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Nair NU, Greninger P, Zhang X, Friedman AA, Amzallag A, Cortez E, Sahu AD, Lee JS, Dastur A, Egan RK, Murchie E, Ceribelli M, Crowther GS, Beck E, McClanaghan J, Klump-Thomas C, Boisvert JL, Damon LJ, Wilson KM, Ho J, Tam A, McKnight C, Michael S, Itkin Z, Garnett MJ, Engelman JA, Haber DA, Thomas CJ, Ruppin E, Benes CH. A landscape of response to drug combinations in non-small cell lung cancer. Nat Commun 2023; 14:3830. [PMID: 37380628 PMCID: PMC10307832 DOI: 10.1038/s41467-023-39528-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 06/14/2023] [Indexed: 06/30/2023] Open
Abstract
Combination of anti-cancer drugs is broadly seen as way to overcome the often-limited efficacy of single agents. The design and testing of combinations are however very challenging. Here we present a uniquely large dataset screening over 5000 targeted agent combinations across 81 non-small cell lung cancer cell lines. Our analysis reveals a profound heterogeneity of response across the tumor models. Notably, combinations very rarely result in a strong gain in efficacy over the range of response observable with single agents. Importantly, gain of activity over single agents is more often seen when co-targeting functionally proximal genes, offering a strategy for designing more efficient combinations. Because combinatorial effect is strongly context specific, tumor specificity should be achievable. The resource provided, together with an additional validation screen sheds light on major challenges and opportunities in building efficacious combinations against cancer and provides an opportunity for training computational models for synergy prediction.
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Affiliation(s)
- Nishanth Ulhas Nair
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Xiaohu Zhang
- Howard Hughes Medical Institute, Bethesda, MD, USA
| | - Adam A Friedman
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Arnaud Amzallag
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Eliane Cortez
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Avinash Das Sahu
- University of New Mexico, Comprehensive Cancer Center, Albuquerque, NM, USA
| | - Joo Sang Lee
- Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon, 16419, Republic of Korea
| | - Anahita Dastur
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Regina K Egan
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Ellen Murchie
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | - Erin Beck
- Howard Hughes Medical Institute, Bethesda, MD, USA
| | | | | | | | - Leah J Damon
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Jeffrey Ho
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Angela Tam
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Sam Michael
- Howard Hughes Medical Institute, Bethesda, MD, USA
| | - Zina Itkin
- Howard Hughes Medical Institute, Bethesda, MD, USA
| | - Mathew J Garnett
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK
| | | | - Daniel A Haber
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Bethesda, MD, USA
| | - Craig J Thomas
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institute of Health, Rockville, MD, 20850, USA
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Eytan Ruppin
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Cyril H Benes
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
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Das A, Lee JS, Zhang G, Wang Z, Amzallag A, Boland G, Hannenhalli S, Herlyn M, Benes C, Gutkind JS, Flaherty K, Ruppin E. Abstract LB-149: Genome-wide prediction of synthetic rescue mediators of resistance to targeted and immunotherapy. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-lb-149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Most patients with advanced cancer eventually acquire resistance to targeted therapies, spurring extensive efforts to identify molecular events mediating therapy resistance. Here we demonstrate that many of these molecular events involve synthetic rescue (SR) genetic interactions, where the reduction in cancer cell viability caused by targeted gene inactivation is rescued by an adaptive alteration of another gene (the rescuer).
Methods: Analyzing recently published large scale in vitro functional screens we identify 100,000s candidate SR interactions that show evidence of rescue events in cancer cell lines. We then analyze tumor transcriptomic, genomic, and genetic profiles together with survival and clinical characteristics of 10,000 TCGA cancer patients to identify the few thousand SR interactions that have strong evidence that they are mediators of emerging resistance in patient tumors.
Results: We identify the first rescue network, composed of SR interactions common to many cancer types. The identified SRs successfully match the resistance mediators identified in recently published clinical studies. We perform multiple in vitro analyses in head and neck and lung cancer, showing that targeting predicted rescuer genes successfully re-sensitizes resistant cancer cells, providing specific leads for targeting resistance proactively. We further demonstrate that SR-based combination therapy can improve the progression free survival in mouse xenografts models. Notably, we show that SR interactions successfully predict cancer patients' response in the TCGA compendium, showing performance superior to existing machine learning based predictive models. Finally, we show that SR analysis of melanoma patients successfully identifies known mediators of resistance to checkpoint immunotherapy (reported previously in mice) and suggests new combination therapies that counteract the resistance.
Conclusions: This work presents a new paradigm identifying and harnessing synthetic rescue interactions to counteract resistance to both targeted- and immuno-therapies. Future implementations of this approach will have two broad implications in the precision oncology era: first for determining the most effective treatment regimen based on the molecular characteristics of individual patient’s tumor; second for identifying conjunct drugs to counteract resistance to existing primary therapies, for both targeted and immune checkpoint therapies.
Citation Format: Avinash Das, Joo Sang Lee, Gao Zhang, Zhiyong Wang, Arnaud Amzallag, Genevieve Boland, Sridhar Hannenhalli, Meenhard Herlyn, Cyril Benes, J. Silvio Gutkind, Keity Flaherty, Eytan Ruppin. Genome-wide prediction of synthetic rescue mediators of resistance to targeted and immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-149.
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3
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Yuan TL, Amzallag A, Bagni R, Yi M, Afghani S, Burgan W, Fer N, Strathern LA, Powell K, Smith B, Waters AM, Drubin D, Thomson T, Liao R, Greninger P, Stein GT, Murchie E, Cortez E, Egan RK, Procter L, Bess M, Cheng KT, Lee CS, Lee LC, Fellmann C, Stephens R, Luo J, Lowe SW, Benes CH, McCormick F. Differential Effector Engagement by Oncogenic KRAS. Cell Rep 2019; 22:1889-1902. [PMID: 29444439 DOI: 10.1016/j.celrep.2018.01.051] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 10/02/2017] [Accepted: 01/17/2018] [Indexed: 12/25/2022] Open
Abstract
KRAS can bind numerous effector proteins, which activate different downstream signaling events. The best known are RAF, phosphatidylinositide (PI)-3' kinase, and RalGDS families, but many additional direct and indirect effectors have been reported. We have assessed how these effectors contribute to several major phenotypes in a quantitative way, using an arrayed combinatorial siRNA screen in which we knocked down 41 KRAS effectors nodes in 92 cell lines. We show that every cell line has a unique combination of effector dependencies, but in spite of this heterogeneity, we were able to identify two major subtypes of KRAS mutant cancers of the lung, pancreas, and large intestine, which reflect different KRAS effector engagement and opportunities for therapeutic intervention.
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Affiliation(s)
- Tina L Yuan
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, 1450 3rd Street, San Francisco, CA 94158, USA
| | - Arnaud Amzallag
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Rachel Bagni
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., P.O. Box B, Frederick, MD 21702, USA
| | - Ming Yi
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., P.O. Box B, Frederick, MD 21702, USA
| | - Shervin Afghani
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, 1450 3rd Street, San Francisco, CA 94158, USA
| | - William Burgan
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., P.O. Box B, Frederick, MD 21702, USA
| | - Nicole Fer
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., P.O. Box B, Frederick, MD 21702, USA
| | - Leslie A Strathern
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., P.O. Box B, Frederick, MD 21702, USA
| | - Katie Powell
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., P.O. Box B, Frederick, MD 21702, USA
| | - Brian Smith
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., P.O. Box B, Frederick, MD 21702, USA
| | - Andrew M Waters
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., P.O. Box B, Frederick, MD 21702, USA
| | - David Drubin
- Selventa, One Alewife Center, Suite 330, Cambridge, MA 02140, USA
| | - Ty Thomson
- Selventa, One Alewife Center, Suite 330, Cambridge, MA 02140, USA
| | - Rosy Liao
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Patricia Greninger
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Giovanna T Stein
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Ellen Murchie
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Eliane Cortez
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Regina K Egan
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Lauren Procter
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., P.O. Box B, Frederick, MD 21702, USA
| | - Matthew Bess
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., P.O. Box B, Frederick, MD 21702, USA
| | - Kwong Tai Cheng
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., P.O. Box B, Frederick, MD 21702, USA
| | - Chih-Shia Lee
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Liam Changwoo Lee
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Christof Fellmann
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Robert Stephens
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., P.O. Box B, Frederick, MD 21702, USA
| | - Ji Luo
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Scott W Lowe
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Department of Cancer Biology & Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Howard Hughes Medical Institute, New York, NY 10065, USA
| | - Cyril H Benes
- Center for Cancer Research, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA.
| | - Frank McCormick
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, 1450 3rd Street, San Francisco, CA 94158, USA; Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., P.O. Box B, Frederick, MD 21702, USA.
