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St Paul M, Saibil SD, Kates M, Han S, Lien SC, Laister RC, Hezaveh K, Kloetgen A, Penny S, Guo T, Garcia-Batres C, Smith LK, Chung DC, Elford AR, Sayad A, Pinto D, Mak TW, Hirano N, McGaha T, Ohashi PS. Ex vivo activation of the GCN2 pathway metabolically reprograms T cells, leading to enhanced adoptive cell therapy. Cell Rep Med 2024; 5:101465. [PMID: 38460518 PMCID: PMC10983112 DOI: 10.1016/j.xcrm.2024.101465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 10/14/2023] [Accepted: 02/15/2024] [Indexed: 03/11/2024]
Abstract
The manipulation of T cell metabolism to enhance anti-tumor activity is an area of active investigation. Here, we report that activating the amino acid starvation response in effector CD8+ T cells ex vivo using the general control non-depressible 2 (GCN2) agonist halofuginone (halo) enhances oxidative metabolism and effector function. Mechanistically, we identified autophagy coupled with the CD98-mTOR axis as key downstream mediators of the phenotype induced by halo treatment. The adoptive transfer of halo-treated CD8+ T cells into tumor-bearing mice led to robust tumor control and curative responses. Halo-treated T cells synergized in vivo with a 4-1BB agonistic antibody to control tumor growth in a mouse model resistant to immunotherapy. Importantly, treatment of human CD8+ T cells with halo resulted in similar metabolic and functional reprogramming. These findings demonstrate that activating the amino acid starvation response with the GCN2 agonist halo can enhance T cell metabolism and anti-tumor activity.
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Affiliation(s)
- Michael St Paul
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C1, Canada; Department of Immunology, University of Toronto, Toronto, ON M5S 1C1, Canada
| | - Samuel D Saibil
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C1, Canada; Department of Immunology, University of Toronto, Toronto, ON M5S 1C1, Canada.
| | - Meghan Kates
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C1, Canada; Department of Immunology, University of Toronto, Toronto, ON M5S 1C1, Canada
| | - SeongJun Han
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C1, Canada; Department of Immunology, University of Toronto, Toronto, ON M5S 1C1, Canada
| | - Scott C Lien
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C1, Canada; Department of Immunology, University of Toronto, Toronto, ON M5S 1C1, Canada
| | - Rob C Laister
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Kebria Hezaveh
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Andreas Kloetgen
- Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Susanne Penny
- Human Health Therapeutics Research Centre, National Research Council Canada, Halifax, NS, Canada
| | - Tingxi Guo
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C1, Canada; Department of Immunology, University of Toronto, Toronto, ON M5S 1C1, Canada
| | - Carlos Garcia-Batres
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Logan K Smith
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Douglas C Chung
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C1, Canada; Department of Immunology, University of Toronto, Toronto, ON M5S 1C1, Canada
| | - Alisha R Elford
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Azin Sayad
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Devanand Pinto
- Human Health Therapeutics Research Centre, National Research Council Canada, Halifax, NS, Canada
| | - Tak W Mak
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Naoto Hirano
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C1, Canada; Department of Immunology, University of Toronto, Toronto, ON M5S 1C1, Canada
| | - Tracy McGaha
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C1, Canada; Department of Immunology, University of Toronto, Toronto, ON M5S 1C1, Canada
| | - Pamela S Ohashi
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C1, Canada; Department of Immunology, University of Toronto, Toronto, ON M5S 1C1, Canada.
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2
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Jacquelot N, Xiong L, Cao WHJ, Huang Q, Yu H, Sayad A, Anttila CJA, Baldwin TM, Hickey PF, Amann-Zalcenstein D, Ohashi PS, Nutt SL, Belz GT, Seillet C. PD-1 regulates ILC3-driven intestinal immunity and homeostasis. Mucosal Immunol 2024:S1933-0219(24)00021-7. [PMID: 38492744 DOI: 10.1016/j.mucimm.2024.03.002] [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: 10/19/2023] [Revised: 02/13/2024] [Accepted: 03/08/2024] [Indexed: 03/18/2024]
Abstract
Interleukin-(IL) 22 production by intestinal group 3 innate lymphoid cells (ILC3) is critical to maintain gut homeostasis. However, IL-22 needs to be tightly controlled; reduced IL-22 expression is associated with intestinal epithelial barrier defect while its overexpression promotes tumor development. Here, using a single cell RNAseq approach, we identified a core set of genes associated with increased IL-22 production by ILC3. Among these genes, Programmed cell death 1 (PD-1), extensively studied in the context of cancer and chronic infection, was constitutively expressed on a subset of ILC3. These cells, found in the crypt of the small intestine and colon, displayed superior capacity to produce IL-22. PD-1 expression on ILC3 was dependent on the microbiota and was induced during inflammation in response to IL-23 but, conversely, was reduced in the presence of Notch ligand. PD-1+ ILC3 exhibited distinct metabolic activity with increased glycolytic, lipid and polyamine synthesis associated with augmented proliferation compared with their PD-1- counterparts. Further, PD-1+ ILC3 showed increased expression of mitochondrial antioxidant proteins which enable the cells to maintain their levels of reactive oxygen species (ROS). Loss of PD-1 signaling in ILC3 led to reduced IL-22 production in a cell intrinsic manner. During inflammation, PD-1 expression was increased on NCR- ILC3 while deficiency in PD-1 expression resulted in increased susceptibility to experimental colitis and failure to maintain gut barrier integrity. Collectively, our findings uncover a new function of the PD-1 and highlight the role of PD-1 signaling in the maintenance of gut homeostasis mediated by ILC3 in mice.
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Affiliation(s)
- Nicolas Jacquelot
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1; Arnie Charbonneau Cancer Research Institute, Calgary, AB T2N 4N1, Canada.
| | - Le Xiong
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, 3010, Australia
| | - Wang H J Cao
- Frazer Institute, The University of Queensland, Woolloongabba, Queensland, 4102, Australia
| | - Qiutong Huang
- Frazer Institute, The University of Queensland, Woolloongabba, Queensland, 4102, Australia
| | - Huiyang Yu
- Frazer Institute, The University of Queensland, Woolloongabba, Queensland, 4102, Australia
| | - Azin Sayad
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 2C1, Canada
| | - Casey J A Anttila
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Tracey M Baldwin
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia
| | - Peter F Hickey
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, 3010, Australia
| | - Daniela Amann-Zalcenstein
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, 3010, Australia
| | - Pamela S Ohashi
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 2C1, Canada; Department of Immunology, University of Toronto, Faculty of Medicine, Toronto, Ontario, M5G 2M9, Canada
| | - Stephen L Nutt
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, 3010, Australia
| | - Gabrielle T Belz
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, 3010, Australia; Frazer Institute, The University of Queensland, Woolloongabba, Queensland, 4102, Australia.
| | - Cyril Seillet
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, 3010, Australia.
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3
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Khan S, Chakraborty M, Wu F, Chen N, Wang T, Chan YT, Sayad A, Vásquez JDS, Kotlyar M, Nguyen K, Huang Y, Alibhai FJ, Woo M, Li RK, Husain M, Jurisica I, Gehring AJ, Ohashi PS, Furman D, Tsai S, Winer S, Winer DA. B Cells Promote T Cell Immunosenescence and Mammalian Aging Parameters. bioRxiv 2023:2023.09.12.556363. [PMID: 38529494 PMCID: PMC10962733 DOI: 10.1101/2023.09.12.556363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
A dysregulated adaptive immune system is a key feature of aging, and is associated with age-related chronic diseases and mortality. Most notably, aging is linked to a loss in the diversity of the T cell repertoire and expansion of activated inflammatory age-related T cell subsets, though the main drivers of these processes are largely unknown. Here, we find that T cell aging is directly influenced by B cells. Using multiple models of B cell manipulation and single-cell omics, we find B cells to be a major cell type that is largely responsible for the age-related reduction of naive T cells, their associated differentiation towards pathogenic immunosenescent T cell subsets, and for the clonal restriction of their T cell receptor (TCR). Accordingly, we find that these pathogenic shifts can be therapeutically targeted via CD20 monoclonal antibody treatment. Mechanistically, we uncover a new role for insulin receptor signaling in influencing age-related B cell pathogenicity that in turn induces T cell dysfunction and a decline in healthspan parameters. These results establish B cells as a pivotal force contributing to age-associated adaptive immune dysfunction and healthspan outcomes, and suggest new modalities to manage aging and related multi-morbidity.
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Affiliation(s)
- Saad Khan
- Department of Immunology, University of Toronto, Toronto, ON M5S 1A8, Canada
- Division of Cellular & Molecular Biology, Diabetes Research Group, Toronto General Hospital Research Institute (TGHRI), University Health Network, Toronto, ON M5G 1L7, Canada
- Banting and Best Diabetes Centre, University of Toronto, Toronto, ON M5G 2C4, Canada
| | - Mainak Chakraborty
- Division of Cellular & Molecular Biology, Diabetes Research Group, Toronto General Hospital Research Institute (TGHRI), University Health Network, Toronto, ON M5G 1L7, Canada
- Banting and Best Diabetes Centre, University of Toronto, Toronto, ON M5G 2C4, Canada
| | - Fei Wu
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Nan Chen
- Division of Cellular & Molecular Biology, Diabetes Research Group, Toronto General Hospital Research Institute (TGHRI), University Health Network, Toronto, ON M5G 1L7, Canada
- Banting and Best Diabetes Centre, University of Toronto, Toronto, ON M5G 2C4, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, ON M5S 1A8, Canada
| | - Tao Wang
- Department of Physiology, University of Toronto, ON M5S 1A8, Canada
- Toronto General Hospital Research Institute (TGHRI), University Health Network, Toronto, ON M5G 1L7, Canada
- Ted Rogers Centre for Heart Research, Toronto, ON, M5G 1X8, Canada
| | - Yi Tao Chan
- Department of Immunology, University of Toronto, Toronto, ON M5S 1A8, Canada
- Division of Cellular & Molecular Biology, Diabetes Research Group, Toronto General Hospital Research Institute (TGHRI), University Health Network, Toronto, ON M5G 1L7, Canada
- Banting and Best Diabetes Centre, University of Toronto, Toronto, ON M5G 2C4, Canada
| | - Azin Sayad
- Princess Margaret Cancer Centre, University Health Network, ON M5G 2C1, Canada
| | - Juan Diego Sánchez Vásquez
- Department of Immunology, University of Toronto, Toronto, ON M5S 1A8, Canada
- Toronto General Hospital Research Institute (TGHRI), University Health Network, Toronto, ON M5G 1L7, Canada
| | - Max Kotlyar
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health Network, and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, Toronto, ON M5T 0S8, Canada
| | - Khiem Nguyen
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Yingxiang Huang
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Faisal J. Alibhai
- Toronto General Hospital Research Institute (TGHRI), University Health Network, Toronto, ON M5G 1L7, Canada
| | - Minna Woo
- Department of Immunology, University of Toronto, Toronto, ON M5S 1A8, Canada
- Division of Cellular & Molecular Biology, Diabetes Research Group, Toronto General Hospital Research Institute (TGHRI), University Health Network, Toronto, ON M5G 1L7, Canada
- Banting and Best Diabetes Centre, University of Toronto, Toronto, ON M5G 2C4, Canada
- Division of Endocrinology and Metabolism, Department of Medicine, University Health Network, University of Toronto, ON M5G 1L7, Canada
| | - Ren-Ke Li
- Toronto General Hospital Research Institute (TGHRI), University Health Network, Toronto, ON M5G 1L7, Canada
- Division of Cardiac Surgery, University Health Network, University of Toronto, ON M5G IL7, Canada
| | - Mansoor Husain
- Department of Laboratory Medicine and Pathobiology, University of Toronto, ON M5S 1A8, Canada
- Department of Physiology, University of Toronto, ON M5S 1A8, Canada
- Toronto General Hospital Research Institute (TGHRI), University Health Network, Toronto, ON M5G 1L7, Canada
- Ted Rogers Centre for Heart Research, Toronto, ON, M5G 1X8, Canada
| | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health Network, and Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, Toronto, ON M5T 0S8, Canada
- Departments of Medical Biophysics and Computer Science, and Faculty of Dentistry, University of Toronto, ON M5S 2E4, Canada
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Adam J. Gehring
- Department of Immunology, University of Toronto, Toronto, ON M5S 1A8, Canada
- Toronto Center for Liver Disease & Schwartz Reisman Liver Research Centre, Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Pamela S. Ohashi
- Department of Immunology, University of Toronto, Toronto, ON M5S 1A8, Canada
- Princess Margaret Cancer Centre, University Health Network, ON M5G 2C1, Canada
| | - David Furman
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Sue Tsai
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, AB T6G 2RS, Canada
| | - Shawn Winer
- Department of Laboratory Medicine and Pathobiology, University of Toronto, ON M5S 1A8, Canada
- Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Daniel A. Winer
- Department of Immunology, University of Toronto, Toronto, ON M5S 1A8, Canada
- Division of Cellular & Molecular Biology, Diabetes Research Group, Toronto General Hospital Research Institute (TGHRI), University Health Network, Toronto, ON M5G 1L7, Canada
- Banting and Best Diabetes Centre, University of Toronto, Toronto, ON M5G 2C4, Canada
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
- Department of Laboratory Medicine and Pathobiology, University of Toronto, ON M5S 1A8, Canada
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4
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Sun R, Ge W, Zhu Y, Sayad A, Luna A, Lyu M, Liang S, Tobalina L, Rajapakse VN, Yu C, Zhang H, Fang J, Wu F, Xie H, Saez-Rodriguez J, Ying H, Reinhold WC, Sander C, Pommier Y, Neel BG, Aebersold R, Guo T. Proteomic Dynamics of Breast Cancer Cell Lines Identifies Potential Therapeutic Protein Targets. Mol Cell Proteomics 2023; 22:100602. [PMID: 37343696 PMCID: PMC10392136 DOI: 10.1016/j.mcpro.2023.100602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 04/18/2023] [Accepted: 06/12/2023] [Indexed: 06/23/2023] Open
Abstract
Treatment and relevant targets for breast cancer (BC) remain limited, especially for triple-negative BC (TNBC). We identified 6091 proteins of 76 human BC cell lines using data-independent acquisition (DIA). Integrating our proteomic findings with prior multi-omics datasets, we found that including proteomics data improved drug sensitivity predictions and provided insights into the mechanisms of action. We subsequently profiled the proteomic changes in nine cell lines (five TNBC and four non-TNBC) treated with EGFR/AKT/mTOR inhibitors. In TNBC, metabolism pathways were dysregulated after EGFR/mTOR inhibitor treatment, while RNA modification and cell cycle pathways were affected by AKT inhibitor. This systematic multi-omics and in-depth analysis of the proteome of BC cells can help prioritize potential therapeutic targets and provide insights into adaptive resistance in TNBC.
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Affiliation(s)
- Rui Sun
- Westlake Intelligent Biomarker Discovery Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Weigang Ge
- Bioinformatics Department, Westlake Omics (Hangzhou) Biotechnology Co, Ltd, Hangzhou, Zhejiang, China
| | - Yi Zhu
- Westlake Intelligent Biomarker Discovery Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China; Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Azin Sayad
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Laura and Isaac Perlmutter Cancer Center, New York University Langone Medical Center, New York, New York, USA
| | - Augustin Luna
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA; Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Mengge Lyu
- Westlake Intelligent Biomarker Discovery Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Shuang Liang
- Westlake Intelligent Biomarker Discovery Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
| | - Luis Tobalina
- Bioinformatics and Data Science, Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Vinodh N Rajapakse
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Chenhuan Yu
- Key Laboratory of Experimental Animal and Safety Evaluation, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, China
| | - Huanhuan Zhang
- Key Laboratory of Experimental Animal and Safety Evaluation, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, China
| | - Jie Fang
- Key Laboratory of Experimental Animal and Safety Evaluation, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, China
| | - Fang Wu
- Key Laboratory of Experimental Animal and Safety Evaluation, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, China
| | - Hui Xie
- Key Laboratory of Experimental Animal and Safety Evaluation, Zhejiang Academy of Medical Sciences, Hangzhou, Zhejiang, China
| | - Julio Saez-Rodriguez
- Faculty of Medicine, Institute for Computational Biomedicine, Heidelberg University Hospital, BioQuant, Heidelberg University, Heidelberg, Baden-Württemberg, Germany
| | - Huazhong Ying
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - William C Reinhold
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Chris Sander
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA; Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Yves Pommier
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Benjamin G Neel
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada; Laura and Isaac Perlmutter Cancer Center, New York University Langone Medical Center, New York, New York, USA.
