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Lee M, Lee K, Yu N, Jang I, Choi I, Kim P, Jang YE, Kim B, Kim S, Lee B, Kang J, Lee S. ChimerDB 3.0: an enhanced database for fusion genes from cancer transcriptome and literature data mining. Nucleic Acids Res 2016; 45:D784-D789. [PMID: 27899563 PMCID: PMC5210563 DOI: 10.1093/nar/gkw1083] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 10/24/2016] [Accepted: 10/27/2016] [Indexed: 11/17/2022] Open
Abstract
Fusion gene is an important class of therapeutic targets and prognostic markers in cancer. ChimerDB is a comprehensive database of fusion genes encompassing analysis of deep sequencing data and manual curations. In this update, the database coverage was enhanced considerably by adding two new modules of The Cancer Genome Atlas (TCGA) RNA-Seq analysis and PubMed abstract mining. ChimerDB 3.0 is composed of three modules of ChimerKB, ChimerPub and ChimerSeq. ChimerKB represents a knowledgebase including 1066 fusion genes with manual curation that were compiled from public resources of fusion genes with experimental evidences. ChimerPub includes 2767 fusion genes obtained from text mining of PubMed abstracts. ChimerSeq module is designed to archive the fusion candidates from deep sequencing data. Importantly, we have analyzed RNA-Seq data of the TCGA project covering 4569 patients in 23 cancer types using two reliable programs of FusionScan and TopHat-Fusion. The new user interface supports diverse search options and graphic representation of fusion gene structure. ChimerDB 3.0 is available at http://ercsb.ewha.ac.kr/fusiongene/.
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Affiliation(s)
- Myunggyo Lee
- Department of Bio-Information Science, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Kyubum Lee
- Department of Computer Science and Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Namhee Yu
- Department of Life Science, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Insu Jang
- Korean Bioinformation Center, Korean Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Ikjung Choi
- Ewha Research Center for Systems Biology, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Pora Kim
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Ye Eun Jang
- Department of Bio-Information Science, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Byounggun Kim
- Interdisciplinary Graduate Program in Bioinformatics, Korea University, Seoul 02841, Republic of Korea
| | - Sunkyu Kim
- Interdisciplinary Graduate Program in Bioinformatics, Korea University, Seoul 02841, Republic of Korea
| | - Byungwook Lee
- Korean Bioinformation Center, Korean Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Jaewoo Kang
- Department of Computer Science and Engineering, Korea University, Seoul 02841, Republic of Korea .,Interdisciplinary Graduate Program in Bioinformatics, Korea University, Seoul 02841, Republic of Korea
| | - Sanghyuk Lee
- Department of Bio-Information Science, Ewha Womans University, Seoul 03760, Republic of Korea .,Department of Life Science, Ewha Womans University, Seoul 03760, Republic of Korea.,Ewha Research Center for Systems Biology, Ewha Womans University, Seoul 03760, Republic of Korea
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302
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Pan-cancer analysis of somatic copy-number alterations implicates IRS4 and IGF2 in enhancer hijacking. Nat Genet 2016; 49:65-74. [PMID: 27869826 DOI: 10.1038/ng.3722] [Citation(s) in RCA: 272] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 10/19/2016] [Indexed: 02/06/2023]
Abstract
Extensive prior research focused on somatic copy-number alterations (SCNAs) affecting cancer genes, yet the extent to which recurrent SCNAs exert their influence through rearrangement of cis-regulatory elements (CREs) remains unclear. Here we present a framework for inferring cancer-related gene overexpression resulting from CRE reorganization (e.g., enhancer hijacking) by integrating SCNAs, gene expression data and information on topologically associating domains (TADs). Analysis of 7,416 cancer genomes uncovered several pan-cancer candidate genes, including IRS4, SMARCA1 and TERT. We demonstrate that IRS4 overexpression in lung cancer is associated with recurrent deletions in cis, and we present evidence supporting a tumor-promoting role. We additionally pursued cancer-type-specific analyses and uncovered IGF2 as a target for enhancer hijacking in colorectal cancer. Recurrent tandem duplications intersecting with a TAD boundary mediate de novo formation of a 3D contact domain comprising IGF2 and a lineage-specific super-enhancer, resulting in high-level gene activation. Our framework enables systematic inference of CRE rearrangements mediating dysregulation in cancer.
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303
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Bunn PA. Karnofsky Award 2016: A Lung Cancer Journey, 1973 to 2016. J Clin Oncol 2016; 35:243-252. [PMID: 28056194 DOI: 10.1200/jco.2016.70.4064] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Paul A Bunn
- From University of Colorado Cancer Center, Aurora, CO
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304
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Beaumeunier S, Audoux J, Boureux A, Ruffle F, Commes T, Philippe N, Alves R. On the evaluation of the fidelity of supervised classifiers in the prediction of chimeric RNAs. BioData Min 2016; 9:34. [PMID: 27822312 PMCID: PMC5090896 DOI: 10.1186/s13040-016-0112-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 10/11/2016] [Indexed: 03/11/2023] Open
Abstract
Background High-throughput sequencing technology and bioinformatics have identified chimeric RNAs (chRNAs), raising the possibility of chRNAs expressing particularly in diseases can be used as potential biomarkers in both diagnosis and prognosis. Results The task of discriminating true chRNAs from the false ones poses an interesting Machine Learning (ML) challenge. First of all, the sequencing data may contain false reads due to technical artifacts and during the analysis process, bioinformatics tools may generate false positives due to methodological biases. Moreover, if we succeed to have a proper set of observations (enough sequencing data) about true chRNAs, chances are that the devised model can not be able to generalize beyond it. Like any other machine learning problem, the first big issue is finding the good data to build models. As far as we were concerned, there is no common benchmark data available for chRNAs detection. The definition of a classification baseline is lacking in the related literature too. In this work we are moving towards benchmark data and an evaluation of the fidelity of supervised classifiers in the prediction of chRNAs. Conclusions We proposed a modelization strategy that can be used to increase the tools performances in context of chRNA classification based on a simulated data generator, that permit to continuously integrate new complex chimeric events. The pipeline incorporated a genome mutation process and simulated RNA-seq data. The reads within distinct depth were aligned and analysed by CRAC that integrates genomic location and local coverage, allowing biological predictions at the read scale. Additionally, these reads were functionally annotated and aggregated to form chRNAs events, making it possible to evaluate ML methods (classifiers) performance in both levels of reads and events. Ensemble learning strategies demonstrated to be more robust to this classification problem, providing an average AUC performance of 95 % (ACC=94 %, Kappa=0.87 %). The resulting classification models were also tested on real RNA-seq data from a set of twenty-seven patients with acute myeloid leukemia (AML). Electronic supplementary material The online version of this article (doi:10.1186/s13040-016-0112-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sacha Beaumeunier
- Institut de Médecine Régénératrice et de Biothérapie, INSERM U1183, CHU Montpellier, Montpellier, France ; Institut de Biologie Computationnelle, Université Montpellier, Montpellier, France
| | - Jérôme Audoux
- Institut de Médecine Régénératrice et de Biothérapie, INSERM U1183, CHU Montpellier, Montpellier, France ; Institut de Biologie Computationnelle, Université Montpellier, Montpellier, France
| | - Anthony Boureux
- Institut de Médecine Régénératrice et de Biothérapie, INSERM U1183, CHU Montpellier, Montpellier, France ; Institut de Biologie Computationnelle, Université Montpellier, Montpellier, France
| | - Florence Ruffle
- Institut de Médecine Régénératrice et de Biothérapie, INSERM U1183, CHU Montpellier, Montpellier, France ; Institut de Biologie Computationnelle, Université Montpellier, Montpellier, France
| | - Thérèse Commes
- Institut de Médecine Régénératrice et de Biothérapie, INSERM U1183, CHU Montpellier, Montpellier, France ; Institut de Biologie Computationnelle, Université Montpellier, Montpellier, France
| | - Nicolas Philippe
- Institut de Médecine Régénératrice et de Biothérapie, INSERM U1183, CHU Montpellier, Montpellier, France ; Institut de Biologie Computationnelle, Université Montpellier, Montpellier, France
| | - Ronnie Alves
- Institut de Médecine Régénératrice et de Biothérapie, INSERM U1183, CHU Montpellier, Montpellier, France ; Institut de Biologie Computationnelle, Université Montpellier, Montpellier, France ; Laboratoire d'Informatique, de Robotique et de Microélectronique de Montpellier, Université Montpellier, UMR 5506 CNRS, Montpellier, France ; PPGCC, Universidade Federal do Pará, Belém, Brazil ; Instituto Tecnológico Vale, Belém, Brazil
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305
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Maguire SL, Peck B, Wai PT, Campbell J, Barker H, Gulati A, Daley F, Vyse S, Huang P, Lord CJ, Farnie G, Brennan K, Natrajan R. Three-dimensional modelling identifies novel genetic dependencies associated with breast cancer progression in the isogenic MCF10 model. J Pathol 2016; 240:315-328. [PMID: 27512948 PMCID: PMC5082563 DOI: 10.1002/path.4778] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 07/05/2016] [Accepted: 08/02/2016] [Indexed: 12/21/2022]
Abstract
The initiation and progression of breast cancer from the transformation of the normal epithelium to ductal carcinoma in situ (DCIS) and invasive disease is a complex process involving the acquisition of genetic alterations and changes in gene expression, alongside microenvironmental and recognized histological alterations. Here, we sought to comprehensively characterise the genomic and transcriptomic features of the MCF10 isogenic model of breast cancer progression, and to functionally validate potential driver alterations in three-dimensional (3D) spheroids that may provide insights into breast cancer progression, and identify targetable alterations in conditions more similar to those encountered in vivo. We performed whole genome, exome and RNA sequencing of the MCF10 progression series to catalogue the copy number and mutational and transcriptomic landscapes associated with progression. We identified a number of predicted driver mutations (including PIK3CA and TP53) that were acquired during transformation of non-malignant MCF10A cells to their malignant counterparts that are also present in analysed primary breast cancers from The Cancer Genome Atlas (TCGA). Acquisition of genomic alterations identified MYC amplification and previously undescribed RAB3GAP1-HRAS and UBA2-PDCD2L expressed in-frame fusion genes in malignant cells. Comparison of pathway aberrations associated with progression showed that, when cells are grown as 3D spheroids, they show perturbations of cancer-relevant pathways. Functional interrogation of the dependency on predicted driver events identified alterations in HRAS, PIK3CA and TP53 that selectively decreased cell growth and were associated with progression from preinvasive to invasive disease only when cells were grown as spheroids. Our results have identified changes in the genomic repertoire in cell lines representative of the stages of breast cancer progression, and demonstrate that genetic dependencies can be uncovered when cells are grown in conditions more like those in vivo. The MCF10 progression series therefore represents a good model with which to dissect potential biomarkers and to evaluate therapeutic targets involved in the progression of breast cancer. © 2016 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
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MESH Headings
- Breast Neoplasms/genetics
- Breast Neoplasms/pathology
- Carcinoma, Ductal, Breast/genetics
- Carcinoma, Ductal, Breast/pathology
- Carcinoma, Intraductal, Noninfiltrating/genetics
- Carcinoma, Intraductal, Noninfiltrating/pathology
- Cell Line, Tumor
- Cell Transformation, Neoplastic
- Class I Phosphatidylinositol 3-Kinases
- DNA, Neoplasm/chemistry
- DNA, Neoplasm/genetics
- Disease Progression
- Exome/genetics
- Female
- Gene Expression Regulation, Neoplastic
- Genome
- High-Throughput Nucleotide Sequencing
- Humans
- Models, Biological
- Mutation
- Phosphatidylinositol 3-Kinases/genetics
- Phosphatidylinositol 3-Kinases/metabolism
- Sequence Analysis, DNA
- Spheroids, Cellular
- Transcriptome
- Tumor Suppressor Protein p53/genetics
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Affiliation(s)
- Sarah L Maguire
- The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer, The Institute of Cancer Research, London, UK
| | - Barrie Peck
- The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer, The Institute of Cancer Research, London, UK
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Patty T Wai
- The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer, The Institute of Cancer Research, London, UK
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - James Campbell
- The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer, The Institute of Cancer Research, London, UK
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Holly Barker
- The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer, The Institute of Cancer Research, London, UK
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Aditi Gulati
- The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer, The Institute of Cancer Research, London, UK
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Frances Daley
- The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer, The Institute of Cancer Research, London, UK
| | - Simon Vyse
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
| | - Paul Huang
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
| | - Christopher J Lord
- The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer, The Institute of Cancer Research, London, UK
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Gillian Farnie
- Institute of Cancer Sciences, University of Manchester, Manchester, UK
| | - Keith Brennan
- Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - Rachael Natrajan
- The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer, The Institute of Cancer Research, London, UK.
