151
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Parma B, Ramesh V, Gollavilli PN, Siddiqui A, Pinna L, Schwab A, Marschall S, Zhang S, Pilarsky C, Napoli F, Volante M, Urbanczyk S, Mielenz D, Schrøder HD, Stemmler M, Wurdak H, Ceppi P. Metabolic impairment of non-small cell lung cancers by mitochondrial HSPD1 targeting. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:248. [PMID: 34364401 PMCID: PMC8348813 DOI: 10.1186/s13046-021-02049-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/22/2021] [Indexed: 12/25/2022]
Abstract
Background The identification of novel targets is of paramount importance to develop more effective drugs and improve the treatment of non-small cell lung cancer (NSCLC), the leading cause of cancer-related deaths worldwide. Since cells alter their metabolic rewiring during tumorigenesis and along cancer progression, targeting key metabolic players and metabolism-associated proteins represents a valuable approach with a high therapeutic potential. Metabolic fitness relies on the functionality of heat shock proteins (HSPs), molecular chaperones that facilitate the correct folding of metabolism enzymes and their assembly in macromolecular structures. Methods Gene fitness was determined by bioinformatics analysis from available datasets from genetic screenings. HSPD1 expression was evaluated by immunohistochemistry from formalin-fixed paraffin-embedded tissues from NSCLC patients. Real-time proliferation assays with and without cytotoxicity reagents, colony formation assays and cell cycle analyses were used to monitor growth and drug sensitivity of different NSCLC cells in vitro. In vivo growth was monitored with subcutaneous injections in immune-deficient mice. Cell metabolic activity was analyzed through extracellular metabolic flux analysis. Specific knockouts were introduced by CRISPR/Cas9. Results We show heat shock protein family D member 1 (HSPD1 or HSP60) as a survival gene ubiquitously expressed in NSCLC and associated with poor patients’ prognosis. HSPD1 knockdown or its chemical disruption by the small molecule KHS101 induces a drastic breakdown of oxidative phosphorylation, and suppresses cell proliferation both in vitro and in vivo. By combining drug profiling with transcriptomics and through a whole-genome CRISPR/Cas9 screen, we demonstrate that HSPD1-targeted anti-cancer effects are dependent on oxidative phosphorylation and validated molecular determinants of KHS101 sensitivity, in particular, the creatine-transporter SLC6A8 and the subunit of the cytochrome c oxidase complex COX5B. Conclusions These results highlight mitochondrial metabolism as an attractive target and HSPD1 as a potential theranostic marker for developing therapies to combat NSCLC. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-021-02049-8.
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Affiliation(s)
- Beatrice Parma
- Interdisciplinary Center for Clinical Research (IZKF), Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen, Germany
| | - Vignesh Ramesh
- Interdisciplinary Center for Clinical Research (IZKF), Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen, Germany
| | - Paradesi Naidu Gollavilli
- Interdisciplinary Center for Clinical Research (IZKF), Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen, Germany
| | - Aarif Siddiqui
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Luisa Pinna
- Interdisciplinary Center for Clinical Research (IZKF), Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen, Germany
| | - Annemarie Schwab
- Interdisciplinary Center for Clinical Research (IZKF), Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen, Germany
| | - Sabine Marschall
- Interdisciplinary Center for Clinical Research (IZKF), Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen, Germany
| | - Shuman Zhang
- Department of Surgery, Friedrich-Alexander University of Erlangen- Nuremberg (FAU) and University Hospital of Erlangen, Erlangen, Germany
| | - Christian Pilarsky
- Department of Surgery, Friedrich-Alexander University of Erlangen- Nuremberg (FAU) and University Hospital of Erlangen, Erlangen, Germany
| | - Francesca Napoli
- Department of Oncology At San Luigi Hospital, University of Turin, Orbassano, Turin, Italy
| | - Marco Volante
- Department of Oncology At San Luigi Hospital, University of Turin, Orbassano, Turin, Italy
| | - Sophia Urbanczyk
- Department of Molecular Immunology, Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen, Germany
| | - Dirk Mielenz
- Department of Molecular Immunology, Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen, Germany
| | | | - Marc Stemmler
- Department of Experimental Medicine-I, Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen, Germany
| | - Heiko Wurdak
- Stem Cell and Brain Tumour Group, School of Medicine, University of Leeds, Leeds, LS2 9JT, UK.
| | - Paolo Ceppi
- Interdisciplinary Center for Clinical Research (IZKF), Friedrich-Alexander University of Erlangen-Nuremberg, Erlangen, Germany. .,Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark.
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152
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McKinney DC, McMillan BJ, Ranaghan MJ, Moroco JA, Brousseau M, Mullin-Bernstein Z, O'Keefe M, McCarren P, Mesleh MF, Mulvaney KM, Robinson F, Singh R, Bajrami B, Wagner FF, Hilgraf R, Drysdale MJ, Campbell AJ, Skepner A, Timm DE, Porter D, Kaushik VK, Sellers WR, Ianari A. Discovery of a First-in-Class Inhibitor of the PRMT5-Substrate Adaptor Interaction. J Med Chem 2021; 64:11148-11168. [PMID: 34342224 DOI: 10.1021/acs.jmedchem.1c00507] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
PRMT5 and its substrate adaptor proteins (SAPs), pICln and Riok1, are synthetic lethal dependencies in MTAP-deleted cancer cells. SAPs share a conserved PRMT5 binding motif (PBM) which mediates binding to a surface of PRMT5 distal to the catalytic site. This interaction is required for methylation of several PRMT5 substrates, including histone and spliceosome complexes. We screened for small molecule inhibitors of the PRMT5-PBM interaction and validated a compound series which binds to the PRMT5-PBM interface and directly inhibits binding of SAPs. Mode of action studies revealed the formation of a covalent bond between a halogenated pyridazinone group and cysteine 278 of PRMT5. Optimization of the starting hit produced a lead compound, BRD0639, which engages the target in cells, disrupts PRMT5-RIOK1 complexes, and reduces substrate methylation. BRD0639 is a first-in-class PBM-competitive inhibitor that can support studies of PBM-dependent PRMT5 activities and the development of novel PRMT5 inhibitors that selectively target these functions.
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Affiliation(s)
- David C McKinney
- Center for the Development of Therapeutics, The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Brian J McMillan
- Center for the Development of Therapeutics, The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Matthew J Ranaghan
- Center for the Development of Therapeutics, The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Jamie A Moroco
- Center for the Development of Therapeutics, The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Merissa Brousseau
- Center for the Development of Therapeutics, The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Zachary Mullin-Bernstein
- Cancer Program, The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Meghan O'Keefe
- Center for the Development of Therapeutics, The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Patrick McCarren
- Center for the Development of Therapeutics, The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Michael F Mesleh
- Center for the Development of Therapeutics, The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Kathleen M Mulvaney
- Cancer Program, The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Foxy Robinson
- Cancer Program, The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Ritu Singh
- Center for the Development of Therapeutics, The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Besnik Bajrami
- Center for the Development of Therapeutics, The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Florence F Wagner
- Center for the Development of Therapeutics, The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Robert Hilgraf
- Center for the Development of Therapeutics, The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Martin J Drysdale
- Center for the Development of Therapeutics, The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Arthur J Campbell
- Center for the Development of Therapeutics, The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Adam Skepner
- Center for the Development of Therapeutics, The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - David E Timm
- Department of Biochemistry, University of Utah, 1390 Presidents Circle, Salt Lake City, Utah 84112, United States
| | - Dale Porter
- Cancer Program, The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Virendar K Kaushik
- Center for the Development of Therapeutics, The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - William R Sellers
- Cancer Program, The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States.,Department of Medical Oncology, Dana-Farber Cancer Institute, Department of Medicine, Harvard Medical School, 44 Binney Street, Boston, Massachusetts 02215, United States
| | - Alessandra Ianari
- Cancer Program, The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
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153
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Chiu YC, Zheng S, Wang LJ, Iskra BS, Rao MK, Houghton PJ, Huang Y, Chen Y. Predicting and characterizing a cancer dependency map of tumors with deep learning. SCIENCE ADVANCES 2021; 7:7/34/eabh1275. [PMID: 34417181 PMCID: PMC8378822 DOI: 10.1126/sciadv.abh1275] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 06/29/2021] [Indexed: 05/14/2023]
Abstract
Genome-wide loss-of-function screens have revealed genes essential for cancer cell proliferation, called cancer dependencies. It remains challenging to link cancer dependencies to the molecular compositions of cancer cells or to unscreened cell lines and further to tumors. Here, we present DeepDEP, a deep learning model that predicts cancer dependencies using integrative genomic profiles. It uses a unique unsupervised pretraining that captures unlabeled tumor genomic representations to improve the learning of cancer dependencies. We demonstrated DeepDEP's improvement over conventional machine learning methods and validated the performance with three independent datasets. By systematic model interpretations, we extended the current dependency maps with functional characterizations of dependencies and a proof-of-concept in silico assay of synthetic essentiality. We applied DeepDEP to pan-cancer tumor genomics and built the first pan-cancer synthetic dependency map of 8000 tumors with clinical relevance. In summary, DeepDEP is a novel tool for investigating cancer dependency with rapidly growing genomic resources.
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Affiliation(s)
- Yu-Chiao Chiu
- Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Siyuan Zheng
- Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
- Department of Population Health Sciences, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Li-Ju Wang
- Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Brian S Iskra
- Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Manjeet K Rao
- Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Peter J Houghton
- Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
- Department of Molecular Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Yufei Huang
- University of Pittsburgh Medical Center Hillman Cancer Center, Pittsburgh, PA 15232, USA.
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Yidong Chen
- Greehey Children's Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA.
