1
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Thomas JR, Shelton C, Murphy J, Brittain S, Bray MA, Aspesi P, Concannon J, King FJ, Ihry RJ, Ho DJ, Henault M, Hadjikyriacou A, Neri M, Sigoillot FD, Pham HT, Shum M, Barys L, Jones MD, Martin EJ, Blechschmidt A, Rieffel S, Troxler TJ, Mapa FA, Jenkins JL, Jain RK, Kutchukian PS, Schirle M, Renner S. Enhancing the Small-Scale Screenable Biological Space beyond Known Chemogenomics Libraries with Gray Chemical Matter─Compounds with Novel Mechanisms from High-Throughput Screening Profiles. ACS Chem Biol 2024; 19:938-952. [PMID: 38565185 PMCID: PMC11040606 DOI: 10.1021/acschembio.3c00737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 02/28/2024] [Accepted: 03/01/2024] [Indexed: 04/04/2024]
Abstract
Phenotypic assays have become an established approach to drug discovery. Greater disease relevance is often achieved through cellular models with increased complexity and more detailed readouts, such as gene expression or advanced imaging. However, the intricate nature and cost of these assays impose limitations on their screening capacity, often restricting screens to well-characterized small compound sets such as chemogenomics libraries. Here, we outline a cheminformatics approach to identify a small set of compounds with likely novel mechanisms of action (MoAs), expanding the MoA search space for throughput limited phenotypic assays. Our approach is based on mining existing large-scale, phenotypic high-throughput screening (HTS) data. It enables the identification of chemotypes that exhibit selectivity across multiple cell-based assays, which are characterized by persistent and broad structure activity relationships (SAR). We validate the effectiveness of our approach in broad cellular profiling assays (Cell Painting, DRUG-seq, and Promotor Signature Profiling) and chemical proteomics experiments. These experiments revealed that the compounds behave similarly to known chemogenetic libraries, but with a notable bias toward novel protein targets. To foster collaboration and advance research in this area, we have curated a public set of such compounds based on the PubChem BioAssay dataset and made it available for use by the scientific community.
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Affiliation(s)
- Jason R. Thomas
- Novartis
Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Claude Shelton
- Novartis
Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Jason Murphy
- Novartis
Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Scott Brittain
- Novartis
Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Mark-Anthony Bray
- Novartis
Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Peter Aspesi
- Novartis
Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - John Concannon
- Novartis
Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Frederick J. King
- Novartis
Biomedical Research, San Diego, California 92121, United States
| | - Robert J. Ihry
- Novartis
Biomedical Research, San Diego, California 92121, United States
| | - Daniel J. Ho
- Novartis
Biomedical Research, San Diego, California 92121, United States
| | - Martin Henault
- Novartis
Biomedical Research, Cambridge, Massachusetts 02139, United States
| | | | - Marilisa Neri
- Novartis
Biomedical Research, Basel 4056, Switzerland
| | | | - Helen T. Pham
- Novartis
Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Matthew Shum
- Novartis
Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Louise Barys
- Novartis
Biomedical Research, Basel 4056, Switzerland
| | - Michael D. Jones
- Novartis
Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Eric J. Martin
- Novartis
Biomedical Research, Emeryville, California 94608, United States
| | | | | | | | - Felipa A. Mapa
- Novartis
Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Jeremy L. Jenkins
- Novartis
Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Rishi K. Jain
- Novartis
Biomedical Research, Cambridge, Massachusetts 02139, United States
| | | | - Markus Schirle
- Novartis
Biomedical Research, Cambridge, Massachusetts 02139, United States
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2
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Cimini BA, Chandrasekaran SN, Kost-Alimova M, Miller L, Goodale A, Fritchman B, Byrne P, Garg S, Jamali N, Logan DJ, Concannon JB, Lardeau CH, Mouchet E, Singh S, Shafqat Abbasi H, Aspesi P, Boyd JD, Gilbert T, Gnutt D, Hariharan S, Hernandez D, Hormel G, Juhani K, Melanson M, Mervin LH, Monteverde T, Pilling JE, Skepner A, Swalley SE, Vrcic A, Weisbart E, Williams G, Yu S, Zapiec B, Carpenter AE. Optimizing the Cell Painting assay for image-based profiling. Nat Protoc 2023; 18:1981-2013. [PMID: 37344608 PMCID: PMC10536784 DOI: 10.1038/s41596-023-00840-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 03/28/2023] [Indexed: 06/23/2023]
Abstract
