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Torres MDA, Jones MR, Vom Berg C, Pinto E, Janssen EML. Lethal and sublethal effects towards zebrafish larvae of microcystins and other cyanopeptides produced by cyanobacteria. Aquat Toxicol 2023; 263:106689. [PMID: 37713741 DOI: 10.1016/j.aquatox.2023.106689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/04/2023] [Accepted: 09/07/2023] [Indexed: 09/17/2023]
Abstract
Cyanobacterial blooms affect aquatic ecosystems across the globe and one major concern relates to their toxins such as microcystins (MC). Yet, the ecotoxicological risks, particularly non-lethal effects, associated with other co-produced secondary metabolites remain mostly unknown. Here, we assessed survival, morphological alterations, swimming behaviour and cardiovascular functions of zebrafish (Danio rerio) upon exposure to cyanobacterial extracts of two Brazilian Microcystis strains. We verified that only MIRS-04 produced MCs and identified other co-produced cyanopeptides also for the MC non-producer NPCD-01 by LC-HRMS/MS analysis. Both cyanobacterial extracts, from the MC-producer and non-producer, caused acute toxicity in zebrafish with LC50 values of 0.49 and 0.98 mgdw_biomass/mL, respectively. After exposure to MC-producer extract, additional decreased locomotor activity was observed. The cyanopeptolin (micropeptin K139) contributed 52% of the overall mortality and caused oedemas of the pericardial region. Oedemas of the pericardial area and prevented hatching were also observed upon exposure to the fraction with high abundance of a microginin (Nostoginin BN741) in the extract of the MC non-producer. Our results further add to the yet sparse understanding of lethal and sublethal effects caused by cyanobacterial metabolites other than MCs and the need to better understand the underlying mechanisms of the toxicity. We emphasize the importance of considering mixture toxicity of co-produced metabolites in the ecotoxicological risk assessment of cyanobacterial bloom events, given the importance for predicting adverse outcomes in fish and other organisms.
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Affiliation(s)
| | - Martin R Jones
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom, B15 2TT
| | - Colette Vom Berg
- Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600 Dübendorf, Switzerland
| | - Ernani Pinto
- Centre for Nuclear Energy in Agriculture, University of São Paulo, 13418-260, Piracicaba, Brazil
| | - Elisabeth M-L Janssen
- Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600 Dübendorf, Switzerland.
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2
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Busquet F, Laperrouze J, Jankovic K, Krsmanovic T, Ignasiak T, Leoni B, Apic G, Asole G, Guigó R, Marangio P, Palumbo E, Perez-Lluch S, Wucher V, Vlot AH, Anholt R, Mackay T, Escher BI, Grasse N, Huchthausen J, Massei R, Reemtsma T, Scholz S, Schüürmann G, Bondesson M, Cherbas P, Freedman JH, Glaholt S, Holsopple J, Jacobson SC, Kaufman T, Popodi E, Shaw JJ, Smoot S, Tennessen JM, Churchill G, von Clausbruch CC, Dickmeis T, Hayot G, Pace G, Peravali R, Weiss C, Cistjakova N, Liu X, Slaitas A, Brown JB, Ayerbe R, Cabellos J, Cerro-Gálvez E, Diez-Ortiz M, González V, Martínez R, Vives PS, Barnett R, Lawson T, Lee RG, Sostare E, Viant M, Grafström R, Hongisto V, Kohonen P, Patyra K, Bhaskar PK, Garmendia-Cedillos M, Farooq I, Oliver B, Pohida T, Salem G, Jacobson D, Andrews E, Barnard M, Čavoški A, Chaturvedi A, Colbourne JK, Epps DJT, Holden L, Jones MR, Li X, Müller F, Ormanin-Lewandowska A, Orsini L, Roberts R, Weber RJM, Zhou J, Chung ME, Sanchez JCG, Diwan GD, Singh G, Strähle U, Russell RB, Batista D, Sansone SA, Rocca-Serra P, Du Pasquier D, Lemkine G, Robin-Duchesne B, Tindall A. The Precision Toxicology Initiative. Toxicol Lett 2023:S0378-4274(23)00180-7. [PMID: 37211341 DOI: 10.1016/j.toxlet.2023.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/01/2023] [Accepted: 05/09/2023] [Indexed: 05/23/2023]
Abstract
The goal of PrecisionTox is to overcome conceptual barriers to replacing traditional mammalian chemical safety testing by accelerating the discovery of evolutionarily conserved toxicity pathways that are shared by descent among humans and more distantly related animals. An international consortium is systematically testing the toxicological effects of a diverse set of chemicals on a suite of five model species comprising fruit flies, nematodes, water fleas, and embryos of clawed frogs and zebrafish along with human cell lines. Multiple forms of omics and comparative toxicology data are integrated to map the evolutionary origins of biomolecular interactions, which are predictive of adverse health effects, to major branches of the animal phylogeny. These conserved elements of adverse outcome pathways (AOPs) and their biomarkers are expect to provide mechanistic insight useful for regulating groups of chemicals based on their shared modes of action. PrecisionTox also aims to quantify risk variation within populations by recognizing susceptibility as a heritable trait that varies with genetic diversity. This initiative incorporates legal experts and collaborates with risk managers to address specific needs within European chemicals legislation, including the uptake of new approach methodologies (NAMs) for setting precise regulatory limits on toxic chemicals.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Nico Grasse
- Helmholtz Centre for Environmental Research, DE
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3
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Titmuss E, Milne K, Jones MR, Ng T, Topham JT, Brown SD, Schaeffer DF, Kalloger S, Wilson D, Corbett RD, Williamson LM, Mungall K, Mungall AJ, Holt RA, Nelson BH, Jones SJM, Laskin J, Lim HJ, Marra MA. Immune Activation following Irbesartan Treatment in a Colorectal Cancer Patient: A Case Study. Int J Mol Sci 2023; 24:ijms24065869. [PMID: 36982943 PMCID: PMC10051648 DOI: 10.3390/ijms24065869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 03/14/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
Colorectal cancers are one of the most prevalent tumour types worldwide and, despite the emergence of targeted and biologic therapies, have among the highest mortality rates. The Personalized OncoGenomics (POG) program at BC Cancer performs whole genome and transcriptome analysis (WGTA) to identify specific alterations in an individual's cancer that may be most effectively targeted. Informed using WGTA, a patient with advanced mismatch repair-deficient colorectal cancer was treated with the antihypertensive drug irbesartan and experienced a profound and durable response. We describe the subsequent relapse of this patient and potential mechanisms of response using WGTA and multiplex immunohistochemistry (m-IHC) profiling of biopsies before and after treatment from the same metastatic site of the L3 spine. We did not observe marked differences in the genomic landscape before and after treatment. Analyses revealed an increase in immune signalling and infiltrating immune cells, particularly CD8+ T cells, in the relapsed tumour. These results indicate that the observed anti-tumour response to irbesartan may have been due to an activated immune response. Determining whether there may be other cancer contexts in which irbesartan may be similarly valuable will require additional studies.
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Affiliation(s)
- E Titmuss
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - K Milne
- Deeley Research Centre, BC Cancer, Victoria, BC V8R 6V5, Canada
| | - M R Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - T Ng
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 1Z7, Canada
| | - J T Topham
- Pancreas Centre BC, Vancouver, BC V5Z 1G1, Canada
| | - S D Brown
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | | | - S Kalloger
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 1Z7, Canada
| | - D Wilson
- Department of Medical Oncology, BC Cancer, Vancouver, BC V5Z 4E6, Canada
| | - R D Corbett
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - L M Williamson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - K Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - A J Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - R A Holt
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z2, Canada
| | - B H Nelson
- Deeley Research Centre, BC Cancer, Victoria, BC V8R 6V5, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z2, Canada
| | - S J M Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - J Laskin
- Department of Medical Oncology, BC Cancer, Vancouver, BC V5Z 4E6, Canada
| | - H J Lim
- Department of Medical Oncology, BC Cancer, Vancouver, BC V5Z 4E6, Canada
| | - M A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z2, Canada
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4
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Tessier-Cloutier B, Grewal JK, Jones MR, Pleasance E, Shen Y, Cai E, Dunham C, Hoang L, Horst B, Huntsman DG, Ionescu D, Karnezis AN, Lee AF, Lee CH, Lee TH, Twa DD, Mungall AJ, Mungall K, Naso JR, Ng T, Schaeffer DF, Sheffield BS, Skinnider B, Smith T, Williamson L, Zhong E, Regier DA, Laskin J, Marra MA, Gilks CB, Jones SJ, Yip S. The impact of whole genome and transcriptome analysis (WGTA) on predictive biomarker discovery and diagnostic accuracy of advanced malignancies. J Pathol Clin Res 2022; 8:395-407. [PMID: 35257510 PMCID: PMC9161328 DOI: 10.1002/cjp2.265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 01/15/2022] [Accepted: 02/04/2022] [Indexed: 12/13/2022]
Abstract
In this study, we evaluate the impact of whole genome and transcriptome analysis (WGTA) on predictive molecular profiling and histologic diagnosis in a cohort of advanced malignancies. WGTA was used to generate reports including molecular alterations and site/tissue of origin prediction. Two reviewers analyzed genomic reports, clinical history, and tumor pathology. We used National Comprehensive Cancer Network (NCCN) consensus guidelines, Food and Drug Administration (FDA) approvals, and provincially reimbursed treatments to define genomic biomarkers associated with approved targeted therapeutic options (TTOs). Tumor tissue/site of origin was reassessed for most cases using genomic analysis, including a machine learning algorithm (Supervised Cancer Origin Prediction Using Expression [SCOPE]) trained on The Cancer Genome Atlas data. WGTA was performed on 652 cases, including a range of primary tumor types/tumor sites and 15 malignant tumors of uncertain histogenesis (MTUH). At the time WGTA was performed, alterations associated with an approved TTO were identified in 39 (6%) cases; 3 of these were not identified through routine pathology workup. In seven (1%) cases, the pathology workup either failed, was not performed, or gave a different result from the WGTA. Approved TTOs identified by WGTA increased to 103 (16%) when applying 2021 guidelines. The histopathologic diagnosis was reviewed in 389 cases and agreed with the diagnostic consensus after WGTA in 94% of non‐MTUH cases (n = 374). The remainder included situations where the morphologic diagnosis was changed based on WGTA and clinical data (0.5%), or where the WGTA was non‐contributory (5%). The 15 MTUH were all diagnosed as specific tumor types by WGTA. Tumor board reviews including WGTA agreed with almost all initial predictive molecular profile and histopathologic diagnoses. WGTA was a powerful tool to assign site/tissue of origin in MTUH. Current efforts focus on improving therapeutic predictive power and decreasing cost to enhance use of WGTA data as a routine clinical test.
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Affiliation(s)
- Basile Tessier-Cloutier
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Jasleen K Grewal
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Martin R Jones
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Erin Pleasance
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Yaoqing Shen
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Ellen Cai
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Chris Dunham
- Department of Pathology and Laboratory Medicine, Children's and Women's Health Centre of British Columbia, Vancouver, BC, Canada
| | - Lynn Hoang
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, BC, Canada
| | - Basil Horst
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, BC, Canada
| | - David G Huntsman
- Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada
| | - Diana Ionescu
- Department of Anatomical Pathology, BC Cancer, Vancouver, BC, Canada
| | - Anthony N Karnezis
- Department of Pathology and Laboratory Medicine, UC Davis, Sacramento, CA, USA
| | - Anna F Lee
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, Children's and Women's Health Centre of British Columbia, Vancouver, BC, Canada
| | - Cheng Han Lee
- Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada
| | - Tae Hoon Lee
- Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - David Dw Twa
- Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Karen Mungall
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Julia R Naso
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Tony Ng
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, BC, Canada
| | - David F Schaeffer
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, BC, Canada
| | - Brandon S Sheffield
- Department of Pathology and Laboratory Medicine, William Osler Health System, Brampton, ON, Canada
| | - Brian Skinnider
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, BC, Canada
| | - Tyler Smith
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, BC, Canada
| | - Laura Williamson
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Ellia Zhong
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Dean A Regier
- Cancer Control Research, BC Cancer, Vancouver, BC, Canada
| | - Janessa Laskin
- Division of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - C Blake Gilks
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, BC, Canada
| | - Steven Jm Jones
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Vancouver, BC, Canada
| | - Stephen Yip
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, BC, Canada.,Department of Molecular Oncology, BC Cancer, Vancouver, BC, Canada
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5
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Pleasance E, Bohm A, Williamson LM, Nelson JMT, Shen Y, Bonakdar M, Titmuss E, Csizmok V, Wee K, Hosseinzadeh S, Grisdale CJ, Reisle C, Taylor GA, Lewis E, Jones MR, Bleile D, Sadeghi S, Zhang W, Davies A, Pellegrini B, Wong T, Bowlby R, Chan SK, Mungall KL, Chuah E, Mungall AJ, Moore RA, Zhao Y, Deol B, Fisic A, Fok A, Regier DA, Weymann D, Schaeffer DF, Young S, Yip S, Schrader K, Levasseur N, Taylor SK, Feng X, Tinker A, Savage KJ, Chia S, Gelmon K, Sun S, Lim H, Renouf DJ, Jones SJM, Marra MA, Laskin J. Whole genome and transcriptome analysis enhances precision cancer treatment options. Ann Oncol 2022; 33:939-949. [PMID: 35691590 DOI: 10.1016/j.annonc.2022.05.522] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 05/03/2022] [Accepted: 05/31/2022] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Recent advances are enabling delivery of precision genomic medicine to cancer clinics. While the majority of approaches profile panels of selected genes or hotspot regions, comprehensive data provided by whole genome and transcriptome sequencing and analysis (WGTA) presents an opportunity to align a much larger proportion of patients to therapies. PATIENTS AND METHODS Samples from 570 patients with advanced or metastatic cancer of diverse types enrolled in the Personalized OncoGenomics (POG) program underwent WGTA. DNA-based data, including mutations, copy number, and mutation signatures, were combined with RNA-based data, including gene expression and fusions, to generate comprehensive WGTA profiles. A multidisciplinary molecular tumour board used WGTA profiles to identify and prioritize clinically actionable alterations and inform therapy. Patient responses to WGTA-informed therapies were collected. RESULTS Clinically actionable targets were identified for 83% of patients, 37% of whom received WGTA-informed treatments. RNA expression data were particularly informative, contributing to 67% of WGTA-informed treatments; 25% of treatments were informed by RNA expression alone. Of a total 248 WGTA-informed treatments, 46% resulted in clinical benefit. RNA expression data were comparable to DNA-based mutation and copy number data in aligning to clinically beneficial treatments. Genome signatures also guided therapeutics including platinum, PARP inhibitors, and immunotherapies. Patients accessed WGTA-informed treatments through clinical trials (19%), off-label use (35%), and as standard therapies (46%) including those which would not otherwise have been the next choice of therapy, demonstrating the utility of genomic information to direct use of chemotherapies as well as targeted therapies. CONCLUSIONS Integrating RNA expression and genome data illuminated treatment options that resulted in 46% of treated patients experiencing positive clinical benefit, supporting the use of comprehensive WGTA profiling in clinical cancer care. CLINICAL TRIAL NUMBER NCT02155621.
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Affiliation(s)
- E Pleasance
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver
| | - A Bohm
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver; Department of Medicine, University of British Columbia, Vancouver
| | - L M Williamson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver
| | - J M T Nelson
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver
| | - Y Shen
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver
| | - M Bonakdar
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver
| | - E Titmuss
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver
| | - V Csizmok
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver
| | - K Wee
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver
| | - S Hosseinzadeh
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver; Department of Medicine, University of British Columbia, Vancouver
| | - C J Grisdale
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver
| | - C Reisle
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver
| | - G A Taylor
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver
| | - E Lewis
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver
| | - M R Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver
| | - D Bleile
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver
| | - S Sadeghi
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver
| | - W Zhang
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver
| | - A Davies
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver
| | - B Pellegrini
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver
| | - T Wong
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver
| | - R Bowlby
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver
| | - S K Chan
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver
| | - K L Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver
| | - E Chuah
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver
| | - A J Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver
| | - R A Moore
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver
| | - Y Zhao
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver
| | - B Deol
- Department of Medical Oncology, BC Cancer, Vancouver
| | - A Fisic
- Department of Medical Oncology, BC Cancer, Vancouver
| | - A Fok
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver
| | - D A Regier
- Canadian Centre for Applied Research in Cancer Control, Cancer Control Research, BC Cancer, Vancouver
| | - D Weymann
- Canadian Centre for Applied Research in Cancer Control, Cancer Control Research, BC Cancer, Vancouver
| | - D F Schaeffer
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver; Pancreas Centre BC, Vancouver
| | - S Young
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver
| | - S Yip
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver
| | - K Schrader
- Hereditary Cancer Program, BC Cancer, Vancouver; Department of Medical Genetics, University of British Columbia, Vancouver
| | - N Levasseur
- Department of Medical Oncology, BC Cancer, Vancouver
| | - S K Taylor
- Department of Medical Oncology, BC Cancer, Kelowna
| | - X Feng
- Department of Medical Oncology, BC Cancer, Victoria
| | - A Tinker
- Department of Medical Oncology, BC Cancer, Vancouver
| | - K J Savage
- Department of Medical Oncology, BC Cancer, Vancouver
| | - S Chia
- Department of Medical Oncology, BC Cancer, Vancouver
| | - K Gelmon
- Department of Medical Oncology, BC Cancer, Vancouver
| | - S Sun
- Department of Medical Oncology, BC Cancer, Vancouver
| | - H Lim
- Department of Medical Oncology, BC Cancer, Vancouver
| | - D J Renouf
- Department of Medical Oncology, BC Cancer, Vancouver; Pancreas Centre BC, Vancouver
| | - S J M Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver; Department of Medical Genetics, University of British Columbia, Vancouver; Department of Molecular Biology and Biochemistry, Simon Fraser University, Vancouver, Canada
| | - M A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver; Department of Medical Genetics, University of British Columbia, Vancouver
| | - J Laskin
- Department of Medical Oncology, BC Cancer, Vancouver.
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6
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Reisle C, Williamson LM, Pleasance E, Davies A, Pellegrini B, Bleile DW, Mungall KL, Chuah E, Jones MR, Ma Y, Lewis E, Beckie I, Pham D, Matiello Pletz R, Muhammadzadeh A, Pierce BM, Li J, Stevenson R, Wong H, Bailey L, Reisle A, Douglas M, Bonakdar M, Nelson JMT, Grisdale CJ, Krzywinski M, Fisic A, Mitchell T, Renouf DJ, Yip S, Laskin J, Marra MA, Jones SJM. A platform for oncogenomic reporting and interpretation. Nat Commun 2022; 13:756. [PMID: 35140225 PMCID: PMC8828759 DOI: 10.1038/s41467-022-28348-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 01/14/2022] [Indexed: 01/01/2023] Open
Abstract
Manual interpretation of variants remains rate limiting in precision oncology. The increasing scale and complexity of molecular data generated from comprehensive sequencing of cancer samples requires advanced interpretative platforms as precision oncology expands beyond individual patients to entire populations. To address this unmet need, we introduce a Platform for Oncogenomic Reporting and Interpretation (PORI), comprising an analytic framework that facilitates the interpretation and reporting of somatic variants in cancer. PORI integrates reporting and graph knowledge base tools combined with support for manual curation at the reporting stage. PORI represents an open-source platform alternative to commercial reporting solutions suitable for comprehensive genomic data sets in precision oncology. We demonstrate the utility of PORI by matching 9,961 pan-cancer genome atlas tumours to the graph knowledge base, calculating therapeutically informative alterations, and making available reports describing select individual samples. The interpretation of somatic variants in cancer is challenging due to the scale and complexity of sequencing data. Here, the authors present PORI, an open-source framework for interpreting somatic variants in cancer using graph knowledge base tools, automated reporting, and manual curation.
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Affiliation(s)
- Caralyn Reisle
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada.,Bioinformatics Graduate Program, Faculty of Science, University of British Columbia, Vancouver, BC, Canada
| | | | - Erin Pleasance
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Anna Davies
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | | | - Dustin W Bleile
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Karen L Mungall
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Eric Chuah
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Martin R Jones
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Yussanne Ma
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Eleanor Lewis
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Isaac Beckie
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - David Pham
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | | | | | - Brandon M Pierce
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Jacky Li
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Ross Stevenson
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Hansen Wong
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Lance Bailey
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Abbey Reisle
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Matthew Douglas
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Melika Bonakdar
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | | | | | - Martin Krzywinski
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Ana Fisic
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Teresa Mitchell
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Daniel J Renouf
- Pancreas Centre BC, Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Stephen Yip
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Janessa Laskin
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada. .,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada. .,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.
