1
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Jiménez-Gracia L, Marchese D, Nieto JC, Caratù G, Melón-Ardanaz E, Gudiño V, Roth S, Wise K, Ryan NK, Jensen KB, Hernando-Momblona X, Bernardes JP, Tran F, Sievers LK, Schreiber S, van den Berge M, Kole T, van der Velde PL, Nawijn MC, Rosenstiel P, Batlle E, Butler LM, Parish IA, Plummer J, Gut I, Salas A, Heyn H, Martelotto LG. FixNCut: single-cell genomics through reversible tissue fixation and dissociation. Genome Biol 2024; 25:81. [PMID: 38553769 PMCID: PMC10979608 DOI: 10.1186/s13059-024-03219-5] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 03/18/2024] [Indexed: 04/02/2024] Open
Abstract
The use of single-cell technologies for clinical applications requires disconnecting sampling from downstream processing steps. Early sample preservation can further increase robustness and reproducibility by avoiding artifacts introduced during specimen handling. We present FixNCut, a methodology for the reversible fixation of tissue followed by dissociation that overcomes current limitations. We applied FixNCut to human and mouse tissues to demonstrate the preservation of RNA integrity, sequencing library complexity, and cellular composition, while diminishing stress-related artifacts. Besides single-cell RNA sequencing, FixNCut is compatible with multiple single-cell and spatial technologies, making it a versatile tool for robust and flexible study designs.
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Affiliation(s)
- Laura Jiménez-Gracia
- Centro Nacional de Análisis Genómico (CNAG), 08028, Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Domenica Marchese
- Centro Nacional de Análisis Genómico (CNAG), 08028, Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Juan C Nieto
- Centro Nacional de Análisis Genómico (CNAG), 08028, Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Ginevra Caratù
- Centro Nacional de Análisis Genómico (CNAG), 08028, Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Elisa Melón-Ardanaz
- Inflammatory Bowel Disease Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Victoria Gudiño
- Inflammatory Bowel Disease Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Sara Roth
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia
- Monash University Department of Surgery, Alfred Hospital, Melbourne, VIC, Australia
| | - Kellie Wise
- Adelaide Centre for Epigenetics (ACE), University of Adelaide, Adelaide, South Australia, Australia
- South Australian immunoGENomics Cancer Institute (SAiGENCI), University of Adelaide, Adelaide, South Australia, Australia
- Australian Genomics Research Facility, Adelaide, South Australia, Australia
| | - Natalie K Ryan
- South Australian immunoGENomics Cancer Institute (SAiGENCI), University of Adelaide, Adelaide, South Australia, Australia
- Freemasons Foundation Centre for Men's Health, University of Adelaide, Adelaide, South Australia, Australia
- South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Kirk B Jensen
- Adelaide Centre for Epigenetics (ACE), University of Adelaide, Adelaide, South Australia, Australia
- South Australian immunoGENomics Cancer Institute (SAiGENCI), University of Adelaide, Adelaide, South Australia, Australia
- Australian Genomics Research Facility, Adelaide, South Australia, Australia
| | - Xavier Hernando-Momblona
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Joana P Bernardes
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Florian Tran
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
- Department of Internal Medicine I, University Hospital Schleswig-Holstein (UKSH), Campus Kiel, Kiel, Germany
| | - Laura Katharina Sievers
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
- Department of Internal Medicine I, University Hospital Schleswig-Holstein (UKSH), Campus Kiel, Kiel, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
- Department of Internal Medicine I, University Hospital Schleswig-Holstein (UKSH), Campus Kiel, Kiel, Germany
| | - Maarten van den Berge
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
- Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Tessa Kole
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
- Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Petra L van der Velde
- Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
- Department of Pathology & Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Martijn C Nawijn
- Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
- Department of Pathology & Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Eduard Batlle
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
- ICREA, Barcelona, Spain
| | - Lisa M Butler
- South Australian immunoGENomics Cancer Institute (SAiGENCI), University of Adelaide, Adelaide, South Australia, Australia
- Freemasons Foundation Centre for Men's Health, University of Adelaide, Adelaide, South Australia, Australia
- South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Ian A Parish
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia
| | - Jasmine Plummer
- St Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Ivo Gut
- Centro Nacional de Análisis Genómico (CNAG), 08028, Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Azucena Salas
- Inflammatory Bowel Disease Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Holger Heyn
- Centro Nacional de Análisis Genómico (CNAG), 08028, Barcelona, Spain.
- Universitat de Barcelona (UB), Barcelona, Spain.
- Omniscope, Barcelona, Spain.
| | - Luciano G Martelotto
- Adelaide Centre for Epigenetics (ACE), University of Adelaide, Adelaide, South Australia, Australia.
- South Australian immunoGENomics Cancer Institute (SAiGENCI), University of Adelaide, Adelaide, South Australia, Australia.
- Omniscope, Barcelona, Spain.
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2
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Vandenbempt V, Eski SE, Brahma MK, Li A, Negueruela J, Bruggeman Y, Demine S, Xiao P, Cardozo AK, Baeyens N, Martelotto LG, Singh SP, Mariño E, Gysemans C, Gurzov EN. HAMSAB diet ameliorates dysfunctional signaling in pancreatic islets in autoimmune diabetes. iScience 2024; 27:108694. [PMID: 38213620 PMCID: PMC10783594 DOI: 10.1016/j.isci.2023.108694] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 10/23/2023] [Accepted: 12/05/2023] [Indexed: 01/13/2024] Open
Abstract
An altered gut microbiota is associated with type 1 diabetes (T1D), affecting the production of short-chain fatty acids (SCFA) and glucose homeostasis. We previously demonstrated that enhancing serum acetate and butyrate using a dietary supplement (HAMSAB) improved glycemia in non-obese diabetic (NOD) mice and patients with established T1D. The effects of SCFA on immune-infiltrated islet cells remain to be clarified. Here, we performed single-cell RNA sequencing on islet cells from NOD mice fed an HAMSAB or control diet. HAMSAB induced a regulatory gene expression profile in pancreas-infiltrated immune cells. Moreover, HAMSAB maintained the expression of β-cell functional genes and decreased cellular stress. HAMSAB-fed mice showed preserved pancreatic endocrine cell identity, evaluated by decreased numbers of poly-hormonal cells. Finally, SCFA increased insulin levels in human β-like cells and improved transplantation outcome in NOD/SCID mice. Our findings support the use of metabolite-based diet as attractive approach to improve glucose control in T1D.
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Affiliation(s)
- Valerie Vandenbempt
- Signal Transduction and Metabolism Laboratory, Université libre de Bruxelles, 1070 Brussels, Belgium
| | - Sema Elif Eski
- IRIBHM, Université libre de Bruxelles, 1070 Brussels, Belgium
| | - Manoja K. Brahma
- Signal Transduction and Metabolism Laboratory, Université libre de Bruxelles, 1070 Brussels, Belgium
| | - Ao Li
- Signal Transduction and Metabolism Laboratory, Université libre de Bruxelles, 1070 Brussels, Belgium
| | - Javier Negueruela
- Signal Transduction and Metabolism Laboratory, Université libre de Bruxelles, 1070 Brussels, Belgium
| | - Ylke Bruggeman
- Clinical and Experimental Endocrinology (CEE), Department of Chronic Diseases, Metabolism and Ageing (CHROMETA), Campus Gasthuisberg O&N 1, KU Leuven, 3000 Leuven, Belgium
| | - Stéphane Demine
- Signal Transduction and Metabolism Laboratory, Université libre de Bruxelles, 1070 Brussels, Belgium
| | - Peng Xiao
- Inflammatory and Cell Death Signaling in Diabetes group, Signal Transduction and Metabolism Laboratory, Université libre de Bruxelles, 1070 Brussels, Belgium
| | - Alessandra K. Cardozo
- Inflammatory and Cell Death Signaling in Diabetes group, Signal Transduction and Metabolism Laboratory, Université libre de Bruxelles, 1070 Brussels, Belgium
| | - Nicolas Baeyens
- Laboratoire de Physiologie et de Pharmacologie, Université Libre de Bruxelles, 1000 Brussels, Belgium
| | - Luciano G. Martelotto
- Single Cell and Spatial-Omics Laboratory, Adelaide Centre of Epigenetics, University of Adelaide, Adelaide, SA 5005, Australia
| | | | - Eliana Mariño
- Infection and Immunity Program, Biomedicine Discovery Institute, Department of Biochemistry, Monash University, Melbourne, VIC 3800, Australia
- ImmunoBiota Therapeutics Pty Ltd, Melbourne, VIC 3187, Australia
| | - Conny Gysemans
- Clinical and Experimental Endocrinology (CEE), Department of Chronic Diseases, Metabolism and Ageing (CHROMETA), Campus Gasthuisberg O&N 1, KU Leuven, 3000 Leuven, Belgium
| | - Esteban N. Gurzov
- Signal Transduction and Metabolism Laboratory, Université libre de Bruxelles, 1070 Brussels, Belgium
- WELBIO Department, WEL Research Institute, Avenue Pasteur 6, 1300 Wavre, Belgium
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3
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Vaghjiani VG, Cochrane CR, Jayasekara WSN, Chong WC, Szczepny A, Kumar B, Martelotto LG, McCaw A, Carey K, Kansara M, Thomas DM, Walkley C, Mudge S, Gough DJ, Downie PA, Peacock CD, Matsui W, Watkins DN, Cain JE. Ligand-dependent hedgehog signaling maintains an undifferentiated, malignant osteosarcoma phenotype. Oncogene 2023; 42:3529-3541. [PMID: 37845394 PMCID: PMC10656285 DOI: 10.1038/s41388-023-02864-7] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 09/26/2023] [Accepted: 10/04/2023] [Indexed: 10/18/2023]
Abstract
TP53 and RB1 loss-of-function mutations are common in osteosarcoma. During development, combined loss of TP53 and RB1 function leads to downregulation of autophagy and the aberrant formation of primary cilia, cellular organelles essential for the transmission of canonical Hedgehog (Hh) signaling. Excess cilia formation then leads to hypersensitivity to Hedgehog (Hh) ligand signaling. In mouse and human models, we now show that osteosarcomas with mutations in TP53 and RB1 exhibit enhanced ligand-dependent Hh pathway activation through Smoothened (SMO), a transmembrane signaling molecule required for activation of the canonical Hh pathway. This dependence is mediated by hypersensitivity to Hh ligand and is accompanied by impaired autophagy and increased primary cilia formation and expression of Hh ligand in vivo. Using a conditional genetic mouse model of Trp53 and Rb1 inactivation in osteoblast progenitors, we further show that deletion of Smo converts the highly malignant osteosarcoma phenotype to benign, well differentiated bone tumors. Conversely, conditional overexpression of SHH ligand, or a gain-of-function SMO mutant in committed osteoblast progenitors during development blocks terminal bone differentiation. Finally, we demonstrate that the SMO antagonist sonidegib (LDE225) induces growth arrest and terminal differentiation in vivo in osteosarcomas that express primary cilia and Hh ligand combined with mutations in TP53. These results provide a mechanistic framework for aberrant Hh signaling in osteosarcoma based on defining mutations in the tumor suppressor, TP53.
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Affiliation(s)
| | - Catherine R Cochrane
- Hudson Institute of Medical Research, Clayton, VIC, 3168, Australia
- Department of Molecular and Translational Medicine, School of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, 3800, Australia
| | | | - Wai Chin Chong
- Hudson Institute of Medical Research, Clayton, VIC, 3168, Australia
- Department of Molecular and Translational Medicine, School of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, 3800, Australia
| | - Anette Szczepny
- Hudson Institute of Medical Research, Clayton, VIC, 3168, Australia
| | - Beena Kumar
- Department of Pathology, Monash Medical Centre, Clayton, VIC, 3168, Australia
| | - Luciano G Martelotto
- Department of Molecular and Translational Medicine, School of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, 3800, Australia
| | - Andrew McCaw
- Hudson Institute of Medical Research, Clayton, VIC, 3168, Australia
| | - Kirstyn Carey
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Maya Kansara
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
| | - David M Thomas
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
- St.Vincent's Clinical School, Faculty of Medicine, UNSW, Sydney, NSW, 1466, Australia
| | - Carl Walkley
- St. Vincent's Institute, Fitzroy, VIC, 3065, Australia
- Department of Medicine, St. Vincent's Hospital, University of Melbourne, Fitzroy, VIC, 3065, Australia
| | - Stuart Mudge
- Mayne Pharma International Pty Ltd, Salisbury Sth, SA, 5106, Australia
| | - Daniel J Gough
- Hudson Institute of Medical Research, Clayton, VIC, 3168, Australia
- Department of Molecular and Translational Medicine, School of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, 3800, Australia
| | - Peter A Downie
- Monash Children's Cancer Centre, Monash Children's Hospital, Monash Health, Clayton, VIC, 3168, Australia
- Department of Paediatrics, Monash University, Clayton, VIC, 3168, Australia
| | - Craig D Peacock
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Case Comprehensive Cancer Center, Cleveland, OH, 44106, USA
| | - William Matsui
- Department of Oncology and Livestrong Cancer Institutes, Dell Medical School, University of Texas at Austin, Austin, TX, 78712, USA
| | - D Neil Watkins
- Research Institute in Oncology and Hematology, CancerCare Manitoba, Winnipeg, MB, R3E-0V9, Canada.
- Department of Internal Medicine, Rady Faculty of Heath Sciences, University of Manitoba, Winnipeg, MB, R3A-1R9, Canada.
| | - Jason E Cain
- Hudson Institute of Medical Research, Clayton, VIC, 3168, Australia.
- Department of Molecular and Translational Medicine, School of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, 3800, Australia.
- Department of Paediatrics, Monash University, Clayton, VIC, 3168, Australia.
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4
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Tsui V, Lyu R, Novakovic S, Stringer JM, Dunleavy JE, Granger E, Semple T, Leichter A, Martelotto LG, Merriner DJ, Liu R, McNeill L, Zerafa N, Hoffmann ER, O’Bryan MK, Hutt K, Deans AJ, Heierhorst J, McCarthy DJ, Crismani W. Fancm has dual roles in the limiting of meiotic crossovers and germ cell maintenance in mammals. Cell Genom 2023; 3:100349. [PMID: 37601968 PMCID: PMC10435384 DOI: 10.1016/j.xgen.2023.100349] [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] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 03/30/2023] [Accepted: 06/02/2023] [Indexed: 08/22/2023]
Abstract
Meiotic crossovers are required for accurate chromosome segregation and producing new allelic combinations. Meiotic crossover numbers are tightly regulated within a narrow range, despite an excess of initiating DNA double-strand breaks. Here, we reveal the tumor suppressor FANCM as a meiotic anti-crossover factor in mammals. We use unique large-scale crossover analyses with both single-gamete sequencing and pedigree-based bulk-sequencing datasets to identify a genome-wide increase in crossover frequencies in Fancm-deficient mice. Gametogenesis is heavily perturbed in Fancm loss-of-function mice, which is consistent with the reproductive defects reported in humans with biallelic FANCM mutations. A portion of the gametogenesis defects can be attributed to the cGAS-STING pathway after birth. Despite the gametogenesis phenotypes in Fancm mutants, both sexes are capable of producing offspring. We propose that the anti-crossover function and role in gametogenesis of Fancm are separable and will inform diagnostic pathways for human genomic instability disorders.
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Affiliation(s)
- Vanessa Tsui
- DNA Repair and Recombination Laboratory, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
- The Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Parkville, VIC, Australia
| | - Ruqian Lyu
- Bioinformatics and Cellular Genomics, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
- Melbourne Integrative Genomics, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Stevan Novakovic
- DNA Repair and Recombination Laboratory, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
| | - Jessica M. Stringer
- Ovarian Biology Laboratory, Biomedicine Discovery Institute, Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, Australia
| | - Jessica E.M. Dunleavy
- Male Infertility and Germ Cell Biology Group, School of BioSciences and the Bio21 Institute, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Elissah Granger
- DNA Repair and Recombination Laboratory, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
| | - Tim Semple
- Single Cell Innovation Laboratory, Centre for Cancer Research, University of Melbourne, Parkville, VIC, Australia
| | - Anna Leichter
- Single Cell Innovation Laboratory, Centre for Cancer Research, University of Melbourne, Parkville, VIC, Australia
| | - Luciano G. Martelotto
- Single Cell Innovation Laboratory, Centre for Cancer Research, University of Melbourne, Parkville, VIC, Australia
| | - D. Jo Merriner
- Male Infertility and Germ Cell Biology Group, School of BioSciences and the Bio21 Institute, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Ruijie Liu
- Bioinformatics and Cellular Genomics, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
- Melbourne Integrative Genomics, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Lucy McNeill
- DNA Repair and Recombination Laboratory, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
| | - Nadeen Zerafa
- Ovarian Biology Laboratory, Biomedicine Discovery Institute, Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, Australia
| | - Eva R. Hoffmann
- DNRF Center for Chromosome Stability, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Moira K. O’Bryan
- Male Infertility and Germ Cell Biology Group, School of BioSciences and the Bio21 Institute, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Karla Hutt
- Ovarian Biology Laboratory, Biomedicine Discovery Institute, Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC, Australia
| | - Andrew J. Deans
- The Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Parkville, VIC, Australia
- Genome Stability Unit, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
| | - Jörg Heierhorst
- The Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Parkville, VIC, Australia
- Molecular Genetics Unit, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
| | - Davis J. McCarthy
- Bioinformatics and Cellular Genomics, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
- Melbourne Integrative Genomics, Faculty of Science, The University of Melbourne, Parkville, VIC, Australia
| | - Wayne Crismani
- DNA Repair and Recombination Laboratory, St Vincent’s Institute of Medical Research, Fitzroy, VIC, Australia
- The Faculty of Medicine, Dentistry and Health Science, The University of Melbourne, Parkville, VIC, Australia
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5
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De Rop FV, Hulselmans G, Flerin C, Soler-Vila P, Rafels A, Christiaens V, González-Blas CB, Marchese D, Caratù G, Poovathingal S, Rozenblatt-Rosen O, Slyper M, Luo W, Muus C, Duarte F, Shrestha R, Bagdatli ST, Corces MR, Mamanova L, Knights A, Meyer KB, Mulqueen R, Taherinasab A, Maschmeyer P, Pezoldt J, Lambert CLG, Iglesias M, Najle SR, Dossani ZY, Martelotto LG, Burkett Z, Lebofsky R, Martin-Subero JI, Pillai S, Sebé-Pedrós A, Deplancke B, Teichmann SA, Ludwig LS, Braun TP, Adey AC, Greenleaf WJ, Buenrostro JD, Regev A, Aerts S, Heyn H. Systematic benchmarking of single-cell ATAC-sequencing protocols. Nat Biotechnol 2023:10.1038/s41587-023-01881-x. [PMID: 37537502 DOI: 10.1038/s41587-023-01881-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 06/22/2023] [Indexed: 08/05/2023]
Abstract
Single-cell assay for transposase-accessible chromatin by sequencing (scATAC-seq) has emerged as a powerful tool for dissecting regulatory landscapes and cellular heterogeneity. However, an exploration of systemic biases among scATAC-seq technologies has remained absent. In this study, we benchmark the performance of eight scATAC-seq methods across 47 experiments using human peripheral blood mononuclear cells (PBMCs) as a reference sample and develop PUMATAC, a universal preprocessing pipeline, to handle the various sequencing data formats. Our analyses reveal significant differences in sequencing library complexity and tagmentation specificity, which impact cell-type annotation, genotype demultiplexing, peak calling, differential region accessibility and transcription factor motif enrichment. Our findings underscore the importance of sample extraction, method selection, data processing and total cost of experiments, offering valuable guidance for future research. Finally, our data and analysis pipeline encompasses 169,000 PBMC scATAC-seq profiles and a best practices code repository for scATAC-seq data analysis, which are freely available to extend this benchmarking effort to future protocols.
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Affiliation(s)
- Florian V De Rop
- VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Gert Hulselmans
- VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Chris Flerin
- VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Paula Soler-Vila
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Albert Rafels
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Valerie Christiaens
- VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Carmen Bravo González-Blas
- VIB Center for Brain and Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Domenica Marchese
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Ginevra Caratù
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | | | | | | | - Wendy Luo
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Fabiana Duarte
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rojesh Shrestha
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - M Ryan Corces
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA
| | | | | | | | - Ryan Mulqueen
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Akram Taherinasab
- Division of Hematology & Medical Oncology, Knight Cancer Institute, Oregon Health & Sciences University, Portland, OR, USA
- Division of Oncologic Sciences, Knight Cancer Institute, Oregon Health & Sciences University, Portland, OR, USA
| | - Patrick Maschmeyer
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Jörn Pezoldt
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Camille Lucie Germaine Lambert
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Marta Iglesias
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Sebastián R Najle
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Zain Y Dossani
- Vitalant Research Institute, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Luciano G Martelotto
- Adelaide Centre for Epigenetics and the South Australian Immunogenomics Cancer Institute, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- University of Melbourne Centre for Cancer Research, Victoria Comprehensive Cancer Centre, Melbourne, Victoria, Australia
| | - Zach Burkett
- Digital Biology Group, Bio-Rad, Pleasanton, CA, USA
| | | | - José Ignacio Martin-Subero
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Departament de Fonaments Clínics, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Satish Pillai
- Vitalant Research Institute, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Arnau Sebé-Pedrós
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- ICREA, Barcelona, Spain
| | - Bart Deplancke
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Cambridge, UK
- Department of Physics/Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Leif S Ludwig
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Theodore P Braun
- Division of Hematology & Medical Oncology, Knight Cancer Institute, Oregon Health & Sciences University, Portland, OR, USA
- Division of Oncologic Sciences, Knight Cancer Institute, Oregon Health & Sciences University, Portland, OR, USA
| | - Andrew C Adey
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Jason D Buenrostro
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Koch Institute of Integrative Cancer Research, Cambridge, MA, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Stein Aerts
- VIB Center for Brain and Disease Research, Leuven, Belgium.