In image-based profiling, software extracts thousands of morphological features of cells from multi-channel fluorescence microscopy images, yielding single-cell profiles that can be used for basic research and drug discovery. Powerful applications have been proven, including clustering chemical and genetic perturbations on the basis of their similar morphological impact, identifying disease phenotypes by observing differences in profiles between healthy and diseased cells and predicting assay outcomes by using machine learning, among many others. Here, we provide an updated protocol for the most popular assay for image-based profiling, Cell Painting. Introduced in 2013, it uses six stains imaged in five channels and labels eight diverse components of the cell: DNA, cytoplasmic RNA, nucleoli, actin, Golgi apparatus, plasma membrane, endoplasmic reticulum and mitochondria. The original protocol was updated in 2016 on the basis of several years' experience running it at two sites, after optimizing it by visual stain quality. Here, we describe the work of the Joint Undertaking for Morphological Profiling Cell Painting Consortium, to improve upon the assay via quantitative optimization by measuring the assay's ability to detect morphological phenotypes and group similar perturbations together. The assay gives very robust outputs despite various changes to the protocol, and two vendors' dyes work equivalently well. We present Cell Painting version 3, in which some steps are simplified and several stain concentrations can be reduced, saving costs. Cell culture and image acquisition take 1-2 weeks for typically sized batches of ≤20 plates; feature extraction and data analysis take an additional 1-2 weeks.This protocol is an update to Nat. Protoc. 11, 1757-1774 (2016): https://doi.org/10.1038/nprot.2016.105.
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Affiliation(s)
- Beth A Cimini
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Maria Kost-Alimova
- Center for Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lisa Miller
- Center for Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Amy Goodale
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Briana Fritchman
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Patrick Byrne
- Center for Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Nasim Jamali
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - David J Logan
- Internal Medicine Research Unit, Pfizer Worldwide Research, Development and Medical, Cambridge, MA, USA
| | - John B Concannon
- Chemical Biology & Therapeutics Department, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | | | | | - Shantanu Singh
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Peter Aspesi
- Chemical Biology & Therapeutics Department, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Justin D Boyd
- Internal Medicine Research Unit, Pfizer Worldwide Research, Development and Medical, Cambridge, MA, USA
| | - Tamara Gilbert
- Internal Medicine Research Unit, Pfizer Worldwide Research, Development and Medical, Cambridge, MA, USA
| | - David Gnutt
- Bayer AG, Research & Development, Pharmaceuticals, Wuppertal, Germany
| | | | - Desiree Hernandez
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Michelle Melanson
- Center for Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | | | - Adam Skepner
- Center for Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Anita Vrcic
- Center for Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Erin Weisbart
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Guy Williams
- AstraZeneca BioPharmaceuticals R&D, Cambridge, UK
| | - Shan Yu
- Takeda Development Center Americas, Inc., San Diego, CA, USA
| | | | - Anne E Carpenter
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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3
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Rago F, Rodrigues LU, Bonney M, Sprouffske K, Kurth E, Elliott G, Ambrose J, Aspesi P, Oborski J, Chen JT, McDonald ER, Mapa FA, Ruddy DA, Kauffmann A, Abrams T, Bhang HEC, Jagani Z. Exquisite Sensitivity to Dual BRG1/BRM ATPase Inhibitors Reveals Broad SWI/SNF Dependencies in Acute Myeloid Leukemia. Mol Cancer Res 2021; 20:361-372. [PMID: 34799403 DOI: 10.1158/1541-7786.mcr-21-0390] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 10/03/2021] [Accepted: 11/15/2021] [Indexed: 11/16/2022]
Abstract
Various subunits of mammalian SWI/SNF chromatin remodeling complexes display loss-of-function mutations characteristic of tumor suppressors in different cancers, but an additional role for SWI/SNF supporting cell survival in distinct cancer contexts is emerging. In particular, genetic dependence on the catalytic subunit BRG1/SMARCA4 has been observed in acute myeloid leukemia (AML), yet the feasibility of direct therapeutic targeting of SWI/SNF catalytic activity in leukemia remains unknown. Here, we evaluated the activity of dual BRG1/BRM ATPase inhibitors across a genetically diverse panel of cancer cell lines and observed that hematopoietic cancer cell lines were among the most sensitive compared to other lineages. This result was striking in comparison to data from pooled short hairpin RNA screens, which showed that only a subset of leukemia cell lines display sensitivity to BRG1 knockdown. We demonstrate that combined genetic knockdown of BRG1 and BRM is required to recapitulate the effects of dual inhibitors, suggesting that SWI/SNF dependency in human leukemia extends beyond a predominantly BRG1-driven mechanism. Through gene expression and chromatin accessibility studies, we show that the dual inhibitors act at genomic loci associated with oncogenic transcription factors, and observe a downregulation of leukemic pathway genes including MYC, a well-established target of BRG1 activity in AML. Overall, small molecule inhibition of BRG1/BRM induced common transcriptional responses across leukemia models resulting in a spectrum of cellular phenotypes. Implications: Our studies reveal the breadth of SWI/SNF dependency in leukemia and support targeting SWI/SNF catalytic function as a potential therapeutic strategy in AML.