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Mahadevan KK, Arora KS, Amzallag A, Williams E, Kulkarni AS, Fernandez-Del Castillo C, Lillemoe KD, Bardeesy N, Hong TS, Ferrone CR, Ting DT, Deshpande V. Quasimesenchymal phenotype predicts systemic metastasis in pancreatic ductal adenocarcinoma. Mod Pathol 2019; 32:844-854. [PMID: 30683911 PMCID: PMC7755428 DOI: 10.1038/s41379-018-0196-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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: 08/22/2018] [Revised: 12/04/2018] [Accepted: 12/05/2018] [Indexed: 01/07/2023]
Abstract
Metastasis following surgical resection is a leading cause of mortality in pancreatic ductal adenocarcinoma. Epithelial-mesenchymal transition is thought to play an important role in metastasis, although its clinical relevance in metastasis remains uncertain. We evaluated a panel of RNA in-situ hybridization probes for epithelial-mesenchymal transition-related genes expressed in circulating tumor cells. We assessed the predictive value of this panel for metastasis in pancreatic ductal adenocarcinoma and, to determine if the phenotype is generalizable between cancers, in colonic adenocarcinoma. One hundred fifty-eight pancreatic ductal adenocarcinomas and 205 colonic adenocarcinomas were classified as epithelial or quasimesenchymal phenotype using dual colorimetric RNA-in-situ hybridization. SMAD4 expression on pancreatic ductal adenocarcinomas was assessed by immunohistochemistry. Pancreatic ductal adenocarcinomas with quasimesenchymal phenotype had a significantly shorter disease-specific survival (P = 0.031) and metastasis-free survival (P = 0.0001) than those with an epithelial phenotype. Pancreatic ductal adenocarcinomas with SMAD4 loss also had lower disease-specific survival (P = 0.041) and metastasis-free survival (P = 0.001) than those with intact SMAD4. However, the quasimesenchymal phenotype proved a more robust predictor of metastases-area under the curve for quasimesenchymal = 0.8; SMAD4 = 0.6. The quasimesenchymal phenotype also predicted metastasis-free survival (P = 0.004) in colonic adenocarcinoma. Epithelial-mesenchymal transition defined two phenotypes with distinct metastatic capabilities-epithelial phenotype tumors with predominantly organ-confined disease and quasimesenchymal phenotype with high risk of metastatic disease in two epithelial malignancies. Collectively, this work validates the relevance of epithelial-mesenchymal transition in human gastrointestinal tumors.
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Affiliation(s)
- Krishnan K Mahadevan
- Department of Pathology, Massachusetts General Hospital, Boston, MA and Harvard Medical School, Boston, MA, USA
| | - Kshitij S Arora
- Department of Pathology, Massachusetts General Hospital, Boston, MA and Harvard Medical School, Boston, MA, USA
| | - Arnaud Amzallag
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA and Harvard Medical School, Boston, MA, USA
| | - Erik Williams
- Department of Pathology, Massachusetts General Hospital, Boston, MA and Harvard Medical School, Boston, MA, USA
| | - Anupriya S Kulkarni
- Department of Medicine, Division of Oncology, Massachusetts General Hospital, Boston, MA and Harvard Medical School, Boston, MA, USA
| | | | - Keith D Lillemoe
- Department of Surgery, Massachusetts General Hospital, Boston, MA and Harvard Medical School, Boston, MA, USA
| | - Nabeel Bardeesy
- Department of Medicine, Division of Oncology, Massachusetts General Hospital, Boston, MA and Harvard Medical School, Boston, MA, USA
| | - Theodore S Hong
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA and Harvard Medical School, Boston, MA, USA
| | - Cristina R Ferrone
- Department of Surgery, Massachusetts General Hospital, Boston, MA and Harvard Medical School, Boston, MA, USA
| | - David T Ting
- Department of Medicine, Division of Oncology, Massachusetts General Hospital, Boston, MA and Harvard Medical School, Boston, MA, USA
| | - Vikram Deshpande
- Department of Pathology, Massachusetts General Hospital, Boston, MA and Harvard Medical School, Boston, MA, USA.
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5
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Sahu AD, S Lee J, Wang Z, Zhang G, Iglesias-Bartolome R, Tian T, Wei Z, Miao B, Nair NU, Ponomarova O, Friedman AA, Amzallag A, Moll T, Kasumova G, Greninger P, Egan RK, Damon LJ, Frederick DT, Jerby-Arnon L, Wagner A, Cheng K, Park SG, Robinson W, Gardner K, Boland G, Hannenhalli S, Herlyn M, Benes C, Flaherty K, Luo J, Gutkind JS, Ruppin E. Genome-wide prediction of synthetic rescue mediators of resistance to targeted and immunotherapy. Mol Syst Biol 2019; 15:e8323. [PMID: 30858180 PMCID: PMC6413886 DOI: 10.15252/msb.20188323] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 12/31/2018] [Accepted: 01/21/2019] [Indexed: 01/09/2023] Open
Abstract
Most patients with advanced cancer eventually acquire resistance to targeted therapies, spurring extensive efforts to identify molecular events mediating therapy resistance. Many of these events involve synthetic rescue (SR) interactions, where the reduction in cancer cell viability caused by targeted gene inactivation is rescued by an adaptive alteration of another gene (the rescuer). Here, we perform a genome-wide in silico prediction of SR rescuer genes by analyzing tumor transcriptomics and survival data of 10,000 TCGA cancer patients. Predicted SR interactions are validated in new experimental screens. We show that SR interactions can successfully predict cancer patients' response and emerging resistance. Inhibiting predicted rescuer genes sensitizes resistant cancer cells to therapies synergistically, providing initial leads for developing combinatorial approaches to overcome resistance proactively. Finally, we show that the SR analysis of melanoma patients successfully identifies known mediators of resistance to immunotherapy and predicts novel rescuers.
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Affiliation(s)
- Avinash Das Sahu
- Department of Biostatistics and Computational Biology, Harvard School of Public Health, Boston, MA, USA
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
- University of Maryland Institute of Advanced Computer Science (UMIACS), University of Maryland, College Park, MD, USA
| | - Joo S Lee
- University of Maryland Institute of Advanced Computer Science (UMIACS), University of Maryland, College Park, MD, USA
- Cancer Data Science Lab, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Zhiyong Wang
- Department of Pharmacology & Moores Cancer Center, University of California, San Diego La Jolla, CA, USA
| | - Gao Zhang
- Molecular and Cellular Oncogenesis Program and Melanoma Research Center, The Wistar Institute, Philadelphia, PA, USA
- Department of Neurosurgery and The Preston Robert Tisch Brain Tumor Center, Duke University, Durham, NC, USA
| | | | - Tian Tian
- New Jersey Institute of Technology, Newark, NJ, USA
| | - Zhi Wei
- New Jersey Institute of Technology, Newark, NJ, USA
| | - Benchun Miao
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Nishanth Ulhas Nair
- University of Maryland Institute of Advanced Computer Science (UMIACS), University of Maryland, College Park, MD, USA
- Cancer Data Science Lab, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Olga Ponomarova
- University of Massachusetts Medical School, Worcester, MA, USA
| | - Adam A Friedman
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Arnaud Amzallag
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Tabea Moll
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Gyulnara Kasumova
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Patricia Greninger
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Regina K Egan
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Leah J Damon
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Dennie T Frederick
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Livnat Jerby-Arnon
- Schools of Computer Science & Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Allon Wagner
- Department of Electrical Engineering and Computer Science, the Center for Computational Biology, University of California, Berkeley, CA, USA
| | - Kuoyuan Cheng
- University of Maryland Institute of Advanced Computer Science (UMIACS), University of Maryland, College Park, MD, USA
| | - Seung Gu Park
- Department of Biostatistics and Computational Biology, Harvard School of Public Health, Boston, MA, USA
| | - Welles Robinson
- University of Maryland Institute of Advanced Computer Science (UMIACS), University of Maryland, College Park, MD, USA
| | - Kevin Gardner
- Cancer Data Science Lab, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Genevieve Boland
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Sridhar Hannenhalli
- University of Maryland Institute of Advanced Computer Science (UMIACS), University of Maryland, College Park, MD, USA
| | - Meenhard Herlyn
- Molecular and Cellular Oncogenesis Program and Melanoma Research Center, The Wistar Institute, Philadelphia, PA, USA
| | - Cyril Benes
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Keith Flaherty
- Department of Medicine and Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Ji Luo
- National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - J Silvio Gutkind
- Department of Pharmacology & Moores Cancer Center, University of California, San Diego La Jolla, CA, USA
| | - Eytan Ruppin
- University of Maryland Institute of Advanced Computer Science (UMIACS), University of Maryland, College Park, MD, USA
- Cancer Data Science Lab, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Schools of Computer Science & Medicine, Tel-Aviv University, Tel-Aviv, Israel
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Amzallag A, Ramaswamy S, Benes CH. Statistical assessment and visualization of synergies for large-scale sparse drug combination datasets. BMC Bioinformatics 2019; 20:83. [PMID: 30777010 PMCID: PMC6378741 DOI: 10.1186/s12859-019-2642-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 01/21/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Drug combinations have the potential to improve efficacy while limiting toxicity. To robustly identify synergistic combinations, high-throughput screens using full dose-response surface are desirable but require an impractical number of data points. Screening of a sparse number of doses per drug allows to screen large numbers of drug pairs, but complicates statistical assessment of synergy. Furthermore, since the number of pairwise combinations grows with the square of the number of drugs, exploration of large screens necessitates advanced visualization tools. RESULTS We describe a statistical and visualization framework for the analysis of large-scale drug combination screens. We developed an approach suitable for datasets with large number of drugs pairs even if small number of data points are available per drug pair. We demonstrate our approach using a systematic screen of all possible pairs among 108 cancer drugs applied to melanoma cell lines. In this dataset only two dose-response data points per drug pair and two data points per single drug test were available. We used a Bliss-based linear model, effectively borrowing data from the drug pairs to obtain robust estimations of the singlet viabilities, consequently yielding better estimates of drug synergy. Our method improves data consistency across dosing thus likely reducing the number of false positives. The approach allows to compute p values accounting for standard errors of the modeled singlets and combination viabilities. We further develop a synergy specificity score that distinguishes specific synergies from those arising with promiscuous drugs. Finally, we developed a summarized interactive visualization in a web application, providing efficient access to any of the 439,000 data points in the combination matrix ( http://www.cmtlab.org:3000/combo_app.html ). The code of the analysis and the web application is available at https://github.com/arnaudmgh/synergy-screen . CONCLUSIONS We show that statistical modeling of single drug response from drug combination data can help determine significance of synergy and antagonism in drug combination screens with few data point per drug pair. We provide a web application for the rapid exploration of large combinatorial drug screen. All codes are available to the community, as a resource for further analysis of published data and for analysis of other drug screens.