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7
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Jones MR, Subbe CP, Thorpe C, Pickwick C. Frailty Status and Outcomes of COVID-19 Patients Admitted to an Intensive Care Unit. J Frailty Aging 2022; 11:242-243. [PMID: 35441204 PMCID: PMC8821774 DOI: 10.14283/jfa.2022.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- M R Jones
- Matthew Rhys Jones, Cardiff University School of Medicine, Cardiff, United Kingdom,
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8
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Dubas K, Szewczyk S, Białek R, Burdziński G, Jones MR, Gibasiewicz K. Antagonistic Effects of Point Mutations on Charge Recombination and a New View of Primary Charge Separation in Photosynthetic Proteins. J Phys Chem B 2021; 125:8742-8756. [PMID: 34328746 PMCID: PMC8389993 DOI: 10.1021/acs.jpcb.1c03978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Light-induced electron-transfer
reactions were investigated in
wild-type and three mutant Rhodobacter sphaeroides reaction centers with the secondary electron acceptor (ubiquinone
QA) either removed or permanently reduced. Under such conditions,
charge separation between the primary electron donor (bacteriochlorophyll
dimer, P) and the electron acceptor (bacteriopheophytin, HA) was followed by P+HA– →
PHA charge recombination. Two reaction centers were used
that had different single amino-acid mutations that brought about
either a 3-fold acceleration in charge recombination compared to that
in the wild-type protein, or a 3-fold deceleration. In a third mutant
in which the two single amino-acid mutations were combined, charge
recombination was similar to that in the wild type. In all cases,
data from transient absorption measurements were analyzed using similar
models. The modeling included the energetic relaxation of the charge-separated
states caused by protein dynamics and evidenced the appearance of
an intermediate charge-separated state, P+BA–, with BA being the bacteriochlorophyll
located between P and HA. In all cases, mixing of the states
P+BA– and P+HA– was observed and explained in terms of
electron delocalization over BA and HA. This
delocalization, together with picosecond protein relaxation, underlies
a new view of primary charge separation in photosynthesis.
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Affiliation(s)
- K Dubas
- Faculty of Physics, Adam Mickiewicz University, ul. Uniwersytetu Poznanskiego 2, 61-614 Poznań, Poland.,Department of Optometry, Poznan University of Medical Sciences, ul. Rokietnicka 5d, 60-806 Poznań, Poland
| | - S Szewczyk
- Faculty of Physics, Adam Mickiewicz University, ul. Uniwersytetu Poznanskiego 2, 61-614 Poznań, Poland
| | - R Białek
- Faculty of Physics, Adam Mickiewicz University, ul. Uniwersytetu Poznanskiego 2, 61-614 Poznań, Poland
| | - G Burdziński
- Faculty of Physics, Adam Mickiewicz University, ul. Uniwersytetu Poznanskiego 2, 61-614 Poznań, Poland
| | - M R Jones
- School of Biochemistry, Medical Sciences Building, University of Bristol, University Walk, Bristol, BS8 1TD, U.K
| | - K Gibasiewicz
- Faculty of Physics, Adam Mickiewicz University, ul. Uniwersytetu Poznanskiego 2, 61-614 Poznań, Poland
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9
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Jones MR, Pinto E, Torres MA, Dörr F, Mazur-Marzec H, Szubert K, Tartaglione L, Dell'Aversano C, Miles CO, Beach DG, McCarron P, Sivonen K, Fewer DP, Jokela J, Janssen EML. CyanoMetDB, a comprehensive public database of secondary metabolites from cyanobacteria. Water Res 2021; 196:117017. [PMID: 33765498 DOI: 10.1016/j.watres.2021.117017] [Citation(s) in RCA: 103] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 02/26/2021] [Accepted: 03/06/2021] [Indexed: 05/06/2023]
Abstract
Harmful cyanobacterial blooms, which frequently contain toxic secondary metabolites, are reported in aquatic environments around the world. More than two thousand cyanobacterial secondary metabolites have been reported from diverse sources over the past fifty years. A comprehensive, publically-accessible database detailing these secondary metabolites would facilitate research into their occurrence, functions and toxicological risks. To address this need we created CyanoMetDB, a highly curated, flat-file, openly-accessible database of cyanobacterial secondary metabolites collated from 850 peer-reviewed articles published between 1967 and 2020. CyanoMetDB contains 2010 cyanobacterial metabolites and 99 structurally related compounds. This has nearly doubled the number of entries with complete literature metadata and structural composition information compared to previously available open access databases. The dataset includes microcytsins, cyanopeptolins, other depsipeptides, anabaenopeptins, microginins, aeruginosins, cyclamides, cryptophycins, saxitoxins, spumigins, microviridins, and anatoxins among other metabolite classes. A comprehensive database dedicated to cyanobacterial secondary metabolites facilitates: (1) the detection and dereplication of known cyanobacterial toxins and secondary metabolites; (2) the identification of novel natural products from cyanobacteria; (3) research on biosynthesis of cyanobacterial secondary metabolites, including substructure searches; and (4) the investigation of their abundance, persistence, and toxicity in natural environments.
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Affiliation(s)
- Martin R Jones
- Department of Environmental Chemistry, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600 Duebendorf, Switzerland
| | - Ernani Pinto
- Centre for Nuclear Energy in Agriculture, University of São Paulo, CEP 13418-260 Piracicaba, SP, Brazil
| | - Mariana A Torres
- School of Pharmaceutical Sciences, University of São Paulo, CEP 05508-900, São Paulo - SP, Brazil
| | - Fabiane Dörr
- School of Pharmaceutical Sciences, University of São Paulo, CEP 05508-900, São Paulo - SP, Brazil
| | - Hanna Mazur-Marzec
- Division of Marine Biotechnology, University of Gdansk, Al. Marszałka Piłsudskiego 46, 81-378 Gdynia, Poland
| | - Karolina Szubert
- Division of Marine Biotechnology, University of Gdansk, Al. Marszałka Piłsudskiego 46, 81-378 Gdynia, Poland
| | - Luciana Tartaglione
- Department of Pharmacy, School of Medicine and Surgery, University of Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| | - Carmela Dell'Aversano
- Department of Pharmacy, School of Medicine and Surgery, University of Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| | - Christopher O Miles
- Biotoxin Metrology, National Research Council Canada, 1411 Oxford Street, Nova Scotia, Halifax B3H 3Z1, Canada
| | - Daniel G Beach
- Biotoxin Metrology, National Research Council Canada, 1411 Oxford Street, Nova Scotia, Halifax B3H 3Z1, Canada
| | - Pearse McCarron
- Biotoxin Metrology, National Research Council Canada, 1411 Oxford Street, Nova Scotia, Halifax B3H 3Z1, Canada
| | - Kaarina Sivonen
- Department of Microbiology, University of Helsinki, 00014 Helsinki, Finland
| | - David P Fewer
- Department of Microbiology, University of Helsinki, 00014 Helsinki, Finland
| | - Jouni Jokela
- Department of Microbiology, University of Helsinki, 00014 Helsinki, Finland
| | - Elisabeth M-L Janssen
- Department of Environmental Chemistry, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600 Duebendorf, Switzerland.
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10
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Cadranel J, Liu SV, Duruisseaux M, Branden E, Goto Y, Weinberg BA, Heining C, Schlenk RF, Cheema P, Jones MR, Drilon A, Trombetta D, Muscarella LA, Tolba K, Gounant V, Cseh A, Solca F, Laskin JJ, Renouf DJ. Therapeutic Potential of Afatinib in NRG1 Fusion-Driven Solid Tumors: A Case Series. Oncologist 2021; 26:7-16. [PMID: 32852072 PMCID: PMC7794194 DOI: 10.1634/theoncologist.2020-0379] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 08/04/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Neuregulin 1 (NRG1) fusions, which activate ErbB signaling, are rare oncogenic drivers in multiple tumor types. Afatinib is a pan-ErbB family inhibitor that may be an effective treatment for NRG1 fusion-driven tumors. PATIENTS AND METHODS This report summarizes pertinent details, including best tumor response to treatment, for six patients with metastatic NRG1 fusion-positive tumors treated with afatinib. RESULTS The six cases include four female and two male patients who ranged in age from 34 to 69 years. Five of the cases are patients with lung cancer, including two patients with invasive mucinous adenocarcinoma and three patients with nonmucinous adenocarcinoma. The sixth case is a patient with colorectal cancer. NRG1 fusion partners for the patients with lung cancer were either CD74 or SDC4. The patient with colorectal cancer harbored a novel POMK-NRG1 fusion and a KRAS mutation. Two patients received afatinib as first- or second-line therapy, three patients received the drug as third- to fifth-line therapy, and one patient received afatinib as fifteenth-line therapy. Best response with afatinib was stable disease in two patients (duration up to 16 months when combined with local therapies) and partial response (PR) of >18 months in three patients, including one with ongoing PR after 27 months. The remaining patient had a PR of 5 months with afatinib 40 mg/day, then another 6 months after an increase to 50 mg/day. CONCLUSION This report reviews previously published metastatic NRG1 fusion-positive tumors treated with afatinib and summarizes six previously unpublished cases. The latter include several with a prolonged response to treatment (>18 months), as well as the first report of efficacy in NRG1 fusion-positive colorectal cancer. This adds to the growing body of evidence suggesting that afatinib can be effective in patients with NRG1 fusion-positive tumors. KEY POINTS NRG1 fusions activate ErbB signaling and have been identified as oncogenic drivers in multiple solid tumor types. Afatinib is a pan-ErbB family inhibitor authorized for the treatment of advanced non-small cell lung cancer that may be effective in NRG1 fusion-driven tumors. This report summarizes six previously unpublished cases of NRG1 fusion-driven cancers treated with afatinib, including five with metastatic lung cancer and one with metastatic colorectal cancer. Several patients showed a prolonged response of >18 months with afatinib treatment. This case series adds to the evidence suggesting a potential role for afatinib in this area of unmet medical need.
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Affiliation(s)
- Jacques Cadranel
- Assistance Publique Hôpitaux de Paris, Hôpital Tenon and Groupes de recherche clinique Theranoscan and Curamus Sorbonne UniversitéParisFrance
| | - Stephen V. Liu
- Georgetown University Medical CenterWashingtonDistrict of ColumbiaUSA
| | - Michaël Duruisseaux
- Respiratory Department, Louis Pradel Hospital, Hospices Civils de Lyon Cancer InstituteLyonFrance
- Anticancer Antibodies Laboratory, Cancer Research Center of LyonLyonFrance
- Université Claude Bernard Lyon 1, Université de LyonLyonFrance
| | | | | | | | - Christoph Heining
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden and German Cancer Research Center (DKFZ)DresdenGermany
- Center for Personalized Oncology, NCT Dresden and University Hospital Carl Gustav Carus Dresden at Technical University DresdenDresdenGermany
- German Cancer Consortium (DKTK)DresdenGermany
| | - Richard F. Schlenk
- National Center of Tumor Diseases Heidelberg, Heidelberg University Hospital and German Cancer Research CenterHeidelbergGermany
| | - Parneet Cheema
- William Osler Health System, University of TorontoTorontoOntarioCanada
| | - Martin R. Jones
- QIAGEN Digital Insights, QIAGEN Inc.Redwood CityCaliforniaUSA
| | | | - Domenico Trombetta
- Fondazione IRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni RotondoFoggiaItaly
| | - Lucia Anna Muscarella
- Fondazione IRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni RotondoFoggiaItaly
| | - Khaled Tolba
- Oregon Health and Science UniversityPortlandOregonUSA
| | - Valerie Gounant
- Assistance Publique Hôpitaux de Paris, Hôpital Bichat – Claude‐Bernard and Université Paris DescartesParisFrance
| | | | - Flavio Solca
- Boehringer Ingelheim Regional Center Vienna GmbH & Co KGViennaAustria
| | - Janessa J. Laskin
- University of British Columbia, BC CancerVancouverBritish ColumbiaCanada
| | - Daniel J. Renouf
- University of British Columbia, BC CancerVancouverBritish ColumbiaCanada
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11
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Laskin J, Liu SV, Tolba K, Heining C, Schlenk RF, Cheema P, Cadranel J, Jones MR, Drilon A, Cseh A, Gyorffy S, Solca F, Duruisseaux M. NRG1 fusion-driven tumors: biology, detection, and the therapeutic role of afatinib and other ErbB-targeting agents. Ann Oncol 2020; 31:1693-1703. [PMID: 32916265 DOI: 10.1016/j.annonc.2020.08.2335] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 08/03/2020] [Accepted: 08/31/2020] [Indexed: 10/23/2022] Open
Abstract
Oncogenic gene fusions are hybrid genes that result from structural DNA rearrangements, leading to deregulated activity. Fusions involving the neuregulin-1 gene (NRG1) result in ErbB-mediated pathway activation and therefore present a rational candidate for targeted treatment. The most frequently reported NRG1 fusion is CD74-NRG1, which most commonly occurs in patients with invasive mucinous adenocarcinomas (IMAs) of the lung, although several other NRG1 fusion partners have been identified in patients with lung cancer, including ATP1B1, SDC4, and RBPMS. NRG1 fusions are also present in patients with other solid tumors, such as pancreatic ductal adenocarcinoma. In general, NRG1 fusions are rare across different types of cancer, with a reported incidence of <1%, with the notable exception of IMA, which represents ≈2%-10% of lung adenocarcinomas and has a reported incidence of ≈10%-30% for NRG1 fusions. A substantial proportion (≈20%) of NRG1 fusion-positive non-small-cell lung cancer cases are nonmucinous adenocarcinomas. ErbB-targeted treatments, such as afatinib, a pan-ErbB tyrosine kinase inhibitor, are potential therapeutic strategies to address unmet treatment needs in patients harboring NRG1 fusions.
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Affiliation(s)
- J Laskin
- Division of Medical Oncology, Department of Medicine, University of British Columbia, BC Cancer, Vancouver, BC, Canada.
| | - S V Liu
- Georgetown University Medical Center, Washington, USA
| | - K Tolba
- Oregon Health and Science University, Portland, OR, USA
| | - C Heining
- Department of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Dresden and German Cancer Research Center (DKFZ), Dresden, Germany; Center for Personalized Oncology, NCT Dresden and University Hospital Carl Gustav Carus Dresden at Technical University Dresden, Dresden, Germany; German Cancer Consortium (DKTK), Dresden, Germany
| | - R F Schlenk
- National Center of Tumor Diseases Heidelberg, Heidelberg University Hospital and German Cancer Research Center, Heidelberg, Germany
| | - P Cheema
- William Osler Health System, University of Toronto, Toronto, ON, Canada
| | - J Cadranel
- Assistance Publique Hôpitaux de Paris, Hôpital Tenon and Sorbonne Université, Paris, France
| | - M R Jones
- QIAGEN Digital Insights, QIAGEN Inc., Redwood City, CA, USA
| | - A Drilon
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - A Cseh
- Boehringer Ingelheim International GmbH, Ingelheim, Germany
| | - S Gyorffy
- AstraZeneca Canada Ltd, Mississauga, ON, Canada
| | - F Solca
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - M Duruisseaux
- Hospices Civils de Lyon Cancer Institute, Anticancer Antibodies Lab Cancer Research Center of Lyon INSERM 1052 CNRS 528, Université Claude Bernard Lyon 1, Lyon, France
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12
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Pleasance E, Titmuss E, Williamson L, Kwan H, Culibrk L, Zhao EY, Dixon K, Fan K, Bowlby R, Jones MR, Shen Y, Grewal JK, Ashkani J, Wee K, Grisdale CJ, Thibodeau ML, Bozoky Z, Pearson H, Majounie E, Vira T, Shenwai R, Mungall KL, Chuah E, Davies A, Warren M, Reisle C, Bonakdar M, Taylor GA, Csizmok V, Chan SK, Zong Z, Bilobram S, Muhammadzadeh A, D’Souza D, Corbett RD, MacMillan D, Carreira M, Choo C, Bleile D, Sadeghi S, Zhang W, Wong T, Cheng D, Brown SD, Holt RA, Moore RA, Mungall AJ, Zhao Y, Nelson J, Fok A, Ma Y, Lee MKC, Lavoie JM, Mendis S, Karasinska JM, Deol B, Fisic A, Schaeffer DF, Yip S, Schrader K, Regier DA, Weymann D, Chia S, Gelmon K, Tinker A, Sun S, Lim H, Renouf DJ, Laskin J, Jones SJM, Marra MA. Pan-cancer analysis of advanced patient tumors reveals interactions between therapy and genomic landscapes. ACTA ACUST UNITED AC 2020; 1:452-468. [DOI: 10.1038/s43018-020-0050-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 03/05/2020] [Indexed: 02/08/2023]
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13
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Abstract
Harmful cyanobacterial blooms in freshwater ecosystems produce bioactive secondary metabolites including cyanopeptides that pose ecological and human health risks. Only adverse effects of one class of cyanopeptides, microcystins, have been studied extensively and have consequently been included in water quality assessments. Inhibition is a commonly observed effect for enzymes exposed to cyanopeptides and has mostly been investigated for human biologically relevant model enzymes. Here, we investigated the inhibition of ubiquitous aquatic enzymes by cyanobacterial metabolites. Hydrolytic enzymes are utilized in the metabolism of aquatic organisms and extracellularly by heterotrophic bacteria to obtain assimilable substrates. The ubiquitous occurrence of hydrolytic enzymes leads to the co-occurrence with cyanopeptides especially during cyanobacterial blooms. Bacterial leucine aminopeptidase and alkaline phosphatase were exposed to cyanopeptide extracts of different cyanobacterial strains ( Microcystis aeruginosa wild type and microcystin-free mutant, Planktothrix rubescens) and purified cyanopeptides. We observed inhibition of aminopeptidase and phosphatase upon exposure, especially to the apolar fractions of the cyanobacterial extracts. Exposure to the dominant cyanopeptides in these extracts confirmed that purified microcystins, aerucyclamide A and cyanopeptolin A inhibit the aminopeptidase in the low mg L-1 range while the phosphatase was less affected. Inhibition of aquatic enzymes can reduce the turnover of nutrients and carbon substrates and may also impair metabolic functions of grazing organisms.
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Affiliation(s)
- Christine M Egli
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zurich, Switzerland; Eawag, Swiss Federal Institute of Aquatic Science and Technology, Switzerland
| | - Regiane S Natumi
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Switzerland
| | - Martin R Jones
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Switzerland
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14
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Majounie E, Wee K, Williamson LM, Jones MR, Pleasance E, Lim HJ, Ho C, Renouf DJ, Yip S, Jones SJM, Marra MA, Laskin J. Fluorouracil sensitivity in a head and neck squamous cell carcinoma with a somatic DPYD structural variant. Cold Spring Harb Mol Case Stud 2020; 6:mcs.a004713. [PMID: 31871216 PMCID: PMC6996515 DOI: 10.1101/mcs.a004713] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 11/18/2019] [Indexed: 12/13/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is one of the most common cancers worldwide and represents a heterogeneous group of tumors, the majority of which are treated with a combination of surgery, radiation, and chemotherapy. Fluoropyrimidine (5-FU) and its oral prodrug, capecitabine, are commonly prescribed treatments for several solid tumor types including HNSCC. 5-FU-associated toxicity is observed in ∼30% of treated patients and is largely caused by germline polymorphisms in DPYD, which encodes dihydropyrimidine dehydrogenase, a key enzyme of 5-FU catabolism and deactivation. Although the association of germline DPYD alterations with toxicity is well-described, the potential contribution of somatic DPYD alterations to 5-FU sensitivity has not been explored. In a patient with metastatic HNSCC, in-depth genomic and transcriptomic integrative analysis on a biopsy from a metastatic neck lesion revealed alterations in genes that are associated with 5-FU uptake and metabolism. These included a novel somatic structural variant resulting in a partial deletion affecting DPYD, a variant of unknown significance affecting SLC29A1, and homozygous deletion of MTAP. There was no evidence of deleterious germline polymorphisms that have been associated with 5-FU toxicity, indicating a potential vulnerability of the tumor to 5-FU therapy. The discovery of the novel DPYD variant led to the initiation of 5-FU treatment that resulted in a rapid response lasting 17 wk, with subsequent relapse due to unknown resistance mechanisms. This suggests that somatic alterations present in this tumor may serve as markers for tumor sensitivity to 5-FU, aiding in the selection of personalized treatment strategies.