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Affiliation(s)
| | | | - Megan Bonney
- Oncology, Novartis Institutes for Biomedical Research
| | | | - Esther Kurth
- Oncology, Novartis Institutes for Biomedical Research
| | | | - Jessi Ambrose
- Oncology, Novartis Institutes for Biomedical Research
| | - Peter Aspesi
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research
| | - Justin Oborski
- High Throughput Biology, Novartis Institutes for Biomedical Research
| | - Julie T Chen
- Oncology, Novartis Institutes for Biomedical Research
| | | | - Felipa A Mapa
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research
| | - David A Ruddy
- Oncology Drug Discovery, Novartis Institutes for BioMedical Research
| | - Audrey Kauffmann
- Oncology Disease Area, Novartis Institutes for Biomedical Research
| | - Tinya Abrams
- Disease Area Oncology, Novartis Institutes for BioMedical Research
| | | | - Zainab Jagani
- Oncology, Novartis Institutes for Biomedical Research
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4
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Rao P, Tullai J, Aspesi P, Mapa F, Cochran N, Sigoillot F, Roma G, Gleim S, Jacob J, Marchese J, Solomon J. Abstract 2025: Characterization of cancer cell lines made senescent by exposure to ribociclib, doxorubicin, or TGFβ1, and identification of genes required for entry into senescence and senescent cell survival. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-2025] [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
Cellular senescence is a stress-induced state of stable growth arrest characterized by high expression of cell cycle inhibitors; a dramatic change in cell morphology, including an increase in lysosomal content; and secretion of large numbers of proteins involved in immune signaling and extracellular matrix remodeling. The physiological importance of cellular senescence has been attributed to prevention of carcinogenesis, aging, development, and tissue repair, and tumor cells can undergo senescence in response to therapeutic agents. In this work, we sought to validate the senescence-inducing activity of two known inducers (doxorubicin and TGFβ1) and a CDK4/6 inhibitor (ribociclib) and to identify proteins that can kill senescent tumor cells (senolytic targets) if knocked out and to identify downstream components of the tumor cell senescence pathway. Huh7 hepatocellular carcinoma cells and SK-MEL-28 melanoma cells were induced to senescence by treatment with three different agents: ribociclib, low doses of doxorubicin, or TGFβ1. The induction of senescence was confirmed by observing growth arrest, an increase in SA-β-gal staining, dramatic cell morphology changes, loss of c-Myc protein, increased expression of p15, and increased expression of senescence-associated secretory phenotype (SASP) proteins. Induction of SASP components was measured by RNAseq and SOMAscan. All three agents induced a senescent state, with blockage at different stages of the cell cycle observed. Induction of known immune factors, including IL-8 and IL-11, were identified in senescent cells (Huh7). A whole-genome CRISPR screen identified proteins required to enter senescence and those that were incompatible with the senescent state if knocked out. Expected hits were observed (eg, TGFBR1/TGFBR2 for TGFβ1, RB for ribociclib, and TOP2A for doxorubicin) for guide DNAs (gDNAs) that blocked entry into the senescent state. No gDNA candidates for common downstream senescence pathway components were observed, suggesting that these components are essential genes or that they do not exist. gDNA-induced knockouts that were incompatible with the senescent state dropped out of the screen and represent potential senolytic targets. The screen identified BCL2L1 as the only common senolytic hit across multiple senescence-inducing reagents, confirming published reports suggesting it is a senolytic target. These data show that ribociclib, doxorubicin, and TGFβ1 induced senescence in cancer cell lines. Whole-genome CRISPR screens identified senescence pathway components for each of these agents, as well as a common senolytic target.
