1
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Ciriello G, Magnani L, Aitken SJ, Akkari L, Behjati S, Hanahan D, Landau DA, Lopez-Bigas N, Lupiáñez DG, Marine JC, Martin-Villalba A, Natoli G, Obenauf AC, Oricchio E, Scaffidi P, Sottoriva A, Swarbrick A, Tonon G, Vanharanta S, Zuber J. Cancer Evolution: A Multifaceted Affair. Cancer Discov 2024; 14:36-48. [PMID: 38047596 PMCID: PMC10784746 DOI: 10.1158/2159-8290.cd-23-0530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 08/29/2023] [Accepted: 10/23/2023] [Indexed: 12/05/2023]
Abstract
Cancer cells adapt and survive through the acquisition and selection of molecular modifications. This process defines cancer evolution. Building on a theoretical framework based on heritable genetic changes has provided insights into the mechanisms supporting cancer evolution. However, cancer hallmarks also emerge via heritable nongenetic mechanisms, including epigenetic and chromatin topological changes, and interactions between tumor cells and the tumor microenvironment. Recent findings on tumor evolutionary mechanisms draw a multifaceted picture where heterogeneous forces interact and influence each other while shaping tumor progression. A comprehensive characterization of the cancer evolutionary toolkit is required to improve personalized medicine and biomarker discovery. SIGNIFICANCE Tumor evolution is fueled by multiple enabling mechanisms. Importantly, genetic instability, epigenetic reprogramming, and interactions with the tumor microenvironment are neither alternative nor independent evolutionary mechanisms. As demonstrated by findings highlighted in this perspective, experimental and theoretical approaches must account for multiple evolutionary mechanisms and their interactions to ultimately understand, predict, and steer tumor evolution.
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Affiliation(s)
- Giovanni Ciriello
- Swiss Cancer Center Leman, Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Luca Magnani
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
- Breast Epigenetic Plasticity and Evolution Laboratory, Division of Breast Cancer Research, The Institute of Cancer Research, London, United Kingdom
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Sarah J. Aitken
- Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, United Kingdom
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Leila Akkari
- Division of Tumor Biology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Sam Behjati
- Wellcome Sanger Institute, Hinxton, United Kingdom
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
- Department of Paediatrics, University of Cambridge, Cambridge, United Kingdom
| | - Douglas Hanahan
- Swiss Cancer Center Leman, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, Lausanne, Switzerland
| | - Dan A. Landau
- New York Genome Center, New York, New York
- Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, New York
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York
| | - Nuria Lopez-Bigas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Darío G. Lupiáñez
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory for Molecular Cancer Biology, Department of Oncology, KULeuven, Leuven, Belgium
| | - Ana Martin-Villalba
- Department of Molecular Neurobiology, German Cancer Research Center (DFKZ), Heidelberg, Germany
| | - Gioacchino Natoli
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Anna C. Obenauf
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Elisa Oricchio
- Swiss Cancer Center Leman, Lausanne, Switzerland
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Paola Scaffidi
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy
- Cancer Epigenetic Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Andrea Sottoriva
- Computational Biology Research Centre, Human Technopole, Milan, Italy
| | - Alexander Swarbrick
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Darlinghurst, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, Australia
| | - Giovanni Tonon
- Vita-Salute San Raffaele University, Milan, Italy
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Sakari Vanharanta
- Translational Cancer Medicine Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Johannes Zuber
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
- Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
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2
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Gainza P, Wehrle S, Van Hall-Beauvais A, Marchand A, Scheck A, Harteveld Z, Buckley S, Ni D, Tan S, Sverrisson F, Goverde C, Turelli P, Raclot C, Teslenko A, Pacesa M, Rosset S, Georgeon S, Marsden J, Petruzzella A, Liu K, Xu Z, Chai Y, Han P, Gao GF, Oricchio E, Fierz B, Trono D, Stahlberg H, Bronstein M, Correia BE. De novo design of protein interactions with learned surface fingerprints. Nature 2023; 617:176-184. [PMID: 37100904 PMCID: PMC10131520 DOI: 10.1038/s41586-023-05993-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [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: 06/16/2022] [Accepted: 03/21/2023] [Indexed: 04/28/2023]
Abstract
Physical interactions between proteins are essential for most biological processes governing life1. However, the molecular determinants of such interactions have been challenging to understand, even as genomic, proteomic and structural data increase. This knowledge gap has been a major obstacle for the comprehensive understanding of cellular protein-protein interaction networks and for the de novo design of protein binders that are crucial for synthetic biology and translational applications2-9. Here we use a geometric deep-learning framework operating on protein surfaces that generates fingerprints to describe geometric and chemical features that are critical to drive protein-protein interactions10. We hypothesized that these fingerprints capture the key aspects of molecular recognition that represent a new paradigm in the computational design of novel protein interactions. As a proof of principle, we computationally designed several de novo protein binders to engage four protein targets: SARS-CoV-2 spike, PD-1, PD-L1 and CTLA-4. Several designs were experimentally optimized, whereas others were generated purely in silico, reaching nanomolar affinity with structural and mutational characterization showing highly accurate predictions. Overall, our surface-centric approach captures the physical and chemical determinants of molecular recognition, enabling an approach for the de novo design of protein interactions and, more broadly, of artificial proteins with function.
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Affiliation(s)
- Pablo Gainza
- Laboratory of Protein Design and Immunoengineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Monte Rosa Therapeutics, Basel, Switzerland
| | - Sarah Wehrle
- Laboratory of Protein Design and Immunoengineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Alexandra Van Hall-Beauvais
- Laboratory of Protein Design and Immunoengineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Anthony Marchand
- Laboratory of Protein Design and Immunoengineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Andreas Scheck
- Laboratory of Protein Design and Immunoengineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Zander Harteveld
- Laboratory of Protein Design and Immunoengineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Stephen Buckley
- Laboratory of Protein Design and Immunoengineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Dongchun Ni
- Laboratory of Biological Electron Microscopy, Institute of Physics, School of Basic Science, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Shuguang Tan
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Freyr Sverrisson
- Laboratory of Protein Design and Immunoengineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Casper Goverde
- Laboratory of Protein Design and Immunoengineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Priscilla Turelli
- Laboratory of Virology and Genetics, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Charlène Raclot
- Laboratory of Virology and Genetics, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Alexandra Teslenko
- Laboratory of Biophysical Chemistry of Macromolecules, School of Basic Sciences, Institute of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Martin Pacesa
- Laboratory of Protein Design and Immunoengineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Stéphane Rosset
- Laboratory of Protein Design and Immunoengineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Sandrine Georgeon
- Laboratory of Protein Design and Immunoengineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Jane Marsden
- Laboratory of Protein Design and Immunoengineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Aaron Petruzzella
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Kefang Liu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Zepeng Xu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yan Chai
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Pu Han
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - George F Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Elisa Oricchio
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Beat Fierz
- Laboratory of Biophysical Chemistry of Macromolecules, School of Basic Sciences, Institute of Chemical Sciences and Engineering (ISIC), École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Didier Trono
- Laboratory of Virology and Genetics, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Henning Stahlberg
- Laboratory of Biological Electron Microscopy, Institute of Physics, School of Basic Science, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | | | - Bruno E Correia
- Laboratory of Protein Design and Immunoengineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
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3
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Lambuta RA, Nanni L, Liu Y, Diaz-Miyar J, Iyer A, Tavernari D, Katanayeva N, Ciriello G, Oricchio E. Whole-genome doubling drives oncogenic loss of chromatin segregation. Nature 2023; 615:925-933. [PMID: 36922594 PMCID: PMC10060163 DOI: 10.1038/s41586-023-05794-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [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: 02/13/2022] [Accepted: 02/03/2023] [Indexed: 03/17/2023]
Abstract
Whole-genome doubling (WGD) is a recurrent event in human cancers and it promotes chromosomal instability and acquisition of aneuploidies1-8. However, the three-dimensional organization of chromatin in WGD cells and its contribution to oncogenic phenotypes are currently unknown. Here we show that in p53-deficient cells, WGD induces loss of chromatin segregation (LCS). This event is characterized by reduced segregation between short and long chromosomes, A and B subcompartments and adjacent chromatin domains. LCS is driven by the downregulation of CTCF and H3K9me3 in cells that bypassed activation of the tetraploid checkpoint. Longitudinal analyses revealed that LCS primes genomic regions for subcompartment repositioning in WGD cells. This results in chromatin and epigenetic changes associated with oncogene activation in tumours ensuing from WGD cells. Notably, subcompartment repositioning events were largely independent of chromosomal alterations, which indicates that these were complementary mechanisms contributing to tumour development and progression. Overall, LCS initiates chromatin conformation changes that ultimately result in oncogenic epigenetic and transcriptional modifications, which suggests that chromatin evolution is a hallmark of WGD-driven cancer.