- Department of Population Health Sciences, University of Texas Health San Antonio, San Antonio, TX 78229, USA
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154
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Grand RS, Burger L, Gräwe C, Michael AK, Isbel L, Hess D, Hoerner L, Iesmantavicius V, Durdu S, Pregnolato M, Krebs AR, Smallwood SA, Thomä N, Vermeulen M, Schübeler D. BANP opens chromatin and activates CpG-island-regulated genes. Nature 2021; 596:133-137. [PMID: 34234345 DOI: 10.1038/s41586-021-03689-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 06/03/2021] [Indexed: 02/06/2023]
Abstract
The majority of gene transcripts generated by RNA polymerase II in mammalian genomes initiate at CpG island (CGI) promoters1,2, yet our understanding of their regulation remains limited. This is in part due to the incomplete information that we have on transcription factors, their DNA-binding motifs and which genomic binding sites are functional in any given cell type3-5. In addition, there are orphan motifs without known binders, such as the CGCG element, which is associated with highly expressed genes across human tissues and enriched near the transcription start site of a subset of CGI promoters6-8. Here we combine single-molecule footprinting with interaction proteomics to identify BTG3-associated nuclear protein (BANP) as the transcription factor that binds this element in the mouse and human genome. We show that BANP is a strong CGI activator that controls essential metabolic genes in pluripotent stem and terminally differentiated neuronal cells. BANP binding is repelled by DNA methylation of its motif in vitro and in vivo, which epigenetically restricts most binding to CGIs and accounts for differential binding at aberrantly methylated CGI promoters in cancer cells. Upon binding to an unmethylated motif, BANP opens chromatin and phases nucleosomes. These findings establish BANP as a critical activator of a set of essential genes and suggest a model in which the activity of CGI promoters relies on methylation-sensitive transcription factors that are capable of chromatin opening.
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Affiliation(s)
- Ralph S Grand
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Lukas Burger
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Cathrin Gräwe
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Alicia K Michael
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Luke Isbel
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Daniel Hess
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Leslie Hoerner
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | | | - Sevi Durdu
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Marco Pregnolato
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,Faculty of Science, University of Basel, Basel, Switzerland
| | - Arnaud R Krebs
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Nicolas Thomä
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Dirk Schübeler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland. .,Faculty of Science, University of Basel, Basel, Switzerland.
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155
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Mulvaney KM, Blomquist C, Acharya N, Li R, Ranaghan MJ, O'Keefe M, Rodriguez DJ, Young MJ, Kesar D, Pal D, Stokes M, Nelson AJ, Jain SS, Yang A, Mullin-Bernstein Z, Columbus J, Bozal FK, Skepner A, Raymond D, LaRussa S, McKinney DC, Freyzon Y, Baidi Y, Porter D, Aguirre AJ, Ianari A, McMillan B, Sellers WR. Molecular basis for substrate recruitment to the PRMT5 methylosome. Mol Cell 2021; 81:3481-3495.e7. [PMID: 34358446 DOI: 10.1016/j.molcel.2021.07.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 06/07/2021] [Accepted: 07/14/2021] [Indexed: 12/15/2022]
Abstract
PRMT5 is an essential arginine methyltransferase and a therapeutic target in MTAP-null cancers. PRMT5 uses adaptor proteins for substrate recruitment through a previously undefined mechanism. Here, we identify an evolutionarily conserved peptide sequence shared among the three known substrate adaptors (CLNS1A, RIOK1, and COPR5) and show that it is necessary and sufficient for interaction with PRMT5. We demonstrate that PRMT5 uses modular adaptor proteins containing a common binding motif for substrate recruitment, comparable with other enzyme classes such as kinases and E3 ligases. We structurally resolve the interface with PRMT5 and show via genetic perturbation that it is required for methylation of adaptor-recruited substrates including the spliceosome, histones, and ribosomal complexes. Furthermore, disruption of this site affects Sm spliceosome activity, leading to intron retention. Genetic disruption of the PRMT5-substrate adaptor interface impairs growth of MTAP-null tumor cells and is thus a site for development of therapeutic inhibitors of PRMT5.
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Affiliation(s)
| | | | | | | | - Matthew J Ranaghan
- Center for the Development of Therapeutics, Broad Institute, Cambridge, MA, USA
| | - Meghan O'Keefe
- Center for the Development of Therapeutics, Broad Institute, Cambridge, MA, USA
| | | | | | | | | | | | | | | | | | | | | | | | - Adam Skepner
- Center for the Development of Therapeutics, Broad Institute, Cambridge, MA, USA
| | - Donald Raymond
- Center for the Development of Therapeutics, Broad Institute, Cambridge, MA, USA
| | - Salvatore LaRussa
- Center for the Development of Therapeutics, Broad Institute, Cambridge, MA, USA
| | - David C McKinney
- Center for the Development of Therapeutics, Broad Institute, Cambridge, MA, USA
| | | | | | - Dale Porter
- Broad Institute, Cambridge, MA, USA; Cedilla Therapeutics, Cambridge, MA, USA
| | - Andrew J Aguirre
- Broad Institute, Cambridge, MA, USA; Medical Oncology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | | | - Brian McMillan
- Center for the Development of Therapeutics, Broad Institute, Cambridge, MA, USA; Tango Therapeutics, Cambridge, MA, USA
| | - William R Sellers
- Broad Institute, Cambridge, MA, USA; Medical Oncology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.
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156
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Lee E, Szvetecz S, Polli R, Grauel A, Chen J, Judge J, Jaiswal S, Maeda R, Schwartz S, Voedisch B, Piksa M, Japutra C, Sadhasivam L, Wang Y, Carrion A, Isim S, Liang J, Nicholson T, Lei H, Fang Q, Steinkrauss M, Walker D, Wagner J, Cremasco V, Wang HQ, Galli GG, Granda B, Mansfield K, Simmons Q, Nguyen AA, Vincent Jordan N. PAX8 lineage-driven T cell engaging antibody for the treatment of high-grade serous ovarian cancer. Sci Rep 2021; 11:14841. [PMID: 34290299 PMCID: PMC8295318 DOI: 10.1038/s41598-021-93992-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 07/05/2021] [Indexed: 12/03/2022] Open
Abstract
High-grade serous ovarian cancers (HGSOC) represent the most common subtype of ovarian malignancies. Due to the frequency of late-stage diagnosis and high rates of recurrence following standard of care treatments, novel therapies are needed to promote durable responses. We investigated the anti-tumor activity of CD3 T cell engaging bispecific antibodies (TCBs) directed against the PAX8 lineage-driven HGSOC tumor antigen LYPD1 and demonstrated that anti-LYPD1 TCBs induce T cell activation and promote in vivo tumor growth inhibition in LYPD1-expressing HGSOC. To selectively target LYPD1-expressing tumor cells with high expression while sparing cells with low expression, we coupled bivalent low-affinity anti-LYPD1 antigen-binding fragments (Fabs) with the anti-CD3 scFv. In contrast to the monovalent anti-LYPD1 high-affinity TCB (VHP354), the bivalent low-affinity anti-LYPD1 TCB (QZC131) demonstrated antigen density-dependent selectivity and showed tolerability in cynomolgus monkeys at the maximum dose tested of 3 mg/kg. Collectively, these data demonstrate that bivalent TCBs directed against LYPD1 have compelling efficacy and safety profiles to support its use as a treatment for high-grade serous ovarian cancers.
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Affiliation(s)
- Emily Lee
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Sarah Szvetecz
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Ryan Polli
- PKS Oncology, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Angelo Grauel
- Immuno-Oncology, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Jayson Chen
- PCS Toxicology, Novartis Institutes for Biomedical Research, East Hanover, NJ, USA
| | - Joyce Judge
- PCS Toxicology, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Smita Jaiswal
- PCS Toxicology, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Rie Maeda
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Stephanie Schwartz
- Immuno-Oncology, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Bernd Voedisch
- NIBR Biologics Center, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Mateusz Piksa
- NIBR Biologics Center, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Chietara Japutra
- NIBR Biologics Center, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Lingheswar Sadhasivam
- NIBR Biologics Center, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Yiqin Wang
- NIBR Biologics Center, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Ana Carrion
- NIBR Biologics Center, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Sinan Isim
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Jinsheng Liang
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | | | - Hong Lei
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Qing Fang
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | | | - Dana Walker
- PCS Toxicology, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Joel Wagner
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Viviana Cremasco
- Immuno-Oncology, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Hui Qin Wang
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Giorgio G Galli
- Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Brian Granda
- NIBR Biologics Center, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Keith Mansfield
- PCS Toxicology, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Quincey Simmons
- PCS Toxicology, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Andrew Anh Nguyen
- NIBR Biologics Center, Novartis Institutes for Biomedical Research, Cambridge, MA, USA.
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157
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Elmes K, Schmich F, Szczurek E, Jenkins J, Beerenwinkel N, Gavryushkin A. Learning epistatic gene interactions from perturbation screens. PLoS One 2021; 16:e0254491. [PMID: 34255784 PMCID: PMC8277066 DOI: 10.1371/journal.pone.0254491] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 06/28/2021] [Indexed: 11/21/2022] Open
Abstract
The treatment of complex diseases often relies on combinatorial therapy, a strategy where drugs are used to target multiple genes simultaneously. Promising candidate genes for combinatorial perturbation often constitute epistatic genes, i.e., genes which contribute to a phenotype in a non-linear fashion. Experimental identification of the full landscape of genetic interactions by perturbing all gene combinations is prohibitive due to the exponential growth of testable hypotheses. Here we present a model for the inference of pairwise epistatic, including synthetic lethal, gene interactions from siRNA-based perturbation screens. The model exploits the combinatorial nature of siRNA-based screens resulting from the high numbers of sequence-dependent off-target effects, where each siRNA apart from its intended target knocks down hundreds of additional genes. We show that conditional and marginal epistasis can be estimated as interaction coefficients of regression models on perturbation data. We compare two methods, namely glinternet and xyz, for selecting non-zero effects in high dimensions as components of the model, and make recommendations for the appropriate use of each. For data simulated from real RNAi screening libraries, we show that glinternet successfully identifies epistatic gene pairs with high accuracy across a wide range of relevant parameters for the signal-to-noise ratio of observed phenotypes, the effect size of epistasis and the number of observations per double knockdown. xyz is also able to identify interactions from lower dimensional data sets (fewer genes), but is less accurate for many dimensions. Higher accuracy of glinternet, however, comes at the cost of longer running time compared to xyz. The general model is widely applicable and allows mining the wealth of publicly available RNAi screening data for the estimation of epistatic interactions between genes. As a proof of concept, we apply the model to search for interactions, and potential targets for treatment, among previously published sets of siRNA perturbation screens on various pathogens. The identified interactions include both known epistatic interactions as well as novel findings.