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK.
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306
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Choi ES, Lee H, Lee CH, Goh SH. Overexpression of KLHL23 protein from read-through transcription of PHOSPHO2-KLHL23 in gastric cancer increases cell proliferation. FEBS Open Bio 2016; 6:1155-1164. [PMID: 27833855 PMCID: PMC5095152 DOI: 10.1002/2211-5463.12136] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 09/20/2016] [Accepted: 09/28/2016] [Indexed: 01/05/2023] Open
Abstract
Gene fusion, as a prototypical pathognomonic mutation, contributes to genome complexity, and the cis‐transcription‐induced gene fusions generated by read‐through transcription of adjacent genes have been found to be important for tumor development. We screened read‐through transcription events from stomach adenocarcinoma RNA‐seq data and selected three candidates PHOSPHO2‐KLHL23, RPL17‐C18orf32, and PRR5‐ARHGAP8, to assess their biological role in gastric cancer. The expression of all three read‐through fusion transcripts was confirmed in gastric cancer cell lines and paired normal/tumor gastric cancer tissues by real‐time quantitative reverse transcription polymerase chain reaction and their expression was found to be significantly higher in the tumor (P < 0.05; n = 75). The correlation between the expression level and clinicopathological information was statistically analyzed. The level of the PHOSPHO2‐KLHL23 read‐through fusion transcript correlated with the Lauren classification and was significantly associated with the presence of perineural invasion. Overexpression of KLHL23 from PHOSPHO2‐KLHL23 read‐through transcript led to a significant increase in cell proliferation and resistance to anticancer drug treatment. Silencing of KLHL23 expression decreased cyclin D1 levels. The expression of KLHL23 from prevalent read‐through transcripts of PHOSPHO2‐KLHL23 in gastric cancer may undermine the efficacy of anticancer drug treatment.
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Affiliation(s)
- Eun-Seok Choi
- Precision Medicine Branch Research Institute National Cancer Center Goyang Gyeonggi-do Korea; Department of Environmental Medical Biology Institute of Tropical Medicine Yonsei University College of Medicine Seoul Korea
| | - Hanna Lee
- Precision Medicine Branch Research Institute National Cancer Center Goyang Gyeonggi-do Korea
| | - Chang-Hun Lee
- Cancer Cell and Molecular Biology Branch Research Institute National Cancer Center Goyang Gyeonggi-do Korea
| | - Sung-Ho Goh
- Precision Medicine Branch Research Institute National Cancer Center Goyang Gyeonggi-do Korea
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307
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Recurrent MET fusion genes represent a drug target in pediatric glioblastoma. Nat Med 2016; 22:1314-1320. [PMID: 27748748 DOI: 10.1038/nm.4204] [Citation(s) in RCA: 157] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 09/15/2016] [Indexed: 12/18/2022]
Abstract
Pediatric glioblastoma is one of the most common and most deadly brain tumors in childhood. Using an integrative genetic analysis of 53 pediatric glioblastomas and five in vitro model systems, we identified previously unidentified gene fusions involving the MET oncogene in ∼10% of cases. These MET fusions activated mitogen-activated protein kinase (MAPK) signaling and, in cooperation with lesions compromising cell cycle regulation, induced aggressive glial tumors in vivo. MET inhibitors suppressed MET tumor growth in xenograft models. Finally, we treated a pediatric patient bearing a MET-fusion-expressing glioblastoma with the targeted inhibitor crizotinib. This therapy led to substantial tumor shrinkage and associated relief of symptoms, but new treatment-resistant lesions appeared, indicating that combination therapies are likely necessary to achieve a durable clinical response.
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308
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Escalante DA, Wang H, Fundakowski CE. Fusion proteins in head and neck neoplasms: Clinical implications, genetics, and future directions for targeting. Cancer Biol Ther 2016; 17:995-1002. [PMID: 27636353 DOI: 10.1080/15384047.2016.1219823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Fusion proteins resulting from chromosomal rearrangements are known to drive the pathogenesis of a variety of hematological and solid neoplasms such as chronic myeloid leukemia and non-small-cell lung cancer. Efforts to elucidate the role they play in these malignancies have led to important diagnostic and therapeutic triumphs, including the famous development of the tyrosine kinase inhibitor dasatinib targeting the BCR-ABL fusion. Until recently, there has been a paucity of research investigating fusion proteins harbored by head and neck neoplasms. The discovery and characterization of novel fusion proteins in neoplasms originating from the thyroid, nasopharynx, salivary glands, and midline head and neck structures offer substantial contributions to our understanding of the pathogenesis and biological behavior of these neoplasms, while raising new therapeutic and diagnostic opportunities. Further characterization of these fusion proteins promises to facilitate advances on par with those already achieved with regard to hematologic malignancies in the precise, molecularly guided diagnosis and treatment of head and neck neoplasms. The following is a subsite specific review of the clinical implications of fusion proteins in head and neck neoplasms and the future potential for diagnostic targeting.
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Affiliation(s)
- Derek A Escalante
- a Temple University Katz School of Medicine , Philadelphia , PA , USA
| | - He Wang
- a Temple University Katz School of Medicine , Philadelphia , PA , USA.,b Department of Pathology and Lab Medicine , Temple University , Philadelphia , PA , USA
| | - Christopher E Fundakowski
- a Temple University Katz School of Medicine , Philadelphia , PA , USA.,c Department of Otolaryngology - Head & Neck Surgery , Temple University , Philadelphia , PA , USA.,d Department of Surgical Oncology, Fox Chase Cancer Center , Philadelphia , PA , USA
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309
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Marum JE, Branford S. Current developments in molecular monitoring in chronic myeloid leukemia. Ther Adv Hematol 2016; 7:237-251. [PMID: 27695615 PMCID: PMC5026293 DOI: 10.1177/2040620716657994] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Molecular monitoring plays an essential role in the clinical management of chronic myeloid leukemia (CML) patients, and now guides clinical decision making. Quantitative reverse-transcriptase-polymerase-chain-reaction (qRT-PCR) assessment of BCR-ABL1 transcript levels has become the standard of care protocol in CML. However, further developments are required to assess leukemic burden more efficiently, monitor minimal residual disease (MRD), detect mutations that drive resistance to tyrosine kinase inhibitor (TKI) therapy and identify predictors of response to TKI therapy. Cartridge-based BCR-ABL1 quantitation, digital PCR and next generation sequencing are examples of technologies which are currently being explored, evaluated and translated into the clinic. Here we review the emerging molecular methods/technologies currently being developed to advance molecular monitoring in CML.
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Affiliation(s)
- Justine Ellen Marum
- Centre for Cancer Biology, SA Pathology, Adelaide, Australia
- Division of Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Susan Branford
- Centre for Cancer Biology, SA Pathology, Adelaide, Australia
- School of Pharmacy and Medical Science, University of South Australia, Adelaide, SA, Australia
- School of Medicine, University of Adelaide, SA, Adelaide, Australia
- School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
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310
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Panagopoulos I, Torkildsen S, Gorunova L, Ulvmoen A, Tierens A, Zeller B, Heim S. RUNX1 truncation resulting from a cryptic and novel t(6;21)(q25;q22) chromosome translocation in acute myeloid leukemia: A case report. Oncol Rep 2016; 36:2481-2488. [PMID: 27667292 PMCID: PMC5055202 DOI: 10.3892/or.2016.5119] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 08/12/2016] [Indexed: 12/28/2022] Open
Abstract
Fluorescence in situ hybridization examination of a pediatric AML patient whose bone marrow cells carried trisomy 4 and FLT3-ITD mutation, demonstrated that part of the RUNX1 probe had unexpectedly moved to chromosome band 6q25 indicating a cryptic t(6;21)(q25;q22) translocation. RNA sequencing showed fusion of exon 7 of RUNX1 with an intergenic sequence of 6q25 close to the MIR1202 locus, something that was verified by RT-PCR together with Sanger sequencing. The RUNX1 fusion transcript encodes a truncated protein containing the Runt homology domain responsible for both heterodimerization with CBFB and DNA binding, but lacking the proline-, serine-, and threonine-rich (PST) region which is the transcription activation domain at the C terminal end. Which genetic event (+4, FLT3-ITD, t(6;21)-RUNX1 truncation or other, undetected acquired changes) was more pathogenetically important in the present case of AML, remains unknown. The case illustrates that submicroscopic chromosomal rearrangements may accompany visible numerical changes and perhaps should be actively looked for whenever a single trisomy is found. An active search for them may provide both pathogenetic and prognostic novel information.
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Affiliation(s)
- Ioannis Panagopoulos
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, NO-0424 Oslo, Norway
| | - Synne Torkildsen
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, NO-0424 Oslo, Norway
| | - Ludmila Gorunova
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, NO-0424 Oslo, Norway
| | - Aina Ulvmoen
- Pediatric Medicine, Oslo University Hospital, NO-0424 Oslo, Norway
| | - Anne Tierens
- Laboratory Medicine Program, Department of Haematopathology, University Health Network, Toronto, Ontario M5G 2C4, Canada
| | - Bernward Zeller
- Pediatric Medicine, Oslo University Hospital, NO-0424 Oslo, Norway
| | - Sverre Heim
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, NO-0424 Oslo, Norway
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311
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Delespaul L, Lesluyes T, Pérot G, Brulard C, Lartigue L, Baud J, Lagarde P, Le Guellec S, Neuville A, Terrier P, Vince-Ranchère D, Schmidt S, Debant A, Coindre JM, Chibon F. Recurrent TRIO Fusion in Nontranslocation–Related Sarcomas. Clin Cancer Res 2016; 23:857-867. [DOI: 10.1158/1078-0432.ccr-16-0290] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 06/27/2016] [Accepted: 07/27/2016] [Indexed: 11/16/2022]
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312
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Olsen TK, Panagopoulos I, Gorunova L, Micci F, Andersen K, Kilen Andersen H, Meling TR, Due-Tønnessen B, Scheie D, Heim S, Brandal P. Novel fusion genes and chimeric transcripts in ependymal tumors. Genes Chromosomes Cancer 2016; 55:944-953. [PMID: 27401149 DOI: 10.1002/gcc.22392] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 07/03/2016] [Accepted: 07/03/2016] [Indexed: 01/14/2023] Open
Abstract
We have previously identified two ALK rearrangements in a subset of ependymal tumors using a combination of cytogenetic data and RNA sequencing. The aim of this study was to perform an unbiased search for fusion transcripts in our entire series of ependymal tumors. Fusion analysis was performed using the FusionCatcher algorithm on 12 RNA-sequenced ependymal tumors. Candidate transcripts were prioritized based on the software's filtering and manual visualization using the BLAST (Basic Local Alignment Search Tool) and BLAT (BLAST-like alignment tool) tools. Genomic and reverse transcriptase PCR with subsequent Sanger sequencing was used to validate the potential fusions. Fluorescent in situ hybridization (FISH) using locus-specific probes was also performed. A total of 841 candidate chimeric transcripts were identified in the 12 tumors, with an average of 49 unique candidate fusions per tumor. After algorithmic and manual filtering, the final list consisted of 24 potential fusion events. Raw RNA-seq read sequences and PCR validation supports two novel fusion genes: a reciprocal fusion gene involving UQCR10 and C1orf194 in an adult spinal ependymoma and a TSPAN4-CD151 fusion gene in a pediatric infratentorial anaplastic ependymoma. Our previously reported ALK rearrangements and the RELA and YAP1 fusions found in supratentorial ependymomas were until now the only known fusion genes present in ependymal tumors. The chimeric transcripts presented here are the first to be reported in infratentorial or spinal ependymomas. Further studies are required to characterize the genomic rearrangements causing these fusion genes, as well as the frequency and functional importance of the fusions. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Thale Kristin Olsen
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, Oslo University Hospital, Norway. .,Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Norway. .,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Norway.