Citation Format: Pasupuleti Rao, Jennifer Tullai, Peter Aspesi, Felipa Mapa, Nadire Cochran, Frederic Sigoillot, Guglielmo Roma, Scott Gleim, Jaison Jacob, Jason Marchese, Jonathan Solomon. Characterization of cancer cell lines made senescent by exposure to ribociclib, doxorubicin, or TGFβ1, and identification of genes required for entry into senescence and senescent cell survival [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2025.
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Affiliation(s)
- Pasupuleti Rao
- 1Novartis Institutes for BioMedical Research, Cambridge, MA
| | | | - Peter Aspesi
- 1Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Felipa Mapa
- 1Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Nadire Cochran
- 1Novartis Institutes for BioMedical Research, Cambridge, MA
| | | | - Guglielmo Roma
- 2Novartis Institutes for BioMedical Research, Basel, Switzerland
| | - Scott Gleim
- 1Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Jaison Jacob
- 1Novartis Institutes for BioMedical Research, Cambridge, MA
| | - Jason Marchese
- 1Novartis Institutes for BioMedical Research, Cambridge, MA
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5
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Cho H, Shen Q, Zhang LH, Okumura M, Kawakami A, Ambrose J, Sigoillot F, Miller HR, Gleim S, Cobos-Correa A, Wang Y, Piechon P, Roma G, Eggimann F, Moore C, Aspesi P, Mapa FA, Burks H, Ross NT, Krastel P, Hild M, Maimone TJ, Fisher DE, Nomura DK, Tallarico JA, Canham SM, Jenkins JL, Forrester WC. CYP27A1-dependent anti-melanoma activity of limonoid natural products targets mitochondrial metabolism. Cell Chem Biol 2021; 28:1407-1419.e6. [PMID: 33794192 DOI: 10.1016/j.chembiol.2021.03.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 01/24/2021] [Accepted: 03/09/2021] [Indexed: 01/18/2023]
Abstract
Three limonoid natural products with selective anti-proliferative activity against BRAF(V600E) and NRAS(Q61K)-mutation-dependent melanoma cell lines were identified. Differential transcriptome analysis revealed dependency of compound activity on expression of the mitochondrial cytochrome P450 oxidase CYP27A1, a transcriptional target of melanogenesis-associated transcription factor (MITF). We determined that CYP27A1 activity is necessary for the generation of a reactive metabolite that proceeds to inhibit cellular proliferation. A genome-wide small interfering RNA screen in combination with chemical proteomics experiments revealed gene-drug functional epistasis, suggesting that these compounds target mitochondrial biogenesis and inhibit tumor bioenergetics through a covalent mechanism. Our work suggests a strategy for melanoma-specific targeting by exploiting the expression of MITF target gene CYP27A1 and inhibiting mitochondrial oxidative phosphorylation in BRAF mutant melanomas.
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Affiliation(s)
- Hyelim Cho
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Qiong Shen
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Lydia H Zhang
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720, USA
| | - Mikiko Okumura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720, USA
| | - Akinori Kawakami
- Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Jessi Ambrose
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Frederic Sigoillot
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Howard R Miller
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Scott Gleim
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Amanda Cobos-Correa
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland
| | - Ying Wang
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland
| | - Philippe Piechon
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland
| | - Guglielmo Roma
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland
| | - Fabian Eggimann
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland
| | - Charles Moore
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland
| | - Peter Aspesi
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Felipa A Mapa
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Heather Burks
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Nathan T Ross
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Philipp Krastel
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland
| | - Marc Hild
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Thomas J Maimone
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720, USA
| | - David E Fisher
- Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Daniel K Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA; Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA 94720, USA; Innovative Genomics Institute, Berkeley, CA 94720, USA
| | - John A Tallarico
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA; Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720, USA
| | - Stephen M Canham
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA; Novartis-Berkeley Center for Proteomics and Chemistry Technologies, Berkeley, CA 94720, USA
| | - Jeremy L Jenkins
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA.
| | - William C Forrester
- Novartis Institutes for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA.