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland; Faculty of Science, University of Zurich, Zurich, Switzerland.
| | - Tiannan Guo
- Westlake Intelligent Biomarker Discovery Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China; Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
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5
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Kondratyev M, Pesic A, Ketela T, Stickle N, Beswick C, Shalev Z, Marastoni S, Samadian S, Dvorkin-Gheva A, Sayad A, Bashkurov M, Boasquevisque P, Datti A, Pugh TJ, Virtanen C, Moffat J, Grénman RA, Koritzinsky M, Wouters BG. Identification of acquired Notch3 dependency in metastatic Head and Neck Cancer. Commun Biol 2023; 6:538. [PMID: 37202533 DOI: 10.1038/s42003-023-04828-9] [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] [Received: 05/07/2020] [Accepted: 04/11/2023] [Indexed: 05/20/2023] Open
Abstract
During cancer development, tumor cells acquire changes that enable them to invade surrounding tissues and seed metastasis at distant sites. These changes contribute to the aggressiveness of metastatic cancer and interfere with success of therapy. Our comprehensive analysis of "matched" pairs of HNSCC lines derived from primary tumors and corresponding metastatic sites identified several components of Notch3 signaling that are differentially expressed and/or altered in metastatic lines and confer a dependency on this pathway. These components were also shown to be differentially expressed between early and late stages of tumors in a TMA constructed from over 200 HNSCC patients. Finally, we show that suppression of Notch3 improves survival in mice in both subcutaneous and orthotopic models of metastatic HNSCC. Novel treatments targeting components of this pathway may prove effective in targeting metastatic HNSCC cells alone or in combination with conventional therapies.
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Affiliation(s)
- Maria Kondratyev
- Princess Margaret Cancer Centre University Health Network, Toronto, ON, Canada.
| | - Aleksandra Pesic
- Princess Margaret Cancer Centre University Health Network, Toronto, ON, Canada
| | - Troy Ketela
- Princess Margaret Cancer Centre University Health Network, Toronto, ON, Canada
| | - Natalie Stickle
- Princess Margaret Cancer Center, Bioinformatics and HPC Core, Toronto, ON, Canada
| | - Christine Beswick
- Princess Margaret Cancer Centre University Health Network, Toronto, ON, Canada
| | - Zvi Shalev
- Princess Margaret Cancer Centre University Health Network, Toronto, ON, Canada
| | - Stefano Marastoni
- Princess Margaret Cancer Centre University Health Network, Toronto, ON, Canada
| | - Soroush Samadian
- Princess Margaret Cancer Centre University Health Network, Toronto, ON, Canada
| | - Anna Dvorkin-Gheva
- Princess Margaret Cancer Centre University Health Network, Toronto, ON, Canada
| | - Azin Sayad
- Princess Margaret Cancer Centre University Health Network, Toronto, ON, Canada
| | - Mikhail Bashkurov
- SMART High-Content Screening facility at Network Biology Collaborative Centre, Toronto, ON, Canada
| | - Pedro Boasquevisque
- Princess Margaret Cancer Centre University Health Network, Toronto, ON, Canada
| | - Alessandro Datti
- SMART High-Content Screening facility at Network Biology Collaborative Centre, Toronto, ON, Canada
| | - Trevor J Pugh
- Princess Margaret Cancer Centre University Health Network, Toronto, ON, Canada
| | - Carl Virtanen
- Princess Margaret Cancer Center, Bioinformatics and HPC Core, Toronto, ON, Canada
| | - Jason Moffat
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | | | | | - Bradly G Wouters
- Princess Margaret Cancer Centre University Health Network, Toronto, ON, Canada.
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6
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Millar DG, Yang SYC, Sayad A, Zhao Q, Nguyen LT, Warner K, Sangster AG, Nakatsugawa M, Murata K, Wang BX, Shaw P, Clarke B, Bernardini MQ, Pugh T, Thibault P, Hirano N, Perreault C, Ohashi PS. Identification of antigenic epitopes recognized by tumor infiltrating lymphocytes in high grade serous ovarian cancer by multi-omics profiling of the auto-antigen repertoire. Cancer Immunol Immunother 2023:10.1007/s00262-023-03413-7. [PMID: 36943460 DOI: 10.1007/s00262-023-03413-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 02/16/2023] [Indexed: 03/23/2023]
Abstract
Immunotherapeutic strategies aimed at enhancing tumor cell killing by tumor-specific T cells hold great potential for reducing tumor burden and prolonging survival of cancer patients. Although many potential tumor antigens have been described, identifying relevant targets when designing anti-cancer vaccines or targeted cell therapies remains a challenge. To identify novel, potentially immunogenic candidate tumor antigens, we performed integrated tumor transcriptomic, seromic, and proteomic analyses of high grade serous ovarian cancer (HGSC) patient tumor samples. We identified tumor neo-antigens and over-expressed antigens using whole exome and RNA sequencing and examined these in relation to patient-matched auto-antibody repertoires. Focusing on MHC class I epitopes recognized by CD8+ T cells, HLA-binding epitopes were identified or predicted from the highly expressed, mutated, or auto-antibody target antigen, or MHC-associated peptides (MAPs). Recognition of candidate antigenic peptides was assessed within the tumor-infiltrating T lymphocyte (TIL) population expanded from each patient. Known tumor-associated antigens (TAA) and cancer/testis antigens (CTA) were commonly found in the auto-antibody and MAP repertoires and CD8+ TILs recognizing epitopes from these antigens were detected, although neither expression level nor the presence of auto-antibodies correlated with TIL recognition. Auto-antibodies against tumor-mutated antigens were found in most patients, however, no TIL recognition of the highest predicted affinity neo-epitopes was detected. Using high expression level, auto-antibody recognition, and epitope prediction algorithms, we identified epitopes in 5 novel antigens (MOB1A, SOCS3, TUBB, PRKAR1A, CCDC6) recognized by HGSC patient TILs. Furthermore, selection of epitopes from the MAP repertoire identified 5 additional targets commonly recognized by multiple patient TILs. We find that the repertoire of TIL specificities includes recognition of highly expressed and immunogenic self-antigens that are processed and presented by tumors. These results indicate an ongoing autoimmune response against a range of self-antigens targeted by HGSC TILs.
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Affiliation(s)
- Douglas G Millar
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
| | - S Y Cindy Yang
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
| | - Azin Sayad
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
| | - Qingchuan Zhao
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, Canada
| | - Linh T Nguyen
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
| | - Kathrin Warner
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
| | - Ami G Sangster
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
| | - Munehide Nakatsugawa
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
| | - Kenji Murata
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
| | - Ben X Wang
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
| | - Patricia Shaw
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
| | - Blaise Clarke
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
| | - Marcus Q Bernardini
- Division of Gynecologic Oncology, Cancer Clinical Research Unit (CCRU), Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Trevor Pugh
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, Canada
| | - Naoto Hirano
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Claude Perreault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, Canada
| | - Pamela S Ohashi
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada.
- Department of Immunology, University of Toronto, Toronto, ON, Canada.
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7
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Han S, Liu ZQ, Chung DC, Paul MS, Garcia-Batres CR, Sayad A, Elford AR, Gold MJ, Grimshaw N, Ohashi PS. Overproduction of IFNγ by Cbl-b-Deficient CD8+ T Cells Provides Resistance against Regulatory T Cells and Induces Potent Antitumor Immunity. Cancer Immunol Res 2022; 10:437-452. [PMID: 35181779 PMCID: PMC9662906 DOI: 10.1158/2326-6066.cir-20-0973] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 11/27/2020] [Revised: 11/22/2021] [Accepted: 02/15/2022] [Indexed: 01/07/2023]
Abstract
Regulatory T cells (Treg) are an integral component of the adaptive immune system that negatively affect antitumor immunity. Here, we investigated the role of the E3 ubiquitin ligase casitas B-lineage lymphoma-b (Cbl-b) in establishing CD8+ T-cell resistance to Treg-mediated suppression to enhance antitumor immunity. Transcriptomic analyses suggested that Cbl-b regulates pathways associated with cytokine signaling and cellular proliferation. We showed that the hypersecretion of IFNγ by Cbl-b-deficient CD8+ T cells selectively attenuated CD8+ T-cell suppression by Tregs. Although IFNγ production by Cbl-b-deficient T cells contributed to phenotypic alterations in Tregs, the cytokine did not attenuate the suppressive function of Tregs. Instead, IFNγ had a profound effect on CD8+ T cells by directly upregulating interferon-stimulated genes and modulating T-cell activation. In murine models of adoptive T-cell therapy, Cbl-b-deficient T cells elicited superior antitumor immune response. Furthermore, Cbl-b-deficient CD8+ T cells were less susceptible to suppression by Tregs in the tumor through the effects of IFNγ. Collectively, this study demonstrates that the hypersecretion of IFNγ serves as a key mechanism by which Cbl-b-deficient CD8+ T cells are rendered resistant to Tregs. See related Spotlight by Wolf and Baier, p. 370.
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Affiliation(s)
- SeongJun Han
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Immunology, University of Toronto, Faculty of Medicine, Toronto, Ontario, Canada
| | - Zhe Qi Liu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Immunology, University of Toronto, Faculty of Medicine, Toronto, Ontario, Canada
| | - Douglas C. Chung
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Immunology, University of Toronto, Faculty of Medicine, Toronto, Ontario, Canada
| | - Michael St. Paul
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Immunology, University of Toronto, Faculty of Medicine, Toronto, Ontario, Canada
| | | | - Azin Sayad
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Alisha R. Elford
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Matthew J. Gold
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Natasha Grimshaw
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Pamela S. Ohashi
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Immunology, University of Toronto, Faculty of Medicine, Toronto, Ontario, Canada.,Corresponding Author: Pamela S. Ohashi, Princess Margaret Cancer Centre, 610 University Avenue, 9-406, Toronto ON M5G 2M9, Canada. Phone: 416-946-4501 ×3689; E-mail:
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8
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Chang CA, Jen J, Jiang S, Sayad A, Mer AS, Brown KR, Nixon AM, Dhabaria A, Tang KH, Venet D, Sotiriou C, Deng J, Wong KK, Adams S, Meyn P, Heguy A, Skok JA, Tsirigos A, Ueberheide B, Moffat J, Singh A, Haibe-Kains B, Khodadadi-Jamayran A, Neel BG. Ontogeny and Vulnerabilities of Drug-Tolerant Persisters in HER2+ Breast Cancer. Cancer Discov 2022; 12:1022-1045. [PMID: 34911733 PMCID: PMC8983469 DOI: 10.1158/2159-8290.cd-20-1265] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [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: 08/29/2020] [Revised: 10/14/2021] [Accepted: 12/10/2021] [Indexed: 11/16/2022]
Abstract
Resistance to targeted therapies is an important clinical problem in HER2-positive (HER2+) breast cancer. "Drug-tolerant persisters" (DTP), a subpopulation of cancer cells that survive via reversible, nongenetic mechanisms, are implicated in resistance to tyrosine kinase inhibitors (TKI) in other malignancies, but DTPs following HER2 TKI exposure have not been well characterized. We found that HER2 TKIs evoke DTPs with a luminal-like or a mesenchymal-like transcriptome. Lentiviral barcoding/single-cell RNA sequencing reveals that HER2+ breast cancer cells cycle stochastically through a "pre-DTP" state, characterized by a G0-like expression signature and enriched for diapause and/or senescence genes. Trajectory analysis/cell sorting shows that pre-DTPs preferentially yield DTPs upon HER2 TKI exposure. Cells with similar transcriptomes are present in HER2+ breast tumors and are associated with poor TKI response. Finally, biochemical experiments indicate that luminal-like DTPs survive via estrogen receptor-dependent induction of SGK3, leading to rewiring of the PI3K/AKT/mTORC1 pathway to enable AKT-independent mTORC1 activation. SIGNIFICANCE DTPs are implicated in resistance to anticancer therapies, but their ontogeny and vulnerabilities remain unclear. We find that HER2 TKI-DTPs emerge from stochastically arising primed cells ("pre-DTPs") that engage either of two distinct transcriptional programs upon TKI exposure. Our results provide new insights into DTP ontogeny and potential therapeutic vulnerabilities. This article is highlighted in the In This Issue feature, p. 873.
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Affiliation(s)
- Chewei Anderson Chang
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Jayu Jen
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York University Langone Health, New York, New York, USA
| | - Shaowen Jiang
- Applied Bioinformatics Laboratories, Office of Science and Research, NYU Grossman School of Medicine, New York University Langone Health, New York, New York, USA
| | - Azin Sayad
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Arvind Singh Mer
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Kevin R. Brown
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | | | - Avantika Dhabaria
- Proteomics Laboratory, Division of Advanced Research and Technology, NYU Grossman School of Medicine, New York University Langone Health, New York, New York, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York University Langone Health, New York, New York, USA
| | - Kwan Ho Tang
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York University Langone Health, New York, New York, USA
| | - David Venet
- Breast Cancer Translational Research Laboratory, Institut Jules Bordet Brussels and Université Libre de Bruxelles (ULB), Belgium
| | - Christos Sotiriou
- Breast Cancer Translational Research Laboratory, Institut Jules Bordet Brussels and Université Libre de Bruxelles (ULB), Belgium.,Medical Oncology Department, Institut Jules Bordet Brussels and Université Libre de Bruxelles (ULB), Belgium
| | - Jiehue Deng
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York University Langone Health, New York, New York, USA.,Division of Hematology and Medical Oncology, Department of Medicine, Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York University Langone Health, New York, New York, USA
| | - Kwok-kin Wong
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York University Langone Health, New York, New York, USA.,Division of Hematology and Medical Oncology, Department of Medicine, Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York University Langone Health, New York, New York, USA
| | - Sylvia Adams
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York University Langone Health, New York, New York, USA.,Division of Hematology and Medical Oncology, Department of Medicine, Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York University Langone Health, New York, New York, USA
| | - Peter Meyn
- Genome Technology Center, Division of Advanced Research Technologies, NYU Grossman School of Medicine, New York University Langone Health, New York, New York, USA
| | - Adriana Heguy
- Genome Technology Center, Division of Advanced Research Technologies, NYU Grossman School of Medicine, New York University Langone Health, New York, New York, USA
| | - Jane A. Skok
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York University Langone Health, New York, New York, USA.,Department of Pathology, NYU Grossman School of Medicine, New York University Langone Health, New York, New York, USA
| | - Aristotelis Tsirigos
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York University Langone Health, New York, New York, USA.,Applied Bioinformatics Laboratories, Office of Science and Research, NYU Grossman School of Medicine, New York University Langone Health, New York, New York, USA.,Department of Pathology, NYU Grossman School of Medicine, New York University Langone Health, New York, New York, USA
| | - Beatrix Ueberheide
- Proteomics Laboratory, Division of Advanced Research and Technology, NYU Grossman School of Medicine, New York University Langone Health, New York, New York, USA.,Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York University Langone Health, New York, New York, USA
| | - Jason Moffat
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Institute of Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Abhyudai Singh
- Department of Electrical and Computer Engineering, University of Delaware, Newark, Delaware, USA.,Department of Biomedical Engineering, University of Delaware, Newark, Delaware, USA
| | - Benjamin Haibe-Kains
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.,Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Vector Institute for Artificial Intelligence, Toronto, Ontario, Canada
| | - Alireza Khodadadi-Jamayran
- Applied Bioinformatics Laboratories, Office of Science and Research, NYU Grossman School of Medicine, New York University Langone Health, New York, New York, USA
| | - Benjamin G. Neel
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York University Langone Health, New York, New York, USA.,Division of Hematology and Medical Oncology, Department of Medicine, Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, New York University Langone Health, New York, New York, USA
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9
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St Paul M, Saibil SD, Han S, Israni-Winger K, Lien SC, Laister RC, Sayad A, Penny S, Amaria RN, Haydu LE, Garcia-Batres CR, Kates M, Mulder DT, Robert-Tissot C, Gold MJ, Tran CW, Elford AR, Nguyen LT, Pugh TJ, Pinto DM, Wargo JA, Ohashi PS. Coenzyme A fuels T cell anti-tumor immunity. Cell Metab 2021; 33:2415-2427.e6. [PMID: 34879240 DOI: 10.1016/j.cmet.2021.11.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 09/20/2021] [Accepted: 11/15/2021] [Indexed: 01/23/2023]
Abstract
Metabolic programming is intricately linked to the anti-tumor properties of T cells. To study the metabolic pathways associated with increased anti-tumor T cell function, we utilized a metabolomics approach to characterize three different CD8+ T cell subsets with varying degrees of anti-tumor activity in murine models, of which IL-22-producing Tc22 cells displayed the most robust anti-tumor activity. Tc22s demonstrated upregulation of the pantothenate/coenzyme A (CoA) pathway and a requirement for oxidative phosphorylation (OXPHOS) for differentiation. Exogenous administration of CoA reprogrammed T cells to increase OXPHOS and adopt the CD8+ Tc22 phenotype independent of polarizing conditions via the transcription factors HIF-1α and the aryl hydrocarbon receptor (AhR). In murine tumor models, treatment of mice with the CoA precursor pantothenate enhanced the efficacy of anti-PDL1 antibody therapy. In patients with melanoma, pre-treatment plasma pantothenic acid levels were positively correlated with the response to anti-PD1 therapy. Collectively, our data demonstrate that pantothenate and its metabolite CoA drive T cell polarization, bioenergetics, and anti-tumor immunity.