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Affiliation(s)
- Elisa Majounie
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 4S6, Canada
| | - Kathleen Wee
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 4S6, Canada
| | - Laura M Williamson
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 4S6, Canada
| | - Martin R Jones
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 4S6, Canada
| | - Erin Pleasance
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 4S6, Canada
| | - Howard J Lim
- Department of Medical Oncology, BC Cancer, Vancouver, British Columbia V5Z 4E6, Canada
| | - Cheryl Ho
- Department of Medical Oncology, BC Cancer, Vancouver, British Columbia V5Z 4E6, Canada
| | - Daniel J Renouf
- Department of Medical Oncology, BC Cancer, Vancouver, British Columbia V5Z 4E6, Canada.,Pancreas Centre BC, Vancouver, British Columbia V5Z 1L8, Canada
| | - Stephen Yip
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 4S6, Canada.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Vancouver, British Columbia V5A 1S6, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 4S6, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada
| | - Janessa Laskin
- Department of Medical Oncology, BC Cancer, Vancouver, British Columbia V5Z 4E6, Canada
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15
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Laperle AH, Sances S, Yucer N, Dardov VJ, Garcia VJ, Ho R, Fulton AN, Jones MR, Roxas KM, Avalos P, West D, Banuelos MG, Shu Z, Murali R, Maidment NT, Van Eyk JE, Tagliati M, Svendsen CN. iPSC modeling of young-onset Parkinson's disease reveals a molecular signature of disease and novel therapeutic candidates. Nat Med 2020; 26:289-299. [PMID: 31988461 DOI: 10.1038/s41591-019-0739-1] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 12/16/2019] [Indexed: 12/21/2022]
Abstract
Young-onset Parkinson's disease (YOPD), defined by onset at <50 years, accounts for approximately 10% of all Parkinson's disease cases and, while some cases are associated with known genetic mutations, most are not. Here induced pluripotent stem cells were generated from control individuals and from patients with YOPD with no known mutations. Following differentiation into cultures containing dopamine neurons, induced pluripotent stem cells from patients with YOPD showed increased accumulation of soluble α-synuclein protein and phosphorylated protein kinase Cα, as well as reduced abundance of lysosomal membrane proteins such as LAMP1. Testing activators of lysosomal function showed that specific phorbol esters, such as PEP005, reduced α-synuclein and phosphorylated protein kinase Cα levels while increasing LAMP1 abundance. Interestingly, the reduction in α-synuclein occurred through proteasomal degradation. PEP005 delivery to mouse striatum also decreased α-synuclein production in vivo. Induced pluripotent stem cell-derived dopaminergic cultures reveal a signature in patients with YOPD who have no known Parkinson's disease-related mutations, suggesting that there might be other genetic contributions to this disorder. This signature was normalized by specific phorbol esters, making them promising therapeutic candidates.
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Affiliation(s)
- A H Laperle
- Cedars-Sinai Board of Governors Regenerative Medicine Institute, Los Angeles, CA, USA
| | - S Sances
- Cedars-Sinai Board of Governors Regenerative Medicine Institute, Los Angeles, CA, USA
| | - N Yucer
- Cedars-Sinai Board of Governors Regenerative Medicine Institute, Los Angeles, CA, USA
| | - V J Dardov
- Cedars-Sinai Board of Governors Regenerative Medicine Institute, Los Angeles, CA, USA
| | - V J Garcia
- Cedars-Sinai Board of Governors Regenerative Medicine Institute, Los Angeles, CA, USA
| | - R Ho
- Cedars-Sinai Board of Governors Regenerative Medicine Institute, Los Angeles, CA, USA
| | - A N Fulton
- Cedars-Sinai Board of Governors Regenerative Medicine Institute, Los Angeles, CA, USA
| | - M R Jones
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - K M Roxas
- Cedars-Sinai Board of Governors Regenerative Medicine Institute, Los Angeles, CA, USA
| | - P Avalos
- Cedars-Sinai Board of Governors Regenerative Medicine Institute, Los Angeles, CA, USA
| | - D West
- Cedars-Sinai Board of Governors Regenerative Medicine Institute, Los Angeles, CA, USA
| | - M G Banuelos
- Cedars-Sinai Board of Governors Regenerative Medicine Institute, Los Angeles, CA, USA
| | - Z Shu
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
| | - R Murali
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Samuel Oschin Comprehensive Cancer Institute, Los Angeles, CA, USA
- Research Division of Immunology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - N T Maidment
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
| | - J E Van Eyk
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - M Tagliati
- Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - C N Svendsen
- Cedars-Sinai Board of Governors Regenerative Medicine Institute, Los Angeles, CA, USA.
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16
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Lever J, Jones MR, Danos AM, Krysiak K, Bonakdar M, Grewal JK, Culibrk L, Griffith OL, Griffith M, Jones SJM. Text-mining clinically relevant cancer biomarkers for curation into the CIViC database. Genome Med 2019; 11:78. [PMID: 31796060 PMCID: PMC6891984 DOI: 10.1186/s13073-019-0686-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 11/07/2019] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Precision oncology involves analysis of individual cancer samples to understand the genes and pathways involved in the development and progression of a cancer. To improve patient care, knowledge of diagnostic, prognostic, predisposing, and drug response markers is essential. Several knowledgebases have been created by different groups to collate evidence for these associations. These include the open-access Clinical Interpretation of Variants in Cancer (CIViC) knowledgebase. These databases rely on time-consuming manual curation from skilled experts who read and interpret the relevant biomedical literature. METHODS To aid in this curation and provide the greatest coverage for these databases, particularly CIViC, we propose the use of text mining approaches to extract these clinically relevant biomarkers from all available published literature. To this end, a group of cancer genomics experts annotated sentences that discussed biomarkers with their clinical associations and achieved good inter-annotator agreement. We then used a supervised learning approach to construct the CIViCmine knowledgebase. RESULTS We extracted 121,589 relevant sentences from PubMed abstracts and PubMed Central Open Access full-text papers. CIViCmine contains over 87,412 biomarkers associated with 8035 genes, 337 drugs, and 572 cancer types, representing 25,818 abstracts and 39,795 full-text publications. CONCLUSIONS Through integration with CIVIC, we provide a prioritized list of curatable clinically relevant cancer biomarkers as well as a resource that is valuable to other knowledgebases and precision cancer analysts in general. All data is publically available and distributed with a Creative Commons Zero license. The CIViCmine knowledgebase is available at http://bionlp.bcgsc.ca/civicmine/.
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Affiliation(s)
- Jake Lever
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
- University of British Columbia, Vancouver, BC, Canada
| | - Martin R Jones
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Arpad M Danos
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Kilannin Krysiak
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Melika Bonakdar
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Jasleen K Grewal
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
- University of British Columbia, Vancouver, BC, Canada
| | - Luka Culibrk
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
- University of British Columbia, Vancouver, BC, Canada
| | - Obi L Griffith
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA.
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA.
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
| | - Malachi Griffith
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA.
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA.
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada.
- University of British Columbia, Vancouver, BC, Canada.
- Simon Fraser University, Burnaby, BC, Canada.
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17
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Laskin JJ, Cadranel J, Renouf DJ, Weinberg BA, Goto Y, Duruisseaux M, Tolba K, Branden E, Doebele RC, Heining C, Schlenk RF, Cheema PK, Jones MR, Trombetta D, Muscarella LA, Cseh A, Solca F, Liu SV. Afatinib as a novel potential treatment option for NRG1 fusion-positive tumors. J Glob Oncol 2019. [DOI: 10.1200/jgo.2019.5.suppl.110] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
110 Background: Neuregulin 1 (NRG1) is a growth factor that binds HER3/4 and activates ErbB signalling pathways. NRG1 gene fusions function as oncogenic drivers and represent a potential therapeutic target across tumour types. Afatinib, an ErbB-family blocker, is a potential treatment option for some patients with NRG1 fusion-positive ( NRG1+) tumours, as supported by preclinical evidence and clinical case reports. Of 13 patients with NRG1+ lung adenocarcinoma (ADC; n = 9), pancreatic ADC (n = 2), cholangiocarcinoma (n = 1), and ovarian cancer (n = 1) treated with afatinib, eight patients achieved a best response of partial response (PR; median duration 7.3 months, range 3–12), three patients had stable disease (SD) and two patients had progressive disease. Methods: Here, we report the clinico-pathological and molecular characteristics and current status of four additional cases of afatinib-treated NRG1+ tumours. Results: Patient 1, 66 year-old female, never-smoker with metastatic non-mucinous lung ADC. CD74-NRG1 fusion was identified, and 5th-line afatinib initiated. PR is ongoing after 16 months. Patient 2, 43 year-old female, non-smoker with advanced invasive mucinous lung ADC. CD74-NRG1 fusion was identified and 3rd-line afatinib initiated (PR, 18 months); treatment is ongoing following local progression. Patient 3, 69 year-old male, with KRAS-mutated metastatic colorectal cancer. Following a right hemicolectomy and liver/lung metastasectomies, a novel POMK-NRG1 fusion was detected and afatinib initiated (SD, 4 months). Eight months after initiation, afatinib treatment is ongoing, in combination with radiotherapy, with SD. Patient 4, 54 year-old male, with KRAS-wild-type metastatic pancreatic cancer. Following progression on chemotherapy, APP-NRG1 fusion was detected as part of the Personalized Oncogenomics study (NCT02155621), and afatinib initiated; PR is ongoing after 7 months. Conclusions: These findings add to a growing body of evidence that afatinib is a potential treatment option for patients with NRG1+ tumours. Prospective study is ongoing/planned in the Drug Rediscovery Protocol trial (DRUP; NCT02925234) and Targeted Agent and Profiling Utilization Registry study (TAPUR; NCT02693535).
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Affiliation(s)
| | - Jacques Cadranel
- Assistance Publique Hôpitaux de Paris, Hôpital Tenon and Sorbonne Université, Paris, France
| | | | | | | | | | - Khaled Tolba
- Oregon Health and Science University, Portland, OR
| | | | | | | | - Richard F. Schlenk
- National Center of Tumor Diseases Heidelberg, Heidelberg University Hospital and German Cancer Research Center, Heidelberg, Germany
| | | | | | - Domenico Trombetta
- Fondazione IRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, Italy
| | - Lucia A. Muscarella
- Fondazione IRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, Italy
| | | | - Flavio Solca
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
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18
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Lee M, Jones MR, Williamson L, Topham JT, Wong HL, Addison S, Denroche R, Jang GH, Karasinska J, McGhie JP, Gill S, Lim HJ, Yip S, Knox JJ, Gallinger S, Laskin JJ, Marra MA, Jones SJM, Schaeffer DF, Renouf DJ. Comprehensive genomic analysis of metastatic pancreatic ductal adenocarcinoma (mPDAC) reveals a significant proportion of clinical actionable aberrations. J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.15_suppl.e15753] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
e15753 Background: Significant progress has been made in the understanding of the genomic landscape of PDAC, but the clinical utility of these data remains uncertain. Methods: As part of the BC Cancer Personalized Oncogenomics (POG) and PanGen studies (NCT02155621, NCT02869802), whole genome analysis and transcriptome sequencing were performed on fresh biopsy and blood sample from 48 mPDAC patients. Genomic findings informed therapy choices including potential eligibility for the CCTG PM.1 molecular basket trial (NCT03297606). Results: Cohort consists of 54.1% male, average age 57.6, 34/48 had ≥2 lines of treatment. 37/48 biopsies were from liver and 27/48 were collected pre-treatment. 8/48 (16.6%) patients had aberrations with strong evidence of clinical actionability. These include 2 germline BRCA2, 1 germline BRCA1, 1 somatic XRCC2 homozygous deletion with strong COSMIC signature 3, all predictive of platinum sensitivity. Patients with XRCC2 deletion and BRCA1 had over 2 years on FOLFIRINOX. Fusions affecting the NRG1 gene were identified in 3/4 patients with KRAS wildtype tumours, which may confer ERRB inhibitor sensitivity. 2/3 NRG1 fusion patients have thus far been treated with the ERBB inhibitor afatinib with radiographic responses noted in both patients. One patient had mismatch repair deficiency, and a high mutational burden, suggestive of immune checkpoint inhibitor sensitivity. Other possible actionable mutations include CCTG PM.1 trial potential eligibility: 4/48 with high homologous recombination defects and 1 germline ATM mutation loss (PARP inhibitor arm), 1/47 ERBB2 amplification (anti-HER2 arm), 2/47 high expression of FGFR1 (Sunitinib arm) and 1/47 with high FLT4 and IGF1R expression (Axitinib arm). Conclusions: More routine use of comprehensive genomic analysis should be considered in mPDAC given finding of high degree of actionability. Importantly, a significant proportion (16.6%) had findings with strong evidence of clinical impact.
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Affiliation(s)
| | | | - Laura Williamson
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | | | - Hui-Li Wong
- Royal Melbourne Hospital, Melbourne, Australia
| | - Sean Addison
- Vancouver General Hospital, Internal Medicine Department, Vancouver, BC, Canada
| | - Rob Denroche
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Gun Ho Jang
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | | | | | | | - Stephen Yip
- Vancouver Coastal Health Research Institute, Vancouver, BC, Canada
| | | | - Steven Gallinger
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | | | - Marco A. Marra
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | | | - David F. Schaeffer
- Department of Pathology & Laboratory Medicine Vancouver General Hospital, Vancouver, BC, Canada
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19
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Stern SA, Weaver HA, Spencer JR, Olkin CB, Gladstone GR, Grundy WM, Moore JM, Cruikshank DP, Elliott HA, McKinnon WB, Parker JW, Verbiscer AJ, Young LA, Aguilar DA, Albers JM, Andert T, Andrews JP, Bagenal F, Banks ME, Bauer BA, Bauman JA, Bechtold KE, Beddingfield CB, Behrooz N, Beisser KB, Benecchi SD, Bernardoni E, Beyer RA, Bhaskaran S, Bierson CJ, Binzel RP, Birath EM, Bird MK, Boone DR, Bowman AF, Bray VJ, Britt DT, Brown LE, Buckley MR, Buie MW, Buratti BJ, Burke LM, Bushman SS, Carcich B, Chaikin AL, Chavez CL, Cheng AF, Colwell EJ, Conard SJ, Conner MP, Conrad CA, Cook JC, Cooper SB, Custodio OS, Dalle Ore CM, Deboy CC, Dharmavaram P, Dhingra RD, Dunn GF, Earle AM, Egan AF, Eisig J, El-Maarry MR, Engelbrecht C, Enke BL, Ercol CJ, Fattig ED, Ferrell CL, Finley TJ, Firer J, Fischetti J, Folkner WM, Fosbury MN, Fountain GH, Freeze JM, Gabasova L, Glaze LS, Green JL, Griffith GA, Guo Y, Hahn M, Hals DW, Hamilton DP, Hamilton SA, Hanley JJ, Harch A, Harmon KA, Hart HM, Hayes J, Hersman CB, Hill ME, Hill TA, Hofgartner JD, Holdridge ME, Horányi M, Hosadurga A, Howard AD, Howett CJA, Jaskulek SE, Jennings DE, Jensen JR, Jones MR, Kang HK, Katz DJ, Kaufmann DE, Kavelaars JJ, Keane JT, Keleher GP, Kinczyk M, Kochte MC, Kollmann P, Krimigis SM, Kruizinga GL, Kusnierkiewicz DY, Lahr MS, Lauer TR, Lawrence GB, Lee JE, Lessac-Chenen EJ, Linscott IR, Lisse CM, Lunsford AW, Mages DM, Mallder VA, Martin NP, May BH, McComas DJ, McNutt RL, Mehoke DS, Mehoke TS, Nelson DS, Nguyen HD, Núñez JI, Ocampo AC, Owen WM, Oxton GK, Parker AH, Pätzold M, Pelgrift JY, Pelletier FJ, Pineau JP, Piquette MR, Porter SB, Protopapa S, Quirico E, Redfern JA, Regiec AL, Reitsema HJ, Reuter DC, Richardson DC, Riedel JE, Ritterbush MA, Robbins SJ, Rodgers DJ, Rogers GD, Rose DM, Rosendall PE, Runyon KD, Ryschkewitsch MG, Saina MM, Salinas MJ, Schenk PM, Scherrer JR, Schlei WR, Schmitt B, Schultz DJ, Schurr DC, Scipioni F, Sepan RL, Shelton RG, Showalter MR, Simon M, Singer KN, Stahlheber EW, Stanbridge DR, Stansberry JA, Steffl AJ, Strobel DF, Stothoff MM, Stryk T, Stuart JR, Summers ME, Tapley MB, Taylor A, Taylor HW, Tedford RM, Throop HB, Turner LS, Umurhan OM, Van Eck J, Velez D, Versteeg MH, Vincent MA, Webbert RW, Weidner SE, Weigle GE, Wendel JR, White OL, Whittenburg KE, Williams BG, Williams KE, Williams SP, Winters HL, Zangari AM, Zurbuchen TH. Initial results from the New Horizons exploration of 2014 MU 69, a small Kuiper Belt object. Science 2019; 364:364/6441/eaaw9771. [PMID: 31097641 DOI: 10.1126/science.aaw9771] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 04/16/2019] [Indexed: 11/02/2022]
Abstract
The Kuiper Belt is a distant region of the outer Solar System. On 1 January 2019, the New Horizons spacecraft flew close to (486958) 2014 MU69, a cold classical Kuiper Belt object approximately 30 kilometers in diameter. Such objects have never been substantially heated by the Sun and are therefore well preserved since their formation. We describe initial results from these encounter observations. MU69 is a bilobed contact binary with a flattened shape, discrete geological units, and noticeable albedo heterogeneity. However, there is little surface color or compositional heterogeneity. No evidence for satellites, rings or other dust structures, a gas coma, or solar wind interactions was detected. MU69's origin appears consistent with pebble cloud collapse followed by a low-velocity merger of its two lobes.