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Affiliation(s)
- Ruxandra A Lambuta
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, EPFL, Écublens, Switzerland
- Swiss Cancer Center Leman, Lausanne, Switzerland
| | - Luca Nanni
- Swiss Cancer Center Leman, Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne (UNIL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Yuanlong Liu
- Swiss Cancer Center Leman, Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne (UNIL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Juan Diaz-Miyar
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, EPFL, Écublens, Switzerland
- Swiss Cancer Center Leman, Lausanne, Switzerland
| | - Arvind Iyer
- Swiss Cancer Center Leman, Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne (UNIL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Daniele Tavernari
- Swiss Cancer Center Leman, Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne (UNIL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Natalya Katanayeva
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, EPFL, Écublens, Switzerland
- Swiss Cancer Center Leman, Lausanne, Switzerland
| | - Giovanni Ciriello
- Swiss Cancer Center Leman, Lausanne, Switzerland.
- Department of Computational Biology, University of Lausanne (UNIL), Lausanne, Switzerland.
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
| | - Elisa Oricchio
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, EPFL, Écublens, Switzerland.
- Swiss Cancer Center Leman, Lausanne, Switzerland.
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4
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Oricchio E. Chromatin organization in red triangles. Nat Rev Genet 2023:10.1038/s41576-023-00582-0. [PMID: 36732639 DOI: 10.1038/s41576-023-00582-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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5
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Liu Y, Nanni L, Sungalee S, Zufferey M, Tavernari D, Mina M, Ceri S, Oricchio E, Ciriello G. Systematic inference and comparison of multi-scale chromatin sub-compartments connects spatial organization to cell phenotypes. Nat Commun 2021; 12:2439. [PMID: 33972523 PMCID: PMC8110550 DOI: 10.1038/s41467-021-22666-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 03/16/2021] [Indexed: 12/21/2022] Open
Abstract
Chromatin compartmentalization reflects biological activity. However, inference of chromatin sub-compartments and compartment domains from chromosome conformation capture (Hi-C) experiments is limited by data resolution. As a result, these have been characterized only in a few cell types and systematic comparisons across multiple tissues and conditions are missing. Here, we present Calder, an algorithmic approach that enables the identification of multi-scale sub-compartments at variable data resolution. Calder allows to infer and compare chromatin sub-compartments and compartment domains in >100 cell lines. Our results reveal sub-compartments enriched for poised chromatin states and undergoing spatial repositioning during lineage differentiation and oncogenic transformation.
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Affiliation(s)
- Yuanlong Liu
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Cancer Center Leman, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Luca Nanni
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Cancer Center Leman, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Electronics, Information, and Bioengineering, Politecnico di Milano, Milan, Italy
| | - Stephanie Sungalee
- Swiss Cancer Center Leman, Lausanne, Switzerland
- Swiss Institute for Experimental Cancer Research (ISREC) School of Life Sciences, EPFL, Épalinges, Switzerland
| | - Marie Zufferey
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Cancer Center Leman, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Daniele Tavernari
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Cancer Center Leman, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Marco Mina
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Cancer Center Leman, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Stefano Ceri
- Department of Electronics, Information, and Bioengineering, Politecnico di Milano, Milan, Italy
| | - Elisa Oricchio
- Swiss Cancer Center Leman, Lausanne, Switzerland
- Swiss Institute for Experimental Cancer Research (ISREC) School of Life Sciences, EPFL, Épalinges, Switzerland
| | - Giovanni Ciriello
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
- Swiss Cancer Center Leman, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
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6
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Tavernari D, Battistello E, Dheilly E, Petruzzella AS, Mina M, Sordet-Dessimoz J, Peters S, Krueger T, Gfeller D, Riggi N, Oricchio E, Letovanec I, Ciriello G. Nongenetic Evolution Drives Lung Adenocarcinoma Spatial Heterogeneity and Progression. Cancer Discov 2021; 11:1490-1507. [PMID: 33563664 DOI: 10.1158/2159-8290.cd-20-1274] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 12/21/2020] [Accepted: 01/22/2021] [Indexed: 11/16/2022]
Abstract
Cancer evolution determines molecular and morphologic intratumor heterogeneity and challenges the design of effective treatments. In lung adenocarcinoma, disease progression and prognosis are associated with the appearance of morphologically diverse tumor regions, termed histologic patterns. However, the link between molecular and histologic features remains elusive. Here, we generated multiomics and spatially resolved molecular profiles of histologic patterns from primary lung adenocarcinoma, which we integrated with molecular data from >2,000 patients. The transition from indolent to aggressive patterns was not driven by genetic alterations but by epigenetic and transcriptional reprogramming reshaping cancer cell identity. A signature quantifying this transition was an independent predictor of patient prognosis in multiple human cohorts. Within individual tumors, highly multiplexed protein spatial profiling revealed coexistence of immune desert, inflamed, and excluded regions, which matched histologic pattern composition. Our results provide a detailed molecular map of lung adenocarcinoma intratumor spatial heterogeneity, tracing nongenetic routes of cancer evolution. SIGNIFICANCE: Lung adenocarcinomas are classified based on histologic pattern prevalence. However, individual tumors exhibit multiple patterns with unknown molecular features. We characterized nongenetic mechanisms underlying intratumor patterns and molecular markers predicting patient prognosis. Intratumor patterns determined diverse immune microenvironments, warranting their study in the context of current immunotherapies.This article is highlighted in the In This Issue feature, p. 1307.
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Affiliation(s)
- Daniele Tavernari
- Swiss Cancer Center Leman, Lausanne, Switzerland.,Department of Computational Biology, University of Lausanne (UNIL), Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Elena Battistello
- Swiss Cancer Center Leman, Lausanne, Switzerland.,Department of Computational Biology, University of Lausanne (UNIL), Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Swiss Institute for Experimental Cancer Research (ISREC), EPFL, Lausanne, Switzerland
| | - Elie Dheilly
- Swiss Cancer Center Leman, Lausanne, Switzerland.,Swiss Institute for Experimental Cancer Research (ISREC), EPFL, Lausanne, Switzerland
| | - Aaron S Petruzzella
- Swiss Cancer Center Leman, Lausanne, Switzerland.,Swiss Institute for Experimental Cancer Research (ISREC), EPFL, Lausanne, Switzerland
| | - Marco Mina
- Swiss Cancer Center Leman, Lausanne, Switzerland.,Department of Computational Biology, University of Lausanne (UNIL), Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | - Solange Peters
- Swiss Cancer Center Leman, Lausanne, Switzerland.,Department of Oncology, University Hospital of Lausanne (CHUV), Lausanne, Switzerland
| | - Thorsten Krueger
- Division of Thoracic Surgery, University Hospital of Lausanne (CHUV), Lausanne, Switzerland
| | - David Gfeller
- Swiss Cancer Center Leman, Lausanne, Switzerland.,Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne (UNIL), Lausanne, Switzerland
| | - Nicolo Riggi
- Swiss Cancer Center Leman, Lausanne, Switzerland.,Institute of Pathology, University Hospital of Lausanne (CHUV), Lausanne, Switzerland
| | - Elisa Oricchio
- Swiss Cancer Center Leman, Lausanne, Switzerland.,Swiss Institute for Experimental Cancer Research (ISREC), EPFL, Lausanne, Switzerland
| | - Igor Letovanec
- Swiss Cancer Center Leman, Lausanne, Switzerland. .,Institute of Pathology, University Hospital of Lausanne (CHUV), Lausanne, Switzerland.,Department of Pathology, Central Institute, Hôpital du Valais, Sion, Switzerland
| | - Giovanni Ciriello
- Swiss Cancer Center Leman, Lausanne, Switzerland. .,Department of Computational Biology, University of Lausanne (UNIL), Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
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7
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Sesterhenn F, Yang C, Bonet J, Cramer JT, Wen X, Wang Y, Chiang CI, Abriata LA, Kucharska I, Castoro G, Vollers SS, Galloux M, Dheilly E, Rosset S, Corthésy P, Georgeon S, Villard M, Richard CA, Descamps D, Delgado T, Oricchio E, Rameix-Welti MA, Más V, Ervin S, Eléouët JF, Riffault S, Bates JT, Julien JP, Li Y, Jardetzky T, Krey T, Correia BE. De novo protein design enables the precise induction of RSV-neutralizing antibodies. Science 2020; 368:eaay5051. [PMID: 32409444 PMCID: PMC7391827 DOI: 10.1126/science.aay5051] [Citation(s) in RCA: 109] [Impact Index Per Article: 27.3] [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: 06/24/2019] [Revised: 01/30/2020] [Accepted: 04/08/2020] [Indexed: 12/27/2022]
Abstract
De novo protein design has been successful in expanding the natural protein repertoire. However, most de novo proteins lack biological function, presenting a major methodological challenge. In vaccinology, the induction of precise antibody responses remains a cornerstone for next-generation vaccines. Here, we present a protein design algorithm called TopoBuilder, with which we engineered epitope-focused immunogens displaying complex structural motifs. In both mice and nonhuman primates, cocktails of three de novo-designed immunogens induced robust neutralizing responses against the respiratory syncytial virus. Furthermore, the immunogens refocused preexisting antibody responses toward defined neutralization epitopes. Overall, our design approach opens the possibility of targeting specific epitopes for the development of vaccines and therapeutic antibodies and, more generally, will be applicable to the design of de novo proteins displaying complex functional motifs.