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Affiliation(s)
- Michael St Paul
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada; Department of Immunology, University of Toronto, Toronto, ON M5S 1C1, Canada
| | - Samuel D Saibil
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada; Department of Immunology, University of Toronto, Toronto, ON M5S 1C1, Canada
| | - SeongJun Han
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada; Department of Immunology, University of Toronto, Toronto, ON M5S 1C1, Canada
| | - Kavita Israni-Winger
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada; Department of Immunology, University of Toronto, Toronto, ON M5S 1C1, Canada
| | - Scott C Lien
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada; Department of Immunology, University of Toronto, Toronto, ON M5S 1C1, Canada
| | - Rob C Laister
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Azin Sayad
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Susanne Penny
- National Research Council, Human Health Therapeutics, Halifax, NS B3H 3Z1, Canada
| | - Rodabe N Amaria
- Department of Melanoma Medical Oncology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lauren E Haydu
- Department of Surgical Oncology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Meghan Kates
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada; Department of Immunology, University of Toronto, Toronto, ON M5S 1C1, Canada
| | - David T Mulder
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Céline Robert-Tissot
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Matthew J Gold
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Charles W Tran
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada; Department of Immunology, University of Toronto, Toronto, ON M5S 1C1, Canada
| | - Alisha R Elford
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Linh T Nguyen
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Devanand M Pinto
- National Research Council, Human Health Therapeutics, Halifax, NS B3H 3Z1, Canada
| | - Jennifer A Wargo
- Department of Surgical Oncology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Pamela S Ohashi
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada; Department of Immunology, University of Toronto, Toronto, ON M5S 1C1, Canada.
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10
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St Paul M, Saibil SD, Lien SC, Han S, Sayad A, Mulder DT, Garcia-Batres CR, Elford AR, Israni-Winger K, Robert-Tissot C, Zon M, Katz SR, Shaw PA, Clarke BA, Bernardini MQ, Nguyen LT, Haibe-Kains B, Pugh TJ, Ohashi PS. IL6 Induces an IL22 + CD8 + T-cell Subset with Potent Antitumor Function. Cancer Immunol Res 2020; 8:321-333. [PMID: 31964625 DOI: 10.1158/2326-6066.cir-19-0521] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 10/30/2019] [Accepted: 01/13/2020] [Indexed: 11/16/2022]
Abstract
CD8+ T cells can be polarized into several different subsets as defined by the cytokines they produce and the transcription factors that govern their differentiation. Here, we identified the polarizing conditions to induce an IL22-producing CD8+ Tc22 subset, which is dependent on IL6 and the aryl hydrocarbon receptor transcription factor. Further characterization showed that this subset was highly cytolytic and expressed a distinct cytokine profile and transcriptome relative to other subsets. In addition, polarized Tc22 were able to control tumor growth as well as, if not better than, the traditional IFNγ-producing Tc1 subset. Tc22s were also found to infiltrate the tumors of human patients with ovarian cancer, comprising up to approximately 30% of expanded CD8+ tumor-infiltrating lymphocytes (TIL). Importantly, IL22 production in these CD8+ TILs correlated with improved recurrence-free survival. Given the antitumor properties of Tc22 cells, it may be prudent to polarize T cells to the Tc22 lineage when using chimeric antigen receptor (CAR)-T or T-cell receptor (TCR) transduction-based immunotherapies.
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MESH Headings
- Animals
- Basic Helix-Loop-Helix Transcription Factors/immunology
- Cell Polarity/immunology
- Female
- Humans
- Immunotherapy, Adoptive/methods
- Interleukin-6/biosynthesis
- Interleukin-6/genetics
- Interleukin-6/immunology
- Interleukin-6/pharmacology
- Interleukins/immunology
- Lymphocytes, Tumor-Infiltrating/drug effects
- Lymphocytes, Tumor-Infiltrating/immunology
- Melanoma, Experimental/genetics
- Melanoma, Experimental/immunology
- Melanoma, Experimental/pathology
- Melanoma, Experimental/therapy
- Mice, Inbred C57BL
- Mice, Knockout
- Mice, Transgenic
- Ovarian Neoplasms/genetics
- Ovarian Neoplasms/immunology
- Ovarian Neoplasms/pathology
- Ovarian Neoplasms/therapy
- Receptors, Antigen, T-Cell/immunology
- Receptors, Antigen, T-Cell/metabolism
- Receptors, Aryl Hydrocarbon/immunology
- T-Box Domain Proteins/immunology
- T-Lymphocyte Subsets/drug effects
- T-Lymphocyte Subsets/immunology
- T-Lymphocytes, Cytotoxic/drug effects
- T-Lymphocytes, Cytotoxic/immunology
- T-Lymphocytes, Helper-Inducer/drug effects
- T-Lymphocytes, Helper-Inducer/immunology
- Transcriptome
- Tumor Cells, Cultured
- Interleukin-22
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Affiliation(s)
- Michael St Paul
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Samuel D Saibil
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Scott C Lien
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - SeongJun Han
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Azin Sayad
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - David T Mulder
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | | | - Alisha R Elford
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Kavita Israni-Winger
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Céline Robert-Tissot
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Michael Zon
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Sarah Rachel Katz
- Division of Gynecologic Oncology, University Health Network, Toronto, Ontario, Canada
| | - Patricia A Shaw
- Department of Laboratory Medicine and Pathobiology, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Blaise A Clarke
- Department of Laboratory Medicine and Pathobiology, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Marcus Q Bernardini
- Division of Gynecologic Oncology, University Health Network, Toronto, Ontario, Canada
| | - Linh T Nguyen
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Benjamin Haibe-Kains
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Vector Institute for Artificial Intelligence, Toronto, Ontario, Canada
| | - Trevor J Pugh
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Pamela S Ohashi
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada.
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
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11
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MacGregor HL, Sayad A, Elia A, Wang BX, Katz SR, Shaw PA, Clarke BA, Crome SQ, Robert-Tissot C, Bernardini MQ, Nguyen LT, Ohashi PS. High expression of B7-H3 on stromal cells defines tumor and stromal compartments in epithelial ovarian cancer and is associated with limited immune activation. J Immunother Cancer 2019; 7:357. [PMID: 31892360 PMCID: PMC6937725 DOI: 10.1186/s40425-019-0816-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [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: 07/25/2019] [Accepted: 11/11/2019] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND B7-H3 and B7-H4 are highly expressed by many human malignancies making them attractive immunotherapeutic targets. However, their expression patterns and immune contexts in epithelial ovarian cancer have not been well characterized. METHODS We used flow cytometry, immunohistochemistry, and genomic analyses to determine the patterns of B7-H3, B7-H4, and PD-L1 expression by tumor, stromal, and immune cells in the ovarian tumor microenvironment (TME). We analyzed immune cell frequency and expression of PD-1, TIM3, LAG3, ICOS, TIA-1, granzyme B, 2B4, CD107a, and GITR on T cells; CD20, CD22, IgD, BTLA, and CD27 on B cells; CD16 on monocytes; and B7-H3, B7-H4, PD-L1, PD-L2, ICOSL, CD40, CD86, and CLEC9a on antigen-presenting cells by flow cytometry. We determined intratumoral cellular location of immune cells using immunohistochemistry. We compared differences in immune infiltration in tumors with low or high tumor-to-stroma ratio and in tumors from the same or unrelated patients. RESULTS On non-immune cells, B7-H4 expression was restricted to tumor cells whereas B7-H3 was expressed by both tumor and stromal cells. Stromal cells of the ovarian TME expressed high levels of B7-H3 compared to tumor cells. We used this differential expression to assess the tumor-to-stroma ratio of ovarian tumors and found that high tumor-to-stroma ratio was associated with increased expression of CD16 by monocytes, increased frequencies of PD-1high CD8+ T cells, increased PD-L1 expression by APCs, and decreased CLEC9a expression by APCs. We found that expression of PD-L1 or CD86 on APCs and the proportion of PD-1high CD4+ T cells were strongly correlated on immune cells from tumors within the same patient, whereas expression of CD40 and ICOSL on APCs and the proportion of PD-1high CD8+ T cells were not. CONCLUSIONS This study provides insight into the expression patterns of B7-H3 and B7-H4 in the ovarian TME. Further, we demonstrate an association between the tumor-to-stroma ratio and the phenotype of tumor-infiltrating immune cells. We also find that some but not all immune parameters show consistency between peritoneal metastatic sites. These data have implications for the design of immunotherapies targeting these B7 molecules in epithelial ovarian cancer.
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Affiliation(s)
- Heather L MacGregor
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Azin Sayad
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Andrew Elia
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Ben X Wang
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Sarah Rachel Katz
- Division of Gynecologic Oncology, University Health Network, Toronto, Ontario, Canada
| | - Patricia A Shaw
- Department of Laboratory Medicine and Pathobiology, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Blaise A Clarke
- Department of Laboratory Medicine and Pathobiology, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Sarah Q Crome
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada.,Toronto General Hospital Research Institute, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Celine Robert-Tissot
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Marcus Q Bernardini
- Division of Gynecologic Oncology, University Health Network, Toronto, Ontario, Canada
| | - Linh T Nguyen
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Pamela S Ohashi
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada. .,Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada. .,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
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12
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MacGregor HL, Garcia-Batres C, Sayad A, Elia A, Berman HK, Toker A, Katz SR, Shaw PA, Clarke BA, Crome SQ, Robert-Tissot C, Bernardini MQ, Nguyen LT, Ohashi PS. Tumor cell expression of B7-H4 correlates with higher frequencies of tumor-infiltrating APCs and higher CXCL17 expression in human epithelial ovarian cancer. Oncoimmunology 2019; 8:e1665460. [PMID: 31741762 PMCID: PMC6844312 DOI: 10.1080/2162402x.2019.1665460] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 08/29/2019] [Accepted: 08/31/2019] [Indexed: 01/05/2023] Open
Abstract
B7-H4, an immune suppressive member of the B7 family, is highly expressed in a wide variety of human malignancies making it an attractive immunotherapeutic target. However, the association between B7-H4 expression in the tumor microenvironment and the immune infiltrate has not been comprehensively examined. To evaluate the immune tumor microenvironment, we analyzed epithelial ovarian tumors from 28 patients using flow cytometry, immunohistochemistry, functional, and genomic analyses. We determined B7-H4 expression patterns and compared the immune infiltrates of tumors with high and low surface expression of B7-H4. Frequencies and phenotypes of tumor and immune cells were determined using multiple flow cytometry panels. Immunohistochemistry was used to analyze cellular infiltration and location. Publicly available datasets were interrogated to determine intratumoral cytokine and chemokine expression. We found that B7-H4 was predominantly expressed by tumor cells in the epithelial ovarian tumor microenvironment. Surface expression of B7-H4 on tumor cells was correlated with higher levels of infiltrating mature antigen-presenting cells. Further, expression of CXCL17, a monocyte and dendritic cell chemoattractant, correlated strongly with B7-H4 expression. T cells expressed activation markers, but T cells expressing a combination of markers associated with T cell activation/exhaustion phenotype were not prevalent. Overall, our data suggest that B7-H4 is associated with a pro-inflammatory tumor microenvironment.
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Affiliation(s)
- Heather L. MacGregor
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Carlos Garcia-Batres
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Azin Sayad
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Andrew Elia
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Hal K. Berman
- Department of Laboratory Medicine and Pathobiology, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Aras Toker
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Sarah Rachel Katz
- Division of Gynecologic Oncology, University Health Network, Toronto, Ontario, Canada
| | - Patricia A. Shaw
- Department of Laboratory Medicine and Pathobiology, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Blaise A. Clarke
- Department of Laboratory Medicine and Pathobiology, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Sarah Q. Crome
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
- Toronto General Hospital Research Institute, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Celine Robert-Tissot
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Marcus Q. Bernardini
- Division of Gynecologic Oncology, University Health Network, Toronto, Ontario, Canada
| | - Linh T. Nguyen
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Pamela S. Ohashi
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
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13
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Kondratyev M, Pesic A, Sayad A, Ketela T, Stickle N, Virtanen C, Moffat J, Ailles L, Koritzinsky M, Wouters B. Abstract 3054: Cell surface targets in head and neck cancer. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-3054] [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
HNSCC is 6th most common malignancy in the world. Despite advances in diagnosis and treatment, the survival rates remain low due in large part to metastatic disease. The underlying biology associated with metastatic disease and poor outcome in HNSCC remains unclear. Importantly, metastatic cells acquire new properties that permit them to invade surrounding tissues and seed metastasis at distant sites. While these acquired properties contribute to aggressiveness of metastatic cancer and interfere with success of therapies, they can also potentially be exploited to target metastatic cells selectively, sparing toxicity in normal tissues. We used functional genomic technologies to identify new potential therapeutic targets for advanced disease in HNSCC. These targets were identified by conducting whole genome shRNA screens in matched sets of cell lines derived from primary tumors and their respective metastatic sites, with the goal of identifying genes that become essential for cell survival only following metastasis. Since hypoxia is an important attribute of aggressive and therapy resistant subpopulations of HNSCC tumor cells, we also aimed to identify genes that became essential when cells are exposed to hypoxia. We are particularly interested in the identification of contextual synthetic lethal oncogenes expressed on the cell surface, as those are easily targetable by therapeutic antibodies. To identify these targets, we performed high-throughput flow cytometry screening that enables evaluation of 370 validated cell surface antibodies. Cell surface targets differentially expressed in metastatic lines included CECAM and CCR6 that were previously reported to be implicated in metastasis and tumor progression as well as Thy1, a known marker of stem cells involved in regulation of cell adhesion. Cell surface targets induced under hypoxic conditions across the cell lines included CA9, an enzyme that is known to regulate pH in hypoxic cells and be associated with tumor progression, as well as CD338, CD264 and CD312, that were previously associated with stemness in a few models of cancer. Interestingly, the described proteins were also found to be differentially essential in the shRNA screens, highlighting their functional importance in tumor progression and hypoxia survival. We are currently investigating the role of these proteins in HNSCC metastasis utilizing our unique collection of matched pairs of HNSCC lines from multiple patients. Moreover, we are utilizing our pipeline of patient derived HNSCC xenografts to test the effect of knocking down the described genes in patient tumors. We are also testing the expression of selected hits in histological sections of patient tumorsthe 400-patient TMA by immunohistochemistry looking for correlation with tumor grade, aggressiveness, levels of hypoxia as well as presence/absence of metastasis in the patient.