- Department of Human Genetics, KU Leuven, Leuven, Belgium.
| | - Holger Heyn
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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6
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Mathiyalagan P, Martelotto LG, Ounzain S, El-Osta A, Uchida S. Editorial: RNA-chromatin interactions: Biology, mechanism, disease and therapeutics. Front Genet 2023; 13:1069427. [PMID: 36712845 PMCID: PMC9877285 DOI: 10.3389/fgene.2022.1069427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 12/23/2022] [Indexed: 01/13/2023] Open
Affiliation(s)
- Prabhu Mathiyalagan
- Center for Human Genetics and Genomics, New York University, New York City, NY, United States,*Correspondence: Prabhu Mathiyalagan,
| | - Luciano G. Martelotto
- Adelaide Centre for Epigenetics, South Australian Immunogenomics Cancer Institute, The University of Adelaide, Adelaide, SA, Australia
| | | | - Assam El-Osta
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Shizuka Uchida
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, Copenhagen, Denmark
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7
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Gruber E, So J, Lewis AC, Franich R, Cole R, Martelotto LG, Rogers AJ, Vidacs E, Fraser P, Stanley K, Jones L, Trigos A, Thio N, Li J, Nicolay B, Daigle S, Tron AE, Hyer ML, Shortt J, Johnstone RW, Kats LM. Inhibition of mutant IDH1 promotes cycling of acute myeloid leukemia stem cells. Cell Rep 2022; 40:111182. [PMID: 35977494 DOI: 10.1016/j.celrep.2022.111182] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/09/2022] [Accepted: 07/19/2022] [Indexed: 11/24/2022] Open
Abstract
Approximately 20% of acute myeloid leukemia (AML) patients carry mutations in IDH1 or IDH2 that result in over-production of the oncometabolite D-2-hydroxyglutarate (2-HG). Small molecule inhibitors that block 2-HG synthesis can induce complete morphological remission; however, almost all patients eventually acquire drug resistance and relapse. Using a multi-allelic mouse model of IDH1-mutant AML, we demonstrate that the clinical IDH1 inhibitor AG-120 (ivosidenib) exerts cell-type-dependent effects on leukemic cells, promoting delayed disease regression. Although single-agent AG-120 treatment does not fully eradicate the disease, it increases cycling of rare leukemia stem cells and triggers transcriptional upregulation of the pyrimidine salvage pathway. Accordingly, AG-120 sensitizes IDH1-mutant AML to azacitidine, with the combination of AG-120 and azacitidine showing vastly improved efficacy in vivo. Our data highlight the impact of non-genetic heterogeneity on treatment response and provide a mechanistic rationale for the observed combinatorial effect of AG-120 and azacitidine in patients.
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Affiliation(s)
- Emily Gruber
- The Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
| | - Joan So
- The Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia
| | | | - Rheana Franich
- The Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
| | - Rachel Cole
- The Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
| | - Luciano G Martelotto
- The University of Melbourne Centre for Cancer Research, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Amy J Rogers
- The Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
| | - Eva Vidacs
- The Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
| | - Peter Fraser
- The Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
| | - Kym Stanley
- The Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
| | - Lisa Jones
- The Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
| | - Anna Trigos
- The Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
| | - Niko Thio
- The Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
| | - Jason Li
- The Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia
| | | | - Scott Daigle
- Agios Pharmaceuticals, Inc., Cambridge, MA 02139, USA; Servier Pharmaceuticals, Boston, MA 02210, USA
| | - Adriana E Tron
- Agios Pharmaceuticals, Inc., Cambridge, MA 02139, USA; Servier Pharmaceuticals, Boston, MA 02210, USA
| | - Marc L Hyer
- Agios Pharmaceuticals, Inc., Cambridge, MA 02139, USA; Servier Pharmaceuticals, Boston, MA 02210, USA
| | - Jake Shortt
- The Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia; School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC 3068, Australia; Monash Haematology, Monash Health, Clayton, VIC 3068, Australia
| | - Ricky W Johnstone
- The Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia
| | - Lev M Kats
- The Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC 3052, Australia.
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8
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Salmon JM, Todorovski I, Stanley KL, Bruedigam C, Kearney CJ, Martelotto LG, Rossello F, Semple T, Arnau GM, Zethoven M, Bots M, Bjelosevic S, Cluse LA, Fraser PJ, Litalien V, Vidacs E, McArthur K, Matthews AY, Gressier E, de Weerd NA, Lichte J, Kelly MJ, Hogg SJ, Hertzog PJ, Kats LM, Vervoort SJ, De Carvalho DD, Scheu S, Bedoui S, Kile BT, Lane SW, Perkins AC, Wei AH, Dominguez PM, Johnstone RW. Epigenetic Activation of Plasmacytoid DCs Drives IFNAR-Dependent Therapeutic Differentiation of AML. Cancer Discov 2022; 12:1560-1579. [PMID: 35311997 PMCID: PMC9355625 DOI: 10.1158/2159-8290.cd-20-1145] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 08/10/2020] [Revised: 10/28/2021] [Accepted: 03/16/2022] [Indexed: 01/07/2023]
Abstract
Pharmacologic inhibition of epigenetic enzymes can have therapeutic benefit against hematologic malignancies. In addition to affecting tumor cell growth and proliferation, these epigenetic agents may induce antitumor immunity. Here, we discovered a novel immunoregulatory mechanism through inhibition of histone deacetylases (HDAC). In models of acute myeloid leukemia (AML), leukemia cell differentiation and therapeutic benefit mediated by the HDAC inhibitor (HDACi) panobinostat required activation of the type I interferon (IFN) pathway. Plasmacytoid dendritic cells (pDC) produced type I IFN after panobinostat treatment, through transcriptional activation of IFN genes concomitant with increased H3K27 acetylation at these loci. Depletion of pDCs abrogated panobinostat-mediated induction of type I IFN signaling in leukemia cells and impaired therapeutic efficacy, whereas combined treatment with panobinostat and IFNα improved outcomes in preclinical models. These discoveries offer a new therapeutic approach for AML and demonstrate that epigenetic rewiring of pDCs enhances antitumor immunity, opening the possibility of exploiting this approach for immunotherapies. SIGNIFICANCE We demonstrate that HDACis induce terminal differentiation of AML through epigenetic remodeling of pDCs, resulting in production of type I IFN that is important for the therapeutic effects of HDACis. The study demonstrates the important functional interplay between the immune system and leukemias in response to HDAC inhibition. This article is highlighted in the In This Issue feature, p. 1397.
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Affiliation(s)
- Jessica M. Salmon
- Translational Haematology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Australian Centre for Blood Diseases, Monash University and The Alfred Hospital, Melbourne, Australia
| | - Izabela Todorovski
- Translational Haematology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Kym L. Stanley
- Translational Haematology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Claudia Bruedigam
- Cancer Program, Queensland Institute of Medical Research (QIMR) Berghofer Medical Research Institute, Brisbane, Queensland, Australia.,School of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Conor J. Kearney
- Translational Haematology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Luciano G. Martelotto
- Single Cell Innovation Lab, Department of Clinical Pathology, University of Melbourne, Parkville, Victoria, Australia
| | - Fernando Rossello
- Single Cell Innovation Lab, Department of Clinical Pathology, University of Melbourne, Parkville, Victoria, Australia.,University of Melbourne Centre for Cancer Research, The University of Melbourne, Melbourne, Victoria, Australia
| | - Timothy Semple
- Molecular Genomics Core, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Gisela Mir Arnau
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia.,Molecular Genomics Core, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Magnus Zethoven
- Translational Haematology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Michael Bots
- Laboratory of Clinical Chemistry, Academic Medical Center, University of Amsterdam, the Netherlands
| | - Stefan Bjelosevic
- Translational Haematology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Leonie A. Cluse
- Translational Haematology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Peter J. Fraser
- Translational Haematology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Veronique Litalien
- Australian Centre for Blood Diseases, Monash University and The Alfred Hospital, Melbourne, Australia
| | - Eva Vidacs
- Translational Haematology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Kate McArthur
- Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Antony Y. Matthews
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia; Department of Molecular and Translational Sciences, Monash University Clayton Victoria, Australia
| | - Elise Gressier
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia
| | - Nicole A. de Weerd
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia; Department of Molecular and Translational Sciences, Monash University Clayton Victoria, Australia
| | - Jens Lichte
- Institute of Medical Microbiology and Hospital Hygiene, University of Düsseldorf, Düsseldorf, Germany
| | - Madison J. Kelly
- Translational Haematology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Simon J. Hogg
- Translational Haematology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Paul J. Hertzog
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia; Department of Molecular and Translational Sciences, Monash University Clayton Victoria, Australia
| | - Lev M. Kats
- Translational Haematology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Stephin J. Vervoort
- Translational Haematology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Daniel D. De Carvalho
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Stefanie Scheu
- Institute of Medical Microbiology and Hospital Hygiene, University of Düsseldorf, Düsseldorf, Germany
| | - Sammy Bedoui
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia
| | - Benjamin T. Kile
- Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia.,Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Steven W. Lane
- Cancer Program, Queensland Institute of Medical Research (QIMR) Berghofer Medical Research Institute, Brisbane, Queensland, Australia.,School of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Andrew C. Perkins
- Australian Centre for Blood Diseases, Monash University and The Alfred Hospital, Melbourne, Australia
| | - Andrew H. Wei
- Australian Centre for Blood Diseases, Monash University and The Alfred Hospital, Melbourne, Australia
| | - Pilar M. Dominguez
- Translational Haematology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia.,Corresponding Authors: Ricky W. Johnstone, Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, Victoria 3000, Australia. Phone: 61-855-97133; E-mail: ; and Pilar M. Dominguez, Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, Victoria 3000, Australia. Phone: 61-481-880-373; E-mail:
| | - Ricky W. Johnstone
- Translational Haematology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia.,Corresponding Authors: Ricky W. Johnstone, Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, Victoria 3000, Australia. Phone: 61-855-97133; E-mail: ; and Pilar M. Dominguez, Peter MacCallum Cancer Centre, 305 Grattan Street, Melbourne, Victoria 3000, Australia. Phone: 61-481-880-373; E-mail:
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9
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Gularte-Mérida R, Smith S, Bowman AS, da Cruz Paula A, Chatila W, Bielski CM, Vyas M, Borsu L, Zehir A, Martelotto LG, Shia J, Yaeger R, Fang F, Gardner R, Luo R, Schatz MC, Shen R, Weigelt B, Sánchez-Vega F, Reis-Filho JS, Hechtman JF. Same-Cell Co-Occurrence of RAS Hotspot and BRAF V600E Mutations in Treatment-Naive Colorectal Cancer. JCO Precis Oncol 2022; 6:e2100365. [PMID: 35235413 PMCID: PMC8906458 DOI: 10.1200/po.21.00365] [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
PURPOSE Mitogen-activated protein kinase pathway-activating mutations occur in the majority of colorectal cancer (CRC) cases and show mutual exclusivity. We identified 47 epidermal growth factor receptor/BRAF inhibitor-naive CRC patients with dual RAS hotspot/BRAF V600E mutations (CRC-DD) from a cohort of 4,561 CRC patients with clinical next-generation sequencing results. We aimed to define the molecular phenotypes of the CRC-DD and to test if the dual RAS hotspot/BRAF V600E mutations coexist within the same cell. MATERIALS AND METHODS We developed a single-cell genotyping method with a mutation detection rate of 96.3% and a genotype prediction accuracy of 92.1%. Mutations in the CRC-DD cohort were analyzed for clonality, allelic imbalance, copy number, and overall survival. RESULTS Application of single-cell genotyping to four CRC-DD revealed the co-occurrence of both mutations in the following percentages of cells per case: NRAS G13D/KRAS G12C, 95%; KRAS G12D/NRAS G12V, 48%; BRAF V600E/KRAS G12D, 44%; and KRAS G12D/NRAS G13V, 14%, respectively. Allelic imbalance favoring the oncogenic allele was less frequent in CRC-DD (24 of 76, 31.5%, somatic mutations) compared with a curated cohort of CRC with a single-driver mutation (CRC-SD; 119 of 232 mutations, 51.3%; P = .013). Microsatellite instability-high status was enriched in CRC-DD compared with CRC-SD (23% v 11.4%, P = .028). Of the seven CRC-DD cases with multiregional sequencing, five retained both driver mutations throughout all sequenced tumor sites. Both CRC-DD cases with discordant multiregional sequencing were microsatellite instability-high. CONCLUSION Our findings indicate that dual-driver mutations occur in a rare subset of CRC, often within the same tumor cells and across multiple tumor sites. Their presence and a lower rate of allelic imbalance may be related to dose-dependent signaling within the mitogen-activated protein kinase pathway.
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Affiliation(s)
- Rodrigo Gularte-Mérida
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY,Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY,Rodrigo Gularte Mérida, PhD, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY 10065; e-mail:
| | - Shaleigh Smith
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY,Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Anita S. Bowman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Walid Chatila
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Craig M. Bielski
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Monika Vyas
- Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA
| | - Laetitia Borsu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Jinru Shia
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Rona Yaeger
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Fang Fang
- Flow Cytometry Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Rui Gardner
- Flow Cytometry Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ruibang Luo
- Department of Computer Science, John Hopkins University, Baltimore, MD
| | - Michael C. Schatz
- Department of Computer Science, John Hopkins University, Baltimore, MD
| | - Ronglai Shen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Francisco Sánchez-Vega
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY,Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jorge S. Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jaclyn F. Hechtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
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10
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Fennell KA, Vassiliadis D, Lam EYN, Martelotto LG, Balic JJ, Hollizeck S, Weber TS, Semple T, Wang Q, Miles DC, MacPherson L, Chan YC, Guirguis AA, Kats LM, Wong ES, Dawson SJ, Naik SH, Dawson MA. Non-genetic determinants of malignant clonal fitness at single-cell resolution. Nature 2021; 601:125-131. [PMID: 34880496 DOI: 10.1038/s41586-021-04206-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 10/30/2021] [Indexed: 12/14/2022]
Abstract
All cancers emerge after a period of clonal selection and subsequent clonal expansion. Although the evolutionary principles imparted by genetic intratumour heterogeneity are becoming increasingly clear1, little is known about the non-genetic mechanisms that contribute to intratumour heterogeneity and malignant clonal fitness2. Here, using single-cell profiling and lineage tracing (SPLINTR)-an expressed barcoding strategy-we trace isogenic clones in three clinically relevant mouse models of acute myeloid leukaemia. We find that malignant clonal dominance is a cell-intrinsic and heritable property that is facilitated by the repression of antigen presentation and increased expression of the secretory leukocyte peptidase inhibitor gene (Slpi), which we genetically validate as a regulator of acute myeloid leukaemia. Increased transcriptional heterogeneity is a feature that enables clonal fitness in diverse tissues and immune microenvironments and in the context of clonal competition between genetically distinct clones. Similar to haematopoietic stem cells3, leukaemia stem cells (LSCs) display heritable clone-intrinsic properties of high, and low clonal output that contribute to the overall tumour mass. We demonstrate that LSC clonal output dictates sensitivity to chemotherapy and, although high- and low-output clones adapt differently to therapeutic pressure, they coordinately emerge from minimal residual disease with increased expression of the LSC program. Together, these data provide fundamental insights into the non-genetic transcriptional processes that underpin malignant clonal fitness and may inform future therapeutic strategies.
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Affiliation(s)
- Katie A Fennell
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Dane Vassiliadis
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Enid Y N Lam
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Luciano G Martelotto
- The University of Melbourne Centre for Cancer Research, The University of Melbourne, Melbourne, Victoria, Australia
| | - Jesse J Balic
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Sebastian Hollizeck
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Tom S Weber
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia.,The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Timothy Semple
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,The University of Melbourne Centre for Cancer Research, The University of Melbourne, Melbourne, Victoria, Australia
| | - Qing Wang
- Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia
| | - Denise C Miles
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia.,The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Laura MacPherson
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Yih-Chih Chan
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Andrew A Guirguis
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Lev M Kats
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Emily S Wong
- Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia.,School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, New South Wales, Australia
| | - Sarah-Jane Dawson
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia.,The University of Melbourne Centre for Cancer Research, The University of Melbourne, Melbourne, Victoria, Australia
| | - Shalin H Naik
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia.,The Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Mark A Dawson
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia. .,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia. .,The University of Melbourne Centre for Cancer Research, The University of Melbourne, Melbourne, Victoria, Australia.
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11
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Lelliott EJ, Kong IY, Zethoven M, Ramsbottom KM, Martelotto LG, Meyran D, Jiang Zhu J, Costacurta M, Kirby L, Sandow JJ, Lim L, Dominguez PM, Todorovski I, Haynes NM, Beavis PA, Neeson PJ, Hawkins ED, McArthur GA, Parish IA, Johnstone RW, Oliaro J, Sheppard KE, Kearney CJ, Vervoort SJ. CDK4/6 inhibition promotes anti-tumor immunity through the induction of T cell memory. Cancer Discov 2021; 11:2582-2601. [PMID: 33990344 DOI: 10.1158/2159-8290.cd-20-1554] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 04/05/2021] [Accepted: 05/12/2021] [Indexed: 11/16/2022]
Abstract
Pharmacological inhibitors of cyclin dependent kinases 4 and 6 (CDK4/6) are an approved treatment for hormone receptor-positive breast cancer and are currently under evaluation across hundreds of clinical trials for other cancer types. The clinical success of these inhibitors is largely attributed to well-defined tumor-intrinsic cytostatic mechanisms, while their emerging role as immunomodulatory agents is less understood. Using integrated epigenomic, transcriptomic and proteomic analyses, we demonstrated a novel action of CDK4/6 inhibitors in promoting the phenotypic and functional acquisition of immunological T cell memory. Short-term priming with a CDK4/6 inhibitor promoted long-term endogenous anti-tumor T cell immunity in mice, enhanced the persistence and therapeutic efficacy of chimeric antigen receptor (CAR)-T cells, and induced an RB-dependent T cell phenotype supportive of favorable responses to immune checkpoint blockade in melanoma patients. Together, these mechanistic insights significantly broaden the prospective utility of CDK4/6 inhibitors as clinical tools to boost anti-tumor T cell immunity.
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Affiliation(s)
| | - Isabella Y Kong
- Inflammation, Walter and Eliza Hall Institute of Medical Research
| | | | | | | | | | | | | | - Laura Kirby
- Cancer Research, Peter MacCallum Cancer Centre
| | - Jarrod J Sandow
- Advanced Biology and Technology, The Walter and Eliza Hall Institute
| | - Lydia Lim
- Division of Research, Peter MacCallum Cancer Centre
| | | | | | - Nicole M Haynes
- Sir Peter MacCallum Department of Oncology, Peter MacCallum Cancer Centre
| | - Paul A Beavis
- Cancer Immunology Program, Peter MacCallum Cancer Research Centre
| | - Paul J Neeson
- Cancer Immunology Research, Peter MacCallum Cancer Centre
| | - Edwin D Hawkins
- Immunology Division, Walter and Eliza Hall Institute of Medical Research
| | | | - Ian A Parish
- Cancer Immunology Program, Peter MacCallum Cancer Research Centre
| | | | | | | | | | - Stephin J Vervoort
- Gene Regulation Laboratory, Cancer Therapeutics Program, Peter MacCallum Cancer Centre
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12
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Gherardin NA, Waldeck K, Caneborg A, Martelotto LG, Balachander S, Zethoven M, Petrone PM, Pattison A, Wilmott JS, Quiñones-Parra SM, Rossello F, Posner A, Wong A, Weppler AM, Shannon KF, Hong A, Ferguson PM, Jakrot V, Raleigh J, Hatzimihalis A, Neeson PJ, Deleso P, Johnston M, Chua M, Becker JC, Sandhu S, McArthur GA, Gill AJ, Scolyer RA, Hicks RJ, Godfrey DI, Tothill RW. γδ T Cells in Merkel Cell Carcinomas Have a Proinflammatory Profile Prognostic of Patient Survival. Cancer Immunol Res 2021; 9:612-623. [PMID: 33674358 DOI: 10.1158/2326-6066.cir-20-0817] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 01/14/2021] [Accepted: 03/03/2021] [Indexed: 11/16/2022]
Abstract
Merkel cell carcinomas (MCC) are immunogenic skin cancers associated with viral infection or UV mutagenesis. To study T-cell infiltrates in MCC, we analyzed 58 MCC lesions from 39 patients using multiplex-IHC/immunofluorescence (m-IHC/IF). CD4+ or CD8+ T cells comprised the majority of infiltrating T lymphocytes in most tumors. However, almost half of the tumors harbored prominent CD4/CD8 double-negative (DN) T-cell infiltrates (>20% DN T cells), and in 12% of cases, DN T cells represented the majority of T cells. Flow cytometric analysis of single-cell suspensions from fresh tumors identified DN T cells as predominantly Vδ2- γδ T cells. In the context of γδ T-cell inflammation, these cells expressed PD-1 and LAG3, which is consistent with a suppressed or exhausted phenotype, and CD103, which indicates tissue residency. Furthermore, single-cell RNA sequencing (scRNA-seq) identified a transcriptional profile of γδ T cells suggestive of proinflammatory potential. T-cell receptor (TCR) analysis confirmed clonal expansion of Vδ1 and Vδ3 clonotypes, and functional studies using cloned γδ TCRs demonstrated restriction of these for CD1c and MR1 antigen-presenting molecules. On the basis of a 13-gene γδ T-cell signature derived from scRNA-seq analysis, gene-set enrichment on bulk RNA-seq data showed a positive correlation between enrichment scores and DN T-cell infiltrates. An improved disease-specific survival was evident for patients with high enrichment scores, and complete responses to anti-PD-1/PD-L1 treatment were observed in three of four cases with high enrichment scores. Thus, γδ T-cell infiltration may serve as a prognostic biomarker and should be explored for therapeutic interventions.See related Spotlight on p. 600.