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6
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Monaco KA, Delach S, Yuan J, Mishina Y, Fordjour P, Labrot E, McKay D, Guo R, Higgins S, Wang HQ, Liang J, Bui K, Green J, Aspesi P, Ambrose J, Mapa F, Griner L, Jaskelioff M, Fuller J, Crawford K, Pardee G, Widger S, Hammerman PS, Engelman JA, Stuart DD, Cooke VG, Caponigro G. LXH254, a Potent and Selective ARAF-Sparing Inhibitor of BRAF and CRAF for the Treatment of MAPK-Driven Tumors. Clin Cancer Res 2020; 27:2061-2073. [DOI: 10.1158/1078-0432.ccr-20-2563] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 10/02/2020] [Accepted: 12/16/2020] [Indexed: 11/16/2022]
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7
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Canham SM, Wang Y, Cornett A, Auld DS, Baeschlin DK, Patoor M, Skaanderup PR, Honda A, Llamas L, Wendel G, Mapa FA, Aspesi P, Labbé-Giguère N, Gamber GG, Palacios DS, Schuffenhauer A, Deng Z, Nigsch F, Frederiksen M, Bushell SM, Rothman D, Jain RK, Hemmerle H, Briner K, Porter JA, Tallarico JA, Jenkins JL. Systematic Chemogenetic Library Assembly. Cell Chem Biol 2020; 27:1124-1129. [PMID: 32707038 DOI: 10.1016/j.chembiol.2020.07.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 06/03/2020] [Accepted: 07/02/2020] [Indexed: 12/22/2022]
Abstract
Chemogenetic libraries, collections of well-defined chemical probes, provide tremendous value to biomedical research but require substantial effort to ensure diversity as well as quality of the contents. We have assembled a chemogenetic library by data mining and crowdsourcing institutional expertise. We are sharing our approach, lessons learned, and disclosing our current collection of 4,185 compounds with their primary annotated gene targets (https://github.com/Novartis/MoaBox). This physical collection is regularly updated and used broadly both within Novartis and in collaboration with external partners.
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Affiliation(s)
- Stephen M Canham
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA.
| | - Yuan Wang
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Allen Cornett
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Douglas S Auld
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA.
| | - Daniel K Baeschlin
- Novartis Institute for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland
| | - Maude Patoor
- Novartis Institute for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland
| | - Philip R Skaanderup
- Novartis Institute for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland
| | - Ayako Honda
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Luis Llamas
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Greg Wendel
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Felipa A Mapa
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Peter Aspesi
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Nancy Labbé-Giguère
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Gabriel G Gamber
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Daniel S Palacios
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Ansgar Schuffenhauer
- Novartis Institute for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland
| | - Zhan Deng
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Florian Nigsch
- Novartis Institute for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland
| | - Mathias Frederiksen
- Novartis Institute for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland
| | - Simon M Bushell
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Deborah Rothman
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Rishi K Jain
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Horst Hemmerle
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Karin Briner
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Jeffery A Porter
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - John A Tallarico
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Jeremy L Jenkins
- Novartis Institute for BioMedical Research, 181 Massachusetts Avenue, Cambridge, MA 02139, USA.
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8
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Barretina J, Caponigro G, Stransky N, Venkatesan K, Margolin AA, Kim S, Wilson CJ, Lehár J, Kryukov GV, Sonkin D, Reddy A, Liu M, Murray L, Berger MF, Monahan JE, Morais P, Meltzer J, Korejwa A, Jané-Valbuena J, Mapa FA, Thibault J, Bric-Furlong E, Raman P, Shipway A, Engels IH, Cheng J, Yu GK, Yu J, Aspesi P, de Silva M, Jagtap K, Jones MD, Wang L, Hatton C, Palescandolo E, Gupta S, Mahan S, Sougnez C, Onofrio RC, Liefeld T, MacConaill L, Winckler W, Reich M, Li N, Mesirov JP, Gabriel SB, Getz G, Ardlie K, Chan V, Myer VE, Weber BL, Porter J, Warmuth M, Finan P, Harris JL, Meyerson M, Golub TR, Morrissey MP, Sellers WR, Schlegel R, Garraway LA. Addendum: The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 2018; 565:E5-E6. [PMID: 30559381 DOI: 10.1038/s41586-018-0722-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jordi Barretina
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA.,Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA.,Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Giordano Caponigro
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Nicolas Stransky
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Kavitha Venkatesan
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Adam A Margolin
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA.,Sage Bionetworks, 1100 Fairview Ave. N., Seattle, Washington, 98109, USA
| | - Sungjoon Kim
- Genomics Institute of the Novartis Research Foundation, San Diego, California, 92121, USA