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Affiliation(s)
- Fabian Sesterhenn
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne CH-1015, Switzerland
| | - Che Yang
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne CH-1015, Switzerland
| | - Jaume Bonet
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne CH-1015, Switzerland
| | - Johannes T Cramer
- Institute of Virology, Hannover Medical School, Hannover 30625, Germany
| | - Xiaolin Wen
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Yimeng Wang
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA
| | - Chi-I Chiang
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA
| | - Luciano A Abriata
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne CH-1015, Switzerland
| | - Iga Kucharska
- Program in Molecular Medicine, Hospital for Sick Children Research Institute, Toronto, Ontario M5G 0A4, Canada
- Departments of Biochemistry and Immunology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Giacomo Castoro
- Institute of Virology, Hannover Medical School, Hannover 30625, Germany
| | - Sabrina S Vollers
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne CH-1015, Switzerland
| | - Marie Galloux
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350 Jouy-en-Josas, France
| | - Elie Dheilly
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
| | - Stéphane Rosset
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne CH-1015, Switzerland
| | - Patricia Corthésy
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne CH-1015, Switzerland
| | - Sandrine Georgeon
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne CH-1015, Switzerland
| | - Mélanie Villard
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne CH-1015, Switzerland
| | | | - Delphyne Descamps
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350 Jouy-en-Josas, France
| | - Teresa Delgado
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Madrid, Spain
| | - Elisa Oricchio
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland
| | | | - Vicente Más
- Centro Nacional de Microbiología, Instituto de Salud Carlos III, 28220 Madrid, Spain
| | - Sean Ervin
- Wake Forest Baptist Medical Center, Winston Salem, NC 27157, USA
| | | | - Sabine Riffault
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350 Jouy-en-Josas, France
| | - John T Bates
- University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Jean-Philippe Julien
- Program in Molecular Medicine, Hospital for Sick Children Research Institute, Toronto, Ontario M5G 0A4, Canada
- Departments of Biochemistry and Immunology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Yuxing Li
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA
- Department of Microbiology and Immunology & Center of Biomolecular Therapeutics, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Theodore Jardetzky
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Thomas Krey
- Institute of Virology, Hannover Medical School, Hannover 30625, Germany
- German Center for Infection Research (DZIF), 38124 Braunschweig, Germany
- Institute of Biochemistry, Center of Structural and Cell Biology in Medicine, University of Luebeck, D-23538 Luebeck, Germany
- Excellence Cluster 2155 RESIST, Hannover Medical School, 30625 Hannover, Germany
- Centre for Structural Systems Biology (CSSB), 22607 Hamburg, Germany
| | - Bruno E Correia
- Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland.
- Swiss Institute of Bioinformatics (SIB), Lausanne CH-1015, Switzerland
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8
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Dheilly E, Battistello E, Katanayeva N, Sungalee S, Michaux J, Duns G, Wehrle S, Sordet-Dessimoz J, Mina M, Racle J, Farinha P, Coukos G, Gfeller D, Mottok A, Kridel R, Correia BE, Steidl C, Bassani-Sternberg M, Ciriello G, Zoete V, Oricchio E. Cathepsin S Regulates Antigen Processing and T Cell Activity in Non-Hodgkin Lymphoma. Cancer Cell 2020; 37:674-689.e12. [PMID: 32330455 DOI: 10.1016/j.ccell.2020.03.016] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 11/14/2019] [Accepted: 03/18/2020] [Indexed: 10/24/2022]
Abstract
Genomic alterations in cancer cells can influence the immune system to favor tumor growth. In non-Hodgkin lymphoma, physiological interactions between B cells and the germinal center microenvironment are coopted to sustain cancer cell proliferation. We found that follicular lymphoma patients harbor a recurrent hotspot mutation targeting tyrosine 132 (Y132D) in cathepsin S (CTSS) that enhances protein activity. CTSS regulates antigen processing and CD4+ and CD8+ T cell-mediated immune responses. Loss of CTSS activity reduces lymphoma growth by limiting communication with CD4+ T follicular helper cells while inducing antigen diversification and activation of CD8+ T cells. Overall, our results suggest that CTSS inhibition has non-redundant therapeutic potential to enhance anti-tumor immune responses in indolent and aggressive lymphomas.
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Affiliation(s)
- Elie Dheilly
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, EPFL, Lausanne, 1015 Switzerland; Swiss Cancer Center Leman (SCCL), Lausanne, 1015 Switzerland
| | - Elena Battistello
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, EPFL, Lausanne, 1015 Switzerland; Swiss Cancer Center Leman (SCCL), Lausanne, 1015 Switzerland; Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics (SIB), Lausanne 1015, Switzerland
| | - Natalya Katanayeva
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, EPFL, Lausanne, 1015 Switzerland; Swiss Cancer Center Leman (SCCL), Lausanne, 1015 Switzerland
| | - Stephanie Sungalee
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, EPFL, Lausanne, 1015 Switzerland; Swiss Cancer Center Leman (SCCL), Lausanne, 1015 Switzerland
| | - Justine Michaux
- Swiss Cancer Center Leman (SCCL), Lausanne, 1015 Switzerland; Ludwig Institute for Cancer Research and Department of Oncology, University of Lausanne, Lausanne, Switzerland; Department of Oncology, University Hospital of Lausanne, Lausanne, Switzerland
| | - Gerben Duns
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, BC, Canada
| | - Sarah Wehrle
- Institute of Bioengineering, EPFL, 1015 Lausanne, Switzerland
| | | | - Marco Mina
- Swiss Cancer Center Leman (SCCL), Lausanne, 1015 Switzerland; Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics (SIB), Lausanne 1015, Switzerland
| | - Julien Racle
- Swiss Cancer Center Leman (SCCL), Lausanne, 1015 Switzerland; Swiss Institute of Bioinformatics (SIB), Lausanne 1015, Switzerland; Ludwig Institute for Cancer Research and Department of Oncology, University of Lausanne, Lausanne, Switzerland; Department of Oncology, University Hospital of Lausanne, Lausanne, Switzerland
| | - Pedro Farinha
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, BC, Canada
| | - George Coukos
- Swiss Cancer Center Leman (SCCL), Lausanne, 1015 Switzerland; Ludwig Institute for Cancer Research and Department of Oncology, University of Lausanne, Lausanne, Switzerland; Department of Oncology, University Hospital of Lausanne, Lausanne, Switzerland
| | - David Gfeller
- Swiss Cancer Center Leman (SCCL), Lausanne, 1015 Switzerland; Swiss Institute of Bioinformatics (SIB), Lausanne 1015, Switzerland; Ludwig Institute for Cancer Research and Department of Oncology, University of Lausanne, Lausanne, Switzerland; Department of Oncology, University Hospital of Lausanne, Lausanne, Switzerland
| | - Anja Mottok
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Germany
| | | | - Bruno E Correia
- Swiss Institute of Bioinformatics (SIB), Lausanne 1015, Switzerland; Institute of Bioengineering, EPFL, 1015 Lausanne, Switzerland
| | - Christian Steidl
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, BC, Canada
| | - Michal Bassani-Sternberg
- Swiss Cancer Center Leman (SCCL), Lausanne, 1015 Switzerland; Ludwig Institute for Cancer Research and Department of Oncology, University of Lausanne, Lausanne, Switzerland; Department of Oncology, University Hospital of Lausanne, Lausanne, Switzerland
| | - Giovanni Ciriello
- Swiss Cancer Center Leman (SCCL), Lausanne, 1015 Switzerland; Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics (SIB), Lausanne 1015, Switzerland
| | - Vincent Zoete
- Swiss Cancer Center Leman (SCCL), Lausanne, 1015 Switzerland; Swiss Institute of Bioinformatics (SIB), Lausanne 1015, Switzerland; Ludwig Institute for Cancer Research and Department of Oncology, University of Lausanne, Lausanne, Switzerland; Molecular Modeling Group, SIB, Lausanne, Switzerland
| | - Elisa Oricchio
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, EPFL, Lausanne, 1015 Switzerland; Swiss Cancer Center Leman (SCCL), Lausanne, 1015 Switzerland.