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Affiliation(s)
- Nicholas A Gherardin
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Melbourne, Victoria, Australia
| | - Kelly Waldeck
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Alex Caneborg
- Department of Clinical Pathology and Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia
| | - Luciano G Martelotto
- Department of Clinical Pathology and Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia
| | - Shiva Balachander
- Department of Clinical Pathology and Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia
| | - Magnus Zethoven
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Pasquale M Petrone
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Andrew Pattison
- Department of Clinical Pathology and Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia
| | - James S Wilmott
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Sergio M Quiñones-Parra
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Fernando Rossello
- Department of Clinical Pathology and Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia
| | - Atara Posner
- Department of Clinical Pathology and Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia
| | - Annie Wong
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Alison M Weppler
- Medical Oncology Department, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Kerwin F Shannon
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - Angela Hong
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - Peter M Ferguson
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - Valerie Jakrot
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia
| | - Jeanette Raleigh
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Athena Hatzimihalis
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Paul J Neeson
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Paolo Deleso
- Radiation Oncology Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Meredith Johnston
- Radiation Oncology Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Liverpool Hospital, Sydney, New South Wales, Australia
| | - Margaret Chua
- Radiation Oncology Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Juergen C Becker
- German Cancer Consortium (DKTK), Translational Skin Cancer Research, University Medicine Essen, Essen and DKFZ, Heidelberg, Germany
| | - Shahneen Sandhu
- Medical Oncology Department, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Grant A McArthur
- Medical Oncology Department, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Anthony J Gill
- Cancer Diagnosis and Pathology Group, Kolling Institute of Medical, Research and The University of Sydney, Sydney, New South Wales, Australia
| | - Richard A Scolyer
- Melanoma Institute Australia, The University of Sydney, Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia.,New South Wales Health Pathology, Sydney, New South Wales, Australia
| | - Rodney J Hicks
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia.,Cancer Imaging Department, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Dale I Godfrey
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, University of Melbourne, Melbourne, Victoria, Australia
| | - Richard W Tothill
- Department of Clinical Pathology and Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia. .,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
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13
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Lelliott EJ, Mangiola S, Ramsbottom KM, Zethoven M, Lim L, Lau PKH, Oliver AJ, Martelotto LG, Kirby L, Martin C, Patel RP, Slater A, Cullinane C, Papenfuss AT, Haynes NM, McArthur GA, Oliaro J, Sheppard KE. Combined BRAF, MEK, and CDK4/6 Inhibition Depletes Intratumoral Immune-Potentiating Myeloid Populations in Melanoma. Cancer Immunol Res 2020; 9:136-146. [PMID: 33303574 DOI: 10.1158/2326-6066.cir-20-0401] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 09/14/2020] [Accepted: 12/04/2020] [Indexed: 11/16/2022]
Abstract
Combined inhibition of BRAF, MEK, and CDK4/6 is currently under evaluation in clinical trials for patients with melanoma harboring a BRAFV600 mutation. While this triple therapy has potent tumor-intrinsic effects, the impact of this combination on antitumor immunity remains unexplored. Here, using a syngeneic BrafV600ECdkn2a-/-Pten-/- melanoma model, we demonstrated that triple therapy promoted durable tumor control through tumor-intrinsic mechanisms and promoted immunogenic cell death and T-cell infiltration. Despite this, tumors treated with triple therapy were unresponsive to immune checkpoint blockade (ICB). Flow cytometric and single-cell RNA sequencing analyses of tumor-infiltrating immune populations revealed that triple therapy markedly depleted proinflammatory macrophages and cross-priming CD103+ dendritic cells, the absence of which correlated with poor overall survival and clinical responses to ICB in patients with melanoma. Indeed, immune populations isolated from tumors of mice treated with triple therapy failed to stimulate T-cell responses ex vivo While combined BRAF, MEK, and CDK4/6 inhibition demonstrates favorable tumor-intrinsic activity, these data suggest that collateral effects on tumor-infiltrating myeloid populations may impact antitumor immunity. These findings have important implications for the design of combination strategies and clinical trials that incorporate BRAF, MEK, and CDK4/6 inhibition with immunotherapy for the treatment of patients with melanoma.
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Affiliation(s)
- Emily J Lelliott
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Stefano Mangiola
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Kelly M Ramsbottom
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Magnus Zethoven
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Lydia Lim
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Peter K H Lau
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Amanda J Oliver
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Luciano G Martelotto
- Single Cell Innovation Laboratory, The University of Melbourne, Parkville, Victoria, Australia
| | - Laura Kirby
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Claire Martin
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Riyaben P Patel
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Alison Slater
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Carleen Cullinane
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Anthony T Papenfuss
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Nicole M Haynes
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Grant A McArthur
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Jane Oliaro
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia.,Department of Immunology, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Karen E Sheppard
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia. .,Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia.,Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria, Australia
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14
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Alidousty C, Duerbaum N, Wagener-Ryczek S, Baar T, Martelotto LG, Heydt C, Siemanowski J, Holz B, Binot E, Fassunke J, Merkelbach-Bruse S, Wolf J, Kron A, Buettner R, Schultheis AM. Prevalence and potential biological role of TERT amplifications in ALK translocated adenocarcinoma of the lung. Histopathology 2020; 78:578-585. [PMID: 32946634 DOI: 10.1111/his.14256] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 06/10/2020] [Accepted: 09/11/2020] [Indexed: 12/20/2022]
Abstract
AIMS The advent of specific ALK-targeting drugs has radically changed the outcome of patients with ALK translocated non-small-cell lung cancer (NSCLC). However, emerging resistance to treatment with ALK inhibitors in these patients remains a major concern. In previous studies, we analysed two ALK+ patient cohorts (TP53 wild-type/TP53 mutated) in terms of copy number alterations. All patients belonging to the TP53 wild-type group had mainly genetically stable genomes, with one exception showing chromosomal instability and amplifications of several gene loci, including TERT. Here, we aimed to determine the prevalence of TERT amplifications in these ALK+ lung cancer patients by analysing an independent cohort of 109 ALK translocated cases. We further analysed the copy numbers of numerous cancer-relevant genes and other genetic aberrations. METHODS AND RESULTS The prevalence of TERT amplifications was determined by means of FISH analyses. Copy numbers of 87 cancer-relevant genes were determined by NanoString nCounter® technology, FoundationOne® and lung-specific NGS panels in some of these TERT-amplified samples, and clinical data on patients with TERT-amplified tumours were collected. Our data revealed that five (4.6%) of all 109 analysed ALK+ patients harboured amplification of TERT and that these patients had genetically unstable genomes. CONCLUSIONS Our preliminary study shows that ALK+ adenocarcinomas should be evaluated in the context of their genomic background in order to more clearly understand and predict patients' individual course of disease.
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Affiliation(s)
| | - Nicolai Duerbaum
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | | | - Till Baar
- Faculty of Medicine, Institute of Medical Statistics and Computational Biology, University of Cologne, Cologne, Germany
| | | | - Carina Heydt
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | - Janna Siemanowski
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | - Barbara Holz
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | - Elke Binot
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | - Jana Fassunke
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | | | - Jürgen Wolf
- Network Genomic Medicine, Cologne, Germany.,Lung Cancer Group Cologne, Department I of Internal Medicine, University Hospital of Cologne, Cologne, Germany.,Center for Integrated Oncology Koeln Bonn, Cologne, Germany
| | - Anna Kron
- Network Genomic Medicine, Cologne, Germany.,Lung Cancer Group Cologne, Department I of Internal Medicine, University Hospital of Cologne, Cologne, Germany.,Center for Integrated Oncology Koeln Bonn, Cologne, Germany
| | - Reinhard Buettner
- Institute of Pathology, University Hospital Cologne, Cologne, Germany.,Network Genomic Medicine, Cologne, Germany.,Center for Integrated Oncology Koeln Bonn, Cologne, Germany
| | - Anne M Schultheis
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
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15
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Abstract
Unravelling spatio-temporal patterns of gene expression is crucial to understanding core biological principles from embryogenesis to disease. Here we review emerging technologies, providing automated, high-throughput, spatially resolved quantitative gene expression data. Novel techniques expand on current benchmark protocols, expediting their incorporation into ongoing research. These approaches digitally reconstruct patterns of embryonic expression in three dimensions, and have successfully identified novel domains of expression, cell types, and tissue features. Such technologies pave the way for unbiased and exhaustive recapitulation of gene expression levels in spatial and quantitative terms, promoting understanding of the molecular origin of developmental defects, and improving medical diagnostics.
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Affiliation(s)
- Lisa N Waylen
- Australian Regenerative Medicine Institute and Systems Biology Institute, Monash University, Clayton, VIC, Australia
| | - Hieu T Nim
- Australian Regenerative Medicine Institute and Systems Biology Institute, Monash University, Clayton, VIC, Australia
- Transcriptomics and Bioinformatics Group, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Luciano G Martelotto
- Single Cell Core Laboratory, Harvard Medical School, Department of System Biology, Boston, MA, USA
| | - Mirana Ramialison
- Australian Regenerative Medicine Institute and Systems Biology Institute, Monash University, Clayton, VIC, Australia.
- Transcriptomics and Bioinformatics Group, Murdoch Children's Research Institute, Parkville, VIC, Australia.
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16
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Verghese E, Martelotto LG, Cain JE, Williams TM, Wise AF, Hill PA, Langham RG, Watkins DN, Ricardo SD, Deane JA. Renal epithelial cells retain primary cilia during human acute renal allograft rejection injury. BMC Res Notes 2019; 12:718. [PMID: 31676011 PMCID: PMC6824085 DOI: 10.1186/s13104-019-4738-6] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Accepted: 10/16/2019] [Indexed: 01/03/2023] Open
Abstract
Objectives Primary cilia are sensory organelles which co-ordinate several developmental/repair pathways including hedgehog signalling. Studies of human renal allografts suffering acute tubular necrosis have shown that length of primary cilia borne by epithelial cells doubles throughout the nephron and collecting duct, and then normalises as renal function returns. Conversely the loss of primary cilia has been reported in chronic allograft rejection and linked to defective hedgehog signalling. We investigated the fate of primary cilia in renal allografts suffering acute rejection. Results Here we observed that in renal allografts undergoing acute rejection, primary cilia were retained, with their length increasing 1 week after transplantation and remaining elevated. We used a mouse model of acute renal injury to demonstrate that elongated renal primary cilia in the injured renal tubule show evidence of smoothened accumulation, a biomarker for activation of hedgehog signalling. We conclude that primary cilium-mediated activation of hedgehog signalling is still possible during the acute phase of renal allograft rejection.
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Affiliation(s)
- Elizabeth Verghese
- Biomedical and Health Sciences, Victoria University, St Albans, Australia.
| | - Luciano G Martelotto
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Australia.,Centre for Cancer Research, VCCC, University of Melbourne, Melbourne, Australia
| | - Jason E Cain
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Australia
| | - Timothy M Williams
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Australia
| | - Andrea F Wise
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Australia
| | - Prudence A Hill
- Department of Anatomical Pathology, St Vincent's Hospital, Melbourne, Australia
| | - Robyn G Langham
- Department of Nephrology, St Vincent's Hospital, Melbourne, VIC, Australia.,Monash Rural Health, Monash University, Clayton, VIC, Australia
| | - D Neil Watkins
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Australia.,The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, Darlinghurst, NSW, Australia
| | - Sharon D Ricardo
- Department of Anatomy and Developmental Biology, Monash University, Clayton, Australia
| | - James A Deane
- Department of Obstetrics and Gynaecology, Monash University, Clayton, Australia.
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17
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Marini KD, Croucher DR, McCloy RA, Vaghjiani V, Gonzalez-Rajal A, Hastings JF, Chin V, Szczepny A, Kostyrko K, Marquez C, Jayasekara WSN, Alamgeer M, Boolell V, Han JZR, Waugh T, Lee HC, Oakes SR, Kumar B, Harrison CA, Hedger MP, Lorensuhewa N, Kita B, Barrow R, Robinson BW, de Kretser DM, Wu J, Ganju V, Sweet-Cordero EA, Burgess A, Martelotto LG, Rossello FJ, Cain JE, Watkins DN. Inhibition of activin signaling in lung adenocarcinoma increases the therapeutic index of platinum chemotherapy. Sci Transl Med 2019; 10:10/451/eaat3504. [PMID: 30045976 DOI: 10.1126/scitranslmed.aat3504] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 05/30/2018] [Indexed: 12/14/2022]
Abstract
Resistance to platinum chemotherapy is a long-standing problem in the management of lung adenocarcinoma. Using a whole-genome synthetic lethal RNA interference screen, we identified activin signaling as a critical mediator of innate platinum resistance. The transforming growth factor-β (TGFβ) superfamily ligands activin A and growth differentiation factor 11 (GDF11) mediated resistance via their cognate receptors through TGFβ-activated kinase 1 (TAK1), rather than through the SMAD family of transcription factors. Inhibition of activin receptor signaling or blockade of activin A and GDF11 by the endogenous protein follistatin overcame this resistance. Consistent with the role of activin signaling in acute renal injury, both therapeutic interventions attenuated acute cisplatin-induced nephrotoxicity, its major dose-limiting side effect. This cancer-specific enhancement of platinum-induced cell death has the potential to dramatically improve the safety and efficacy of chemotherapy in lung cancer patients.
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Affiliation(s)
- Kieren D Marini
- Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - David R Croucher
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia.,St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, Darlinghurst, New South Wales 2010, Australia.,School of Medicine, University College Dublin, Belfield, Dublin D04 V1W8, Ireland
| | - Rachael A McCloy
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia
| | - Vijesh Vaghjiani
- Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia
| | - Alvaro Gonzalez-Rajal
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia
| | - Jordan F Hastings
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia
| | - Venessa Chin
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia.,Department of Medical Oncology, St. Vincent's Hospital, Darlinghurst, New South Wales 2010, Australia
| | - Anette Szczepny
- Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia
| | - Kaja Kostyrko
- Department of Pediatrics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Cesar Marquez
- Department of Pediatrics, University of California San Francisco, San Francisco, CA 94158, USA
| | | | - Muhammad Alamgeer
- Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria 3800, Australia.,Department of Medical Oncology, Monash Medical Centre, East Bentleigh, Victoria 3165, Australia
| | - Vishal Boolell
- Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Department of Medical Oncology, Monash Medical Centre, East Bentleigh, Victoria 3165, Australia
| | - Jeremy Z R Han
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia
| | - Todd Waugh
- Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia
| | - Hong Ching Lee
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia
| | - Samantha R Oakes
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia.,St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, Darlinghurst, New South Wales 2010, Australia
| | - Beena Kumar
- Department of Pathology, Monash Medical Centre, Clayton, Victoria 3168, Australia
| | - Craig A Harrison
- Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Mark P Hedger
- Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria 3800, Australia
| | | | - Badia Kita
- Paranta Biosciences Limited, Melbourne, Victoria 3004, Australia
| | - Ross Barrow
- Paranta Biosciences Limited, Melbourne, Victoria 3004, Australia
| | - Bruce W Robinson
- School of Medicine and Pharmacology, Queen Elizabeth II Medical Centre Unit, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - David M de Kretser
- Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria 3800, Australia.,Paranta Biosciences Limited, Melbourne, Victoria 3004, Australia
| | - Jianmin Wu
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia.,St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, Darlinghurst, New South Wales 2010, Australia.,Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Beijing, China.,Center for Cancer Bioinformatics, Peking University Cancer Hospital and Institute, Hai-Dian District, Beijing 100142, China
| | - Vinod Ganju
- Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.,Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria 3800, Australia
| | | | - Andrew Burgess
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia.,ANZAC Research Institute, Concord, New South Wales 2139, Australia
| | - Luciano G Martelotto
- Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria 3800, Australia.,Center for Cancer Research, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Fernando J Rossello
- Australian Regenerative Medicine Institute, Clayton, Victoria 3800, Australia.,Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Jason E Cain
- Hudson Institute of Medical Research, Clayton, Victoria 3168, Australia.
| | - D Neil Watkins
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia. .,St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales Sydney, Darlinghurst, New South Wales 2010, Australia.,Department of Thoracic Medicine, St. Vincent's Hospital, Darlinghurst, New South Wales 2010, Australia
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18
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Bell CC, Fennell KA, Chan YC, Rambow F, Yeung MM, Vassiliadis D, Lara L, Yeh P, Martelotto LG, Rogiers A, Kremer BE, Barbash O, Mohammad HP, Johanson TM, Burr ML, Dhar A, Karpinich N, Tian L, Tyler DS, MacPherson L, Shi J, Pinnawala N, Yew Fong C, Papenfuss AT, Grimmond SM, Dawson SJ, Allan RS, Kruger RG, Vakoc CR, Goode DL, Naik SH, Gilan O, Lam EYN, Marine JC, Prinjha RK, Dawson MA. Targeting enhancer switching overcomes non-genetic drug resistance in acute myeloid leukaemia. Nat Commun 2019; 10:2723. [PMID: 31222014 PMCID: PMC6586637 DOI: 10.1038/s41467-019-10652-9] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [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: 03/13/2019] [Accepted: 05/21/2019] [Indexed: 12/16/2022] Open
Abstract
Non-genetic drug resistance is increasingly recognised in various cancers. Molecular insights into this process are lacking and it is unknown whether stable non-genetic resistance can be overcome. Using single cell RNA-sequencing of paired drug naïve and resistant AML patient samples and cellular barcoding in a unique mouse model of non-genetic resistance, here we demonstrate that transcriptional plasticity drives stable epigenetic resistance. With a CRISPR-Cas9 screen we identify regulators of enhancer function as important modulators of the resistant cell state. We show that inhibition of Lsd1 (Kdm1a) is able to overcome stable epigenetic resistance by facilitating the binding of the pioneer factor, Pu.1 and cofactor, Irf8, to nucleate new enhancers that regulate the expression of key survival genes. This enhancer switching results in the re-distribution of transcriptional co-activators, including Brd4, and provides the opportunity to disable their activity and overcome epigenetic resistance. Together these findings highlight key principles to help counteract non-genetic drug resistance.
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MESH Headings
- Animals
- Antineoplastic Agents/pharmacology
- Antineoplastic Agents/therapeutic use
- Bone Marrow/pathology
- CRISPR-Cas Systems/genetics
- Cell Line, Tumor
- Drug Resistance, Neoplasm/drug effects
- Epigenesis, Genetic/drug effects
- Female
- Gene Expression Regulation, Leukemic/drug effects
- HEK293 Cells
- Humans
- Kaplan-Meier Estimate
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/mortality
- Leukemia, Myeloid, Acute/pathology
- Mice
- Mice, Inbred C57BL
- Sequence Analysis, RNA
- Single-Cell Analysis
- Trans-Activators/antagonists & inhibitors
- Trans-Activators/genetics
- Trans-Activators/metabolism
- Transcription, Genetic/drug effects
- Treatment Outcome
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Charles C Bell
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Katie A Fennell
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Yih-Chih Chan
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Florian Rambow
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, KU Leuven, Leuven, Belgium
| | - Miriam M Yeung
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Dane Vassiliadis
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Luis Lara
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Paul Yeh
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
- Department of Haematology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | | | - Aljosja Rogiers
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, KU Leuven, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Brandon E Kremer
- Epigenetics DPU, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | - Olena Barbash
- Epigenetics DPU, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | - Helai P Mohammad
- Epigenetics DPU, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | - Timothy M Johanson
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Marian L Burr
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Arindam Dhar
- Epigenetics DPU, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | | | - Luyi Tian
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Dean S Tyler
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Laura MacPherson
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Junwei Shi
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Nathan Pinnawala
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Chun Yew Fong
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Anthony T Papenfuss
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Sean M Grimmond
- Centre for Cancer Research, University of Melbourne, Melbourne, VIC, Australia
| | - Sarah-Jane Dawson
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
- Centre for Cancer Research, University of Melbourne, Melbourne, VIC, Australia
| | - Rhys S Allan
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Ryan G Kruger
- Epigenetics DPU, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | | | - David L Goode
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Shalin H Naik
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Omer Gilan
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Enid Y N Lam
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, KU Leuven, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Rab K Prinjha
- Epigenetics DPU, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | - Mark A Dawson
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia.
- Department of Haematology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.
- Centre for Cancer Research, University of Melbourne, Melbourne, VIC, Australia.
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19
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Alidousty C, Baar T, Martelotto LG, Heydt C, Wagener S, Fassunke J, Duerbaum N, Scheel AH, Frank S, Holz B, Binot E, Kron A, Merkelbach‐Bruse S, Ihle MA, Wolf J, Buettner R, Schultheis AM. Genetic instability and recurrent MYC amplification in ALK-translocated NSCLC: a central role of TP53 mutations. J Pathol 2018; 246:67-76. [PMID: 29885057 PMCID: PMC6120547 DOI: 10.1002/path.5110] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 04/30/2018] [Accepted: 06/05/2018] [Indexed: 12/12/2022]
Abstract
The anaplastic lymphoma kinase (ALK) rearrangement defines a distinct molecular subtype of non-small cell lung cancer (NSCLC). Despite the excellent initial efficacy of ALK inhibitors in patients with ALK+ lung cancer, resistance occurs almost inevitably. To date, there is no reliable biomarker allowing the identification of patients at higher risk of relapse. Here, we analysed a subset of 53 ALK+ tumours with and without TP53 mutation and ALK+ NSCLC cell lines by NanoString nCounter technology. We found that the co-occurrence of early TP53 mutations in ALK+ NSCLC can lead to chromosomal instability: 24% of TP53-mutated patients showed amplifications of known cancer genes such as MYC (14%), CCND1 (10%), TERT (5%), BIRC2 (5%), ORAOV1 (5%), and YAP1 (5%). MYC-overexpressing ALK+ TP53-mutated cells had a proliferative advantage compared to wild-type cells. ChIP-Seq data revealed MYC-binding sites within the promoter region of EML4, and MYC overexpression in ALK+ TP53-mutated cells resulted in an upregulation of EML4-ALK, indicating a potential MYC-dependent resistance mechanism in patients with increased MYC copy number. Our study reveals that ALK+ NSCLC represents a more heterogeneous subgroup of tumours than initially thought, and that TP53 mutations in that particular cancer type define a subset of tumours that harbour chromosomal instability, leading to the co-occurrence of pathogenic aberrations. © 2018 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
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Affiliation(s)
| | - Till Baar
- University of Cologne, Faculty of Medicine, Institute of Medical Statistics and Computational BiologyCologneGermany
| | | | - Carina Heydt
- University Hospital Cologne, Institute of PathologyCologneGermany
| | - Svenja Wagener
- University Hospital Cologne, Institute of PathologyCologneGermany
| | - Jana Fassunke
- University Hospital Cologne, Institute of PathologyCologneGermany
| | - Nicolai Duerbaum
- University Hospital Cologne, Institute of PathologyCologneGermany
| | - Andreas H Scheel
- University Hospital Cologne, Institute of PathologyCologneGermany
| | - Sandra Frank
- University Hospital Cologne, Institute of PathologyCologneGermany
| | - Barbara Holz
- University Hospital Cologne, Institute of PathologyCologneGermany
| | - Elke Binot
- University Hospital Cologne, Institute of PathologyCologneGermany
| | - Anna Kron
- Network Genomic MedicineCologneGermany
| | | | - Michaela A Ihle
- University Hospital Cologne, Institute of PathologyCologneGermany
| | - Jürgen Wolf
- Network Genomic MedicineCologneGermany
- Lung Cancer Group Cologne, Department I for Internal MedicineUniversity Hospital of CologneCologneGermany
- Center for Integrated Oncology Cologne BonnGermany
| | - Reinhard Buettner
- University Hospital Cologne, Institute of PathologyCologneGermany
- Network Genomic MedicineCologneGermany
- Lung Cancer Group Cologne, Department I for Internal MedicineUniversity Hospital of CologneCologneGermany
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20
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Kim J, Geyer FC, Martelotto LG, Ng CKY, Lim RS, Selenica P, Li A, Pareja F, Fusco N, Edelweiss M, Mariani O, Badve S, Vincent-Salomon A, Norton L, Reis-Filho JS, Weigelt B. Abstract P2-05-03: Novel driver genetic alterations in MYB-NFIB-negative breast adenoid cystic carcinomas. Cancer Res 2018. [DOI: 10.1158/1538-7445.sabcs17-p2-05-03] [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
Introduction: Breast adenoid cystic carcinoma (AdCC) is a rare type of triple-negative breast cancer associated with an indolent clinical behavior. AdCCs provide a clear example of genotypic-phenotypic correlation with the majority harboring the MYB-NFIB fusion gene. In this study, we sought to identify alternative driver genetic alterations in breast AdCCs lacking the MYB-NFIB fusion gene.