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Affiliation(s)
- Arnaud Amzallag
- 0000 0004 0386 9924grid.32224.35The Center of Cancer Research, Massachusetts General Hospital, 149 13th Street, Charlestown, MA 02129 USA ,000000041936754Xgrid.38142.3cHarvard Medical School, Boston, MA USA ,grid.66859.34Broad Institute of Harvard and MIT, Cambridge, MA USA ,Current Address: PatientsLikeMe, 160 Second Street, Cambridge, MA 02142 USA
| | - Sridhar Ramaswamy
- 0000 0004 0386 9924grid.32224.35The Center of Cancer Research, Massachusetts General Hospital, 149 13th Street, Charlestown, MA 02129 USA ,000000041936754Xgrid.38142.3cHarvard Medical School, Boston, MA USA ,grid.66859.34Broad Institute of Harvard and MIT, Cambridge, MA USA ,000000041936754Xgrid.38142.3cHarvard Stem Cell Institute, Cambridge, MA USA ,Harvard-Ludwig Center for Cancer Research, Boston, MA USA
| | - Cyril H. Benes
- 0000 0004 0386 9924grid.32224.35The Center of Cancer Research, Massachusetts General Hospital, 149 13th Street, Charlestown, MA 02129 USA ,000000041936754Xgrid.38142.3cHarvard Medical School, Boston, MA USA
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7
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Lee JS, Das A, Jerby-Arnon L, Arafeh R, Auslander N, Davidson M, McGarry L, James D, Amzallag A, Park SG, Cheng K, Robinson W, Atias D, Stossel C, Buzhor E, Stein G, Waterfall JJ, Meltzer PS, Golan T, Hannenhalli S, Gottlieb E, Benes CH, Samuels Y, Shanks E, Ruppin E. Harnessing synthetic lethality to predict the response to cancer treatment. Nat Commun 2018; 9:2546. [PMID: 29959327 PMCID: PMC6026173 DOI: 10.1038/s41467-018-04647-1] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 05/15/2018] [Indexed: 12/21/2022] Open
Abstract
While synthetic lethality (SL) holds promise in developing effective cancer therapies, SL candidates found via experimental screens often have limited translational value. Here we present a data-driven approach, ISLE (identification of clinically relevant synthetic lethality), that mines TCGA cohort to identify the most likely clinically relevant SL interactions (cSLi) from a given candidate set of lab-screened SLi. We first validate ISLE via a benchmark of large-scale drug response screens and by predicting drug efficacy in mouse xenograft models. We then experimentally test a select set of predicted cSLi via new screening experiments, validating their predicted context-specific sensitivity in hypoxic vs normoxic conditions and demonstrating cSLi's utility in predicting synergistic drug combinations. We show that cSLi can successfully predict patients' drug treatment response and provide patient stratification signatures. ISLE thus complements existing actionable mutation-based methods for precision cancer therapy, offering an opportunity to expand its scope to the whole genome.
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Affiliation(s)
- Joo Sang Lee
- Center for Bioinformatics and Computational Biology, University of Maryland Institute of Advanced Computer Science (UMIACS) & Department of Computer Science, University of Maryland, College Park, MD, 20742, USA
- Cancer Data Science Lab, National Cancer Institute, National Institute of Health, Bethesda, MD, 20892, USA
| | - Avinash Das
- Center for Bioinformatics and Computational Biology, University of Maryland Institute of Advanced Computer Science (UMIACS) & Department of Computer Science, University of Maryland, College Park, MD, 20742, USA
| | - Livnat Jerby-Arnon
- The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Rand Arafeh
- Department of Molecular Cell Biology, Weizmann Institute, Rehovot, 7610001, Israel
| | - Noam Auslander
- Center for Bioinformatics and Computational Biology, University of Maryland Institute of Advanced Computer Science (UMIACS) & Department of Computer Science, University of Maryland, College Park, MD, 20742, USA
- Cancer Data Science Lab, National Cancer Institute, National Institute of Health, Bethesda, MD, 20892, USA
| | - Matthew Davidson
- Cancer Research UK, Beatson Institute, Switchback Road, Glasgow, G61 1BD, Scotland, UK
| | - Lynn McGarry
- Cancer Research UK, Beatson Institute, Switchback Road, Glasgow, G61 1BD, Scotland, UK
| | - Daniel James
- Cancer Research UK, Beatson Institute, Switchback Road, Glasgow, G61 1BD, Scotland, UK
| | - Arnaud Amzallag
- Massachusetts General Hospital Center for Cancer Research, Charlestown, MA, 02129, USA
- Harvard Medical School, Boston, MA, 02114, USA
- PatientsLikeMe, 160 Second Street, Cambridge, MA, 02142, USA
| | - Seung Gu Park
- Center for Bioinformatics and Computational Biology, University of Maryland Institute of Advanced Computer Science (UMIACS) & Department of Computer Science, University of Maryland, College Park, MD, 20742, USA
| | - Kuoyuan Cheng
- Center for Bioinformatics and Computational Biology, University of Maryland Institute of Advanced Computer Science (UMIACS) & Department of Computer Science, University of Maryland, College Park, MD, 20742, USA
- Cancer Data Science Lab, National Cancer Institute, National Institute of Health, Bethesda, MD, 20892, USA
| | - Welles Robinson
- Center for Bioinformatics and Computational Biology, University of Maryland Institute of Advanced Computer Science (UMIACS) & Department of Computer Science, University of Maryland, College Park, MD, 20742, USA
- Cancer Data Science Lab, National Cancer Institute, National Institute of Health, Bethesda, MD, 20892, USA
| | - Dikla Atias
- Division of Oncology, Sheba Medical Center Tel Hashomer, Ramat-Gan, 5262100, Israel
| | - Chani Stossel
- Division of Oncology, Sheba Medical Center Tel Hashomer, Ramat-Gan, 5262100, Israel
| | - Ella Buzhor
- Division of Oncology, Sheba Medical Center Tel Hashomer, Ramat-Gan, 5262100, Israel
| | - Gidi Stein
- The Sackler School of Medicine, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Joshua J Waterfall
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Paul S Meltzer
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Talia Golan
- Division of Oncology, Sheba Medical Center Tel Hashomer, Ramat-Gan, 5262100, Israel
- The Sackler School of Medicine, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Sridhar Hannenhalli
- Center for Bioinformatics and Computational Biology, University of Maryland Institute of Advanced Computer Science (UMIACS) & Department of Computer Science, University of Maryland, College Park, MD, 20742, USA
| | - Eyal Gottlieb
- Cancer Research UK, Beatson Institute, Switchback Road, Glasgow, G61 1BD, Scotland, UK
| | - Cyril H Benes
- Massachusetts General Hospital Center for Cancer Research, Charlestown, MA, 02129, USA
- Harvard Medical School, Boston, MA, 02114, USA
| | - Yardena Samuels
- Department of Molecular Cell Biology, Weizmann Institute, Rehovot, 7610001, Israel
| | - Emma Shanks
- Cancer Research UK, Beatson Institute, Switchback Road, Glasgow, G61 1BD, Scotland, UK
| | - Eytan Ruppin
- Center for Bioinformatics and Computational Biology, University of Maryland Institute of Advanced Computer Science (UMIACS) & Department of Computer Science, University of Maryland, College Park, MD, 20742, USA.
- Cancer Data Science Lab, National Cancer Institute, National Institute of Health, Bethesda, MD, 20892, USA.
- The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, 6997801, Israel.
- The Sackler School of Medicine, Tel Aviv University, Tel Aviv, 6997801, Israel.