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9
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Donaldson-Collier MC, Sungalee S, Zufferey M, Tavernari D, Katanayeva N, Battistello E, Mina M, Douglass KM, Rey T, Raynaud F, Manley S, Ciriello G, Oricchio E. EZH2 oncogenic mutations drive epigenetic, transcriptional, and structural changes within chromatin domains. Nat Genet 2019; 51:517-528. [PMID: 30692681 DOI: 10.1038/s41588-018-0338-y] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 12/17/2018] [Indexed: 12/16/2022]
Abstract
Chromatin is organized into topologically associating domains (TADs) enriched in distinct histone marks. In cancer, gain-of-function mutations in the gene encoding the enhancer of zeste homolog 2 protein (EZH2) lead to a genome-wide increase in histone-3 Lys27 trimethylation (H3K27me3) associated with transcriptional repression. However, the effects of these epigenetic changes on the structure and function of chromatin domains have not been explored. Here, we found a functional interplay between TADs and epigenetic and transcriptional changes mediated by mutated EZH2. Altered EZH2 (p.Tyr646* (EZH2Y646X)) led to silencing of entire domains, synergistically inactivating multiple tumor suppressors. Intra-TAD gene silencing was coupled with changes of interactions between gene promoter regions. Notably, gene expression and chromatin interactions were restored by pharmacological inhibition of EZH2Y646X. Our results indicate that EZH2Y646X alters the topology and function of chromatin domains to promote synergistic oncogenic programs.
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Affiliation(s)
- Maria C Donaldson-Collier
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Science, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Stephanie Sungalee
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Science, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Marie Zufferey
- Department of Computational Biology, University of Lausanne (UNIL), Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Daniele Tavernari
- Department of Computational Biology, University of Lausanne (UNIL), Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Natalya Katanayeva
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Science, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Elena Battistello
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Science, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Department of Computational Biology, University of Lausanne (UNIL), Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Marco Mina
- Department of Computational Biology, University of Lausanne (UNIL), Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Kyle M Douglass
- Institute of Physics, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Timo Rey
- Institute of Physics, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Franck Raynaud
- Department of Computational Biology, University of Lausanne (UNIL), Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Suliana Manley
- Institute of Physics, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Giovanni Ciriello
- Department of Computational Biology, University of Lausanne (UNIL), Lausanne, Switzerland. .,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
| | - Elisa Oricchio
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Science, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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10
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Zufferey M, Tavernari D, Oricchio E, Ciriello G. Comparison of computational methods for the identification of topologically associating domains. Genome Biol 2018; 19:217. [PMID: 30526631 PMCID: PMC6288901 DOI: 10.1186/s13059-018-1596-9] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 11/26/2018] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Chromatin folding gives rise to structural elements among which are clusters of densely interacting DNA regions termed topologically associating domains (TADs). TADs have been characterized across multiple species, tissue types, and differentiation stages, sometimes in association with regulation of biological functions. The reliability and reproducibility of these findings are intrinsically related with the correct identification of these domains from high-throughput chromatin conformation capture (Hi-C) experiments. RESULTS Here, we test and compare 22 computational methods to identify TADs across 20 different conditions. We find that TAD sizes and numbers vary significantly among callers and data resolutions, challenging the definition of an average TAD size, but strengthening the hypothesis that TADs are hierarchically organized domains, rather than disjoint structural elements. Performances of these methods differ based on data resolution and normalization strategy, but a core set of TAD callers consistently retrieve reproducible domains, even at low sequencing depths, that are enriched for TAD-associated biological features. CONCLUSIONS This study provides a reference for the analysis of chromatin domains from Hi-C experiments and useful guidelines for choosing a suitable approach based on the experimental design, available data, and biological question of interest.
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Affiliation(s)
- Marie Zufferey
- Department of Computational Biology, University of Lausanne (UNIL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Daniele Tavernari
- Department of Computational Biology, University of Lausanne (UNIL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Elisa Oricchio
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Giovanni Ciriello
- Department of Computational Biology, University of Lausanne (UNIL), Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
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11
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Oricchio E, Katanayeva N, Donaldson MC, Sungalee S, Pasion JP, Béguelin W, Battistello E, Sanghvi VR, Jiang M, Jiang Y, Teater M, Parmigiani A, Budanov AV, Chan FC, Shah SP, Kridel R, Melnick AM, Ciriello G, Wendel HG. Genetic and epigenetic inactivation of SESTRIN1 controls mTORC1 and response to EZH2 inhibition in follicular lymphoma. Sci Transl Med 2018; 9:9/396/eaak9969. [PMID: 28659443 DOI: 10.1126/scitranslmed.aak9969] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 02/03/2017] [Accepted: 06/05/2017] [Indexed: 12/14/2022]
Abstract
Follicular lymphoma (FL) is an incurable form of B cell lymphoma. Genomic studies have cataloged common genetic lesions in FL such as translocation t(14;18), frequent losses of chromosome 6q, and mutations in epigenetic regulators such as EZH2 Using a focused genetic screen, we identified SESTRIN1 as a relevant target of the 6q deletion and demonstrate tumor suppression by SESTRIN1 in vivo. Moreover, SESTRIN1 is a direct target of the lymphoma-specific EZH2 gain-of-function mutation (EZH2Y641X ). SESTRIN1 inactivation disrupts p53-mediated control of mammalian target of rapamycin complex 1 (mTORC1) and enables mRNA translation under genotoxic stress. SESTRIN1 loss represents an alternative to RRAGC mutations that maintain mTORC1 activity under nutrient starvation. The antitumor efficacy of pharmacological EZH2 inhibition depends on SESTRIN1, indicating that mTORC1 control is a critical function of EZH2 in lymphoma. Conversely, EZH2Y641X mutant lymphomas show increased sensitivity to RapaLink-1, a bifunctional mTOR inhibitor. Hence, SESTRIN1 contributes to the genetic and epigenetic control of mTORC1 in lymphoma and influences responses to targeted therapies.
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Affiliation(s)
- Elisa Oricchio
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Natalya Katanayeva
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Maria Christine Donaldson
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Stephanie Sungalee
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Joyce P Pasion
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Wendy Béguelin
- Division of Hematology/Oncology, Weill Cornell Medical College, Cornell University, 1300 York Avenue, New York, NY 10065, USA
| | - Elena Battistello
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.,Department of Computational Biology, University of Lausanne, 1005 Lausanne, Switzerland
| | - Viraj R Sanghvi
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Man Jiang
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Yanwen Jiang
- Institute for Computational Biomedicine, Weill Cornell Medical College, Cornell University, New York, NY 10065, USA
| | - Matt Teater
- Institute for Computational Biomedicine, Weill Cornell Medical College, Cornell University, New York, NY 10065, USA
| | - Anita Parmigiani
- Department of Human and Molecular Genetics, Goodwin Research Laboratories, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Andrei V Budanov
- Department of Human and Molecular Genetics, Goodwin Research Laboratories, Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA.,School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Pearse Street, Dublin 2, Ireland
| | - Fong Chun Chan
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada.,Bioinformatics Graduate Program, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sohrab P Shah
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Molecular Oncology, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Robert Kridel
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada.,Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Ari M Melnick
- Division of Hematology/Oncology, Weill Cornell Medical College, Cornell University, 1300 York Avenue, New York, NY 10065, USA
| | - Giovanni Ciriello
- Department of Computational Biology, University of Lausanne, 1005 Lausanne, Switzerland
| | - Hans-Guido Wendel
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
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12
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Mina M, Raynaud F, Tavernari D, Battistello E, Sungalee S, Saghafinia S, Laessle T, Sanchez-Vega F, Schultz N, Oricchio E, Ciriello G. Interrogating functional dependencies between genomic alterations can facilitate precision medicine approaches in cancer. Ann Oncol 2017. [DOI: 10.1093/annonc/mdx508.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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13
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Abstract
SESTRIN1 is a tumor suppressor in follicular lymphoma that controls mTORC1 activity and it is inactivated by chromosomal deletions or epigenetically silenced by mutant EZH2Y641X. Pharmacological inhibition of EZH2 promotes SESTRIN1 re-expression and it restores its tumor suppressive activity, suggesting the possibility to epigenetically control mTORC1 activity.
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Affiliation(s)
- Maria C Donaldson
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Natalya Katanayeva
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Elisa Oricchio
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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14
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Mina M, Raynaud F, Tavernari D, Battistello E, Sungalee S, Saghafinia S, Laessle T, Sanchez-Vega F, Schultz N, Oricchio E, Ciriello G. Conditional Selection of Genomic Alterations Dictates Cancer Evolution and Oncogenic Dependencies. Cancer Cell 2017; 32:155-168.e6. [PMID: 28756993 DOI: 10.1016/j.ccell.2017.06.010] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 06/05/2017] [Accepted: 06/26/2017] [Indexed: 02/07/2023]
Abstract
Cancer evolves through the emergence and selection of molecular alterations. Cancer genome profiling has revealed that specific events are more or less likely to be co-selected, suggesting that the selection of one event depends on the others. However, the nature of these evolutionary dependencies and their impact remain unclear. Here, we designed SELECT, an algorithmic approach to systematically identify evolutionary dependencies from alteration patterns. By analyzing 6,456 genomes from multiple tumor types, we constructed a map of oncogenic dependencies associated with cellular pathways, transcriptional readouts, and therapeutic response. Finally, modeling of cancer evolution shows that alteration dependencies emerge only under conditional selection. These results provide a framework for the design of strategies to predict cancer progression and therapeutic response.