Methods: Nucleic acids obtained from four breast AdCCs lacking the MYB-NFIB fusion gene as defined by reverse transcription (RT)-PCR and/or fluorescence in situ hybridization (FISH) were subjected to RNA-sequencing (n=3), whole-genome (n=2) and/or targeted (n=1) massively parallel sequencing. Sequencing data were analyzed using state-of-the-art bioinformatics algorithms, and potential alternative driver genetic alterations were validated using orthogonal sequencing and molecular pathology methods.
Results: RNA-sequencing revealed the presence of MYBL1-ACTN1 or MYBL1-NFIB fusion genes in two breast AdCCs, which were validated by whole-genome sequencing and/or MYBL1 FISH analysis. Both MYBL1 fusion gene-positive cases were found to overexpress MYBL1 as defined by quantitative RT-PCR analysis. In the third MYB-NFIB-negative breast AdCC studied, a high-level MYB gene amplification coupled with overexpression of MYB at the mRNA and protein levels was identified. In the fourth breast AdCC, which expressed high levels of MYB, whole-genome and RNA-sequencing revealed no definite alternative driver alteration, however, a MYBL2 intronic mutation was found in this case, which was associated with high levels of MYBL2 mRNA expression. In this case, single sample gene set enrichment analysis revealed activation of pathways similar to those activated in AdCCs harboring the MYB-NFIB or MYBL1 fusions genes.
Conclusion: We demonstrate that in breast AdCCs lacking the MYB-NFIB fusion gene MYBL1 rearrangements and MYB amplification are likely alternative driver genetic events. Given that activation of MYB/MYBL1 and their downstream targets can be driven by the MYB-NFIB fusion gene, MYBL1 rearrangements, MYB amplification or other yet to be validated mechanisms (e.g. MYBL2 non-coding mutations), our findings further suggest that breast AdCCs constitute a convergent phenotype.
Citation Format: Kim J, Geyer FC, Martelotto LG, Ng CKY, Lim RS, Selenica P, Li A, Pareja F, Fusco N, Edelweiss M, Mariani O, Badve S, Vincent-Salomon A, Norton L, Reis-Filho JS, Weigelt B. Novel driver genetic alterations in MYB-NFIB-negative breast adenoid cystic carcinomas [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P2-05-03.
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Affiliation(s)
- J Kim
- Memorial Sloan Kettering Cancer Center, New York, NY; Institut Curie, Paris, France; IU Health Pathology Laboratory, Indiana University, Indianapolis, IN
| | - FC Geyer
- Memorial Sloan Kettering Cancer Center, New York, NY; Institut Curie, Paris, France; IU Health Pathology Laboratory, Indiana University, Indianapolis, IN
| | - LG Martelotto
- Memorial Sloan Kettering Cancer Center, New York, NY; Institut Curie, Paris, France; IU Health Pathology Laboratory, Indiana University, Indianapolis, IN
| | - CKY Ng
- Memorial Sloan Kettering Cancer Center, New York, NY; Institut Curie, Paris, France; IU Health Pathology Laboratory, Indiana University, Indianapolis, IN
| | - RS Lim
- Memorial Sloan Kettering Cancer Center, New York, NY; Institut Curie, Paris, France; IU Health Pathology Laboratory, Indiana University, Indianapolis, IN
| | - P Selenica
- Memorial Sloan Kettering Cancer Center, New York, NY; Institut Curie, Paris, France; IU Health Pathology Laboratory, Indiana University, Indianapolis, IN
| | - A Li
- Memorial Sloan Kettering Cancer Center, New York, NY; Institut Curie, Paris, France; IU Health Pathology Laboratory, Indiana University, Indianapolis, IN
| | - F Pareja
- Memorial Sloan Kettering Cancer Center, New York, NY; Institut Curie, Paris, France; IU Health Pathology Laboratory, Indiana University, Indianapolis, IN
| | - N Fusco
- Memorial Sloan Kettering Cancer Center, New York, NY; Institut Curie, Paris, France; IU Health Pathology Laboratory, Indiana University, Indianapolis, IN
| | - M Edelweiss
- Memorial Sloan Kettering Cancer Center, New York, NY; Institut Curie, Paris, France; IU Health Pathology Laboratory, Indiana University, Indianapolis, IN
| | - O Mariani
- Memorial Sloan Kettering Cancer Center, New York, NY; Institut Curie, Paris, France; IU Health Pathology Laboratory, Indiana University, Indianapolis, IN
| | - S Badve
- Memorial Sloan Kettering Cancer Center, New York, NY; Institut Curie, Paris, France; IU Health Pathology Laboratory, Indiana University, Indianapolis, IN
| | - A Vincent-Salomon
- Memorial Sloan Kettering Cancer Center, New York, NY; Institut Curie, Paris, France; IU Health Pathology Laboratory, Indiana University, Indianapolis, IN
| | - L Norton
- Memorial Sloan Kettering Cancer Center, New York, NY; Institut Curie, Paris, France; IU Health Pathology Laboratory, Indiana University, Indianapolis, IN
| | - JS Reis-Filho
- Memorial Sloan Kettering Cancer Center, New York, NY; Institut Curie, Paris, France; IU Health Pathology Laboratory, Indiana University, Indianapolis, IN
| | - B Weigelt
- Memorial Sloan Kettering Cancer Center, New York, NY; Institut Curie, Paris, France; IU Health Pathology Laboratory, Indiana University, Indianapolis, IN
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21
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Geyer FC, Li A, Papanastasiou AD, Smith A, Selenica P, Burke KA, Edelweiss M, Wen HC, Piscuoglio S, Schultheis AM, Martelotto LG, Pareja F, Kumar R, Brandes A, Lozada J, Macedo GS, Muenst S, Terracciano LM, Jungbluth A, Foschini MP, Wen HY, Brogi E, Palazzo J, Rubin BP, Ng CKY, Norton L, Varga Z, Ellis IO, Rakha E, Chandarlapatty S, Weigelt B, Reis-Filho JS. Abstract PD4-13: Estrogen receptor-negative breast adenomyoepitheliomas are driven by co-occurring HRAS hotspot and PI3K pathway gene mutations: A genetic and functional analysis. Cancer Res 2018. [DOI: 10.1158/1538-7445.sabcs17-pd4-13] [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
Introduction:Adenomyoepithelioma (AME) of the breast is a rare biphasic tumor, characterized by epithelial and myoepithelial differentiation. Although AMEs have an indolent clinical course, a subset may progress to carcinoma and metastasize. We sought to define the mutational landscape of AMEs and investigate the functional impact of recurrent pathogenic mutations identified in these tumors.
Methods: Thirty-one AMEs were subjected to whole-exome sequencing (WES, n=8) or massively parallel sequencing targeting all coding regions of 410 key cancer genes and intronic and regulatory regions of selected genes (n=23). Somatic genetic alterations were defined using state-of-the-art bioinformatics algorithms. In an additional set of 12 AMEs, Sanger sequencing analysis of HRAS, PIK3CA and AKT1 was performed. Non-tumorigenic estrogen receptor (ER)-negative mammary epithelial cells (i.e. MCF10A, MCF10A with a PIK3CA H1047R mutation knock-in and MCF12A) were utilized for functional studies using both conventional monolayer and three-dimensional (3D) culture assays.
Results: 27 (63%) and 16 (37%) AMEs were ER-positive and ER-negative, respectively. ER-negativity was significantly associated with histologic features predictive of a more aggressive behavior, with a higher number of mutations and copy number alterations, and with a distinct mutational profile as compared to ER-positive AMEs. Of the 27 ER-positive AMEs, 12 cases (44%) harbored PIK3CA hotspot mutations, and 5 PIK3CA wild-type cases displayed E17K AKT1 hotspot mutations. By contrast, of the 16 ER-negative AMEs, 9 (56%), 9 (56%) and 3 (19%) harbored HRAS, PIK3CA (mostly E545K and H1047R hotspots) and PIK3R1 mutations, respectively. Strikingly, all HRAS mutations were restricted to ER-negative AMEs, affected the hotspot codon Q61 (Q61R/K), and all but one co-occurred with PIK3CA or PIK3R1 mutations. In addition, HRAS Q61 hotspot mutations were significantly associated with necrosis (p=0.01) and high mitotic rates (p=0.03). CDKN2A homozygous deletions were also detected only in ER-negative AMEs (19%) and found to be significantly associated with progression to carcinoma (p=0.001). Forced expression of HRAS Q61R in MCF10A and MCF12A cells resulted in i) increased proliferation and transformation, ii) an irregular growth pattern in 3D organotypic cell cultures, iii) partial loss of the epithelial phenotype, and iv) acquisition of myoepithelial differentiation, which was more overt in PIK3CA-mutant MCF10A cells. HRAS Q61Rinduced hyperactivation of the PI3K pathway, but both PI3K and MAPK pathways likely contributed to the RAS-mediated proliferation, which was completely arrested by combined AKT and MEK inhibition.
Conclusion: AMEs are phenotypically and genetically heterogeneous. Whilst pathogenic mutations in PI3K pathway-related genes occur across the spectrum of lesions, HRAS Q61 hotspot mutations are restricted to ER-negative AMEs. Our genomic and functional analyses indicate that HRAS Q61 mutations are driver events in the pathogenesis of ER-negative AMEs and, in conjunction with mutant PIK3CA, may lead to the acquisition of myoepithelial differentiation in breast epithelial cells.
Citation Format: Geyer FC, Li A, Papanastasiou AD, Smith A, Selenica P, Burke KA, Edelweiss M, Wen H-C, Piscuoglio S, Schultheis AM, Martelotto LG, Pareja F, Kumar R, Brandes A, Lozada J, Macedo GS, Muenst S, Terracciano LM, Jungbluth A, Foschini MP, Wen HY, Brogi E, Palazzo J, Rubin BP, Ng CKY, Norton L, Varga Z, Ellis IO, Rakha E, Chandarlapatty S, Weigelt B, Reis-Filho JS. Estrogen receptor-negative breast adenomyoepitheliomas are driven by co-occurring HRAS hotspot and PI3K pathway gene mutations: A genetic and functional analysis [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr PD4-13.
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Affiliation(s)
- FC Geyer
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - A Li
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - AD Papanastasiou
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - A Smith
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - P Selenica
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - KA Burke
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - M Edelweiss
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - H-C Wen
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - S Piscuoglio
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - AM Schultheis
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - LG Martelotto
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - F Pareja
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - R Kumar
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - A Brandes
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - J Lozada
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - GS Macedo
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - S Muenst
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - LM Terracciano
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - A Jungbluth
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - MP Foschini
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - HY Wen
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - E Brogi
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - J Palazzo
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - BP Rubin
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - CKY Ng
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - L Norton
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - Z Varga
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - IO Ellis
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - E Rakha
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - S Chandarlapatty
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - B Weigelt
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
| | - JS Reis-Filho
- Memorial Sloan Kettering Cancer Center, New York, NY; University of Basel, Basel, Switzerland; Bellaria Hospital, University of Bologna, Bologna, Italy; Thomas Jefferson University Hospital, Philadelphia, PA; Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH; Institute of Surgical Pathology, University Hospital Zurich, Zurich, Switzerland; University of Nottingham, Nottingham, United Kingdom
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22
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Kim J, Geyer FC, Martelotto LG, Ng CKY, Lim RS, Selenica P, Li A, Pareja F, Fusco N, Edelweiss M, Kumar R, Gularte-Merida R, Forbes AN, Khurana E, Mariani O, Badve S, Vincent-Salomon A, Norton L, Reis-Filho JS, Weigelt B. MYBL1 rearrangements and MYB amplification in breast adenoid cystic carcinomas lacking the MYB-NFIB fusion gene. J Pathol 2018; 244:143-150. [PMID: 29149504 PMCID: PMC5839480 DOI: 10.1002/path.5006] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [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: 06/02/2017] [Revised: 11/03/2017] [Accepted: 11/11/2017] [Indexed: 01/14/2023]
Abstract
Breast adenoid cystic carcinoma (AdCC), a rare type of triple-negative breast cancer, has been shown to be driven by MYB pathway activation, most often underpinned by the MYB-NFIB fusion gene. Alternative genetic mechanisms, such as MYBL1 rearrangements, have been reported in MYB-NFIB-negative salivary gland AdCCs. Here we report on the molecular characterization by massively parallel sequencing of four breast AdCCs lacking the MYB-NFIB fusion gene. In two cases, we identified MYBL1 rearrangements (MYBL1-ACTN1 and MYBL1-NFIB), which were associated with MYBL1 overexpression. A third AdCC harboured a high-level MYB amplification, which resulted in MYB overexpression at the mRNA and protein levels. RNA-sequencing and whole-genome sequencing revealed no definite alternative driver in the fourth AdCC studied, despite high levels of MYB expression and the activation of pathways similar to those activated in MYB-NFIB-positive AdCCs. In this case, a deletion encompassing the last intron and part of exon 15 of MYB, including the binding site of ERG-1, a transcription factor that may downregulate MYB, and the exon 15 splice site, was detected. In conclusion, we demonstrate that MYBL1 rearrangements and MYB amplification probably constitute alternative genetic drivers of breast AdCCs, functioning through MYBL1 or MYB overexpression. These observations emphasize that breast AdCCs probably constitute a convergent phenotype, whereby activation of MYB and MYBL1 and their downstream targets can be driven by the MYB-NFIB fusion gene, MYBL1 rearrangements, MYB amplification, or other yet to be identified mechanisms. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Jisun Kim
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New
York, NY, USA
- Department of Surgery, Ulsan University, College of Medicine, Asan
Medical Center, Seoul, Korea
| | - Felipe C. Geyer
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New
York, NY, USA
| | - Luciano G Martelotto
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New
York, NY, USA
| | - Charlotte K Y Ng
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New
York, NY, USA
- Institute of Pathology, University Hospital Basel and Department of
Biomedicine, University of Basel, Basel, Switzerland
| | - Raymond S Lim
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New
York, NY, USA
| | - Pier Selenica
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New
York, NY, USA
| | - Anqi Li
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New
York, NY, USA
| | - Fresia Pareja
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New
York, NY, USA
| | - Nicola Fusco
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New
York, NY, USA
- Division of Pathology, Fondazione IRCCS Ca’Granda Ospedale
Maggiore Policlinico, University of Milan, Milan, Italy
| | - Marcia Edelweiss
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New
York, NY, USA
| | - Rahul Kumar
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New
York, NY, USA
| | | | - Andre N Forbes
- Institute for Computational Medicine and Department of Physiology
and Biophysics, Weill Cornell Medical College, New York, NY, USA
| | - Ekta Khurana
- Institute for Computational Medicine and Department of Physiology
and Biophysics, Weill Cornell Medical College, New York, NY, USA
| | | | - Sunil Badve
- IU Health Pathology Laboratory, Indiana University, Indianapolis,
IN, USA
| | | | - Larry Norton
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New
York, NY, USA
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New
York, NY, USA
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New
York, NY, USA
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23
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Weigelt B, Comino-Méndez I, de Bruijn I, Tian L, Meisel JL, García-Murillas I, Fribbens C, Cutts R, Martelotto LG, Ng CKY, Lim RS, Selenica P, Piscuoglio S, Aghajanian C, Norton L, Murali R, Hyman DM, Borsu L, Arcila ME, Konner J, Reis-Filho JS, Greenberg RA, Robson ME, Turner NC. Diverse BRCA1 and BRCA2 Reversion Mutations in Circulating Cell-Free DNA of Therapy-Resistant Breast or Ovarian Cancer. Clin Cancer Res 2017. [PMID: 28765325 DOI: 10.1158/1078-0432.ccr-17-0544] [] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Purpose: Resistance to platinum-based chemotherapy or PARP inhibition in germline BRCA1 or BRCA2 mutation carriers may occur through somatic reversion mutations or intragenic deletions that restore BRCA1 or BRCA2 function. We assessed whether BRCA1/2 reversion mutations could be identified in circulating cell-free DNA (cfDNA) of patients with ovarian or breast cancer previously treated with platinum and/or PARP inhibitors.Experimental Design: cfDNA from 24 prospectively accrued patients with germline BRCA1 or BRCA2 mutations, including 19 patients with platinum-resistant/refractory ovarian cancer and five patients with platinum and/or PARP inhibitor pretreated metastatic breast cancer, was subjected to massively parallel sequencing targeting all exons of 141 genes and all exons and introns of BRCA1 and BRCA2 Functional studies were performed to assess the impact of the putative BRCA1/2 reversion mutations on BRCA1/2 function.Results: Diverse and often polyclonal putative BRCA1 or BRCA2 reversion mutations were identified in cfDNA from four patients with ovarian cancer (21%) and from two patients with breast cancer (40%). BRCA2 reversion mutations were detected in cfDNA prior to PARP inhibitor treatment in a patient with breast cancer who did not respond to treatment and were enriched in plasma samples after PARP inhibitor therapy. Foci formation and immunoprecipitation assays suggest that a subset of the putative reversion mutations restored BRCA1/2 function.Conclusions: Putative BRCA1/2 reversion mutations can be detected by cfDNA sequencing analysis in patients with ovarian and breast cancer. Our findings warrant further investigation of cfDNA sequencing to identify putative BRCA1/2 reversion mutations and to aid the selection of patients for PARP inhibition therapy. Clin Cancer Res; 23(21); 6708-20. ©2017 AACR.
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Affiliation(s)
- Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
| | - Iñaki Comino-Méndez
- Breast Cancer Now Research Centre, Institute of Cancer Research, London, United Kingdom
| | - Ino de Bruijn
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Lei Tian
- Department of Cancer Biology, Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jane L Meisel
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, Georgia
| | - Isaac García-Murillas
- Breast Cancer Now Research Centre, Institute of Cancer Research, London, United Kingdom
| | - Charlotte Fribbens
- Breast Cancer Now Research Centre, Institute of Cancer Research, London, United Kingdom.,Breast Unit, The Royal Marsden Hospital, Fulham Road, London, United Kingdom
| | - Ros Cutts
- Breast Cancer Now Research Centre, Institute of Cancer Research, London, United Kingdom
| | - Luciano G Martelotto
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Charlotte K Y Ng
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.,Institute of Pathology, University Hospital Basel, Basel, Switzerland.,Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Raymond S Lim
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Pier Selenica
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Salvatore Piscuoglio
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.,Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Carol Aghajanian
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Larry Norton
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Rajmohan Murali
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David M Hyman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Laetitia Borsu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Maria E Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jason Konner
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Roger A Greenberg
- Department of Cancer Biology, Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Mark E Robson
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nicholas C Turner
- Breast Cancer Now Research Centre, Institute of Cancer Research, London, United Kingdom. .,Breast Unit, The Royal Marsden Hospital, Fulham Road, London, United Kingdom
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24
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Weigelt B, Comino-Méndez I, de Bruijn I, Tian L, Meisel JL, García-Murillas I, Fribbens C, Cutts R, Martelotto LG, Ng CKY, Lim RS, Selenica P, Piscuoglio S, Aghajanian C, Norton L, Murali R, Hyman DM, Borsu L, Arcila ME, Konner J, Reis-Filho JS, Greenberg RA, Robson ME, Turner NC. Diverse BRCA1 and BRCA2 Reversion Mutations in Circulating Cell-Free DNA of Therapy-Resistant Breast or Ovarian Cancer. Clin Cancer Res 2017; 23:6708-6720. [PMID: 28765325 DOI: 10.1158/1078-0432.ccr-17-0544] [Citation(s) in RCA: 172] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 05/24/2017] [Accepted: 07/28/2017] [Indexed: 01/13/2023]
Abstract
Purpose: Resistance to platinum-based chemotherapy or PARP inhibition in germline BRCA1 or BRCA2 mutation carriers may occur through somatic reversion mutations or intragenic deletions that restore BRCA1 or BRCA2 function. We assessed whether BRCA1/2 reversion mutations could be identified in circulating cell-free DNA (cfDNA) of patients with ovarian or breast cancer previously treated with platinum and/or PARP inhibitors.Experimental Design: cfDNA from 24 prospectively accrued patients with germline BRCA1 or BRCA2 mutations, including 19 patients with platinum-resistant/refractory ovarian cancer and five patients with platinum and/or PARP inhibitor pretreated metastatic breast cancer, was subjected to massively parallel sequencing targeting all exons of 141 genes and all exons and introns of BRCA1 and BRCA2 Functional studies were performed to assess the impact of the putative BRCA1/2 reversion mutations on BRCA1/2 function.Results: Diverse and often polyclonal putative BRCA1 or BRCA2 reversion mutations were identified in cfDNA from four patients with ovarian cancer (21%) and from two patients with breast cancer (40%). BRCA2 reversion mutations were detected in cfDNA prior to PARP inhibitor treatment in a patient with breast cancer who did not respond to treatment and were enriched in plasma samples after PARP inhibitor therapy. Foci formation and immunoprecipitation assays suggest that a subset of the putative reversion mutations restored BRCA1/2 function.Conclusions: Putative BRCA1/2 reversion mutations can be detected by cfDNA sequencing analysis in patients with ovarian and breast cancer. Our findings warrant further investigation of cfDNA sequencing to identify putative BRCA1/2 reversion mutations and to aid the selection of patients for PARP inhibition therapy. Clin Cancer Res; 23(21); 6708-20. ©2017 AACR.