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Lee JS, Das A, Jerby-Arnon L, Arafeh R, Davidson M, Amzallag A, Park SG, Cheng K, Robinson W, Atias D, Stossel C, Buzhor E, Stein G, Waterfall JJ, Meltzer PS, Golan T, Hannenhalli S, Gottlieb E, Benes CH, Samuels Y, Shanks E, Ruppin E. Abstract A188: Harnessing synthetic lethality to predict the response to cancer treatments. Mol Cancer Ther 2018. [DOI: 10.1158/1535-7163.targ-17-a188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Synthetic lethality (SL) describes an interaction between a pair of genes whereby their double knockout is lethal, while their respective knockout is not. The identification of SL interactions (SLi) via large-scale genomic screens offers promising opportunities for developing selective therapies in cancer. However, our analysis of the TCGA cohort shows that many of the interactions do not carry predictive signal of patient survival or drug response. Here we present a data-driven approach termed ISLE (Identification of clinically relevant Synthetic LEthality) that mines the TCGA cohort to identify a subset of clinically relevant SL interactions (cSLi). ISLE consists of the following inference steps, analysis of tumor, cell line, and gene evolutionary data. We first create an initial pool of SL pairs identified through direct double knockout screens/isogenic cell line screens or inferred from large-scale shRNA/sgRNA single-gene knockout screens. Starting from this initial SL pool, ISLE first identifies putative SL gene pairs whose co-inactivation is under-represented in tumors, testifying that it is selected against. Second, it prioritizes candidate SL pairs whose co-inactivation is associated with improved patient’s prognosis, testifying that it may hamper tumor progression. Finally, it prioritizes SL-gene pairs with similar evolutionary phylogenetic profiles based on the notion that SL interactions are conserved across multiple species. We validate the identified SL pairs using an unseen large-scale in vitro drug response screen by showing the SL pairs marks a decent prediction accuracy (AUC~0.8). We compare ISLE’s performance to the standard supervised drug response prediction approaches in DREAM challenges, and our prediction based on generic pretreatment tumor samples (from TCGA) was within top 3 in prediction accuracy among the top predictors. ISLE-based approach also successfully distinguishes responders vs nonresponders to drug treatment (for >70% of drugs) in mouse xenografts using the activity profile of the drug target’s SL-partners. We then experimentally show the utility of SL in predicting synergistic drug combinations in patient-derived cell lines based on the notion that the two drugs whose targets have SL interactions are synergistic. Most importantly, we demonstrate for the first time that an SL network can successfully predict the treatment outcome in cancer patients in multiple large-scale patient datasets including TCGA, where cSLi are successfully predict patients’ response for more than 70% of cancer drugs. ISLE is predictive of patients’ response for the majority of current cancer drugs without any drug-specific training. Of paramount importance, the predictions of ISLE are based on SLi between (potentially) all genes in the cancer genome, thus prioritizing treatments for patients whose tumors do not bear specific actionable mutations in cancer driver genes, offering a novel approach to precision-based cancer therapy.
Citation Format: Joo S. Lee, Avinash Das, Livnat Jerby-Arnon, Rand Arafeh, Matthew Davidson, Arnaud Amzallag, Seung Gu Park, Kuoyuan Cheng, Welles Robinson, Dikla Atias, Chani Stossel, Ella Buzhor, Gidi Stein, Joshua J. Waterfall, Paul S. Meltzer, Talia Golan, Sridhar Hannenhalli, Eyal Gottlieb, Cyril H. Benes, Yardena Samuels, Emma Shanks, Eytan Ruppin. Harnessing synthetic lethality to predict the response to cancer treatments [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2017 Oct 26-30; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Ther 2018;17(1 Suppl):Abstract nr A188.
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Affiliation(s)
- Joo S. Lee
- 1University of Maryland, College Park, MD
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9
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Lee JS, Das A, Jerby-Arnon L, Atias D, Amzallag A, Benes CH, Golan T, Ruppin E. Abstract PR09: Harnessing synthetic lethality to predict clinical outcomes of cancer treatment. Mol Cancer Ther 2017. [DOI: 10.1158/1538-8514.synthleth-pr09] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Significance: The identification of Synthetic Lethal interactions (SLi) have long been considered a foundation for the advancement of cancer treatment. The rapidly accumulating large-scale patient data now provides a golden opportunity to infer SLi directly from patient samples. Here we present a new data-driven approach termed ISLE for identifying SLi, which is then shown to be predictive of clinical outcomes of cancer treatment in an unsupervised manner, for the first time.
Methods: ISLE consists of four inference steps, analyzing tumor, cell line and gene evolutionary data: It first identifies putative SL gene pairs whose co-inactivation is underrepresented in tumors, testifying that they are selected against. Second, it further prioritizes candidate SL pairs whose co-inactivation is associated with better prognosis in patients, testifying that they may hamper tumor progression. Finally, it eliminates false positive SLi using gene essentiality screens (testifying to causal SLi relations) and prioritizing SLi paired genes with similar evolutionary phylogenetic profiles.
Results: We applied ISLE to analyze the TCGA tumor collection and generated the first clinically-derived pan-cancer SL-network, composed of SLi common across many cancer types. We validated that these SLi match the known, experimentally identified SLi (AUC=0.87), and show that the SL-network is predictive of patient survival in an independent breast cancer dataset (METABRIC). Based on the predicted SLi, we predicted drug response in a wide variety of in vitro, mouse xenograft and patient data, altogether encompassing >700 single drugs and >5,000 drug combinations in >1,000 cell lines, 375 xenograft models and >5,000 patient samples. Importantly, these predictions were performed in an unsupervised manner, reducing the known risk of over-fitting the data commonly associated with supervised prediction methods. SL-derived predictions are based on computing an SL-score that estimates the efficacy of a given drug in a given tumor based on the latter's omics data. The SL-score counts the number of inactive SL-partners of a given drug target(s) in the given tumor, reflecting the notion that a drug is likely to be more effective in tumors where many of its targets' SL-partners are inactive. The predicted SL-scores show significant correlations (R > 0.4) with large-scale in vitro and in vivo drug response screens for the majority of drugs tested. Based on the conjecture that synergism between drugs may be mediated by underlying SLi between their targets, we additionally provide accurate predictions of drug synergism for both in vitro and in vivo drug combination screens (AUC~0.8). Most importantly, we demonstrate for the first time that an SL-network can successfully predict the treatment outcome in cancer patients in multiple large-scale patient datasets including the TCGA, where SLis successfully predict patients' response for 75% of cancer drugs.
Conclusions: ISLE is predictive of the patients' response for the majority of current cancer drugs. Of paramount importance, the predictions of ISLE are based on SLi between (potentially) all genes in the cancer genome, thus prioritizing treatments for patients whose tumors do not bear specific actionable mutations in cancer driver genes, offering a novel approach to precision-based cancer therapy. The predictive performance of ISLE is likely to further improve with the expected rapid accumulation of additional cancer omics and clinical phenotypic data.
Citation Format: Joo Sang Lee, Avinash Das, Livnat Jerby-Arnon, Dikla Atias, Arnaud Amzallag, Cyril H. Benes, Talia Golan, Eytan Ruppin. Harnessing synthetic lethality to predict clinical outcomes of cancer treatment [abstract]. In: Proceedings of the AACR Precision Medicine Series: Opportunities and Challenges of Exploiting Synthetic Lethality in Cancer; Jan 4-7, 2017; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2017;16(10 Suppl):Abstract nr PR09.
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10
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Lapek JD, Greninger P, Morris R, Amzallag A, Pruteanu-Malinici I, Benes CH, Haas W. Detection of dysregulated protein-association networks by high-throughput proteomics predicts cancer vulnerabilities. Nat Biotechnol 2017; 35:983-989. [PMID: 28892078 PMCID: PMC5683351 DOI: 10.1038/nbt.3955] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 08/08/2017] [Indexed: 12/17/2022]
Abstract
The formation of protein complexes and the co-regulation of the cellular concentrations of proteins are essential mechanisms for cellular signaling and for maintaining homeostasis. Here we use isobaric-labeling multiplexed proteomics to analyze protein co-regulation and show that this allows the identification of protein-protein associations with high accuracy. We apply this 'interactome mapping by high-throughput quantitative proteome analysis' (IMAHP) method to a panel of 41 breast cancer cell lines and show that deviations of the observed protein co-regulations in specific cell lines from the consensus network affects cellular fitness. Furthermore, these aberrant interactions serve as biomarkers that predict the drug sensitivity of cell lines in screens across 195 drugs. We expect that IMAHP can be broadly used to gain insight into how changing landscapes of protein-protein associations affect the phenotype of biological systems.
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Affiliation(s)
- John D Lapek
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Charlestown, Massachusetts, USA
| | - Patricia Greninger
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Charlestown, Massachusetts, USA
| | - Robert Morris
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Charlestown, Massachusetts, USA
| | - Arnaud Amzallag
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Charlestown, Massachusetts, USA
| | - Iulian Pruteanu-Malinici
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Charlestown, Massachusetts, USA
| | - Cyril H Benes
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Charlestown, Massachusetts, USA
| | - Wilhelm Haas
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Charlestown, Massachusetts, USA
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11
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Lee JS, Das A, Jerby-Arnon L, Park SG, Davidson M, Atias D, Amzallag A, Stossel C, Buzhor E, Robinson W, Cheng K, Waterfall JJ, Meltzer PS, Hannenhalli S, Benes CH, Golan T, Shanks E, Ruppin E. Abstract 543: Harnessing synthetic lethality to predict clinical outcomes of cancer treatment. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Significance: The identification of Synthetic Lethal interactions (SLi) has long been considered a foundation for the advancement of cancer treatment. The rapidly accumulating large-scale patient data now provides a golden opportunity to infer SLi directly from patient samples. Here we present a new data-driven approach termed ISLE for identifying SLi, which is then shown to be predictive of clinical outcomes of cancer treatment in an unsupervised manner, for the first time.