| | - Ioannis Panagopoulos
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, Oslo University Hospital, Norway.,Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Norway
| | - Ludmila Gorunova
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, Oslo University Hospital, Norway.,Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Norway
| | - Francesca Micci
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, Oslo University Hospital, Norway.,Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Norway
| | - Kristin Andersen
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, Oslo University Hospital, Norway
| | - Hege Kilen Andersen
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, Oslo University Hospital, Norway
| | | | | | - David Scheie
- Department of Pathology, Rigshospitalet, Copenhagen, Denmark.,Department of Pathology, Oslo University Hospital, Norway
| | - Sverre Heim
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, Oslo University Hospital, Norway.,Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Norway
| | - Petter Brandal
- Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, Oslo University Hospital, Norway.,Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, Norway.,Department of Oncology, Oslo University Hospital-The Norwegian Radium Hospital, Norway
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313
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Guo T, Gaykalova DA, Considine M, Wheelan S, Pallavajjala A, Bishop JA, Westra WH, Ideker T, Koch WM, Khan Z, Fertig EJ, Califano JA. Characterization of functionally active gene fusions in human papillomavirus related oropharyngeal squamous cell carcinoma. Int J Cancer 2016; 139:373-82. [PMID: 26949921 PMCID: PMC5579720 DOI: 10.1002/ijc.30081] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 02/24/2016] [Indexed: 01/04/2023]
Abstract
The Cancer Genome Atlas (TCGA) sequencing analysis of head and neck squamous cell carcinoma (HNSCC) recently reported on gene fusions, however, few human papillomavirus (HPV) positive samples were included, and the functional relevance of identified fusions was not explored. We therefore performed an independent analysis of gene fusions in HPV-positive oropharyngeal SCC (OPSCC). RNA sequencing was performed on 47 HPV-positive OPSCC primary tumors and 25 normal mucosal samples from cancer unaffected controls on an Illumina TruSeq platform. MapSplice2 was used for alignment and identification of fusion candidates. Putative fusions with less than five spanning reads, detected in normal tissues, or that mapped to the same gene were filtered out. Selected fusions were validated by RT-PCR and Sanger sequencing. Within 47 HPV-positive OPSCC tumors, 282 gene fusions were identified. Most fusions (85.1%) occurred in a single tumor, and the remaining fusions recurred in 2-16 tumors. Gene fusions were associated with significant up regulation of 16 genes (including EGFR and ERBB4) and down regulation of four genes (PTPRT, ZNF750, DLG2, SLCO5A1). Expression of these genes followed similar patterns of up regulation and down regulation in tumors without these fusions compared to normal tissue. Five of six gene fusions selected for validation were confirmed through RT-PCR and sequencing. This integrative analysis provides a method of prioritizing functionally relevant gene fusions that may be expanded to other tumor types. These results demonstrate that gene fusions may be one mechanism by which functionally relevant genes are altered in HPV-positive OPSCC.
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Affiliation(s)
- Theresa Guo
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, MD
| | - Daria A Gaykalova
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, MD
| | - Michael Considine
- Division of Oncology Biostatistics, Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD
| | - Sarah Wheelan
- Division of Oncology Biostatistics, Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD
| | - Aparna Pallavajjala
- Division of Oncology Biostatistics, Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD
| | - Justin A Bishop
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD
| | - William H Westra
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD
| | - Trey Ideker
- Department of Medicine, University of California San Diego, San Diego, CA
| | - Wayne M Koch
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, MD
| | - Zubair Khan
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, MD
| | - Elana J Fertig
- Division of Oncology Biostatistics, Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD
| | - Joseph A Califano
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, MD
- Division of Otolaryngology-Head and Neck Surgery, Department of Surgery, Moores Cancer Center, University of California, San Diego, CA
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314
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Hofree M, Carter H, Kreisberg JF, Bandyopadhyay S, Mischel PS, Friend S, Ideker T. Challenges in identifying cancer genes by analysis of exome sequencing data. Nat Commun 2016; 7:12096. [PMID: 27417679 PMCID: PMC4947162 DOI: 10.1038/ncomms12096] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Accepted: 05/31/2016] [Indexed: 12/11/2022] Open
Abstract
Massively parallel sequencing has permitted an unprecedented examination of the cancer exome, leading to predictions that all genes important to cancer will soon be identified by genetic analysis of tumours. To examine this potential, here we evaluate the ability of state-of-the-art sequence analysis methods to specifically recover known cancer genes. While some cancer genes are identified by analysis of recurrence, spatial clustering or predicted impact of somatic mutations, many remain undetected due to lack of power to discriminate driver mutations from the background mutational load (13-60% recall of cancer genes impacted by somatic single-nucleotide variants, depending on the method). Cancer genes not detected by mutation recurrence also tend to be missed by all types of exome analysis. Nonetheless, these genes are implicated by other experiments such as functional genetic screens and expression profiling. These challenges are only partially addressed by increasing sample size and will likely hold even as greater numbers of tumours are analysed.
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Affiliation(s)
- Matan Hofree
- Cancer Cell Map Initiative (CCMI), 9500 Gilman Drive, La Jolla, California 92093, USA
- Department of Computer Science and Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
- Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Hannah Carter
- Department of Computer Science and Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
- Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
- Moores Cancer Center, University of California San Diego, 3855 Health Sciences Drive, La Jolla, California 92093, USA
| | - Jason F. Kreisberg
- Cancer Cell Map Initiative (CCMI), 9500 Gilman Drive, La Jolla, California 92093, USA
- Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Sourav Bandyopadhyay
- Diller Family Comprehensive Cancer Center, University of California San Francisco, 1600 Divisadero Street, San Francisco, California 94115, USA
| | - Paul S. Mischel
- Ludwig Institute for Cancer Research, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
| | - Stephen Friend
- Sage Bionetworks, Seattle, 110 Fairview Avenue North, Seattle, Washington 98109, USA
| | - Trey Ideker
- Cancer Cell Map Initiative (CCMI), 9500 Gilman Drive, La Jolla, California 92093, USA
- Department of Computer Science and Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
- Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
- Moores Cancer Center, University of California San Diego, 3855 Health Sciences Drive, La Jolla, California 92093, USA
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315
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Cajaiba MM, Jennings LJ, George D, Perlman EJ. Expanding the spectrum of ALK-rearranged renal cell carcinomas in children: Identification of a novel HOOK1-ALK fusion transcript. Genes Chromosomes Cancer 2016; 55:814-7. [PMID: 27225638 DOI: 10.1002/gcc.22382] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 05/23/2016] [Accepted: 05/24/2016] [Indexed: 12/15/2022] Open
Affiliation(s)
- Mariana M Cajaiba
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago and Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Lawrence J Jennings
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago and Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - David George
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago and Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Elizabeth J Perlman
- Department of Pathology and Laboratory Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago and Northwestern University Feinberg School of Medicine, Chicago, Illinois
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316
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Veeraraghavan J, Ma J, Hu Y, Wang XS. Recurrent and pathological gene fusions in breast cancer: current advances in genomic discovery and clinical implications. Breast Cancer Res Treat 2016; 158:219-32. [PMID: 27372070 DOI: 10.1007/s10549-016-3876-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 06/18/2016] [Indexed: 12/22/2022]
Abstract
Gene fusions have long been considered principally as the oncogenic events of hematologic malignancies, but have recently gained wide attention in solid tumors due to several milestone discoveries and the advancement of deep sequencing technologies. With the progress in deep sequencing studies of breast cancer transcriptomes and genomes, the discovery of recurrent and pathological gene fusions in breast cancer is on the focus. Recently, driven by new deep sequencing studies, several recurrent or pathological gene fusions have been identified in breast cancer, including ESR1-CCDC170, SEC16A-NOTCH1, SEC22B-NOTCH2, and ESR1-YAP1 etc. More important, most of these gene fusions are preferentially identified in the more aggressive breast cancers, such as luminal B, basal-like, or endocrine-resistant breast cancer, suggesting recurrent gene fusions as additional key driver events in these tumors other than the known drivers such as the estrogen receptor. In this paper, we have comprehensively summarized the newly identified recurrent or pathological gene fusion events in breast cancer, reviewed the contributions of new genomic and deep sequencing technologies to new fusion discovery and the integrative bioinformatics tools to analyze these data, highlighted the biological relevance and clinical implications of these fusion discoveries, and discussed future directions of gene fusion research in breast cancer.
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Affiliation(s)
- Jamunarani Veeraraghavan
- Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jiacheng Ma
- Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yiheng Hu
- Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Xiao-Song Wang
- Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA. .,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA. .,University of Pittsburgh Cancer Institute, University of Pittsburgh, Pittsburgh, PA, 15232, USA. .,Department of Pathology, University of Pittsburgh, Pittsburgh, PA, 15232, USA. .,Hillman Cancer Center, Research Pavilion, University of Pittsburgh Cancer Institute, 5117 Centre Avenue, Room G.5a, Pittsburgh, PA, 15213, USA.
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317
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Wang K, Russell JS, McDermott JD, Elvin JA, Khaira D, Johnson A, Jennings TA, Ali SM, Murray M, Marshall C, Oldham DS, Washburn D, Wong SJ, Chmielecki J, Yelensky R, Lipson D, Miller VA, Stephens PJ, Serracino HS, Ross JS, Bowles DW. Profiling of 149 Salivary Duct Carcinomas, Carcinoma Ex Pleomorphic Adenomas, and Adenocarcinomas, Not Otherwise Specified Reveals Actionable Genomic Alterations. Clin Cancer Res 2016; 22:6061-6068. [DOI: 10.1158/1078-0432.ccr-15-2568] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 05/10/2016] [Accepted: 05/23/2016] [Indexed: 11/16/2022]
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318
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Shaver TM, Lehmann BD, Beeler JS, Li CI, Li Z, Jin H, Stricker TP, Shyr Y, Pietenpol JA. Diverse, Biologically Relevant, and Targetable Gene Rearrangements in Triple-Negative Breast Cancer and Other Malignancies. Cancer Res 2016; 76:4850-60. [PMID: 27231203 DOI: 10.1158/0008-5472.can-16-0058] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 05/11/2016] [Indexed: 12/20/2022]
Abstract
Triple-negative breast cancer (TNBC) and other molecularly heterogeneous malignancies present a significant clinical challenge due to a lack of high-frequency "driver" alterations amenable to therapeutic intervention. These cancers often exhibit genomic instability, resulting in chromosomal rearrangements that affect the structure and expression of protein-coding genes. However, identification of these rearrangements remains technically challenging. Using a newly developed approach that quantitatively predicts gene rearrangements in tumor-derived genetic material, we identified and characterized a novel oncogenic fusion involving the MER proto-oncogene tyrosine kinase (MERTK) and discovered a clinical occurrence and cell line model of the targetable FGFR3-TACC3 fusion in TNBC. Expanding our analysis to other malignancies, we identified a diverse array of novel and known hybrid transcripts, including rearrangements between noncoding regions and clinically relevant genes such as ALK, CSF1R, and CD274/PD-L1 The over 1,000 genetic alterations we identified highlight the importance of considering noncoding gene rearrangement partners, and the targetable gene fusions identified in TNBC demonstrate the need to advance gene fusion detection for molecularly heterogeneous cancers. Cancer Res; 76(16); 4850-60. ©2016 AACR.