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Affiliation(s)
- Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
| | - Iñaki Comino-Méndez
- Breast Cancer Now Research Centre, Institute of Cancer Research, London, United Kingdom
| | - Ino de Bruijn
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Lei Tian
- Department of Cancer Biology, Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jane L Meisel
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, Georgia
| | - Isaac García-Murillas
- Breast Cancer Now Research Centre, Institute of Cancer Research, London, United Kingdom
| | - Charlotte Fribbens
- Breast Cancer Now Research Centre, Institute of Cancer Research, London, United Kingdom.,Breast Unit, The Royal Marsden Hospital, Fulham Road, London, United Kingdom
| | - Ros Cutts
- Breast Cancer Now Research Centre, Institute of Cancer Research, London, United Kingdom
| | - Luciano G Martelotto
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Charlotte K Y Ng
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.,Institute of Pathology, University Hospital Basel, Basel, Switzerland.,Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Raymond S Lim
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Pier Selenica
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Salvatore Piscuoglio
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.,Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Carol Aghajanian
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Larry Norton
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Rajmohan Murali
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David M Hyman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Laetitia Borsu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Maria E Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jason Konner
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Roger A Greenberg
- Department of Cancer Biology, Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Mark E Robson
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nicholas C Turner
- Breast Cancer Now Research Centre, Institute of Cancer Research, London, United Kingdom. .,Breast Unit, The Royal Marsden Hospital, Fulham Road, London, United Kingdom
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25
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Geyer FC, Burke KA, Li A, Papanastatiou AD, Pareja F, Schulteis AS, Ng CK, Piscuoglio S, Edelweiss M, Martelotto LG, Selenica P, Filippo MR, Macedo GS, Jungbluth A, Wen HY, Palazzo J, Varga Z, Rakha E, Ellis IO, Rubin B, Weigelt B, Reis-Filho JS. Abstract 3379: Massively parallel sequencing analysis of breast adenomyoepitheliomas reveals the heterogeneity of the disease and identifies a subset driven by HRAS hotspot mutations. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-3379] [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
Adenomyoepithelioma (AME) is a rare biphasic proliferative breast lesion, which may resemble salivary gland epithelial-myoepithelial carcinomas (EMCs). Most AMEs have an indolent clinical course, but malignant transformation and local and distant recurrences have been reported. We sought to define the mutational landscape of AMEs and investigate the functional impact of recurrent likely pathogenic mutations identified in these tumors. Nineteen AMEs were subjected to whole-exome massively parallel sequencing (MPS, n=7) or targeted capture MPS using MSK-IMPACT assay (n=12). Somatic genetic alterations and the cancer cell fraction of mutations were defined using state-of-the-art bioinformatics algorithms. Selected genes (i.e. HRAS and PIK3CA) were subjected to Sanger sequencing in a series of 17 additional AMEs (total n=36). Non-tumorigenic mammary epithelial cells (i.e. MCF10A, MCF10A with the PIK3CAH1047R mutation and MCF12A), which are estrogen receptor (ER)-negative, were utilized for 2D and 3D functional studies. Of 36 cases, 22 were ER-positive and 14 were ER-negative. MPS analysis revealed a low mutation burden and HRASQ61 and PIK3CA hotspot mutations in 6/19 (32%) and 11/19 (58%) AMEs, respectively. All HRASQ61 and all but one PIK3CA mutations were clonal. ER-positive and ER-negative AMEs were fundamentally histologically and genetically distinct. Whilst ER-positive AMEs displayed recurrent PIK3CA mutations (50%, 11/22) but lacked HRAS mutations, ER-negative AMEs displayed, in addition to PIK3CA mutations (57%, 8/14), recurrent HRASQ61 mutations (57%, 8/14). HRASQ61 mutations co-occurred with PIK3CA mutations (50%, 4/8), PIK3R1 deletions (12.5%, 1/8) and/or CDKN2A homozygous deletions (25%, 2/8). HRASQ61 mutations, but not PIK3CA mutations, were significantly associated with ER-negativity (100% vs 21%), concurrent carcinoma (50% vs 7%), axillary metastases (38% vs 0%), high proliferation (63% vs 4%), necrosis (63% vs 11%) and nuclear pleomorphism (75% vs 29%). In vitro forced HRASQ61R expression in MCF10A and MCF12A cells resulted in increased proliferation and transformation. In 3D organotypic cell cultures, forced HRASQ61R resulted in a highly disorganized growth pattern, a partial loss of epithelial phenotype and acquisition of aberrant myoepithelial differentiation, which was more overt in PIK3CA-mutant MCF10A cells. In conclusion, AMEs are phenotypically and genetically heterogeneous. Whilst PIK3CA hotspot mutations occur across the spectrum of lesions, HRASQ61 hotspot mutations are restricted to ER-negative AMEs, which should arguably be classified as breast EMCs. Our genomic and functional analyses are consistent with the notion that HRASQ61 mutations are driver events in the pathogenesis of ER-negative AMEs and may be sufficient for the acquisition of myoepithelial differentiation in breast cells.
Citation Format: Felipe C. Geyer, Kathleen A. Burke, Anqi Li, Anastasios D. Papanastatiou, Fresia Pareja, Anne S. Schulteis, Charlotte K. Ng, Salvatore Piscuoglio, Marcia Edelweiss, Luciano G. Martelotto, Pier Selenica, Maria R. Filippo, Gabriel S. Macedo, Achim Jungbluth, Hannah Y. Wen, Juan Palazzo, Zsuzsanna Varga, Emad Rakha, Ian O. Ellis, Brian Rubin, Britta Weigelt, Jorge S. Reis-Filho. Massively parallel sequencing analysis of breast adenomyoepitheliomas reveals the heterogeneity of the disease and identifies a subset driven by HRAS hotspot mutations [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 3379. doi:10.1158/1538-7445.AM2017-3379
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Affiliation(s)
| | | | - Anqi Li
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Fresia Pareja
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | | | | - Pier Selenica
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | - Hannah Y. Wen
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Juan Palazzo
- 2Thomas Jefferson University Hospital, Philadelphia, Philadelphia, PA
| | | | - Emad Rakha
- 4Nottingham University Hospitals, Nottingham, United Kingdom
| | - Ian O. Ellis
- 4Nottingham University Hospitals, Nottingham, United Kingdom
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26
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Mutter RW, Riaz N, Ng CK, Delsite R, Piscuoglio S, Edelweiss M, Martelotto LG, Sakr RA, King TA, Giri DD, Drobnjak M, Brogi E, Bindra R, Bernheim G, Lim RS, Blecua P, Desrichard A, Higginson D, Towers R, Jiang R, Lee W, Weigelt B, Reis-Filho JS, Powell SN. Bi-allelic alterations in DNA repair genes underpin homologous recombination DNA repair defects in breast cancer. J Pathol 2017; 242:165-177. [PMID: 28299801 DOI: 10.1002/path.4890] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [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: 10/09/2016] [Revised: 02/06/2017] [Accepted: 02/20/2017] [Indexed: 01/07/2023]
Abstract
Homologous recombination (HR) DNA repair-deficient (HRD) breast cancers have been shown to be sensitive to DNA repair targeted therapies. Burgeoning evidence suggests that sporadic breast cancers, lacking germline BRCA1/BRCA2 mutations, may also be HRD. We developed a functional ex vivo RAD51-based test to identify HRD primary breast cancers. An integrated approach examining methylation, gene expression, and whole-exome sequencing was employed to ascertain the aetiology of HRD. Functional HRD breast cancers displayed genomic features of lack of competent HR, including large-scale state transitions and specific mutational signatures. Somatic and/or germline genetic alterations resulting in bi-allelic loss-of-function of HR genes underpinned functional HRD in 89% of cases, and were observed in only one of the 15 HR-proficient samples tested. These findings indicate the importance of a comprehensive genetic assessment of bi-allelic alterations in the HR pathway to deliver a precision medicine-based approach to select patients for therapies targeting tumour-specific DNA repair defects. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Robert W Mutter
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Radiation Oncology, Mayo Clinic, Rochester, MN, USA
| | - Nadeem Riaz
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Charlotte Ky Ng
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rob Delsite
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Salvatore Piscuoglio
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marcia Edelweiss
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Luciano G Martelotto
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rita A Sakr
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tari A King
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dilip D Giri
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria Drobnjak
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Edi Brogi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ranjit Bindra
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Radiation Oncology, Yale, New Haven, CT, USA
| | - Giana Bernheim
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Raymond S Lim
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pedro Blecua
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexis Desrichard
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dan Higginson
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Russell Towers
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ruomu Jiang
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - William Lee
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Simon N Powell
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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27
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Spraggon L, Martelotto LG, Hmeljak J, Hitchman TD, Wang J, Wang L, Slotkin EK, Fan PD, Reis-Filho JS, Ladanyi M. Generation of conditional oncogenic chromosomal translocations using CRISPR-Cas9 genomic editing and homology-directed repair. J Pathol 2017; 242:102-112. [PMID: 28188619 DOI: 10.1002/path.4883] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [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: 01/17/2017] [Revised: 01/27/2017] [Accepted: 01/30/2017] [Indexed: 01/11/2023]
Abstract
Chromosomal rearrangements encoding oncogenic fusion proteins are found in a wide variety of malignancies. The use of programmable nucleases to generate specific double-strand breaks in endogenous loci, followed by non-homologous end joining DNA repair, has allowed several of these translocations to be generated as constitutively expressed fusion genes within a cell population. Here, we describe a novel approach that combines CRISPR-Cas9 technology with homology-directed repair to engineer, capture, and modulate the expression of chromosomal translocation products in a human cell line. We have applied this approach to the genetic modelling of t(11;22)(q24;q12) and t(11;22)(p13;q12), translocation products of the EWSR1 gene and its 3' fusion partners FLI1 and WT1, present in Ewing's sarcoma and desmoplastic small round cell tumour, respectively. Our innovative approach allows for temporal control of the expression of engineered endogenous chromosomal rearrangements, and provides a means to generate models to study tumours driven by fusion genes. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Lee Spraggon
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Luciano G Martelotto
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Julija Hmeljak
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tyler D Hitchman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jiang Wang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lu Wang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Emily K Slotkin
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pang-Dian Fan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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28
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Geyer FC, Burke KA, Macedo GS, Piscuoglio S, Ng CK, Martelotto LG, Papanastatiou AD, De Filippo MR, Schultheis AM, Brogi E, Robson M, Wen YH, Weigelt B, Schnitt SJ, Tung N, Reis-Filho JS. Abstract S2-02: The landscape of somatic genetic alterations in BRCA1 and BRCA2 breast cancers. Cancer Res 2017. [DOI: 10.1158/1538-7445.sabcs16-s2-02] [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
Introduction: Women carrying BRCA1 or BRCA2 germline mutations have a 45-80% lifetime risk of developing breast cancer (BC). BRCA1 and BRCA2 are perceived as bona fide tumor suppressor genes, whereby bi-allelic inactivation in tumor cells is required for tumorigenesis. Recent studies have indicated that loss of heterozygosity (LOH) of the wild-type allele of BRCA1 may be heterogeneous and constitute a late event. Therefore, additional somatic events prior to full BRCA1/2 inactivation may be required for tumorigenesis. Given that the somatic events that result in the development of BRCA1/2-BCs and their chronology are not understood, here we sought to define the genomic landscape of BRCA1/2-BCs and whether LOH of BRCA1/2 wild-type allele and/or mutations affecting additional tumor suppressor genes would be clonal or subclonal in these cancers.
Methods: We retrieved 29 BRCA1-BCs and 10 BRCA2-BCs from the Pathology Departments of the authors' institutions. DNA extracted from microdissected tumor and normal breast samples was subjected to targeted capture massively parallel sequencing using either the MSK-IMPACT assay or an assay targeting all exons of 254 genes recurrently mutated in BC or related to DNA repair. Somatic single nucleotide variants, small insertions and deletions and copy number alterations affecting genes present in both sequencing assays (111 genes) were defined using state-of-the-art bioinformatics algorithms. ABSOLUTE and FACETS were employed to define clonal (i.e. present virtually in 100% of the cancer cells of a given case) and subclonal mutations and the presence of LOH of the BRCA1 and BRCA2 wild-type alleles.
Results: Our analysis revealed bi-allelic inactivation of BRCA1 in 28 of 29 BRCA1-BCs (93% harbored LOH of the BRCA1 wild-type allele and 3% harbored a second somatic BRCA1 pathogenic mutation). The only BRCA1-BC lacking bi-allelic inactivation of BRCA1 was an estrogen receptor-positive lobular carcinoma, lacking genomic features consistent with homologous recombination DNA repair defects, diagnosed at 62 years of age. Bi-allelic inactivation of BRCA2 was found in all cases (100% of harbored LOH of the BRCA2 wild-type allele). A clonal somatic 'second hit' resulting in bi-allelic inactivation of BRCA1 or BRCA2 was detected in 76% and 100% of BRCA1-BCs and BRCA2-BCs, respectively. In BRCA1-BCs, TP53 mutations were detected in 76% of cases, and these mutations were found to be clonal in 58% of cases. The repertoire of somatic mutations affecting BRCA1-BCs included clonal somatic mutations or homozygous deletions of known tumor suppressor genes, such as PTEN, RB1, CDKN2A and NF1. In contrast, only 10% of the BRCA2-BCs harbored TP53 somatic mutations. Though clonal somatic mutations in several cancer genes were detected, 40% of BRCA2-BCs had no mutations affecting the cancer genes analyzed.
Conclusions: Bi-allelic inactivation of BRCA1 and BRCA2 are frequent events in BRCA1-BCs and BRCA2-BCs, respectively. In a subset of BRCA1-BCs, however, the second 'hit' appeared to be subclonal, whereas mutations affecting TP53 and other tumor suppressor genes were clonal, supporting the notion that at least in a subset of these tumors, loss of the wild-type allele of BRCA1 may be preceded by inactivation of another tumor suppressor gene.
Citation Format: Geyer FC, Burke KA, Macedo GS, Piscuoglio S, Ng CK, Martelotto LG, Papanastatiou AD, De Filippo MR, Schultheis AM, Brogi E, Robson M, Wen YH, Weigelt B, Schnitt SJ, Tung N, Reis-Filho JS. The landscape of somatic genetic alterations in BRCA1 and BRCA2 breast cancers [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr S2-02.
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Affiliation(s)
- FC Geyer
- Memorial Sloan Kettering Cancer Center, New York, NY; Beth Israel Deaconess Medical School, Boston, MA
| | - KA Burke
- Memorial Sloan Kettering Cancer Center, New York, NY; Beth Israel Deaconess Medical School, Boston, MA
| | - GS Macedo
- Memorial Sloan Kettering Cancer Center, New York, NY; Beth Israel Deaconess Medical School, Boston, MA
| | - S Piscuoglio
- Memorial Sloan Kettering Cancer Center, New York, NY; Beth Israel Deaconess Medical School, Boston, MA
| | - CK Ng
- Memorial Sloan Kettering Cancer Center, New York, NY; Beth Israel Deaconess Medical School, Boston, MA
| | - LG Martelotto
- Memorial Sloan Kettering Cancer Center, New York, NY; Beth Israel Deaconess Medical School, Boston, MA
| | - AD Papanastatiou
- Memorial Sloan Kettering Cancer Center, New York, NY; Beth Israel Deaconess Medical School, Boston, MA
| | - MR De Filippo
- Memorial Sloan Kettering Cancer Center, New York, NY; Beth Israel Deaconess Medical School, Boston, MA
| | - AM Schultheis
- Memorial Sloan Kettering Cancer Center, New York, NY; Beth Israel Deaconess Medical School, Boston, MA
| | - E Brogi
- Memorial Sloan Kettering Cancer Center, New York, NY; Beth Israel Deaconess Medical School, Boston, MA
| | - M Robson
- Memorial Sloan Kettering Cancer Center, New York, NY; Beth Israel Deaconess Medical School, Boston, MA
| | - YH Wen
- Memorial Sloan Kettering Cancer Center, New York, NY; Beth Israel Deaconess Medical School, Boston, MA
| | - B Weigelt
- Memorial Sloan Kettering Cancer Center, New York, NY; Beth Israel Deaconess Medical School, Boston, MA
| | - SJ Schnitt
- Memorial Sloan Kettering Cancer Center, New York, NY; Beth Israel Deaconess Medical School, Boston, MA
| | - N Tung
- Memorial Sloan Kettering Cancer Center, New York, NY; Beth Israel Deaconess Medical School, Boston, MA
| | - JS Reis-Filho
- Memorial Sloan Kettering Cancer Center, New York, NY; Beth Israel Deaconess Medical School, Boston, MA
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29
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Martelotto LG, Baslan T, Kendall J, Geyer FC, Burke KA, Spraggon L, Piscuoglio S, Chadalavada K, Nanjangud G, Ng CKY, Moody P, D'Italia S, Rodgers L, Cox H, da Cruz Paula A, Stepansky A, Schizas M, Wen HY, King TA, Norton L, Weigelt B, Hicks JB, Reis-Filho JS. Whole-genome single-cell copy number profiling from formalin-fixed paraffin-embedded samples. Nat Med 2017; 23:376-385. [PMID: 28165479 PMCID: PMC5608257 DOI: 10.1038/nm.4279] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 01/09/2017] [Indexed: 12/16/2022]
Abstract
A substantial proportion of tumors consist of genotypically distinct subpopulations of cancer cells. This intratumor genetic heterogeneity poses a substantial challenge for the implementation of precision medicine. Single-cell genomics constitutes a powerful approach to resolve complex mixtures of cancer cells by tracing cell lineages and discovering cryptic genetic variations that would otherwise be obscured in tumor bulk analyses. Because of the chemical alterations that result from formalin fixation, single-cell genomic approaches have largely remained limited to fresh or rapidly frozen specimens. Here we describe the development and validation of a robust and accurate methodology to perform whole-genome copy-number profiling of single nuclei obtained from formalin-fixed paraffin-embedded clinical tumor samples. We applied the single-cell sequencing approach described here to study the progression from in situ to invasive breast cancer, which revealed that ductal carcinomas in situ show intratumor genetic heterogeneity at diagnosis and that these lesions may progress to invasive breast cancer through a variety of evolutionary processes.
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Affiliation(s)
- Luciano G Martelotto
- Department of Pathology, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Timour Baslan
- Cold Spring Harbor Laboratory (CSHL), Cold Spring Harbor, New York, USA.,Department of Molecular and Cellular Biology, Stony Brook University, New York, New York, USA
| | - Jude Kendall
- Cold Spring Harbor Laboratory (CSHL), Cold Spring Harbor, New York, USA
| | - Felipe C Geyer
- Department of Pathology, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Kathleen A Burke
- Department of Pathology, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Lee Spraggon
- Department of Pathology, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Salvatore Piscuoglio
- Department of Pathology, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Kalyani Chadalavada
- Molecular Cytogenetics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Gouri Nanjangud
- Molecular Cytogenetics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Charlotte K Y Ng
- Department of Pathology, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Pamela Moody
- Cold Spring Harbor Laboratory (CSHL), Cold Spring Harbor, New York, USA
| | - Sean D'Italia
- Cold Spring Harbor Laboratory (CSHL), Cold Spring Harbor, New York, USA
| | - Linda Rodgers
- Cold Spring Harbor Laboratory (CSHL), Cold Spring Harbor, New York, USA
| | - Hilary Cox
- Cold Spring Harbor Laboratory (CSHL), Cold Spring Harbor, New York, USA
| | - Arnaud da Cruz Paula
- Department of Pathology, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA.,Instituto Português de Oncologia, Porto, Portugal
| | - Asya Stepansky
- Cold Spring Harbor Laboratory (CSHL), Cold Spring Harbor, New York, USA
| | - Michail Schizas
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Hannah Y Wen
- Department of Pathology, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Tari A King
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Larry Norton
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - James B Hicks
- Cold Spring Harbor Laboratory (CSHL), Cold Spring Harbor, New York, USA
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
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30
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Fusco N, Geyer FC, De Filippo MR, Martelotto LG, Ng CKY, Piscuoglio S, Guerini-Rocco E, Schultheis AM, Fuhrmann L, Wang L, Jungbluth AA, Burke KA, Lim RS, Vincent-Salomon A, Bamba M, Moritani S, Badve SS, Ichihara S, Ellis IO, Reis-Filho JS, Weigelt B. Genetic events in the progression of adenoid cystic carcinoma of the breast to high-grade triple-negative breast cancer. Mod Pathol 2016; 29:1292-1305. [PMID: 27491809 PMCID: PMC5083185 DOI: 10.1038/modpathol.2016.134] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [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: 04/08/2016] [Revised: 05/30/2016] [Accepted: 05/31/2016] [Indexed: 01/01/2023]
Abstract
Adenoid cystic carcinoma of the breast is a rare histological type of triple-negative breast cancer with an indolent clinical behavior, often driven by the MYB-NFIB fusion gene. Here we sought to define the repertoire of somatic genetic alterations in two adenoid cystic carcinomas associated with high-grade triple-negative breast cancer. The different components of each case were subjected to copy number profiling and massively parallel sequencing targeting all exons and selected regulatory and intronic regions of 488 genes. Reverse transcription PCR and fluorescence in situ hybridization were employed to investigate the presence of the MYB-NFIB translocation. The MYB-NFIB fusion gene was detected in both adenoid cystic carcinomas and their associated high-grade triple-negative breast cancer components. Although the distinct components of both cases displayed similar patterns of gene copy number alterations, massively parallel sequencing analysis revealed intratumor genetic heterogeneity. In case 1, progression from the trabecular adenoid cystic carcinoma to the high-grade triple-negative breast cancer was found to involve clonal shifts with enrichment of mutations affecting EP300, NOTCH1, ERBB2 and FGFR1 in the high-grade triple-negative breast cancer. In case 2, a clonal KMT2C mutation was present in the cribriform adenoid cystic carcinoma, solid adenoid cystic carcinoma and high-grade triple-negative breast cancer components, whereas a mutation affecting MYB was present only in the solid and high-grade triple-negative breast cancer areas and additional three mutations targeting STAG2, KDM6A and CDK12 were restricted to the high-grade triple-negative breast cancer. In conclusion, adenoid cystic carcinomas of the breast with high-grade transformation are underpinned by the MYB-NFIB fusion gene and, akin to other forms of cancer, may be constituted by a mosaic of cancer cell clones at diagnosis. The progression from adenoid cystic carcinoma to high-grade triple-negative breast cancer of no special type may involve the selection of neoplastic clones and/or the acquisition of additional genetic alterations.