Methods: ISLE consists of four inference steps, analyzing tumor, cell line and gene evolutionary data: It first identifies putative SL gene pairs whose co-inactivation is underrepresented in tumors, testifying that they are selected against. Second, it further prioritizes candidate SL pairs whose co-inactivation is associated with better prognosis in patients, testifying that they may hamper tumor progression. Finally, it eliminates false positive SLi using gene essentiality screens (testifying to causal SLi relations) and prioritizing SLi paired genes with similar evolutionary phylogenetic profiles.
Results: We applied ISLE to analyze the TCGA tumor collection and generated the first clinically-derived pan-cancer SL-network, composed of SLi common across many cancer types. We validated that these SLi match the known, experimentally identified SLi (AUC=0.87), and show that the SL-network is predictive of patient survival in an independent breast cancer dataset (METABRIC). Based on the predicted SLi, we predicted drug response of single agents and drug combinations in a wide variety of in vitro, mouse xenograft and patient data, altogether encompassing >700 single drugs and >5,000 drug combinations in >1,000 cell lines, 375 xenograft models and >5,000 patient samples. Of note, these predictions were performed in an unsupervised manner, reducing the known risk of over-fitting the data commonly associated with supervised prediction methods. Our prediction is based on the notion that a drug is likely to be more effective in tumors where many of its targets’ SL-partners are inactive, and drug synergism may be mediated by underlying SLi between their targets. Most importantly, we demonstrate for the first time that an SL-network can successfully predict the treatment outcome in cancer patients in multiple large-scale patient datasets including the TCGA, where SLis successfully predict patients’ response for 75% of cancer drugs.
Conclusions: ISLE is predictive of the patients’ response for the majority of current cancer drugs. Of paramount importance, the predictions of ISLE are based on SLi between (potentially) all genes in the cancer genome, thus prioritizing treatments for patients whose tumors do not bear specific actionable mutations in cancer driver genes, offering a novel approach to precision-based cancer therapy. The predictive performance of ISLE is likely to further improve with the expected rapid accumulation of additional patient data.
Citation Format: Joo Sang Lee, Avinash Das, Livnat Jerby-Arnon, Seung Gu Park, Matthew Davidson, Dikla Atias, Arnaud Amzallag, Chani Stossel, Ella Buzhor, Welles Robinson, Kuoyuan Cheng, Joshua J. Waterfall, Paul S. Meltzer, Sridhar Hannenhalli, Cyril H. Benes, Talia Golan, Emma Shanks, Eytan Ruppin. Harnessing synthetic lethality to predict clinical outcomes of cancer treatment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 543. doi:10.1158/1538-7445.AM2017-543
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Conery AR, Centore RC, Spillane KL, Follmer NE, Bommi-Reddy A, Hatton C, Bryant BM, Greninger P, Amzallag A, Benes CH, Mertz JA, Sims RJ. Abstract B19: Targeting dependencies within apoptotic pathways through inhibition of BET bromodomains. Clin Cancer Res 2017. [DOI: 10.1158/1557-3265.pmccavuln16-b19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Cancer is driven in large part by dysregulated transcriptional programs that allow for the acquisition of the many ‘Hallmarks of Cancer.' Multiple regulatory factors are essential for the establishment and maintenance of these cancer-specific transcriptional programs, and this dependence creates vulnerabilities that can be therapeutically targeted. Here we describe a selective dependence on the bromodomain and extraterminal (BET) family of proteins for the reprogramming of apoptotic signaling networks and demonstrate how this dependence can be predicted prior to therapeutic intervention. We demonstrate in phenotypically sensitive cell lines that BET inhibition results in a rapid and robust transcriptional response among regulators of apoptosis, and that this transcriptional response is correlated with changes in the apoptotic threshold of target cells and subsequent apoptosis. We show that the robustness of the apoptotic response, and not that of the cytostatic response, predicts phenotypic sensitivity to BETi. Consistent with this, we observed that acquired BETi tolerance in two disparate cellular models is driven by dysregulated expression of anti-apoptotic BCL2 family proteins, and that genetic or pharmacological manipulation of apoptotic signaling can modify the phenotypic response to BETi. We further demonstrate that the basal expression levels of a set of apoptotic factors significantly predict preclinical response to BETi, and in particular note that BETi preferentially targets those cells that are dependent on BCL2 for survival. Our findings suggest that tumor cells have acquired a dependence on BET bromodomain function to evade apoptosis, and highlight opportunities to exploit this dependence in the clinic through rational patient selection and drug combination strategies.
Citation Format: Andrew R. Conery, Richard C. Centore, Kerry L. Spillane, Nicole E. Follmer, Archana Bommi-Reddy, Charlie Hatton, Barbara M. Bryant, Patricia Greninger, Arnaud Amzallag, Cyril H. Benes, Jennifer A. Mertz, Robert J. Sims, III. Targeting dependencies within apoptotic pathways through inhibition of BET bromodomains. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Targeting the Vulnerabilities of Cancer; May 16-19, 2016; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(1_Suppl):Abstract nr B19.
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13
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Conery AR, Centore RC, Spillane KL, Follmer NE, Bommi-Reddy A, Hatton C, Bryant BM, Greninger P, Amzallag A, Benes CH, Mertz JA, Sims RJ. Preclinical Anticancer Efficacy of BET Bromodomain Inhibitors Is Determined by the Apoptotic Response. Cancer Res 2016; 76:1313-9. [PMID: 26759243 DOI: 10.1158/0008-5472.can-15-1458] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 12/28/2015] [Indexed: 11/16/2022]
Abstract
Small-molecule inhibitors of the bromodomain and extraterminal (BET) family of proteins are being tested in clinical trials for a variety of cancers, but patient selection strategies remain limited. This challenge is partly attributed to the heterogeneous responses elicited by BET inhibition (BETi), including cellular differentiation, senescence, and death. In this study, we performed phenotypic and gene-expression analyses of treatment-naive and engineered tolerant cell lines representing human melanoma and leukemia to elucidate the dominant features defining response to BETi. We found that de novo and acquired tolerance to BETi is driven by the robustness of the apoptotic response, and that genetic or pharmacologic manipulation of the apoptotic signaling network can modify the phenotypic response to BETi. We further reveal that the expression signatures of the apoptotic genes BCL2, BCL2L1, and BAD significantly predict response to BETi. Taken together, our findings highlight the apoptotic program as a determinant of response to BETi, and provide a molecular basis for patient stratification and combination therapy development.
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Affiliation(s)
- Andrew R Conery
- Constellation Pharmaceuticals, Inc., Cambridge, Massachusetts
| | | | | | | | | | - Charlie Hatton
- Constellation Pharmaceuticals, Inc., Cambridge, Massachusetts
| | | | - Patricia Greninger
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Arnaud Amzallag
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Cyril H Benes
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | | | - Robert J Sims
- Constellation Pharmaceuticals, Inc., Cambridge, Massachusetts.
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14
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Friedman AA, Amzallag A, Pruteanu-Malinici I, Baniya S, Cooper ZA, Piris A, Hargreaves L, Igras V, Frederick DT, Lawrence DP, Haber DA, Flaherty KT, Wargo JA, Ramaswamy S, Benes CH, Fisher DE. Landscape of Targeted Anti-Cancer Drug Synergies in Melanoma Identifies a Novel BRAF-VEGFR/PDGFR Combination Treatment. PLoS One 2015; 10:e0140310. [PMID: 26461489 PMCID: PMC4604168 DOI: 10.1371/journal.pone.0140310] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Accepted: 09/24/2015] [Indexed: 12/12/2022] Open
Abstract
A newer generation of anti-cancer drugs targeting underlying somatic genetic driver events have resulted in high single-agent or single-pathway response rates in selected patients, but few patients achieve complete responses and a sizeable fraction of patients relapse within a year. Thus, there is a pressing need for identification of combinations of targeted agents which induce more complete responses and prevent disease progression. We describe the results of a combination screen of an unprecedented scale in mammalian cells performed using a collection of targeted, clinically tractable agents across a large panel of melanoma cell lines. We find that even the most synergistic drug pairs are effective only in a discrete number of cell lines, underlying a strong context dependency for synergy, with strong, widespread synergies often corresponding to non-specific or off-target drug effects such as multidrug resistance protein 1 (MDR1) transporter inhibition. We identified drugs sensitizing cell lines that are BRAFV600E mutant but intrinsically resistant to BRAF inhibitor PLX4720, including the vascular endothelial growth factor receptor/kinase insert domain receptor (VEGFR/KDR) and platelet derived growth factor receptor (PDGFR) family inhibitor cediranib. The combination of cediranib and PLX4720 induced apoptosis in vitro and tumor regression in animal models. This synergistic interaction is likely due to engagement of multiple receptor tyrosine kinases (RTKs), demonstrating the potential of drug- rather than gene-specific combination discovery approaches. Patients with elevated biopsy KDR expression showed decreased progression free survival in trials of mitogen-activated protein kinase (MAPK) kinase pathway inhibitors. Thus, high-throughput unbiased screening of targeted drug combinations, with appropriate library selection and mechanistic follow-up, can yield clinically-actionable drug combinations.