Citation Format: Maria Kondratyev, Aleksandra Pesic, Azin Sayad, Troy Ketela, Natalie Stickle, Carl Virtanen, Jason Moffat, Laurie Ailles, Marianne Koritzinsky, Brad Wouters. Cell surface targets in head and neck cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3054.
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Affiliation(s)
| | | | - Azin Sayad
- 1University Health Network, Toronto, Ontario, Canada
| | - Troy Ketela
- 1University Health Network, Toronto, Ontario, Canada
| | | | - Carl Virtanen
- 1University Health Network, Toronto, Ontario, Canada
| | - Jason Moffat
- 2University of Toronto, Toronto, Ontario, Canada
| | - Laurie Ailles
- 1University Health Network, Toronto, Ontario, Canada
| | | | - Brad Wouters
- 1University Health Network, Toronto, Ontario, Canada
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14
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Kondratyev M, Pesic A, Ketela T, Sayad A, Marastoni S, Mofat J, Virtanen C, Stickle N, Grenman R, Wouters B. Abstract 407: Novel targets in metastatic HNSCC. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-407] [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
Head and neck carcinoma (HNSCC) is 6th most common malignancy in the world. Despite advances in diagnosis and treatment, the survival rates remain low due in large part to metastatic disease. The underlying biology associated with metastatic disease and poor outcome in HNSCC remains unclear. Importantly, metastatic cells acquire new properties that permit them to invade surrounding tissues and seed metastasis at distant sites. While these acquired properties contribute to aggressiveness of metastatic cancer and interfere with success of therapies, they can also potentially be exploited to target metastatic cells selectively, sparing toxicity in normal tissues. The idea behind this selective targeting is based on discovering molecular pathways that became essential in metastatic cells, and then exploiting this vulnerability through targeted agents. We used functional genomic technologies to identify new potential therapeutic targets for advanced disease in HNSCC. These targets were identified by conducting whole genome shRNA screens in matched sets of cell lines derived from primary tumors and their respective metastatic sites, with the goal of identifying genes that become essential for cell survival only following metastasis. Since hypoxia is an important attribute of aggressive and therapy resistant subpopulations of HNSCC tumor cells, we also aimed to identify genes that became essential when cells are exposed to hypoxia. To complement the functional screens data, we performed targeted sequencing of the most commonly altered genes in HNSCC as reported by the TCGA profiled gene expression in the HNSCC cell lines cultured under normoxia and hypoxia using Illumina microarrays. These analyses led to the discovery of genes that are differentially essential in metastatic cells as well as in cells exposed to hypoxic conditions. Utilizing CRISPR technology, we assembled a library of guide RNAs targeting the discovered hits and are currently validating the top identified genes using both in vitro and in vivo systems. To validate hits that are essential in metastatic cells in vivo, we engineered selected “matched” pairs of HNSCC cell lines to express CAS9 protein upon induction with doxycycline. The cells are then transduced with the library of guides and injected subcutaneously into mice; tumors from control and doxycycline treated animals are compared. The difference in genes that are essential for growth of tumors seeded by primary tumor derived and metastasis derived HNSCC cell lines is then assessed in a quantitative manner.
Citation Format: Maria Kondratyev, Aleksandra Pesic, Troy Ketela, Azin Sayad, Stephano Marastoni, Jason Mofat, Carl Virtanen, Natalie Stickle, Reider Grenman, Brad Wouters. Novel targets in metastatic HNSCC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 407.
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Affiliation(s)
| | | | - Troy Ketela
- 1University Health Network, Toronto, Ontario, Canada
| | - Azin Sayad
- 1University Health Network, Toronto, Ontario, Canada
| | | | - Jason Mofat
- 2University of Toronto, Toronto, Ontario, Canada
| | - Carl Virtanen
- 1University Health Network, Toronto, Ontario, Canada
| | | | - Reider Grenman
- 3Turku University and Turku University Hospital, Turku, Finland
| | - Brad Wouters
- 1University Health Network, Toronto, Ontario, Canada
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15
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Cybulska P, Stewart JM, Sayad A, Virtanen C, Shaw PA, Clarke B, Stickle N, Bernardini MQ, Neel BG. A Genomically Characterized Collection of High-Grade Serous Ovarian Cancer Xenografts for Preclinical Testing. The American Journal of Pathology 2018; 188:1120-1131. [DOI: 10.1016/j.ajpath.2018.01.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Revised: 12/06/2017] [Accepted: 01/16/2018] [Indexed: 10/18/2022]
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16
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Gu S, Sayad A, Chan G, Yang W, Lu Z, Virtanen C, Van Etten RA, Neel BG. SHP2 is required for BCR-ABL1-induced hematologic neoplasia. Leukemia 2017; 32:203-213. [PMID: 28804122 PMCID: PMC6005183 DOI: 10.1038/leu.2017.250] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [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: 03/31/2017] [Revised: 07/14/2017] [Accepted: 07/18/2017] [Indexed: 12/16/2022]
Abstract
BCR-ABL1-targeting tyrosine kinase inhibitors (TKIs) have revolutionized treatment of Philadelphia chromosome-positive (Ph+) hematologic neoplasms. Nevertheless, acquired TKI resistance remains a major problem in chronic myeloid leukemia (CML), and TKIs are less effective against Ph+ B-cell acute lymphoblastic leukemia (B-ALL). GAB2, a scaffolding adaptor that binds and activates SHP2, is essential for leukemogenesis by BCR-ABL1, and a GAB2 mutant lacking SHP2 binding cannot mediate leukemogenesis. Using a genetic loss-of-function approach and bone marrow transplantation (BMT) models for CML and BCR-ABL1+ B-ALL, we show that SHP2 is required for BCR-ABL1-evoked myeloid and lymphoid neoplasia. Ptpn11 deletion impairs initiation and maintenance of CML-like myeloproliferative neoplasm, and compromises induction of BCR-ABL1+ B-ALL. SHP2, and specifically, its SH2 domains, PTP activity and C-terminal tyrosines, is essential for BCR-ABL1+, but not WT, pre-B cell proliferation. The MEK/ERK pathway is regulated by SHP2 in WT and BCR-ABL1+ pre-B cells, but is only required for the proliferation of BCR-ABL1+ cells. SHP2 is required for SRC family kinase (SFK) activation only in BCR-ABL1+ pre-B cells. RNAseq reveals distinct SHP2-dependent transcriptional programs in BCR-ABL1+ and WT pre-B cells. Our results suggest that SHP2, via SFKs and ERK, represses MXD3/4 to facilitate a MYC-dependent proliferation program in BCR-ABL1-transformed pre-B cells.
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Affiliation(s)
- S Gu
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Center, Toronto, Ontario, Canada
| | - A Sayad
- Princess Margaret Cancer Center, Toronto, Ontario, Canada
| | - G Chan
- Princess Margaret Cancer Center, Toronto, Ontario, Canada
| | - W Yang
- Department of Orthopaedics, Brown University Alpert Medical School, Providence, RI, USA
| | - Z Lu
- Princess Margaret Cancer Center, Toronto, Ontario, Canada
| | - C Virtanen
- Princess Margaret Cancer Center, Toronto, Ontario, Canada
| | - R A Van Etten
- Chao Family Comprehensive Cancer Center, Division of Hematology/Oncology, University of California, Irvine, Irvine, CA, USA
| | - B G Neel
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Center, Toronto, Ontario, Canada
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17
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Kondratyev M, Pesic A, Ketela T, Sayad A, Marastoni S, Virtanen C, Ailles L, Samadian S, Bashkurov M, Koritzinsky M, Wouters B. Abstract 3020: Novel therapeutic targets in head and neck cancer. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-3020] [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
HNSCC is 6th most common malignancy in the world. Despite advances in diagnosis and treatment, the survival rates remain low due to frequent recurrences the biology of which remains unclear. Using functional genomic technologies, we identified new therapeutic targets for metastatic disease in HNSCC. Whole genome shRNA screens were conducted in matched sets of cell lines derived from primary tumors and respective metastatic sites, identifying genes essential for cell survival only following metastasis. To test if knockdown of selected targets inhibits metastasis in a therapeutic setting, we established orthotropic model of HNSCC that metastasize to lymph nodes in the mouse. Components of Notch pathway were identified as essential for survival of cells derived from metastatic sites. Whole exome sequencing identified a novel mutation in one of the EGF domains of Notch3 that was acquired only in the metastatic line. Utilizing CRISPR methodology, we established that “fixing” the mutation results in reversal of metastatic phenotype of the cells, making them Notch independent similar to their primary tumor counterparts. Mutations in EGF domains have been reported to influence interaction with specific ligands, dictating which ligand can activate Notch signaling. Our data indicate that a distinct set of target genes is induced upon interaction between Notch3 and Jag2 ligand. Furthermore, our results indicate that suppression of Notch3 improves survival in mice bearing orthotropic tumors derived from the metastatic HNSCC lines. Overall, our data demonstrate that metastatic cells from head and neck tumors acquire dependency on Notch3 signaling. Novel treatments targeting components of this pathway may prove effective in targeting metastatic cells alone or in combination with conventional therapies.
Citation Format: Maria Kondratyev, Aleksandra Pesic, Troy Ketela, Azin Sayad, Stephano Marastoni, Carl Virtanen, Laurie Ailles, Soroush Samadian, Mikhail Bashkurov, Marianne Koritzinsky, Brad Wouters. Novel therapeutic targets in head and neck cancer [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 3020. doi:10.1158/1538-7445.AM2017-3020
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18
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Saremi L, Lotfipanah S, Mohammadi M, Hosseinzadeh H, Sayad A, Saltanatpour Z. Association of HFE gene mutations with nonalcoholic fatty liver disease in the Iranian population. Cell Mol Biol (Noisy-le-grand) 2016; 62:123-128. [PMID: 27894410 DOI: 10.14715/cmb/2016.62.12.21] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Accepted: 11/26/2016] [Indexed: 11/18/2022]
Abstract
To determine whether the HFE gene variants H63D and C282Y are associated with NAFLD in persons with type 2 diabetes, we conducted a case-control study including 145 case of NAFLD patients with a history of type 2 diabetes and 145 matching control. The genomic DNA was extracted from the peripheral venous blood and the genotyping of HFE gene mutations was analyzed using the PCR-RFLP technique. Statistical analysis was performed using SPSS 12.0 software by χ2 test, t test and ANOVA (P<0.05). Data showed no increased frequency of HFE mutations in persons with type 2 diabetes and no association between H63D mutation and NAFLD in the study population. Also, we analyzed index of physiological variables including FBS, lipid profile (TC, TG, LDL-C, and HDL-C), BMI, HbA1c, and micro albuminuria and Cr levels). Data showed there are no relationship between these indexes and HFE gene mutations and either NAFLD as a complication of diabetes. But our results showed a relationship between C282Y mutation and NAFLD in persons with type 2 diabetes. C282Y mutation might be a genetic marker of NAFLD in Iranian population.
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Affiliation(s)
- L Saremi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - S Lotfipanah
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - M Mohammadi
- Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - H Hosseinzadeh
- Department of Biology, Faculty of Science, Yazd University, Yazd, Iran
| | - A Sayad
- Department of Medical Genetics, Shahid Beheshti University of Medical Science, Tehran, Iran
| | - Z Saltanatpour
- Department of Molecular Medicine, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran.
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19
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Kondratyev M, Pesic A, Marastoni S, Ketela T, Moffat J, Virtanen C, Sayad A, Bashkurov M, Dati A, Ailles L, Grenman R, Koritzinsky M, Wouters B. Abstract 3794: Novel therapeutic targets in head and neck cancer. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-3794] [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
HNSCC is 6th most common malignancy in the world. Despite advances in diagnosis and treatment, the survival rates remain low due to frequent recurrences the biology of which remains unclear. Using functional genomic technologies we identified new therapeutic targets for metastatic disease in HNSCC. Whole genome shRNA screens were conducted in matched sets of cell lines derived from primary tumors and respective metastatic sites, identifying genes essential for cell survival only following metastasis. To test if knockdown of selected targets inhibits metastasis in a therapeutic setting, we established orthotropic model of HNSCC that metastasize to lymph nodes in the mouse. Components of Notch pathway were identified as essential for survival of cells derived from metastatic sites. Whole exome sequencing identified a novel mutation in one of the EGF domains of Notch3 that was acquired only in the metastatic line. Mutations in EGF domains have been reported to influence interaction with specific ligands, dictating which ligand can activate Notch signaling. Our data indicate that metastatic, but not primary tumor cells, undergo apoptosis upon knockdown of Notch3 and that a distinct set of target genes is induced upon interaction between Notch3 and Jag2 ligand. Furthermore, our results indicate that suppression of Notch3 improves survival in mice bearing orthotropic tumors derived from the metastatic HNSCC lines. Our data demonstrate that metastatic cells from head and neck tumors acquire dependency on Notch3 signaling. Novel treatments targeting components of this pathway may prove effective in targeting metastatic cells alone or in combination with conventional therapies.
Citation Format: Maria Kondratyev, Aleksandra Pesic, Stephano Marastoni, Troy Ketela, Jason Moffat, Carl Virtanen, Azin Sayad, Mikhail Bashkurov, Alessandro Dati, Laurie Ailles, Reidar Grenman, Marianne Koritzinsky, Brad Wouters. Novel therapeutic targets in head and neck cancer. [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 3794.
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Affiliation(s)
| | | | | | - Troy Ketela
- 3Banting & Best Department of Medical Research, Toronto, Ontario, Canada
| | - Jason Moffat
- 3Banting & Best Department of Medical Research, Toronto, Ontario, Canada
| | - Carl Virtanen
- 4Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Azin Sayad
- 4Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Mikhail Bashkurov
- 5Samuel Lunenfeld Research Institute – Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Alessandro Dati
- 5Samuel Lunenfeld Research Institute – Mount Sinai Hospital, Toronto, Ontario, Canada
| | | | - Reidar Grenman
- 6Dept. of Otorhinolaryngology - Head and Neck Surgery, Turku University and Turku University Hospital, Turku, Finland
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20
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Marcotte R, Sayad A, Brown KR, Sanchez-Garcia F, Reimand J, Haider M, Virtanen C, Bradner JE, Bader GD, Mills GB, Pe'er D, Moffat J, Neel BG. Functional Genomic Landscape of Human Breast Cancer Drivers, Vulnerabilities, and Resistance. Cell 2016; 164:293-309. [PMID: 26771497 DOI: 10.1016/j.cell.2015.11.062] [Citation(s) in RCA: 301] [Impact Index Per Article: 37.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 10/09/2015] [Accepted: 11/23/2015] [Indexed: 12/12/2022]
Abstract
Large-scale genomic studies have identified multiple somatic aberrations in breast cancer, including copy number alterations and point mutations. Still, identifying causal variants and emergent vulnerabilities that arise as a consequence of genetic alterations remain major challenges. We performed whole-genome small hairpin RNA (shRNA) "dropout screens" on 77 breast cancer cell lines. Using a hierarchical linear regression algorithm to score our screen results and integrate them with accompanying detailed genetic and proteomic information, we identify vulnerabilities in breast cancer, including candidate "drivers," and reveal general functional genomic properties of cancer cells. Comparisons of gene essentiality with drug sensitivity data suggest potential resistance mechanisms, effects of existing anti-cancer drugs, and opportunities for combination therapy. Finally, we demonstrate the utility of this large dataset by identifying BRD4 as a potential target in luminal breast cancer and PIK3CA mutations as a resistance determinant for BET-inhibitors.