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Affiliation(s)
- Nicola Fusco
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
- Division of Pathology, Fondazione IRCCS Ca’ Granda – Ospedale Maggiore Policlinico, Milan, Italy
| | - Felipe C Geyer
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Pathology, Hospital Israelita Albert Einstein, Instituto Israelita de Ensino e Pesquisa, São Paulo, Brazil
| | - Maria R De Filippo
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Charlotte K Y Ng
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Elena Guerini-Rocco
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Pathology, European Institute of Oncology, Milan, Italy
| | - Anne M Schultheis
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Lu Wang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Achim A Jungbluth
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kathleen A Burke
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Raymond S Lim
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Masamichi Bamba
- Department of Pathology and Laboratory Medicine, Saiseikai Shiga Hospital, Imperial Gift Foundation Inc., Shiga, Japan
| | - Suzuko Moritani
- Division of Diagnostic Pathology, Shiga University of Medical Science, Shiga, Japan
| | - Sunil S Badve
- Department of Pathology, Indiana University School of Medicine, Indianapolis, IN
| | - Shu Ichihara
- Department of Pathology, Nagoya National Hospital, Nagoya, Japan
| | - Ian O Ellis
- Department of Pathology, University of Nottingham, Nottingham, UK
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
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31
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Chiang S, Weigelt B, Wen HC, Pareja F, Raghavendra A, Martelotto LG, Burke KA, Basili T, Li A, Geyer FC, Piscuoglio S, Ng CKY, Jungbluth AA, Balss J, Pusch S, Baker GM, Cole KS, von Deimling A, Batten JM, Marotti JD, Soh HC, McCalip BL, Serrano J, Lim RS, Siziopikou KP, Lu S, Liu X, Hammour T, Brogi E, Snuderl M, Iafrate AJ, Reis-Filho JS, Schnitt SJ. IDH2 Mutations Define a Unique Subtype of Breast Cancer with Altered Nuclear Polarity. Cancer Res 2016; 76:7118-7129. [PMID: 27913435 DOI: 10.1158/0008-5472.can-16-0298] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 10/06/2016] [Accepted: 10/06/2016] [Indexed: 01/04/2023]
Abstract
Solid papillary carcinoma with reverse polarity (SPCRP) is a rare breast cancer subtype with an obscure etiology. In this study, we sought to describe its unique histopathologic features and to identify the genetic alterations that underpin SPCRP using massively parallel whole-exome and targeted sequencing. The morphologic and immunohistochemical features of SPCRP support the invasive nature of this subtype. Ten of 13 (77%) SPCRPs harbored hotspot mutations at R172 of the isocitrate dehydrogenase IDH2, of which 8 of 10 displayed concurrent pathogenic mutations affecting PIK3CA or PIK3R1 One of the IDH2 wild-type SPCRPs harbored a TET2 Q548* truncating mutation coupled with a PIK3CA H1047R hotspot mutation. Functional studies demonstrated that IDH2 and PIK3CA hotspot mutations are likely drivers of SPCRP, resulting in its reversed nuclear polarization phenotype. Our results offer a molecular definition of SPCRP as a distinct breast cancer subtype. Concurrent IDH2 and PIK3CA mutations may help diagnose SPCRP and possibly direct effective treatment. Cancer Res; 76(24); 7118-29. ©2016 AACR.
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Affiliation(s)
- Sarah Chiang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Huei-Chi Wen
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Fresia Pareja
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ashwini Raghavendra
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Luciano G Martelotto
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kathleen A Burke
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Thais Basili
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Anqi Li
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Felipe C Geyer
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Salvatore Piscuoglio
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Charlotte K Y Ng
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Achim A Jungbluth
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jörg Balss
- German Consortium of Translational Cancer Research (DKTK), Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan Pusch
- German Consortium of Translational Cancer Research (DKTK), Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Kimberly S Cole
- Department of Pathology, University of Iowa Hospital and Clinics, Iowa City, Iowa
| | - Andreas von Deimling
- German Consortium of Translational Cancer Research (DKTK), Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Neuropathology, Institute of Pathology, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany
| | - Julie M Batten
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Jonathan D Marotti
- Department of Pathology, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire
| | - Hwei-Choo Soh
- Pathology North, North Shore Private Hospital, New South Wales, Australia
| | | | - Jonathan Serrano
- Department of Pathology, New York University Langone Medical Center and Medical School, New York, New York
| | - Raymond S Lim
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kalliopi P Siziopikou
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Song Lu
- Department of Pathology, Mon General Hospital, Morgantown, West Virginia
| | | | | | - Edi Brogi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Matija Snuderl
- Department of Pathology, New York University Langone Medical Center and Medical School, New York, New York
| | - A John Iafrate
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts.,Department of Pathology, Harvard Medical School, Boston, Massachusetts
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Stuart J Schnitt
- Department of Pathology, Harvard Medical School, Boston, Massachusetts. .,Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts
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32
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Macedo GS, Burke KA, Piscuoglio S, Ng CKY, Geyer FC, Martelotto LG, Papanastatiou AD, De Filippo MR, Schultheis AM, Brogi E, Robson ME, Wen HY, Weigelt B, Reis-Filho JS. Abstract 100: The landscape of somatic genetic alterations in BRCA1 and BRCA2 breast cancers. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-100] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: BRCA1 or BRCA2 germline mutations account for a substantial proportion of hereditary breast cancers. The majority of BRCA1-associated breast cancers are of triple-negative phenotype (estrogen receptor (ER)-, progesterone receptor (PR)- and HER2-negative) and harbor TP53 somatic mutations. BRCA2-associated cancers are less homogeneous and often ER-positive. Systematic analyses of the profiles of somatic genetic alterations in BRCA1- and BRCA2-breast cancers have yet to be reported. Here we sought to determine the repertoire of somatic mutations and copy number alterations (CNAs) in breast cancers occurring in patients with BRCA1 or BRCA2 germline mutations..
Methods: Eleven BRCA1- and five BRCA2-associated breast cancers were microdissected. DNA was extracted from microdissected frozen tumor-normal pairs and subjected to targeted capture massively parallel sequencing using the MSK-IMPACT platform, which includes all exons and selected introns and regulatory regions of 410 key cancer genes. Somatic single nucleotide variants, small insertions and deletions, CNAs and the cancer cell fraction (CCF) of each alteration were defined using state-of-the-art bioinformatics algorithms.
Results: 82% (9/11) and 18% (2/11) of BRCA1-breast cancers were triple-negative and ER-positive/HER2-negative, respectively. All BRCA2-cancers were ER-positive, of which one was HER2-positive. Sequencing analysis revealed a median of four (2-11) and two (0-6) non-synonymous somatic mutations in BRCA1- and BRCA2-breast cancers, respectively. Within BRCA1-breast cancers all but one (10/11, 91%) harbored TP53 clonal somatic mutations, and clonal somatic loss of the BRCA1 wild-type allele was found in 8 of these cases. The BRCA1-breast cancer lacking these alterations was ER-positive and the only case harboring a PIK3CA mutation. Additional clonal mutations identified in BRCA1-breast cancers included somatic mutations affecting EGFR and RB1. Subclonal mutations in known cancer genes (e.g. GATA3 and PTEN) were also identified, suggesting intra-tumor genetic heterogeneity. All BRCA2-breast cancers analyzed displayed clonal loss of the wild-type of BRCA2, but no gene was found to be recurrently mutated.
Conclusions: BRCA1- and BRCA2-breast cancers are both characterized by clonal inactivation of the BRCA1 and BRCA2 wild-type alleles, respectively, which likely constitute early genetic events. Within BRCA1-breast cancers, TP53 mutations are highly recurrent and clonal, and may precede somatic loss of the BRCA1 wild-type allele, as the latter was subclonal in one case harboring a clonal TP53 somatic mutation.
Citation Format: Gabriel S. Macedo, Kathleen A. Burke, Salvatore Piscuoglio, Charlotte K. Y. Ng, Felipe C. Geyer, Luciano G. Martelotto, Anastasios D. Papanastatiou, Maria R. De Filippo, Anne M. Schultheis, Edi Brogi, Mark E. Robson, Hannah Y. Wen, Britta Weigelt, Jorge S. Reis-Filho. The landscape of somatic genetic alterations in BRCA1 and BRCA2 breast cancers. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 100.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Edi Brogi
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Hannah Y. Wen
- Memorial Sloan Kettering Cancer Center, New York, NY
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33
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Chiang S, Weigelt B, Wen HC, Piscuoglio S, Martelotto LG, Ng CKY, Balss J, Baker G, Cole KS, von Deimling A, Batten JM, Marotti JD, Soh HC, McCalip BL, Lim RS, Siziopikou KP, Burke R, Lu S, Liu X, Hammour T, Brogi E, Iafrate AJ, Reis-Filho JS, Schnitt SJ. Abstract 138: Solid papillary carcinoma with reverse polarization are driven by IDH2 and PI3K pathway mutations. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-138] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Solid papillary carcinoma with reverse polarization (SPCRP) is a rare breast cancer subtype, whose most striking morphologic feature is the presence of back-to-back columnar epithelial cells with nuclei situated in an apical rather than in the normal basal location. We sought to characterize the morphologic and genetic landscape of SPCRP and determine whether it represents a distinct subtype of breast cancer underpinned by highly recurrent disease-specific genetic alterations.
Material and Methods: Archival sections of 13 SPCRPs were subjected to microdissection. DNA samples extracted from microdissected tumor and matched normal samples were subjected to whole exome sequencing (n = 2) on an Illumina HiSeq2000, and DNA samples from tumors were further subjected to targeted massively parallel sequencing (n = 1), SNaPshot profiling (n = 7) and/or Sanger sequencing. State-of-the-art bioinformatics methods were used to define somatic mutations. Non-malignant breast epithelial MCF10A cells with and without somatic PIK3CA H1047R knock-in were used to assess the functional impact of the mutations identified by sequencing of SPCRPs in two- and three-dimensional cell culture systems.
Results: Ten of 13 (77%) SPCRPs were found to harbor IDH2 R172 hotspot mutations, and eight of these cases had concurrent pathogenic mutations affecting PIK3CA or PIK3R1, in particular PIK3CA H1047R hotspot mutations. Functional monolayer and three-dimensional cell culture studies demonstrated that IDH2 R172 and PIK3CA mutations constitute likely drivers of this tumor and contribute to its unusual nuclear polarization phenotype.
Conclusions: Our results suggest that SPCRP is a distinct subtype of breast cancer underpinned by IDH2 hotspot mutations in conjunction with mutations affecting canonical genes of the PI3K pathway. Given that IDH2 hotspot mutations have not been described in breast cancer to date, these may be used as a diagnostic ancillary marker for SPCRPs. Furthermore, IDH2 mutations may serve as a potential therapeutic target in SPCRP patients with disseminated disease.
Citation Format: Sarah Chiang, Britta Weigelt, Huei-Chi Wen, Salvatore Piscuoglio, Luciano G. Martelotto, Charlotte K Y Ng, Jörg Balss, Gabrielle Baker, Kimberly S. Cole, Andreas von Deimling, Julie M. Batten, Jonathan D. Marotti, Hwei-Choo Soh, Benjamin L. McCalip, Raymond S. Lim, Kalliopi P. Siziopikou, Randi Burke, Song Lu, Xiaolong Liu, Tarek Hammour, Edi Brogi, A John Iafrate, Jorge S. Reis-Filho, Stuart J. Schnitt. Solid papillary carcinoma with reverse polarization are driven by IDH2 and PI3K pathway mutations. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 138.
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Affiliation(s)
- Sarah Chiang
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Huei-Chi Wen
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | - Jörg Balss
- 2German Consortium of Translational Cancer Research (DKTK), Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Gabrielle Baker
- 3Department of Pathology, University of Chicago, Chicago, IL
| | - Kimberly S. Cole
- 4Memorial Sloan Kettering Cancer CenterDepartment of Pathology, Montefiore Medical Center and Albert Einstein College of Medicine, New York, NY
| | - Andreas von Deimling
- 5Department of Neuropathology, Institute of Pathology, INF 224, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany
| | - Julie M. Batten
- 6Department of Pathology, Massachusetts General Hospital, Boston, MA
| | | | - Hwei-Choo Soh
- 8Pathology North, North Shore Private Hospital, Sydney, Australia
| | | | | | - Kalliopi P. Siziopikou
- 10Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL
| | | | - Song Lu
- 12Department of Pathology, Mon General Hospital, Morgantown, WV
| | | | | | - Edi Brogi
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - A John Iafrate
- 6Department of Pathology, Massachusetts General Hospital, Boston, MA
| | | | - Stuart J. Schnitt
- 15Department of Pathology, Beth Israel Deaconess Medical Center, Boston, MA
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Piscuoglio S, Ng CKY, Murray MP, Guerini-Rocco E, Martelotto LG, Geyer FC, Bidard FC, Berman S, Fusco N, Sakr RA, Eberle CA, De Mattos-Arruda L, Macedo GS, Akram M, Baslan T, Hicks JB, King TA, Brogi E, Norton L, Weigelt B, Hudis CA, Reis-Filho JS. The Genomic Landscape of Male Breast Cancers. Clin Cancer Res 2016; 22:4045-56. [PMID: 26960396 DOI: 10.1158/1078-0432.ccr-15-2840] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 02/29/2016] [Indexed: 01/07/2023]
Abstract
PURPOSE Male breast cancer is rare, and its genomic landscape has yet to be fully characterized. Lacking studies in men, treatment of males with breast cancer is extrapolated from results in females with breast cancer. We sought to define whether male breast cancers harbor somatic genetic alterations in genes frequently altered in female breast cancers. EXPERIMENTAL DESIGN All male breast cancers were estrogen receptor-positive, and all but two were HER2-negative. Fifty-nine male breast cancers were subtyped by immunohistochemistry, and tumor-normal pairs were microdissected and subjected to massively parallel sequencing targeting all exons of 241 genes frequently mutated in female breast cancers or DNA-repair related. The repertoires of somatic mutations and copy number alterations of male breast cancers were compared with that of subtype-matched female breast cancers. RESULTS Twenty-nine percent and 71% of male breast cancers were immunohistochemically classified as luminal A-like or luminal B-like, respectively. Male breast cancers displayed a heterogeneous repertoire of somatic genetic alterations that to some extent recapitulated that of estrogen receptor (ER)-positive/HER2-negative female breast cancers, including recurrent mutations affecting PIK3CA (20%) and GATA3 (15%). ER-positive/HER2-negative male breast cancers, however, less frequently harbored 16q losses, and PIK3CA and TP53 mutations than ER-positive/HER2-negative female breast cancers. In addition, male breast cancers were found to be significantly enriched for mutations affecting DNA repair-related genes. CONCLUSIONS Male breast cancers less frequently harbor somatic genetic alterations typical of ER-positive/HER2-negative female breast cancers, such as PIK3CA and TP53 mutations and losses of 16q, suggesting that at least a subset of male breast cancers are driven by a distinct repertoire of somatic changes. Given the genomic differences, caution may be needed in the application of biologic and therapeutic findings from studies of female breast cancers to male breast cancers. Clin Cancer Res; 22(16); 4045-56. ©2016 AACR.
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Affiliation(s)
- Salvatore Piscuoglio
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Charlotte K Y Ng
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Melissa P Murray
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Elena Guerini-Rocco
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York. Department of Pathology, European Institute of Oncology, Milan, Italy
| | - Luciano G Martelotto
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Felipe C Geyer
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York. Department of Pathology, Hospital Israelita Albert Einstein, Instituto Israelita de Ensino e Pesquisa, São Paulo, Brazil
| | - Francois-Clement Bidard
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York. Department of Medical Oncology, Institut Curie, Paris, France
| | - Samuel Berman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nicola Fusco
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York. Division of Pathology, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Rita A Sakr
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Carey A Eberle
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Gabriel S Macedo
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Muzaffar Akram
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Timour Baslan
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York. Department of Molecular and Cellular Biology, Stony Brook University, Stony Brook, New York. Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - James B Hicks
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
| | - Tari A King
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Edi Brogi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Larry Norton
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Clifford A Hudis
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
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Piscuoglio S, Ng CK, Murray M, Burke KA, Edelweiss M, Geyer FC, Macedo GS, Inagaki A, Papanastasiou AD, Martelotto LG, Marchio C, Lim RS, Ioris RA, Nahar PK, Bruijn ID, Smyth L, Akram M, Ross D, Petrini JH, Norton L, Solit DB, Baselga J, Brogi E, Ladanyi M, Weigelt B, Reis-Filho JS. Massively parallel sequencing of phyllodes tumours of the breast reveals actionable mutations, and TERT promoter hotspot mutations and TERT gene amplification as likely drivers of progression. J Pathol 2016; 238:508-18. [PMID: 26832993 DOI: 10.1002/path.4672] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [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: 10/12/2015] [Revised: 10/20/2015] [Accepted: 10/21/2015] [Indexed: 12/25/2022]
Abstract
Phyllodes tumours (PTs) are breast fibroepithelial lesions that are graded based on histological criteria as benign, borderline or malignant. PTs may recur locally. Borderline PTs and malignant PTs may metastasize to distant sites. Breast fibroepithelial lesions, including PTs and fibroadenomas, are characterized by recurrent MED12 exon 2 somatic mutations. We sought to define the repertoire of somatic genetic alterations in PTs and whether these may assist in the differential diagnosis of these lesions. We collected 100 fibroadenomas, 40 benign PTs, 14 borderline PTs and 22 malignant PTs; six, six and 13 benign, borderline and malignant PTs, respectively, and their matched normal tissue, were subjected to targeted massively parallel sequencing (MPS) using the MSK-IMPACT sequencing assay. Recurrent MED12 mutations were found in 56% of PTs; in addition, mutations affecting cancer genes (eg TP53, RB1, SETD2 and EGFR) were exclusively detected in borderline and malignant PTs. We found a novel recurrent clonal hotspot mutation in the TERT promoter (-124 C>T) in 52% and TERT gene amplification in 4% of PTs. Laser capture microdissection revealed that these mutations were restricted to the mesenchymal component of PTs. Sequencing analysis of the entire cohort revealed that the frequency of TERT alterations increased from benign (18%) to borderline (57%) and to malignant PTs (68%; p < 0.01), and TERT alterations were associated with increased levels of TERT mRNA (p < 0.001). No TERT alterations were observed in fibroadenomas. An analysis of TERT promoter sequencing and gene amplification distinguished PTs from fibroadenomas with a sensitivity and a positive predictive value of 100% (CI 95.38-100%) and 100% (CI 85.86-100%), respectively, and a sensitivity and a negative predictive value of 39% (CI 28.65-51.36%) and 68% (CI 60.21-75.78%), respectively. Our results suggest that TERT alterations may drive the progression of PTs, and may assist in the differential diagnosis between PTs and fibroadenomas. Copyright © 2015 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
| | - Charlotte Ky Ng
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Melissa Murray
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Kathleen A Burke
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Marcia Edelweiss
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Felipe C Geyer
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA.,Department of Pathology, Hospital Israelita Albert Einstein, Instituto Israelita de Ensino e Pesquisa, São Paulo, Brazil
| | - Gabriel S Macedo
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Akiko Inagaki
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Anastasios D Papanastasiou
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA.,Department of Pathology, Patras General Hospital, Greece
| | | | - Caterina Marchio
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA.,Department of Medical Sciences, University of Turin, Italy
| | - Raymond S Lim
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Rafael A Ioris
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Pooja K Nahar
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Ino De Bruijn
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Lillian Smyth
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Muzaffar Akram
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Dara Ross
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - John H Petrini
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Larry Norton
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - David B Solit
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA.,Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Jose Baselga
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Edi Brogi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
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Piscuoglio S, Fusco N, Ng CKY, Martelotto LG, da Cruz Paula A, Katabi N, Rubin BP, Skálová A, Weinreb I, Weigelt B, Reis-Filho JS. Lack of PRKD2 and PRKD3 kinase domain somatic mutations in PRKD1 wild-type classic polymorphous low-grade adenocarcinomas of the salivary gland. Histopathology 2016; 68:1055-62. [PMID: 26426580 DOI: 10.1111/his.12883] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [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: 08/12/2015] [Accepted: 09/25/2015] [Indexed: 02/02/2023]
Abstract
AIMS Polymorphous low-grade adenocarcinoma (PLGA) is the second most common intra-oral salivary gland malignancy. The vast majority of PLGAs harbour a PRKD1 E710D hot-spot somatic mutation or somatic rearrangements of PRKD1, PRKD2 or PRKD3. Given the kinase domain homology among PRKD1, PRKD2 and PRKD3, we sought to define whether PLGAs lacking PRKD1 somatic mutations or PRKD gene family rearrangements would be driven by somatic mutations affecting the kinase domains of PRKD2 or PRKD3. METHODS AND RESULTS DNA was extracted from eight microdissected PLGAs lacking PRKD1 somatic mutations or PRKD gene family rearrangements. Samples were thoroughly centrally reviewed, microdissected and subjected to Sanger sequencing of the kinase domains of the PRKD2 and PRKD3 genes. None of the PLGAs lacking PRKD1 somatic mutations or PRKD gene family rearrangements harboured somatic mutations in the kinase domains of the PRKD2 or PRKD3 genes. CONCLUSION PLGAs lacking PRKD1 somatic mutations or PRKD gene family rearrangements are unlikely to harbour somatic mutations in the kinase domains of PRKD2 or PRKD3. Further studies are warranted to define the driver genetic events in this subgroup of PLGAs.
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Affiliation(s)
- Salvatore Piscuoglio
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nicola Fusco
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Division of Pathology, Fondazione IRCCS Ca' Granda - Ospedale Maggiore Policlinico, Milan, Italy
| | - Charlotte K Y Ng
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Luciano G Martelotto
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Arnaud da Cruz Paula
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Instituto Português de Oncologia, Oporto, Portugal
| | - Nora Katabi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Brian P Rubin
- Department of Pathology, Robert J Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Alena Skálová
- Department of Pathology, Medical Faculty of Charles University, Plzen, Czech Republic
| | - Ilan Weinreb
- Department of Pathology, University Health Network, Toronto, Ontario, Canada
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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Piscuoglio S, Burke KA, Ng CKY, Papanastasiou AD, Geyer FC, Macedo GS, Martelotto LG, de Bruijn I, De Filippo MR, Schultheis AM, Ioris RA, Levine DA, Soslow RA, Rubin BP, Reis-Filho JS, Weigelt B. Uterine adenosarcomas are mesenchymal neoplasms. J Pathol 2015; 238:381-8. [PMID: 26592504 DOI: 10.1002/path.4675] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [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: 10/05/2015] [Revised: 11/10/2015] [Accepted: 11/17/2015] [Indexed: 12/25/2022]
Abstract
Uterine adenosarcomas (UAs) are biphasic lesions composed of a malignant mesenchymal (ie stromal) component and an epithelial component. UAs are generally low-grade and have a favourable prognosis, but may display sarcomatous overgrowth (SO), which is associated with a worse outcome. We hypothesized that, akin to breast fibroepithelial lesions, UAs are mesenchymal neoplasms in which clonal somatic genetic alterations are restricted to the mesenchymal component. To characterize the somatic genetic alterations in UAs and to test this hypothesis, we subjected 20 UAs to a combination of whole-exome (n = 6), targeted capture (n = 13) massively parallel sequencing (MPS) and/or RNA sequencing (n = 6). Only three genes, FGFR2, KMT2C and DICER1, were recurrently mutated, all in 2/19 cases; however, 26% (5/19) and 21% (4/19) of UAs harboured MDM2/CDK4/HMGA2 and TERT gene amplification, respectively, and two cases harboured fusion genes involving NCOA family members. Using a combination of laser-capture microdissection and in situ techniques, we demonstrated that the somatic genetic alterations detected by MPS were restricted to the mesenchymal component. Furthermore, mitochondrial DNA sequencing of microdissected samples revealed that epithelial and mesenchymal components of UAs were clonally unrelated. In conclusion, here we provide evidence that UAs are genetically heterogeneous lesions and mesenchymal neoplasms.