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Affiliation(s)
- Adam A. Friedman
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts, United States of America
- Dermatology and Cutaneous Biology Research Center, Massachusetts General Hospital, Charlestown, Massachusetts, United States of America
- * E-mail: (AAF); (CHB); (DEF)
| | - Arnaud Amzallag
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Iulian Pruteanu-Malinici
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Subash Baniya
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts, United States of America
- Dermatology and Cutaneous Biology Research Center, Massachusetts General Hospital, Charlestown, Massachusetts, United States of America
| | - Zachary A. Cooper
- Department of Surgical Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas, United States of America
- Department of Genomic Medicine, University of Texas M.D. Anderson Cancer Center, Houston, Texas, United States of America
| | - Adriano Piris
- Division of Dermatopathology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Leeza Hargreaves
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts, United States of America
- Dermatology and Cutaneous Biology Research Center, Massachusetts General Hospital, Charlestown, Massachusetts, United States of America
| | - Vivien Igras
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts, United States of America
- Dermatology and Cutaneous Biology Research Center, Massachusetts General Hospital, Charlestown, Massachusetts, United States of America
| | - Dennie T. Frederick
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Donald P. Lawrence
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Daniel A. Haber
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Keith T. Flaherty
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jennifer A. Wargo
- Department of Surgical Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas, United States of America
- Department of Genomic Medicine, University of Texas M.D. Anderson Cancer Center, Houston, Texas, United States of America
| | - Sridhar Ramaswamy
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Cyril H. Benes
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (AAF); (CHB); (DEF)
| | - David E. Fisher
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts, United States of America
- Dermatology and Cutaneous Biology Research Center, Massachusetts General Hospital, Charlestown, Massachusetts, United States of America
- * E-mail: (AAF); (CHB); (DEF)
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Yuan TL, Bagni R, Yi M, Amzallag A, Afghani S, Beam K, Burgan W, Fer N, Garvey L, Smith B, Waters A, Stephens R, Benes C, McCormick F. Abstract 4690: Next-generation screen for integrative subtyping and target discovery for KRAS-mutant cancer. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-4690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Mutations in the small GTPase, KRAS, are found in ∼140,000 new cases of cancer every year in the United States. This heterogeneous class of cancers manifests primarily as adenocarcinomas of the lung, colon and pancreas. These cancers display a wide spectrum of KRAS-dependency and differentially activate downstream effector signaling. The tumors further diverge in their array of co-occurring secondary mutations, expression signatures and KRAS mutant allele. Ultimately, the sole trait these cancers share in common is an obstinate resistance to chemo- and targeted-therapies, making identification of effective treatments an urgent need. To identify treatments for such a heterogeneous class of cancers, we developed a strategy to stratify KRAS-mutant cell lines into subtypes by integrating next-generation RNAi screening and “Omics” database mining. Each subtype is characterized by unique biomarkers and distinct patterns of effector dependency, both of which represent potential targets for personalized therapeutic strategies.
Our RNAi screen systematically evaluates sensitivity to siRNA-mediated knockdown of 40 KRAS effector nodes in a panel of 135 lung, colorectal and pancreatic cancer cell lines. Data is analyzed on the single cell level, through the simultaneous measurement of 5 functional parameters. This single-cell, multi-dimensional approach allows for a comprehensive assessment of cellular homeostasis, with unprecedented depth and dynamic range that allows robust classification of cell lines by similarity. We identify subtypes of KRAS-mutant cell lines that rely on particular effector pathways such as the RAL, RSK, MTOR and autophagy pathways, which are not engaged by all KRAS-mutant cell lines, and thus may represent targets for personalized treatment. We further identify widely shared dependencies such as on the RAF, glycolytic and cell cycle pathways. Through integrative data mining of exome, transcriptome and drug/siRNA sensitivity databases for each KRAS-mutant subtype, we can identify unique biomarkers that will serve to stratify patients in the clinic and recommend personalized treatment strategies.
Citation Format: Tina L. Yuan, Rachel Bagni, Ming Yi, Arnaud Amzallag, Shervin Afghani, Katie Beam, William Burgan, Nicole Fer, Leslie Garvey, Brian Smith, Andrew Waters, Robert Stephens, Cyril Benes, Frank McCormick. Next-generation screen for integrative subtyping and target discovery for KRAS-mutant cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4690. doi:10.1158/1538-7445.AM2015-4690
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Affiliation(s)
- Tina L. Yuan
- 1UCSF Helen Diller Comprehensive Cancer Center, San Francisco, CA
| | - Rachel Bagni
- 2Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Ming Yi
- 2Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Arnaud Amzallag
- 3Massachusetts General Hospital Cancer Center, Department of Medicine and Harvard Medical School, Boston, MA
| | - Shervin Afghani
- 1UCSF Helen Diller Comprehensive Cancer Center, San Francisco, CA
| | - Katie Beam
- 2Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD
| | - William Burgan
- 2Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Nicole Fer
- 2Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Leslie Garvey
- 2Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Brian Smith
- 2Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Andrew Waters
- 2Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Robert Stephens
- 2Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Cyril Benes
- 3Massachusetts General Hospital Cancer Center, Department of Medicine and Harvard Medical School, Boston, MA
| | - Frank McCormick
- 1UCSF Helen Diller Comprehensive Cancer Center, San Francisco, CA
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16
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Amzallag A, Yuan TL, Bagni R, Yi M, Stephens R, Ramawamy S, McCormick F, Benes CH. Abstract LB-247: Querying the RAS genomic network with siRNAs and and flow cytometry: Automatic, multidimensional phenotyping of 135 cancer cell lines by Gaussian mixture fitting and expectation maximization. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-lb-247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
To discover novel therapeutic modalities and genomic predictors of response, large screen utilizing small molecules or sh/siRNA are performed on increasingly large collections of cancer cell lines. However these screens suffer from two main limitations: 1) the off-target effects of the probes 2) the coarse measurement of the cellular response that cannot distinguish between different outcomes such as proliferation block and apoptosis.
Here we profile 50 lung cancer cell lines using highly specific combinations of siRNAs against effector nodes of KRAS, and measured several characteristics of phenotypic response by flow cytometry including viability, level of reactive oxygen species and cell membrane integrity.
For each assay [node-cell line], typically 25,000 events were measured. We often observed multi modal distributions following node silencing. We used the expectation maximization algorithm to fit the different cell populations induced by the gene silencing. This allows us to automatically extract the proportion of dying cells, and also provides estimates of the cell growth impairment. Assessment of replicates shows that our results are highly reproducible, provide an accurate estimate of the proportion of dying cells, and reveal the complexity of multi-modal response of KRAS cancer cell lines to perturbation of key signaling nodes. Using the genomic profiling and pharmaceutical screen of the same cell lines, we reveal the association of specific node silencing with 1) the basal genomic state of the cell lines 2) the activity of a panel of drugs with the goal of identifying new targeting modalities and patient selection strategies for KRAS mutant cancers.
Citation Format: Arnaud Amzallag, Tina L. Yuan, Rachel Bagni, Ming Yi, Robert Stephens, Sridhar Ramawamy, Frank McCormick, Cyril H. Benes. Querying the RAS genomic network with siRNAs and and flow cytometry: Automatic, multidimensional phenotyping of 135 cancer cell lines by Gaussian mixture fitting and expectation maximization. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr LB-247. doi:10.1158/1538-7445.AM2015-LB-247
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Affiliation(s)
| | | | - Rachel Bagni
- 3Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Ming Yi
- 3Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Robert Stephens
- 3Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD
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Kim WJ, Wittner BS, Amzallag A, Brannigan BW, Ting DT, Ramaswamy S, Maheswaran S, Haber DA. The WTX Tumor Suppressor Interacts with the Transcriptional Corepressor TRIM28. J Biol Chem 2015; 290:14381-90. [PMID: 25882849 DOI: 10.1074/jbc.m114.631945] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Indexed: 02/05/2023] Open
Abstract
WTX encodes a tumor suppressor implicated in the pediatric kidney cancer Wilms tumor and in mesenchymal differentiation with potentially distinct functions in the cytoplasm, at the plasma membrane, and in the nucleus. Although modulating components of the WNT signaling pathway is a proposed function for cytoplasmic and membrane-bound WTX, its nuclear properties are not well understood. Here we report that the transcriptional corepressor TRIM28 is the major binding partner for nuclear WTX. WTX interacted with the coiled coil domain of TRIM28 required for its binding to Krüppel-associated box domains of transcription factors and for its chromatin recruitment through its own coiled coil and proline-rich domains. Knockdown of endogenous WTX reduced the recruitment of TRIM28 to a chromatinized reporter sequence and its ability to repress a target transcript. In mouse embryonic stem cells where TRIM28 plays a major role in repressing endogenous retroviruses and long interspersed elements, knockdown of either TRIM28 or WTX combined with single molecule RNA sequencing revealed a highly significant shared set of differentially regulated transcripts, including derepression of non-coding repetitive sequences and their neighboring protein encoding genes (p < 1e-20). In mesenchymal precursor cells, depletion of WTX and TRIM28 resulted in analogous β-catenin-independent defects in adipogenic and osteogenic differentiation, and knockdown of WTX reduced TRIM28 binding to Pparγ promoter. Together, the physical and functional interaction between WTX and TRIM28 suggests that the nuclear fraction of WTX plays a role in epigenetic silencing, an effect that may contribute to its function as a regulator of cellular differentiation and tumorigenesis.