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Affiliation(s)
- Kieran Elmes
- Department of Computer Science, University of Otago, Dunedin, New Zealand
| | - Fabian Schmich
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Ewa Szczurek
- Institute of Informatics, University of Warsaw, Warsaw, Poland
| | - Jeremy Jenkins
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, United States of America
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
- * E-mail: (NB); (AG)
| | - Alex Gavryushkin
- Department of Computer Science, University of Otago, Dunedin, New Zealand
- School of Mathematics and Statistics, University of Canterbury, Christchurch, New Zealand
- * E-mail: (NB); (AG)
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158
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Okutachi S, Manoharan GB, Kiriazis A, Laurini C, Catillon M, McCormick F, Yli-Kauhaluoma J, Abankwa D. A Covalent Calmodulin Inhibitor as a Tool to Study Cellular Mechanisms of K-Ras-Driven Stemness. Front Cell Dev Biol 2021; 9:665673. [PMID: 34307350 PMCID: PMC8296985 DOI: 10.3389/fcell.2021.665673] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 06/04/2021] [Indexed: 11/23/2022] Open
Abstract
Recently, the highly mutated oncoprotein K-Ras4B (hereafter K-Ras) was shown to drive cancer cell stemness in conjunction with calmodulin (CaM). We previously showed that the covalent CaM inhibitor ophiobolin A (OphA) can potently inhibit K-Ras stemness activity. However, OphA, a fungus-derived natural product, exhibits an unspecific, broad toxicity across all phyla. Here we identified a less toxic, functional analog of OphA that can efficiently inactivate CaM by covalent inhibition. We analyzed a small series of benzazulenones, which bear some structural similarity to OphA and can be synthesized in only six steps. We identified the formyl aminobenzazulenone 1, here named Calmirasone1, as a novel and potent covalent CaM inhibitor. Calmirasone1 has a 4-fold increased affinity for CaM as compared to OphA and was active against K-Ras in cells within minutes, as compared to hours required by OphA. Calmirasone1 displayed a 2.5–4.5-fold higher selectivity for KRAS over BRAF mutant 3D spheroid growth than OphA, suggesting improved relative on-target activity. Importantly, Calmirasone1 has a 40–260-fold lower unspecific toxic effect on HRAS mutant cells, while it reaches almost 50% of the activity of novel K-RasG12C specific inhibitors in 3D spheroid assays. Our results suggest that Calmirasone1 can serve as a new tool compound to further investigate the cancer cell biology of the K-Ras and CaM associated stemness activities.
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Affiliation(s)
- Sunday Okutachi
- Cancer Cell Biology and Drug Discovery Group, Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Ganesh Babu Manoharan
- Cancer Cell Biology and Drug Discovery Group, Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Alexandros Kiriazis
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Christina Laurini
- Cancer Cell Biology and Drug Discovery Group, Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Marie Catillon
- Cancer Cell Biology and Drug Discovery Group, Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Frank McCormick
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States.,Frederick National Laboratory for Cancer Research, Cancer Research Technology Program, Leidos Biomedical Research, Inc., National Cancer Institute RAS Initiative, Frederick, MD, United States
| | - Jari Yli-Kauhaluoma
- Drug Research Program, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland
| | - Daniel Abankwa
- Cancer Cell Biology and Drug Discovery Group, Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
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Setton J, Zinda M, Riaz N, Durocher D, Zimmermann M, Koehler M, Reis-Filho JS, Powell SN. Synthetic Lethality in Cancer Therapeutics: The Next Generation. Cancer Discov 2021; 11:1626-1635. [PMID: 33795234 PMCID: PMC8295179 DOI: 10.1158/2159-8290.cd-20-1503] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 01/01/2021] [Accepted: 02/23/2021] [Indexed: 12/25/2022]
Abstract
Synthetic lethality (SL) provides a conceptual framework for tackling targets that are not classically "druggable," including loss-of-function mutations in tumor suppressor genes required for carcinogenesis. Recent technological advances have led to an inflection point in our understanding of genetic interaction networks and ability to identify a wide array of novel SL drug targets. Here, we review concepts and lessons emerging from first-generation trials aimed at testing SL drugs, discuss how the nature of the targeted lesion can influence therapeutic outcomes, and highlight the need to develop clinical biomarkers distinct from those based on the paradigms developed to target activated oncogenes. SIGNIFICANCE: SL offers an approach for the targeting of loss of function of tumor suppressor and DNA repair genes, as well as of amplification and/or overexpression of genes that cannot be targeted directly. A next generation of tumor-specific alterations targetable through SL has emerged from high-throughput CRISPR technology, heralding not only new opportunities for drug development, but also important challenges in the development of optimal predictive biomarkers.
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Affiliation(s)
- Jeremy Setton
- Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Nadeem Riaz
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Daniel Durocher
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | | | | | - Simon N Powell
- Memorial Sloan Kettering Cancer Center, New York, New York.
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160
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Clemons NJ, Phillips WA. Trapping Colorectal Cancer Into a Dead-end. Gastroenterology 2021; 161:33-35. [PMID: 33798528 DOI: 10.1053/j.gastro.2021.03.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 03/29/2021] [Indexed: 12/02/2022]
Affiliation(s)
- Nicholas J Clemons
- Cancer Research, Peter MacCallum Cancer Centre, Victoria, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia.
| | - Wayne A Phillips
- Cancer Research, Peter MacCallum Cancer Centre, Victoria, Australia; Sir Peter MacCallum Department of Oncology, Department of Surgery (St. Vincent's Hospital), The University of Melbourne, Parkville, Victoria, Australia.
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161
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Inoue A, Robinson FS, Minelli R, Tomihara H, Rizi BS, Rose JL, Kodama T, Srinivasan S, Harris AL, Zuniga AM, Mullinax RA, Ma X, Seth S, Daniele JR, Peoples MD, Loponte S, Akdemir KC, Khor TO, Feng N, Roszik J, Sobieski MM, Brunell D, Stephan C, Giuliani V, Deem AK, Shingu T, Deribe YL, Menter DG, Heffernan TP, Viale A, Bristow CA, Kopetz S, Draetta GF, Genovese G, Carugo A. Sequential Administration of XPO1 and ATR Inhibitors Enhances Therapeutic Response in TP53-mutated Colorectal Cancer. Gastroenterology 2021; 161:196-210. [PMID: 33745946 PMCID: PMC8238881 DOI: 10.1053/j.gastro.2021.03.022] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 02/24/2021] [Accepted: 03/05/2021] [Indexed: 12/20/2022]
Abstract
BACKGROUND & AIMS Understanding the mechanisms by which tumors adapt to therapy is critical for developing effective combination therapeutic approaches to improve clinical outcomes for patients with cancer. METHODS To identify promising and clinically actionable targets for managing colorectal cancer (CRC), we conducted a patient-centered functional genomics platform that includes approximately 200 genes and paired this with a high-throughput drug screen that includes 262 compounds in four patient-derived xenografts (PDXs) from patients with CRC. RESULTS Both screening methods identified exportin 1 (XPO1) inhibitors as drivers of DNA damage-induced lethality in CRC. Molecular characterization of the cellular response to XPO1 inhibition uncovered an adaptive mechanism that limited the duration of response in TP53-mutated, but not in TP53-wild-type CRC models. Comprehensive proteomic and transcriptomic characterization revealed that the ATM/ATR-CHK1/2 axes were selectively engaged in TP53-mutant CRC cells upon XPO1 inhibitor treatment and that this response was required for adapting to therapy and escaping cell death. Administration of KPT-8602, an XPO1 inhibitor, followed by AZD-6738, an ATR inhibitor, resulted in dramatic antitumor effects and prolonged survival in TP53-mutant models of CRC. CONCLUSIONS Our findings anticipate tremendous therapeutic benefit and support the further evaluation of XPO1 inhibitors, especially in combination with DNA damage checkpoint inhibitors, to elicit an enduring clinical response in patients with CRC harboring TP53 mutations.
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Affiliation(s)
- Akira Inoue
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas; Department of Gastroenterological Surgery, Osaka General Medical Center, Osaka, Japan.
| | - Frederick S Robinson
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas; Translational Research to Advance Therapeutics and Innovation in Oncology (TRACTION) platform, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rosalba Minelli
- Translational Research to Advance Therapeutics and Innovation in Oncology (TRACTION) platform, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Hideo Tomihara
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Bahar Salimian Rizi
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Johnathon L Rose
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Takahiro Kodama
- Department of Gastroenterology and Hepatology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Sanjana Srinivasan
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Angela L Harris
- Translational Research to Advance Therapeutics and Innovation in Oncology (TRACTION) platform, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Andy M Zuniga
- Translational Research to Advance Therapeutics and Innovation in Oncology (TRACTION) platform, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Robert A Mullinax
- Translational Research to Advance Therapeutics and Innovation in Oncology (TRACTION) platform, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Xiaoyan Ma
- Translational Research to Advance Therapeutics and Innovation in Oncology (TRACTION) platform, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sahil Seth
- Translational Research to Advance Therapeutics and Innovation in Oncology (TRACTION) platform, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Joseph R Daniele
- Translational Research to Advance Therapeutics and Innovation in Oncology (TRACTION) platform, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Michael D Peoples
- Translational Research to Advance Therapeutics and Innovation in Oncology (TRACTION) platform, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sara Loponte
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kadir C Akdemir
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Tin Oo Khor
- Translational Research to Advance Therapeutics and Innovation in Oncology (TRACTION) platform, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ningping Feng
- Translational Research to Advance Therapeutics and Innovation in Oncology (TRACTION) platform, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jason Roszik
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Mary M Sobieski
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, Texas
| | - David Brunell
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, Texas
| | - Clifford Stephan
- Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University, Houston, Texas
| | - Virginia Giuliani
- Translational Research to Advance Therapeutics and Innovation in Oncology (TRACTION) platform, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Angela K Deem
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas; Translational Research to Advance Therapeutics and Innovation in Oncology (TRACTION) platform, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Takashi Shingu
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Yonathan Lissanu Deribe
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - David G Menter
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Timothy P Heffernan
- Translational Research to Advance Therapeutics and Innovation in Oncology (TRACTION) platform, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Andrea Viale
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Christopher A Bristow
- Translational Research to Advance Therapeutics and Innovation in Oncology (TRACTION) platform, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Giulio F Draetta
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Giannicola Genovese
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas; Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Alessandro Carugo
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas; Translational Research to Advance Therapeutics and Innovation in Oncology (TRACTION) platform, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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162
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Lopes R, Sprouffske K, Sheng C, Uijttewaal ECH, Wesdorp AE, Dahinden J, Wengert S, Diaz-Miyar J, Yildiz U, Bleu M, Apfel V, Mermet-Meillon F, Krese R, Eder M, Olsen AV, Hoppe P, Knehr J, Carbone W, Cuttat R, Waldt A, Altorfer M, Naumann U, Weischenfeldt J, deWeck A, Kauffmann A, Roma G, Schübeler D, Galli GG. Systematic dissection of transcriptional regulatory networks by genome-scale and single-cell CRISPR screens. SCIENCE ADVANCES 2021; 7:eabf5733. [PMID: 34215580 PMCID: PMC11057712 DOI: 10.1126/sciadv.abf5733] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 05/21/2021] [Indexed: 06/13/2023]
Abstract
Millions of putative transcriptional regulatory elements (TREs) have been cataloged in the human genome, yet their functional relevance in specific pathophysiological settings remains to be determined. This is critical to understand how oncogenic transcription factors (TFs) engage specific TREs to impose transcriptional programs underlying malignant phenotypes. Here, we combine cutting edge CRISPR screens and epigenomic profiling to functionally survey ≈15,000 TREs engaged by estrogen receptor (ER). We show that ER exerts its oncogenic role in breast cancer by engaging TREs enriched in GATA3, TFAP2C, and H3K27Ac signal. These TREs control critical downstream TFs, among which TFAP2C plays an essential role in ER-driven cell proliferation. Together, our work reveals novel insights into a critical oncogenic transcription program and provides a framework to map regulatory networks, enabling to dissect the function of the noncoding genome of cancer cells.