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Affiliation(s)
- S A Stern
- Southwest Research Institute, Boulder, CO 80302, USA.
| | - H A Weaver
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - J R Spencer
- Southwest Research Institute, Boulder, CO 80302, USA
| | - C B Olkin
- Southwest Research Institute, Boulder, CO 80302, USA
| | - G R Gladstone
- Southwest Research Institute, San Antonio, TX 78238, USA
| | - W M Grundy
- Lowell Observatory, Flagstaff, AZ 86001, USA
| | - J M Moore
- NASA Ames Research Center, Space Science Division, Moffett Field, CA 94035, USA
| | - D P Cruikshank
- NASA Ames Research Center, Space Science Division, Moffett Field, CA 94035, USA
| | - H A Elliott
- Southwest Research Institute, San Antonio, TX 78238, USA.,Department of Physics and Astronomy, University of Texas, San Antonio, TX 78249, USA
| | - W B McKinnon
- Department of Earth and Planetary Sciences and McDonnell Center for the Space Sciences, Washington University, St. Louis, MO 63130, USA
| | - J Wm Parker
- Southwest Research Institute, Boulder, CO 80302, USA
| | - A J Verbiscer
- Department of Astronomy, University of Virginia, Charlottesville, VA 22904, USA
| | - L A Young
- Southwest Research Institute, Boulder, CO 80302, USA
| | - D A Aguilar
- Independent consultant, Carbondale, CO 81623, USA
| | - J M Albers
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - T Andert
- Universität der Bundeswehr München, Neubiberg 85577, Germany
| | - J P Andrews
- Southwest Research Institute, Boulder, CO 80302, USA
| | - F Bagenal
- Laboratory for Atmospheric and Space Physics, University of Colorado, Boulder, CO 80303, USA
| | - M E Banks
- NASA Goddard Space Flight Center, Greenbelt, MD 20771, USA
| | - B A Bauer
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | | | - K E Bechtold
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - C B Beddingfield
- NASA Ames Research Center, Space Science Division, Moffett Field, CA 94035, USA.,SETI Institute, Mountain View, CA 94043, USA
| | - N Behrooz
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - K B Beisser
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - S D Benecchi
- Planetary Science Institute, Tucson, AZ 85719, USA
| | - E Bernardoni
- Laboratory for Atmospheric and Space Physics, University of Colorado, Boulder, CO 80303, USA
| | - R A Beyer
- NASA Ames Research Center, Space Science Division, Moffett Field, CA 94035, USA.,SETI Institute, Mountain View, CA 94043, USA
| | - S Bhaskaran
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA
| | - C J Bierson
- Earth and Planetary Science Department, University of California, Santa Cruz, CA 95064, USA
| | - R P Binzel
- Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - E M Birath
- Southwest Research Institute, Boulder, CO 80302, USA
| | - M K Bird
- Argelander-Institut für Astronomie, University of Bonn, Bonn D-53121, Germany.,Rheinisches Institut für Umweltforschung, Universität zu Köln, Cologne 50931, Germany
| | - D R Boone
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA
| | - A F Bowman
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - V J Bray
- Lunar and Planetary Laboratory, University of Arizona, Tucson, AZ 85721, USA
| | - D T Britt
- Department of Physics, University of Central Florida, Orlando, FL 32816, USA
| | - L E Brown
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - M R Buckley
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - M W Buie
- Southwest Research Institute, Boulder, CO 80302, USA
| | - B J Buratti
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA
| | - L M Burke
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - S S Bushman
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - B Carcich
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA.,Cornell University, Ithaca, NY 14853, USA
| | - A L Chaikin
- Independent science writer, Arlington, VT 05250, USA
| | - C L Chavez
- NASA Ames Research Center, Space Science Division, Moffett Field, CA 94035, USA.,SETI Institute, Mountain View, CA 94043, USA
| | - A F Cheng
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - E J Colwell
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - S J Conard
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - M P Conner
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - C A Conrad
- Southwest Research Institute, Boulder, CO 80302, USA
| | - J C Cook
- Pinhead Institute, Telluride, CO 81435, USA
| | - S B Cooper
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - O S Custodio
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - C M Dalle Ore
- NASA Ames Research Center, Space Science Division, Moffett Field, CA 94035, USA.,SETI Institute, Mountain View, CA 94043, USA
| | - C C Deboy
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - P Dharmavaram
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | | | - G F Dunn
- Southwest Research Institute, San Antonio, TX 78238, USA
| | - A M Earle
- Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - A F Egan
- Southwest Research Institute, Boulder, CO 80302, USA
| | - J Eisig
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - M R El-Maarry
- Department of Earth and Planetary Sciences, Birkbeck, University of London, London WC1E 7HX, UK
| | - C Engelbrecht
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - B L Enke
- Southwest Research Institute, Boulder, CO 80302, USA
| | - C J Ercol
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - E D Fattig
- Southwest Research Institute, San Antonio, TX 78238, USA
| | - C L Ferrell
- Southwest Research Institute, Boulder, CO 80302, USA
| | - T J Finley
- Southwest Research Institute, Boulder, CO 80302, USA
| | - J Firer
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | | | - W M Folkner
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA
| | - M N Fosbury
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - G H Fountain
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - J M Freeze
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - L Gabasova
- University Grenoble Alpes, Centre National de la Recherche Scientifique, Institut de Planétologie et d'Astrophysique de Grenoble, 38000 Grenoble, France
| | - L S Glaze
- NASA Headquarters, Washington, DC 20546, USA
| | - J L Green
- NASA Headquarters, Washington, DC 20546, USA
| | - G A Griffith
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - Y Guo
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - M Hahn
- Rheinisches Institut für Umweltforschung, Universität zu Köln, Cologne 50931, Germany
| | - D W Hals
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - D P Hamilton
- Department of Astronomy, University of Maryland, College Park, MD 20742, USA
| | - S A Hamilton
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - J J Hanley
- Southwest Research Institute, San Antonio, TX 78238, USA
| | - A Harch
- Cornell University, Ithaca, NY 14853, USA
| | - K A Harmon
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA
| | - H M Hart
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - J Hayes
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - C B Hersman
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - M E Hill
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - T A Hill
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - J D Hofgartner
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA
| | - M E Holdridge
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - M Horányi
- Laboratory for Atmospheric and Space Physics, University of Colorado, Boulder, CO 80303, USA
| | - A Hosadurga
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - A D Howard
- Department of Environmental Sciences, University of Virginia, Charlottesville, VA 22904, USA
| | - C J A Howett
- Southwest Research Institute, Boulder, CO 80302, USA
| | - S E Jaskulek
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - D E Jennings
- NASA Goddard Space Flight Center, Greenbelt, MD 20771, USA
| | - J R Jensen
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - M R Jones
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - H K Kang
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - D J Katz
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - D E Kaufmann
- Southwest Research Institute, Boulder, CO 80302, USA
| | - J J Kavelaars
- National Research Council of Canada, Victoria, BC V9E 2E7, Canada
| | - J T Keane
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA
| | - G P Keleher
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - M Kinczyk
- Marine, Earth, and Atmospheric Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - M C Kochte
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - P Kollmann
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - S M Krimigis
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - G L Kruizinga
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA
| | - D Y Kusnierkiewicz
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - M S Lahr
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - T R Lauer
- National Optical Astronomy Observatory, Tucson, AZ 26732, USA
| | - G B Lawrence
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - J E Lee
- NASA Marshall Space Flight Center, Huntsville, AL 35812, USA
| | | | - I R Linscott
- Independent consultant, Mountain View, CA 94043, USA
| | - C M Lisse
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - A W Lunsford
- NASA Goddard Space Flight Center, Greenbelt, MD 20771, USA
| | - D M Mages
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA
| | - V A Mallder
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - N P Martin
- Independent consultant, Crested Butte, CO 81224, USA
| | - B H May
- Independent collaborator, Windlesham GU20 6YW, UK
| | - D J McComas
- Southwest Research Institute, San Antonio, TX 78238, USA.,Department of Astrophysical Sciences, Princeton University, Princeton, NJ 08544, USA
| | - R L McNutt
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - D S Mehoke
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - T S Mehoke
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | | | - H D Nguyen
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - J I Núñez
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - A C Ocampo
- NASA Headquarters, Washington, DC 20546, USA
| | - W M Owen
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA
| | - G K Oxton
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - A H Parker
- Southwest Research Institute, Boulder, CO 80302, USA
| | - M Pätzold
- Rheinisches Institut für Umweltforschung, Universität zu Köln, Cologne 50931, Germany
| | | | | | - J P Pineau
- Stellar Solutions, Palo Alto, CA 94306, USA
| | - M R Piquette
- Laboratory for Atmospheric and Space Physics, University of Colorado, Boulder, CO 80303, USA
| | - S B Porter
- Southwest Research Institute, Boulder, CO 80302, USA
| | - S Protopapa
- Southwest Research Institute, Boulder, CO 80302, USA
| | - E Quirico
- University Grenoble Alpes, Centre National de la Recherche Scientifique, Institut de Planétologie et d'Astrophysique de Grenoble, 38000 Grenoble, France
| | - J A Redfern
- Southwest Research Institute, Boulder, CO 80302, USA
| | - A L Regiec
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | | | - D C Reuter
- NASA Goddard Space Flight Center, Greenbelt, MD 20771, USA
| | - D C Richardson
- Department of Astronomy, University of Maryland, College Park, MD 20742, USA
| | - J E Riedel
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA
| | - M A Ritterbush
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA
| | - S J Robbins
- Southwest Research Institute, Boulder, CO 80302, USA
| | - D J Rodgers
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - G D Rogers
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - D M Rose
- Southwest Research Institute, Boulder, CO 80302, USA
| | - P E Rosendall
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - K D Runyon
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - M G Ryschkewitsch
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - M M Saina
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | | | - P M Schenk
- Lunar and Planetary Institute, Houston, TX 77058, USA
| | - J R Scherrer
- Southwest Research Institute, San Antonio, TX 78238, USA
| | - W R Schlei
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - B Schmitt
- University Grenoble Alpes, Centre National de la Recherche Scientifique, Institut de Planétologie et d'Astrophysique de Grenoble, 38000 Grenoble, France
| | - D J Schultz
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - D C Schurr
- NASA Headquarters, Washington, DC 20546, USA
| | - F Scipioni
- NASA Ames Research Center, Space Science Division, Moffett Field, CA 94035, USA.,SETI Institute, Mountain View, CA 94043, USA
| | - R L Sepan
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - R G Shelton
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | | | - M Simon
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - K N Singer
- Southwest Research Institute, Boulder, CO 80302, USA
| | - E W Stahlheber
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | | | - J A Stansberry
- Space Telescope Science Institute, Baltimore, MD 21218, USA
| | - A J Steffl
- Southwest Research Institute, Boulder, CO 80302, USA
| | - D F Strobel
- Johns Hopkins University, Baltimore, MD 21218, USA
| | - M M Stothoff
- Southwest Research Institute, San Antonio, TX 78238, USA
| | - T Stryk
- Roane State Community College, Oak Ridge, TN 37830, USA
| | - J R Stuart
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA
| | - M E Summers
- George Mason University, Fairfax, VA 22030, USA
| | - M B Tapley
- Southwest Research Institute, San Antonio, TX 78238, USA
| | - A Taylor
- KinetX Aerospace, Tempe, AZ 85284, USA
| | - H W Taylor
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - R M Tedford
- Southwest Research Institute, Boulder, CO 80302, USA
| | - H B Throop
- Planetary Science Institute, Tucson, AZ 85719, USA
| | - L S Turner
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - O M Umurhan
- NASA Ames Research Center, Space Science Division, Moffett Field, CA 94035, USA.,SETI Institute, Mountain View, CA 94043, USA
| | - J Van Eck
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - D Velez
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA
| | - M H Versteeg
- Southwest Research Institute, San Antonio, TX 78238, USA
| | - M A Vincent
- Southwest Research Institute, Boulder, CO 80302, USA
| | - R W Webbert
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - S E Weidner
- Department of Astrophysical Sciences, Princeton University, Princeton, NJ 08544, USA
| | - G E Weigle
- Independent consultant, Burden, KS 67019, USA
| | - J R Wendel
- NASA Headquarters, Washington, DC 20546, USA
| | - O L White
- NASA Ames Research Center, Space Science Division, Moffett Field, CA 94035, USA.,SETI Institute, Mountain View, CA 94043, USA
| | - K E Whittenburg
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | | | | | - S P Williams
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - H L Winters
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - A M Zangari
- Southwest Research Institute, Boulder, CO 80302, USA
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20
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Jones MR, Williamson LM, Topham JT, Lee MKC, Goytain A, Ho J, Denroche RE, Jang G, Pleasance E, Shen Y, Karasinska JM, McGhie JP, Gill S, Lim HJ, Moore MJ, Wong HL, Ng T, Yip S, Zhang W, Sadeghi S, Reisle C, Mungall AJ, Mungall KL, Moore RA, Ma Y, Knox JJ, Gallinger S, Laskin J, Marra MA, Schaeffer DF, Jones SJM, Renouf DJ. NRG1 Gene Fusions Are Recurrent, Clinically Actionable Gene Rearrangements in KRAS Wild-Type Pancreatic Ductal Adenocarcinoma. Clin Cancer Res 2019; 25:4674-4681. [PMID: 31068372 DOI: 10.1158/1078-0432.ccr-19-0191] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 03/07/2019] [Accepted: 04/15/2019] [Indexed: 01/28/2023]
Abstract
PURPOSE Gene fusions involving neuregulin 1 (NRG1) have been noted in multiple cancer types and have potential therapeutic implications. Although varying results have been reported in other cancer types, the efficacy of the HER-family kinase inhibitor afatinib in the treatment of NRG1 fusion-positive pancreatic ductal adenocarcinoma is not fully understood. EXPERIMENTAL DESIGN Forty-seven patients with pancreatic ductal adenocarcinoma received comprehensive whole-genome and transcriptome sequencing and analysis. Two patients with gene fusions involving NRG1 received afatinib treatment, with response measured by pretreatment and posttreatment PET/CT imaging. RESULTS Three of 47 (6%) patients with advanced pancreatic ductal adenocarcinoma were identified as KRAS wild type by whole-genome sequencing. All KRAS wild-type tumors were positive for gene fusions involving the ERBB3 ligand NRG1. Two of 3 patients with NRG1 fusion-positive tumors were treated with afatinib and demonstrated a significant and rapid response while on therapy. CONCLUSIONS This work adds to a growing body of evidence that NRG1 gene fusions are recurrent, therapeutically actionable genomic events in pancreatic cancers. Based on the clinical outcomes described here, patients with KRAS wild-type tumors harboring NRG1 gene fusions may benefit from treatment with afatinib.See related commentary by Aguirre, p. 4589.
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Affiliation(s)
- Martin R Jones
- BC Cancer, Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Laura M Williamson
- BC Cancer, Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | | | - Michael K C Lee
- BC Cancer, Division of Medical Oncology, Vancouver, British Columbia, Canada
| | - Angela Goytain
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Julie Ho
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Robert E Denroche
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - GunHo Jang
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Erin Pleasance
- BC Cancer, Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Yaoquing Shen
- BC Cancer, Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | | | - John P McGhie
- BC Cancer, Division of Medical Oncology, Vancouver, British Columbia, Canada
| | - Sharlene Gill
- BC Cancer, Division of Medical Oncology, Vancouver, British Columbia, Canada
| | - Howard J Lim
- BC Cancer, Division of Medical Oncology, Vancouver, British Columbia, Canada
| | - Malcolm J Moore
- Division of Medical Oncology, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Hui-Li Wong
- BC Cancer, Division of Medical Oncology, Vancouver, British Columbia, Canada
| | - Tony Ng
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Stephen Yip
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Wei Zhang
- BC Cancer, Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Sara Sadeghi
- BC Cancer, Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Carolyn Reisle
- BC Cancer, Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Andrew J Mungall
- BC Cancer, Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Karen L Mungall
- BC Cancer, Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Richard A Moore
- BC Cancer, Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Yussanne Ma
- BC Cancer, Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Jennifer J Knox
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Division of Medical Oncology, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Steven Gallinger
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Janessa Laskin
- BC Cancer, Division of Medical Oncology, Vancouver, British Columbia, Canada
| | - Marco A Marra
- BC Cancer, Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - David F Schaeffer
- Pancreas Centre British Columbia, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Steven J M Jones
- BC Cancer, Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Vancouver, British Columbia, Canada
| | - Daniel J Renouf
- Pancreas Centre British Columbia, Vancouver, Canada.
- BC Cancer, Division of Medical Oncology, Vancouver, British Columbia, Canada
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21
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Teter B, Morihara T, Lim GP, Chu T, Jones MR, Zuo X, Paul RM, Frautschy SA, Cole GM. Curcumin restores innate immune Alzheimer's disease risk gene expression to ameliorate Alzheimer pathogenesis. Neurobiol Dis 2019; 127:432-448. [PMID: 30951849 DOI: 10.1016/j.nbd.2019.02.015] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 02/15/2019] [Accepted: 02/20/2019] [Indexed: 01/28/2023] Open
Abstract
Alzheimer's disease (AD) genetics implies a causal role for innate immune genes, TREM2 and CD33, products that oppose each other in the downstream Syk tyrosine kinase pathway, activating microglial phagocytosis of amyloid (Aβ). We report effects of low (Curc-lo) and high (Curc-hi) doses of curcumin on neuroinflammation in APPsw transgenic mice. Results showed that Curc-lo decreased CD33 and increased TREM2 expression (predicted to decrease AD risk) and also increased TyroBP, which controls a neuroinflammatory gene network implicated in AD as well as phagocytosis markers CD68 and Arg1. Curc-lo coordinately restored tightly correlated relationships between these genes' expression levels, and decreased expression of genes characteristic of toxic pro-inflammatory M1 microglia (CD11b, iNOS, COX-2, IL1β). In contrast, very high dose curcumin did not show these effects, failed to clear amyloid plaques, and dysregulated gene expression relationships. Curc-lo stimulated microglial migration to and phagocytosis of amyloid plaques both in vivo and in ex vivo assays of sections of human AD brain and of mouse brain. Curcumin also reduced levels of miR-155, a micro-RNA reported to drive a neurodegenerative microglial phenotype. In conditions without amyloid (human microglial cells in vitro, aged wild-type mice), Curc-lo similarly decreased CD33 and increased TREM2. Like curcumin, anti-Aβ antibody (also reported to engage the Syk pathway, increase CD68, and decrease amyloid burden in human and mouse brain) increased TREM2 in APPsw mice and decreased amyloid in human AD sections ex vivo. We conclude that curcumin is an immunomodulatory treatment capable of emulating anti-Aβ vaccine in stimulating phagocytic clearance of amyloid by reducing CD33 and increasing TREM2 and TyroBP, while restoring neuroinflammatory networks implicated in neurodegenerative diseases.
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Affiliation(s)
- B Teter
- Departments of Neurology, Geriatric Research Education and Clinical Centerand, University of California, Los Angeles (UCLA), United States of America; Departments of Veterans Affairs Greater Los Angeles Healthcare System, Geriatric Research Education and Clinical Center, University of California, Los Angeles (UCLA), United States of America; Alzheimer's Translational Center, Veterans Administration (Research 151), Bldg. 114, Rm. 114-1, 11301 Wilshire Blvd, Los Angeles, CA 90073, United States of America.
| | - T Morihara
- Departments of Neurology, Geriatric Research Education and Clinical Centerand, University of California, Los Angeles (UCLA), United States of America; Departments of Veterans Affairs Greater Los Angeles Healthcare System, Geriatric Research Education and Clinical Center, University of California, Los Angeles (UCLA), United States of America.
| | - G P Lim
- Departments of Neurology, Geriatric Research Education and Clinical Centerand, University of California, Los Angeles (UCLA), United States of America; Departments of Veterans Affairs Greater Los Angeles Healthcare System, Geriatric Research Education and Clinical Center, University of California, Los Angeles (UCLA), United States of America
| | - T Chu
- Departments of Neurology, Geriatric Research Education and Clinical Centerand, University of California, Los Angeles (UCLA), United States of America; Departments of Veterans Affairs Greater Los Angeles Healthcare System, Geriatric Research Education and Clinical Center, University of California, Los Angeles (UCLA), United States of America
| | - M R Jones
- Departments of Neurology, Geriatric Research Education and Clinical Centerand, University of California, Los Angeles (UCLA), United States of America
| | - X Zuo
- Departments of Neurology, Geriatric Research Education and Clinical Centerand, University of California, Los Angeles (UCLA), United States of America; Departments of Veterans Affairs Greater Los Angeles Healthcare System, Geriatric Research Education and Clinical Center, University of California, Los Angeles (UCLA), United States of America
| | - R M Paul
- Departments of Neurology, Geriatric Research Education and Clinical Centerand, University of California, Los Angeles (UCLA), United States of America; Departments of Medicine, University of California, Los Angeles (UCLA), United States of America
| | - S A Frautschy
- Departments of Neurology, Geriatric Research Education and Clinical Centerand, University of California, Los Angeles (UCLA), United States of America; Departments of Medicine, University of California, Los Angeles (UCLA), United States of America; Departments of Veterans Affairs Greater Los Angeles Healthcare System, Geriatric Research Education and Clinical Center, University of California, Los Angeles (UCLA), United States of America.
| | - G M Cole
- Departments of Neurology, Geriatric Research Education and Clinical Centerand, University of California, Los Angeles (UCLA), United States of America; Departments of Medicine, University of California, Los Angeles (UCLA), United States of America; Departments of Veterans Affairs Greater Los Angeles Healthcare System, Geriatric Research Education and Clinical Center, University of California, Los Angeles (UCLA), United States of America.
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22
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Thibodeau ML, Zhao EY, Reisle C, Ch'ng C, Wong HL, Shen Y, Jones MR, Lim HJ, Young S, Cremin C, Pleasance E, Zhang W, Holt R, Eirew P, Karasinska J, Kalloger SE, Taylor G, Majounie E, Bonakdar M, Zong Z, Bleile D, Chiu R, Birol I, Gelmon K, Lohrisch C, Mungall KL, Mungall AJ, Moore R, Ma YP, Fok A, Yip S, Karsan A, Huntsman D, Schaeffer DF, Laskin J, Marra MA, Renouf DJ, Jones SJM, Schrader KA. Base excision repair deficiency signatures implicate germline and somatic MUTYH aberrations in pancreatic ductal adenocarcinoma and breast cancer oncogenesis. Cold Spring Harb Mol Case Stud 2019; 5:mcs.a003681. [PMID: 30833417 PMCID: PMC6549570 DOI: 10.1101/mcs.a003681] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 02/17/2019] [Indexed: 12/21/2022] Open
Abstract
We report a case of early-onset pancreatic ductal adenocarcinoma in a patient harboring biallelic MUTYH germline mutations, whose tumor featured somatic mutational signatures consistent with defective MUTYH-mediated base excision repair and the associated driver KRAS transversion mutation p.Gly12Cys. Analysis of an additional 730 advanced cancer cases (N = 731) was undertaken to determine whether the mutational signatures were also present in tumors from germline MUTYH heterozygote carriers or if instead the signatures were only seen in those with biallelic loss of function. We identified two patients with breast cancer each carrying a pathogenic germline MUTYH variant with a somatic MUTYH copy loss leading to the germline variant being homozygous in the tumor and demonstrating the same somatic signatures. Our results suggest that monoallelic inactivation of MUTYH is not sufficient for C:G>A:T transversion signatures previously linked to MUTYH deficiency to arise (N = 9), but that biallelic complete loss of MUTYH function can cause such signatures to arise even in tumors not classically seen in MUTYH-associated polyposis (N = 3). Although defective MUTYH is not the only determinant of these signatures, MUTYH germline variants may be present in a subset of patients with tumors demonstrating elevated somatic signatures possibly suggestive of MUTYH deficiency (e.g., COSMIC Signature 18, SigProfiler SBS18/SBS36, SignatureAnalyzer SBS18/SBS36).