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Affiliation(s)
- Timothy M Shaver
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee. Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Brian D Lehmann
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee. Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee.
| | - J Scott Beeler
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee. Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Chung-I Li
- Department of Statistics, National Cheng Kung University, Tainan, Taiwan
| | - Zhu Li
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee. Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Hailing Jin
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee. Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Thomas P Stricker
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Yu Shyr
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, Tennessee. Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jennifer A Pietenpol
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee. Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee.
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319
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Zheng S, Cherniack AD, Dewal N, Moffitt RA, Danilova L, Murray BA, Lerario AM, Else T, Knijnenburg TA, Ciriello G, Kim S, Assie G, Morozova O, Akbani R, Shih J, Hoadley KA, Choueiri TK, Waldmann J, Mete O, Robertson AG, Wu HT, Raphael BJ, Shao L, Meyerson M, Demeure MJ, Beuschlein F, Gill AJ, Sidhu SB, Almeida MQ, Fragoso MCBV, Cope LM, Kebebew E, Habra MA, Whitsett TG, Bussey KJ, Rainey WE, Asa SL, Bertherat J, Fassnacht M, Wheeler DA, Hammer GD, Giordano TJ, Verhaak RGW. Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma. Cancer Cell 2016; 29:723-736. [PMID: 27165744 PMCID: PMC4864952 DOI: 10.1016/j.ccell.2016.04.002] [Citation(s) in RCA: 375] [Impact Index Per Article: 46.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 12/08/2015] [Accepted: 04/05/2016] [Indexed: 01/08/2023]
Abstract
We describe a comprehensive genomic characterization of adrenocortical carcinoma (ACC). Using this dataset, we expand the catalogue of known ACC driver genes to include PRKAR1A, RPL22, TERF2, CCNE1, and NF1. Genome wide DNA copy-number analysis revealed frequent occurrence of massive DNA loss followed by whole-genome doubling (WGD), which was associated with aggressive clinical course, suggesting WGD is a hallmark of disease progression. Corroborating this hypothesis were increased TERT expression, decreased telomere length, and activation of cell-cycle programs. Integrated subtype analysis identified three ACC subtypes with distinct clinical outcome and molecular alterations which could be captured by a 68-CpG probe DNA-methylation signature, proposing a strategy for clinical stratification of patients based on molecular markers.
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Affiliation(s)
- Siyuan Zheng
- Departments of Genomic Medicine, Bioinformatics, and Computational Biology, Endocrine Neoplasia and Hormonal Disorders, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Andrew D Cherniack
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Ninad Dewal
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard A Moffitt
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ludmila Danilova
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University, Baltimore, MD 21287, USA
| | - Bradley A Murray
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Antonio M Lerario
- Unidade de Suprarrenal, Laboratório de Hormônios e Genética Molecular LIM42, Serviço de Endocrinologia e Metabologia, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-900, Brazil; Departments of Cell & Developmental Biology, Pathology, Molecular & Integrative Physiology, Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA; University of Michigan Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Tobias Else
- Departments of Cell & Developmental Biology, Pathology, Molecular & Integrative Physiology, Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA; University of Michigan Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Giovanni Ciriello
- Department of Computational Biology, University of Lausanne, Rue du Bugnon 27, 1005 Lausanne, Switzerland; Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Seungchan Kim
- Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Guillaume Assie
- Inserm U1016, CNRS UMR 8104, Institut Cochin, 75014 Paris, France; Faculté de Médecine Paris Descartes, Université Paris Descartes, Sorbonne Paris Cité, 75006 Paris, France; Department of Endocrinology, Referral Center for Rare Adrenal Diseases, Assistance Publique Hôpitaux de Paris, Hôpital Cochin, 75014 Paris, France; European Network for the Study of Adrenal Tumors, 75014 Paris, France
| | - Olena Morozova
- University of California Santa Cruz Genomics Institute, University California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Rehan Akbani
- Departments of Genomic Medicine, Bioinformatics, and Computational Biology, Endocrine Neoplasia and Hormonal Disorders, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Juliann Shih
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Katherine A Hoadley
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Toni K Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Jens Waldmann
- European Network for the Study of Adrenal Tumors, 75014 Paris, France; Department of Visceral, Thoracic and Vascular Surgery, University Hospital Giessen and Marburg, Campus Marburg, General Surgery, Endocrine Center, 34501 Marburg, Germany
| | - Ozgur Mete
- Department of Laboratory Medicine and Pathobiology, University Health Network, Toronto, ON M5G 2C4, Canada
| | - A Gordon Robertson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC V5Z 4S6, Canada
| | - Hsin-Ta Wu
- Department of Computer Science, Brown University, Providence, RI 02906, USA
| | - Benjamin J Raphael
- Department of Computer Science, Brown University, Providence, RI 02906, USA
| | - Lina Shao
- Departments of Cell & Developmental Biology, Pathology, Molecular & Integrative Physiology, Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Matthew Meyerson
- The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Department of Pathology, Harvard Medical School, Boston, MA 02215, USA
| | | | - Felix Beuschlein
- European Network for the Study of Adrenal Tumors, 75014 Paris, France; Endocrine Research Unit, Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, 80336 Munich, Germany
| | - Anthony J Gill
- Cancer Diagnosis and Pathology Group and Cancer Genetics Laboratory, Kolling Institute of Medical Research, University of Sydney, Sydney, NSW 2006, Australia; Department of Anatomical Pathology, Royal North Shore Hospital, St Leonards, NSW 2065, Australia
| | - Stan B Sidhu
- Cancer Diagnosis and Pathology Group and Cancer Genetics Laboratory, Kolling Institute of Medical Research, University of Sydney, Sydney, NSW 2006, Australia; Endocrine Surgical Unit, Royal North Shore Hospital, St Leonards, NSW 2065, Australia
| | - Madson Q Almeida
- Unidade de Suprarrenal, Laboratório de Hormônios e Genética Molecular LIM42, Serviço de Endocrinologia e Metabologia, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-900, Brazil; Instituto do Câncer do Estado de São Paulo (ICESP), Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-900, Brazil
| | - Maria C B V Fragoso
- Unidade de Suprarrenal, Laboratório de Hormônios e Genética Molecular LIM42, Serviço de Endocrinologia e Metabologia, Hospital das Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-900, Brazil; Instituto do Câncer do Estado de São Paulo (ICESP), Faculdade de Medicina da Universidade de São Paulo, São Paulo 05403-900, Brazil
| | - Leslie M Cope
- The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University, Baltimore, MD 21287, USA
| | - Electron Kebebew
- Endocrine Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mouhammed A Habra
- Departments of Genomic Medicine, Bioinformatics, and Computational Biology, Endocrine Neoplasia and Hormonal Disorders, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Kimberly J Bussey
- Translational Genomics Research Institute, Phoenix, AZ 85004, USA; NantOmics, LLC, The Biodesign Institute, Arizona State University, Tempe, AZ 85287-5001, USA
| | - William E Rainey
- Departments of Cell & Developmental Biology, Pathology, Molecular & Integrative Physiology, Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA; University of Michigan Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sylvia L Asa
- Department of Laboratory Medicine and Pathobiology, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Jérôme Bertherat
- Inserm U1016, CNRS UMR 8104, Institut Cochin, 75014 Paris, France; Faculté de Médecine Paris Descartes, Université Paris Descartes, Sorbonne Paris Cité, 75006 Paris, France; Department of Endocrinology, Referral Center for Rare Adrenal Diseases, Assistance Publique Hôpitaux de Paris, Hôpital Cochin, 75014 Paris, France; European Network for the Study of Adrenal Tumors, 75014 Paris, France
| | - Martin Fassnacht
- European Network for the Study of Adrenal Tumors, 75014 Paris, France; Endocrine and Diabetes Unit, Department of Internal Medicine I, University Hospital Würzburg, 97080 Würzburg, Germany; Comprehensive Cancer Center Mainfranken, University of Würzburg, 97080 Würzburg, Germany
| | - David A Wheeler
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gary D Hammer
- Departments of Cell & Developmental Biology, Pathology, Molecular & Integrative Physiology, Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA; University of Michigan Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Thomas J Giordano
- Departments of Cell & Developmental Biology, Pathology, Molecular & Integrative Physiology, Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA; University of Michigan Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Roel G W Verhaak
- Departments of Genomic Medicine, Bioinformatics, and Computational Biology, Endocrine Neoplasia and Hormonal Disorders, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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320
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Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas. Nat Genet 2016; 48:607-16. [PMID: 27158780 PMCID: PMC4884143 DOI: 10.1038/ng.3564] [Citation(s) in RCA: 811] [Impact Index Per Article: 101.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 04/12/2016] [Indexed: 12/13/2022]
Abstract
To compare lung adenocarcinoma (ADC) and lung squamous cell carcinoma (SqCC) and to identify new drivers of lung carcinogenesis, we examined the exome sequences and copy number profiles of 660 lung ADC and 484 lung SqCC tumor-normal pairs. Recurrent alterations in lung SqCCs were more similar to those of other squamous carcinomas than to alterations in lung ADCs. New significantly mutated genes included PPP3CA, DOT1L, and FTSJD1 in lung ADC, RASA1 in lung SqCC, and KLF5, EP300, and CREBBP in both tumor types. New amplification peaks encompassed MIR21 in lung ADC, MIR205 in lung SqCC, and MAPK1 in both. Lung ADCs lacking receptor tyrosine kinase-Ras-Raf pathway alterations had mutations in SOS1, VAV1, RASA1, and ARHGAP35. Regarding neoantigens, 47% of the lung ADC and 53% of the lung SqCC tumors had at least five predicted neoepitopes. Although targeted therapies for lung ADC and SqCC are largely distinct, immunotherapies may aid in treatment for both subtypes.
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321
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Yang L, Lee MS, Lu H, Oh DY, Kim YJ, Park D, Park G, Ren X, Bristow CA, Haseley PS, Lee S, Pantazi A, Kucherlapati R, Park WY, Scott KL, Choi YL, Park PJ. Analyzing Somatic Genome Rearrangements in Human Cancers by Using Whole-Exome Sequencing. Am J Hum Genet 2016; 98:843-856. [PMID: 27153396 PMCID: PMC4863662 DOI: 10.1016/j.ajhg.2016.03.017] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 03/14/2016] [Indexed: 12/21/2022] Open
Abstract
Although exome sequencing data are generated primarily to detect single-nucleotide variants and indels, they can also be used to identify a subset of genomic rearrangements whose breakpoints are located in or near exons. Using >4,600 tumor and normal pairs across 15 cancer types, we identified over 9,000 high confidence somatic rearrangements, including a large number of gene fusions. We find that the 5' fusion partners of functional fusions are often housekeeping genes, whereas the 3' fusion partners are enriched in tyrosine kinases. We establish the oncogenic potential of ROR1-DNAJC6 and CEP85L-ROS1 fusions by showing that they can promote cell proliferation in vitro and tumor formation in vivo. Furthermore, we found that ∼4% of the samples have massively rearranged chromosomes, many of which are associated with upregulation of oncogenes such as ERBB2 and TERT. Although the sensitivity of detecting structural alterations from exomes is considerably lower than that from whole genomes, this approach will be fruitful for the multitude of exomes that have been and will be generated, both in cancer and in other diseases.