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Affiliation(s)
- Richard Marcotte
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Azin Sayad
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Kevin R Brown
- The Donnelly Centre, University of Toronto, ON M5S 3E1, Canada
| | | | - Jüri Reimand
- The Donnelly Centre, University of Toronto, ON M5S 3E1, Canada
| | - Maliha Haider
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Carl Virtanen
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Department of Medicine, Harvard Medical School, Boston, MA 02215, USA
| | - Gary D Bader
- The Donnelly Centre, University of Toronto, ON M5S 3E1, Canada
| | - Gordon B Mills
- Department of Systems Biology, Sheikh Khalifa Al Nahyan Ben Zayed Institute for Personalized Cancer Therapy, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Dana Pe'er
- Columbia University, New York, NY 10027, USA
| | - Jason Moffat
- The Donnelly Centre, University of Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, ON M5S 3E1, Canada
| | - Benjamin G Neel
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Laura and Isaac Perlmutter Cancer Centre, NYU-Langone Medical Center, NY 10016, USA.
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21
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Hsu T, Simon L, Neill N, marcotte R, Sayad A, Karlin K, Lagisetti C, Cooper T, Webb T, Neel B, Shaw C, Westbrook T(. Abstract PR02: The spliceosome is a therapeutic vulnerability in MYC-driven breast cancer. Mol Cancer Res 2016. [DOI: 10.1158/1557-3125.advbc15-pr02] [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
c-MYC (MYC) hyperactivation is one of the most common drivers of human breast cancer and correlates with poor prognosis. Despite intensive study, the MYC oncogene remains recalcitrant to therapeutic inhibition. Like other classic oncogenes, hyperactivation of MYC leads to collateral stresses onto breast cancer cells, suggesting that tumors harbor unique vulnerabilities arising from oncogenic activation of MYC. Herein, we discover the spliceosome as a new target of oncogenic stress in MYC-driven cancers. We demonstrate that core components of the spliceosome and its catalytic activity are required to tolerate oncogenic MYC. Notably, MYC hyperactivation induces global changes in mRNA metabolism and increases the burden on the core spliceosome to process pre-mRNA. In primary human breast cancers, MYC hyperactivation is associated with altered splicing efficiency. In contrast to normal mammary epithelium, partial inhibition of the spliceosome in MYC-hyperactivated breast cancers leads to global intron retention, widespread defects in pre-mRNA maturation, and deregulation of essential cell processes. Importantly, genetic or pharmacologic inhibition of the spliceosome in vivo impairs survival, tumorigenicity, and metastatic proclivity of MYC-dependent breast cancers. Collectively, these data suggest that oncogenic MYC confers a collateral stress on splicing and that components of the spliceosome are therapeutic entry points for aggressive MYC-driven breast cancers.
Citation Format: Tiffany Hsu, Lukas Simon, Nicholas Neill, richard marcotte, Azin Sayad, Kristen Karlin, Chandraiah Lagisetti, Thomas Cooper, Thomas Webb, Benjamin Neel, Chad Shaw, Thomas (“Trey”) Westbrook. The spliceosome is a therapeutic vulnerability in MYC-driven breast cancer. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Breast Cancer Research; Oct 17-20, 2015; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Res 2016;14(2_Suppl):Abstract nr PR02.
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Affiliation(s)
| | | | | | | | - Azin Sayad
- 2Princess Margaret Cancer Center, Toronto, ON, Canada,
| | | | | | | | | | - Benjamin Neel
- 2Princess Margaret Cancer Center, Toronto, ON, Canada,
| | - Chad Shaw
- 1Baylor College of Medicine, Houston, TX,
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Gu S, Lheureux S, Sayad A, Ben-David LH, Vyarvelska I, Cybulska P, Bernardini M, Rosen B, Oza A, Neel BG. Abstract PR16: Computational modeling of serous ovarian carcinoma dynamics: Implications for screening and therapy. Clin Cancer Res 2016. [DOI: 10.1158/1557-3265.ovca15-pr16] [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
High-grade serous ovarian carcinoma (HG-SOC) is the most common subtype of ovarian cancer and has the worst prognosis. There is intense controversy on whether the temporal order of cytoreductive surgery and chemotherapy affects treatment outcome, with the main options being primary debulking surgery with adjuvant chemotherapy (PDS) versus neo-adjuvant chemotherapy with interval debulking surgery (NACT). Although some studies report that PDS-treated patients survive significantly longer than those receiving NACT, other reports showed no significant difference patient outcome. To address this question in an unbiased way, we used computational modeling and simulated HG-SOC progression dynamics with different treatments.
We developed a mathematical framework to predict the evolution of chemotherapy resistance, and populated our model with clinical data from nearly 300 patients receiving PDS or NACT from multiple institutes. After estimating the rates of proliferation and mutation of carcinoma cells, we determined that most HG-SOC patients likely harbor chemotherapy-resistant cancer cells at diagnosis. Furthermore, we predicted the effects of PDS and NACT on the number of sensitive and resistant cells, as well as patient survival following treatment, and found that our model closely recapitulated clinical observations in both training and test sets. Based on our results, we predict that PDS with optimal debulking (<1mm residual tumor) has the potential to be curative because surgery can sometimes remove all chemo-resistant cells, while adjuvant chemotherapy depletes the remaining chemo-sensitive cells. By contrast, NACT is unlikely to cure the disease because it depletes chemo-sensitive cells that can mark the location of accompanying “passenger” chemo-resistant cells. Our model also predicts that PDS should have a better outcome than NACT, when controlled for residual tumor size.
Finally, we evaluated the potential benefits of early diagnosis of naive or relapsed HG-SOC. We recapitualted the clinical finding that CA125-based earlier diagnosis of relapsed cancer does not improve survival compared to physical-symptom-based diagnosis. We also predict that more sensitive detection methods (such as ctDNA-based diagnosis) are unlikely to improve survival post-relapse with current chemotherapy, because earlier diagnosis does not decrease the number of chemo-resistant cells, which are already enriched at recurrence. By contrast, our model predicts that with sufficiently sensitive assays, early detection of treatment-naive HG-SOC could improve survival time and increase chance of cure.
This abstract is also presented as Poster B19.
Citation Format: Shengqing Gu, Stephanie Lheureux, Azin Sayad, Liat Hogen Ben-David, Iryna Vyarvelska, Paulina Cybulska, Marcus Bernardini, Barry Rosen, Amit Oza, Benjamin G. Neel. Computational modeling of serous ovarian carcinoma dynamics: Implications for screening and therapy. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research: Exploiting Vulnerabilities; Oct 17-20, 2015; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(2 Suppl):Abstract nr PR16.
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Affiliation(s)
- Shengqing Gu
- 1University of Toronto, Toronto, ON, Canada,
- 4Princess Margaret Cancer Center, Toronto, ON, Canada
| | | | - Azin Sayad
- 2University Health Network, Toronto, ON, Canada,
| | | | | | | | | | - Barry Rosen
- 2University Health Network, Toronto, ON, Canada,
| | - Amit Oza
- 2University Health Network, Toronto, ON, Canada,
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23
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Taheri M, Valipour E, Rasuli S, Sayad A, Movafagh A, Mahdi Eftekharian M, Mazdeh M. Evaluation of migraine in patients with ischaemic stroke. Acta Clin Belg 2015; 70:403-7. [PMID: 26138909 DOI: 10.1179/2295333715y.0000000040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
An association between migraine and ischaemic stroke has been observed for many years, but the exact mechanisms by which migraine can lead to stroke are still unknown. The purpose of this study was to determine the prevalence of migraine headaches in patients with ischaemic stroke. In this prospective cohort study, we assessed 323 patients with ischaemic stroke; these diagnoses were assigned based on the International Headache Society criteria for migraine with or without aura. Patients were recruited without major risk factors such as stroke, hypertension, hyperlipidaemia, diabetes, taking oral contraceptive pills, history of drug abuse and trauma in issue of their Stroke. Data were collected via a written questionnaire upon admission and were analysed with SPSS version 16 software. Comparisons were performed using Mann-Whitney's U test and chi-square and t-test. Migraine headache was present in 11.2% (36 of 323) of patients, 8.1% of women and 3.1% of men. Migraine prevalence was highest in the age over 60 years. There was a history of migraine without aura for over 2 years in 6.2% of patients with ischaemic stroke. Also, we found no significant correlation between migraine headache and location of the lesion in patients with ischaemic stroke.
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Affiliation(s)
- M Taheri
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences , Tehran, Iran
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24
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Marcotte R, Sayad A, Iorio C, Moffat J, Neel BG. Abstract A2-07: Integrative functional genomics of breast cancer. Cancer Res 2015. [DOI: 10.1158/1538-7445.transcagen-a2-07] [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
Breast cancer is the most common invasive malignancy and second leading cause of cancer death in women. Earlier detection and better therapy have led to >85% 5-year survival. Still, half of affected women will die from breast cancer, reflecting incomplete knowledge of how to target this disease. Large-scale genomic technologies enable the identification of genetic/epigenetic abnormalities, but defining which defects are functionally important remains challenging. In addition, the products of many oncogenes and tumor suppressor genes are not “druggable”. However, such abnormalities can cause unanticipated gene/pathway dependencies (“synthetic lethality”), providing alternate avenues for drug development. Lentiviral-based shRNA libraries enable genome-wide screening of cultured cancer cells in a pooled format, facilitating the identification of genes necessary for cancer cell proliferation and survival in cultured cells. If enough lines are tested and companion genomic data are available, “functional” and “genomic” signatures can be compared. Such information can suggest new drug targets, partnered to specific biomarkers.
We screened a panel of > 75 breast cancer cell lines using an 80,000 lentiviral shRNA library targeting 16,000 genes, and integrated the screen results with gene expression, somatic copy-number alteration (SCNA), miRNA expression, somatic mutation and reverse-phase protein array (RPPA) data derived from the same lines. We also developed a new mixed effect regression model (siMEM) that provides increased power for interrogating screen results. The resultant analyses reveal several general features associated with pooled shRNA screens: 1) Increased gene expression, when associated with increased essentiality, specifically enriches for known and novel driver genes. Conversely, high gene expression decreases essentiality for numerous housekeeping genes, likely because of shRNA titration; 2) Increased essentiality with heterozygous copy loss expands the number of reported CYCLOPS and GO genes; 3) Integration of essentiality with recurrent SCNAs identifies novel cis and trans dependencies, suggesting new driver genes and synthetic lethal interactions, respectively. In addition, we identified several classes of gene “dropouts” that are required for survival or growth of most cell lines, irrespective of subtype and several “subtype-specific” genes, whose essentiality is restricted to a defined subtype. These include well-known subtype-specific genes, as well new ones, such as BRD4. We confirmed that BRD4 associates with the estrogen receptor (ER) and acts as an ER co-activator, a function dependent on its BET domain. However, we also found that BRD4 has BET domain-independent functions. Remarkably, the BET domain-dependent functions of BRD4 can be abrogated by PIK3CA mutations, most likely via activation of an estrogen-independent/ER-dependent survival pathway. Consequently, breast cancer lines harboring PIK3CA mutations are resistant to BET domain inhibitors (BET-I), but are sensitive to a combination of BET-I and PI3K pathway inhibitors in vitro and in vivo.
Overall, our study represents an extensive functional genetic survey of breast cancer, reveals complexities between genomic and functional genomic results, uncovers unexpected gene dependencies and suggests potential novel therapeutic targets and drug combinations for genetically defined breast cancer subtypes.
Citation Format: Richard Marcotte, Azin Sayad, Cathy Iorio, Jason Moffat, Benjamin G. Neel. Integrative functional genomics of breast cancer. [abstract]. In: Proceedings of the AACR Special Conference on Translation of the Cancer Genome; Feb 7-9, 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 1):Abstract nr A2-07.
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Affiliation(s)
| | - Azin Sayad
- 1Princess Margaret Cancer Centre, Toronto, ON, Canada,
| | - Cathy Iorio
- 1Princess Margaret Cancer Centre, Toronto, ON, Canada,
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25
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Gu S, Lheureux S, Sayad A, Hogen LF, Vyarvelska I, Cybulska P, Bernardini M, Rosen B, Oza A, Neel BG. Abstract B2-06: Computational modeling of serous ovarian carcinoma dynamics: Implications for screening and therapy. Cancer Res 2015. [DOI: 10.1158/1538-7445.compsysbio-b2-06] [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
High-grade serous ovarian carcinoma (HG-SOC) is the most common subtype of ovarian cancer and has the worst prognosis. There is intense controversy on whether the temporal order of cytoreductive surgery and chemotherapy affects treatment outcome, with the main options being primary debulking surgery with adjuvant chemotherapy (PDS) versus neo-adjuvant chemotherapy with interval debulking surgery (NACT). Although some studies report that PDS-treated patients survive significantly longer than those receiving NACT, other reports showed no significant difference in patient outcome. To address this question in an unbiased way, we used computational modeling and simulated HG-SOC progression dynamics with different treatments.
We developed a mathematical framework to predict the evolution of chemotherapy resistance, and populated our model with survival data from >300 patients receiving PDS or NACT. After estimating the rates of proliferation and mutation of carcinoma cells, we determined that most HG-SOC patients likely harbor chemotherapy-resistant cancer cells at diagnosis. Furthermore, we predicted the effects of PDS and NACT on the number of sensitive and resistant cells, as well as patient survival following treatment, and found that our model closely recapitulated clinical observations in both training and test sets. Based on our results, we predict that PDS with optimal debulking (<1mm residual tumor) has the potential to be curative because surgery can sometimes remove all chemo-resistant cells, while adjuvant chemotherapy depletes the remaining chemo-sensitive cells. By contrast, NACT is unlikely to cure the disease because it depletes chemo-sensitive cells that can mark the location of accompanying “passenger” chemo-resistant cells. Moreover, NACT results in extensive enrichment of chemo-resistant cells before surgery, but the deposits of such cells are typically too small to be visualized at eventual surgery. Our model also predicts that PDS should have a better outcome than NACT, when controlled for residual tumor size.
Finally, we evaluated the potential benefits of early diagnosis of naïve or relapsed HG-SOC. We recapitulated the clinical finding that CA125-based earlier diagnosis of relapsed cancer does not improve survival. We also predict that more sensitive detection methods (such as ctDNA-based diagnosis) are unlikely to improve survival post-relapse with current chemotherapy, because earlier diagnosis does not decrease the number of chemo-resistant cells, which are already enriched at recurrence. By contrast, our model predicts that with sufficiently sensitive assays, early detection could improve survival time and increase chances of cure.
Citation Format: Shengqing Gu, Stephanie Lheureux, Azin Sayad, Liat Frida Hogen, Iryna Vyarvelska, Paulina Cybulska, Marcus Bernardini, Barry Rosen, Amit Oza, Benjamin G. Neel. Computational modeling of serous ovarian carcinoma dynamics: Implications for screening and therapy. [abstract]. In: Proceedings of the AACR Special Conference on Computational and Systems Biology of Cancer; Feb 8-11 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 2):Abstract nr B2-06.
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Affiliation(s)
| | | | - Azin Sayad
- 2University Health Network, Toronto, ON, Canada
| | | | | | | | | | - Barry Rosen
- 2University Health Network, Toronto, ON, Canada
| | - Amit Oza
- 2University Health Network, Toronto, ON, Canada
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26
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Abstract
Abstract
Breast cancer is the most common invasive malignancy and second leading cause of cancer death in women. Earlier detection and better therapy have led to >85% 5-year survival. Still, half of affected women will die from breast cancer, reflecting incomplete knowledge of how to target this disease. Large-scale genomic technologies enable the identification of genetic/epigenetic abnormalities, but defining which defects are functionally important remains challenging. In addition, the products of many oncogenes and tumor suppressor genes are not “druggable”. However, such abnormalities can cause unanticipated gene/pathway dependencies (“synthetic lethality”), providing alternate avenues for drug development. Lentiviral-based shRNA libraries enable genome-wide screening of cultured cancer cells in a pooled format, facilitating the identification of genes necessary for cancer cell proliferation and survival in cultured cells. If enough lines are tested and companion genomic data are available, “functional” and “genomic” signatures can be compared. Such information can suggest new drug targets, partnered to specific biomarkers.