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Affiliation(s)
| | - Kathleen A Burke
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Charlotte K Y Ng
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Anastasios D Papanastasiou
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA.,Department of Pathology, Patras General Hospital, University of Patras, Greece
| | - Felipe C Geyer
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA.,Department of Pathology, Hospital Israelita Albert Einstein, Instituto Israelita de Ensino e Pesquisa, São Paulo, Brazil
| | - Gabriel S Macedo
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | | | - Ino de Bruijn
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Maria R De Filippo
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Anne M Schultheis
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Rafael A Ioris
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Douglas A Levine
- Gynaecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Robert A Soslow
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Brian P Rubin
- Department of Pathology, Cleveland Clinic, Cleveland, OH, USA
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
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Schizas M, Sakr RA, Weigelt B, Ng CKY, Carniello JVS, Giri D, Piscuoglio S, Martelotto LG, Towers R, Andrade VP, Lim R, Solit DB, Reis-Filho JS, King TA. Abstract 2971: Whole exome sequencing reveals heterogeneity within lobular carcinoma in situ (LCIS) and clonal selection in the progression to malignant lesions. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-2971] [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
INTRODUCTION: Lobular carcinoma in situ (LCIS) is considered both a risk factor and non-obligate precursor of low-grade estrogen receptor-positive breast cancer. We sought to define the mutational repertoire, subclone complexity and heterogeneity of LCIS, and whether invasive lobular carcinomas (ILCs) would stem from specific subclones within a LCIS.
METHODS: Patients with a history of LCIS undergoing therapeutic or prophylactic mastectomy were prospectively enrolled in an IRB approved protocol. Frozen tissue blocks were collected, screened for lesions of interest (LCIS, ductal carcinoma in situ (DCIS), ILC, invasive ductal carcinoma (IDC)) and subject to microdissection and DNA extraction. Matched germline DNA was available for all cases. Whole exome sequencing was performed on a HiSeq2000 (Illumina) and data were aligned to the reference human genome hg19 and processed using GATK. SNVs were called using MuTect, and indels were called using a combination of Varscan and Strelka. Purity and ploidy estimates were calculated by ABSOLUTE. Clonal frequencies were estimated using Pyclone.
RESULTS: 30 LCIS, 10 ILCs, 6 IDCs and 7 DCIS from 15 patients qualified for data analysis, resulting in 18 LCIS-ILC pairs, 22 LCIS-LCIS pairs, 12 LCIS-DCIS pairs, and 14 LCIS-IDC pairs for comparison. 9/18 (50%) LCIS-ILC pairs and 8/22 (36%) LCIS-LCIS pairs were clonally related, supported by several shared mutations (median 18, range 7-81 for LCIS-ILC; median 14, range 5-22 for LCIS-LCIS). All related LCIS-ILC pairs and 6/8 related LCIS-LCIS pairs shared a pathogenic CDH1 mutation; 75% of related LCIS-ILC pairs also shared a PIK3CA hotspot mutation. 7/12 (58%) LCIS-DCIS pairs were found to be clonally related but the number of shared mutations was generally lower than that found in LCIS-ILC pairs (median 9, range 2-11). No evidence of a clonal relationship was found in any of the LCIS-IDC pairs tested. Clonal composition analysis revealed that samples of LCIS display intra-lesion genetic heterogeneity in the form of the presence of a minor clone in 70% of cases. In one case, the LCIS minor subclone (∼15%) constituted the major clone in the ILC and in another case the LCIS minor subclone constituted the major clone in the associated DCIS. The majority of the clonally related lesions were located in the same quadrant of the breast, however evidence of clonality was found in 5 LCIS-LCIS and 3 LCIS-DCIS pairs located in separate quadrants of the breast.
CONCLUSIONS: Intra-lesion genetic heterogeneity is a common phenomenon in LCIS. The dominant clone of a LCIS may not always be the clone directly involved in the progression to malignancy. The spatial relationships of clonally related lesions in this study suggest that anatomy does not always infer clonality, as lesions located in separate quadrants of the breast may be clonally related.
Citation Format: Michail Schizas, Rita A. Sakr, Britta Weigelt, Charlotte KY Ng, Jose Victor S. Carniello, Dilip Giri, Salvatore Piscuoglio, Luciano G. Martelotto, Russell Towers, Victor P. Andrade, Raymond Lim, David B. Solit, Jorge S. Reis-Filho, Tari A. King. Whole exome sequencing reveals heterogeneity within lobular carcinoma in situ (LCIS) and clonal selection in the progression to malignant lesions. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2971. doi:10.1158/1538-7445.AM2015-2971
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Martelotto LG, Sakr RA, Baslan T, Rodgers L, Cox H, Kendall J, King TA, Weigelt B, Hicks J, Reis-Filho JS. Abstract 4735: Single-cell sequencing from formalin-fixed paraffin-embedded breast cancers: a powerful tool to address intratumor genetic heterogeneity. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-4735] [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: At diagnosis, tumors often consist of multiple, genotypically distinct cell populations. Genome sequencing of single cells has opened new avenues of investigation, yet the application of this technology remains limited to fresh/frozen tissue samples. Here, we describe and validate a method to perform single-cell massively parallel sequencing using DNA extracted from individual nuclei from FFPE tumor samples.
Methods: Tissue sections are deparaffinized and the area of interest microdissected, DNA is reverse-crosslinked and the extracellular matrix is digested. Extracted single nuclei are then FACS-sorted, lysed and the whole genome repaired using a broad-spectrum DNA-repair enzyme cocktail. Repaired DNA is whole genome amplified (WGA) using GenomePlex WGA4 (Sigma-Aldrich) with modifications for heavily damaged genomic templates. Illumina sequencing libraries are generated using standard approaches followed by multiplex sequencing on an Illumina HiSeq2000. To obtain copy number (CN) profiles, single-cell sequencing data are mapped to the reference genome with PCR duplicates removed. Uniquely mapped reads are allocated and counted in genomic intervals of variable length (bins) with CN states roughly proportional to the number of allocated sequencing reads. Bin counts are then normalized on the basis of GC-content, segmented and transformed to CN values to identify long contiguous regions of equivalent CN.
Results: As a proof-of-principle we performed single-cell CN profiling on two aneuploid synchronous ductal carcinomas in situ (DCIS)/invasive ductal carcinomas (IDCs), where both FFPE and frozen material was available. Using our novel methodology, 24 single nuclei were multiplexed/lesion. An average of 3 million reads/cell (average coverage of 0.1X/cell) was obtained, providing sufficient data to infer CN profiles of single cells accurately. These data were successfully employed to identify non-neoplastic cells and distinct clonal lineages of neoplastic cells within each lesion. The data obtained from the analysis of FFPE samples were concordant with those obtained from the analysis of matched frozen samples.
Conclusions: We developed a robust procedure to perform single-cell massively parallel sequencing of individual nuclei isolated from FFPE samples, providing the opportunity to unlock pathology archives for studies aiming to catalog and dissect the biological and clinical relevance of intra-tumor genetic heterogeneity.
Citation Format: Luciano G. Martelotto, Rita A. Sakr, Timour Baslan, Linda Rodgers, Hilary Cox, Jude Kendall, Tari A. King, Britta Weigelt, James Hicks, Jorge S. Reis-Filho. Single-cell sequencing from formalin-fixed paraffin-embedded breast cancers: a powerful tool to address intratumor genetic heterogeneity. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4735. doi:10.1158/1538-7445.AM2015-4735
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Affiliation(s)
| | - Rita A. Sakr
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Timour Baslan
- 2Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
| | - Linda Rodgers
- 2Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
| | - Hilary Cox
- 2Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
| | - Jude Kendall
- 2Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
| | - Tari A. King
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - James Hicks
- 2Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
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Sakr RA, Martelotto LG, Baslan T, Ng CKY, Kendall J, Rodgers L, Cox H, Riggs M, D'Itali S, Stepansky A, Olvera N, King TA, Weigelt B, Reis-Filho JS, Hicks J. Abstract 2989: Intra-tumor heterogeneity and clonal changes in the progression of DCIS to invasiveness: Combined tumor bulk and single cell analysis. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-2989] [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
INTRODUCTION: Ductal carcinoma in situ (DCIS) is a clonal intraductal proliferation of epithelial cells which acts as a non-obligate precursor of invasive breast cancer (IBC), yet the genetic events leading to the acquisition of invasive behavior remain unclear. We hypothesize that DCIS is composed of mosaics of genetically diverse tumor cell clones, and that the process of invasion is an evolutionary bottleneck. To test this hypothesis we performed a detailed characterization of the repertoire of genetic alterations and intra-tumor genetic heterogeneity in synchronously diagnosed DCIS and IBC using NextGen sequencing of bulk tumor and single cells.
METHODS: DNA extracted from fresh frozen, microdissected DCIS, IBC and adjacent normal tissue was subjected to whole exome sequencing on an Illumina HiSeq2000. Reads were aligned to the reference human genome hg19. Single nucleotide variants (SNVs) were called by MuTect, and gene copy number alterations were determined using VarScan2. Single nuclei were isolated from 100μm serial sections microdissected to separate DCIS and IBC. Individual nuclei were FACS-sorted into a 96-well plate, lysed and whole genome amplified. Amplified DNA samples were barcoded, pooled and sequenced on a HiSeq2000. Single cell sequencing data were mapped to the reference genome and uniquely mapped reads were allocated into bins, normalized, segmented and CN values generated.
RESULTS: In 6 cases of synchronous DCIS and IBC, a median of 41 and 47 non-synonymous mutations were found in each component, respectively. The somatic mutations identified in both DCIS and adjacent IBC components affected known driver breast cancer genes, including AKT1, PIK3CA, GATA3, MAP2K4 and TP53. Interestingly, we also found mutations restricted to either DCIS or IBC: ATRX (IBC-3); ALK and PKD2 (IBC-5); ESR1 (DCIS-5). The gene copy number profiles of matched DCIS and IBC were similar in all 6 pairs, however we also identified gene copy number alterations restricted either to DCIS or IBC: 1q gain (IBC-5); 3p and 3q losses (DCIS-6); 12p homozygous deletion (DCIS-4). Single cell sequencing of two cases (3 and 4) revealed that the majority of cells from both DCIS and IBC were derived from a common precursor lineage with shared copy number losses and gains. Both sets of DCIS-IBC pairs in these cases displayed elements of a subclonal structure with dominant clones alongside genetically diverse derivatives as well as genetic heterogeneity reflected in variable copy number alterations and non-modal clones.
CONCLUSION: Synchronous DCIS and IBC share founder genetic events, but also harbor somatic genetic alterations restricted to either the DCIS or IBC components, demonstrating that although DCIS is a precursor of IBC, intra-tumor genetic heterogeneity is present at the DCIS stage. Changes in clonal composition likely take place in the progression from DCIS to IBC.
Citation Format: Rita A. Sakr, Luciano G. Martelotto, Timour Baslan, Charlotte KY Ng, Jude Kendall, Linda Rodgers, Hilary Cox, Mike Riggs, Sean D'Itali, Asya Stepansky, Narciso Olvera, Tari A. King, Britta Weigelt, Jorge S. Reis-Filho, James Hicks. Intra-tumor heterogeneity and clonal changes in the progression of DCIS to invasiveness: Combined tumor bulk and single cell analysis. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2989. doi:10.1158/1538-7445.AM2015-2989
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Affiliation(s)
- Rita A. Sakr
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Timour Baslan
- 2Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
| | | | - Jude Kendall
- 2Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
| | - Linda Rodgers
- 2Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
| | - Hilary Cox
- 2Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
| | - Mike Riggs
- 2Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
| | - Sean D'Itali
- 2Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
| | | | | | - Tari A. King
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - James Hicks
- 2Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
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Guerini-Rocco E, Hodi Z, Piscuoglio S, Ng CKY, Rakha EA, Schultheis AM, Marchiò C, da Cruz Paula A, De Filippo MR, Martelotto LG, De Mattos-Arruda L, Edelweiss M, Jungbluth AA, Fusco N, Norton L, Weigelt B, Ellis IO, Reis-Filho JS. The repertoire of somatic genetic alterations of acinic cell carcinomas of the breast: an exploratory, hypothesis-generating study. J Pathol 2015; 237:166-78. [PMID: 26011570 DOI: 10.1002/path.4566] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 05/01/2015] [Accepted: 05/19/2015] [Indexed: 12/12/2022]
Abstract
Acinic cell carcinoma (ACC) of the breast is a rare form of triple-negative (that is, oestrogen receptor-negative, progesterone receptor-negative, HER2-negative) salivary gland-type tumour displaying serous acinar differentiation. Despite its triple-negative phenotype, breast ACCs are reported to have an indolent clinical behaviour. Here, we sought to define whether ACCs have a mutational repertoire distinct from that of other triple-negative breast cancers (TNBCs). DNA was extracted from microdissected formalin-fixed, paraffin-embedded sections of tumour and normal tissue from two pure and six mixed breast ACCs. Each tumour component of the mixed cases was microdissected separately. Tumour and normal samples were subjected to targeted capture massively parallel sequencing targeting all exons of 254 genes, including genes most frequently mutated in breast cancer and related to DNA repair. Selected somatic mutations were validated by targeted amplicon resequencing and Sanger sequencing. Akin to other forms of TNBC, the most frequently mutated gene found in breast ACCs was TP53 (one pure and six mixed cases). Additional somatic mutations affecting breast cancer-related genes found in ACCs included PIK3CA, MTOR, CTNNB1, BRCA1, ERBB4, ERBB3, INPP4B, and FGFR2. Copy number alteration analysis revealed complex patterns of gains and losses similar to those of common forms of TNBCs. Of the mixed cases analysed, identical somatic mutations were found in the acinic and the high-grade non-acinic components in two out of four cases analysed, providing evidence of their clonal relatedness. In conclusion, breast ACCs display the hallmark somatic genetic alterations found in high-grade forms of TNBC, including complex patterns of gene copy number alterations and recurrent TP53 mutations. Furthermore, we provide circumstantial genetic evidence to suggest that ACCs may constitute the substrate for the development of more aggressive forms of triple-negative disease.
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Affiliation(s)
- Elena Guerini-Rocco
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,School of Pathology, University of Milan, Italy
| | - Zsolt Hodi
- Department of Pathology, University of Nottingham, Nottingham, UK
| | - Salvatore Piscuoglio
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Charlotte K Y Ng
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Emad A Rakha
- Department of Pathology, University of Nottingham, Nottingham, UK
| | - Anne M Schultheis
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Caterina Marchiò
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medical Sciences, University of Turin, Turin, Italy
| | - Arnaud da Cruz Paula
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria R De Filippo
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Luciano G Martelotto
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Leticia De Mattos-Arruda
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Vall d'Hebron Institute of Oncology, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Marcia Edelweiss
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Achim A Jungbluth
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nicola Fusco
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,School of Pathology, University of Milan, Italy
| | - Larry Norton
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ian O Ellis
- Department of Pathology, University of Nottingham, Nottingham, UK
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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Martelotto LG, De Filippo MR, Ng CKY, Natrajan R, Fuhrmann L, Cyrta J, Piscuoglio S, Wen HC, Lim RS, Shen R, Schultheis AM, Wen YH, Edelweiss M, Mariani O, Stenman G, Chan TA, Colombo PE, Norton L, Vincent-Salomon A, Reis-Filho JS, Weigelt B. Genomic landscape of adenoid cystic carcinoma of the breast. J Pathol 2015; 237:179-89. [PMID: 26095796 DOI: 10.1002/path.4573] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [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: 04/02/2015] [Revised: 05/24/2015] [Accepted: 06/10/2015] [Indexed: 12/31/2022]
Abstract
Adenoid cystic carcinoma (AdCC) is a rare type of triple-negative breast cancer (TNBC) characterized by the presence of the MYB-NFIB fusion gene. The molecular underpinning of breast AdCCs other than the MYB-NFIB fusion gene remains largely unexplored. Here we sought to define the repertoire of somatic genetic alterations of breast AdCCs. We performed whole-exome sequencing, followed by orthogonal validation, of 12 breast AdCCs to determine the landscape of somatic mutations and gene copy number alterations. Fluorescence in situ hybridization and reverse-transcription PCR were used to define the presence of MYB gene rearrangements and MYB-NFIB chimeric transcripts. Unlike common forms of TNBC, we found that AdCCs have a low mutation rate (0.27 non-silent mutations/Mb), lack mutations in TP53 and PIK3CA and display a heterogeneous constellation of known cancer genes affected by somatic mutations, including MYB, BRAF, FBXW7, SMARCA5, SF3B1 and FGFR2. MYB and TLN2 were affected by somatic mutations in two cases each. Akin to salivary gland AdCCs, breast AdCCs were found to harbour mutations targeting chromatin remodelling, cell adhesion, RNA biology, ubiquitination and canonical signalling pathway genes. We observed that, although breast AdCCs had rather simple genomes, they likely display intra-tumour genetic heterogeneity at diagnosis. Taken together, these findings demonstrate that the mutational burden and mutational repertoire of breast AdCCs are more similar to those of salivary gland AdCCs than to those of other types of TNBCs, emphasizing the importance of histological subtyping of TNBCs. Furthermore, our data provide direct evidence that AdCCs harbour a distinctive mutational landscape and genomic structure, irrespective of the disease site of origin.
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Affiliation(s)
| | - Maria R De Filippo
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Charlotte K Y Ng
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Rachael Natrajan
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
| | | | - Joanna Cyrta
- Department of Tumour Biology, Institut Curie, Paris, France
| | | | - Huei-Chi Wen
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Raymond S Lim
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Ronglai Shen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Anne M Schultheis
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Y Hannah Wen
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Marcia Edelweiss
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Odette Mariani
- Department of Tumour Biology, Institut Curie, Paris, France
| | - Göran Stenman
- Sahlgrenska Cancer Center, Department of Pathology, University of Gothenburg, Sweden
| | - Timothy A Chan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, USA
| | | | - Larry Norton
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | | | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
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Fusco N, Colombo PE, Martelotto LG, De Filippo MR, Piscuoglio S, Ng CKY, Lim RS, Jacot W, Vincent-Salomon A, Reis-Filho JS, Weigelt B. Resolving quandaries: basaloid adenoid cystic carcinoma or breast cylindroma? The role of massively parallel sequencing. Histopathology 2015; 68:262-71. [PMID: 25951887 DOI: 10.1111/his.12735] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [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: 03/30/2015] [Accepted: 05/03/2015] [Indexed: 12/23/2022]
Abstract
AIMS The aims of this study were to perform a whole-exome sequencing analysis of a breast cylindroma and to investigate the role of molecular analyses in the differentiation between breast cylindroma, a benign tumour that displays MYB expression, and CYLD gene mutations, and its main differential diagnosis, the breast solid-basaloid adenoid cystic carcinoma, a malignant tumour that is characterized by the presence of the MYB-NFIB fusion gene and MYB overexpression. METHODS AND RESULTS A 66-year-old female underwent quadrantectomy after an irregular dense shadow was discovered in the right breast at the screening mammogram. Histologically, the tumour displayed features suggestive of a solid-basaloid variant of adenoid cystic carcinoma with a differential diagnosis of cylindroma. Fluorescence in situ hybridization, reverse transcription-polymerase chain reaction, immunohistochemistry and whole-exome sequencing revealed absence of the MYB-NFIB fusion gene, low levels of MYB protein expression and a clonal somatic CYLD splice site mutation associated with loss of heterozygosity of the wild-type allele. CONCLUSIONS The results of the histological, immunohistochemical and molecular analyses were consistent with a diagnosis of breast cylindroma, providing a proof-of-principle that the integration of histopathological and molecular approaches can help to differentiate between a low-malignant potential and a benign breast tumour of triple-negative phenotype.
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Affiliation(s)
- Nicola Fusco
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,School of Pathology, University of Milan, Milan, Italy
| | | | - Luciano G Martelotto
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria R De Filippo
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Salvatore Piscuoglio
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Charlotte K Y Ng
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Raymond S Lim
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - William Jacot
- Department of Surgical Oncology, Montpellier Cancer Institute (ICM), Montpellier, France
| | | | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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Piscuoglio S, Murray M, Fusco N, Marchiò C, Loo FL, Martelotto LG, Schultheis AM, Akram M, Weigelt B, Brogi E, Reis-Filho JS. MED12 somatic mutations in fibroadenomas and phyllodes tumours of the breast. Histopathology 2015; 67:719-29. [PMID: 25855048 DOI: 10.1111/his.12712] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [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: 12/26/2014] [Accepted: 04/06/2015] [Indexed: 02/06/2023]
Abstract
AIMS Somatic mutations in exon 2 of the mediator complex subunit 12 (MED12) gene have been identified in 60% of breast fibroadenomas (FAs). The aim of this study was to define whether phyllodes tumours (PTs) would harbour MED12 somatic mutations in a way akin to FAs. METHODS AND RESULTS A collection of 73 fibroepithelial tumours (including 26 FAs, 25 benign PTs, nine borderline PTs and 13 malignant PTs) from 64 patients was retrieved from the authors' institution. Sections from formalin-fixed paraffin-embedded (FFPE) blocks were microdissected to ensure an enrichment in neoplastic stromal elements of >70%. DNA samples extracted from tumour and matched normal tissues were subjected to Sanger sequencing of exon 2 of the MED12 gene. MED12 exon 2 somatic mutations, including 28 somatic single nucleotide variants and 19 insertions and deletions, were found in 65%, 88%, 78% and 8% of FAs, benign PTs, borderline PTs and malignant PTs, respectively. Malignant PTs harboured MED12 exon 2 somatic mutations significantly less frequently than FAs, benign and borderline PTs. CONCLUSIONS Although MED12 exon 2 somatic mutations probably constitute the driver genetic event of most FAs, benign and borderline PTs, our results suggest that the majority of malignant PTs may be driven by other genetic/epigenetic alterations.