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Affiliation(s)
- Lixing Yang
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Mi-Sook Lee
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul 06351, Korea
| | - Hengyu Lu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Doo-Yi Oh
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul 06351, Korea
| | - Yeon Jeong Kim
- Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Korea; Samsung Biomedical Research Institute, Samsung Advanced Institute of Technology (SAIT), Samsung Electronics Co., Seoul 06351, Korea
| | - Donghyun Park
- Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Korea; Samsung Biomedical Research Institute, Samsung Advanced Institute of Technology (SAIT), Samsung Electronics Co., Seoul 06351, Korea
| | - Gahee Park
- Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Korea
| | - Xiaojia Ren
- Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Christopher A Bristow
- Department of Genomic Medicine and Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Psalm S Haseley
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA; Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Soohyun Lee
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Angeliki Pantazi
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Raju Kucherlapati
- Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Woong-Yang Park
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul 06351, Korea; Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Korea
| | - Kenneth L Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yoon-La Choi
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul 06351, Korea; Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea.
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA; Division of Genetics, Brigham and Women's Hospital, Boston, MA 02115, USA; Ludwig Center, Harvard Medical School, Boston, MA 02115, USA.
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322
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Latysheva NS, Babu MM. Discovering and understanding oncogenic gene fusions through data intensive computational approaches. Nucleic Acids Res 2016; 44:4487-503. [PMID: 27105842 PMCID: PMC4889949 DOI: 10.1093/nar/gkw282] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 03/24/2016] [Indexed: 12/21/2022] Open
Abstract
Although gene fusions have been recognized as important drivers of cancer for decades, our understanding of the prevalence and function of gene fusions has been revolutionized by the rise of next-generation sequencing, advances in bioinformatics theory and an increasing capacity for large-scale computational biology. The computational work on gene fusions has been vastly diverse, and the present state of the literature is fragmented. It will be fruitful to merge three camps of gene fusion bioinformatics that appear to rarely cross over: (i) data-intensive computational work characterizing the molecular biology of gene fusions; (ii) development research on fusion detection tools, candidate fusion prioritization algorithms and dedicated fusion databases and (iii) clinical research that seeks to either therapeutically target fusion transcripts and proteins or leverages advances in detection tools to perform large-scale surveys of gene fusion landscapes in specific cancer types. In this review, we unify these different-yet highly complementary and symbiotic-approaches with the view that increased synergy will catalyze advancements in gene fusion identification, characterization and significance evaluation.
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Affiliation(s)
- Natasha S Latysheva
- MRC Laboratory of Molecular Biology, Francis Crick Ave, Cambridge CB2 0QH, United Kingdom
| | - M Madan Babu
- MRC Laboratory of Molecular Biology, Francis Crick Ave, Cambridge CB2 0QH, United Kingdom
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323
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Yakirevich E, Resnick MB, Mangray S, Wheeler M, Jackson CL, Lombardo KA, Lee J, Kim KM, Gill AJ, Wang K, Gowen K, Sun J, Miller VA, Stephens PJ, Ali SM, Ross JS, Safran H. Oncogenic ALK Fusion in Rare and Aggressive Subtype of Colorectal Adenocarcinoma as a Potential Therapeutic Target. Clin Cancer Res 2016; 22:3831-40. [DOI: 10.1158/1078-0432.ccr-15-3000] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 02/18/2016] [Indexed: 11/16/2022]
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324
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Beadling C, Wald AI, Warrick A, Neff TL, Zhong S, Nikiforov YE, Corless CL, Nikiforova MN. A Multiplexed Amplicon Approach for Detecting Gene Fusions by Next-Generation Sequencing. J Mol Diagn 2016; 18:165-75. [DOI: 10.1016/j.jmoldx.2015.10.002] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 10/25/2015] [Accepted: 10/30/2015] [Indexed: 01/05/2023] Open
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325
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Kekeeva T, Tanas A, Kanygina A, Alexeev D, Shikeeva A, Zavalishina L, Andreeva Y, Frank GA, Zaletaev D. Novel fusion transcripts in bladder cancer identified by RNA-seq. Cancer Lett 2016; 374:224-8. [PMID: 26898937 DOI: 10.1016/j.canlet.2016.02.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 01/29/2016] [Accepted: 02/05/2016] [Indexed: 10/25/2022]
Abstract
Urothelial carcinoma (UC) is the most common type of bladder cancer and is the second most frequently diagnosed genitourinary tumor. The identification of fusion genes in bladder cancer might provide new perspectives for its classification and significance. In this study, we present a thorough search on three UC samples for novel fusion transcripts in bladder cancer using high-throughput RNA sequencing. We used stringent requirements for 819 fusion candidates and nominated 10 candidate fusion transcripts. Among them four novel fusion genes SEPT9/CYHR, IGF1R/TTC23, SYT8/TNNI2 and CASZ1/DFFA were validated and characterized in 48 formalin-fixed paraffin-embedded (FFPE) specimens of bladder cancer. Chromosomal rearrangements of regions 17q25, 15q26.3 and 1p36.22 resulting in the fusion transcripts SEPT9/CYHR, IGF1R/TTC23 and CASZ1/DFFA, appeared to be rare or unique events because they were not detected in the 48 UC samples. In contrast, the SYT8/TNNI2 fusion transcript resulting from transcription-induced chimerism by read-through mechanisms was a rather common and tumor-specific event occurring in 37.5% (18/48) of the UC specimens. Further investigation of functional and clinical relevance of novel fusion genes remains to be elucidated to reveal their role in bladder carcinogenesis.
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Affiliation(s)
- T Kekeeva
- Laboratory of Epigenetics, Research Centre for Medical Genetics, Moskvorechie st., 1, Moscow, 115478, Russian Federation; Pathology Department, Russian Medical Academy of Postgraduate Education, Polikarpov st., 12, Moscow, 125284, Russian Federation.
| | - A Tanas
- Laboratory of Epigenetics, Research Centre for Medical Genetics, Moskvorechie st., 1, Moscow, 115478, Russian Federation
| | - A Kanygina
- Department of Molecular Biophysics, Moscow Institute of Physics and Technology, Institutskii Per. 9, Moscow Region, Dolgoprudny, 141700, Russian Federation
| | - D Alexeev
- Medical and Rehabilitation Center of Ministry of Healthcare of Russian Federation, Ivankovskoye, 3, Moscow, 125367, Russian Federation; Department of Molecular Biophysics, Moscow Institute of Physics and Technology, Institutskii Per. 9, Moscow Region, Dolgoprudny, 141700, Russian Federation
| | - A Shikeeva
- Laboratory of Epigenetics, Research Centre for Medical Genetics, Moskvorechie st., 1, Moscow, 115478, Russian Federation; Pathology Department, Russian Medical Academy of Postgraduate Education, Polikarpov st., 12, Moscow, 125284, Russian Federation
| | - L Zavalishina
- Pathology Department, Russian Medical Academy of Postgraduate Education, Polikarpov st., 12, Moscow, 125284, Russian Federation
| | - Y Andreeva
- Pathology Department, Russian Medical Academy of Postgraduate Education, Polikarpov st., 12, Moscow, 125284, Russian Federation
| | - G A Frank
- Pathology Department, Russian Medical Academy of Postgraduate Education, Polikarpov st., 12, Moscow, 125284, Russian Federation
| | - D Zaletaev
- Laboratory of Epigenetics, Research Centre for Medical Genetics, Moskvorechie st., 1, Moscow, 115478, Russian Federation; Laboratory of Human Molecular Genetics, I. M. Sechenov First Moscow State Medical University, Trubetskaya Str., 8, Moscow 119991, Russian Federation
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326
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Andreasen S, Persson M, Kiss K, Homøe P, Heegaard S, Stenman G. Genomic profiling of a combined large cell neuroendocrine carcinoma of the submandibular gland. Oncol Rep 2016; 35:2177-82. [PMID: 26883388 DOI: 10.3892/or.2016.4621] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 01/05/2016] [Indexed: 11/06/2022] Open
Abstract
A 69-year-old female with no previous medical history presented with a rapidly growing submandibular mass. Fine needle aspiration cytology suggested a small-cell carcinoma and PET-CT showed increased 18-FDG uptake in the submandibular mass as well as in a lung mass. Submandibular resection and selective neck dissection was performed and histopathologic examination revealed a combined large-cell neuroendocrine carcinoma (LCNEC) with a squamous component and without lymph node metastases. Resection of the lung tumor revealed a papillary adenocarcinoma that was morphologically distinctly different from the LCNEC. The patient died of her lung cancer after 19 months without evidence of recurrence of the LCNEC. Genomic profiling of the salivary gland LCNEC revealed a hypodiploid genome predominated by losses of whole chromosomes or chromosome arms involving chromosomes 3p, 4, 7q, 10, 11, 13, 16q and gains of 3q and 16p. In addition, there was a segmental gain of 9p23-p22.3 including the NFIB oncogene. Continued studies of salivary gland LCNEC may provide new knowledge concerning potential diagnostic biomarkers and may ultimately also lead to the identification of new treatment targets for patients with these aggressive carcinomas.
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Affiliation(s)
- Simon Andreasen
- Department of Otorhinolaryngology Head and Neck Surgery and Audiology, Rigshospitalet, Copenhagen, Denmark
| | - Marta Persson
- Sahlgrenska Cancer Center, Department of Pathology, University of Gothenburg, Gothenburg, Sweden
| | - Katalin Kiss
- Department of Pathology, Rigshospitalet, Copenhagen, Denmark
| | - Preben Homøe
- Department of Otorhinolaryngology and Maxillofacial Surgery, Køge University Hospital, Køge, Denmark
| | | | - Göran Stenman
- Sahlgrenska Cancer Center, Department of Pathology, University of Gothenburg, Gothenburg, Sweden
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327
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Paratala BS, Dolfi SC, Khiabanian H, Rodriguez-Rodriguez L, Ganesan S, Hirshfield KM. Emerging Role of Genomic Rearrangements in Breast Cancer: Applying Knowledge from Other Cancers. BIOMARKERS IN CANCER 2016; 8:1-14. [PMID: 26917980 PMCID: PMC4756769 DOI: 10.4137/bic.s34417] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 12/28/2015] [Accepted: 12/31/2015] [Indexed: 12/16/2022]
Abstract
Significant advances in our knowledge of cancer genomes are rapidly changing the way we think about tumor biology and the heterogeneity of cancer. Recent successes in genomically-guided treatment approaches accompanied by more sophisticated sequencing techniques have paved the way for deeper investigation into the landscape of genomic rearrangements in cancer. While considerable research on solid tumors has focused on point mutations that directly alter the coding sequence of key genes, far less is known about the role of somatic rearrangements. With many recurring alterations observed across tumor types, there is an obvious need for functional characterization of these genomic biomarkers in order to understand their relevance to tumor biology, therapy, and prognosis. As personalized therapy approaches are turning toward genomic alterations for answers, these biomarkers will become increasingly relevant to the practice of precision medicine. This review discusses the emerging role of genomic rearrangements in breast cancer, with a particular focus on fusion genes. In addition, it raises several key questions on the therapeutic value of such rearrangements and provides a framework to evaluate their significance as predictive and prognostic biomarkers.