We screened a panel of > 75 breast cancer cell lines using an 80,000 lentiviral shRNA library targeting 16,000 genes, and integrated the screen results with gene expression, somatic copy-number alteration (SCNA), miRNA expression, somatic mutation and reverse-phase protein array (RPPA) data derived from the same lines. We also developed a new mixed effect regression model (siMEM) that provides increased power for interrogating screen results. The resultant analyses reveal several general features associated with pooled shRNA screens: 1) Increased gene expression, when associated with increased essentiality, specifically enriches for known and novel driver genes. Conversely, high gene expression decreases essentiality for numerous housekeeping genes, likely because of shRNA titration; 2) Increased essentiality with heterozygous copy loss expands the number of reported CYCLOPS and GO genes; 3) Integration of essentiality with recurrent SCNAs identifies novel cis and trans dependencies, suggesting new driver genes and synthetic lethal interactions, respectively. In addition, we identified several classes of gene “dropouts” that are required for survival or growth of most cell lines, irrespective of subtype and several “subtype-specific” genes, whose essentiality is restricted to a defined subtype. These include well-known subtype-specific genes, as well new ones, such as BRD4. We confirmed that BRD4 associates with the estrogen receptor (ER) and acts as an ER co-activator, a function dependent on its BET domain. However, we also found that BRD4 has BET domain-independent functions. Remarkably, the BET domain-dependent functions of BRD4 can be abrogated by PIK3CA mutations, most likely via activation of an estrogen-independent/ER-dependent survival pathway. Consequently, breast cancer lines harboring PIK3CA mutations are resistant to BET domain inhibitors (BET-I), but are sensitive to a combination of BET-I and PI3K pathway inhibitors in vitro and in vivo.
Overall, our study represents an extensive functional genetic survey of breast cancer, reveals complexities between genomic and functional genomic results, uncovers unexpected gene dependencies and suggests potential novel therapeutic targets and drug combinations for genetically defined breast cancer subtypes.
Citation Format: Richard Marcotte, Azin Sayad, Cathy Iorio, Jason Moffat, Benjamin G. Neel. Integrative functional genomics of breast cancer. [abstract]. In: Proceedings of the AACR Special Conference on Computational and Systems Biology of Cancer; Feb 8-11 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 2):Abstract nr PR14.
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Affiliation(s)
| | - Azin Sayad
- 1Princess Margaret Cancer Centre, Toronto, ON, Canada,
| | - Cathy Iorio
- 1Princess Margaret Cancer Centre, Toronto, ON, Canada,
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27
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Vandenplas Y, De Greef E, Xinias I, Vrani O, Mavroudi A, Hammoud M, Al Refai F, Khalife MC, Sayad A, Noun P, Farah A, Makhoul G, Orel R, Sokhn M, L'Homme A, Mohring MP, Merhi BA, Boulos J, El Masri H, Halut C. Safety of a thickened extensive casein hydrolysate formula. Nutrition 2015; 32:206-12. [PMID: 26704966 DOI: 10.1016/j.nut.2015.08.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [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: 04/06/2015] [Revised: 07/14/2015] [Accepted: 08/08/2015] [Indexed: 12/28/2022]
Abstract
OBJECTIVES Cow's milk allergy (CMA) is treated in formula-fed infants with an extensive protein hydrolysate. This study aimed to evaluate the nutritional safety of a non-thickened and thickened extensively casein hydrolyzed protein formula (NT- and T-eCHF) in infants with CMA. METHODS Infants younger than 6 mo old with a positive cow milk challenge test, positive IgE, or skin prick test for cow milk were selected. Weight and length were followed during the 6 mo intervention with the NT-eCHF and T-eCHF. RESULTS A challenge was performed in 50/71 infants with suspected CMA and was positive in 34/50. All children with confirmed CMA tolerated the eCHF. The T-eCHF leads to a significant improvement of the stool consistency in the whole population and in the subpopulation of infants with proven CMA. Height and weight evolution was satisfactory throughout the 6 mo study. CONCLUSIONS The eCHF fulfills the criteria of a hypoallergenic formula and the NT- and T-eCHF reduced CMA symptoms. Growth was within normal range.
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Affiliation(s)
- Yvan Vandenplas
- UZ Brussel, Department of Pediatrics, Vrije Universiteit Brussel, Brussels, Belgium.
| | - Elisabeth De Greef
- UZ Brussel, Department of Pediatrics, Vrije Universiteit Brussel, Brussels, Belgium
| | - I Xinias
- Department of Pediatrics, Hippocration Hospital, Thessaloniki, Greece
| | - O Vrani
- Department of Pediatrics, Hippocration Hospital, Thessaloniki, Greece
| | - A Mavroudi
- Department of Pediatrics, Hippocration Hospital, Thessaloniki, Greece
| | - M Hammoud
- Faculty of Medicine, Department of Pediatrics, Kuwait University, Kuwait City, Kuwait
| | - F Al Refai
- Faculty of Medicine, Department of Pediatrics, Kuwait University, Kuwait City, Kuwait
| | - M C Khalife
- Holy Spirit University of Kaslik, Kaslikand UH-NDS, Beyruth, Lebanon
| | - A Sayad
- Holy Spirit University of Kaslik, Kaslikand UH-NDS, Beyruth, Lebanon
| | - P Noun
- Holy Spirit University of Kaslik, Kaslikand UH-NDS, Beyruth, Lebanon
| | - A Farah
- Holy Spirit University of Kaslik, Kaslikand UH-NDS, Beyruth, Lebanon
| | | | - R Orel
- University Children's Hospital, Ljubljana, Slovenia
| | - M Sokhn
- University of Balamand, Beirut, Lebanon
| | - A L'Homme
- Department of Pediatrics, La Citadelle Regional Hospital, Liège, Belgium
| | - M P Mohring
- Department of Pediatrics, La Citadelle Regional Hospital, Liège, Belgium
| | | | - J Boulos
- Mount Lebanon Hospital, Beyruth, Lebanon
| | - H El Masri
- Bahman Hospital, Medical Director Dar Hawraa Center, Beyruth, Lebanon
| | - C Halut
- Department of Pediatrics, Regional Hospital, Namur, Belgium
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28
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Hsu TYT, Simon LM, Neill NJ, Marcotte R, Sayad A, Bland CS, Echeverria GV, Sun T, Kurley SJ, Tyagi S, Karlin KL, Dominguez-Vidaña R, Hartman JD, Renwick A, Scorsone K, Bernardi RJ, Skinner SO, Jain A, Orellana M, Lagisetti C, Golding I, Jung SY, Neilson JR, Zhang XHF, Cooper TA, Webb TR, Neel BG, Shaw CA, Westbrook TF. The spliceosome is a therapeutic vulnerability in MYC-driven cancer. Nature 2015; 525:384-8. [PMID: 26331541 PMCID: PMC4831063 DOI: 10.1038/nature14985] [Citation(s) in RCA: 335] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 07/24/2015] [Indexed: 12/14/2022]
Abstract
c-MYC (MYC) overexpression or hyperactivation is one of the most common drivers of human cancer. Despite intensive study, the MYC oncogene remains recalcitrant to therapeutic inhibition. MYC is a transcription factor, and many of its pro-tumorigenic functions have been attributed to its ability to regulate gene expression programs1–3. Notably, oncogenic MYC activation has also been shown to increase total RNA and protein production in many tissue and disease contexts4–7. While such increases in RNA and protein production may endow cancer cells with pro-tumor hallmarks, this elevation in synthesis may also generate new or heightened burden on MYC-driven cancer cells to properly process these macromolecules8. Herein, we discover the spliceosome as a new target of oncogenic stress in MYC-driven cancers. We identify BUD31 as a MYC-synthetic lethal gene, and demonstrate that BUD31 is a component of the core spliceosome required for its assembly and catalytic activity. Core spliceosomal factors (SF3B1, U2AF1, and others) associated with BUD31 are also required to tolerate oncogenic MYC. Notably, MYC hyperactivation induces an increase in total pre-mRNA synthesis, suggesting an increased burden on the core spliceosome to process pre-mRNA. In contrast to normal cells, partial inhibition of the spliceosome in MYC-hyperactivated cells leads to global intron retention, widespread defects in pre-mRNA maturation, and deregulation of many essential cell processes. Importantly, genetic or pharmacologic inhibition of the spliceosome in vivo impairs survival, tumorigenicity, and metastatic proclivity of MYC-dependent breast cancers. Collectively, these data suggest that oncogenic MYC confers a collateral stress on splicing and that components of the spliceosome may be therapeutic entry points for aggressive MYC-driven cancers.
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Affiliation(s)
- Tiffany Y-T Hsu
- Verna &Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.,Interdepartmental Program in Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, Texas 77030, USA.,Medical Scientist Training Program, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Lukas M Simon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Nicholas J Neill
- Verna &Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Richard Marcotte
- Princess Margaret Cancer Centre, University Health Network, Toronto M5G 2C4, Canada
| | - Azin Sayad
- Princess Margaret Cancer Centre, University Health Network, Toronto M5G 2C4, Canada
| | - Christopher S Bland
- Verna &Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Gloria V Echeverria
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Tingting Sun
- Verna &Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Sarah J Kurley
- Verna &Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Siddhartha Tyagi
- Verna &Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Kristen L Karlin
- Verna &Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Rocio Dominguez-Vidaña
- Verna &Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.,Interdepartmental Program in Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Jessica D Hartman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Alexander Renwick
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Kathleen Scorsone
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Ronald J Bernardi
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Samuel O Skinner
- Verna &Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Physics, University of Illinois, Urbana, Illinois 61801, USA
| | - Antrix Jain
- Verna &Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Mayra Orellana
- Verna &Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Chandraiah Lagisetti
- Center for Chemical Biology, Bioscience Division, SRI International, Menlo Park, California 94025, USA
| | - Ido Golding
- Verna &Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Physics, University of Illinois, Urbana, Illinois 61801, USA
| | - Sung Y Jung
- Verna &Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Joel R Neilson
- Interdepartmental Program in Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Xiang H-F Zhang
- The Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Thomas A Cooper
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Thomas R Webb
- Center for Chemical Biology, Bioscience Division, SRI International, Menlo Park, California 94025, USA
| | - Benjamin G Neel
- Princess Margaret Cancer Centre, University Health Network, Toronto M5G 2C4, Canada.,Department of Medical Biophysics, University of Toronto, Toronto M5S 2J7, Canada
| | - Chad A Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Thomas F Westbrook
- Verna &Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA.,Interdepartmental Program in Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
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Gu S, Hogen L, Lheureux S, Sayad A, Vyarvelska I, Cybulska P, Bernardini M, Rosen B, Oza A, Neel BG. Abstract LB-307: Computational modeling of serous ovarian carcinoma dynamics: Implications for screening and therapy. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-lb-307] [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
High-grade serous ovarian carcinoma (HG-SOC) is the most common subtype of ovarian cancer and has the worst prognosis. There is intense controversy on whether the temporal order of cytoreductive surgery and chemotherapy affects treatment outcome, with the main options being primary debulking surgery with adjuvant chemotherapy (PDS) versus neo-adjuvant chemotherapy with interval debulking surgery (NACT). Although some studies report that PDS-treated patients survive significantly longer than those receiving NACT, other reports showed no significant difference in patient outcome. To address this question in an unbiased way, we used computational modeling to simulate HG-SOC progression dynamics with different treatments.
We adapted a mathematical framework to predict the evolution of chemotherapy resistance, and populated our model with survival data from >300 patients receiving PDS or NACT. After estimating the mutation rate of carcinoma cells and cancer cell number at diagnosis, we determined that most HG-SOC patients likely harbor chemotherapy-resistant cancer cells at diagnosis. Furthermore, we predicted the effects of PDS and NACT on the number of sensitive and resistant cells, as well as patient survival following treatment, and found that our model closely recapitulated clinical observations in both training and test sets. Based on our results, we predict that PDS with optimal debulking (<1mm residual tumor) has the potential to be curative because surgery can sometimes remove all chemo-resistant cells, while adjuvant chemotherapy depletes the remaining chemo-sensitive cells. By contrast, NACT is unlikely to cure the disease because neo-adjuvant chemotherapy depletes chemo-sensitive cells that can mark the location of accompanying “passenger” chemo-resistant cells. As a result, it leads to extensive enrichment of chemo-resistant cells before surgery, but the deposits of such cells are typically too small to be visualized at eventual surgery. Our model also predicts that PDS should have a better outcome than NACT, when controlled for residual tumor size.
Finally, we evaluated the potential benefits of early diagnosis of naïve or relapsed HG-SOC. We recapitulated the clinical finding that CA125-based earlier diagnosis of relapsed cancer does not improve survival. We also predict that more sensitive detection methods (such as ctDNA-based diagnosis) are unlikely to improve survival post-relapse with current chemotherapy, because earlier diagnosis does not decrease the number of chemo-resistant cells, which are already enriched at recurrence. By contrast, our model predicts that with sufficiently sensitive assays, early detection could improve survival time and increase chances of cure.
Note: This abstract was not presented at the meeting.
Citation Format: Shengqing Gu, Liat Hogen, Stephanie Lheureux, Azin Sayad, Iryna Vyarvelska, Paulina Cybulska, Marcus Bernardini, Barry Rosen, Amit Oza, Benjamin G. Neel. Computational modeling of serous ovarian carcinoma dynamics: Implications for screening and therapy. [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 LB-307. doi:10.1158/1538-7445.AM2015-LB-307
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Affiliation(s)
- Shengqing Gu
- 1University of Toronto, Toronto, Ontario, Canada
| | - Liat Hogen
- 2University Health Network, Toronto, Ontario, Canada
| | | | - Azin Sayad
- 2University Health Network, Toronto, Ontario, Canada
| | | | | | | | - Barry Rosen
- 2University Health Network, Toronto, Ontario, Canada
| | - Amit Oza
- 2University Health Network, Toronto, Ontario, Canada
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Movafagh A, Sayad A, Hashemi M, Darvish H, Zare-Abdollahi D, Emamalizadeh B, Shahvaisizadeh F, Mansouri N, Mortazavi-Tabatabaei SA. Rare chromosome structural aberration characterizing oncology malignancy. Gulf J Oncolog 2015; 1:71-78. [PMID: 26003108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/02/2015] [Indexed: 06/04/2023]
Abstract
UNLABELLED Ring chromosome aberration are rare abnormality potentially involving any chromosome in patients diagnosing in Oncology. The present review and case study has focused on the ring chromosome associated with oncology malignancies. MATERIAL AND METHODS An electronic peer review article search was performed systematically to obtain relevant literature with the CINAHL, Google scholar, and Pub Med databases. The keywords included marker, abnormalities, structural, Ring chromosome. The inclusion criteria for the review were that the documents were original quantitative research and published in English. This was also initiated using Medline, Mitelman database (http://cgap.nci.nih.gov/Chromosomes/Mitelman), Danish cytogenetic register and other pertinent web references on ring chromosomes in Oncology malignancies. Articles that were not directly relevant to the present objective were excluded. Also the un-stimulated bone marrow specimen of present case manipulated with Methotrexate cells culture synchronization and finally was treated by GTGbanding technique. RESULTS Ring chromosome was observed in 10% of the total cells. Cytogenetic analysis demonstrated apparently ring (15) 46, XY, r(15) karyotype. The clinical findings revealed history of nausea, loss of appetite, diarrhea, night sweats, and a weight loss, anemia and diagnosed as accelerated CML. CONCLUSION Our finding adds to the spectrum of both morphology and genetic rearrangements in oncology malignancies. Additional future analyses in similar subject will be necessary to draw firm conclusions.