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Affiliation(s)
- Salvatore Piscuoglio
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Melissa Murray
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nicola Fusco
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,School of Pathology, University of Milan, Milan, Italy
| | - Caterina Marchiò
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medical Sciences, University of Turin, Turin, Italy
| | - Florence L Loo
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Luciano G Martelotto
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anne M Schultheis
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Muzaffar Akram
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Edi Brogi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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45
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Ng CKY, Martelotto LG, Gauthier A, Wen HC, Piscuoglio S, Lim RS, Cowell CF, Wilkerson PM, Wai P, Rodrigues DN, Arnould L, Geyer FC, Bromberg SE, Lacroix-Triki M, Penault-Llorca F, Giard S, Sastre-Garau X, Natrajan R, Norton L, Cottu PH, Weigelt B, Vincent-Salomon A, Reis-Filho JS. Intra-tumor genetic heterogeneity and alternative driver genetic alterations in breast cancers with heterogeneous HER2 gene amplification. Genome Biol 2015; 16:107. [PMID: 25994018 PMCID: PMC4440518 DOI: 10.1186/s13059-015-0657-6] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [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: 11/05/2014] [Accepted: 04/20/2015] [Indexed: 01/08/2023] Open
Abstract
Background HER2 is overexpressed and amplified in approximately 15% of invasive breast cancers, and is the molecular target and predictive marker of response to anti-HER2 agents. In a subset of these cases, heterogeneous distribution of HER2 gene amplification can be found, which creates clinically challenging scenarios. Currently, breast cancers with HER2 amplification/overexpression in just over 10% of cancer cells are considered HER2-positive for clinical purposes; however, it is unclear as to whether the HER2-negative components of such tumors would be driven by distinct genetic alterations. Here we sought to characterize the pathologic and genetic features of the HER2-positive and HER2-negative components of breast cancers with heterogeneous HER2 gene amplification and to define the repertoire of potential driver genetic alterations in the HER2-negative components of these cases. Results We separately analyzed the HER2-negative and HER2-positive components of 12 HER2 heterogeneous breast cancers using gene copy number profiling and massively parallel sequencing, and identified potential driver genetic alterations restricted to the HER2-negative cells in each case. In vitro experiments provided functional evidence to suggest that BRF2 and DSN1 overexpression/amplification, and the HER2 I767M mutation may be alterations that compensate for the lack of HER2 amplification in the HER2-negative components of HER2 heterogeneous breast cancers. Conclusions Our results indicate that even driver genetic alterations, such as HER2 gene amplification, can be heterogeneously distributed within a cancer, and that the HER2-negative components are likely driven by genetic alterations not present in the HER2-positive components, including BRF2 and DSN1 amplification and HER2 somatic mutations. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0657-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Charlotte K Y Ng
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
| | - Luciano G Martelotto
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
| | - Arnaud Gauthier
- Department of Tumor Biology, Institut Curie, 75248, Paris, France.
| | - Huei-Chi Wen
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
| | - Salvatore Piscuoglio
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
| | - Raymond S Lim
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
| | - Catherine F Cowell
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
| | - Paul M Wilkerson
- The Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, SW3 6JB, UK.
| | - Patty Wai
- The Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, SW3 6JB, UK.
| | - Daniel N Rodrigues
- The Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, SW3 6JB, UK.
| | - Laurent Arnould
- Department of Pathology and CRB Ferdinand Cabanne, Centre Georges Francois Leclerc, 21000, Dijon, France.
| | - Felipe C Geyer
- Departments of Anatomic Pathology and Oncology, Hospital Israelita Albert Einstein, São Paulo, 05652-900, Brazil.
| | - Silvio E Bromberg
- Departments of Anatomic Pathology and Oncology, Hospital Israelita Albert Einstein, São Paulo, 05652-900, Brazil.
| | - Magali Lacroix-Triki
- Department of Pathology, Institut Claudius Regaud, IUCT-Oncopole, 31059, Toulouse, France.
| | - Frederique Penault-Llorca
- Department of Pathology, Centre Jean Perrin, and University of Auvergne, 63000, Clermont Ferrand, France.
| | - Sylvia Giard
- Department of Pathology, Centre Oscar Lambret, 59000, Lille, France.
| | | | - Rachael Natrajan
- The Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, SW3 6JB, UK.
| | - Larry Norton
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
| | - Paul H Cottu
- Department of Medical Oncology, Institut Curie, 75248, Paris, France.
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
| | | | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA. .,Affiliate Member, Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA. .,Affiliate Member, Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
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Ng CKY, Weigelt B, Piscuoglio S, Wen YH, De Filippo MR, Martelotto LG, Natrajan R, Lim R, Brogi E, Norton L, Vincent-Salomon A, Reis-Filho JS. Abstract P2-03-08: Mutational landscape of metaplastic breast carcinomas. Cancer Res 2015. [DOI: 10.1158/1538-7445.sabcs14-p2-03-08] [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
Introduction: Metaplastic breast carcinoma (MBC) is an aggressive histologic type of breast cancer, which preferentially displays a triple-negative phenotype. These tumors are characterized by the presence of malignant cells exhibiting differentiation towards squamous epithelium or mesenchymal elements, including spindle, chondroid, osseous and rhabdoid differentiation. Unlike other rare histologic types of breast cancer such as adenoid cystic and secretory carcinomas, which are underpinned by the MYB-NFIB and ETV6-NTRK3 fusion genes respectively, pathognomonic genetic alterations have not been identified in MBC. It has been suggested, however, that the frequency of PIK3CA somatic mutations would be significantly higher in MBCs than in other forms of triple-negative disease. Here we sought to characterize the mutational landscape of MBCs by means of high-depth whole exome sequencing analysis.
Material and Methods: Twenty-one triple-negative MBCs were retrieved from the authors’ institutions. Representative sections from frozen blocks were microdissected to ensure tumor cell content greater than 50%. DNA samples extracted from microdissected tumor and matched peripheral blood leukocytes were subjected to high-depth (250x) whole exome sequencing on an Illumina GAIIx or HiSeq2000. Somatic point mutations were called using MuTect and somatic insertions and deletions (indels) were called using Strelka, Varscan2 and Haplotype Caller. Potentially pathogenic mutations were predicted using computational algorithms including PolyPhen-2, Mutation Taster, Mutation Assessor, CHASM and FATHMM. Significantly mutated genes were identified using MutSigCV. Pathway and network enrichment analysis of mutations was performed with Ingenuity Pathway Analysis and HOTNET. The genomic landscape of MBCs was compared with that of triple-negative breast cancers (TNBCs) analyzed as part of The Cancer Genome Atlas project.
Results: A mean of 135 somatic non-synonymous point mutations and indels were identified per MBC. The most frequently mutated gene was TP53, found in 12/21 cases (57%), and the only significantly mutated gene as defined by MutSigCV (q<0.01). The repertoire of somatic mutations found in MBCs was qualitatively similar to that of TNBCs of no special type, and recurrently mutated genes were altered at similar frequencies in MBCs and TNBCs of no special type. When somatic mutations were annotated in pathways and networks, MBCs were found to have potentially pathogenic mutations affecting genes directly related to the PI3K pathway, including pathogenic non-synonymous mutations affecting PIK3CA, PIK3R1, PIK3R2, PIK3C2B, PIK3C2G and PTEN, significantly more frequently than TNBCs of no special type (10 out of 21 MBCs vs. 11 out of 62 TNBCs; Fisher's exact test p-value=0.0099).
Conclusion: The majority (57%) of MBCs harbored non-synonymous mutations affecting TP53. While the frequencies of mutations affecting recurrently mutated genes in MBCs are similar to those found in other forms of TNBCs, MBCs significantly more frequently harbor mutations affecting PI3K pathway-related genes than TNBCs of no special type.
Citation Format: Charlotte KY Ng, Britta Weigelt, Salvatore Piscuoglio, Y Hannah Wen, Maria R De Filippo, Luciano G Martelotto, Rachael Natrajan, Raymond Lim, Edi Brogi, Larry Norton, Anne Vincent-Salomon, Jorge S Reis-Filho. Mutational landscape of metaplastic breast carcinomas [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P2-03-08.
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Affiliation(s)
| | | | | | | | | | | | - Rachael Natrajan
- 2Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research
| | | | - Edi Brogi
- 1Memorial Sloan Kettering Cancer Center
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Martelotto LG, Ng CK, De Filippo MR, Zhang Y, Piscuoglio S, Lim RS, Shen R, Norton L, Reis-Filho JS, Weigelt B. Benchmarking mutation effect prediction algorithms using functionally validated cancer-related missense mutations. Genome Biol 2014; 15:484. [PMID: 25348012 PMCID: PMC4232638 DOI: 10.1186/s13059-014-0484-1] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [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: 06/13/2014] [Accepted: 09/30/2014] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Massively parallel sequencing studies have led to the identification of a large number of mutations present in a minority of cancers of a given site. Hence, methods to identify the likely pathogenic mutations that are worth exploring experimentally and clinically are required. We sought to compare the performance of 15 mutation effect prediction algorithms and their agreement. As a hypothesis-generating aim, we sought to define whether combinations of prediction algorithms would improve the functional effect predictions of specific mutations. RESULTS Literature and database mining of single nucleotide variants (SNVs) affecting 15 cancer genes was performed to identify mutations supported by functional evidence or hereditary disease association to be classified either as non-neutral (n = 849) or neutral (n = 140) with respect to their impact on protein function. These SNVs were employed to test the performance of 15 mutation effect prediction algorithms. The accuracy of the prediction algorithms varies considerably. Although all algorithms perform consistently well in terms of positive predictive value, their negative predictive value varies substantially. Cancer-specific mutation effect predictors display no-to-almost perfect agreement in their predictions of these SNVs, whereas the non-cancer-specific predictors showed no-to-moderate agreement. Combinations of predictors modestly improve accuracy and significantly improve negative predictive values. CONCLUSIONS The information provided by mutation effect predictors is not equivalent. No algorithm is able to predict sufficiently accurately SNVs that should be taken forward for experimental or clinical testing. Combining algorithms aggregates orthogonal information and may result in improvements in the negative predictive value of mutation effect predictions.
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Affiliation(s)
- Luciano G Martelotto
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
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Weinreb I, Piscuoglio S, Martelotto LG, Waggott D, Ng CKY, Perez-Ordonez B, Harding NJ, Alfaro J, Chu KC, Viale A, Fusco N, da Cruz Paula A, Marchio C, Sakr RA, Lim R, Thompson LDR, Chiosea SI, Seethala RR, Skalova A, Stelow EB, Fonseca I, Assaad A, How C, Wang J, de Borja R, Chan-Seng-Yue M, Howlett CJ, Nichols AC, Wen YH, Katabi N, Buchner N, Mullen L, Kislinger T, Wouters BG, Liu FF, Norton L, McPherson JD, Rubin BP, Clarke BA, Weigelt B, Boutros PC, Reis-Filho JS. Hotspot activating PRKD1 somatic mutations in polymorphous low-grade adenocarcinomas of the salivary glands. Nat Genet 2014; 46:1166-9. [PMID: 25240283 DOI: 10.1038/ng.3096] [Citation(s) in RCA: 153] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 08/27/2014] [Indexed: 12/15/2022]
Abstract
Polymorphous low-grade adenocarcinoma (PLGA) is the second most frequent type of malignant tumor of the minor salivary glands. We identified PRKD1 hotspot mutations encoding p.Glu710Asp in 72.9% of PLGAs but not in other salivary gland tumors. Functional studies demonstrated that this kinase-activating alteration likely constitutes a driver of PLGA.
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Affiliation(s)
- Ilan Weinreb
- Department of Pathology, University Health Network, Toronto, Ontario, Canada
| | - Salvatore Piscuoglio
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Luciano G Martelotto
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Daryl Waggott
- 1] Informatics and Bio-Computing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada. [2] Ontario Cancer Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, Onatrio, Canada. [3] Campbell Family Institute for Cancer Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Charlotte K Y Ng
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | | | - Nicholas J Harding
- Informatics and Bio-Computing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Javier Alfaro
- 1] Informatics and Bio-Computing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada. [2] Ontario Cancer Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, Onatrio, Canada. [3] Campbell Family Institute for Cancer Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada. [4] Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Kenneth C Chu
- Informatics and Bio-Computing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Agnes Viale
- Integrated Genomics Operation, Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Nicola Fusco
- 1] Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA. [2] School of Pathology, University of Milan, Milan, Italy
| | - Arnaud da Cruz Paula
- 1] Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA. [2] Instituto Português de Oncologia, Oporto, Portugal
| | - Caterina Marchio
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Rita A Sakr
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Raymond Lim
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Lester D R Thompson
- Department of Pathology, Kaiser Permanente, Woodland Hills Medical Center, Woodland Hills, California, USA
| | - Simion I Chiosea
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Raja R Seethala
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Alena Skalova
- Department of Pathology and Laboratory Medicine, Charles University in Prague, Plzen, Czech Republic
| | - Edward B Stelow
- Department of Pathology, University of Virginia Medical Center, Charlottesville, Virginia, USA
| | - Isabel Fonseca
- 1] Instituto Português de Oncologia Francisco Gentil, Lisbon, Portugal. [2] Faculdade de Medicina de Lisboa, Lisbon, Portugal
| | - Adel Assaad
- Department of Pathology, Virginia Mason Hospital and Seattle Medical Center, Seattle, Washington, USA
| | - Christine How
- 1] Ontario Cancer Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, Onatrio, Canada. [2] Campbell Family Institute for Cancer Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Jianxin Wang
- Informatics and Bio-Computing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Richard de Borja
- Informatics and Bio-Computing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Michelle Chan-Seng-Yue
- Informatics and Bio-Computing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | | | - Y Hannah Wen
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Nora Katabi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Nicholas Buchner
- Cancer Genomics Platform, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Laura Mullen
- Cancer Genomics Platform, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Thomas Kislinger
- 1] Ontario Cancer Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, Onatrio, Canada. [2] Campbell Family Institute for Cancer Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada. [3] Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Bradly G Wouters
- 1] Ontario Cancer Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, Onatrio, Canada. [2] Campbell Family Institute for Cancer Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada. [3] Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Fei-Fei Liu
- 1] Ontario Cancer Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, Onatrio, Canada. [2] Campbell Family Institute for Cancer Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada. [3] Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada. [4] Department of Radiation Oncology, Princess Margaret Hospital and University of Toronto, Toronto, Ontario, Canada
| | - Larry Norton
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - John D McPherson
- 1] Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada. [2] Department of Pathology, Virginia Mason Hospital and Seattle Medical Center, Seattle, Washington, USA
| | - Brian P Rubin
- 1] Department of Molecular Genetics, Lerner Research Institute, Cleveland, Ohio, USA. [2] Robert J. Tomsich Pathology and Laboratory Medicine Institute, Taussig Cancer Center, Cleveland Clinic, Cleveland, Ohio, USA
| | - Blaise A Clarke
- Department of Pathology, University Health Network, Toronto, Ontario, Canada
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Paul C Boutros
- 1] Informatics and Bio-Computing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada. [2] Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada. [3] Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Jorge S Reis-Filho
- 1] Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA. [2]
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Piscuoglio S, Ng CKY, Martelotto LG, Eberle CA, Cowell CF, Natrajan R, Bidard FC, De Mattos-Arruda L, Wilkerson PM, Mariani O, Vincent-Salomon A, Weigelt B, Reis-Filho JS. Integrative genomic and transcriptomic characterization of papillary carcinomas of the breast. Mol Oncol 2014; 8:1588-602. [PMID: 25041824 PMCID: PMC5037246 DOI: 10.1016/j.molonc.2014.06.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [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: 03/09/2014] [Revised: 06/08/2014] [Accepted: 06/17/2014] [Indexed: 02/06/2023] Open
Abstract
Papillary carcinoma (PC) is a rare type of breast cancer, which comprises three histologic subtypes: encapsulated PC (EPC), solid PC (SPC) and invasive PC (IPC). Microarray‐based gene expression and Affymetrix SNP 6.0 gene copy number profiling, and RNA‐sequencing revealed that PCs are luminal breast cancers that display transcriptomic profiles distinct from those of grade‐ and estrogen receptor (ER)‐matched invasive ductal carcinomas of no special type (IDC‐NSTs), and that the papillary histologic pattern is unlikely to be underpinned by a highly recurrent expressed fusion gene or a highly recurrent expressed mutation. Despite displaying similar patterns of gene copy number alterations, significant differences in the transcriptomic profiles of EPCs, SPCs and IPCs were found, and may account for their different histologic features. Papillary carcinomas of the breast display distinctive transcriptomic profiles. Proliferation‐related genes are expressed at low levels in papillary carcinomas. Papillary carcinomas are unlikely to be underpinned by a highly recurrent fusion gene. Papillary carcinomas are unlikely to be underpinned by a highly recurrent expressed mutation.
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Affiliation(s)
- Salvatore Piscuoglio
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York 10065, NY, USA
| | - Charlotte K Y Ng
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York 10065, NY, USA
| | - Luciano G Martelotto
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York 10065, NY, USA
| | - Carey A Eberle
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York 10065, NY, USA
| | - Catherine F Cowell
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York 10065, NY, USA
| | - Rachael Natrajan
- The Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, UK
| | - François-Clement Bidard
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York 10065, NY, USA; Institut Curie, Department of Biopathology and INSERM U934, Paris, France
| | - Leticia De Mattos-Arruda
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York 10065, NY, USA
| | - Paul M Wilkerson
- The Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, UK
| | - Odette Mariani
- Institut Curie, Department of Biopathology and INSERM U934, Paris, France
| | | | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York 10065, NY, USA
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York 10065, NY, USA.
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Piscuoglio S, Ng CKY, Martelotto LG, Cowell CF, Natrajan R, Bidard FC, Wilkerson PM, Mariani O, Vincent-Salomon A, Weigelt B, Reis-Filho JS. Abstract P4-04-08: Genomic and transcriptomic characterization of papillary carcinomas of the breast. Cancer Res 2013. [DOI: 10.1158/0008-5472.sabcs13-p4-04-08] [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
Introduction: Papillary carcinomas (PCs) are a rare (<1%) special histological type of breast cancer that often affects postmenopausal women, and has an overall favorable outcome. Based on their histological characteristics, these tumors are classified into three different subtypes, namely encapsulated papillary carcinomas (EPC), solid papillary carcinomas (SPC) and invasive papillary carcinomas (IPC). In this study, we sought i) to investigate whether PCs constitute a molecular entity distinct from grade- and ER-matched invasive ductal carcinomas of no special type (IDC-NST) at the transcriptomic level, ii) to investigate whether EPC, SPC and IPC display distinct transcriptomic profiles, iii) to characterize the repertoire of copy number alterations in the different subtypes of PC, and iv) to identify recurrent fusion genes that may be potential drivers of this disease.
Material and methods: DNA and RNA were extracted from microdissected PCs (4 SPCs, 5 IPCs and 7 EPCs) and grade- and ER-matched IDC-NSTs (RNA only). 16 PCs and 16 grade- and ER-matched IDC-NSTs were subjected to gene expression profiling using the Illumina Human HT-12 v4 platform. Genes differentially expressed between the PC subtypes were identified using SAM, and functional annotation of these genes was performed using DAVID. Intrinsic molecular subtypes were determined using the PAM50 single sample predictor. Copy number profiling was performed using Affymetrix Human SNP 6.0 arrays with DNA extracted from 16 PCs. In addition, 8 PCs (3 IPCs, 3 EPCs, 2 SPCs) were subjected to paired-end massively parallel RNA sequencing (Illumina GAIIx). Putative expressed fusion transcripts were identified using validated algorithms (i.e. deFuse and Chimerascan), and confirmed by reverse transcription PCR.
Results: PCs were preferentially of histological grade I/II (82%) and ER-positive (100%). Unsupervised analysis revealed that PC subtypes show a high degree of similarity at the transcriptomic level, and form clusters distinct from grade- and ER-matched IDC-NSTs. Compared with IDC-NSTs, PCs displayed reduced expression of genes related to cell motility, adhesion and extracellular matrix. PAM50 subtyping classified 87.5%, 50% and 100% of EPCs, SPCs and IPCs as of luminal subtypes, respectively. 12.5% of EPCs were classified as of basal-like subtype, and 50% of SPCs as of HER2-enriched subtype. At the genomic level, PC subtypes displayed similar patterns of gene copy number aberrations. Five in-frame fusion genes, USF1-CCDC38, MDC1-SFTA2, DLD-LMBR1, PDCL-DENND1A and SUGT1-NOL6, were identified and validated in PCs, however none of these were recurrent in the cases included in this study.
Conclusion: Our results demonstrate that the majority of PCs are of luminal subtype, and support the contention that at the transcriptomic level, PCs are distinct from grade- and ER-matched IDC-NSTs. Our findings also demonstrate that unlike some other histological special types of breast cancer, PCs are not underpinned by a highly recurrent expressed fusion gene.
Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P4-04-08.
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Affiliation(s)
- S Piscuoglio
- Memorial Sloan-Kettering Cancer Center, New York, NY; The Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, United Kingdom; Institut Curie, Paris, France
| | - CKY Ng
- Memorial Sloan-Kettering Cancer Center, New York, NY; The Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, United Kingdom; Institut Curie, Paris, France
| | - LG Martelotto
- Memorial Sloan-Kettering Cancer Center, New York, NY; The Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, United Kingdom; Institut Curie, Paris, France
| | - CF Cowell
- Memorial Sloan-Kettering Cancer Center, New York, NY; The Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, United Kingdom; Institut Curie, Paris, France
| | - R Natrajan
- Memorial Sloan-Kettering Cancer Center, New York, NY; The Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, United Kingdom; Institut Curie, Paris, France
| | - F-C Bidard
- Memorial Sloan-Kettering Cancer Center, New York, NY; The Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, United Kingdom; Institut Curie, Paris, France
| | - PM Wilkerson
- Memorial Sloan-Kettering Cancer Center, New York, NY; The Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, United Kingdom; Institut Curie, Paris, France
| | - O Mariani
- Memorial Sloan-Kettering Cancer Center, New York, NY; The Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, United Kingdom; Institut Curie, Paris, France
| | - A Vincent-Salomon
- Memorial Sloan-Kettering Cancer Center, New York, NY; The Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, United Kingdom; Institut Curie, Paris, France
| | - B Weigelt
- Memorial Sloan-Kettering Cancer Center, New York, NY; The Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, United Kingdom; Institut Curie, Paris, France
| | - JS Reis-Filho
- Memorial Sloan-Kettering Cancer Center, New York, NY; The Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, United Kingdom; Institut Curie, Paris, France
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