| | - Christopher J Wilson
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Joseph Lehár
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Gregory V Kryukov
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Dmitriy Sonkin
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Anupama Reddy
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Manway Liu
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Lauren Murray
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Michael F Berger
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA.,Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York, 10065, USA
| | - John E Monahan
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Paula Morais
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Jodi Meltzer
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Adam Korejwa
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Judit Jané-Valbuena
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Felipa A Mapa
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Joseph Thibault
- Genomics Institute of the Novartis Research Foundation, San Diego, California, 92121, USA
| | - Eva Bric-Furlong
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Pichai Raman
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Aaron Shipway
- Genomics Institute of the Novartis Research Foundation, San Diego, California, 92121, USA
| | - Ingo H Engels
- Genomics Institute of the Novartis Research Foundation, San Diego, California, 92121, USA
| | - Jill Cheng
- Novartis Institutes for Biomedical Research, Emeryville, California, 94608, USA
| | - Guoying K Yu
- Novartis Institutes for Biomedical Research, Emeryville, California, 94608, USA
| | - Jianjun Yu
- Novartis Institutes for Biomedical Research, Emeryville, California, 94608, USA
| | - Peter Aspesi
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Melanie de Silva
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Kalpana Jagtap
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Michael D Jones
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Li Wang
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Charles Hatton
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Emanuele Palescandolo
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Supriya Gupta
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Scott Mahan
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Carrie Sougnez
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Robert C Onofrio
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Ted Liefeld
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Laura MacConaill
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Wendy Winckler
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Michael Reich
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Nanxin Li
- Genomics Institute of the Novartis Research Foundation, San Diego, California, 92121, USA
| | - Jill P Mesirov
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Stacey B Gabriel
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Gad Getz
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Kristin Ardlie
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA
| | - Vivien Chan
- Novartis Institutes for Biomedical Research, Emeryville, California, 94608, USA
| | - Vic E Myer
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Barbara L Weber
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Jeff Porter
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Markus Warmuth
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Peter Finan
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Jennifer L Harris
- Genomics Institute of the Novartis Research Foundation, San Diego, California, 92121, USA
| | - Matthew Meyerson
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA.,Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Todd R Golub
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA.,Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, 02115, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland, 20815, USA
| | - Michael P Morrissey
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - William R Sellers
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA
| | - Robert Schlegel
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, 02139, USA.
| | - Levi A Garraway
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, 02142, USA. .,Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA. .,Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA.
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9
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Krastel P, Roggo S, Schirle M, Ross NT, Perruccio F, Aspesi P, Aust T, Buntin K, Estoppey D, Liechty B, Mapa F, Memmert K, Miller H, Pan X, Riedl R, Thibaut C, Thomas J, Wagner T, Weber E, Xie X, Schmitt EK, Hoepfner D. Nannocystin A: an Elongation Factor 1 Inhibitor from Myxobacteria with Differential Anti-Cancer Properties. Angew Chem Int Ed Engl 2015; 54:10149-54. [DOI: 10.1002/anie.201505069] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Indexed: 12/21/2022]
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10
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Krastel P, Roggo S, Schirle M, Ross NT, Perruccio F, Aspesi P, Aust T, Buntin K, Estoppey D, Liechty B, Mapa F, Memmert K, Miller H, Pan X, Riedl R, Thibaut C, Thomas J, Wagner T, Weber E, Xie X, Schmitt EK, Hoepfner D. Nannocystin A: an Elongation Factor 1 Inhibitor from Myxobacteria with Differential Anti-Cancer Properties. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201505069] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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11