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Affiliation(s)
- My Linh Thibodeau
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada.,Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada.,Hereditary Cancer Program, BC Cancer, Vancouver, British Columbia V5Z 1H5, Canada
| | - Eric Y Zhao
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Caralyn Reisle
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Carolyn Ch'ng
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Hui-Li Wong
- Department of Medical Oncology, BC Cancer, Vancouver, British Columbia V5Z 4E6, Canada
| | - Yaoqing Shen
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Martin R Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Howard J Lim
- Department of Medical Oncology, BC Cancer, Vancouver, British Columbia V5Z 4E6, Canada
| | - Sean Young
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada.,Cancer Genetics and Genomics Laboratory, BC Cancer, Vancouver, British Columbia V5Z 4E6, Canada
| | - Carol Cremin
- Hereditary Cancer Program, BC Cancer, Vancouver, British Columbia V5Z 1H5, Canada.,Pancreas Centre BC, Vancouver, British Columbia V5Z 1L8, Canada
| | - Erin Pleasance
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Wei Zhang
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Robert Holt
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada.,Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Peter Eirew
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia V5Z 1L3, Canada
| | | | - Steve E Kalloger
- Pancreas Centre BC, Vancouver, British Columbia V5Z 1L8, Canada.,School of Population and Public Health, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.,The Canadian Centre for Applied Research in Cancer Control, Vancouver, British Columbia V5Z 1L3, Canada.,Department of Pathology and Laboratory Medicine, BC Cancer, Vancouver, British Columbia V5Z 4E6, Canada
| | - Greg Taylor
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Elisa Majounie
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Melika Bonakdar
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Zusheng Zong
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Dustin Bleile
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Readman Chiu
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Inanc Birol
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada.,Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Karen Gelmon
- Department of Medical Oncology, BC Cancer, Vancouver, British Columbia V5Z 4E6, Canada
| | - Caroline Lohrisch
- Department of Medical Oncology, BC Cancer, Vancouver, British Columbia V5Z 4E6, Canada
| | - Karen L Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Richard Moore
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Yussanne P Ma
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Alexandra Fok
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada.,Hereditary Cancer Program, BC Cancer, Vancouver, British Columbia V5Z 1H5, Canada
| | - Stephen Yip
- Cancer Genetics and Genomics Laboratory, BC Cancer, Vancouver, British Columbia V5Z 4E6, Canada.,Department of Pathology & Laboratory Medicine, Vancouver General Hospital, Vancouver, British Columbia V5Z 1M9, Canada
| | - Aly Karsan
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada.,Department of Pathology and Laboratory Medicine, BC Cancer, Vancouver, British Columbia V5Z 4E6, Canada
| | - David Huntsman
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada.,Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia V5Z 1L3, Canada.,Department of Pathology & Laboratory Medicine, Vancouver General Hospital, Vancouver, British Columbia V5Z 1M9, Canada
| | - David F Schaeffer
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V6T 2B5, Canada.,Pancreas Centre BC, Vancouver, British Columbia V5Z 1L8, Canada.,Department of Pathology & Laboratory Medicine, Vancouver General Hospital, Vancouver, British Columbia V5Z 1M9, Canada
| | - Janessa Laskin
- Department of Medical Oncology, BC Cancer, Vancouver, British Columbia V5Z 4E6, Canada
| | - Marco A Marra
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada.,Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Daniel J Renouf
- Department of Medical Oncology, BC Cancer, Vancouver, British Columbia V5Z 4E6, Canada.,Pancreas Centre BC, Vancouver, British Columbia V5Z 1L8, Canada
| | - Steven J M Jones
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada.,Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia V5Z 4S6, Canada
| | - Kasmintan A Schrader
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada.,Hereditary Cancer Program, BC Cancer, Vancouver, British Columbia V5Z 1H5, Canada.,Pancreas Centre BC, Vancouver, British Columbia V5Z 1L8, Canada.,Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia V5Z 1L3, Canada
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23
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Zuo H, Ueland PM, Midttun Ø, Tell GS, Fanidi A, Zheng W, Shu X, Xiang Y, Wu J, Prentice R, Pettinger M, Thomson CA, Giles GG, Hodge A, Cai Q, Blot WJ, Johansson M, Hultdin J, Grankvist K, Stevens VL, McCullough ML, Weinstein SJ, Albanes D, Ziegler RG, Freedman ND, Caporaso NE, Langhammer A, Hveem K, Næss M, Buring JE, Lee I, Gaziano JM, Severi G, Zhang X, Stampfer MJ, Han J, Zeleniuch-Jacquotte A, Marchand LL, Yuan J, Wang R, Koh W, Gao Y, Ericson U, Visvanathan K, Jones MR, Relton C, Brennan P, Johansson M, Ulvik A. Vitamin B6 catabolism and lung cancer risk: results from the Lung Cancer Cohort Consortium (LC3). Ann Oncol 2019; 30:478-485. [PMID: 30698666 PMCID: PMC6442648 DOI: 10.1093/annonc/mdz002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Increased vitamin B6 catabolism related to inflammation, as measured by the PAr index (the ratio of 4-pyridoxic acid over the sum of pyridoxal and pyridoxal-5'-phosphate), has been positively associated with lung cancer risk in two prospective European studies. However, the extent to which this association translates to more diverse populations is not known. MATERIALS AND METHODS For this study, we included 5323 incident lung cancer cases and 5323 controls individually matched by age, sex, and smoking status within each of 20 prospective cohorts from the Lung Cancer Cohort Consortium. Cohort-specific odds ratios (ORs) and 95% confidence intervals (CIs) for the association between PAr and lung cancer risk were calculated using conditional logistic regression and pooled using random-effects models. RESULTS PAr was positively associated with lung cancer risk in a dose-response fashion. Comparing the fourth versus first quartiles of PAr resulted in an OR of 1.38 (95% CI: 1.19-1.59) for overall lung cancer risk. The association between PAr and lung cancer risk was most prominent in former smokers (OR: 1.69, 95% CI: 1.36-2.10), men (OR: 1.60, 95% CI: 1.28-2.00), and for cancers diagnosed within 3 years of blood draw (OR: 1.73, 95% CI: 1.34-2.23). CONCLUSION Based on pre-diagnostic data from 20 cohorts across 4 continents, this study confirms that increased vitamin B6 catabolism related to inflammation and immune activation is associated with a higher risk of developing lung cancer. Moreover, PAr may be a pre-diagnostic marker of lung cancer rather than a causal factor.
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Affiliation(s)
- H Zuo
- Department of Global Public Health and Primary Care, University of Bergen, Bergen.
| | - P M Ueland
- Department of Clinical Science, University of Bergen, Bergen; Laboratory of Medicine and Pathology, Haukeland University Hospital, Bergen
| | | | - G S Tell
- Department of Global Public Health and Primary Care, University of Bergen, Bergen
| | - A Fanidi
- Genetic Epidemiology Group, International Agency for Research on Cancer, Lyon, France; MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - W Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, USA
| | - X Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, USA
| | - Y Xiang
- State Key Laboratory of Oncogene and Related Genes & Department of Epidemiology, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - J Wu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, USA
| | - R Prentice
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle
| | - M Pettinger
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle
| | - C A Thomson
- Health Promotion Sciences, Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, USA
| | - G G Giles
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Australia
| | - A Hodge
- Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Australia
| | - Q Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, USA
| | - W J Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, USA
| | - M Johansson
- Department of Radiation Sciences, Oncology, Umeå University, Umeå
| | - J Hultdin
- Department of Medical Biosciences, Clinical Chemistry, Umeå University, Umeå, Sweden
| | - K Grankvist
- Department of Medical Biosciences, Clinical Chemistry, Umeå University, Umeå, Sweden
| | - V L Stevens
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta
| | - M L McCullough
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta
| | - S J Weinstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, USA
| | - D Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, USA
| | - R G Ziegler
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, USA
| | - N D Freedman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, USA
| | - N E Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, USA
| | - A Langhammer
- HUNT Research Centre, Department of Public Health and Nursing, Faculty of Medicine and Health Science, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - K Hveem
- HUNT Research Centre, Department of Public Health and Nursing, Faculty of Medicine and Health Science, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - M Næss
- HUNT Research Centre, Department of Public Health and Nursing, Faculty of Medicine and Health Science, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
| | - J E Buring
- Division of Preventive Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston
| | - I Lee
- Division of Preventive Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston
| | - J M Gaziano
- Division of Aging, Brigham and Women's Hospital, Boston; VA Boston Healthcare System, Boston, USA
| | - G Severi
- Human Genetics Foundation (HuGeF), Torin, Italy; CESP (U1018 INSERM), Université Paris-Saclay, USQ, Villejuif, France
| | - X Zhang
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston
| | - M J Stampfer
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston; Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston
| | - J Han
- Department of Epidemiology, Richard M. Fairbanks School of Public Health, Melvin & Bren Simon Cancer Center, Indiana University, Indianapolis
| | | | - L L Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu
| | - J Yuan
- Division of Cancer Control and Population Sciences, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh; Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, USA
| | - R Wang
- Division of Cancer Control and Population Sciences, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh
| | - W Koh
- Duke-NUS Medical School, Singapore and Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Y Gao
- Department of Epidemiology, Shanghai Cancer Institute, Shanghai Jiaotong University, Shanghai, China
| | - U Ericson
- Department of Clinical Sciences Malmö, Lund University, Lund, Sweden
| | - K Visvanathan
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health and Johns Hopkins Sidney Kimmel Comprehensive Center, School of Medicine, Baltimore, USA
| | - M R Jones
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health and Johns Hopkins Sidney Kimmel Comprehensive Center, School of Medicine, Baltimore, USA
| | - C Relton
- Institute of Genetic Medicine, Newcastle University, Newcastle; MRC Integrative Epidemiology Unit, School of Social & Community Medicine, University of Bristol, Bristol, UK
| | - P Brennan
- Genetic Epidemiology Group, International Agency for Research on Cancer, Lyon, France
| | - M Johansson
- Genetic Epidemiology Group, International Agency for Research on Cancer, Lyon, France
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24
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Lee M, Jones MR, Williamson L, Topham JT, Addison S, Wong HL, Denroche R, Jang GH, Karasinska J, McGhie JP, Gill S, Lim HJ, Yip S, Knox JJ, Gallinger S, Laskin JJ, Marra MA, Jones SJM, Sschaeffer DF, Renouf DJ. Comprehensive genomic analysis of metastatic pancreatic ductal adenocarcinoma (mPDAC) reveals a significant proportion of clinical actionable aberrations. J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.4_suppl.273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
273 Background: Substantial progress has been made in the understanding of the genomic landscape of PDAC, but the clinical utility of these data remains uncertain. Methods: As part of the BC Cancer Personalized Oncogenomics (POG) and PanGen studies, whole genome analysis and transcriptome sequencing were performed on fresh biopsy and blood sample from 47 mPDAC patients. Genomic findings informed therapy choices including potential eligibility for the CCTG PM.1 molecular basket trial. Results: Cohort consists of 53% male, average age 57.8, 34/47 had ≥2 lines of treatment. 37/47 biopsies were from liver and 26/47 were collected pre-treatment. 8/47 (17%) patients had aberrations with strong evidence of clinical actionability. These include 2 germline BRCA2, 1 germline BRCA1, 1 somatic XRCC2 homozygous deletion with strong COSMIC signature 3, all predictive of platinum sensitivity. Patients with XRCC2 deletion and BRCA1 had over 2 years on FOLFIRINOX. Fusions affecting the NRG1 gene were identified in 3 patients, all with KRAS wildtype tumours, which may confer ERRB inhibitor sensitivity. 1/3 NRG1 fusion patients had thus far been treated with the ERBB inhibitor afatinib, with reduction of CA19-9 from >120,000 to 7246 and dramatic response noted on PET CT imaging one month post treatment. One patient had mismatch repair deficiency, and a high mutational burden, suggestive of immune checkpoint inhibitor sensitivity. In total 85% (40/47) sequenced mPDAC patients had potentially actionable mutations which includes CCTG PM.1 trial eligibility: 24/47 with cell cycle dysregulation (CDK4/6 inhibitor arm), 4/47 with high homologous recombination defects (PARP inhibitor arm), 1/47 ERBB2 amplification (anti-HER2 arm), 2/47 high expression of FGFR1 (Sunitinib arm) and 1/47 with high FLT4 and IGF1R expression (Axitinib arm). Conclusions: More routine use of comprehensive genomic analysis should be considered in mPDAC given finding of high degree of actionability. Importantly, a significant proportion (17%) had findings with strong evidence of clinical impact.(NCT02155621, NCT02869802, NCT03297606)
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Affiliation(s)
- Michael Lee
- British Columbia Cancer Agency, Vancouver, BC, Canada
| | | | - Laura Williamson
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | | | - Sean Addison
- Vancouver General Hospital, Internal Medicine Department, Vancouver, BC, Canada
| | - Hui-Li Wong
- Royal Melbourne Hospital, Abbotsford, Australia
| | - Rob Denroche
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Gun Ho Jang
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | | | | | | | - Stephen Yip
- Vancouver Coastal Health Research Institute, Vancouver, BC, Canada
| | | | | | | | - Marco A. Marra
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | | | - David F Sschaeffer
- Department of Pathology & Laboratory Medicine Vancouver General Hospital, Vancouver, BC, Canada
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25
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Abstract
OBJECTIVE Brain computer interface (BCI) technology can be important for those unable to communicate due to loss of muscle control. Given that the P300 Speller provides a relatively slow rate of communication, highly accurate classification is of great importance. Previous studies have shown that alternative stimuli (e.g. faces) can improve BCI speed and accuracy. The present study uses two new alternative stimuli, locations and graspable tools. Functional MRI studies have shown that images of familiar locations produce brain responses in the parahippocampal place area and graspable tools produce brain responses in premotor cortex. APPROACH The current studies show that location and tool stimuli produce unique and discriminable brain responses that can be used to improve offline classification accuracy. Experiment 1 presented face stimuli and location stimuli and Experiment 2 presented location and tool stimuli. MAIN RESULTS In both experiments, offline results showed that a stimulus specific classifier provided higher accuracy, speed, and bit rate. SIGNIFICANCE This study was used to provide preliminary offline support for using unique stimuli to improve speed and accuracy of the P300 Speller. Additional experiments should be conducted to examine the online efficacy of this novel paradigm.
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Affiliation(s)
- M R Jones
- East Tennessee State University, 1276 Gilbreath Dr, Johnson City, TN 37614, United States of America
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26
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Brower MA, Hai Y, Jones MR, Guo X, Chen YDI, Rotter JI, Krauss RM, Legro RS, Azziz R, Goodarzi MO. Bidirectional Mendelian randomization to explore the causal relationships between body mass index and polycystic ovary syndrome. Hum Reprod 2019; 34:127-136. [PMID: 30496407 PMCID: PMC6295958 DOI: 10.1093/humrep/dey343] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 10/17/2018] [Accepted: 11/01/2018] [Indexed: 11/14/2022] Open
Abstract
STUDY QUESTION What are the causal relationships between polycystic ovary syndrome (PCOS) and body mass index (BMI)? SUMMARY ANSWER Bidirectional Mendelian randomization analyses suggest that increased BMI is causal for PCOS while the reverse is not the case. WHAT IS KNOWN ALREADY The contribution of obesity to the pathogenesis of PCOS is controversial. To date, published genetic studies addressing this question have generated conflicting results and have not utilized the full extent of known single nucleotide polymorphisms associated with body mass index (BMI). STUDY DESIGN, SIZE, DURATION This cross-sectional Mendelian randomization (MR) and genetic association study was conducted in 750 individuals of European origin and with PCOS and 1567 BMI-matched controls. PARTICIPANTS/MATERIALS, SETTING, METHODS Cases and controls were matched for BMI as well as for distribution of weight categories (normal weight, overweight, obese). Two-sample MR using inverse variance weighting (IVW) was conducted using a 92-SNP instrument variable for BMI with PCOS as the outcome, followed by two-sample MR with a 16-SNP instrument variable for PCOS with BMI as the outcome. Sensitivity analyses included MR-Egger and maximum likelihood methods. Secondary analyses assessed associations of genetic risk scores and individual SNPs with PCOS, BMI and quantitative androgen-related and glucose homeostasis-related traits. MAIN RESULTS AND THE ROLE OF CHANCE Each standard deviation genetically higher BMI was associated with a 4.89 (95% CI 1.46-16.32) higher odds of PCOS. Conversely, genetic risk of PCOS did not influence BMI. Sensitivity analyses yielded directionally consistent results. The genetic risk score of 92 BMI SNPs was associated with the diagnosis of PCOS (OR 1.043, 95% CI 1.009-1.078, P = 0.012). Of the 92 BMI risk variants evaluated, none were associated individually with PCOS after considering multiple testing. The association of FTO SNP rs1421085 with BMI was stronger in women with PCOS (β = 0.071, P = 0.0006) than in controls (β = 0.046, P = 0.065). LIMITATIONS, REASONS FOR CAUTION The current sample size, while providing good power for MR and genetic risk score analyses, had limited power to demonstrate association of individual SNPs with PCOS. Cases and controls were not matched for age; however, this was mitigated by adjusting analyses for age. Dietary and lifestyle data, which could have been used to explore the greater association of the FTO SNP with BMI in women with PCOS, was not available. WIDER IMPLICATIONS OF THE FINDINGS Increasing BMI appears to be causal for PCOS but having PCOS does not appear to affect BMI. This study used the most comprehensive set of SNPs for BMI currently available. Prior studies using fewer SNPs had yielded conflicting results and may have been confounded because cases and controls were not matched for weight categories. The current results highlight the potential utility of weight management in the prevention and treatment of PCOS. STUDY FUNDING/COMPETING INTEREST(S) National Institutes of Health Grants R01-HD29364 and K24-HD01346 (to R.A.), Grant R01-DK79888 (to M.O.G.), Grant U54-HD034449 (to R.S.L.), Grant U19-HL069757 (to R.M.K.). The funders had no influence on the data collection, analyses or conclusions of the study. No conflict of interests to declare. TRIAL REGISTRATION NUMBER N/A.