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Affiliation(s)
- Rui Lopes
- Disease area Oncology, Novartis Institute for Biomedical Research, CH-4002 Basel, Switzerland.
| | - Kathleen Sprouffske
- Disease area Oncology, Novartis Institute for Biomedical Research, CH-4002 Basel, Switzerland
| | - Caibin Sheng
- Disease area Oncology, Novartis Institute for Biomedical Research, CH-4002 Basel, Switzerland
| | - Esther C H Uijttewaal
- Disease area Oncology, Novartis Institute for Biomedical Research, CH-4002 Basel, Switzerland
| | - Adriana Emma Wesdorp
- Disease area Oncology, Novartis Institute for Biomedical Research, CH-4002 Basel, Switzerland
| | - Jan Dahinden
- Disease area Oncology, Novartis Institute for Biomedical Research, CH-4002 Basel, Switzerland
| | - Simon Wengert
- Disease area Oncology, Novartis Institute for Biomedical Research, CH-4002 Basel, Switzerland
| | - Juan Diaz-Miyar
- Disease area Oncology, Novartis Institute for Biomedical Research, CH-4002 Basel, Switzerland
| | - Umut Yildiz
- Disease area Oncology, Novartis Institute for Biomedical Research, CH-4002 Basel, Switzerland
| | - Melusine Bleu
- Disease area Oncology, Novartis Institute for Biomedical Research, CH-4002 Basel, Switzerland
| | - Verena Apfel
- Disease area Oncology, Novartis Institute for Biomedical Research, CH-4002 Basel, Switzerland
| | - Fanny Mermet-Meillon
- Disease area Oncology, Novartis Institute for Biomedical Research, CH-4002 Basel, Switzerland
| | - Rok Krese
- Disease area Oncology, Novartis Institute for Biomedical Research, CH-4002 Basel, Switzerland
| | - Mathias Eder
- Disease area Oncology, Novartis Institute for Biomedical Research, CH-4002 Basel, Switzerland
| | - André Vidas Olsen
- Biotech Research and Innovation Centre (BRIC), The Finsen Laboratory, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Philipp Hoppe
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Judith Knehr
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Walter Carbone
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Rachel Cuttat
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Annick Waldt
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Marc Altorfer
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Ulrike Naumann
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Joachim Weischenfeldt
- Biotech Research and Innovation Centre (BRIC), The Finsen Laboratory, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Antoine deWeck
- Disease area Oncology, Novartis Institute for Biomedical Research, CH-4002 Basel, Switzerland
| | - Audrey Kauffmann
- Disease area Oncology, Novartis Institute for Biomedical Research, CH-4002 Basel, Switzerland
| | - Guglielmo Roma
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Dirk Schübeler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Faculty of Sciences, University of Basel, Basel, Switzerland
| | - Giorgio G Galli
- Disease area Oncology, Novartis Institute for Biomedical Research, CH-4002 Basel, Switzerland.
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Navarro-Carrasco E, Lazo PA. VRK1 Depletion Facilitates the Synthetic Lethality of Temozolomide and Olaparib in Glioblastoma Cells. Front Cell Dev Biol 2021; 9:683038. [PMID: 34195200 PMCID: PMC8237761 DOI: 10.3389/fcell.2021.683038] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 05/13/2021] [Indexed: 12/12/2022] Open
Abstract
Background Glioblastomas treated with temozolomide frequently develop resistance to pharmacological treatments. Therefore, there is a need to find alternative drug targets to reduce treatment resistance based on tumor dependencies. A possibility is to target simultaneously two proteins from different DNA-damage repair pathways to facilitate tumor cell death. Therefore, we tested whether targeting the human chromatin kinase VRK1 by RNA interference can identify this protein as a novel molecular target to reduce the dependence on temozolomide in combination with olaparib, based on synthetic lethality. Materials and Methods Depletion of VRK1, an enzyme that regulates chromatin dynamic reorganization and facilitates resistance to DNA damage, was performed in glioblastoma cells treated with temozolomide, an alkylating agent used for GBM treatment; and olaparib, an inhibitor of PARP-1, used as sensitizer. Two genetically different human glioblastoma cell lines, LN-18 and LN-229, were used for these experiments. The effect on the DNA-damage response was followed by determination of sequential steps in this process: H4K16ac, γH2AX, H4K20me2, and 53BP1. Results The combination of temozolomide and olaparib increased DNA damage detected by labeling free DNA ends, and chromatin relaxation detected by H4K16ac. The combination of both drugs, at lower doses, resulted in an increase in the DNA damage response detected by the formation of γH2AX and 53BP1 foci. VRK1 depletion did not prevent the generation of DNA damage in TUNEL assays, but significantly impaired the DNA damage response induced by temozolomide and olaparib, and mediated by γH2AX, H4K20me2, and 53BP1. The combination of these drugs in VRK1 depleted cells resulted in an increase of glioblastoma cell death detected by annexin V and the processing of PARP-1 and caspase-3. Conclusion Depletion of the chromatin kinase VRK1 promotes tumor cell death at lower doses of a combination of temozolomide and olaparib treatments, and can be a novel alternative target for therapies based on synthetic lethality.
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Affiliation(s)
- Elena Navarro-Carrasco
- Molecular Mechanisms of Cancer Program, Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Salamanca, Salamanca, Spain.,Instituto de Investigación Biomédica de Salamanca-IBSAL, Hospital Universitario de Salamanca, Salamanca, Spain
| | - Pedro A Lazo
- Molecular Mechanisms of Cancer Program, Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad de Salamanca, Salamanca, Spain.,Instituto de Investigación Biomédica de Salamanca-IBSAL, Hospital Universitario de Salamanca, Salamanca, Spain
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165
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Rossiter NJ, Huggler KS, Adelmann CH, Keys HR, Soens RW, Sabatini DM, Cantor JR. CRISPR screens in physiologic medium reveal conditionally essential genes in human cells. Cell Metab 2021; 33:1248-1263.e9. [PMID: 33651980 PMCID: PMC8172426 DOI: 10.1016/j.cmet.2021.02.005] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 11/04/2020] [Accepted: 02/03/2021] [Indexed: 12/18/2022]
Abstract
Forward genetic screens across hundreds of cancer cell lines have started to define the genetic dependencies of proliferating human cells and how these vary by genotype and lineage. Most screens, however, have been carried out in culture media that poorly reflect metabolite availability in human blood. Here, we performed CRISPR-based screens in traditional versus human plasma-like medium (HPLM). Sets of conditionally essential genes in human cancer cell lines span several cellular processes and vary with both natural cell-intrinsic diversity and the combination of basal and serum components that comprise typical media. Notably, we traced the causes for each of three conditional CRISPR phenotypes to the availability of metabolites uniquely defined in HPLM versus conventional media. Our findings reveal the profound impact of medium composition on gene essentiality in human cells, and also suggest general strategies for using genetic screens in HPLM to uncover new cancer vulnerabilities and gene-nutrient interactions.
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Affiliation(s)
| | - Kimberly S Huggler
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Charles H Adelmann
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Heather R Keys
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Ross W Soens
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - David M Sabatini
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Jason R Cantor
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA; University of Wisconsin Carbone Cancer Center, Madison, WI 53705, USA.
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166
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Wainberg M, Kamber RA, Balsubramani A, Meyers RM, Sinnott-Armstrong N, Hornburg D, Jiang L, Chan J, Jian R, Gu M, Shcherbina A, Dubreuil MM, Spees K, Meuleman W, Snyder MP, Bassik MC, Kundaje A. A genome-wide atlas of co-essential modules assigns function to uncharacterized genes. Nat Genet 2021; 53:638-649. [PMID: 33859415 PMCID: PMC8763319 DOI: 10.1038/s41588-021-00840-z] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 03/09/2021] [Indexed: 02/01/2023]
Abstract
A central question in the post-genomic era is how genes interact to form biological pathways. Measurements of gene dependency across hundreds of cell lines have been used to cluster genes into 'co-essential' pathways, but this approach has been limited by ubiquitous false positives. In the present study, we develop a statistical method that enables robust identification of gene co-essentiality and yields a genome-wide set of functional modules. This atlas recapitulates diverse pathways and protein complexes, and predicts the functions of 108 uncharacterized genes. Validating top predictions, we show that TMEM189 encodes plasmanylethanolamine desaturase, a key enzyme for plasmalogen synthesis. We also show that C15orf57 encodes a protein that binds the AP2 complex, localizes to clathrin-coated pits and enables efficient transferrin uptake. Finally, we provide an interactive webtool for the community to explore our results, which establish co-essentiality profiling as a powerful resource for biological pathway identification and discovery of new gene functions.