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Affiliation(s)
- Marco Mina
- Department of Computational Biology, University of Lausanne (UNIL), 1011 Lausanne, Vaud, Switzerland; Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Franck Raynaud
- Department of Computational Biology, University of Lausanne (UNIL), 1011 Lausanne, Vaud, Switzerland; Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Daniele Tavernari
- Department of Computational Biology, University of Lausanne (UNIL), 1011 Lausanne, Vaud, Switzerland; Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Elena Battistello
- Department of Computational Biology, University of Lausanne (UNIL), 1011 Lausanne, Vaud, Switzerland; Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland; Swiss Institute for Experimental Cancer Research (ISREC), Ecole Polytechnique Federale Lausanne (EPFL), 1015 Lausanne, Vaud, Switzerland
| | - Stephanie Sungalee
- Swiss Institute for Experimental Cancer Research (ISREC), Ecole Polytechnique Federale Lausanne (EPFL), 1015 Lausanne, Vaud, Switzerland
| | - Sadegh Saghafinia
- Department of Computational Biology, University of Lausanne (UNIL), 1011 Lausanne, Vaud, Switzerland; Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland; Swiss Institute for Experimental Cancer Research (ISREC), Ecole Polytechnique Federale Lausanne (EPFL), 1015 Lausanne, Vaud, Switzerland
| | - Titouan Laessle
- Department of Computational Biology, University of Lausanne (UNIL), 1011 Lausanne, Vaud, Switzerland
| | - Francisco Sanchez-Vega
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nikolaus Schultz
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elisa Oricchio
- Swiss Institute for Experimental Cancer Research (ISREC), Ecole Polytechnique Federale Lausanne (EPFL), 1015 Lausanne, Vaud, Switzerland
| | - Giovanni Ciriello
- Department of Computational Biology, University of Lausanne (UNIL), 1011 Lausanne, Vaud, Switzerland; Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
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15
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Boice M, Salloum D, Mourcin F, Sanghvi V, Amin R, Oricchio E, Jiang M, Mottok A, Denis-Lagache N, Ciriello G, Tam W, Teruya-Feldstein J, de Stanchina E, Chan WC, Malek SN, Ennishi D, Brentjens RJ, Gascoyne RD, Cogné M, Tarte K, Wendel HG. Loss of the HVEM Tumor Suppressor in Lymphoma and Restoration by Modified CAR-T Cells. Cell 2016; 167:405-418.e13. [PMID: 27693350 DOI: 10.1016/j.cell.2016.08.032] [Citation(s) in RCA: 174] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 07/09/2016] [Accepted: 08/16/2016] [Indexed: 12/31/2022]
Abstract
The HVEM (TNFRSF14) receptor gene is among the most frequently mutated genes in germinal center lymphomas. We report that loss of HVEM leads to cell-autonomous activation of B cell proliferation and drives the development of GC lymphomas in vivo. HVEM-deficient lymphoma B cells also induce a tumor-supportive microenvironment marked by exacerbated lymphoid stroma activation and increased recruitment of T follicular helper (TFH) cells. These changes result from the disruption of inhibitory cell-cell interactions between the HVEM and BTLA (B and T lymphocyte attenuator) receptors. Accordingly, administration of the HVEM ectodomain protein (solHVEM(P37-V202)) binds BTLA and restores tumor suppression. To deliver solHVEM to lymphomas in vivo, we engineered CD19-targeted chimeric antigen receptor (CAR) T cells that produce solHVEM locally and continuously. These modified CAR-T cells show enhanced therapeutic activity against xenografted lymphomas. Hence, the HVEM-BTLA axis opposes lymphoma development, and our study illustrates the use of CAR-T cells as "micro-pharmacies" able to deliver an anti-cancer protein.
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Affiliation(s)
- Michael Boice
- Cancer Biology & Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA; Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA
| | - Darin Salloum
- Cancer Biology & Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Frederic Mourcin
- INSERM U917, Equipe labellisée Ligue contre le Cancer, Université Rennes 1, EFS Bretagne, CHU Rennes, 35000 Rennes, France
| | - Viraj Sanghvi
- Cancer Biology & Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Rada Amin
- INSERM U917, Equipe labellisée Ligue contre le Cancer, Université Rennes 1, EFS Bretagne, CHU Rennes, 35000 Rennes, France
| | - Elisa Oricchio
- Swiss Institute for Cancer Research (ISREC), EPFL SV-Batiment 19, 1003 Lausanne, Switzerland
| | - Man Jiang
- Cancer Biology & Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Anja Mottok
- Centre for Lymphoid Cancer, British Columbia Cancer Agency and Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V5Z 1L3, Canada
| | - Nicolas Denis-Lagache
- Centre National de la Recherche Scientifque, UMR 7276, Université de Limoges, 8700 Limoges, France
| | - Giovanni Ciriello
- Department of Computational Biology, University of Lausanne, Rue du Bugnon 27, 1005 Lausanne, Switzerland; The Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Wayne Tam
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical School, New York, NY 10065, USA
| | | | - Elisa de Stanchina
- Antitumor Assessment Core Facility and Molecular Pharmacology Department, Memorial-Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Wing C Chan
- Department of Pathology, City of Hope, Duarte, CA 91010, USA
| | - Sami N Malek
- Division of Hematology and Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Daisuke Ennishi
- Centre for Lymphoid Cancer, British Columbia Cancer Agency and Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V5Z 1L3, Canada
| | - Renier J Brentjens
- Department of Medicine, Memorial-Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Randy D Gascoyne
- Centre for Lymphoid Cancer, British Columbia Cancer Agency and Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V5Z 1L3, Canada
| | - Michel Cogné
- Centre National de la Recherche Scientifque, UMR 7276, Université de Limoges, 8700 Limoges, France
| | - Karin Tarte
- INSERM U917, Equipe labellisée Ligue contre le Cancer, Université Rennes 1, EFS Bretagne, CHU Rennes, 35000 Rennes, France.
| | - Hans-Guido Wendel
- Cancer Biology & Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.
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16
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Abstract
Recombinant antibody phage library technology provides multiple advantages, including that human antibodies can be generated against proteins that are highly conserved between species. We used this technology to isolate and characterize an anti-EphA2 single-chain antibody. We show that the antibody binds the antigen with 1:1 stoichiometry and has high specificity for EphA2. The crystal structure of the complex reveals that the antibody targets the same receptor surface cavity as the ephrin ligand. Specifically, a lengthy CDR-H3 loop protrudes deep into the ligand-binding cavity, with several hydrophobic residues at its tip forming an anchor-like structure buried within the hydrophobic Eph pocket, in a way similar to the ephrin receptor-binding loop in the Eph/ephrin structures. Consequently, the antibody blocks ephrin binding to EphA2. Furthermore, it induces apoptosis and reduces cell proliferation in lymphoma cells lines. Since Ephs are important mediators of tumorigenesis, such antibodies could have applications both in research and therapy.
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Affiliation(s)
- Yehuda Goldgur
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center , New York, NY , USA
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17
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Oricchio E, Wendel HG. Genomic studies indicate a novel combination therapy for follicular lymphoma. Mol Cell Oncol 2014; 8:e969640. [PMID: 35419485 PMCID: PMC8997257 DOI: 10.4161/23723548.2014.969640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Follicular lymphoma (FL) is an incurable form of B-cell lymphoma. Genomic alterations that inactivate RB signaling are surprisingly common in indolent FL. We show that FLs that are positive for phosphorylated RB respond to dual CDK4/BCL2 inhibition. Our results imply that RB phosphorylation identifies patients likely to benefit from such dual intervention.
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Affiliation(s)
- Elisa Oricchio
- Cancer Biology & Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Hans-Guido Wendel
- Cancer Biology & Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
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18
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Oricchio E, Papapetrou EP, Lafaille F, Ganat YM, Kriks S, Ortega-Molina A, Mark WH, Teruya-Feldstein J, Huse JT, Reuter V, Sadelain M, Studer L, Wendel HG. A cell engineering strategy to enhance the safety of stem cell therapies. Cell Rep 2014; 8:1677-1685. [PMID: 25242333 PMCID: PMC4177332 DOI: 10.1016/j.celrep.2014.08.039] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [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: 03/06/2014] [Revised: 07/25/2014] [Accepted: 08/16/2014] [Indexed: 11/17/2022] Open
Abstract
The long-term risk of malignancy associated with stem cell therapies is a significant concern in the clinical application of this exciting technology. We report a cancer-selective strategy to enhance the safety of stem cell therapies. Briefly, using a cell engineering approach, we show that aggressive cancers derived from human or murine induced pluripotent stem cells (iPSCs) and embryonic stem cells (ESCs) are strikingly sensitive to temporary MYC blockade. On the other hand, differentiated tissues derived from human or mouse iPSCs can readily tolerate temporary MYC inactivation. In cancer cells, endogenous MYC is required to maintain the metabolic and epigenetic functions of the embryonic and cancer-specific pyruvate kinase M2 isoform (PKM2). In summary, our results implicate PKM2 in cancer's increased MYC dependence and indicate dominant MYC inhibition as a cancer-selective fail-safe for stem cell therapies.