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Affiliation(s)
- A Movafagh
- Department of Medical Genetics, Pediatric Neurology Research Center, Mofid Hospital, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - A Sayad
- Department of Medical Genetics, Pediatric Neurology Research Center, Mofid Hospital, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - M Hashemi
- Department of Molecular Genetics, Islamic, Azad University, Tehran Medical Sciences Branch, Tehran, Iran
| | - H Darvish
- Department of Medical Genetics, Pediatric Neurology Research Center, Mofid Hospital, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - D Zare-Abdollahi
- Department of Medical Genetics, Pediatric Neurology Research Center, Mofid Hospital, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - B Emamalizadeh
- Department of Medical Genetics, Pediatric Neurology Research Center, Mofid Hospital, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - F Shahvaisizadeh
- Department of Medical Genetics, Pediatric Neurology Research Center, Mofid Hospital, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - N Mansouri
- Department of Medical Genetics, Pediatric Neurology Research Center, Mofid Hospital, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - S A Mortazavi-Tabatabaei
- Proteomics Research Center, School of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Sayad A. The association of −330 interleukin-2 gene polymorphism and HLA-DR15 allele in Iranian patients with multiple sclerosis. Int J Immunogenet 2014; 41:330-4. [DOI: 10.1111/iji.12132] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 04/27/2014] [Accepted: 05/04/2014] [Indexed: 02/05/2023]
Affiliation(s)
- A. Sayad
- Department of Medical Genetics; Shahid Beheshti University of Medical Sciences; Tehran Iran
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Petschnigg J, Groisman B, Kotlyar M, Taipale M, Zheng Y, Kurat CF, Sayad A, Sierra JR, Mattiazzi Usaj M, Snider J, Nachman A, Krykbaeva I, Tsao MS, Moffat J, Pawson T, Lindquist S, Jurisica I, Stagljar I. The mammalian-membrane two-hybrid assay (MaMTH) for probing membrane-protein interactions in human cells. Nat Methods 2014; 11:585-92. [PMID: 24658140 DOI: 10.1038/nmeth.2895] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 01/23/2014] [Indexed: 12/19/2022]
Abstract
Cell signaling, one of key processes in both normal cellular function and disease, is coordinated by numerous interactions between membrane proteins that change in response to stimuli. We present a split ubiquitin-based method for detection of integral membrane protein-protein interactions (PPIs) in human cells, termed mammalian-membrane two-hybrid assay (MaMTH). We show that this technology detects stimulus (hormone or agonist)-dependent and phosphorylation-dependent PPIs. MaMTH can detect changes in PPIs conferred by mutations such as those in oncogenic ErbB receptor variants or by treatment with drugs such as the tyrosine kinase inhibitor erlotinib. Using MaMTH as a screening assay, we identified CRKII as an interactor of oncogenic EGFR(L858R) and showed that CRKII promotes persistent activation of aberrant signaling in non-small cell lung cancer cells. MaMTH is a powerful tool for investigating the dynamic interactomes of human integral membrane proteins.
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Affiliation(s)
- Julia Petschnigg
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Bella Groisman
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Max Kotlyar
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Mikko Taipale
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
| | - Yong Zheng
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Christoph F Kurat
- 1] Donnelly Centre, University of Toronto, Toronto, Ontario, Canada. [2]
| | - Azin Sayad
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - J Rafael Sierra
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | | | - Jamie Snider
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Alex Nachman
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Irina Krykbaeva
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
| | - Ming-Sound Tsao
- 1] Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada. [2] Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada. [3] Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Jason Moffat
- 1] Donnelly Centre, University of Toronto, Toronto, Ontario, Canada. [2] Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Tony Pawson
- 1] Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada. [2]
| | - Susan Lindquist
- 1] Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA. [2] Howard Hughes Medical Institute, Cambridge, Massachusetts, USA. [3] Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Igor Jurisica
- 1] Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada. [2] Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada. [3] Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Igor Stagljar
- 1] Donnelly Centre, University of Toronto, Toronto, Ontario, Canada. [2] Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada. [3] Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
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Mansouri N, Movafagh A, Sayad A, Ghafouri-Fard S, Darvish H, Zare-Abdollahi D, Emamalizadeh B, Shahvaisizadeh F, Ghaedi H, Bastami M, Kayyal M, Hashemi M, Heidari MH, Nejatizadeh A, Zamani M. Hepatitis B virus infection in patients with blood disorders: a concise review in pediatric study. Iran J Ped Hematol Oncol 2014; 4:178-87. [PMID: 25598959 PMCID: PMC4293518] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 10/28/2014] [Indexed: 10/29/2022]
Abstract
Childhood Hepatitis B virus (HBV) infection causes both medical and public health challenges. Infants who acquire HBV parentally have up to 90% risk of developing chronic HBV infection. It is now estimated that approximately 10% of worldwide cancers are attributable to viral infection, with the vast majority (>85 %) occurring in the developing world. In this distribution, elevated rate and prevalence of HBV marker have been found in patients with malignancies as compared to the general population. By reviewing the web-based search for all Persian and English types of scientific peer review published articles initiated using Iran Medex, MEDLINE/PubMed, CINAHL and other pertinent references on websites about HBV and HCV blood disorders. The high prevalence of HBV and HCV infective markers was detected in patients with different malignancies. Moreover, identification of high prevalence of HBV infective markers in leukemia patients proposed strong association between hepatitis viral infections and leukemia.
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Affiliation(s)
- N Mansouri
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - A Movafagh
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Corresponding Author: Movafagh A PhD, Department of Medical Genetics, Pediatric Neurology Research Center, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - A Sayad
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - S Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - H Darvish
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - D Zare-Abdollahi
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - B Emamalizadeh
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - F Shahvaisizadeh
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - H Ghaedi
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - M Bastami
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - M Kayyal
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - M Hashemi
- Department of Genetics, Islamic Azad University, Tehran, Iran.
| | - MH Heidari
- Department of Medical Anatomy, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - A Nejatizadeh
- Department of Medical Genetics, Molecular Medicine Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, Iran.
| | - M Zamani
- Department of Neurogenetics, Iranian Center of Neurological Research, Tehran, Iran. ,Department of Medical Genetics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
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Marcotte R, Sayad A, Iorio C, Haider M, Moffat J, Neel BG. Abstract PR07: Integrative functional genomics of breast cancer. Mol Cancer Res 2013. [DOI: 10.1158/1557-3125.advbc-pr07] [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
Cancer is a disease of the genome. Using genomic approaches alone, it is difficult to ascertain which variants drive pathogenesis because most of these are functionally irrelevant passenger mutations. Highly recurrent events point to drivers; however, the majority of genomic alterations in tumors occur at low frequency. In addition, the products of many oncogenes and tumor suppressor genes are not druggable. However, such abnormalities can cause unanticipated gene/pathway dependencies (synthetic lethality), providing alternate avenues for drug development. Lentiviral-based shRNA libraries enables genome-wide screening of cultured cancer cells in a pooled format, facilitating the identification of genes necessary for cancer cell proliferation and survival in cultured cells. We screened a panel of > 75 breast cancer cell lines using an 80,000 lentiviral shRNA library targeting 16,000 genes and integrated these screen results with gene expression, copy-number variation (CNV), and somatic mutations derived from the same lines. We identified several classes of gene dropouts, which are required for survival or growth of all (or some) cell lines, irrespective of subtype and several subtype-specific genes, whose essentiality is restricted to a defined subtype. These include well-known HER2 subtype-specific genes, ERBB2, ERBB3, and TFAP2C and luminal subtype-specific gene FOXA1, SPDEF, GATA3, and ESR1. In addition, the unprecedented number of lines allows the identification of synthetic lethal interaction with common breast cancer somatic mutations or CNV such as PIK3CA and PTEN or 9p21 deletion, respectively, which encodes the CDKN2A, CDKN2B, and MTAP genes. Finally, integration of gene expression, copy number variation, and functional screening results identified potential biomarkers with common genetic changes and functional drivers. Overall, our study represents an extensive functional genetic survey of breast cancer, reveals complexities between genomic and functional genomic results, and uncovers several unexpected gene dependencies and potential novel therapeutic target for each subtype.
This abstract is also presented as Poster A033.
Citation Format: Richard Marcotte, Azin Sayad, Cathy Iorio, Maliha Haider, Jason Moffat, Benjamin G. Neel. Integrative functional genomics of breast cancer. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Breast Cancer Research: Genetics, Biology, and Clinical Applications; Oct 3-6, 2013; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2013;11(10 Suppl):Abstract nr PR07.
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Affiliation(s)
| | - Azin Sayad
- 1Ontario Cancer Institute, Toronto, ON, Canada,
| | - Cathy Iorio
- 1Ontario Cancer Institute, Toronto, ON, Canada,
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Marcotte R, Sayad A, Haider M, Brown K, Ketela T, Moffat J, Neel BG. Abstract PR01: Functional characterization of breast cancer using pooled lentivirus shRNA screens. Mol Cancer Ther 2013. [DOI: 10.1158/1535-7163.pms-pr01] [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
Breast cancer is the most common invasive malignancy and the second leading cause of cancer death in U.S. women. Early detection and improved therapy have led to >85% 5-year survival, but still, half of currently affected women will succumb from metastatic disease. This poor outcome reflects our incomplete knowledge of essential genes driving tumor proliferation for each subtype. From genomic data alone, it can be difficult to access which genetic alterations drive pathogenesis because most of these are functionally irrelevant “passenger” mutations. Even if an oncogene or tumor suppressor is identified, these often are not amenable to targeted therapy. However, unanticipated gene/pathway dependencies can arise as a consequence of these genetic abnormalities in cancer cells (“synthetic lethality”). The recent development of lentiviral-based shRNA libraries enables genome-wide screening of cultured cancer cells in a pooled format, facilitating the identification of genes necessary for cancer cell proliferation and survival in cell culture as well as potential synthetic lethal interactions. The overall objectives of this project were to identify subtype-specific targets and synthetic lethal interactions for common mutations in human breast cancer using genome-wide shRNA screens, as well as to compare “functional genomic” and genomic classification schemes. We screened a panel of > 75 breast cancer lines using an 80,000 lentiviral shRNA library targeting 16,000 genes in a pooled format. We identified several classes of gene “dropouts,” including general essential genes, which are required for survival or growth in more than 70% of all cell lines, irrespective of subtype. Using a newly developed scoring algorithm that allows for precise measurement of statistical significance between two groups, we also identified several “subtype-specific” genes, whose essentiality is restricted to a defined subtype. These include well-known HER2 subtype-specific genes, ERBB2, ERBB3, and TFAP2C and luminal subtype-specific gene FOXA1, SPDEF, GATA3, ESR1, and CCDN1 as well as newly identified BRD4 and CHD4. These two genes were further validated as luminal-specific and results to explain their luminal subtype-specificity will be presented. In addition, the unprecedented number of lines allows the identification of synthetic lethal interaction with common breast cancer somatic mutation such as PIK3CA and PTEN. Finally, integration of gene expression, copy number variation, and functional screening results identified potential biomarkers with common genetic changes and functional drivers. Overall, our study represents an extensive functional genetic survey of four major breast cancer subtypes, reveals complexities between genomic and functional genomic results, and uncovers several unexpected gene dependencies and potential novel therapeutic target for each subtype.
This abstract is also presented as Poster A22.
Citation Format: Richard Marcotte, Azin Sayad, Maliha Haider, Kevin Brown, Troy Ketela, Jason Moffat, Benjamin G. Neel. Functional characterization of breast cancer using pooled lentivirus shRNA screens. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Synthetic Lethal Approaches to Cancer Vulnerabilities; May 17-20, 2013; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(5 Suppl):Abstract nr PR01.
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Affiliation(s)
- Richard Marcotte
- 1Ontario Cancer Institute, University Health Network, Toronto, ON, Canada,
| | - Azin Sayad
- 1Ontario Cancer Institute, University Health Network, Toronto, ON, Canada,
| | - Maliha Haider
- 1Ontario Cancer Institute, University Health Network, Toronto, ON, Canada,
| | | | | | | | - Benjamin G. Neel
- 1Ontario Cancer Institute, University Health Network, Toronto, ON, Canada,
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Marcotte R, Brown K, Sayad A, Haider M, Ketela T, Moffat J, Neel BG. Abstract 5084: Functional genomic classification of breast cancer using pooled lentivirus shRNA screens. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-5084] [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
Targeted therapies for most breast cancers are lacking because our knowledge of essential genes driving tumor proliferation is still primitive for each subtype. Although ongoing intensive efforts to genetically characterize large numbers of breast tumors are providing a plethora of new data on genomic abnormalities (e.g., amplifications, deletions, somatic mutations), it can be difficult to access which of these actively drive pathogenesis. Even if an oncogene or tumor suppressor is identified, these often are not amenable to targeted therapy (eg. KRAS, c-MYC, p53, etc). However, unanticipated gene/pathway dependencies can arise as a consequence of these genetic abnormalities in cancer cells (“synthetic lethality”). The recent development of lentiviral-based shRNA libraries enables genome-wide screening of cultured cancer cells in a pooled format, facilitating the identification of genes necessary for cancer cell proliferation and survival in cell culture as well as potential synthetic lethal interactions. The overall objective of this project was to identify subtype-specific targets for human breast cancer using a genome-wide shRNA screen, as well as to compare “functional genomic” and genomic classification schemes. We screened a panel of 53 breast cancer lines using an 80,000 lentiviral shRNA library targeting 16,000 genes in a pooled format. We identified several classes of gene “dropouts,” including general essential genes, which are required for survival or growth in more than 70% of all cell lines, irrespective of subtype. Most of these were enriched in housekeeping functions, although several genes involved in cellular signal transduction also were identified, including mTORC1, RAPTOR, TGFBR2, DDR1 and DDR2. In addition, we observed several “subtype-specific” genes, whose essentiality is restricted to a defined subtype. Furthermore, unsupervised and supervised clustering of our functional screening results identified potential “drivers” unique to each subtype. These include amplified/overexpressed genes such as ERBB2, ERBB3, FOXA1, SPDEF, TFAP2C, and CCDN1 known to be specific to the luminal and HER2 subtypes, respectively. Finally, integration of gene expression, copy number variation, and functional screening results identified potential synthetic lethal interactions with common genetic changes. Our study represents an extensive functional genetic survey of three major breast cancer subtypes, reveals complexities between genomic and functional genomic results, and uncovers several unexpected gene dependencies and potential novel therapeutic target for each subtype.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5084. doi:1538-7445.AM2012-5084
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Affiliation(s)
| | - Kevin Brown
- 2University of Toronto, Toronto, Ontario, Canada
| | - Azin Sayad
- 2University of Toronto, Toronto, Ontario, Canada
| | | | - Troy Ketela
- 2University of Toronto, Toronto, Ontario, Canada
| | - Jason Moffat
- 2University of Toronto, Toronto, Ontario, Canada
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Samuel N, Lemire M, Wilson G, Sayad A, Muthuswamy L, Moffat J, Hudson TJ. Abstract 1853: Identification and characterization of genes in regions of recurrent genomic gain as putative therapeutic targets in pancreatic ductal adenocarcinoma. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-1853] [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
Pancreatic ductal adenocarcinoma (PDAC) is the fourth leading cause of cancer-related mortality in the United States. PDAC presents with the worst prognosis of all solid tumors and the 5-year survival rate for patients with advanced PDAC is only 2%. Current chemotherapies fail to attenuate the aggressiveness of this disease and as such, novel therapeutic strategies are needed. The purpose of our study is to identify putative therapeutic targets in PDAC and characterize the role of a target gene in tumor progression. Towards this aim, we sought to identify genes which are recurrently gained or amplified in pancreatic tumors. If increased copy of specific genes confers neoplastic properties, selective targeting of such genes may have therapeutic implications. We obtained publically available copy number alteration data on 60 PDAC genomes characterized in four independent PDAC studies. Using bioinformatics and computational approaches, we identified 20 genomic loci that are gained in at least one sample in three of the four PDAC datasets. Our integrated analysis of the genes mapping to these 20 loci results in a catalogue of 710 protein-coding genes and 46 miRNA genes, which are candidate targets for further analysis. In order to delineate appropriate biological models for functional validation of these genes in PDAC, we obtained SNP array-based copy number data using the Illumina OmniExpress platform and gene expression analysis from Illumina HT-12 BeadChip arrays from 30 human PDAC cell lines. We identified genes from our candidate gene list in which copy number alteration and gene expression are correlated as computed by a Spearman rank correlation coefficient, α. This gene set was enriched for genes with high correlation between copy number and expression in comparison to simulated gene sets (p = 0.007). Our data suggest that Epithelial cell-transforming sequence 2 oncogene (ECT2) on 3q26.3 is a strong candidate for functional validation. This gene encodes a Rho-specific guanine exchange factor involved in various cellular processes including regulation of G1-to-S phase transition in cell-cycle progression. To validate our in silico findings, we have designed experiments to investigate the role of ECT2 amplification in PDAC, using the 30 human PDAC cell lines we have genetically analyzed. This will be accomplished through differential inhibition of the ECT2 protein, using RNAi and small molcules, in cell lines in which ECT2 is amplified, compared to appropriate control lines. In conclusion, we have identified a set of candidate target genes in PDAC and are currently validating the role of one of these targets, ECT2, in PDAC tumor progression.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 1853. doi:1538-7445.AM2012-1853
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Affiliation(s)
| | - Mathieu Lemire
- 2Ontario Institute for Cancer Research, Toronto, ON, Ontario, Canada
| | - Gavin Wilson
- 1University of Toronto, Toronto, Ontario, Canada
| | - Azin Sayad
- 3Ontario Cancer Institute, Toronto, ON, Ontario, Canada
| | | | - Jason Moffat
- 1University of Toronto, Toronto, Ontario, Canada
| | - Thomas J. Hudson
- 2Ontario Institute for Cancer Research, Toronto, ON, Ontario, Canada
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Sayad A, Akbari MT, Pajouhi M, Mostafavi F, Zamani M. The influence of the HLA-DRB, HLA-DQB and polymorphic positions of the HLA-DRβ1 and HLA-DQβ1 molecules on risk of Iranian type 1 diabetes mellitus patients. Int J Immunogenet 2012; 39:429-36. [PMID: 22494469 DOI: 10.1111/j.1744-313x.2012.01116.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Type 1 Diabetes mellitus (T1D) is an autoimmune and multifactorial disease. HLA-DRB1 and DQB1 loci have the strongest association with T1D. This study aimed at investigating (i) susceptibility or protection of alleles, genotypes and haplotypes of HLA-DRB1 and DQB1 loci; and (ii) highly polymorphic amino acid residues of HLA-DRβ1 and DQβ1 in 105 Iranian T1D patients and 100 controls. The results indicated that DRB1*04:01, 03:01, DQB1*03:02, 02:01 alleles, DRB1*03:01/04:01, 03:01/13:03, DQB1*02:01/03:02 genotypes, DRB1*04:01-DQB1*03:02, DRB1*03:01-DQB1*02:01, DRB1*07:01-DQB1*03:03 haplotypes had positive association with T1D. In contrast, HLA-DRB1*15:01, 13:01, DQB1*03:01, 06:01 alleles, DRB1*11:01/15:01, DQB1*03:01/06:01, 03:01/05:01 genotypes and DRB1*15:01-DQB1*06:01, DRB1*11:01-DQB1*03:01 haplotypes had negative association with T1D. Analysis of amino acid sequence of HLA-DRβ1 and DQβ1 revealed that DRβ1(Lys71+) and DQβ1(Asp57-) were significantly more frequent in patients than in controls and had a positive effect in the development of T1D. Haplotype analysis demonstrated that HLA-DRB1(Lys71+) allele provided major susceptibility for T1D, and DQβ1(Asp57-) had an additive effect. We designed an allele-specific primer to develop an easy, quick and cost-benefit method to detect the DRβ1(Lys71+) . This method can identify all 114 DRB1 alleles encoding DRβ1(Lys71+) by three PCR reactions. The PcPPV and PcNPV were also calculated to determine the impact of HLA genotype testing at amino acid positions. It showed that the DRβ1(Lys71+/+) genotype carrier had 1% absolute risk of developing T1D.