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Affiliation(s)
- Michael Wainberg
- Department of Genetics, Stanford University, Stanford, CA, USA,Department of Computer Science, Stanford University, Stanford, CA, USA,These authors contributed equally: Michael Wainberg, Roarke A. Kamber, Akshay Balsubramani
| | - Roarke A. Kamber
- Department of Genetics, Stanford University, Stanford, CA, USA,These authors contributed equally: Michael Wainberg, Roarke A. Kamber, Akshay Balsubramani
| | - Akshay Balsubramani
- Department of Genetics, Stanford University, Stanford, CA, USA,These authors contributed equally: Michael Wainberg, Roarke A. Kamber, Akshay Balsubramani
| | - Robin M. Meyers
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Daniel Hornburg
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Lihua Jiang
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Joanne Chan
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Ruiqi Jian
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Mingxin Gu
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Anna Shcherbina
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Kaitlyn Spees
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | | | - Michael C. Bassik
- Department of Genetics, Stanford University, Stanford, CA, USA,Chemistry, Engineering, and Medicine for Human Health, Stanford University, Stanford, CA, USA,Correspondence and requests for materials should be addressed to M.C.B. or A.K. ;
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, CA, USA,Department of Computer Science, Stanford University, Stanford, CA, USA,Correspondence and requests for materials should be addressed to M.C.B. or A.K. ;
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167
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Kerselidou D, Dohai BS, Nelson DR, Daakour S, De Cock N, Hassoun ZAO, Kim DK, Olivet J, El Assal DC, Jaiswal A, Alzahmi A, Saha D, Pain C, Matthijssens F, Lemaitre P, Herfs M, Chapuis J, Ghesquiere B, Vertommen D, Kriechbaumer V, Knoops K, Lopez-Iglesias C, van Zandvoort M, Lambert JC, Hanson J, Desmet C, Thiry M, Lauersen KJ, Vidal M, Van Vlierberghe P, Dequiedt F, Salehi-Ashtiani K, Twizere JC. Alternative glycosylation controls endoplasmic reticulum dynamics and tubular extension in mammalian cells. SCIENCE ADVANCES 2021; 7:7/19/eabe8349. [PMID: 33962942 PMCID: PMC8104865 DOI: 10.1126/sciadv.abe8349] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 03/18/2021] [Indexed: 05/28/2023]
Abstract
The endoplasmic reticulum (ER) is a central eukaryotic organelle with a tubular network made of hairpin proteins linked by hydrolysis of guanosine triphosphate nucleotides. Among posttranslational modifications initiated at the ER level, glycosylation is the most common reaction. However, our understanding of the impact of glycosylation on the ER structure remains unclear. Here, we show that exostosin-1 (EXT1) glycosyltransferase, an enzyme involved in N-glycosylation, is a key regulator of ER morphology and dynamics. We have integrated multiomics and superresolution imaging to characterize the broad effect of EXT1 inactivation, including the ER shape-dynamics-function relationships in mammalian cells. We have observed that inactivating EXT1 induces cell enlargement and enhances metabolic switches such as protein secretion. In particular, suppressing EXT1 in mouse thymocytes causes developmental dysfunctions associated with the ER network extension. Last, our data illuminate the physical and functional aspects of the ER proteome-glycome-lipidome structure axis, with implications in biotechnology and medicine.
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Affiliation(s)
- Despoina Kerselidou
- Laboratory of Viral Interactomes, GIGA Institute, University of Liege, Liege, Belgium
- Laboratory of Gene expression and Cancer, GIGA Institute, University of Liege, Liege, Belgium
| | - Bushra Saeed Dohai
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE
| | - David R Nelson
- Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, UAE
| | - Sarah Daakour
- Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, UAE
| | - Nicolas De Cock
- TERRA Teaching and Research Centre, University of Liege, Liege, Belgium
| | - Zahra Al Oula Hassoun
- Laboratory of Gene expression and Cancer, GIGA Institute, University of Liege, Liege, Belgium
| | - Dae-Kyum Kim
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Julien Olivet
- Laboratory of Viral Interactomes, GIGA Institute, University of Liege, Liege, Belgium
| | - Diana C El Assal
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Ashish Jaiswal
- Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, UAE
| | - Amnah Alzahmi
- Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, UAE
| | - Deeya Saha
- Laboratory of Viral Interactomes, GIGA Institute, University of Liege, Liege, Belgium
- Laboratory of Gene expression and Cancer, GIGA Institute, University of Liege, Liege, Belgium
| | - Charlotte Pain
- Plant Cell Biology, Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Filip Matthijssens
- Department of Biomolecular Medicine and Center for Medical Genetics, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Pierre Lemaitre
- GIGA-I3 Unit, GIGA Institute, University of Liege, Liege, Belgium
| | - Michael Herfs
- GIGA-Cancer Unit, GIGA Institute, University of Liege, Liege, Belgium
| | - Julien Chapuis
- Laboratory of Excellence Distalz, INSERM Unit 1167, Pasteur Institute of Lille, Lille, France
| | - Bart Ghesquiere
- Metabolomics Expertise Center, Center for Cancer Biology, VIB Center for Cancer Biology, Leuven, Belgium
| | - Didier Vertommen
- de Duve Institute, Catholic University of Louvain, Brussels, Belgium
| | - Verena Kriechbaumer
- Plant Cell Biology, Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Kèvin Knoops
- Microscopy CORE Lab, Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, Netherlands
| | - Carmen Lopez-Iglesias
- Microscopy CORE Lab, Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, Netherlands
| | - Marc van Zandvoort
- Department of Cell Biology, School for Cardiovascular Diseases (CARIM), School for Nutrition and Translational Research in Metabolism (NUTRIM), School for Mental health and Neuroscience (MHeNS), and School for Oncology and Developmental Biology (GROW), Maastricht University, Maastricht, Netherlands
| | - Jean-Charles Lambert
- Laboratory of Excellence Distalz, INSERM Unit 1167, Pasteur Institute of Lille, Lille, France
| | - Julien Hanson
- GIGA-Molecular Pharmacology, University of Liege, Liege, Belgium
| | | | - Marc Thiry
- Laboratory of cell and tissue Biology, GIGA-Neurosciences, University of Liege, Liege, Belgium
| | - Kyle J Lauersen
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Marc Vidal
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Pieter Van Vlierberghe
- Department of Biomolecular Medicine and Center for Medical Genetics, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Franck Dequiedt
- Laboratory of Gene expression and Cancer, GIGA Institute, University of Liege, Liege, Belgium.
| | - Kourosh Salehi-Ashtiani
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE.
- Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, UAE
| | - Jean-Claude Twizere
- Laboratory of Viral Interactomes, GIGA Institute, University of Liege, Liege, Belgium.
- TERRA Teaching and Research Centre, University of Liege, Liege, Belgium
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
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168
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De Fusco C, Schimpl M, Börjesson U, Cheung T, Collie I, Evans L, Narasimhan P, Stubbs C, Vazquez-Chantada M, Wagner DJ, Grondine M, Sanders MG, Tentarelli S, Underwood E, Argyrou A, Smith JM, Lynch JT, Chiarparin E, Robb G, Bagal SK, Scott JS. Fragment-Based Design of a Potent MAT2a Inhibitor and in Vivo Evaluation in an MTAP Null Xenograft Model. J Med Chem 2021; 64:6814-6826. [PMID: 33900758 DOI: 10.1021/acs.jmedchem.1c00067] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
MAT2a is a methionine adenosyltransferase that synthesizes the essential metabolite S-adenosylmethionine (SAM) from methionine and ATP. Tumors bearing the co-deletion of p16 and MTAP genes have been shown to be sensitive to MAT2a inhibition, making it an attractive target for treatment of MTAP-deleted cancers. A fragment-based lead generation campaign identified weak but efficient hits binding in a known allosteric site. By use of structure-guided design and systematic SAR exploration, the hits were elaborated through a merging and growing strategy into an arylquinazolinone series of potent MAT2a inhibitors. The selected in vivo tool compound 28 reduced SAM-dependent methylation events in cells and inhibited proliferation of MTAP-null cells in vitro. In vivo studies showed that 28 was able to induce antitumor response in an MTAP knockout HCT116 xenograft model.
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Affiliation(s)
- Claudia De Fusco
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Marianne Schimpl
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Ulf Börjesson
- Discovery Sciences, R&D, AstraZeneca, Gothenburg SE-431 83, Sweden
| | - Tony Cheung
- Oncology R&D, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Iain Collie
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Laura Evans
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | | | | | | | - David J Wagner
- Oncology R&D, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Michael Grondine
- Oncology R&D, AstraZeneca, Boston, Massachusetts 02451, United States
| | | | - Sharon Tentarelli
- Oncology R&D, AstraZeneca, Boston, Massachusetts 02451, United States
| | | | - Argyrides Argyrou
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - James M Smith
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - James T Lynch
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | | | - Graeme Robb
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Sharan K Bagal
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - James S Scott
- Oncology R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
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169
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Bleu M, Mermet-Meillon F, Apfel V, Barys L, Holzer L, Bachmann Salvy M, Lopes R, Amorim Monteiro Barbosa I, Delmas C, Hinniger A, Chau S, Kaufmann M, Haenni S, Berneiser K, Wahle M, Moravec I, Vissières A, Poetsch T, Ahrné E, Carte N, Voshol J, Bechter E, Hamon J, Meyerhofer M, Erdmann D, Fischer M, Stachyra T, Freuler F, Gutmann S, Fernández C, Schmelzle T, Naumann U, Roma G, Lawrenson K, Nieto-Oberhuber C, Cobos-Correa A, Ferretti S, Schübeler D, Galli GG. PAX8 and MECOM are interaction partners driving ovarian cancer. Nat Commun 2021; 12:2442. [PMID: 33903593 PMCID: PMC8076227 DOI: 10.1038/s41467-021-22708-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 03/26/2021] [Indexed: 11/25/2022] Open
Abstract
The transcription factor PAX8 is critical for the development of the thyroid and urogenital system. Comprehensive genomic screens furthermore indicate an additional oncogenic role for PAX8 in renal and ovarian cancers. While a plethora of PAX8-regulated genes in different contexts have been proposed, we still lack a mechanistic understanding of how PAX8 engages molecular complexes to drive disease-relevant oncogenic transcriptional programs. Here we show that protein isoforms originating from the MECOM locus form a complex with PAX8. These include MDS1-EVI1 (also called PRDM3) for which we map its interaction with PAX8 in vitro and in vivo. We show that PAX8 binds a large number of genomic sites and forms transcriptional hubs. At a subset of these, PAX8 together with PRDM3 regulates a specific gene expression module involved in adhesion and extracellular matrix. This gene module correlates with PAX8 and MECOM expression in large scale profiling of cell lines, patient-derived xenografts (PDXs) and clinical cases and stratifies gynecological cancer cases with worse prognosis. PRDM3 is amplified in ovarian cancers and we show that the MECOM locus and PAX8 sustain in vivo tumor growth, further supporting that the identified function of the MECOM locus underlies PAX8-driven oncogenic functions in ovarian cancer.