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Affiliation(s)
- M A Brower
- Department of Obstetrics and Gynecology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Y Hai
- Department of Statistics, University of Auckland, Auckland, New Zealand
- Institute for Translational Genomics and Population Sciences and Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - M R Jones
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - X Guo
- Institute for Translational Genomics and Population Sciences and Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Y -D I Chen
- Institute for Translational Genomics and Population Sciences and Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - J I Rotter
- Institute for Translational Genomics and Population Sciences and Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - R M Krauss
- Children’s Hospital of Oakland Research Institute, Oakland, CA, USA
| | - R S Legro
- Department of Obstetrics and Gynecology, Pennsylvania State College of Medicine, Hershey, PA, USA
| | - R Azziz
- Departments of Obstetrics and Gynecology and Medicine, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - M O Goodarzi
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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27
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Lever J, Gakkhar S, Gottlieb M, Rashnavadi T, Lin S, Siu C, Smith M, Jones MR, Krzywinski M, Jones SJM, Wren J. A collaborative filtering-based approach to biomedical knowledge discovery. Bioinformatics 2018; 34:652-659. [PMID: 29028901 DOI: 10.1093/bioinformatics/btx613] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 09/25/2017] [Indexed: 01/19/2023] Open
Abstract
Motivation The increase in publication rates makes it challenging for an individual researcher to stay abreast of all relevant research in order to find novel research hypotheses. Literature-based discovery methods make use of knowledge graphs built using text mining and can infer future associations between biomedical concepts that will likely occur in new publications. These predictions are a valuable resource for researchers to explore a research topic. Current methods for prediction are based on the local structure of the knowledge graph. A method that uses global knowledge from across the knowledge graph needs to be developed in order to make knowledge discovery a frequently used tool by researchers. Results We propose an approach based on the singular value decomposition (SVD) that is able to combine data from across the knowledge graph through a reduced representation. Using cooccurrence data extracted from published literature, we show that SVD performs better than the leading methods for scoring discoveries. We also show the diminishing predictive power of knowledge discovery as we compare our predictions with real associations that appear further into the future. Finally, we examine the strengths and weaknesses of the SVD approach against another well-performing system using several predicted associations. Availability and implementation All code and results files for this analysis can be accessed at https://github.com/jakelever/knowledgediscovery. Contact sjones@bcgsc.ca. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jake Lever
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC V5Z 4S6, Canada.,University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Sitanshu Gakkhar
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC V5Z 4S6, Canada
| | - Michael Gottlieb
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC V5Z 4S6, Canada
| | - Tahereh Rashnavadi
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC V5Z 4S6, Canada
| | - Santina Lin
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC V5Z 4S6, Canada
| | - Celia Siu
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC V5Z 4S6, Canada
| | - Maia Smith
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC V5Z 4S6, Canada
| | - Martin R Jones
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC V5Z 4S6, Canada
| | - Martin Krzywinski
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC V5Z 4S6, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC V5Z 4S6, Canada.,University of British Columbia, Vancouver, BC V6T 1Z1, Canada.,Simon Fraser University, Burnaby, BC V5A 1S6, Canada
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28
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Wong HL, Zhao EY, Jones MR, Reisle CR, Eirew P, Pleasance E, Grande BM, Karasinska JM, Kalloger SE, Lim HJ, Shen Y, Yip S, Morin RD, Laskin J, Marra MA, Jones SJ, Schrader KA, Schaeffer DF, Renouf DJ. Temporal Dynamics of Genomic Alterations in a BRCA1 Germline-Mutated Pancreatic Cancer With Low Genomic Instability Burden but Exceptional Response to Fluorouracil, Oxaliplatin, Leucovorin, and Irinotecan. JCO Precis Oncol 2018; 2:PO.18.00057. [PMID: 32913994 PMCID: PMC7446469 DOI: 10.1200/po.18.00057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Affiliation(s)
- Hui-li Wong
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Eric Y. Zhao
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Martin R. Jones
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Caralyn R. Reisle
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Peter Eirew
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Erin Pleasance
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Bruno M. Grande
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Joanna M. Karasinska
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Steve E. Kalloger
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Howard J. Lim
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Yaoqing Shen
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Stephen Yip
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Ryan D. Morin
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Janessa Laskin
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Marco A. Marra
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Steven J.M. Jones
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Kasmintan A. Schrader
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - David F. Schaeffer
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Daniel J. Renouf
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
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Jones MR, Shen Y, Pleasance E, Majounie E, Williamson L, Zhao E, Chuah E, Mungall KL, Mungall AJ, Moore RA, Ma Y, Yip S, Lim H, Renouf D, Jones SJ, Jaskin J, Marra MA. Abstract 4340: Integrating whole genome and transcriptome analysis to inform treatment decisions in the metastatic cancer clinical setting. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-4340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Genomic analysis is an established clinical tool for positioning patients to specific treatment rationales. However, given the vast range of genomic complexity that is observed between tumors the extent to which genomic characterization must be applied in order to generate a true picture of the actionable and informative genomic events in an individual's tumour is still a matter for intense debate. Historically, cost and the complexity of the bioinformatics analysis needed has limited the adoption of comprehensive genomic characterization. However with the emerging clinical significance of genomic signatures, mutation burden and immunogenomic profiling, information that can best be recovered from comprehensive genomic analyses, a better understanding of the utility of extensive genomic characterization of tumours in a clinical setting is needed. For the past 6 years, the Personalized Oncogenomics Project (POG) at the BC Cancer Agency has used paired tumour/normal Whole Genome and Transcriptome Analysis (WGTA) to comprehensively characterize tumour samples from patients with incurable metastatic cancer to inform treatment planning for each patient within a clinically relevant timeframe. To date tumours from over 700 patients have been genomically profiled using this approach. These data represent a cohort of tumours from the post-treatment metastatic setting that have been comprehensively characterized at a whole genome level augmented by comprehensive clinical annotation, including information about the primary diagnosis, progression of the disease and treatment history, as well as follow-up information including the response of the tumour to genome analysis-informed therapy. We will discuss findings from this powerful genomic cohort focusing on aspects that are particularly well represented by using a WGTA approach including; mutation signatures of biological and clinical significance, integration of expression data to complement genomic findings and highlighting the discovery of novel NRG1 gene fusions as a demonstration of how using a comprehensive multi-omic approach for genomic analysis to infer the oncogenic impact of novel genomic events can impact patient care.
Citation Format: Martin R. Jones, Yaoqing Shen, Erin Pleasance, Elisa Majounie, Laura Williamson, Eric Zhao, Eric Chuah, Karen L. Mungall, Andrew J. Mungall, Richard A. Moore, Yussanne Ma, Stephen Yip, Howard Lim, Daniel Renouf, Steven J. Jones, Janesssa Jaskin, Marco A. Marra. Integrating whole genome and transcriptome analysis to inform treatment decisions in the metastatic cancer clinical setting [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4340.
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Affiliation(s)
| | | | | | | | | | - Eric Zhao
- BCGSC, Vancouver, British Columbia, Canada
| | - Eric Chuah
- BCGSC, Vancouver, British Columbia, Canada
| | | | | | | | | | | | - Howard Lim
- BCGSC, Vancouver, British Columbia, Canada
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30
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Zhao EY, Pleasance ED, Jones MR, Shen Y, Reisle CR, Mungall AJ, Moore R, Zhao Y, Renouf DJ, Laskin JJ, Marra MA, Jones SJM. Evolution of genomic instability in metastatic cancer. J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.15_suppl.12008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | - Erin D Pleasance
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | | | | | - Caralyn R Reisle
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Andrew J. Mungall
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Richard Moore
- BC Cancer Agency - Genome Sciences Centre, Vancouver, BC, Canada
| | - Yongjun Zhao
- BC Cancer Agency - Genome Sciences Centre, Vancouver, BC, Canada
| | | | - Janessa J. Laskin
- Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Marco A. Marra
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Steven J. M. Jones
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
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31
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Jones MR, Lim H, Shen Y, Pleasance E, Ch'ng C, Reisle C, Leelakumari S, Zhao C, Yip S, Ho J, Zhong E, Ng T, Ionescu D, Schaeffer DF, Mungall AJ, Mungall KL, Zhao Y, Moore RA, Ma Y, Chia S, Ho C, Renouf DJ, Gelmon K, Jones SJM, Marra MA, Laskin J. Successful targeting of the NRG1 pathway indicates novel treatment strategy for metastatic cancer. Ann Oncol 2018; 28:3092-3097. [PMID: 28950338 DOI: 10.1093/annonc/mdx523] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Background NRG1 fusion-positive lung cancers have emerged as potentially actionable events in lung cancer, but clinical support is currently limited and no evidence of efficacy of this approach in cancers beyond lung has been shown. Patients and methods Here, we describe two patients with advanced cancers refractory to standard therapies. Patient 1 had lung adenocarcinoma and patient 2 cholangiocarcinoma. Whole-genome and transcriptome sequencing were carried out for these cases with select findings validated by fluorescence in situ hybridization. Results Both tumors were found to be positive for NRG1 gene fusions. In patient 1, an SDC4-NRG1 gene fusion was detected, similar gene fusions having been described in lung cancers previously. In patient 2, a novel ATP1B1-NRG1 gene fusion was detected. Cholangiocarcinoma is not a disease type in which NRG1 fusions had been described previously. Integrative genome analysis was used to assess the potential functional significance of the detected genomic events including the gene fusions, prioritizing therapeutic strategies targeting the HER-family of growth factor receptors. Both patients were treated with the pan HER-family kinase inhibitor afatinib and both displayed significant and durable response to treatment. Upon progression sites of disease were sequenced. The lack of obvious genomic events to describe the disease progression indicated that broad transcriptomic or epigenetic mechanisms could be attributed to the lack of prolonged response to afatinib. Conclusion These observations lend further support to the use of pan HER-tyrosine kinase inhibitors for the treatment of NRG1 fusion-positive in both cancers of lung and hepatocellular origin and indicate more broadly that cancers found to be NRG1 fusion-positive may benefit from such a clinical approach regardless of their site of origin. Clinical trial information Personalized Oncogenomics (POG) Program of British Columbia: Utilization of Genomic Analysis to Better Understand Tumour Heterogeneity and Evolution (NCT02155621).
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Affiliation(s)
- M R Jones
- Canada's Michael Smith Genome Sciences Centre
| | - H Lim
- Division of Medical Oncology, BC Cancer Agency, Vancouver
| | - Y Shen
- Canada's Michael Smith Genome Sciences Centre
| | - E Pleasance
- Canada's Michael Smith Genome Sciences Centre
| | - C Ch'ng
- Canada's Michael Smith Genome Sciences Centre
| | - C Reisle
- Canada's Michael Smith Genome Sciences Centre
| | | | - C Zhao
- Canada's Michael Smith Genome Sciences Centre
| | - S Yip
- Department of Pathology & Laboratory Medicine, Vancouver General Hospital, Vancouver
| | - J Ho
- Department of Pathology & Laboratory Medicine, Vancouver General Hospital, Vancouver
| | - E Zhong
- Department of Pathology & Laboratory Medicine, Vancouver General Hospital, Vancouver
| | - T Ng
- Department of Pathology & Laboratory Medicine, Vancouver General Hospital, Vancouver
| | - D Ionescu
- Department of Pathology & Laboratory Medicine, BC Cancer Agency, Vancouver
| | - D F Schaeffer
- Department of Pathology & Laboratory Medicine, Vancouver General Hospital, Vancouver
| | - A J Mungall
- Canada's Michael Smith Genome Sciences Centre
| | - K L Mungall
- Canada's Michael Smith Genome Sciences Centre
| | - Y Zhao
- Canada's Michael Smith Genome Sciences Centre
| | - R A Moore
- Canada's Michael Smith Genome Sciences Centre
| | - Y Ma
- Canada's Michael Smith Genome Sciences Centre
| | - S Chia
- Division of Medical Oncology, BC Cancer Agency, Vancouver
| | - C Ho
- Division of Medical Oncology, BC Cancer Agency, Vancouver
| | - D J Renouf
- Division of Medical Oncology, BC Cancer Agency, Vancouver
| | - K Gelmon
- Division of Medical Oncology, BC Cancer Agency, Vancouver
| | - S J M Jones
- Canada's Michael Smith Genome Sciences Centre.,Department of Medical Genetics, University of British Columbia, Vancouver.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Vancouver, Canada
| | - M A Marra
- Canada's Michael Smith Genome Sciences Centre.,Department of Medical Genetics, University of British Columbia, Vancouver
| | - J Laskin
- Division of Medical Oncology, BC Cancer Agency, Vancouver
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32
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Newton Y, Rassekh SR, Deyell RJ, Shen Y, Jones MR, Dunham C, Yip S, Leelakumari S, Zhu J, McColl D, Swatloski T, Salama SR, Ng T, Hendson G, Lee AF, Ma Y, Moore R, Mungall AJ, Haussler D, Stuart JM, Jantzen C, Laskin J, Jones SJM, Marra MA, Morozova O. Comparative RNA-Sequencing Analysis Benefits a Pediatric Patient With Relapsed Cancer. JCO Precis Oncol 2018; 2. [PMID: 31372595 PMCID: PMC6675034 DOI: 10.1200/po.17.00198] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Clinical detection of sequence and structural variants in known cancer genes points to viable treatment options for a minority of children with cancer.1 To increase the number of children who benefit from genomic profiling, gene expression information must be considered alongside mutations.2,3 Although high expression has been used to nominate drug targets for pediatric cancers,4,5 its utility has not been evaluated in a systematic way.6 We describe a child with a rare sarcoma that was profiled with whole-genome and RNA sequencing (RNA-Seq) techniques. Although the tumor did not harbor DNA mutations targetable by available therapies, incorporation of gene expression information derived from RNA-Seq analysis led to a therapy that produced a significant clinical response. We use this case to describe a framework for inclusion of gene expression into the clinical genomic evaluation of pediatric tumors.
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Affiliation(s)
- Yulia Newton
- University of California Santa Cruz Genomics Institute, Mailstop CBSE, 1156 High St, Santa Cruz, CA 95064
| | - S Rod Rassekh
- British Columbia Children's Hospital and British Columbia Children's Hospital Research Institute
| | - Rebecca J Deyell
- British Columbia Children's Hospital and British Columbia Children's Hospital Research Institute
| | - Yaoqing Shen
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Martin R Jones
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Chris Dunham
- British Columbia Children's Hospital and British Columbia Children's Hospital Research Institute
| | | | - Sreeja Leelakumari
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Jingchun Zhu
- University of California Santa Cruz Genomics Institute, Mailstop CBSE, 1156 High St, Santa Cruz, CA 95064
| | - Duncan McColl
- University of California Santa Cruz Genomics Institute, Mailstop CBSE, 1156 High St, Santa Cruz, CA 95064
| | - Teresa Swatloski
- University of California Santa Cruz Genomics Institute, Mailstop CBSE, 1156 High St, Santa Cruz, CA 95064
| | - Sofie R Salama
- University of California Santa Cruz Genomics Institute, Mailstop CBSE, 1156 High St, Santa Cruz, CA 95064
| | | | - Glenda Hendson
- British Columbia Children's Hospital and British Columbia Children's Hospital Research Institute
| | - Anna F Lee
- British Columbia Children's Hospital and British Columbia Children's Hospital Research Institute
| | - Yussanne Ma
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Richard Moore
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - David Haussler
- University of California Santa Cruz Genomics Institute, Mailstop CBSE, 1156 High St, Santa Cruz, CA 95064
| | - Joshua M Stuart
- University of California Santa Cruz Genomics Institute, Mailstop CBSE, 1156 High St, Santa Cruz, CA 95064
| | - Colleen Jantzen
- British Columbia Children's Hospital and British Columbia Children's Hospital Research Institute
| | | | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Olena Morozova
- University of California Santa Cruz Genomics Institute, Mailstop CBSE, 1156 High St, Santa Cruz, CA 95064
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Chahal M, Pleasance E, Grewal J, Zhao E, Ng T, Chapman E, Jones MR, Shen Y, Mungall KL, Bonakdar M, Taylor GA, Ma Y, Mungall AJ, Moore RA, Lim H, Renouf D, Yip S, Jones SJM, Marra MA, Laskin J. Personalized oncogenomic analysis of metastatic adenoid cystic carcinoma: using whole-genome sequencing to inform clinical decision-making. Cold Spring Harb Mol Case Stud 2018; 4:mcs.a002626. [PMID: 29610392 PMCID: PMC5880267 DOI: 10.1101/mcs.a002626] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 02/13/2018] [Indexed: 12/19/2022] Open
Abstract
Metastatic adenoid cystic carcinomas (ACCs) can cause significant morbidity and mortality. Because of their slow growth and relative rarity, there is limited evidence for systemic therapy regimens. Recently, molecular profiling studies have begun to reveal the genetic landscape of these poorly understood cancers, and new treatment possibilities are beginning to emerge. The objective is to use whole-genome and transcriptome sequencing and analysis to better understand the genetic alterations underlying the pathology of metastatic and rare ACCs and determine potentially actionable therapeutic targets. We report five cases of metastatic ACC, not originating in the salivary glands, in patients enrolled in the Personalized Oncogenomics (POG) Program at the BC Cancer Agency. Genomic workup included whole-genome and transcriptome sequencing, detailed analysis of tumor alterations, and integration with existing knowledge of drug–target combinations to identify potential therapeutic targets. Analysis reveals low mutational burden in these five ACC cases, and mutation signatures that are commonly observed in multiple cancer types. Notably, the only recurrent structural aberration identified was the well-described MYB-NFIB fusion that was present in four of five cases, and one case exhibited a closely related MYBL1-NFIB fusion. Recurrent mutations were also identified in BAP1 and BCOR, with additional mutations in individual samples affecting NOTCH1 and the epigenetic regulators ARID2, SMARCA2, and SMARCB1. Copy changes were rare, and they included amplification of MYC and homozygous loss of CDKN2A in individual samples. Genomic analysis revealed therapeutic targets in all five cases and served to inform a therapeutic choice in three of the cases to date.
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Affiliation(s)
- Manik Chahal
- Department of Medicine, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Erin Pleasance
- British Columbia Cancer Agency, Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 4E6, Canada
| | - Jasleen Grewal
- British Columbia Cancer Agency, Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 4E6, Canada
| | - Eric Zhao
- British Columbia Cancer Agency, Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 4E6, Canada
| | - Tony Ng
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Erin Chapman
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Martin R Jones
- British Columbia Cancer Agency, Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 4E6, Canada
| | - Yaoqing Shen
- British Columbia Cancer Agency, Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 4E6, Canada
| | - Karen L Mungall
- British Columbia Cancer Agency, Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 4E6, Canada
| | - Melika Bonakdar
- British Columbia Cancer Agency, Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 4E6, Canada
| | - Gregory A Taylor
- British Columbia Cancer Agency, Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 4E6, Canada
| | - Yussanne Ma
- British Columbia Cancer Agency, Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 4E6, Canada
| | - Andrew J Mungall
- British Columbia Cancer Agency, Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 4E6, Canada
| | - Richard A Moore
- British Columbia Cancer Agency, Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 4E6, Canada
| | - Howard Lim
- British Columbia Cancer Agency, Division of Medical Oncology, Vancouver, British Columbia V5Z 4E6, Canada
| | - Daniel Renouf
- British Columbia Cancer Agency, Division of Medical Oncology, Vancouver, British Columbia V5Z 4E6, Canada
| | - Stephen Yip
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Steven J M Jones
- British Columbia Cancer Agency, Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 4E6, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Marco A Marra
- British Columbia Cancer Agency, Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia V5Z 4E6, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Janessa Laskin
- British Columbia Cancer Agency, Division of Medical Oncology, Vancouver, British Columbia V5Z 4E6, Canada
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34
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Thibodeau ML, Bonakdar M, Zhao E, Mungall KL, Reisle C, Zhang W, Bye MH, Thiessen N, Bleile D, Mungall AJ, Ma YP, Jones MR, Renouf DJ, Lim HJ, Yip S, Ng T, Ho C, Laskin J, Marra MA, Schrader KA, Jones SJM. Whole genome and whole transcriptome genomic profiling of a metastatic eccrine porocarcinoma. NPJ Precis Oncol 2018; 2:8. [PMID: 29872726 PMCID: PMC5871832 DOI: 10.1038/s41698-018-0050-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 01/26/2018] [Accepted: 02/01/2018] [Indexed: 12/31/2022] Open
Abstract
Eccrine porocarcinomas (EPs) are rare malignant tumours of the intraepidermic sweat gland duct and most often arise from benign eccrine poromas. Some recurrent somatic genomic events have been identified in these malignancies, but very little is known about the complexity of their molecular pathophysiology. We describe the whole genome and whole transcriptome genomic profiling of a metastatic EP in a 66-year-old male patient with a previous history of localized porocarcinoma of the scalp. Whole genome and whole transcriptome genomic profiling was performed on the metastatic EP. Whole genome sequencing was performed on blood-derived DNA in order to allow a comparison between germline and somatic events. We found somatic copy losses of several tumour suppressor genes including APC, PTEN and CDKN2A, CDKN2B and CDKN1A. We identified a somatic hemizygous CDKN2A pathogenic splice site variant. De novo transcriptome assembly revealed abnormal splicing of CDKN2A p14ARF and p16INK4a. Elevated expression of oncogenes EGFR and NOTCH1 was noted and no somatic mutations were found in these genes. Wnt pathway somatic alterations were also observed. In conclusion, our results suggest that the molecular pathophysiology of malignant EP features high complexity and subtle interactions of multiple key genes. Cell cycle dysregulation and CDKN2A loss of function was found to be a new potential driver in EP tumourigenesis. Moreover, the combination of somatic copy number variants and abnormal gene expression perhaps partly related to epigenetic mechanisms, all likely contribute to the development of this rare malignancy in our patient.