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Affiliation(s)
- Bhavna S. Paratala
- Department of Medicine, Division of Medical Oncology, Rutgers Cancer Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
- Department of Cellular and Molecular Pharmacology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, USA
| | - Sonia C. Dolfi
- Department of Medicine, Division of Medical Oncology, Rutgers Cancer Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Hossein Khiabanian
- Department of Pathology, Division of Medical Informatics, Rutgers Cancer Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Lorna Rodriguez-Rodriguez
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, Rutgers Cancer Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Shridar Ganesan
- Department of Medicine, Division of Medical Oncology, Rutgers Cancer Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Kim M. Hirshfield
- Department of Medicine, Division of Medical Oncology, Rutgers Cancer Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
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328
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Whole-Genome Sequencing Reveals Diverse Models of Structural Variations in Esophageal Squamous Cell Carcinoma. Am J Hum Genet 2016; 98:256-74. [PMID: 26833333 PMCID: PMC4746371 DOI: 10.1016/j.ajhg.2015.12.013] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Accepted: 12/15/2015] [Indexed: 01/02/2023] Open
Abstract
Comprehensive identification of somatic structural variations (SVs) and understanding their mutational mechanisms in cancer might contribute to understanding biological differences and help to identify new therapeutic targets. Unfortunately, characterization of complex SVs across the whole genome and the mutational mechanisms underlying esophageal squamous cell carcinoma (ESCC) is largely unclear. To define a comprehensive catalog of somatic SVs, affected target genes, and their underlying mechanisms in ESCC, we re-analyzed whole-genome sequencing (WGS) data from 31 ESCCs using Meerkat algorithm to predict somatic SVs and Patchwork to determine copy-number changes. We found deletions and translocations with NHEJ and alt-EJ signature as the dominant SV types, and 16% of deletions were complex deletions. SVs frequently led to disruption of cancer-associated genes (e.g., CDKN2A and NOTCH1) with different mutational mechanisms. Moreover, chromothripsis, kataegis, and breakage-fusion-bridge (BFB) were identified as contributing to locally mis-arranged chromosomes that occurred in 55% of ESCCs. These genomic catastrophes led to amplification of oncogene through chromothripsis-derived double-minute chromosome formation (e.g., FGFR1 and LETM2) or BFB-affected chromosomes (e.g., CCND1, EGFR, ERBB2, MMPs, and MYC), with approximately 30% of ESCCs harboring BFB-derived CCND1 amplification. Furthermore, analyses of copy-number alterations reveal high frequency of whole-genome duplication (WGD) and recurrent focal amplification of CDCA7 that might act as a potential oncogene in ESCC. Our findings reveal molecular defects such as chromothripsis and BFB in malignant transformation of ESCCs and demonstrate diverse models of SVs-derived target genes in ESCCs. These genome-wide SV profiles and their underlying mechanisms provide preventive, diagnostic, and therapeutic implications for ESCCs.
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329
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Babiceanu M, Qin F, Xie Z, Jia Y, Lopez K, Janus N, Facemire L, Kumar S, Pang Y, Qi Y, Lazar IM, Li H. Recurrent chimeric fusion RNAs in non-cancer tissues and cells. Nucleic Acids Res 2016; 44:2859-72. [PMID: 26837576 PMCID: PMC4824105 DOI: 10.1093/nar/gkw032] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 01/11/2016] [Indexed: 11/13/2022] Open
Abstract
Gene fusions and their products (RNA and protein) were once thought to be unique features to cancer. However, chimeric RNAs can also be found in normal cells. Here, we performed, curated and analyzed nearly 300 RNA-Seq libraries covering 30 different non-neoplastic human tissues and cells as well as 15 mouse tissues. A large number of fusion transcripts were found. Most fusions were detected only once, while 291 were seen in more than one sample. We focused on the recurrent fusions and performed RNA and protein level validations on a subset. We characterized these fusions based on various features of the fusions, and their parental genes. They tend to be expressed at higher levels relative to their parental genes than the non-recurrent ones. Over half of the recurrent fusions involve neighboring genes transcribing in the same direction. A few sequence motifs were found enriched close to the fusion junction sites. We performed functional analyses on a few widely expressed fusions, and found that silencing them resulted in dramatic reduction in normal cell growth and/or motility. Most chimeras use canonical splicing sites, thus are likely products of 'intergenic splicing'. We also explored the implications of these non-pathological fusions in cancer and in evolution.
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Affiliation(s)
- Mihaela Babiceanu
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Fujun Qin
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Zhongqiu Xie
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Yuemeng Jia
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Kevin Lopez
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Nick Janus
- Department of Computer Science, University of Virginia, Charlottesville, VA 22908, USA
| | - Loryn Facemire
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Shailesh Kumar
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Yuwei Pang
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
| | - Yanjun Qi
- Department of Computer Science, University of Virginia, Charlottesville, VA 22908, USA
| | - Iulia M Lazar
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
| | - Hui Li
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
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330
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Abstract
Over the past decade, rapid advances in genomics, proteomics and functional genomics technologies that enable in-depth interrogation of cancer genomes and proteomes and high-throughput analysis of gene function have enabled characterization of the kinome 'at large' in human cancers, providing crucial insights into how members of the protein kinase superfamily are dysregulated in malignancy, the context-dependent functional role of specific kinases in cancer and how kinome remodelling modulates sensitivity to anticancer drugs. The power of these complementary approaches, and the insights gained from them, form the basis of this Analysis article.
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Affiliation(s)
- Emmy D G Fleuren
- Department of Medical Oncology, Radboud University Medical Centre, Geert Grooteplein-Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Luxi Zhang
- Cancer Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
- University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Jianmin Wu
- Cancer Division, Kinghorn Cancer Centre, Garvan Institute of Medical Research, 370 Victoria Street, Sydney, New South Wales 2010, Australia
| | - Roger J Daly
- Cancer Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
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331
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Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A, Szcześniak MW, Gaffney DJ, Elo LL, Zhang X, Mortazavi A. A survey of best practices for RNA-seq data analysis. Genome Biol 2016; 17:13. [PMID: 26813401 PMCID: PMC4728800 DOI: 10.1186/s13059-016-0881-8] [Citation(s) in RCA: 1358] [Impact Index Per Article: 169.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
RNA-sequencing (RNA-seq) has a wide variety of applications, but no single analysis pipeline can be used in all cases. We review all of the major steps in RNA-seq data analysis, including experimental design, quality control, read alignment, quantification of gene and transcript levels, visualization, differential gene expression, alternative splicing, functional analysis, gene fusion detection and eQTL mapping. We highlight the challenges associated with each step. We discuss the analysis of small RNAs and the integration of RNA-seq with other functional genomics techniques. Finally, we discuss the outlook for novel technologies that are changing the state of the art in transcriptomics.
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Affiliation(s)
- Ana Conesa
- Institute for Food and Agricultural Sciences, Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32603, USA. .,Centro de Investigación Príncipe Felipe, Genomics of Gene Expression Laboratory, 46012, Valencia, Spain.
| | - Pedro Madrigal
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. .,Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Anne McLaren Laboratory for Regenerative Medicine, Department of Surgery, University of Cambridge, Cambridge, CB2 0SZ, UK.
| | - Sonia Tarazona
- Centro de Investigación Príncipe Felipe, Genomics of Gene Expression Laboratory, 46012, Valencia, Spain.,Department of Applied Statistics, Operations Research and Quality, Universidad Politécnica de Valencia, 46020, Valencia, Spain
| | - David Gomez-Cabrero
- Unit of Computational Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, 171 77, Stockholm, Sweden.,Center for Molecular Medicine, Karolinska Institutet, 17177, Stockholm, Sweden.,Unit of Clinical Epidemiology, Department of Medicine, Karolinska University Hospital, L8, 17176, Stockholm, Sweden.,Science for Life Laboratory, 17121, Solna, Sweden
| | - Alejandra Cervera
- Systems Biology Laboratory, Institute of Biomedicine and Genome-Scale Biology Research Program, University of Helsinki, 00014, Helsinki, Finland
| | - Andrew McPherson
- School of Computing Science, Simon Fraser University, Burnaby, V5A 1S6, BC, Canada
| | - Michał Wojciech Szcześniak
- Department of Bioinformatics, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznań, 61-614, Poznań, Poland
| | - Daniel J Gaffney
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Laura L Elo
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, FI-20520, Turku, Finland
| | - Xuegong Zhang
- Key Lab of Bioinformatics/Bioinformatics Division, TNLIST and Department of Automation, Tsinghua University, Beijing, 100084, China.,School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Ali Mortazavi
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, 92697-2300, USA. .,Center for Complex Biological Systems, University of California, Irvine, Irvine, CA, 92697, USA.
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332
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Subbannayya Y, Pinto SM, Gowda H, Prasad TSK. Proteogenomics for understanding oncology: recent advances and future prospects. Expert Rev Proteomics 2016; 13:297-308. [PMID: 26697917 DOI: 10.1586/14789450.2016.1136217] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The concept of proteogenomics has emerged rapidly as a valuable approach to integrate mass spectrometry-derived proteomic data with genomic and transcriptomic data. It is used to harness the full potential of the former dataset in the discovery of potential biomarkers, therapeutic targets and novel proteins associated with various biological processes including diseases. Proteogenomic strategies have been successfully utilized to identify novel genes and redefine annotation of existing gene models in various genomes. In recent years, this approach has been extended to the field of cancer biology to unravel complexities in the tumor genomes and proteomes. Standard proteomics workflows employing translated cancer genomes and transcriptomes can potentially identify peptides from mutant proteins, splice variants and fusion proteins in the tumor proteome, which in addition to the currently available biomarker panels can serve as potential diagnostic and prognostic biomarkers, besides having therapeutic utility. This review focuses on the role of proteogenomics to understand cancer biology.
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Affiliation(s)
- Yashwanth Subbannayya
- a YU-IOB Center for Systems Biology and Molecular Medicine , Yenepoya University , Mangalore, India.,b Institute of Bioinformatics , Bangalore , India
| | - Sneha M Pinto
- a YU-IOB Center for Systems Biology and Molecular Medicine , Yenepoya University , Mangalore, India.,b Institute of Bioinformatics , Bangalore , India
| | - Harsha Gowda
- a YU-IOB Center for Systems Biology and Molecular Medicine , Yenepoya University , Mangalore, India.,b Institute of Bioinformatics , Bangalore , India
| | - T S Keshava Prasad
- a YU-IOB Center for Systems Biology and Molecular Medicine , Yenepoya University , Mangalore, India.,b Institute of Bioinformatics , Bangalore , India.,c NIMHANS-IOB Proteomics and Bioinformatics Laboratory, Neurobiology Research Centre , National Institute of Mental Health and Neurosciences , Bangalore , India
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333
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Erdem-Eraslan L, van den Bent MJ, Hoogstrate Y, Naz-Khan H, Stubbs A, van der Spek P, Böttcher R, Gao Y, de Wit M, Taal W, Oosterkamp HM, Walenkamp A, Beerepoot LV, Hanse MCJ, Buter J, Honkoop AH, van der Holt B, Vernhout RM, Sillevis Smitt PAE, Kros JM, French PJ. Identification of Patients with Recurrent Glioblastoma Who May Benefit from Combined Bevacizumab and CCNU Therapy: A Report from the BELOB Trial. Cancer Res 2016; 76:525-34. [PMID: 26762204 DOI: 10.1158/0008-5472.can-15-0776] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 10/08/2015] [Indexed: 11/16/2022]
Abstract
The results from the randomized phase II BELOB trial provided evidence for a potential benefit of bevacizumab (beva), a humanized monoclonal antibody against circulating VEGF-A, when added to CCNU chemotherapy in patients with recurrent glioblastoma (GBM). In this study, we performed gene expression profiling (DASL and RNA-seq) of formalin-fixed, paraffin-embedded tumor material from participants of the BELOB trial to identify patients with recurrent GBM who benefitted most from beva+CCNU treatment. We demonstrate that tumors assigned to the IGS-18 or "classical" subtype and treated with beva+CCNU showed a significant benefit in progression-free survival and a trend toward benefit in overall survival, whereas other subtypes did not exhibit such benefit. In particular, expression of FMO4 and OSBPL3 was associated with treatment response. Importantly, the improved outcome in the beva+CCNU treatment arm was not explained by an uneven distribution of prognostically favorable subtypes as all molecular glioma subtypes were evenly distributed along the different study arms. The RNA-seq analysis also highlighted genetic alterations, including mutations, gene fusions, and copy number changes, within this well-defined cohort of tumors that may serve as useful predictive or prognostic biomarkers of patient outcome. Further validation of the identified molecular markers may enable the future stratification of recurrent GBM patients into appropriate treatment regimens.