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Affiliation(s)
- Elisa Oricchio
- Cancer Biology & Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Eirini P Papapetrou
- Center for Cell Engineering, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Fabien Lafaille
- Developmental Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Yosif M Ganat
- Developmental Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Sonja Kriks
- Developmental Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Ana Ortega-Molina
- Cancer Biology & Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Willie H Mark
- Mouse Genetics Core, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Julie Teruya-Feldstein
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Jason T Huse
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Victor Reuter
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Michel Sadelain
- Center for Cell Engineering, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA; Molecular Pharmacology and Chemistry Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Lorenz Studer
- Center for Cell Engineering, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA; Developmental Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Hans-Guido Wendel
- Cancer Biology & Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.
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19
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Oricchio E, Ciriello G, Jiang M, Boice MH, Schatz JH, Heguy A, Viale A, de Stanchina E, Teruya-Feldstein J, Bouska A, McKeithan T, Sander C, Tam W, Seshan VE, Chan WC, Chaganti RSK, Wendel HG. Frequent disruption of the RB pathway in indolent follicular lymphoma suggests a new combination therapy. ACTA ACUST UNITED AC 2014; 211:1379-91. [PMID: 24913233 PMCID: PMC4076578 DOI: 10.1084/jem.20132120] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [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: 01/15/2023]
Abstract
Loss of cell cycle controls is a hallmark of cancer and has a well-established role in aggressive B cell malignancies. However, the role of such lesions in indolent follicular lymphoma (FL) is unclear and individual lesions have been observed with low frequency. By analyzing genomic data from two large cohorts of indolent FLs, we identify a pattern of mutually exclusive (P = 0.003) genomic lesions that impair the retinoblastoma (RB) pathway in nearly 50% of FLs. These alterations include homozygous and heterozygous deletions of the p16/CDKN2a/b (7%) and RB1 (12%) loci, and more frequent gains of chromosome 12 that include CDK4 (29%). These aberrations are associated with high-risk disease by the FL prognostic index (FLIPI), and studies in a murine FL model confirm their pathogenic role in indolent FL. Increased CDK4 kinase activity toward RB1 is readily measured in tumor samples and indicates an opportunity for CDK4 inhibition. We find that dual CDK4 and BCL2 inhibitor treatment is safe and effective against available models of FL. In summary, frequent RB pathway lesions in indolent, high-risk FLs indicate an untapped therapeutic opportunity.
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Affiliation(s)
- Elisa Oricchio
- Cancer Biology & Genetics Program, Computational Biology Program, Department of Medicine, Human Oncology and Pathogenesis Program, Genomics Core Facility, Molecular Pharmacology Program, Department of Pathology, Department of Epidemiology and Biostatistics, and Cell Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065
| | - Giovanni Ciriello
- Cancer Biology & Genetics Program, Computational Biology Program, Department of Medicine, Human Oncology and Pathogenesis Program, Genomics Core Facility, Molecular Pharmacology Program, Department of Pathology, Department of Epidemiology and Biostatistics, and Cell Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065
| | - Man Jiang
- Cancer Biology & Genetics Program, Computational Biology Program, Department of Medicine, Human Oncology and Pathogenesis Program, Genomics Core Facility, Molecular Pharmacology Program, Department of Pathology, Department of Epidemiology and Biostatistics, and Cell Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065
| | - Michael H Boice
- Cancer Biology & Genetics Program, Computational Biology Program, Department of Medicine, Human Oncology and Pathogenesis Program, Genomics Core Facility, Molecular Pharmacology Program, Department of Pathology, Department of Epidemiology and Biostatistics, and Cell Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065
| | - Jonathan H Schatz
- Cancer Biology & Genetics Program, Computational Biology Program, Department of Medicine, Human Oncology and Pathogenesis Program, Genomics Core Facility, Molecular Pharmacology Program, Department of Pathology, Department of Epidemiology and Biostatistics, and Cell Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065Cancer Biology & Genetics Program, Computational Biology Program, Department of Medicine, Human Oncology and Pathogenesis Program, Genomics Core Facility, Molecular Pharmacology Program, Department of Pathology, Department of Epidemiology and Biostatistics, and Cell Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065
| | - Adriana Heguy
- Cancer Biology & Genetics Program, Computational Biology Program, Department of Medicine, Human Oncology and Pathogenesis Program, Genomics Core Facility, Molecular Pharmacology Program, Department of Pathology, Department of Epidemiology and Biostatistics, and Cell Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065
| | - Agnes Viale
- Cancer Biology & Genetics Program, Computational Biology Program, Department of Medicine, Human Oncology and Pathogenesis Program, Genomics Core Facility, Molecular Pharmacology Program, Department of Pathology, Department of Epidemiology and Biostatistics, and Cell Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065
| | - Elisa de Stanchina
- Cancer Biology & Genetics Program, Computational Biology Program, Department of Medicine, Human Oncology and Pathogenesis Program, Genomics Core Facility, Molecular Pharmacology Program, Department of Pathology, Department of Epidemiology and Biostatistics, and Cell Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065
| | - Julie Teruya-Feldstein
- Cancer Biology & Genetics Program, Computational Biology Program, Department of Medicine, Human Oncology and Pathogenesis Program, Genomics Core Facility, Molecular Pharmacology Program, Department of Pathology, Department of Epidemiology and Biostatistics, and Cell Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065
| | - Alyssa Bouska
- Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198
| | - Tim McKeithan
- Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198
| | - Chris Sander
- Cancer Biology & Genetics Program, Computational Biology Program, Department of Medicine, Human Oncology and Pathogenesis Program, Genomics Core Facility, Molecular Pharmacology Program, Department of Pathology, Department of Epidemiology and Biostatistics, and Cell Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065
| | - Wayne Tam
- Department of Pathology, Weill-Cornell Medical School, New York, NY 10065
| | - Venkatraman E Seshan
- Cancer Biology & Genetics Program, Computational Biology Program, Department of Medicine, Human Oncology and Pathogenesis Program, Genomics Core Facility, Molecular Pharmacology Program, Department of Pathology, Department of Epidemiology and Biostatistics, and Cell Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065
| | - Wing-Chung Chan
- Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198
| | - R S K Chaganti
- Cancer Biology & Genetics Program, Computational Biology Program, Department of Medicine, Human Oncology and Pathogenesis Program, Genomics Core Facility, Molecular Pharmacology Program, Department of Pathology, Department of Epidemiology and Biostatistics, and Cell Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065
| | - Hans-Guido Wendel
- Cancer Biology & Genetics Program, Computational Biology Program, Department of Medicine, Human Oncology and Pathogenesis Program, Genomics Core Facility, Molecular Pharmacology Program, Department of Pathology, Department of Epidemiology and Biostatistics, and Cell Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065
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20
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Abstract
Recent technological advances allow analysis of genomic changes in cancer in unprecedented detail. The next challenge is to prioritize the multitude of genetic aberrations found and identify therapeutic opportunities. We recently completed a study that illustrates the use of unbiased genetic screens and murine cancer models to find therapeutic targets among complex genomic data. We genetically dissected the common deletion of chromosome 6q and identified the ephrin receptor A7 (EPHA7) as a tumor suppressor in lymphoma. Notably, EPHA7 encodes a soluble splice variant that acts as an extrinsic tumor suppressor. Accordingly, we developed an antibody-based strategy to specifically deliver EPHA7 back to tumors that have lost this gene. Recent sequencing studies have implicated EPHA7 in lung cancer and other tumors, suggesting a broader therapeutic potential for antibody-mediated delivery of this tumor suppressor for cancer therapy. Together, our comprehensive approach provides new insights into cancer biology and may directly lead to the development of new cancer therapies.
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Affiliation(s)
- Elisa Oricchio
- Cancer Biology & Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA.
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21
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Abstract
The functional annotation of the cancer genome can reveal new opportunities for cancer therapies. The wealth of genomic data on various cancers has not yet been mined for clinically and therapeutically useful information. We use cross-comparisons of genomic data with the results of unbiased genetic screens to prioritize genomic changes for further study. In this manner, we have identified a soluble variant of the ephrin receptor A7 (EPHA7 (TR) ) as a tumor suppressor that is lost in lymphoma. We also developed antibody-based delivery to restore this tumor suppressor to the cancer cells in situ. We will discuss our strategy of screening genomic data, specific findings concerning EPHA7 and the potential for future discoveries.