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Affiliation(s)
- My Linh Thibodeau
- Department of Medical Genetics, University of British Columbia, C201–4500 Oak Street, Vancouver, BC V6H 3N1 Canada
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
| | - Melika Bonakdar
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
| | - Eric Zhao
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
| | - Karen L. Mungall
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
| | - Caralyn Reisle
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
| | - Wei Zhang
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
| | - Morgan H. Bye
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
| | - Nina Thiessen
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
| | - Dustin Bleile
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
| | - Andrew J. Mungall
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
| | - Yussanne P. Ma
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
| | - Martin R. Jones
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
| | - Daniel J. Renouf
- Department of Medical Oncology, British Columbia Cancer Agency, 600 West 10th Avenue, Vancouver, BC V5Z 4E6 Canada
| | - Howard J. Lim
- Department of Medical Oncology, British Columbia Cancer Agency, 600 West 10th Avenue, Vancouver, BC V5Z 4E6 Canada
| | - Stephen Yip
- Department of Pathology & Laboratory Medicine, Vancouver General Hospital, 910 West 10th Avenue, Vancouver, BC V5Z 1M9 Canada
| | - Tony Ng
- Department of Pathology & Laboratory Medicine, Vancouver General Hospital, 910 West 10th Avenue, Vancouver, BC V5Z 1M9 Canada
| | - Cheryl Ho
- Department of Medical Oncology, British Columbia Cancer Agency, 600 West 10th Avenue, Vancouver, BC V5Z 4E6 Canada
| | - Janessa Laskin
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
- Department of Medical Oncology, British Columbia Cancer Agency, 600 West 10th Avenue, Vancouver, BC V5Z 4E6 Canada
| | - Marco A. Marra
- Department of Medical Genetics, University of British Columbia, C201–4500 Oak Street, Vancouver, BC V6H 3N1 Canada
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
| | - Kasmintan A. Schrader
- Hereditary Cancer Program, Department of Medical Genetics, British Columbia Cancer Agency, 614–750 West Broadway, Vancouver, BC V5Z 1H5 Canada
| | - Steven J. M. Jones
- Department of Medical Genetics, University of British Columbia, C201–4500 Oak Street, Vancouver, BC V6H 3N1 Canada
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
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Hung SS, Meissner B, Chavez EA, Ben-Neriah S, Ennishi D, Jones MR, Shulha HP, Chan FC, Boyle M, Kridel R, Gascoyne RD, Mungall AJ, Marra MA, Scott DW, Connors JM, Steidl C. Assessment of Capture and Amplicon-Based Approaches for the Development of a Targeted Next-Generation Sequencing Pipeline to Personalize Lymphoma Management. J Mol Diagn 2018; 20:203-214. [PMID: 29429887 DOI: 10.1016/j.jmoldx.2017.11.010] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 10/24/2017] [Accepted: 11/03/2017] [Indexed: 01/30/2023] Open
Abstract
Targeted next-generation sequencing panels are increasingly used to assess the value of gene mutations for clinical diagnostic purposes. For assay development, amplicon-based methods have been preferentially used on the basis of short preparation time and small DNA input amounts. However, capture sequencing has emerged as an alternative approach because of high testing accuracy. We compared capture hybridization and amplicon sequencing approaches using fresh-frozen and formalin-fixed, paraffin-embedded tumor samples from eight lymphoma patients. Next, we developed a targeted sequencing pipeline using a 32-gene panel for accurate detection of actionable mutations in formalin-fixed, paraffin-embedded tumor samples of the most common lymphocytic malignancies: chronic lymphocytic leukemia, diffuse large B-cell lymphoma, and follicular lymphoma. We show that hybrid capture is superior to amplicon sequencing by providing deep more uniform coverage and yielding higher sensitivity for variant calling. Sanger sequencing of 588 variants identified specificity limits of thresholds for mutation calling, and orthogonal validation on 66 cases indicated 93% concordance with whole-genome sequencing. The developed pipeline and assay identified at least one actionable mutation in 91% of tumors from 219 lymphoma patients and revealed subtype-specific mutation patterns and frequencies consistent with the literature. This pipeline is an accurate and sensitive method for identifying actionable gene mutations in routinely acquired biopsy materials, suggesting further assessment of capture-based assays in the context of personalized lymphoma management.
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Affiliation(s)
- Stacy S Hung
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Barbara Meissner
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Elizabeth A Chavez
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Susana Ben-Neriah
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Daisuke Ennishi
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Martin R Jones
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Hennady P Shulha
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Fong Chun Chan
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Merrill Boyle
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Robert Kridel
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Randy D Gascoyne
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, British Columbia, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Andrew J Mungall
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Marco A Marra
- Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - David W Scott
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Joseph M Connors
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Christian Steidl
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, British Columbia, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.
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Shen Y, Jones MR, Pleasance E, Bonakdar M, Ch'ng C, Reisle C, Williamson L, Majounie E, Taylor G, Chan S, Pierce B, Zhang W, Muhammadzadeh A, Zhao EY, Bleile D, Mungall K, Thiessen N, Chuah E, Wong T, Corbett R, Ma Y, Moore RA, Mungall AJ, Zhao Y, Yip S, Lee AF, Rassekh R, Deyell R, Lim H, Renouf D, Roscoe R, Jones SJ, Laskin J, Marra MA. Abstract A184: Clinical application of whole genome and transcriptome sequencing in cancer care. Mol Cancer Ther 2018. [DOI: 10.1158/1535-7163.targ-17-a184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Aim: To investigate feasibility and utility of whole genome and RNA sequencing in cancer care. The use of comprehensive personal genomic information to guide cancer treatment decisions has gained momentum in recent years. Here we present the Personalized Oncogenomics (POG) project launched at British Columbia Cancer Agency in 2012. This project uses paired tumor/normal whole genome and transcriptome sequencing to characterize a patient's tumor and inform treatment options within a clinically relevant time frame. In the past 5 years, around 600 patients with metastatic cancers (including 49 pediatric cases) have been sequenced and analyzed, representing over 50 cancer types. The breadth and depth of data in POG enable the detection of multiple types of alterations, from simple mutations, indels, and copy number changes, to more complex alterations such as gene fusion, mutation signatures, and homologous recombination deficiency score. Incorporation of gene expression data through transcriptome sequencing informs on the impact of observed genomic alterations, and provides information regarding specific diagnosis via expression comparison to other cancer subtypes. All genomic and transcriptomic variants are integrated to build a personalized tumor-specific molecular profile, identify actionable items supported by an in-house knowledgebase and publically available molecular oncology, and characterize each individual tumor by intensive pathway analysis and literature search. Such multidimensional data also impose challenges in interpretation and communication. We developed a pipeline to translate complex genomic data into clinically actionable and hypothetical recommendations for the treatment of individual patients. The pipeline produces two reports: a panel-like report that contains known SNVs and fusions with therapeutic relevance from a collection of more than 4000 events, and a second comprehensive and manually curated report to fully characterize the tumor using the whole genome and transcriptome datasets. Genomic data are presented and discussed at a multidisciplinary molecular tumor board consisting of medical oncologists, pathologists, bioinformaticians, geneticists, and biologists. This approach has enabled clinicians to make informed clinical decisions based on the genomic data integrated with other clinical features, as well as to form new treatment-related hypothesis. POG has shown that use of both whole genome and transcriptome sequencing allows identification of therapeutic targets in a significant proportion of patients. Almost 80% cases were found to have one or more actionable alterations (100% in pediatric cases), and almost one-third of these are defined only using RNA data. Based on molecular tumor board discussion, patients are directed to clinical trials, positioned to genomically informed standard-of-care options, or treated with off-label drugs. With demonstrated effectiveness, the integrative approach developed by POG not only provides molecular insight and treatment options into individual tumors, but also provides a rich resource of molecular data with matched clinical information that will aid our understanding of tumor biology and therapy response mechanisms to inform treatment strategies in the future.
Citation Format: Yaoqing Shen, Martin R. Jones, Erin Pleasance, Melika Bonakdar, Carolyn Ch'ng, Caralyn Reisle, Laura Williamson, Elisa Majounie, Greg Taylor, Simon Chan, Brandon Pierce, Wei Zhang, Amir Muhammadzadeh, Eric Y. Zhao, Dustin Bleile, Karen Mungall, Nina Thiessen, Eric Chuah, Tina Wong, Richard Corbett, Yussanne Ma, Richard A. Moore, Andrew J. Mungall, Yongjun Zhao, Stephen Yip, Anna F. Lee, Rod Rassekh, Rebecca Deyell, Howard Lim, Daniel Renouf, Robyn Roscoe, Steven J.M Jones, Janessa Laskin, Marco A. Marra. Clinical application of whole genome and transcriptome sequencing in cancer care [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2017 Oct 26-30; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Ther 2018;17(1 Suppl):Abstract nr A184.
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Affiliation(s)
- Yaoqing Shen
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Martin R. Jones
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Erin Pleasance
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Melika Bonakdar
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Carolyn Ch'ng
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Caralyn Reisle
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Laura Williamson
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Elisa Majounie
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Greg Taylor
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Simon Chan
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Brandon Pierce
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Wei Zhang
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Amir Muhammadzadeh
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Eric Y. Zhao
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Dustin Bleile
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Karen Mungall
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Nina Thiessen
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Eric Chuah
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Tina Wong
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Richard Corbett
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Yussanne Ma
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Richard A. Moore
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Andrew J. Mungall
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Yongjun Zhao
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Stephen Yip
- 2Department of Pathology & Laboratory Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Anna F. Lee
- 2Department of Pathology & Laboratory Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Rod Rassekh
- 3Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Rebecca Deyell
- 3Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Howard Lim
- 4Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Daniel Renouf
- 4Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Robyn Roscoe
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Steven J.M Jones
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Janessa Laskin
- 4Department of Medical Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Marco A. Marra
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
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Stucki S, Orozco-terWengel P, Forester BR, Duruz S, Colli L, Masembe C, Negrini R, Landguth E, Jones MR, Bruford MW, Taberlet P, Joost S. High performance computation of landscape genomic models including local indicators of spatial association. Mol Ecol Resour 2017. [PMID: 27801969 DOI: 10.1111/1755-0998.1262] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
With the increasing availability of both molecular and topo-climatic data, the main challenges facing landscape genomics - that is the combination of landscape ecology with population genomics - include processing large numbers of models and distinguishing between selection and demographic processes (e.g. population structure). Several methods address the latter, either by estimating a null model of population history or by simultaneously inferring environmental and demographic effects. Here we present samβada, an approach designed to study signatures of local adaptation, with special emphasis on high performance computing of large-scale genetic and environmental data sets. samβada identifies candidate loci using genotype-environment associations while also incorporating multivariate analyses to assess the effect of many environmental predictor variables. This enables the inclusion of explanatory variables representing population structure into the models to lower the occurrences of spurious genotype-environment associations. In addition, samβada calculates local indicators of spatial association for candidate loci to provide information on whether similar genotypes tend to cluster in space, which constitutes a useful indication of the possible kinship between individuals. To test the usefulness of this approach, we carried out a simulation study and analysed a data set from Ugandan cattle to detect signatures of local adaptation with samβada, bayenv, lfmm and an FST outlier method (FDIST approach in arlequin) and compare their results. samβada - an open source software for Windows, Linux and Mac OS X available at http://lasig.epfl.ch/sambada - outperforms other approaches and better suits whole-genome sequence data processing.
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Affiliation(s)
- S Stucki
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - P Orozco-terWengel
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Cardiff, CF10 3AX, UK
| | - B R Forester
- Nicholas School of the Environment, University Program in Ecology, Duke University, Durham, NC, 27708, USA
| | - S Duruz
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - L Colli
- BioDNA - Centro di Ricerca sulla Biodiversità e sul DNA Antico, Istituto di Zootecnica, Università Cattolica del S. Cuore, via E. Parmense 84, 29100, Piacenza, Italy
| | - C Masembe
- Department of Zoology, Entomology and Fisheries Sciences, College of Natural Sciences, Makerere University, Box 7062, Kampala, Uganda
| | - R Negrini
- BioDNA - Centro di Ricerca sulla Biodiversità e sul DNA Antico, Istituto di Zootecnica, Università Cattolica del S. Cuore, via E. Parmense 84, 29100, Piacenza, Italy
- Associazione Italiana Allevatori, 00161, Roma, Italy
| | - E Landguth
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA
| | - M R Jones
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA
| | - M W Bruford
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Cardiff, CF10 3AX, UK
| | - P Taberlet
- Laboratoire d'Ecologie Alpine (LECA), CNRS, Grenoble, 38000, France
- Laboratoire d'Ecologie Alpine (LECA), Univ. Grenoble Alpes, Grenoble, 38000, France
| | - S Joost
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
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Zhao EY, Shen Y, Pleasance E, Kasaian K, Jones MR, Ch'ng C, Reisle C, Eirew P, Mungall K, Thiessen N, Ma Y, Fok A, Mungall AJ, Zhao Y, Moore R, Villa D, Shenkier T, Lohrisch C, Chia S, Yip S, Gelmon K, Lim H, Sun S, Schrader KA, Young S, Karsan A, Roscoe R, Laskin J, Marra MA, Jones SJ. Abstract 2473: Breast cancer whole genomes link homologous recombination deficiency (HRD) with therapeutic outcomes. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-2473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Homologous recombination deficiency (HRD) is common in cancer - germline BRCA1 & BRCA2 mutations account for 5-10% of breast cancers and confer 85% lifetime risk. HRD cancers exhibit genomic instability and sensitivity to platinum-based therapy and PARP inhibitors. While not all causes of HRD are known, recent sequencing efforts have revealed genome-wide somatic mutation signatures that characterize the HRD genomic instability phenotype, also known as “BRCA-ness”. This provides a promising new assay to predict sensitivity to platinum-based therapy. Here, we integrate two whole-genome sequencing metrics to assess their association with therapeutic outcomes in a breast cancer cohort.
Methods: Whole-genome sequencing of 47 breast cancer tumors (100x coverage) and matched normals (60x) was performed on an Illumina HiSeq. Alignment, assembly, SNV calling, and loss of heterozygosity (LOH) detection were performed with BWA, ABySS, Strelka, and APOLLOH respectively. SNV signatures were deciphered by non-negative matrix factorization with Monte Carlo resampling. An HRD score comprised of LOH, telomeric allelic imbalance (TAI), and large scale transition (LST) counts was computed. Clinical endpoints were obtained by retrospective review of treatment and imaging reports. Analysis is ongoing in an independent validation cohort of 62 sequenced cases.
Results: The HRD-linked SNV signature was significantly associated with radiographic clinical response (CR) to platinum-based therapy (p=0.015). Logistic regression demonstrated a 59% improved odds of CR to platinum-based therapy per 1000 somatic SNVs attributed to HRD (odds ratio 1.16-2.50). Tumors carried up to 10,246 such SNVs and all patients with CR were among the top quartile. The LOH-TAI-LST score was correlated with SNV signature (r=0.6, p=7×10-6) and associated with CR (p=0.025). Notably, elevated HRD signatures associated with CR were identified in tumors with wild-type BRCA1/BRCA2 or variants of unknown significance. Tumors with above median HRD signatures were associated with a 69-day longer time to treatment failure and an 18% daily decreased probability of treatment failure per 1000 HRD-attributed SNVs (hazard ratio 0.71-0.95, p = 0.007).
Discussion: We found that HRD mutation signatures are associated with clinical response and longer time to treatment failure with platinum-based therapy. While similar benefits were observed in patients with somatic bi-allelic loss of BRCA1/BRCA2, such cases are less common (8% of our cohort) compared to those with elevated HRD signature. Thus, mutation signature methods may identify patients who stand to benefit from platinum-based therapy missed by BRCA screening alone.
Citation Format: Eric Y. Zhao, Yaoqing Shen, Erin Pleasance, Katayoon Kasaian, Martin R. Jones, Carolyn Ch'ng, Caralyn Reisle, Peter Eirew, Karen Mungall, Nina Thiessen, Yussanne Ma, Alexandra Fok, Andrew J. Mungall, Yongjun Zhao, Richard Moore, Diego Villa, Tamara Shenkier, Caroline Lohrisch, Stephen Chia, Stephen Yip, Karen Gelmon, Howard Lim, Sophie Sun, Kasmintan A. Schrader, Sean Young, Aly Karsan, Robyn Roscoe, Janessa Laskin, Marco A. Marra, Steven J. Jones. Breast cancer whole genomes link homologous recombination deficiency (HRD) with therapeutic outcomes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2473. doi:10.1158/1538-7445.AM2017-2473
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Affiliation(s)
- Eric Y. Zhao
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Yaoqing Shen
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Erin Pleasance
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Katayoon Kasaian
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Martin R. Jones
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Carolyn Ch'ng
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Caralyn Reisle
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Peter Eirew
- 2British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Karen Mungall
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Nina Thiessen
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Yussanne Ma
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Alexandra Fok
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Andrew J. Mungall
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Yongjun Zhao
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Richard Moore
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Diego Villa
- 2British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Tamara Shenkier
- 2British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Caroline Lohrisch
- 2British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Stephen Chia
- 2British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Stephen Yip
- 3The University of British Columbia, Vancouver, British Columbia, Canada
| | - Karen Gelmon
- 2British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Howard Lim
- 2British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Sophie Sun
- 2British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | | | - Sean Young
- 3The University of British Columbia, Vancouver, British Columbia, Canada
| | - Aly Karsan
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Robyn Roscoe
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Janessa Laskin
- 2British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Marco A. Marra
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Steven J. Jones
- 1Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
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Lawson TN, Weber RJM, Jones MR, Chetwynd AJ, Rodrı́guez-Blanco G, Di Guida R, Viant MR, Dunn WB. msPurity: Automated Evaluation of Precursor Ion Purity for Mass Spectrometry-Based Fragmentation in Metabolomics. Anal Chem 2017; 89:2432-2439. [DOI: 10.1021/acs.analchem.6b04358] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Thomas N. Lawson
- School
of Biosciences and ‡Phenome Centre Birmingham, College of Life and Environmental
Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Ralf J. M. Weber
- School
of Biosciences and ‡Phenome Centre Birmingham, College of Life and Environmental
Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Martin R. Jones
- School
of Biosciences and ‡Phenome Centre Birmingham, College of Life and Environmental
Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Andrew J. Chetwynd
- School
of Biosciences and ‡Phenome Centre Birmingham, College of Life and Environmental
Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Giovanny Rodrı́guez-Blanco
- School
of Biosciences and ‡Phenome Centre Birmingham, College of Life and Environmental
Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Riccardo Di Guida
- School
of Biosciences and ‡Phenome Centre Birmingham, College of Life and Environmental
Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Mark R. Viant
- School
of Biosciences and ‡Phenome Centre Birmingham, College of Life and Environmental
Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Warwick B. Dunn
- School
of Biosciences and ‡Phenome Centre Birmingham, College of Life and Environmental
Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
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40
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Viant MR, Kurland IJ, Jones MR, Dunn WB. How close are we to complete annotation of metabolomes? Curr Opin Chem Biol 2017; 36:64-69. [PMID: 28113135 PMCID: PMC5337156 DOI: 10.1016/j.cbpa.2017.01.001] [Citation(s) in RCA: 165] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 12/28/2016] [Accepted: 01/02/2017] [Indexed: 01/04/2023]
Abstract
The metabolome describes the full complement of the tens to hundreds of thousands of low molecular weight metabolites present within a biological system. Identification of the metabolome is critical for discovering the maximum amount of biochemical knowledge from metabolomics datasets. Yet no exhaustive experimental characterisation of any organismal metabolome has been reported to date, dramatically contrasting with the genome sequencing of thousands of plants, animals and microbes. Here, we review the status of metabolome annotation and describe advances in the analytical methodologies being applied. In part through new international coordination, we conclude that we are now entering a new era of metabolome annotation.
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Affiliation(s)
- Mark R Viant
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK; Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
| | - Irwin J Kurland
- Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Martin R Jones
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Warwick B Dunn
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK; Phenome Centre Birmingham, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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41
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Stucki S, Orozco-terWengel P, Forester BR, Duruz S, Colli L, Masembe C, Negrini R, Landguth E, Jones MR, Bruford MW, Taberlet P, Joost S. High performance computation of landscape genomic models including local indicators of spatial association. Mol Ecol Resour 2016; 17:1072-1089. [PMID: 27801969 DOI: 10.1111/1755-0998.12629] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 08/05/2016] [Accepted: 09/19/2016] [Indexed: 12/11/2022]
Abstract
With the increasing availability of both molecular and topo-climatic data, the main challenges facing landscape genomics - that is the combination of landscape ecology with population genomics - include processing large numbers of models and distinguishing between selection and demographic processes (e.g. population structure). Several methods address the latter, either by estimating a null model of population history or by simultaneously inferring environmental and demographic effects. Here we present samβada, an approach designed to study signatures of local adaptation, with special emphasis on high performance computing of large-scale genetic and environmental data sets. samβada identifies candidate loci using genotype-environment associations while also incorporating multivariate analyses to assess the effect of many environmental predictor variables. This enables the inclusion of explanatory variables representing population structure into the models to lower the occurrences of spurious genotype-environment associations. In addition, samβada calculates local indicators of spatial association for candidate loci to provide information on whether similar genotypes tend to cluster in space, which constitutes a useful indication of the possible kinship between individuals. To test the usefulness of this approach, we carried out a simulation study and analysed a data set from Ugandan cattle to detect signatures of local adaptation with samβada, bayenv, lfmm and an FST outlier method (FDIST approach in arlequin) and compare their results. samβada - an open source software for Windows, Linux and Mac OS X available at http://lasig.epfl.ch/sambada - outperforms other approaches and better suits whole-genome sequence data processing.