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Affiliation(s)
- Lale Erdem-Eraslan
- Department of Neurology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | | | - Youri Hoogstrate
- Department of Urology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands. Bioinformatics, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Hina Naz-Khan
- Bioinformatics, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Andrew Stubbs
- Bioinformatics, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | | | - René Böttcher
- Department of Urology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Ya Gao
- Department of Neurology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Maurice de Wit
- Department of Neurology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Walter Taal
- Department of Neurology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Hendrika M Oosterkamp
- Department of Medical Oncology, Medical Center Haaglanden, The Hague, the Netherlands
| | - Annemiek Walenkamp
- Department of Medical Oncology, University Medical Center Groningen, Groningen, the Netherlands
| | | | - Monique C J Hanse
- Department of Neurology, Catharina Hospital Eindhoven, the Netherlands
| | - Jan Buter
- Department of Oncology, VU University Medical Center, Amsterdam, the Netherlands
| | - Aafke H Honkoop
- Department of Internal Medicine, Isala Kliniek, Zwolle, the Netherlands
| | - Bronno van der Holt
- Clinical Trial Center, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - René M Vernhout
- Clinical Trial Center, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | | | - Johan M Kros
- Pathology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Pim J French
- Department of Neurology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands.
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334
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Pagan M, Kloos RT, Lin CF, Travers KJ, Matsuzaki H, Tom EY, Kim SY, Wong MG, Stewart AC, Huang J, Walsh PS, Monroe RJ, Kennedy GC. The diagnostic application of RNA sequencing in patients with thyroid cancer: an analysis of 851 variants and 133 fusions in 524 genes. BMC Bioinformatics 2016; 17 Suppl 1:6. [PMID: 26818556 PMCID: PMC4895782 DOI: 10.1186/s12859-015-0849-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Background Thyroid carcinomas are known to harbor oncogenic driver mutations and advances in sequencing technology now allow the detection of these in fine needle aspiration biopsies (FNA). Recent work by The Cancer Genome Atlas (TCGA) Research Network has expanded the number of genetic alterations detected in papillary thyroid carcinomas (PTC). We sought to investigate the prevalence of these and other genetic alterations in diverse subtypes of thyroid nodules beyond PTC, including a variety of samples with benign histopathology. This is the first clinical evaluation of a large panel of TCGA-reported genomic alterations in thyroid FNAs. Results In FNAs, genetic alterations were detected in 19/44 malignant samples (43 % sensitivity) and in 7/44 histopathology benign samples (84 % specificity). Overall, after adding a cohort of tissue samples, 38/76 (50 %) of histopathology malignant samples were found to harbor a genetic alteration, while 15/75 (20 %) of benign samples were also mutated. The most frequently mutated malignant subtypes were medullary thyroid carcinoma (9/12, 75 %) and PTC (14/30, 47 %). Additionally, follicular adenoma, a benign subtype of thyroid neoplasm, was also found to harbor mutations (12/29, 41 %). Frequently mutated genes in malignant samples included BRAF (20/76, 26 %) and RAS (9/76, 12 %). Of the TSHR variants detected, (6/7, 86 %) were in benign nodules. In a direct comparison of the same FNA also tested by an RNA-based gene expression classifier (GEC), the sensitivity of genetic alterations alone was 42 %, compared to the 91 % sensitivity achieved by the GEC. The specificity based only on genetic alterations was 84 %, compared to 77 % specificity with the GEC. Conclusions While the genomic landscape of all thyroid neoplasm subtypes will inevitably be elucidated, caution should be used in the early adoption of published mutations as the sole predictor of malignancy in thyroid. The largest set of such mutations known to date detects only a portion of thyroid carcinomas in preoperative FNAs in our cohort and thus is not sufficient to rule out cancer. Due to the finding that variants are also found in benign nodules, testing only GEC suspicious nodules may be helpful in avoiding false positives and altering the extent of treatment when selected mutations are found. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0849-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | - Ed Y Tom
- Veracyte, Inc., South San Francisco, CA, USA
| | - Su Yeon Kim
- Veracyte, Inc., South San Francisco, CA, USA
| | - Mei G Wong
- Veracyte, Inc., South San Francisco, CA, USA
| | | | - Jing Huang
- Veracyte, Inc., South San Francisco, CA, USA
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335
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Narang P, Dhapola P, Chowdhury S. BreCAN-DB: a repository cum browser of personalized DNA breakpoint profiles of cancer genomes. Nucleic Acids Res 2016; 44:D952-8. [PMID: 26586806 PMCID: PMC4702892 DOI: 10.1093/nar/gkv1264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Revised: 10/29/2015] [Accepted: 11/03/2015] [Indexed: 11/20/2022] Open
Abstract
BreCAN-DB (http://brecandb.igib.res.in) is a repository cum browser of whole genome somatic DNA breakpoint profiles of cancer genomes, mapped at single nucleotide resolution using deep sequencing data. These breakpoints are associated with deletions, insertions, inversions, tandem duplications, translocations and a combination of these structural genomic alterations. The current release of BreCAN-DB features breakpoint profiles from 99 cancer-normal pairs, comprising five cancer types. We identified DNA breakpoints across genomes using high-coverage next-generation sequencing data obtained from TCGA and dbGaP. Further, in these cancer genomes, we methodically identified breakpoint hotspots which were significantly enriched with somatic structural alterations. To visualize the breakpoint profiles, a next-generation genome browser was integrated with BreCAN-DB. Moreover, we also included previously reported breakpoint profiles from 138 cancer-normal pairs, spanning 10 cancer types into the browser. Additionally, BreCAN-DB allows one to identify breakpoint hotspots in user uploaded data set. We have also included a functionality to query overlap of any breakpoint profile with regions of user's interest. Users can download breakpoint profiles from the database or may submit their data to be integrated in BreCAN-DB. We believe that BreCAN-DB will be useful resource for genomics scientific community and is a step towards personalized cancer genomics.
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Affiliation(s)
- Pankaj Narang
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Parashar Dhapola
- GNR Center for Genome Informatics, Institute of Genomics and Integrative Biology, CSIR, Delhi, India
| | - Shantanu Chowdhury
- GNR Center for Genome Informatics, Institute of Genomics and Integrative Biology, CSIR, Delhi, India Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, CSIR, Delhi, India
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336
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Tamura R, Yoshihara K, Yamawaki K, Suda K, Ishiguro T, Adachi S, Okuda S, Inoue I, Verhaak RGW, Enomoto T. Novel kinase fusion transcripts found in endometrial cancer. Sci Rep 2015; 5:18657. [PMID: 26689674 PMCID: PMC4687039 DOI: 10.1038/srep18657] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 11/20/2015] [Indexed: 11/09/2022] Open
Abstract
Recent advances in RNA-sequencing technology have enabled the discovery of gene fusion transcripts in the transcriptome of cancer cells. However, it remains difficult to differentiate the therapeutically targetable fusions from passenger events. We have analyzed RNA-sequencing data and DNA copy number data from 25 endometrial cancer cell lines to identify potential therapeutically targetable fusion transcripts, and have identified 124 high-confidence fusion transcripts, of which 69% are associated with gene amplifications. As targetable fusion candidates, we focused on three in-frame kinase fusion transcripts that retain a kinase domain (CPQ-PRKDC, CAPZA2-MET, and VGLL4-PRKG1). We detected only CPQ-PRKDC fusion transcript in three of 122 primary endometrial cancer tissues. Cell proliferation of the fusion-positive cell line was inhibited by knocking down the expression of wild-type PRKDC but not by blocking the CPQ-PRKDC fusion transcript expression. Quantitative real-time RT-PCR demonstrated that the expression of the CPQ-PRKDC fusion transcript was significantly lower than that of wild-type PRKDC, corresponding to a low transcript allele fraction of this fusion, based on RNA-sequencing read counts. In endometrial cancers, the CPQ-PRKDC fusion transcript may be a passenger aberration related to gene amplification. Our findings suggest that transcript allele fraction is a useful predictor to find bona-fide therapeutic-targetable fusion transcripts.
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Affiliation(s)
- Ryo Tamura
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Kosuke Yoshihara
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Kaoru Yamawaki
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Kazuaki Suda
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Tatsuya Ishiguro
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Sosuke Adachi
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Shujiro Okuda
- Department of Bioinformatics, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Ituro Inoue
- Division of Human Genetics, National Institute of Genetics, Mishima, Japan
| | - Roel G W Verhaak
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Genome Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Takayuki Enomoto
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
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337
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Kumar-Sinha C, Kalyana-Sundaram S, Chinnaiyan AM. Landscape of gene fusions in epithelial cancers: seq and ye shall find. Genome Med 2015; 7:129. [PMID: 26684754 PMCID: PMC4683719 DOI: 10.1186/s13073-015-0252-1] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Enabled by high-throughput sequencing approaches, epithelial cancers across a range of tissue types are seen to harbor gene fusions as integral to their landscape of somatic aberrations. Although many gene fusions are found at high frequency in several rare solid cancers, apart from fusions involving the ETS family of transcription factors which have been seen in approximately 50% of prostate cancers, several other common solid cancers have been shown to harbor recurrent gene fusions at low frequencies. On the other hand, many gene fusions involving oncogenes, such as those encoding ALK, RAF or FGFR kinase families, have been detected across multiple different epithelial carcinomas. Tumor-specific gene fusions can serve as diagnostic biomarkers or help define molecular subtypes of tumors; for example, gene fusions involving oncogenes such as ERG, ETV1, TFE3, NUT, POU5F1, NFIB, PLAG1, and PAX8 are diagnostically useful. Tumors with fusions involving therapeutically targetable genes such as ALK, RET, BRAF, RAF1, FGFR1-4, and NOTCH1-3 have immediate implications for precision medicine across tissue types. Thus, ongoing cancer genomic and transcriptomic analyses for clinical sequencing need to delineate the landscape of gene fusions. Prioritization of potential oncogenic "drivers" from "passenger" fusions, and functional characterization of potentially actionable gene fusions across diverse tissue types, will help translate these findings into clinical applications. Here, we review recent advances in gene fusion discovery and the prospects for medicine.