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Barretina J, Caponigro G, Stransky N, Venkatesan K, Margolin AA, Kim S, J.Wilson C, Lehár J, Kryukov GV, Sonkin D, Reddy A, Liu M, Murray L, Berger MF, Monahan JE, Morais P, Meltzer J, Korejwa A, Jané-Valbuena J, Mapa FA, Thibault J, Bric-Furlong E, Raman P, Shipway A, Engels IH, Cheng J, Yu GK, Yu J, Aspesi P, de Silva M, Jagtap K, Jones MD, Wang L, Hatton C, Palescandolo E, Gupta S, Mahan S, Sougnez C, Onofrio RC, Liefeld T, MacConaill L, Winckler W, Reich M, Li N, Mesirov JP, Gabriel SB, Getz G, Ardlie K, Chan V, Myer VE, Weber BL, Porter J, Warmuth M, Finan P, Harris JL, Meyerson M, Golub TR, Morrissey MP, Sellers WR, Schlegel R, Garraway LA. Addendum: The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 2012. [DOI: 10.1038/nature11735] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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12
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Barretina J, Caponigro G, Stransky N, Venkatesan K, Margolin AA, Kim S, Wilson CJ, Lehár J, Kryukov GV, Sonkin D, Reddy A, Liu M, Murray L, Berger MF, Monahan JE, Morais P, Meltzer J, Korejwa A, Jané-Valbuena J, Mapa FA, Thibault J, Bric-Furlong E, Raman P, Shipway A, Engels IH, Cheng J, Yu GK, Yu J, Aspesi P, de Silva M, Jagtap K, Jones MD, Wang L, Hatton C, Palescandolo E, Gupta S, Mahan S, Sougnez C, Onofrio RC, Liefeld T, MacConaill L, Winckler W, Reich M, Li N, Mesirov JP, Gabriel SB, Getz G, Ardlie K, Chan V, Myer VE, Weber BL, Porter J, Warmuth M, Finan P, Harris JL, Meyerson M, Golub TR, Morrissey MP, Sellers WR, Schlegel R, Garraway LA. The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 2012; 483:603-7. [PMID: 22460905 PMCID: PMC3320027 DOI: 10.1038/nature11003] [Citation(s) in RCA: 5289] [Impact Index Per Article: 440.8] [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: 07/25/2011] [Accepted: 03/01/2012] [Indexed: 02/07/2023]
Abstract
The systematic translation of cancer genomic data into knowledge of tumour biology and therapeutic possibilities remains challenging. Such efforts should be greatly aided by robust preclinical model systems that reflect the genomic diversity of human cancers and for which detailed genetic and pharmacological annotation is available. Here we describe the Cancer Cell Line Encyclopedia (CCLE): a compilation of gene expression, chromosomal copy number and massively parallel sequencing data from 947 human cancer cell lines. When coupled with pharmacological profiles for 24 anticancer drugs across 479 of the cell lines, this collection allowed identification of genetic, lineage, and gene-expression-based predictors of drug sensitivity. In addition to known predictors, we found that plasma cell lineage correlated with sensitivity to IGF1 receptor inhibitors; AHR expression was associated with MEK inhibitor efficacy in NRAS-mutant lines; and SLFN11 expression predicted sensitivity to topoisomerase inhibitors. Together, our results indicate that large, annotated cell-line collections may help to enable preclinical stratification schemata for anticancer agents. The generation of genetic predictions of drug response in the preclinical setting and their incorporation into cancer clinical trial design could speed the emergence of 'personalized' therapeutic regimens.
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MESH Headings
- Antineoplastic Agents/pharmacology
- Cell Line, Tumor
- Cell Lineage
- Chromosomes, Human/genetics
- Clinical Trials as Topic/methods
- Databases, Factual
- Drug Screening Assays, Antitumor/methods
- Encyclopedias as Topic
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic
- Genes, ras/genetics
- Genome, Human/genetics
- Genomics
- Humans
- Mitogen-Activated Protein Kinase Kinases/antagonists & inhibitors
- Mitogen-Activated Protein Kinase Kinases/metabolism
- Models, Biological
- Neoplasms/drug therapy
- Neoplasms/genetics
- Neoplasms/metabolism
- Neoplasms/pathology
- Pharmacogenetics
- Plasma Cells/cytology
- Plasma Cells/drug effects
- Plasma Cells/metabolism
- Precision Medicine/methods
- Receptor, IGF Type 1/antagonists & inhibitors
- Receptor, IGF Type 1/metabolism
- Receptors, Aryl Hydrocarbon/genetics
- Receptors, Aryl Hydrocarbon/metabolism
- Sequence Analysis, DNA
- Topoisomerase Inhibitors/pharmacology
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Affiliation(s)
- Jordi Barretina
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Giordano Caponigro
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Nicolas Stransky
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Kavitha Venkatesan
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Adam A. Margolin
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Sungjoon Kim
- Genomics Institute of the Novartis Research Foundation, San Diego, California 92121, USA
| | | | - Joseph Lehár
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Gregory V. Kryukov
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Dmitriy Sonkin
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Anupama Reddy
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Manway Liu
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Lauren Murray
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Michael F. Berger
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - John E. Monahan
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Paula Morais
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Jodi Meltzer
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Adam Korejwa
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Judit Jané-Valbuena
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Felipa A. Mapa