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Affiliation(s)
- Melusine Bleu
- Disease area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Fanny Mermet-Meillon
- Disease area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Verena Apfel
- Disease area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Louise Barys
- Disease area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Laura Holzer
- Disease area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | | | - Rui Lopes
- Disease area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | | | - Cecile Delmas
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Alexandra Hinniger
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Suzanne Chau
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Markus Kaufmann
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Simon Haenni
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Karolin Berneiser
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
- Biozentrum, University of Basel, Basel, Switzerland
| | - Maria Wahle
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Ivana Moravec
- Analytical Sciences and Imaging, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Alexandra Vissières
- Analytical Sciences and Imaging, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Tania Poetsch
- Analytical Sciences and Imaging, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Erik Ahrné
- Analytical Sciences and Imaging, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Nathalie Carte
- Analytical Sciences and Imaging, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Johannes Voshol
- Analytical Sciences and Imaging, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Elisabeth Bechter
- Disease area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Jacques Hamon
- Disease area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Marco Meyerhofer
- Disease area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Dirk Erdmann
- Disease area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Matteo Fischer
- Disease area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Therese Stachyra
- Disease area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Felix Freuler
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Sascha Gutmann
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - César Fernández
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Tobias Schmelzle
- Disease area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Ulrike Naumann
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Guglielmo Roma
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Kate Lawrenson
- Cedars-Sinai Women's Cancer Program at the Samuel Oschin Cancer Center, Los Angeles, CA, USA
| | | | - Amanda Cobos-Correa
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Stephane Ferretti
- Disease area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Dirk Schübeler
- Friedrich Miescher Institute for Biomedical Research, University of Basel, Basel, Switzerland
- Faculty of Science, University of Basel, Basel, Switzerland
| | - Giorgio Giacomo Galli
- Disease area Oncology, Novartis Institutes for Biomedical Research, Basel, Switzerland.
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170
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Chang L, Ruiz P, Ito T, Sellers WR. Targeting pan-essential genes in cancer: Challenges and opportunities. Cancer Cell 2021; 39:466-479. [PMID: 33450197 PMCID: PMC8157671 DOI: 10.1016/j.ccell.2020.12.008] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 12/02/2020] [Accepted: 12/09/2020] [Indexed: 12/22/2022]
Abstract
Despite remarkable successes in the clinic, cancer targeted therapy development remains challenging and the failure rate is disappointingly high. This problem is partly due to the misapplication of the targeted therapy paradigm to therapeutics targeting pan-essential genes, which can result in therapeutics whereby efficacy is attenuated by dose-limiting toxicity. Here we summarize the key features of successful chemotherapy and targeted therapy agents, and use case studies to outline recurrent challenges to drug development efforts targeting pan-essential genes. Finally, we suggest strategies to avoid previous pitfalls for ongoing and future development of pan-essential therapeutics.
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Affiliation(s)
- Liang Chang
- Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Paloma Ruiz
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Takahiro Ito
- Broad Institute of Harvard and MIT, Cambridge, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - William R Sellers
- Broad Institute of Harvard and MIT, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
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171
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Kingsley LJ, He X, McNeill M, Nelson J, Nikulin V, Ma Z, Lu W, Zhou VW, Manuia M, Kreusch A, Gao MY, Witmer D, Vaillancourt MT, Lu M, Greenblatt S, Lee C, Vashisht A, Bender S, Spraggon G, Michellys PY, Jia Y, Haling JR, Lelais G. Structure-Based Design of Selective LONP1 Inhibitors for Probing In Vitro Biology. J Med Chem 2021; 64:4857-4869. [PMID: 33821636 DOI: 10.1021/acs.jmedchem.0c02152] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
LONP1 is an AAA+ protease that maintains mitochondrial homeostasis by removing damaged or misfolded proteins. Elevated activity and expression of LONP1 promotes cancer cell proliferation and resistance to apoptosis-inducing reagents. Despite the importance of LONP1 in human biology and disease, very few LONP1 inhibitors have been described in the literature. Herein, we report the development of selective boronic acid-based LONP1 inhibitors using structure-based drug design as well as the first structures of human LONP1 bound to various inhibitors. Our efforts led to several nanomolar LONP1 inhibitors with little to no activity against the 20S proteasome that serve as tool compounds to investigate LONP1 biology.
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Affiliation(s)
- Laura J Kingsley
- Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Dr., San Diego, California 92121, United States
| | - Xiaohui He
- Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Dr., San Diego, California 92121, United States
| | - Matthew McNeill
- Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Dr., San Diego, California 92121, United States
| | - John Nelson
- Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Dr., San Diego, California 92121, United States
| | - Victor Nikulin
- Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Dr., San Diego, California 92121, United States
| | - Zhiwei Ma
- Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Dr., San Diego, California 92121, United States
| | - Wenshuo Lu
- Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Dr., San Diego, California 92121, United States
| | - Vicki W Zhou
- Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Dr., San Diego, California 92121, United States
| | - Mari Manuia
- Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Dr., San Diego, California 92121, United States
| | - Andreas Kreusch
- Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Dr., San Diego, California 92121, United States
| | - Mu-Yun Gao
- Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Dr., San Diego, California 92121, United States
| | - Darbi Witmer
- Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Dr., San Diego, California 92121, United States
| | - Mei-Ting Vaillancourt
- Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Dr., San Diego, California 92121, United States
| | - Min Lu
- Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Dr., San Diego, California 92121, United States
| | - Sarah Greenblatt
- Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Dr., San Diego, California 92121, United States
| | - Christian Lee
- Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Dr., San Diego, California 92121, United States
| | - Ajay Vashisht
- Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Dr., San Diego, California 92121, United States
| | - Steven Bender
- Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Dr., San Diego, California 92121, United States
| | - Glen Spraggon
- Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Dr., San Diego, California 92121, United States
| | - Pierre-Yves Michellys
- Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Dr., San Diego, California 92121, United States
| | - Yong Jia
- Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Dr., San Diego, California 92121, United States
| | - Jacob R Haling
- Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Dr., San Diego, California 92121, United States
| | - Gérald Lelais
- Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Dr., San Diego, California 92121, United States
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172
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Cui X, Han L, Liu Y, Li Y, Sun W, Song B, Zhou W, Zhang Y, Wang H. siGCD: a web server to explore survival interaction of genes, cells and drugs in human cancers. Brief Bioinform 2021; 22:6210070. [PMID: 33822887 DOI: 10.1093/bib/bbab058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 01/19/2021] [Accepted: 02/12/2021] [Indexed: 11/13/2022] Open
Abstract
It is pivotal and remains challenge for cancer precision treatment to identify the survival outcome interactions between genes, cells and drugs. Here, we present siGCD, a web-based tool for analysis and visualization of the survival interaction of Genes, Cells and Drugs in human cancers. siGCD utilizes the cancer heterogeneity to simulate the manipulated gene expression, cell infiltration and drug treatment, which overcomes the data and experimental limitations. To illustrate the performance of siGCD, we identified the survival interaction partners of EGFR (gene level), T cells (cell level) and sorafenib (drug level), and our prediction was consistent with previous reports. Moreover, we validate the synergistic effect of regorafenib and glyburide, and found that glyburide could significantly improve the regorafenib response. These results demonstrate that siGCD could benefit cancer precision medicine in a wide range of advantageous application scenarios including gene regulatory network construction, immune cell regulatory gene identification, drug (especially multiple target drugs) response biomarker screening and combination therapeutic design.
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Affiliation(s)
- XiuLiang Cui
- National Center for Liver Cancer, the Second Military Medical University, Shanghai 200438, China
| | - Lu Han
- Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China.,State Key Laboratory of Toxicology and Medical Countermeasures, Beijing China
| | - Yang Liu
- Institute for Hepatology, The Second Affiliated Hospital, South University of Science and Technology, 29 Bulan Road, Longgang District, Shenzhen 518112, China
| | - Ying Li
- Department of Pharmacy, Eastern Hepatobiliary Surgery Hospital, the Second Military Medical University, Shanghai 200438, China
| | - Wen Sun
- National Center for Liver Cancer, the Second Military Medical University, Shanghai 200438, China
| | - Bin Song
- Department of Pancreatic Surgery, Changhai Hospital, Second Military Medical University, Shanghai 200438, China
| | - Wenxia Zhou
- Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China.,State Key Laboratory of Toxicology and Medical Countermeasures, Beijing China
| | - Yongxiang Zhang
- Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China.,State Key Laboratory of Toxicology and Medical Countermeasures, Beijing China
| | - Hongyang Wang
- National Center for Liver Cancer, the Second Military Medical University, Shanghai 200438, China.,International Cooperation Laboratory on Signal Transduction, Eastern Hepatobiliary Surgery Hospital/Institute, the Second Military Medical University, 200438, Shanghai, China
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173
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Wu X, Yang X, Xiong Y, Li R, Ito T, Ahmed TA, Karoulia Z, Adamopoulos C, Wang H, Wang L, Xie L, Liu J, Ueberheide B, Aaronson SA, Chen X, Buchanan SG, Sellers WR, Jin J, Poulikakos PI. Distinct CDK6 complexes determine tumor cell response to CDK4/6 inhibitors and degraders. NATURE CANCER 2021; 2:429-443. [PMID: 34568836 PMCID: PMC8462800 DOI: 10.1038/s43018-021-00174-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 01/21/2021] [Indexed: 12/26/2022]
Abstract
CDK4/6 inhibitors (CDK4/6i) are effective in metastatic breast cancer, but they have been only modestly effective in most other tumor types. Here we show that tumors expressing low CDK6 rely on CDK4 function, and are exquisitely sensitive to CDK4/6i. In contrast, tumor cells expressing both CDK4 and CDK6 have increased reliance on CDK6 to ensure cell cycle progression. We discovered that CDK4/6i and CDK4/6 degraders potently bind and inhibit CDK6 selectively in tumors in which CDK6 is highly thermo-unstable and strongly associated with the HSP90/CDC37 complex. In contrast, CDK4/6i and CDK4/6 degraders are ineffective in antagonizing tumor cells expressing thermostable CDK6, due to their weaker binding to CDK6 in these cells. Thus, we uncover a general mechanism of intrinsic resistance to CDK4/6i and CDK4/6i-derived degraders and the need for novel inhibitors targeting the CDK4/6i-resistant, thermostable form of CDK6 for application as cancer therapeutics.