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Affiliation(s)
- Woo Jae Kim
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, Massachusetts 02129 and
| | - Ben S Wittner
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, Massachusetts 02129 and
| | - Arnaud Amzallag
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, Massachusetts 02129 and
| | - Brian W Brannigan
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, Massachusetts 02129 and
| | - David T Ting
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, Massachusetts 02129 and From the Departments of Medicine and
| | - Sridhar Ramaswamy
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, Massachusetts 02129 and From the Departments of Medicine and
| | - Shyamala Maheswaran
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, Massachusetts 02129 and Surgery
| | - Daniel A Haber
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, Massachusetts 02129 and From the Departments of Medicine and Howard Hughes Medical Institute, Chevy Chase, Maryland 20815
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18
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Crystal AS, Shaw AT, Sequist LV, Friboulet L, Niederst MJ, Lockerman EL, Frias RL, Gainor JF, Amzallag A, Greninger P, Lee D, Kalsy A, Gomez-Caraballo M, Elamine L, Howe E, Hur W, Lifshits E, Robinson HE, Katayama R, Faber AC, Awad MM, Ramaswamy S, Mino-Kenudson M, Iafrate AJ, Benes CH, Engelman JA. Patient-derived models of acquired resistance can identify effective drug combinations for cancer. Science 2014; 346:1480-6. [PMID: 25394791 DOI: 10.1126/science.1254721] [Citation(s) in RCA: 554] [Impact Index Per Article: 55.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Targeted cancer therapies have produced substantial clinical responses, but most tumors develop resistance to these drugs. Here, we describe a pharmacogenomic platform that facilitates rapid discovery of drug combinations that can overcome resistance. We established cell culture models derived from biopsy samples of lung cancer patients whose disease had progressed while on treatment with epidermal growth factor receptor (EGFR) or anaplastic lymphoma kinase (ALK) tyrosine kinase inhibitors and then subjected these cells to genetic analyses and a pharmacological screen. Multiple effective drug combinations were identified. For example, the combination of ALK and MAPK kinase (MEK) inhibitors was active in an ALK-positive resistant tumor that had developed a MAP2K1 activating mutation, and the combination of EGFR and fibroblast growth factor receptor (FGFR) inhibitors was active in an EGFR mutant resistant cancer with a mutation in FGFR3. Combined ALK and SRC (pp60c-src) inhibition was effective in several ALK-driven patient-derived models, a result not predicted by genetic analysis alone. With further refinements, this strategy could help direct therapeutic choices for individual patients.
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Affiliation(s)
- Adam S Crystal
- Massachusetts General Hospital Cancer Center, Department of Medicine and Harvard Medical School, Boston, MA 02114, USA
| | - Alice T Shaw
- Massachusetts General Hospital Cancer Center, Department of Medicine and Harvard Medical School, Boston, MA 02114, USA
| | - Lecia V Sequist
- Massachusetts General Hospital Cancer Center, Department of Medicine and Harvard Medical School, Boston, MA 02114, USA
| | - Luc Friboulet
- Massachusetts General Hospital Cancer Center, Department of Medicine and Harvard Medical School, Boston, MA 02114, USA
| | - Matthew J Niederst
- Massachusetts General Hospital Cancer Center, Department of Medicine and Harvard Medical School, Boston, MA 02114, USA
| | - Elizabeth L Lockerman
- Massachusetts General Hospital Cancer Center, Department of Medicine and Harvard Medical School, Boston, MA 02114, USA
| | - Rosa L Frias
- Massachusetts General Hospital Cancer Center, Department of Medicine and Harvard Medical School, Boston, MA 02114, USA
| | - Justin F Gainor
- Massachusetts General Hospital Cancer Center, Department of Medicine and Harvard Medical School, Boston, MA 02114, USA
| | - Arnaud Amzallag
- Massachusetts General Hospital Cancer Center, Department of Medicine and Harvard Medical School, Boston, MA 02114, USA
| | - Patricia Greninger
- Massachusetts General Hospital Cancer Center, Department of Medicine and Harvard Medical School, Boston, MA 02114, USA
| | - Dana Lee
- Massachusetts General Hospital Cancer Center, Department of Medicine and Harvard Medical School, Boston, MA 02114, USA
| | - Anuj Kalsy
- Massachusetts General Hospital Cancer Center, Department of Medicine and Harvard Medical School, Boston, MA 02114, USA
| | - Maria Gomez-Caraballo
- Massachusetts General Hospital Cancer Center, Department of Medicine and Harvard Medical School, Boston, MA 02114, USA
| | - Leila Elamine
- Massachusetts General Hospital Cancer Center, Department of Medicine and Harvard Medical School, Boston, MA 02114, USA
| | - Emily Howe
- Massachusetts General Hospital Cancer Center, Department of Medicine and Harvard Medical School, Boston, MA 02114, USA
| | - Wooyoung Hur
- Dana-Farber Cancer Institute, Department of Biological Chemistry and Molecular Pharmacology and Harvard Medical School, Boston, MA 02115, USA. Chemical Kinomics Research Center, Korea Institute of Science and Technology, Seoul, 136-791, South Korea
| | - Eugene Lifshits
- Massachusetts General Hospital Cancer Center, Department of Medicine and Harvard Medical School, Boston, MA 02114, USA
| | - Hayley E Robinson
- Massachusetts General Hospital Cancer Center, Department of Pathology and Harvard Medical School, Boston, MA 02114, USA
| | - Ryohei Katayama
- Massachusetts General Hospital Cancer Center, Department of Medicine and Harvard Medical School, Boston, MA 02114, USA
| | - Anthony C Faber
- Massachusetts General Hospital Cancer Center, Department of Medicine and Harvard Medical School, Boston, MA 02114, USA
| | - Mark M Awad
- Massachusetts General Hospital Cancer Center, Department of Medicine and Harvard Medical School, Boston, MA 02114, USA
| | - Sridhar Ramaswamy
- Massachusetts General Hospital Cancer Center, Department of Medicine and Harvard Medical School, Boston, MA 02114, USA
| | - Mari Mino-Kenudson
- Massachusetts General Hospital Cancer Center, Department of Pathology and Harvard Medical School, Boston, MA 02114, USA
| | - A John Iafrate
- Massachusetts General Hospital Cancer Center, Department of Pathology and Harvard Medical School, Boston, MA 02114, USA
| | - Cyril H Benes
- Massachusetts General Hospital Cancer Center, Department of Medicine and Harvard Medical School, Boston, MA 02114, USA.
| | - Jeffrey A Engelman
- Massachusetts General Hospital Cancer Center, Department of Medicine and Harvard Medical School, Boston, MA 02114, USA.
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Korenjak M, Kwon E, Morris RT, Anderssen E, Amzallag A, Ramaswamy S, Dyson NJ. dREAM co-operates with insulator-binding proteins and regulates expression at divergently paired genes. Nucleic Acids Res 2014; 42:8939-53. [PMID: 25053843 PMCID: PMC4132727 DOI: 10.1093/nar/gku609] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [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: 12/30/2022] Open
Abstract
dREAM complexes represent the predominant form of E2F/RBF repressor complexes in Drosophila. dREAM associates with thousands of sites in the fly genome but its mechanism of action is unknown. To understand the genomic context in which dREAM acts we examined the distribution and localization of Drosophila E2F and dREAM proteins. Here we report a striking and unexpected overlap between dE2F2/dREAM sites and binding sites for the insulator-binding proteins CP190 and Beaf-32. Genetic assays show that these components functionally co-operate and chromatin immunoprecipitation experiments on mutant animals demonstrate that dE2F2 is important for association of CP190 with chromatin. dE2F2/dREAM binding sites are enriched at divergently transcribed genes, and the majority of genes upregulated by dE2F2 depletion represent the repressed half of a differentially expressed, divergently transcribed pair of genes. Analysis of mutant animals confirms that dREAM and CP190 are similarly required for transcriptional integrity at these gene pairs and suggest that dREAM functions in concert with CP190 to establish boundaries between repressed/activated genes. Consistent with the idea that dREAM co-operates with insulator-binding proteins, genomic regions bound by dREAM possess enhancer-blocking activity that depends on multiple dREAM components. These findings suggest that dREAM functions in the organization of transcriptional domains.