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Affiliation(s)
- Chandan Kumar-Sinha
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
| | - Shanker Kalyana-Sundaram
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
- Howard Hughes Medical Institute, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
- Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
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338
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Mertens F, Antonescu CR, Mitelman F. Gene fusions in soft tissue tumors: Recurrent and overlapping pathogenetic themes. Genes Chromosomes Cancer 2015; 55:291-310. [PMID: 26684580 DOI: 10.1002/gcc.22335] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 11/01/2015] [Accepted: 11/01/2015] [Indexed: 12/21/2022] Open
Abstract
Gene fusions have been described in approximately one-third of soft tissue tumors (STT); of the 142 different fusions that have been reported, more than half are recurrent in the same histologic subtype. These gene fusions constitute pivotal driver mutations, and detailed studies of their cellular effects have provided important knowledge about pathogenetic mechanisms in STT. Furthermore, most fusions are strongly associated with a particular histotype, serving as ideal molecular diagnostic markers. In recent years, it has also become apparent that some chimeric proteins, directly or indirectly, constitute excellent treatment targets, making the detection of gene fusions in STT ever more important. Indeed, pharmacological treatment of STT displaying fusions that activate protein kinases, such as ALK and ROS1, or growth factors, such as PDGFB, is already in clinical use. However, the vast majority (52/78) of recurrent gene fusions create structurally altered and/or deregulated transcription factors, and a small but growing subset develops through rearranged chromatin regulators. The present review provides an overview of the spectrum of currently recognized gene fusions in STT, and, on the basis of the protein class involved, the mechanisms by which they exert their oncogenic effect are discussed.
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Affiliation(s)
- Fredrik Mertens
- Department of Clinical Genetics, University and Regional Laboratories, Lund University, Lund, Sweden
| | | | - Felix Mitelman
- Department of Clinical Genetics, University and Regional Laboratories, Lund University, Lund, Sweden
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339
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Zhao M, Kim P, Mitra R, Zhao J, Zhao Z. TSGene 2.0: an updated literature-based knowledgebase for tumor suppressor genes. Nucleic Acids Res 2015; 44:D1023-31. [PMID: 26590405 PMCID: PMC4702895 DOI: 10.1093/nar/gkv1268] [Citation(s) in RCA: 262] [Impact Index Per Article: 29.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 11/03/2015] [Indexed: 11/14/2022] Open
Abstract
Tumor suppressor genes (TSGs) are a major type of gatekeeper genes in the cell growth. A knowledgebase with the systematic collection and curation of TSGs in multiple cancer types is critically important for further studying their biological functions as well as for developing therapeutic strategies. Since its development in 2012, the Tumor Suppressor Gene database (TSGene), has become a popular resource in the cancer research community. Here, we reported the TSGene version 2.0, which has substantial updates of contents (e.g. up-to-date literature and pan-cancer genomic data collection and curation), data types (noncoding RNAs and protein-coding genes) and content accessibility. Specifically, the current TSGene 2.0 contains 1217 human TSGs (1018 protein-coding and 199 non-coding genes) curated from over 9000 articles. Additionally, TSGene 2.0 provides thousands of expression and mutation patterns derived from pan-cancer data of The Cancer Genome Atlas. A new web interface is available at http://bioinfo.mc.vanderbilt.edu/TSGene/. Systematic analyses of 199 non-coding TSGs provide numerous cancer-specific non-coding mutational events for further screening and clinical use. Intriguingly, we identified 49 protein-coding TSGs that were consistently down-regulated in 11 cancer types. In summary, TSGene 2.0, which is the only available database for TSGs, provides the most updated TSGs and their features in pan-cancer.
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Affiliation(s)
- Min Zhao
- School of Engineering, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Pora Kim
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Ramkrishna Mitra
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Junfei Zhao
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Zhongming Zhao
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, TN 37212, USA School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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340
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Korla PK, Cheng J, Huang CH, Tsai JJP, Liu YH, Kurubanjerdjit N, Hsieh WT, Chen HY, Ng KL. FARE-CAFE: a database of functional and regulatory elements of cancer-associated fusion events. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2015; 2015:bav086. [PMID: 26384373 PMCID: PMC4684693 DOI: 10.1093/database/bav086] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 08/18/2015] [Indexed: 01/08/2023]
Abstract
Chromosomal translocation (CT) is of enormous clinical interest because this disorder is associated with various major solid tumors and leukemia. A tumor-specific fusion gene event may occur when a translocation joins two separate genes. Currently, various CT databases provide information about fusion genes and their genomic elements. However, no database of the roles of fusion genes, in terms of essential functional and regulatory elements in oncogenesis, is available. FARE-CAFE is a unique combination of CTs, fusion proteins, protein domains, domain–domain interactions, protein–protein interactions, transcription factors and microRNAs, with subsequent experimental information, which cannot be found in any other CT database. Genomic DNA information including, for example, manually collected exact locations of the first and second break points, sequences and karyotypes of fusion genes are included. FARE-CAFE will substantially facilitate the cancer biologist’s mission of elucidating the pathogenesis of various types of cancer. This database will ultimately help to develop ‘novel’ therapeutic approaches. Database URL:http://ppi.bioinfo.asia.edu.tw/FARE-CAFE
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Affiliation(s)
- Praveen Kumar Korla
- Department of Bioinformatics and Medical Engineering, Asia University, Taichung 41354, Taiwan
| | - Jack Cheng
- Graduate Institute of Integrated Medicine, College of Chinese Medicine, China Medical University, Taichung 40402, Taiwan
| | - Chien-Hung Huang
- Department of Computer Science and Information Engineering, National Formosa University, Yunlin 632, Taiwan
| | - Jeffrey J P Tsai
- Department of Bioinformatics and Medical Engineering, Asia University, Taichung 41354, Taiwan
| | - Yu-Hsuan Liu
- Department of Computer Science and Information Engineering, National Formosa University, Yunlin 632, Taiwan
| | | | - Wen-Tsong Hsieh
- Department of Pharmacology, China Medical University, Taichung 40402, Taiwan
| | - Huey-Yi Chen
- Department of Obstetrics and Gynecology, China Medical University Hospital, China Medical University, Taichung 40402, Taiwan, and
| | - Ka-Lok Ng
- Department of Bioinformatics and Medical Engineering, Asia University, Taichung 41354, Taiwan, Department of Medical Research, China Medical University Hospital, China Medical University, Taichung 40402, Taiwan
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341
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Griffith M, Walker JR, Spies NC, Ainscough BJ, Griffith OL. Informatics for RNA Sequencing: A Web Resource for Analysis on the Cloud. PLoS Comput Biol 2015; 11:e1004393. [PMID: 26248053 PMCID: PMC4527835 DOI: 10.1371/journal.pcbi.1004393] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Massively parallel RNA sequencing (RNA-seq) has rapidly become the assay of choice for interrogating RNA transcript abundance and diversity. This article provides a detailed introduction to fundamental RNA-seq molecular biology and informatics concepts. We make available open-access RNA-seq tutorials that cover cloud computing, tool installation, relevant file formats, reference genomes, transcriptome annotations, quality-control strategies, expression, differential expression, and alternative splicing analysis methods. These tutorials and additional training resources are accompanied by complete analysis pipelines and test datasets made available without encumbrance at www.rnaseq.wiki.
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Affiliation(s)
- Malachi Griffith
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Jason R. Walker
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Nicholas C. Spies
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Benjamin J. Ainscough
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Obi L. Griffith
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
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342
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Abstract
Structural chromosome rearrangements may result in the exchange of coding or regulatory DNA sequences between genes. Many such gene fusions are strong driver mutations in neoplasia and have provided fundamental insights into the disease mechanisms that are involved in tumorigenesis. The close association between the type of gene fusion and the tumour phenotype makes gene fusions ideal for diagnostic purposes, enabling the subclassification of otherwise seemingly identical disease entities. In addition, many gene fusions add important information for risk stratification, and increasing numbers of chimeric proteins encoded by the gene fusions serve as specific targets for treatment, resulting in dramatically improved patient outcomes. In this Timeline article, we describe the spectrum of gene fusions in cancer and how the methods to identify them have evolved, and also discuss conceptual implications of current, sequencing-based approaches for detection.
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Affiliation(s)
- Fredrik Mertens
- Department of Clinical Genetics, Lund University and Skåne University Hospital, SE-221 85 Lund, Sweden
| | - Bertil Johansson
- Department of Clinical Genetics, Lund University and Skåne University Hospital, SE-221 85 Lund, Sweden
| | - Thoas Fioretos
- Department of Clinical Genetics, Lund University and Skåne University Hospital, SE-221 85 Lund, Sweden
| | - Felix Mitelman
- Department of Clinical Genetics, Lund University and Skåne University Hospital, SE-221 85 Lund, Sweden
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343
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Subbiah V, Berry J, Roxas M, Guha-Thakurta N, Subbiah IM, Ali SM, McMahon C, Miller V, Cascone T, Pai S, Tang Z, Heymach JV. Systemic and CNS activity of the RET inhibitor vandetanib combined with the mTOR inhibitor everolimus in KIF5B-RET re-arranged non-small cell lung cancer with brain metastases. Lung Cancer 2015; 89:76-9. [PMID: 25982012 DOI: 10.1016/j.lungcan.2015.04.004] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 04/06/2015] [Accepted: 04/12/2015] [Indexed: 10/23/2022]
Abstract
In-frame fusion KIF5B (the-kinesin-family-5B-gene)-RET transcripts have been characterized in 1-2% of non-small cell lung cancers and are known oncogenic drivers. The RET tyrosine kinase inhibitor, vandetanib, suppresses fusion-induced, anchorage-independent growth activity. In vitro studies have shown that vandetanib is a high-affinity substrate of breast cancer resistance protein (Bcrp1/Abcg2) but is not transported by P-glycoprotein (P-gp), limiting its blood-brain barrier penetration. A co-administration strategy to enhance the brain accumulation of vandetanib by modulating P-gp/Abcb1- and Bcrp1/Abcg2-mediated efflux with mTOR inhibitors, specifically everolimus, was shown to increase the blood-brain barrier penetration. We report the first bench-to-bedside evidence that RET inhibitor combined with an mTOR inhibitor is active against brain-metastatic RET-rearranged lung cancer and the first evidence of blood-brain barrier penetration. A 74-year-old female with progressive adenocarcinoma of the lung (wild-type EGFR and no ALK rearrangement) presented for therapy options. A deletion of 5'RET was revealed by FISH assay, indicating RET-gene rearrangement. Because of progressive disease in the brain, she was enrolled in a clinical trial with vandetanib and everolimus (NCT01582191). Comprehensive genomic profiling revealed fusion of KIF5B (the-kinesin-family-5B-gene) and RET, in addition to AKT2 gene amplification. After two cycles of therapy a repeat MRI brain showed a decrease in the intracranial disease burden and PET/CT showed systemic response as well. Interestingly, AKT2 amplification seen is a critical component of the PI3K/mTOR pathway, alterations of which has been associated with both de novo and acquired resistance to targeted therapy. The addition of everolimus may have both overcome the AKT2 amplification to produce a response in addition to its direct effects on the RET gene. Our case report forms the first evidence of blood-brain barrier penetration by vandetanib in combination with everolimus. Further research is required in this setting.
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Affiliation(s)
- Vivek Subbiah
- The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, United States.
| | - Jenny Berry
- The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, United States
| | - Michael Roxas
- The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, United States
| | - Nandita Guha-Thakurta
- The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, United States
| | - Ishwaria Mohan Subbiah
- The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, United States
| | - Siraj M Ali
- Foundation Medicine, Boston, MA, United States
| | | | | | - Tina Cascone
- The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, United States
| | - Shobha Pai
- The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, United States
| | - Zhenya Tang
- The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, United States
| | - John V Heymach
- The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, United States
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