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Joseph Thibault
- Genomics Institute of the Novartis Research Foundation, San Diego, California 92121, USA
| | - Eva Bric-Furlong
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Pichai Raman
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Aaron Shipway
- Genomics Institute of the Novartis Research Foundation, San Diego, California 92121, USA
| | - Ingo H. Engels
- Genomics Institute of the Novartis Research Foundation, San Diego, California 92121, USA
| | - Jill Cheng
- Novartis Institutes for Biomedical Research, Emeryville, California 94608, USA
| | - Guoying K. Yu
- Novartis Institutes for Biomedical Research, Emeryville, California 94608, USA
| | - Jianjun Yu
- Novartis Institutes for Biomedical Research, Emeryville, California 94608, USA
| | - Peter Aspesi
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Melanie de Silva
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Kalpana Jagtap
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Michael D. Jones
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Li Wang
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Charles Hatton
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Emanuele Palescandolo
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Supriya Gupta
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Scott Mahan
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Carrie Sougnez
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Robert C. Onofrio
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Ted Liefeld
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Laura MacConaill
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Wendy Winckler
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Michael Reich
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Nanxin Li
- Genomics Institute of the Novartis Research Foundation, San Diego, California 92121, USA
| | - Jill P. Mesirov
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Stacey B. Gabriel
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Gad Getz
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Kristin Ardlie
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Vivien Chan
- Novartis Institutes for Biomedical Research, Emeryville, California 94608, USA
| | - Vic E. Myer
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Barbara L. Weber
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Jeff Porter
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Markus Warmuth
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Peter Finan
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Jennifer L. Harris
- Genomics Institute of the Novartis Research Foundation, San Diego, California 92121, USA
| | - Matthew Meyerson
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Todd R. Golub
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Michael P. Morrissey
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - William R. Sellers
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Robert Schlegel
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Levi A. Garraway
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
- Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
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13
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Barretina J, Caponigro G, Stransky N, Venkatesan K, Margolin AA, Kim S, Wilson CJ, Lehár J, Kryukov GV, Sonkin D, Reddy A, Liu M, Murray L, Berger MF, Monahan JE, Morais P, Meltzer J, Korejwa A, Jané-Valbuena J, Mapa FA, Thibault J, Bric-Furlong E, Raman P, Shipway A, Engels IH, Cheng J, Yu GK, Yu J, Aspesi P, de Silva M, Jagtap K, Jones MD, Wang L, Hatton C, Palescandolo E, Gupta S, Mahan S, Sougnez C, Onofrio RC, Liefeld T, MacConaill L, Winckler W, Reich M, Li N, Mesirov JP, Gabriel SB, Getz G, Ardlie K, Chan V, Myer VE, Weber BL, Porter J, Warmuth M, Finan P, Harris JL, Meyerson M, Golub TR, Morrissey MP, Sellers WR, Schlegel R, Garraway LA. The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 2012. [PMID: 22460905 DOI: 10.1038/nature1100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The systematic translation of cancer genomic data into knowledge of tumour biology and therapeutic possibilities remains challenging. Such efforts should be greatly aided by robust preclinical model systems that reflect the genomic diversity of human cancers and for which detailed genetic and pharmacological annotation is available. Here we describe the Cancer Cell Line Encyclopedia (CCLE): a compilation of gene expression, chromosomal copy number and massively parallel sequencing data from 947 human cancer cell lines. When coupled with pharmacological profiles for 24 anticancer drugs across 479 of the cell lines, this collection allowed identification of genetic, lineage, and gene-expression-based predictors of drug sensitivity. In addition to known predictors, we found that plasma cell lineage correlated with sensitivity to IGF1 receptor inhibitors; AHR expression was associated with MEK inhibitor efficacy in NRAS-mutant lines; and SLFN11 expression predicted sensitivity to topoisomerase inhibitors. Together, our results indicate that large, annotated cell-line collections may help to enable preclinical stratification schemata for anticancer agents. The generation of genetic predictions of drug response in the preclinical setting and their incorporation into cancer clinical trial design could speed the emergence of 'personalized' therapeutic regimens.
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Affiliation(s)
- Jordi Barretina
- The Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
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