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Affiliation(s)
- Xuewei Wu
- Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Xiaobao Yang
- Department of Pharmacological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yan Xiong
- Department of Pharmacological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ruitong Li
- The Broad Institute of Harvard and MIT, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Takahiro Ito
- The Broad Institute of Harvard and MIT, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Tamer A Ahmed
- Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zoi Karoulia
- Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Christos Adamopoulos
- Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hong Wang
- Eli Lilly and Company, Indianapolis, IN, USA
| | - Li Wang
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, USA
| | - Ling Xie
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, USA
| | - Jing Liu
- Department of Pharmacological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Beatrix Ueberheide
- Department of Biochemistry and Molecular Pharmacology, New York University, New York, NY, USA
| | - Stuart A Aaronson
- Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Xian Chen
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, USA
| | | | - William R Sellers
- The Broad Institute of Harvard and MIT, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Jian Jin
- Department of Pharmacological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Poulikos I Poulikakos
- Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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174
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Dharia NV, Kugener G, Guenther LM, Malone CF, Durbin AD, Hong AL, Howard TP, Bandopadhayay P, Wechsler CS, Fung I, Warren AC, Dempster JM, Krill-Burger JM, Paolella BR, Moh P, Jha N, Tang A, Montgomery P, Boehm JS, Hahn WC, Roberts CWM, McFarland JM, Tsherniak A, Golub TR, Vazquez F, Stegmaier K. A first-generation pediatric cancer dependency map. Nat Genet 2021; 53:529-538. [PMID: 33753930 PMCID: PMC8049517 DOI: 10.1038/s41588-021-00819-w] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 02/16/2021] [Indexed: 01/31/2023]
Abstract
Exciting therapeutic targets are emerging from CRISPR-based screens of high mutational-burden adult cancers. A key question, however, is whether functional genomic approaches will yield new targets in pediatric cancers, known for remarkably few mutations, which often encode proteins considered challenging drug targets. To address this, we created a first-generation pediatric cancer dependency map representing 13 pediatric solid and brain tumor types. Eighty-two pediatric cancer cell lines were subjected to genome-scale CRISPR-Cas9 loss-of-function screening to identify genes required for cell survival. In contrast to the finding that pediatric cancers harbor fewer somatic mutations, we found a similar complexity of genetic dependencies in pediatric cancer cell lines compared to that in adult models. Findings from the pediatric cancer dependency map provide preclinical support for ongoing precision medicine clinical trials. The vulnerabilities observed in pediatric cancers were often distinct from those in adult cancer, indicating that repurposing adult oncology drugs will be insufficient to address childhood cancers.
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Affiliation(s)
- Neekesh V Dharia
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Guillaume Kugener
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Lillian M Guenther
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Clare F Malone
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Adam D Durbin
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Oncology, Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Andrew L Hong
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Pediatrics, Emory University and Department of Hematology and Oncology, Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Thomas P Howard
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Pratiti Bandopadhayay
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Caroline S Wechsler
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Iris Fung
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | | | | | - Phoebe Moh
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- University of Maryland, College Park, MD, USA
| | - Nishant Jha
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Andrew Tang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Jesse S Boehm
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - William C Hahn
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Charles W M Roberts
- Department of Oncology, Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | | | - Todd R Golub
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Francisca Vazquez
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Harvard Medical School, Boston, MA, USA.
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175
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Cupido T, Jones NH, Grasso MJ, Pisa R, Kapoor TM. A chemical genetics approach to examine the functions of AAA proteins. Nat Struct Mol Biol 2021; 28:388-397. [PMID: 33782614 DOI: 10.1038/s41594-021-00575-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 02/18/2021] [Indexed: 12/12/2022]
Abstract
The structural conservation across the AAA (ATPases associated with diverse cellular activities) protein family makes designing selective chemical inhibitors challenging. Here, we identify a triazolopyridine-based fragment that binds the AAA domain of human katanin, a microtubule-severing protein. We have developed a model for compound binding and designed ASPIR-1 (allele-specific, proximity-induced reactivity-based inhibitor-1), a cell-permeable compound that selectively inhibits katanin with an engineered cysteine mutation. Only in cells expressing mutant katanin does ASPIR-1 treatment increase the accumulation of CAMSAP2 at microtubule minus ends, confirming specific on-target cellular activity. Importantly, ASPIR-1 also selectively inhibits engineered cysteine mutants of human VPS4B and FIGL1-AAA proteins, involved in organelle dynamics and genome stability, respectively. Structural studies confirm our model for compound binding at the AAA ATPase site and the proximity-induced reactivity-based inhibition. Together, our findings suggest a chemical genetics approach to decipher AAA protein functions across essential cellular processes and to test hypotheses for developing therapeutics.
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Affiliation(s)
- Tommaso Cupido
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY, USA
| | - Natalie H Jones
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY, USA.,Tri-Institutional PhD Program in Chemical Biology, The Rockefeller University, New York, NY, USA
| | - Michael J Grasso
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY, USA
| | - Rudolf Pisa
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY, USA.,Tri-Institutional PhD Program in Chemical Biology, The Rockefeller University, New York, NY, USA
| | - Tarun M Kapoor
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY, USA.
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176
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Yip HYK, Papa A. Signaling Pathways in Cancer: Therapeutic Targets, Combinatorial Treatments, and New Developments. Cells 2021; 10:659. [PMID: 33809714 PMCID: PMC8002322 DOI: 10.3390/cells10030659] [Citation(s) in RCA: 193] [Impact Index Per Article: 64.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/12/2021] [Accepted: 03/13/2021] [Indexed: 12/13/2022] Open
Abstract
Molecular alterations in cancer genes and associated signaling pathways are used to inform new treatments for precision medicine in cancer. Small molecule inhibitors and monoclonal antibodies directed at relevant cancer-related proteins have been instrumental in delivering successful treatments of some blood malignancies (e.g., imatinib with chronic myelogenous leukemia (CML)) and solid tumors (e.g., tamoxifen with ER positive breast cancer and trastuzumab for HER2-positive breast cancer). However, inherent limitations such as drug toxicity, as well as acquisition of de novo or acquired mechanisms of resistance, still cause treatment failure. Here we provide an up-to-date review of the successes and limitations of current targeted therapies for cancer treatment and highlight how recent technological advances have provided a new level of understanding of the molecular complexity underpinning resistance to cancer therapies. We also raise three basic questions concerning cancer drug discovery based on molecular markers and alterations of selected signaling pathways, and further discuss how combination therapies may become the preferable approach over monotherapy for cancer treatments. Finally, we consider novel therapeutic developments that may complement drug delivery and significantly improve clinical response and outcomes of cancer patients.
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Affiliation(s)
| | - Antonella Papa
- Cancer Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia;
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177
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Crowe MS, Zavorotinskaya T, Voliva CF, Shirley MD, Wang Y, Ruddy DA, Rakiec DP, Engelman JA, Stuart DD, Freeman AK. RAF-Mutant Melanomas Differentially Depend on ERK2 Over ERK1 to Support Aberrant MAPK Pathway Activation and Cell Proliferation. Mol Cancer Res 2021; 19:1063-1075. [PMID: 33707308 DOI: 10.1158/1541-7786.mcr-20-1022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 02/11/2021] [Accepted: 03/05/2021] [Indexed: 11/16/2022]
Abstract
Half of advanced human melanomas are driven by mutant BRAF and dependent on MAPK signaling. Interestingly, the results of three independent genetic screens highlight a dependency of BRAF-mutant melanoma cell lines on BRAF and ERK2, but not ERK1. ERK2 is expressed higher in melanoma compared with other cancer types and higher than ERK1 within melanoma. However, ERK1 and ERK2 are similarly required in primary human melanocytes transformed with mutant BRAF and are expressed at a similar, lower amount compared with established cancer cell lines. ERK1 can compensate for ERK2 loss as seen by expression of ERK1 rescuing the proliferation arrest mediated by ERK2 loss (both by shRNA or inhibition by an ERK inhibitor). ERK2 knockdown, as opposed to ERK1 knockdown, led to more robust suppression of MAPK signaling as seen by RNA-sequencing, qRT-PCR, and Western blot analysis. In addition, treatment with MAPK pathway inhibitors led to gene expression changes that closely resembled those seen upon knockdown of ERK2 but not ERK1. Together, these data demonstrate that ERK2 drives BRAF-mutant melanoma gene expression and proliferation as a function of its higher expression compared with ERK1. Selective inhibition of ERK2 for the treatment of melanomas may spare the toxicity associated with pan-ERK inhibition in normal tissues. IMPLICATIONS: BRAF-mutant melanomas overexpress and depend on ERK2 but not ERK1, suggesting that ERK2-selective inhibition may be toxicity sparing.