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Affiliation(s)
- Elisa Oricchio
- Cancer Biology & Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
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22
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Oricchio E, Nanjangud G, Wolfe AL, Schatz JH, Mavrakis KJ, Jiang M, Liu X, Bruno J, Heguy A, Olshen AB, Socci ND, Teruya-Feldstein J, Weis-Garcia F, Tam W, Shaknovich R, Melnick A, Himanen JP, Chaganti RSK, Wendel HG. The Eph-receptor A7 is a soluble tumor suppressor for follicular lymphoma. Cell 2011; 147:554-64. [PMID: 22036564 DOI: 10.1016/j.cell.2011.09.035] [Citation(s) in RCA: 134] [Impact Index Per Article: 10.3] [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: 02/28/2011] [Revised: 06/16/2011] [Accepted: 09/21/2011] [Indexed: 01/28/2023]
Abstract
Insights into cancer genetics can lead to therapeutic opportunities. By cross-referencing chromosomal changes with an unbiased genetic screen we identify the ephrin receptor A7 (EPHA7) as a tumor suppressor in follicular lymphoma (FL). EPHA7 is a target of 6q deletions and inactivated in 72% of FLs. Knockdown of EPHA7 drives lymphoma development in a murine FL model. In analogy to its physiological function in brain development, a soluble splice variant of EPHA7 (EPHA7(TR)) interferes with another Eph-receptor and blocks oncogenic signals in lymphoma cells. Consistent with this drug-like activity, administration of the purified EPHA7(TR) protein produces antitumor effects against xenografted human lymphomas. Further, by fusing EPHA7(TR) to the anti-CD20 antibody (rituximab) we can directly target this tumor suppressor to lymphomas in vivo. Our study attests to the power of combining descriptive tumor genomics with functional screens and reveals EPHA7(TR) as tumor suppressor with immediate therapeutic potential.
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MESH Headings
- Animals
- Antibodies, Monoclonal, Murine-Derived/therapeutic use
- Cell Line, Tumor
- Chromosomes, Human, Pair 6
- Genes, Tumor Suppressor
- Genomics
- Humans
- Lymphoma, Follicular/drug therapy
- Lymphoma, Follicular/genetics
- Lymphoma, Follicular/metabolism
- Male
- Mice
- Neoplasm Transplantation
- RNA Interference
- Receptor, EphA7/metabolism
- Rituximab
- Transplantation, Heterologous
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Affiliation(s)
- Elisa Oricchio
- Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
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23
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Schatz JH, Oricchio E, Wolfe AL, Jiang M, Linkov I, Maragulia J, Shi W, Zhang Z, Vinagolu RK, Pagano NC, Porco JA, Teruya-Feldstein J, Rosen N, Zelenetz AD, Pelletier J, Wendel HG. Targeting cap-dependent translation blocks converging survival signals by AKT and PIM kinases in lymphoma. J Biophys Biochem Cytol 2011. [DOI: 10.1083/jcb1945oia9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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24
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Schatz JH, Oricchio E, Wolfe AL, Jiang M, Linkov I, Maragulia J, Shi W, Zhang Z, Rajasekhar VK, Pagano NC, Porco JA, Teruya-Feldstein J, Rosen N, Zelenetz AD, Pelletier J, Wendel HG. Targeting cap-dependent translation blocks converging survival signals by AKT and PIM kinases in lymphoma. J Exp Med 2011; 208:1799-807. [PMID: 21859846 PMCID: PMC3171093 DOI: 10.1084/jem.20110846] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [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: 04/28/2011] [Accepted: 07/27/2011] [Indexed: 12/18/2022] Open
Abstract
New anticancer drugs that target oncogenic signaling molecules have greatly improved the treatment of certain cancers. However, resistance to targeted therapeutics is a major clinical problem and the redundancy of oncogenic signaling pathways provides back-up mechanisms that allow cancer cells to escape. For example, the AKT and PIM kinases produce parallel oncogenic signals and share many molecular targets, including activators of cap-dependent translation. Here, we show that PIM kinase expression can affect the clinical outcome of lymphoma chemotherapy. We observe the same in animal lymphoma models. Whereas chemoresistance caused by AKT is readily reversed with rapamycin, PIM-mediated resistance is refractory to mTORC1 inhibition. However, both PIM- and AKT-expressing lymphomas depend on cap-dependent translation, and genetic or pharmacological blockade of the translation initiation complex is highly effective against these tumors. The therapeutic effect of blocking cap-dependent translation is mediated, at least in part, by decreased production of short-lived oncoproteins including c-MYC, Cyclin D1, MCL1, and the PIM1/2 kinases themselves. Hence, targeting the convergence of oncogenic survival signals on translation initiation is an effective alternative to combinations of kinase inhibitors.
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Affiliation(s)
- Jonathan H. Schatz
- Cancer Biology and Genetics Program, Stem Cell Center and Developmental Biology Program, and Program in Molecular Pharmacology, Sloan-Kettering Institute for Cancer Research, New York, NY 10065
- Department of Medicine, Department of Pathology, and Department of Biostatistics and Epidemiology, Memorial Sloan-Kettering Cancer Center, New York, NY 10065
| | - Elisa Oricchio
- Cancer Biology and Genetics Program, Stem Cell Center and Developmental Biology Program, and Program in Molecular Pharmacology, Sloan-Kettering Institute for Cancer Research, New York, NY 10065
| | - Andrew L. Wolfe
- Cancer Biology and Genetics Program, Stem Cell Center and Developmental Biology Program, and Program in Molecular Pharmacology, Sloan-Kettering Institute for Cancer Research, New York, NY 10065
- Weill Cornell Graduate School of Medical Science, New York, NY 10065
| | - Man Jiang
- Cancer Biology and Genetics Program, Stem Cell Center and Developmental Biology Program, and Program in Molecular Pharmacology, Sloan-Kettering Institute for Cancer Research, New York, NY 10065
| | - Irina Linkov
- Department of Medicine, Department of Pathology, and Department of Biostatistics and Epidemiology, Memorial Sloan-Kettering Cancer Center, New York, NY 10065
| | - Jocelyn Maragulia
- Department of Medicine, Department of Pathology, and Department of Biostatistics and Epidemiology, Memorial Sloan-Kettering Cancer Center, New York, NY 10065
| | - Weiji Shi
- Department of Medicine, Department of Pathology, and Department of Biostatistics and Epidemiology, Memorial Sloan-Kettering Cancer Center, New York, NY 10065
| | - Zhigang Zhang
- Department of Medicine, Department of Pathology, and Department of Biostatistics and Epidemiology, Memorial Sloan-Kettering Cancer Center, New York, NY 10065
| | - Vinagolu K. Rajasekhar
- Cancer Biology and Genetics Program, Stem Cell Center and Developmental Biology Program, and Program in Molecular Pharmacology, Sloan-Kettering Institute for Cancer Research, New York, NY 10065
| | - Nen C. Pagano
- Cancer Biology and Genetics Program, Stem Cell Center and Developmental Biology Program, and Program in Molecular Pharmacology, Sloan-Kettering Institute for Cancer Research, New York, NY 10065
| | - John A. Porco
- Department of Chemistry, Center for Chemical Methodology and Library Development, Boston University, Boston, MA 02215
| | - Julie Teruya-Feldstein
- Department of Medicine, Department of Pathology, and Department of Biostatistics and Epidemiology, Memorial Sloan-Kettering Cancer Center, New York, NY 10065
| | - Neal Rosen
- Cancer Biology and Genetics Program, Stem Cell Center and Developmental Biology Program, and Program in Molecular Pharmacology, Sloan-Kettering Institute for Cancer Research, New York, NY 10065
- Department of Medicine, Department of Pathology, and Department of Biostatistics and Epidemiology, Memorial Sloan-Kettering Cancer Center, New York, NY 10065
| | - Andrew D. Zelenetz
- Department of Medicine, Department of Pathology, and Department of Biostatistics and Epidemiology, Memorial Sloan-Kettering Cancer Center, New York, NY 10065
| | - Jerry Pelletier
- Department of Biochemistry and Rosalind and Morris Goodman Cancer Center, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Hans-Guido Wendel
- Cancer Biology and Genetics Program, Stem Cell Center and Developmental Biology Program, and Program in Molecular Pharmacology, Sloan-Kettering Institute for Cancer Research, New York, NY 10065
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25
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Oricchio E, Wolfe AL, Schatz JH, Mavrakis KJ, Wendel HG. Mouse models of cancer as biological filters for complex genomic data. Dis Model Mech 2010; 3:701-4. [PMID: 20876355 DOI: 10.1242/dmm.006296] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Genetically and pathologically accurate mouse models of leukemia and lymphoma have been developed in recent years. Adoptive transfer of genetically modified hematopoietic progenitor cells enables rapid and highly controlled gain- and loss-of-function studies for these types of cancer. In this Commentary, we discuss how these highly versatile experimental approaches can be used as biological filters to pinpoint transformation-relevant activities from complex cancer genome data. We anticipate that the functional identification of genetic 'drivers' using mouse models of leukemia and lymphoma will facilitate the development of molecular diagnostics and mechanism-based therapies for patients that suffer from these diseases.