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Affiliation(s)
- A Sayad
- Department of Neurogenetics, Iranian Centre of Neurological Research, Tehran
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Marcotte R, Brown KR, Suarez F, Sayad A, Karamboulas K, Krzyzanowski PM, Sircoulomb F, Medrano M, Fedyshyn Y, Koh JL, van Dyk D, Fedyshyn B, Luhova M, Brito GC, Vizeacoumar FJ, Vizeacoumar FS, Datti A, Kasimer D, Buzina A, Mero P, Misquitta C, Normand J, Haider M, Ketela T, Wrana JL, Rottapel R, Neel BG, Moffat J. Essential gene profiles in breast, pancreatic, and ovarian cancer cells. Cancer Discov 2012; 2:172-189. [PMID: 22585861 PMCID: PMC5057396 DOI: 10.1158/2159-8290.cd-11-0224] [Citation(s) in RCA: 234] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
UNLABELLED Genomic analyses are yielding a host of new information on the multiple genetic abnormalities associated with specific types of cancer. A comprehensive description of cancer-associated genetic abnormalities can improve our ability to classify tumors into clinically relevant subgroups and, on occasion, identify mutant genes that drive the cancer phenotype ("drivers"). More often, though, the functional significance of cancer-associated mutations is difficult to discern. Genome-wide pooled short hairpin RNA (shRNA) screens enable global identification of the genes essential for cancer cell survival and proliferation, providing a "functional genomic" map of human cancer to complement genomic studies. Using a lentiviral shRNA library targeting ~16,000 genes and a newly developed, dynamic scoring approach, we identified essential gene profiles in 72 breast, pancreatic, and ovarian cancer cell lines. Integrating our results with current and future genomic data should facilitate the systematic identification of drivers, unanticipated synthetic lethal relationships, and functional vulnerabilities of these tumor types. SIGNIFICANCE This study presents a resource of genome-scale, pooled shRNA screens for 72 breast, pancreatic, and ovarian cancer cell lines that will serve as a functional complement to genomics data, facilitate construction of essential gene profiles, help uncover synthetic lethal relationships, and identify uncharacterized genetic vulnerabilities in these tumor types. SIGNIFICANCE This study presents a resource of genome-scale, pooled shRNA screens for 72 breast, pancreatic, and ovarian cancer cell lines that will serve as a functional complement to genomics data, facilitate construction of essential gene profiles, help uncover synthetic lethal relationships, and identify uncharacterized genetic vulnerabilities in these tumor types.
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Affiliation(s)
- Richard Marcotte
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital University Health Network, Toronto, Canada
| | - Kevin R. Brown
- Donnelly Centre and Banting & Best Department of Medical Research, University of Toronto, Toronto, Canada
- Ontario Institute for Cancer Research, Toronto, Canada
| | - Fernando Suarez
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital University Health Network, Toronto, Canada
| | - Azin Sayad
- Donnelly Centre and Banting & Best Department of Medical Research, University of Toronto, Toronto, Canada
| | - Konstantina Karamboulas
- Donnelly Centre and Banting & Best Department of Medical Research, University of Toronto, Toronto, Canada
| | - Paul M. Krzyzanowski
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital University Health Network, Toronto, Canada
| | - Fabrice Sircoulomb
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital University Health Network, Toronto, Canada
| | - Mauricio Medrano
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital University Health Network, Toronto, Canada
| | - Yaroslav Fedyshyn
- Donnelly Centre and Banting & Best Department of Medical Research, University of Toronto, Toronto, Canada
| | - Judice L.Y. Koh
- Donnelly Centre and Banting & Best Department of Medical Research, University of Toronto, Toronto, Canada
- Ontario Institute for Cancer Research, Toronto, Canada
| | - Dewald van Dyk
- Donnelly Centre and Banting & Best Department of Medical Research, University of Toronto, Toronto, Canada
| | - Bodhana Fedyshyn
- Donnelly Centre and Banting & Best Department of Medical Research, University of Toronto, Toronto, Canada
| | - Marianna Luhova
- Donnelly Centre and Banting & Best Department of Medical Research, University of Toronto, Toronto, Canada
| | | | - Franco J. Vizeacoumar
- Donnelly Centre and Banting & Best Department of Medical Research, University of Toronto, Toronto, Canada
| | | | - Alessandro Datti
- Samuel Lunenfeld Research Institute, Toronto, Canada
- Department of Experimental Medicine and Biochemical Sciences, University of Perugia, Perugia, Italy
| | - Dahlia Kasimer
- Donnelly Centre and Banting & Best Department of Medical Research, University of Toronto, Toronto, Canada
| | - Alla Buzina
- Donnelly Centre and Banting & Best Department of Medical Research, University of Toronto, Toronto, Canada
| | - Patricia Mero
- Donnelly Centre and Banting & Best Department of Medical Research, University of Toronto, Toronto, Canada
| | - Christine Misquitta
- Donnelly Centre and Banting & Best Department of Medical Research, University of Toronto, Toronto, Canada
| | - Josee Normand
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital University Health Network, Toronto, Canada
| | - Maliha Haider
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital University Health Network, Toronto, Canada
| | - Troy Ketela
- Donnelly Centre and Banting & Best Department of Medical Research, University of Toronto, Toronto, Canada
- Ontario Institute for Cancer Research, Toronto, Canada
| | - Jeffrey L. Wrana
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Samuel Lunenfeld Research Institute, Toronto, Canada
| | - Robert Rottapel
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital University Health Network, Toronto, Canada
- Ontario Institute for Cancer Research, Toronto, Canada
| | - Benjamin G. Neel
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital University Health Network, Toronto, Canada
| | - Jason Moffat
- Donnelly Centre and Banting & Best Department of Medical Research, University of Toronto, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
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Koh JLY, Brown KR, Sayad A, Kasimer D, Ketela T, Moffat J. COLT-Cancer: functional genetic screening resource for essential genes in human cancer cell lines. Nucleic Acids Res 2011; 40:D957-63. [PMID: 22102578 PMCID: PMC3245009 DOI: 10.1093/nar/gkr959] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Genome-wide pooled shRNA screens enable global identification of the genes essential for cancer cell survival and proliferation and provide a ‘functional genetic’ map of human cancer to complement genomic studies. Using a lentiviral shRNA library targeting approximately 16 000 human genes and a newly developed scoring approach, we identified essential gene profiles in more than 70 breast, pancreatic and ovarian cancer cell lines. We developed a web-accessible database system for capturing information from each step in our standardized screening pipeline and a gene-centric search tool for exploring shRNA activities within a given cell line or across multiple cell lines. The database consists of a laboratory information and management system for tracking each step of a pooled shRNA screen as well as a web interface for querying and visualization of shRNA and gene-level performance across multiple cancer cell lines. COLT-Cancer Version 1.0 is currently accessible at http://colt.ccbr.utoronto.ca/cancer.
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Affiliation(s)
- Judice L Y Koh
- Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, 160 College St, Toronto, ON M5S 3E1, Canada M5G 0A3
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Annan RB, Lee AY, Reid ID, Sayad A, Whiteway M, Hallett M, Thomas DY. A biochemical genomics screen for substrates of Ste20p kinase enables the in silico prediction of novel substrates. PLoS One 2009; 4:e8279. [PMID: 20020052 PMCID: PMC2791418 DOI: 10.1371/journal.pone.0008279] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2009] [Accepted: 11/19/2009] [Indexed: 01/13/2023] Open
Abstract
The Ste20/PAK family is involved in many cellular processes, including the regulation of actin-based cytoskeletal dynamics and the activation of MAPK signaling pathways. Despite its numerous roles, few of its substrates have been identified. To better characterize the roles of the yeast Ste20p kinase, we developed an in vitro biochemical genomics screen to identify its substrates. When applied to 539 purified yeast proteins, the screen reported 14 targets of Ste20p phosphorylation. We used the data resulting from our screen to build an in silico predictor to identify Ste20p substrates on a proteome-wide basis. Since kinase-substrate specificity is often mediated by additional binding events at sites distal to the phosphorylation site, the predictor uses the presence/absence of multiple sequence motifs to evaluate potential substrates. Statistical validation estimates a threefold improvement in substrate recovery over random predictions, despite the lack of a single dominant motif that can characterize Ste20p phosphorylation. The set of predicted substrates significantly overrepresents elements of the genetic and physical interaction networks surrounding Ste20p, suggesting that some of the predicted substrates are in vivo targets. We validated this combined experimental and computational approach for identifying kinase substrates by confirming the in vitro phosphorylation of polarisome components Bni1p and Bud6p, thus suggesting a mechanism by which Ste20p effects polarized growth.
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Affiliation(s)
- Robert B Annan
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada.
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Taurog JD, Maika SD, Satumtira N, Dorris ML, McLean IL, Yanagisawa H, Sayad A, Stagg AJ, Fox GM, Lê O'Brien A, Rehman M, Zhou M, Weiner AL, Splawski JB, Richardson JA, Hammer RE. Inflammatory disease in HLA-B27 transgenic rats. Immunol Rev 1999; 169:209-23. [PMID: 10450519 DOI: 10.1111/j.1600-065x.1999.tb01317.x] [Citation(s) in RCA: 173] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
UNLABELLED A spontaneous inflammatory disease in rats transgenic for HLA-B27 resembles the B27-associated human spondyloarthropathies. Colitis and arthritis, the two most important features, require T cells, gut bacteria, and high expression of B27 in bone marrow-derived cells. Control rats with HLA-B7 remain healthy. Most rats with HLA-Cw6 (associated with psoriasis vulgaris) remain healthy; a minority develop mild and transient disease. Rats with a mutant B27 with a Cys67-->Ser substitution resemble wild-type B27 transgenics, but with a lower prevalence of arthritis. A similar phenotype is seen in B27 rats co-expressing a viral peptide that binds B27. Disease-prone LEW but not F344 B27 rats develop high serum IgA levels concurrent with disease progression. Colitis is associated with high interferon-gamma, arthritis with high interleukin-6. Disease is similar in B27 LEW, F344, and PVG rats, but the DA background is protective. CONCLUSIONS The spondyloarthropathy-like disease in rats is specific for HLA-B27 but does not require Cys67. Arthritis but not colitis is particularly sensitive to B27 peptide-binding specificity. Genetic background exerts a strong influence, but some phenotypic differences exist between permissive strains that do not influence disease susceptibility. The data favor a role for B27 peptide presentation in arthritis, but other mechanisms to explain the role of B27 have not been excluded.
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Affiliation(s)
- J D Taurog
- Harold C. Simmons Arthritis Research Center, University of Texas Southwestern Medical Center, Dallas 75235-8884, USA.
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Zhou M, Sayad A, Simmons WA, Jones RC, Maika SD, Satumtira N, Dorris ML, Gaskell SJ, Bordoli RS, Sartor RB, Slaughter CA, Richardson JA, Hammer RE, Taurog JD. The specificity of peptides bound to human histocompatibility leukocyte antigen (HLA)-B27 influences the prevalence of arthritis in HLA-B27 transgenic rats. J Exp Med 1998; 188:877-86. [PMID: 9730889 PMCID: PMC2213380 DOI: 10.1084/jem.188.5.877] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.0] [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: 04/10/1998] [Revised: 06/17/1998] [Indexed: 11/15/2022] Open
Abstract
Human histocompatibility leukocyte antigen B27 is highly associated with the rheumatic diseases termed spondyloarthropathies, but the mechanism is not known. B27 transgenic rats develop a spontaneous disease resembling the human spondyloarthropathies that includes arthritis and colitis. To investigate whether this disease requires the binding of specific peptides to B27, we made a minigene construct in which a peptide from influenza nucleoprotein, NP383-391 (SRYWAIRTR), which binds B27 with high affinity, is targeted directly to the ER by the signal peptide of the adenovirus E3/gp19 protein. Rats transgenic for this minigene, NP1, were made and bred with B27 rats. The production of the NP383-391 peptide in B27(+)NP1(+) rats was confirmed immunologically and by mass spectrometry. The NP1 product displaced approximately 90% of the 3H-Arg-labeled endogenous peptide fraction in B27(+)NP1(+) spleen cells. Male B27(+)NP1(+) rats had a significantly reduced prevalence of arthritis, compared with B27(+)NP- males or B27(+) males with a control construct, NP2, whereas colitis was not significantly affected by the NP1 transgene. These findings support the hypothesis that B27-related arthritis requires binding of a specific peptide or set of peptides to B27, and they demonstrate a method for efficient transgenic targeting of peptides to the ER.
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Affiliation(s)
- M Zhou
- Harold C. Simmons Arthritis Research Center, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas 75235, USA
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