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Affiliation(s)
- S Stucki
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - P Orozco-terWengel
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Cardiff, CF10 3AX, UK
| | - B R Forester
- Nicholas School of the Environment, University Program in Ecology, Duke University, Durham, NC, 27708, USA
| | - S Duruz
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - L Colli
- BioDNA - Centro di Ricerca sulla Biodiversità e sul DNA Antico, Istituto di Zootecnica, Università Cattolica del S. Cuore, via E. Parmense 84, 29100, Piacenza, Italy
| | - C Masembe
- Department of Zoology, Entomology and Fisheries Sciences, College of Natural Sciences, Makerere University, Box 7062, Kampala, Uganda
| | - R Negrini
- BioDNA - Centro di Ricerca sulla Biodiversità e sul DNA Antico, Istituto di Zootecnica, Università Cattolica del S. Cuore, via E. Parmense 84, 29100, Piacenza, Italy.,Associazione Italiana Allevatori, 00161, Roma, Italy
| | - E Landguth
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA
| | - M R Jones
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA
| | | | - M W Bruford
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Cardiff, CF10 3AX, UK
| | - P Taberlet
- Laboratoire d'Ecologie Alpine (LECA), CNRS, Grenoble, 38000, France.,Laboratoire d'Ecologie Alpine (LECA), Univ. Grenoble Alpes, Grenoble, 38000, France
| | - S Joost
- Laboratory of Geographic Information Systems (LASIG), School of Architecture, Civil and Environmental Engineering (ENAC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
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Villalón E, Jones MR, Sibigtroth C, Zino SJ, Dale JM, Landayan DS, Shen H, Cornelison DDW, Garcia ML. Muscle spindle alterations precede onset of sensorimotor deficits in Charcot-Marie-Tooth type 2E. Genes Brain Behav 2016; 16:260-270. [PMID: 27643807 DOI: 10.1111/gbb.12341] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 09/11/2016] [Accepted: 09/14/2016] [Indexed: 02/01/2023]
Abstract
Charcot-Marie-Tooth (CMT) is the most common inherited peripheral neuropathy, affecting approximately 2.8 million people. The CMT leads to distal neuropathy that is characterized by reduced motor nerve conduction velocity, ataxia, muscle atrophy and sensory loss. We generated a mouse model of CMT type 2E (CMT2E) expressing human neurofilament light E396K (hNF-LE396K ), which develops decreased motor nerve conduction velocity, ataxia and muscle atrophy by 4 months of age. Symptomatic hNF-LE396K mice developed phenotypes that were consistent with proprioceptive sensory defects as well as reduced sensitivity to mechanical stimulation, while thermal sensitivity and auditory brainstem responses were unaltered. Progression from presymptomatic to symptomatic included a 50% loss of large diameter sensory axons within the fifth lumbar dorsal root of hNF-LE396K mice. Owing to proprioceptive deficits and loss of large diameter sensory axons, we analyzed muscle spindle morphology in presymptomatic and symptomatic hNF-LE396K and hNF-L control mice. Muscle spindle cross-sectional area and volume were reduced in all hNF-LE396K mice analyzed, suggesting that alterations in muscle spindle morphology occurred prior to the onset of typical CMT pathology. These data suggested that CMT2E pathology initiated in the muscle spindles altering the proprioceptive sensory system. Early sensory pathology in CMT2E could provide a unifying hypothesis for the convergence of pathology observed in CMT.
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Affiliation(s)
- E Villalón
- Division of Biological Sciences, Columbia, MO, USA.,C. S. Bond Life Sciences Center, Columbia, MO, USA
| | - M R Jones
- Division of Biological Sciences, Columbia, MO, USA.,C. S. Bond Life Sciences Center, Columbia, MO, USA
| | - C Sibigtroth
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri-Columbia, Columbia, MO, USA
| | - S J Zino
- Division of Biological Sciences, Columbia, MO, USA.,C. S. Bond Life Sciences Center, Columbia, MO, USA
| | - J M Dale
- Division of Biological Sciences, Columbia, MO, USA.,C. S. Bond Life Sciences Center, Columbia, MO, USA
| | - D S Landayan
- Quantitative and Systems Biology, University of California Merced, Merced, CA, USA
| | - H Shen
- Institute of Neuroscience, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - D D W Cornelison
- Division of Biological Sciences, Columbia, MO, USA.,C. S. Bond Life Sciences Center, Columbia, MO, USA
| | - M L Garcia
- Division of Biological Sciences, Columbia, MO, USA.,C. S. Bond Life Sciences Center, Columbia, MO, USA
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43
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Dubas K, Baranowski M, Podhorodecki A, Jones MR, Gibasiewicz K. Unified Model of Nanosecond Charge Recombination in Closed Reaction Centers from Rhodobacter sphaeroides: Role of Protein Polarization Dynamics. J Phys Chem B 2016; 120:4890-6. [PMID: 27171418 DOI: 10.1021/acs.jpcb.6b01459] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ongoing questions surround the influence of protein dynamics on rapid processes such as biological electron transfer. Such questions are particularly addressable in light-activated systems. In Rhodobacter sphaeroides reaction centers, charge recombination or back electron transfer from the reduced bacteriopheophytin, HA(-), to the oxidized dimeric bacteriochlorophyll, P(+), may be monitored by both transient absorption spectroscopy and transient fluorescence spectroscopy. Signals measured with both these techniques decay in a similar three-exponential fashion with lifetimes of ∼0.6-0.7, ∼2-4, and ∼10-20 ns, revealing the complex character of this electron transfer reaction. In this study a single kinetic model was developed to connect lifetime and amplitude data from both techniques. The model took into account the possibility that electron transfer from HA(-) to P(+) may occur with transient formation of the state P(+)BA(-). As a result it was possible to model the impact of nanosecond protein relaxation on the free energy levels of both P(+)HA(-) and P(+)BA(-) states relative to that of the singlet excited state of P, P*. Surprisingly, whereas the free energy gap between P* and P(+)HA(-) increased with time in response to protein reorganization, the free energy gap between P* and P(+)BA(-) decreased. This finding may be accounted for by a gradual polarization of the protein environment which stabilizes the state P(+)HA(-) and destabilizes the state P(+)BA(-), favoring productive charge separation over unproductive charge recombination.
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Affiliation(s)
- K Dubas
- Department of Physics, Adam Mickiewicz University , ul. Umultowska 85, 61-614 Poznań, Poland
| | - M Baranowski
- Department of Experimental Physics, Wroclaw University of Technology , Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - A Podhorodecki
- Department of Experimental Physics, Wroclaw University of Technology , Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - M R Jones
- School of Biochemistry, Medical Sciences Building, University of Bristol , University Walk, Bristol, BS8 1TD, U.K
| | - K Gibasiewicz
- Department of Physics, Adam Mickiewicz University , ul. Umultowska 85, 61-614 Poznań, Poland
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Jones MR, Schrader KA, Shen Y, Pleasance E, Ch'ng C, Dar N, Yip S, Renouf DJ, Schein JE, Mungall AJ, Zhao Y, Moore R, Ma Y, Sheffield BS, Ng T, Jones SJM, Marra MA, Laskin J, Lim HJ. Response to angiotensin blockade with irbesartan in a patient with metastatic colorectal cancer. Ann Oncol 2016; 27:801-6. [PMID: 27022066 PMCID: PMC4843189 DOI: 10.1093/annonc/mdw060] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 02/08/2016] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND A patient suffering from metastatic colorectal cancer, treatment-related toxicity and resistance to standard chemotherapy and radiation was assessed as part of a personalized oncogenomics initiative to derive potential alternative therapeutic strategies. PATIENTS AND METHODS Whole-genome and transcriptome sequencing was used to interrogate a metastatic tumor refractory to standard treatments of a patient with mismatch repair-deficient metastatic colorectal cancer. RESULTS Integrative genomic analysis indicated overexpression of the AP-1 transcriptional complex suggesting experimental therapeutic rationales, including blockade of the renin-angiotensin system. This led to the repurposing of the angiotensin II receptor antagonist, irbesartan, as an anticancer therapy, resulting in the patient experiencing a dramatic and durable response. CONCLUSIONS This case highlights the utility of comprehensive integrative genomic profiling and bioinformatics analysis to provide hypothetical rationales for personalized treatment options.
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Affiliation(s)
- M R Jones
- British Columbia Cancer Agency, Canada's Michael Smith Genome Sciences Centre, Vancouver
| | - K A Schrader
- Department of Medical Genetics, University of British Columbia, Vancouver
| | - Y Shen
- British Columbia Cancer Agency, Canada's Michael Smith Genome Sciences Centre, Vancouver
| | - E Pleasance
- British Columbia Cancer Agency, Canada's Michael Smith Genome Sciences Centre, Vancouver
| | - C Ch'ng
- British Columbia Cancer Agency, Canada's Michael Smith Genome Sciences Centre, Vancouver
| | - N Dar
- British Columbia Cancer Agency, Canada's Michael Smith Genome Sciences Centre, Vancouver
| | - S Yip
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver
| | - D J Renouf
- Division of Medical Oncology, British Columbia Cancer Agency, Vancouver
| | - J E Schein
- British Columbia Cancer Agency, Canada's Michael Smith Genome Sciences Centre, Vancouver
| | - A J Mungall
- British Columbia Cancer Agency, Canada's Michael Smith Genome Sciences Centre, Vancouver
| | - Y Zhao
- British Columbia Cancer Agency, Canada's Michael Smith Genome Sciences Centre, Vancouver
| | - R Moore
- British Columbia Cancer Agency, Canada's Michael Smith Genome Sciences Centre, Vancouver
| | - Y Ma
- British Columbia Cancer Agency, Canada's Michael Smith Genome Sciences Centre, Vancouver
| | - B S Sheffield
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver
| | - T Ng
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver
| | - S J M Jones
- British Columbia Cancer Agency, Canada's Michael Smith Genome Sciences Centre, Vancouver Department of Medical Genetics, University of British Columbia, Vancouver Department of Molecular Biology and Biochemistry, Simon Fraser University, Vancouver, Canada
| | - M A Marra
- British Columbia Cancer Agency, Canada's Michael Smith Genome Sciences Centre, Vancouver Department of Medical Genetics, University of British Columbia, Vancouver
| | - J Laskin
- Division of Medical Oncology, British Columbia Cancer Agency, Vancouver
| | - H J Lim
- Division of Medical Oncology, British Columbia Cancer Agency, Vancouver
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Di Guida R, Engel J, Allwood JW, Weber RJM, Jones MR, Sommer U, Viant MR, Dunn WB. Non-targeted UHPLC-MS metabolomic data processing methods: a comparative investigation of normalisation, missing value imputation, transformation and scaling. Metabolomics 2016; 12:93. [PMID: 27123000 PMCID: PMC4831991 DOI: 10.1007/s11306-016-1030-9] [Citation(s) in RCA: 183] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Accepted: 04/05/2016] [Indexed: 12/25/2022]
Abstract
INTRODUCTION The generic metabolomics data processing workflow is constructed with a serial set of processes including peak picking, quality assurance, normalisation, missing value imputation, transformation and scaling. The combination of these processes should present the experimental data in an appropriate structure so to identify the biological changes in a valid and robust manner. OBJECTIVES Currently, different researchers apply different data processing methods and no assessment of the permutations applied to UHPLC-MS datasets has been published. Here we wish to define the most appropriate data processing workflow. METHODS We assess the influence of normalisation, missing value imputation, transformation and scaling methods on univariate and multivariate analysis of UHPLC-MS datasets acquired for different mammalian samples. RESULTS Our studies have shown that once data are filtered, missing values are not correlated with m/z, retention time or response. Following an exhaustive evaluation, we recommend PQN normalisation with no missing value imputation and no transformation or scaling for univariate analysis. For PCA we recommend applying PQN normalisation with Random Forest missing value imputation, glog transformation and no scaling method. For PLS-DA we recommend PQN normalisation, KNN as the missing value imputation method, generalised logarithm transformation and no scaling. These recommendations are based on searching for the biologically important metabolite features independent of their measured abundance. CONCLUSION The appropriate choice of normalisation, missing value imputation, transformation and scaling methods differs depending on the data analysis method and the choice of method is essential to maximise the biological derivations from UHPLC-MS datasets.
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Affiliation(s)
- Riccardo Di Guida
- />School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
- />MRC-ARUK Centre for Musculoskeletal Ageing Research, University of Birmingham, Birmingham, B15 2TT UK
| | - Jasper Engel
- />School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
- />NERC Biomolecular Analysis Facility—Metabolomics Node (NBAF-B), University of Birmingham, Birmingham, B15 2TT UK
| | - J. William Allwood
- />School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
| | - Ralf J. M. Weber
- />School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
| | - Martin R. Jones
- />School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
| | - Ulf Sommer
- />School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
- />NERC Biomolecular Analysis Facility—Metabolomics Node (NBAF-B), University of Birmingham, Birmingham, B15 2TT UK
| | - Mark R. Viant
- />School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
- />NERC Biomolecular Analysis Facility—Metabolomics Node (NBAF-B), University of Birmingham, Birmingham, B15 2TT UK
- />Phenome Centre Birmingham, University of Birmingham, Birmingham, B15 2TT UK
- />Institute of Metabolism and Systems Research, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
| | - Warwick B. Dunn
- />School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
- />MRC-ARUK Centre for Musculoskeletal Ageing Research, University of Birmingham, Birmingham, B15 2TT UK
- />Phenome Centre Birmingham, University of Birmingham, Birmingham, B15 2TT UK
- />Institute of Metabolism and Systems Research, University of Birmingham, Edgbaston, Birmingham, B15 2TT UK
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Jones MR, Martis L, Cantaluppi A. Approaches to correcting protein malnutrition with modified peritoneal dialysis solutions. Contrib Nephrol 2015; 98:174-82. [PMID: 1493729 DOI: 10.1159/000421615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- M R Jones
- Baxter Healthcare Corp., Round Lake, Ill
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Alriyami MZ, Jones MR, Johnsen RC, Banerjee Y, Baillie DL. let-65 is cytoplasmic methionyl tRNA synthetase in C. elegans. Meta Gene 2014; 2:819-30. [PMID: 25606464 PMCID: PMC4287814 DOI: 10.1016/j.mgene.2014.08.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 08/08/2014] [Accepted: 08/11/2014] [Indexed: 02/07/2023] Open
Abstract
Cytoplasmic methionyl tRNA synthetase (MetRS) is one of more than 20 cytoplasmic aminoacyl tRNA synthetase enzymes (ARS). This family of enzymes catalyzes a process fundamental for protein translation. Using a combination of genetic mapping, oligonucleotide array comparative genomic hybridization, and phenotypic correlation, we show that mutations in the essential gene, let-65, reside within the predicted Caenorhabditis elegans homologue of MetRS, which we have named mars-1. We demonstrate that the lethality associated with alleles of let-65 is fully rescued by a transgenic array that spans the mars-1 genomic region. Furthermore, sequence analysis reveals that six let-65 alleles lead to the alteration of highly conserved amino acids.
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Affiliation(s)
- Maha Z Alriyami
- Department of Molecular Biology and Biochemistry, Simon Fraser University Burnaby, 8888 University Drive, Burnaby, BC V5A 1S6 Canada ; Department of Biochemistry, College of Medicine and Health Sciences, Sultan Qaboos University, 35, Al-Khod 123, Oman
| | - Martin R Jones
- Genome Sciences Centre, British Columbia Cancer Research Centre, 600 West 10th Avenue, Vancouver, BC V5Z 4E6, Canada
| | - Robert C Johnsen
- Department of Molecular Biology and Biochemistry, Simon Fraser University Burnaby, 8888 University Drive, Burnaby, BC V5A 1S6 Canada
| | - Yajnavalka Banerjee
- Department of Biochemistry, College of Medicine and Health Sciences, Sultan Qaboos University, 35, Al-Khod 123, Oman
| | - David L Baillie
- Department of Molecular Biology and Biochemistry, Simon Fraser University Burnaby, 8888 University Drive, Burnaby, BC V5A 1S6 Canada
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Given CA, Attizzani GF, Jones MR, Ramsey CN, Brooks WH, Costa MA, Bezerra HG. Frequency-domain optical coherence tomography assessment of human carotid atherosclerosis using saline flush for blood clearance without balloon occlusion. AJNR Am J Neuroradiol 2013; 34:1414-8. [PMID: 23391841 DOI: 10.3174/ajnr.a3411] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
FD-OCT is a new imaging technique that allows unprecedented in vivo microlevel assessment of human carotid plaque morphologic patterns and stent-vessel interactions. Prior reports describing the use of this technique have used balloon occlusion of the target vessel or iodinated contrast media to facilitate imaging. We report, for the first time, in vivo FD-OCT imaging of human carotid arteries without the use of iodinated contrast material or balloon occlusion techniques.
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Affiliation(s)
- C A Given
- Central Baptist Hospital, Baptist Heart and Vascular Institute, Lexington, KY, USA.
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Jones MR, Rose AM, Baillie DL. The ortholog of the human proto-oncogene ROS1 is required for epithelial development in C. elegans. Genesis 2013; 51:545-61. [PMID: 23733356 PMCID: PMC4232869 DOI: 10.1002/dvg.22405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 05/16/2013] [Accepted: 05/20/2013] [Indexed: 12/19/2022]
Abstract
The orphan receptor ROS1 is a human proto-oncogene, mutations of which are found in an increasing number of cancers. Little is known about the role of ROS1, however in vertebrates it has been implicated in promoting differentiation programs in specialized epithelial tissues. In this study we show that the C. elegans ortholog of ROS1, the receptor tyrosine kinase ROL-3, has an essential role in orchestrating the morphogenesis and development of specialized epidermal tissues, highlighting a potentially conserved function in coordinating crosstalk between developing epithelial cells. We also provide evidence of a direct relationship between ROL-3, the mucin SRAP-1, and BCC-1, the homolog of mRNA regulating protein Bicaudal-C. This study answers a longstanding question as to the developmental function of ROL-3, identifies three new genes that are expressed and function in the developing epithelium of C. elegans, and introduces the nematode as a potentially powerful model system for investigating the increasingly important, yet poorly understood, human oncogene ROS1. genesis 51:545–561.
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Affiliation(s)
- Martin R Jones
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada, V6T 1Z4.
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Goodarzi MO, Guo X, Cui J, Jones MR, Haritunians T, Xiang AH, Chen YDI, Taylor KD, Buchanan TA, Hsueh WA, Raffel LJ, Rotter JI. Systematic evaluation of validated type 2 diabetes and glycaemic trait loci for association with insulin clearance. Diabetologia 2013; 56:1282-90. [PMID: 23494448 PMCID: PMC3651757 DOI: 10.1007/s00125-013-2880-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Accepted: 02/12/2013] [Indexed: 12/25/2022]
Abstract
AIMS/HYPOTHESIS Insulin clearance is a highly heritable trait, for which few quantitative trait loci have been discovered. We sought to determine whether validated type 2 diabetes and/or glycaemic trait loci are associated with insulin clearance. METHODS Hyperinsulinaemic-euglycaemic clamps were performed in two Hispanic-American family cohorts totalling 1329 participants in 329 families. The Metabochip was used to fine-map about 50 previously identified loci for type 2 diabetes, fasting glucose, fasting insulin, 2 h glucose or HbA1c. This resulted in 17,930 variants, which were tested for association with clamp-derived insulin clearance via meta-analysis of the two cohorts. RESULTS In the meta-analysis, 38 variants located within seven loci demonstrated association with insulin clearance (p < 0.001). The top signals for each locus were rs10241087 (DGKB/TMEM195 [TMEM195 also known as AGMO]) (p = 4.4 × 10(-5)); chr1:217605433 (LYPLAL1) (p = 3.25 × 10(-4)); rs2380949 (GLIS3) (p = 3.4 × 10(-4)); rs55903902 (FADS1) (p = 5.6 × 10(-4)); rs849334 (JAZF1) (p = 6.4 × 10(-4)); rs35749 (IGF1) (p = 6.7 × 10(-4)); and rs9460557 (CDKAL1) (p = 6.8 × 10(-4)). CONCLUSIONS/INTERPRETATION While the majority of validated loci for type 2 diabetes and related traits do not appear to influence insulin clearance in Hispanics, several of these loci do show evidence of association with this trait. It is therefore possible that these loci could have pleiotropic effects on insulin secretion, insulin sensitivity and insulin clearance.
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Affiliation(s)
- M O Goodarzi
- Division of Endocrinology, Diabetes and Metabolism, Cedars-Sinai Medical Center, 8700 Beverly Blvd, Room B-131, Los Angeles, CA 90048, USA.
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