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Affiliation(s)
- Michael Korenjak
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA 02129, USA
| | - Eunjeong Kwon
- Massachusetts General Hospital, Cutaneous Biology Research Center, Charlestown, MA 02129, USA
| | - Robert T Morris
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA 02129, USA
| | - Endre Anderssen
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA 02129, USA
| | - Arnaud Amzallag
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA 02129, USA
| | - Sridhar Ramaswamy
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA 02129, USA
| | - Nicholas J Dyson
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA 02129, USA
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Foudi A, Kramer DJ, Qin J, Ye D, Behlich AS, Mordecai S, Preffer FI, Amzallag A, Ramaswamy S, Hochedlinger K, Orkin SH, Hock H. Distinct, strict requirements for Gfi-1b in adult bone marrow red cell and platelet generation. ACTA ACUST UNITED AC 2014; 211:909-27. [PMID: 24711581 PMCID: PMC4010908 DOI: 10.1084/jem.20131065] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Strict, lineage-intrinsic requirement for continuous adult Gfi-1b expression at two distinct critical stages of erythropoiesis and megakaryopoiesis. The zinc finger transcriptional repressor Gfi-1b is essential for erythroid and megakaryocytic development in the embryo. Its roles in the maintenance of bone marrow erythropoiesis and thrombopoiesis have not been defined. We investigated Gfi-1b’s adult functions using a loxP-flanked Gfi-1b allele in combination with a novel doxycycline-inducible Cre transgene that efficiently mediates recombination in the bone marrow. We reveal strict, lineage-intrinsic requirements for continuous adult Gfi-1b expression at two distinct critical stages of erythropoiesis and megakaryopoiesis. Induced disruption of Gfi-1b was lethal within 3 wk with severely reduced hemoglobin levels and platelet counts. The erythroid lineage was arrested early in bipotential progenitors, which did not give rise to mature erythroid cells in vitro or in vivo. Yet Gfi-1b−/− progenitors had initiated the erythroid program as they expressed many lineage-restricted genes, including Klf1/Eklf and Erythropoietin receptor. In contrast, the megakaryocytic lineage developed beyond the progenitor stage in Gfi-1b’s absence and was arrested at the promegakaryocyte stage, after nuclear polyploidization, but before cytoplasmic maturation. Genome-wide analyses revealed that Gfi-1b directly regulates a wide spectrum of megakaryocytic and erythroid genes, predominantly repressing their expression. Together our study establishes Gfi-1b as a master transcriptional repressor of adult erythropoiesis and thrombopoiesis.
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Affiliation(s)
- Adlen Foudi
- Cancer Center, 2 Center for Regenerative Medicine, and 3 Department of Pathology, Massachusetts General Hospital, 4 Harvard Medical School, Boston, MA 02114
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21
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Yee AJ, Raz T, Amzallag A, Lipson D, Giladi E, Lopez H, Borger DR, Mino-Kenudson M, Thompson JF, Iafrate AJ, Milos P, Haber DA, Ramaswamy S. Single molecule RNA sequencing of formalin-fixed paraffin-embedded tissue derived from patients with lung cancer. J Clin Oncol 2011. [DOI: 10.1200/jco.2011.29.15_suppl.10550] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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22
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Demurtas D, Amzallag A, Rawdon EJ, Maddocks JH, Dubochet J, Stasiak A. Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles. Nucleic Acids Res 2009; 37:2882-93. [PMID: 19282451 PMCID: PMC2685088 DOI: 10.1093/nar/gkp137] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
We use cryo-electron microscopy (cryo-EM) to study the 3D shapes of 94-bp-long DNA minicircles and address the question of whether cyclization of such short DNA molecules necessitates the formation of sharp, localized kinks in DNA or whether the necessary bending can be redistributed and accomplished within the limits of the elastic, standard model of DNA flexibility. By comparing the shapes of covalently closed, nicked and gapped DNA minicircles, we conclude that 94-bp-long covalently closed and nicked DNA minicircles do not show sharp kinks while gapped DNA molecules, containing very flexible single-stranded regions, do show sharp kinks. We corroborate the results of cryo-EM studies by using Bal31 nuclease to probe for the existence of kinks in 94-bp-long minicircles.
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Affiliation(s)
- Davide Demurtas
- Faculty of Biology and Medicine, Center for Integrative Genomics, University of Lausanne, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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23
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Rougemont J, Amzallag A, Iseli C, Farinelli L, Xenarios I, Naef F. Probabilistic base calling of Solexa sequencing data. BMC Bioinformatics 2008; 9:431. [PMID: 18851737 PMCID: PMC2575221 DOI: 10.1186/1471-2105-9-431] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2008] [Accepted: 10/13/2008] [Indexed: 12/02/2022] Open
Abstract
Background Solexa/Illumina short-read ultra-high throughput DNA sequencing technology produces millions of short tags (up to 36 bases) by parallel sequencing-by-synthesis of DNA colonies. The processing and statistical analysis of such high-throughput data poses new challenges; currently a fair proportion of the tags are routinely discarded due to an inability to match them to a reference sequence, thereby reducing the effective throughput of the technology. Results We propose a novel base calling algorithm using model-based clustering and probability theory to identify ambiguous bases and code them with IUPAC symbols. We also select optimal sub-tags using a score based on information content to remove uncertain bases towards the ends of the reads. Conclusion We show that the method improves genome coverage and number of usable tags as compared with Solexa's data processing pipeline by an average of 15%. An R package is provided which allows fast and accurate base calling of Solexa's fluorescence intensity files and the production of informative diagnostic plots.
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Affiliation(s)
- Jacques Rougemont
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
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Amzallag A, Vaillant C, Jacob M, Unser M, Bednar J, Kahn JD, Dubochet J, Stasiak A, Maddocks JH. 3D reconstruction and comparison of shapes of DNA minicircles observed by cryo-electron microscopy. Nucleic Acids Res 2006; 34:e125. [PMID: 17012274 PMCID: PMC1635295 DOI: 10.1093/nar/gkl675] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We use cryo-electron microscopy to compare 3D shapes of 158 bp long DNA minicircles that differ only in the sequence within an 18 bp block containing either a TATA box or a catabolite activator protein binding site. We present a sorting algorithm that correlates the reconstructed shapes and groups them into distinct categories. We conclude that the presence of the TATA box sequence, which is believed to be easily bent, does not significantly affect the observed shapes.
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Affiliation(s)
- Arnaud Amzallag
- To whom correspondence should be addressed. Tel: +41 21 693 2767; Fax: +41 21 693 5530;
| | | | - Mathews Jacob
- Biomedical Imaging Group, EPFL LIBEcole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Michael Unser
- Biomedical Imaging Group, EPFL LIBEcole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Jan Bednar
- Laboratoire de Spectrometrie Physique, UMR 5588CNRS, 140 Av. de la Physique, BP 87, 38402 St Martin d'Heres Cedex, France
| | - Jason D. Kahn
- Department of Chemistry and Biochemistry, University of MarylandCollege Park, MD 20742-2021, USA
| | - Jacques Dubochet
- Laboratory of Ultrastructural Analysis, University of Lausanne1015 Lausanne, Switzerland
| | - Andrzej Stasiak
- Laboratory of Ultrastructural Analysis, University of Lausanne1015 Lausanne, Switzerland
| | - John H. Maddocks
- To whom correspondence should be addressed. Tel: +41 21 693 2767; Fax: +41 21 693 5530;
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Labrunie P, Valeix B, Jahjah F, Tafani C, Sorensen B, Amzallag A, Malmejac C, Lévy S, Gérard R. [Coronary occlusion immediately following a successful coronary angioplasty. Treatment by repeat angioplasty]. Ann Cardiol Angeiol (Paris) 1985; 34:93-6. [PMID: 3157342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The authors report the case of a 52 year old patient with a significant stenosis of the medial portion of the left anterior descending artery (LAD) with excellent left ventricular function. Transluminal coronary angioplasty (TCA) was indicated following a positive exercise stress test. This was initially performed successfully. Fifteen minutes after the end of the procedure, a total obstruction occurred at the site of dilatation immediately eliciting significant precordial chest pain and massive elevation of the ST segment. Isosorbide dinitrate (ISDN) at a dose of 2 mg was injected into the artery 3 times without success as was an attempt to pass through the obstruction with a guide wire. Another TCA was then attempted without administration of the thrombolytic agent. The dilating catheter passed easily by the obstruction permitting several dilatations which restored rapid coronary artery flow, relieved completely the chest pain, and normalized electrocardiographic abnormalities. This procedure represents a new therapeutic approach to obstruction, an often unpredictable and serious complication of coronary angioplasty in the absence of collateral circulation, thereby preventing the development of a myocardial infarction and an emergency aortocoronary bypass operation.
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Abstract
The order of mutational sites in 10 independently isolated leucine auxotrophys of Escherichia coli K-12 was determined by three-point reciprocal transductions. The sites of mutation mapped in linear sequence in a cluster; all leucine auxotrophic mutations were cotransducible with mutations in the arabinose operon. The mutations were assigned to four complementation groups by abortive transduction tests, designated D, C, B, and A, reading in a clockwise direction from the arabinose operon. Enzyme analyses showed that strains with a mutation in gene A lacked alpha-isopropylmalate synthetase activity (EC 4.1.3), and those with a mutation in gene B lacked beta-isopropylmalate dehydrogenase activity (EC 1.1.1). It is concluded that the gross structure of the leucine operon in E. coli is closely similar to, if not identical with, the gross structure of the leucine operon in Salmonella typhimurium.
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