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Affiliation(s)
- Elisa Oricchio
- Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
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26
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Mavrakis KJ, Wolfe AL, Oricchio E, Palomero T, de Keersmaecker K, McJunkin K, Zuber J, James T, Khan AA, Leslie CS, Parker JS, Paddison PJ, Tam W, Ferrando A, Wendel HG. Genome-wide RNA-mediated interference screen identifies miR-19 targets in Notch-induced T-cell acute lymphoblastic leukaemia. Nat Cell Biol 2010; 12:372-9. [PMID: 20190740 DOI: 10.1038/ncb2037] [Citation(s) in RCA: 269] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2009] [Accepted: 02/05/2010] [Indexed: 01/06/2023]
Abstract
MicroRNAs (miRNAs) have emerged as novel cancer genes. In particular, the miR-17-92 cluster, containing six individual miRNAs, is highly expressed in haematopoietic cancers and promotes lymphomagenesis in vivo. Clinical use of these findings hinges on isolating the oncogenic activity within the 17-92 cluster and defining its relevant target genes. Here we show that miR-19 is sufficient to promote leukaemogenesis in Notch1-induced T-cell acute lymphoblastic leukaemia (T-ALL) in vivo. In concord with the pathogenic importance of this interaction in T-ALL, we report a novel translocation that targets the 17-92 cluster and coincides with a second rearrangement that activates Notch1. To identify the miR-19 targets responsible for its oncogenic action, we conducted a large-scale short hairpin RNA screen for genes whose knockdown can phenocopy miR-19. Strikingly, the results of this screen were enriched for miR-19 target genes, and include Bim (Bcl2L11), AMP-activated kinase (Prkaa1) and the phosphatases Pten and PP2A (Ppp2r5e). Hence, an unbiased, functional genomics approach reveals a coordinate clampdown on several regulators of phosphatidylinositol-3-OH kinase-related survival signals by the leukaemogenic miR-19.
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Affiliation(s)
- Konstantinos J Mavrakis
- Cancer Biology & Genetics Program, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, New York 10021, USA
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27
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Bonaccorsi I, Altieri F, Sciamanna I, Oricchio E, Grillo C, Contartese G, Galati EM. Endogenous reverse transcriptase as a mediator of ursolic acid's anti-proliferative and differentiating effects in human cancer cell lines. Cancer Lett 2008; 263:130-9. [PMID: 18282657 DOI: 10.1016/j.canlet.2007.12.026] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2007] [Revised: 12/07/2007] [Accepted: 12/16/2007] [Indexed: 11/16/2022]
Abstract
Ursolic acid (UA) is a pentacyclic triterpenoid compound that is widely distributed in the plant kingdom and has a broad range of biological effects. Here, we examined the effects of UA on the proliferation and differentiation of human tumor cell lines from melanoma (A375), glioblastoma (U87) and thyroid anaplastic carcinoma (ARO), and on the proliferation of a non-transformed human fibroblast cell line (WI-38). The results show that UA inhibits tumor cell proliferation in a dose- and time-dependent manner. Consistent with this finding, UA treatment promotes differentiation of all of the analyzed tumor cell lines. Interestingly, we found that UA inhibits the endogenous reverse transcriptase (RT) activity in tumor cells, which has recently been shown to be involved in the control of proliferation and differentiation of neoplastic cells. Considering these findings, we suggest that the observed anti-proliferative and differentiating effects of UA may be related to this target.
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Affiliation(s)
- Irene Bonaccorsi
- Pharmaco-Biological Department, School of Pharmacy, University of Messina, Vill. SS. Annunziata, 98168 Messina, Italy
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28
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Oricchio E, Sciamanna I, Beraldi R, Tolstonog GV, Schumann GG, Spadafora C. Distinct roles for LINE-1 and HERV-K retroelements in cell proliferation, differentiation and tumor progression. Oncogene 2007; 26:4226-33. [PMID: 17237820 DOI: 10.1038/sj.onc.1210214] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [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: 12/25/2022]
Abstract
Transformed cells express high levels of non-telomeric reverse-transcriptase (RT) activity of retrotransposon and endogenous retrovirus origin. We previously reported that RT inhibition, either pharmacological or through transient silencing of RT-encoding LINE-1 (L1) elements by RNA interference (RNAi), reduced proliferation, induced differentiation and reprogrammed gene expression in human tumorigenic cell lines. Moreover, the antiretroviral drug efavirenz antagonized tumor progression in animal models in vivo. To get insight into the role of retroelements in tumorigenesis, we have now produced two cell lines derived from A-375 melanoma, in which the expression of either L1 retrotransposon, or HERV-K endogenous retrovirus, was stably suppressed by RNAi. Compared to the parental A-375 cell line, cells with stably interfered L1 expression show a lower proliferation rate, a differentiated morphology and lower tumorigenicity when inoculated in nude mice. L1 silencing modulates expression of several genes and, unexpectedly, also downregulates HERV-K expression. In HERV-K interfered cells, instead, L1 expression was unaffected, and cell proliferation and differentiation remained unchanged compared to parental A-375 cells. In vivo, however, their tumorigenic potential was found to be reduced after inoculation in nude mice. These results suggest that L1 and HERV-K play specific and distinct roles in cell transformation and tumor progression.
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Affiliation(s)
- E Oricchio
- Istituto Superiore di Sanità, Servizio BGSA, Rome, Italy
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Oricchio E, Saladino C, Iacovelli S, Soddu S, Cundari E. Reply to Letter to the Editor. Cell Cycle 2006. [DOI: 10.4161/cc.5.9.2774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Oricchio E, Saladino C, Iacovelli S, Soddu S, Cundari E. ATM is activated by default in mitosis, localizes at centrosomes and monitors mitotic spindle integrity. Cell Cycle 2006; 5:88-92. [PMID: 16319535 DOI: 10.4161/cc.5.1.2269] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We previously showed that ATM is responsible for p53 phosphorylation at Ser15 and localization at centrosomes during mitosis. When p53 centrosomal localization is prevented by inhibiting polymerization of spindle microtubules, a stabilized form of p53 is transmitted to daughter cells that arrest in the next G(1) phase of the cell cycle after exit from mitosis. AT cells are unable to both localize p53 at centrosomes in mitosis and arrest after exposure to mitotic-spindle poisons. Here we show that during mitosis ATM is activated by phosphorylation at Ser1981 and localizes at centrosomes. When mitotic spindle is disrupted by nocodazole, ATM is displaced from centrosomes and colocalizes with phospho-Ser15-p53 under the form of spots dispersed in the mitotic cytoplasm. After release from nocodazole-block, as soon as cells exit mitosis, p53 is redirected to the nucleus and its Ser15 phosphorylation is substituted by phosphorylation at Ser46. We suggest that ATM is activated by default at each mitotic onset and phosphorylates p53 at Ser15 so as to keep it inactive at centrosomes when the spindle is correctly in place or, in case of inactivation of the mitotic spindle, to maintain the memory of a perturbed mitosis.
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Affiliation(s)
- Elisa Oricchio
- Institute of Biology and Molecular Pathology, National Research Council, Rome, Italy
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Tritarelli A, Oricchio E, Ciciarello M, Mangiacasale R, Palena A, Lavia P, Soddu S, Cundari E. p53 localization at centrosomes during mitosis and postmitotic checkpoint are ATM-dependent and require serine 15 phosphorylation. Mol Biol Cell 2004; 15:3751-7. [PMID: 15181149 PMCID: PMC491834 DOI: 10.1091/mbc.e03-12-0900] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.5] [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: 11/11/2022] Open
Abstract
We recently demonstrated that the p53 oncosuppressor associates to centrosomes in mitosis and this association is disrupted by treatments with microtubule-depolymerizing agents. Here, we show that ATM, an upstream activator of p53 after DNA damage, is essential for p53 centrosomal localization and is required for the activation of the postmitotic checkpoint after spindle disruption. In mitosis, p53 failed to associate with centrosomes in two ATM-deficient, ataxiatelangiectasia-derived cell lines. Wild-type ATM gene transfer reestablished the centrosomal localization of p53 in these cells. Furthermore, wild-type p53 protein, but not the p53-S15A mutant, not phosphorylatable by ATM, localized at centrosomes when expressed in p53-null K562 cells. Finally, Ser15 phosphorylation of endogenous p53 was detected at centrosomes upon treatment with phosphatase inhibitors, suggesting that a p53 dephosphorylation step at centrosome contributes to sustain the cell cycle program in cells with normal mitotic spindles. When dissociated from centrosomes by treatments with spindle inhibitors, p53 remained phosphorylated at Ser15. AT cells, which are unable to phosphorylate p53, did not undergo postmitotic proliferation arrest after nocodazole block and release. These data demonstrate that ATM is required for p53 localization at centrosome and support the existence of a surveillance mechanism for inhibiting DNA reduplication downstream of the spindle assembly checkpoint
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Affiliation(s)
- A Tritarelli
- Istituto di Biologia e Patologia Molecolari Consiglio Nazionale delle Ricerche, 00185 Rome, Italy
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