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Affiliation(s)
- Matthew S Crowe
- Oncology, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | | | - Charles F Voliva
- Oncology, Novartis Institutes for BioMedical Research, Emeryville, California
| | - Matthew D Shirley
- Oncology, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Yanqun Wang
- Oncology, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - David A Ruddy
- Oncology, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Daniel P Rakiec
- Oncology, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Jeffery A Engelman
- Oncology, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Darrin D Stuart
- Oncology, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts
| | - Alyson K Freeman
- Oncology, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts.
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178
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Pacini C, Dempster JM, Boyle I, Gonçalves E, Najgebauer H, Karakoc E, van der Meer D, Barthorpe A, Lightfoot H, Jaaks P, McFarland JM, Garnett MJ, Tsherniak A, Iorio F. Integrated cross-study datasets of genetic dependencies in cancer. Nat Commun 2021; 12:1661. [PMID: 33712601 PMCID: PMC7955067 DOI: 10.1038/s41467-021-21898-7] [Citation(s) in RCA: 118] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/18/2021] [Indexed: 01/14/2023] Open
Abstract
CRISPR-Cas9 viability screens are increasingly performed at a genome-wide scale across large panels of cell lines to identify new therapeutic targets for precision cancer therapy. Integrating the datasets resulting from these studies is necessary to adequately represent the heterogeneity of human cancers and to assemble a comprehensive map of cancer genetic vulnerabilities. Here, we integrated the two largest public independent CRISPR-Cas9 screens performed to date (at the Broad and Sanger institutes) by assessing, comparing, and selecting methods for correcting biases due to heterogeneous single-guide RNA efficiency, gene-independent responses to CRISPR-Cas9 targeting originated from copy number alterations, and experimental batch effects. Our integrated datasets recapitulate findings from the individual datasets, provide greater statistical power to cancer- and subtype-specific analyses, unveil additional biomarkers of gene dependency, and improve the detection of common essential genes. We provide the largest integrated resources of CRISPR-Cas9 screens to date and the basis for harmonizing existing and future functional genetics datasets.
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Affiliation(s)
- Clare Pacini
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | | | - Emanuel Gonçalves
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Hanna Najgebauer
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
| | - Emre Karakoc
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Andrew Barthorpe
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Howard Lightfoot
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Patricia Jaaks
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Mathew J Garnett
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Francesco Iorio
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, UK.
- Human Technopole, Milano, Italy.
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179
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Marjon K, Kalev P, Marks K. Cancer Dependencies: PRMT5 and MAT2A in MTAP/p16-Deleted Cancers. ANNUAL REVIEW OF CANCER BIOLOGY 2021. [DOI: 10.1146/annurev-cancerbio-030419-033444] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Discovery of targeted therapies that selectively exploit the genetic inactivation of specific tumor suppressors remains a major challenge. This includes the prevalent deletion of the CDKN2A/ MTAP locus, which was first reported nearly 40 years ago. The more recent advent of RNA interference and functional genomic screening technologies led to the identification of hidden collateral lethalities occurring with passenger deletions of MTAP in cancer cells. In particular, small-molecule inhibition of the type II arginine methyltransferase PRMT5 and the S-adenosylmethionine-producing enzyme MAT2A each presents a precision medicine approach for the treatment of patients whose tumors have homozygous loss of MTAP. In this review, we highlight key aspects of MTAP, PRMT5, and MAT2A biology to provide a conceptual framework for developing novel therapeutic strategies in tumors with MTAP deletion and to summarize ongoing efforts to drug PRMT5 and MAT2A.
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Affiliation(s)
- Katya Marjon
- Agios Pharmaceuticals, Cambridge, Massachusetts 02139, USA
| | - Peter Kalev
- Agios Pharmaceuticals, Cambridge, Massachusetts 02139, USA
| | - Kevin Marks
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
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180
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Jaiswal A, Gautam P, Pietilä EA, Timonen S, Nordström N, Akimov Y, Sipari N, Tanoli Z, Fleischer T, Lehti K, Wennerberg K, Aittokallio T. Multi-modal meta-analysis of cancer cell line omics profiles identifies ECHDC1 as a novel breast tumor suppressor. Mol Syst Biol 2021; 17:e9526. [PMID: 33750001 PMCID: PMC7983037 DOI: 10.15252/msb.20209526] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 02/17/2021] [Accepted: 02/19/2021] [Indexed: 12/12/2022] Open
Abstract
Molecular and functional profiling of cancer cell lines is subject to laboratory-specific experimental practices and data analysis protocols. The current challenge therefore is how to make an integrated use of the omics profiles of cancer cell lines for reliable biological discoveries. Here, we carried out a systematic analysis of nine types of data modalities using meta-analysis of 53 omics studies across 12 research laboratories for 2,018 cell lines. To account for a relatively low consistency observed for certain data modalities, we developed a robust data integration approach that identifies reproducible signals shared among multiple data modalities and studies. We demonstrated the power of the integrative analyses by identifying a novel driver gene, ECHDC1, with tumor suppressive role validated both in breast cancer cells and patient tumors. The multi-modal meta-analysis approach also identified synthetic lethal partners of cancer drivers, including a co-dependency of PTEN deficient endometrial cancer cells on RNA helicases.
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Affiliation(s)
- Alok Jaiswal
- Institute for Molecular Medicine Finland (FIMM)Helsinki Institute of Life Science (HiLIFE)University of HelsinkiHelsinkiFinland
- Present address:
The Broad Institute of MIT and HarvardCambridgeMAUSA
| | - Prson Gautam
- Institute for Molecular Medicine Finland (FIMM)Helsinki Institute of Life Science (HiLIFE)University of HelsinkiHelsinkiFinland
| | - Elina A Pietilä
- Individualized Drug Therapy, Research Programs UnitUniversity of HelsinkiHelsinkiFinland
| | - Sanna Timonen
- Institute for Molecular Medicine Finland (FIMM)Helsinki Institute of Life Science (HiLIFE)University of HelsinkiHelsinkiFinland
- Hematology Research Unit HelsinkiUniversity of Helsinki and Helsinki University Hospital Comprehensive Cancer CenterHelsinkiFinland
- Translational Immunology Research Program and Department of Clinical Chemistry and HematologyUniversity of HelsinkiHelsinkiFinland
| | - Nora Nordström
- Institute for Molecular Medicine Finland (FIMM)Helsinki Institute of Life Science (HiLIFE)University of HelsinkiHelsinkiFinland
| | - Yevhen Akimov
- Institute for Molecular Medicine Finland (FIMM)Helsinki Institute of Life Science (HiLIFE)University of HelsinkiHelsinkiFinland
| | - Nina Sipari
- Viikki Metabolomics UnitHelsinki Institute of Life Science (HiLIFE)University of HelsinkiHelsinkiFinland
| | - Ziaurrehman Tanoli
- Institute for Molecular Medicine Finland (FIMM)Helsinki Institute of Life Science (HiLIFE)University of HelsinkiHelsinkiFinland
| | - Thomas Fleischer
- Department of Cancer GeneticsInstitute for Cancer ResearchOslo University HospitalOsloNorway
| | - Kaisa Lehti
- Individualized Drug Therapy, Research Programs UnitUniversity of HelsinkiHelsinkiFinland
- Department of Microbiology, Tumor and Cell BiologyKarolinska InstitutetStockholmSweden
- Department of Biomedical Laboratory ScienceNorwegian University of Science and TechnologyTrondheimNorway
| | - Krister Wennerberg
- Institute for Molecular Medicine Finland (FIMM)Helsinki Institute of Life Science (HiLIFE)University of HelsinkiHelsinkiFinland
- Biotech Research & Innovation Centre (BRIC) and Novo Nordisk Foundation Center for Stem Cell Biology (DanStem)University of CopenhagenCopenhagenDenmark
| | - Tero Aittokallio
- Institute for Molecular Medicine Finland (FIMM)Helsinki Institute of Life Science (HiLIFE)University of HelsinkiHelsinkiFinland
- Department of Cancer GeneticsInstitute for Cancer ResearchOslo University HospitalOsloNorway
- Department of Mathematics and StatisticsUniversity of TurkuTurkuFinland
- Oslo Centre for Biostatistics and Epidemiology (OCBE)University of OsloOsloNorway
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181
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Thompson NA, Ranzani M, van der Weyden L, Iyer V, Offord V, Droop A, Behan F, Gonçalves E, Speak A, Iorio F, Hewinson J, Harle V, Robertson H, Anderson E, Fu B, Yang F, Zagnoli-Vieira G, Chapman P, Del Castillo Velasco-Herrera M, Garnett MJ, Jackson SP, Adams DJ. Combinatorial CRISPR screen identifies fitness effects of gene paralogues. Nat Commun 2021; 12:1302. [PMID: 33637726 PMCID: PMC7910459 DOI: 10.1038/s41467-021-21478-9] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 01/25/2021] [Indexed: 12/15/2022] Open
Abstract
Genetic redundancy has evolved as a way for human cells to survive the loss of genes that are single copy and essential in other organisms, but also allows tumours to survive despite having highly rearranged genomes. In this study we CRISPR screen 1191 gene pairs, including paralogues and known and predicted synthetic lethal interactions to identify 105 gene combinations whose co-disruption results in a loss of cellular fitness. 27 pairs influence fitness across multiple cell lines including the paralogues FAM50A/FAM50B, two genes of unknown function. Silencing of FAM50B occurs across a range of tumour types and in this context disruption of FAM50A reduces cellular fitness whilst promoting micronucleus formation and extensive perturbation of transcriptional programmes. Our studies reveal the fitness effects of FAM50A/FAM50B in cancer cells.
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Affiliation(s)
- Nicola A Thompson
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Marco Ranzani
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | | | - Vivek Iyer
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Victoria Offord
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Alastair Droop
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Fiona Behan
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Emanuel Gonçalves
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Anneliese Speak
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Francesco Iorio
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
- Human Technopole, Milano, Italy
| | - James Hewinson
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Victoria Harle
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Holly Robertson
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | | | - Beiyuan Fu
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Fengtang Yang
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | | | - Phil Chapman
- Cancer Research UK, Manchester Institute, Manchester, UK
| | | | - Mathew J Garnett
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | | | - David J Adams
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK.
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182
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Abstract
Synthetic lethality is emerging as an important cancer therapeutic paradigm, while the comprehensive selective treatment opportunities for various tumors have not yet been explored. We develop the Synthetic Lethality Knowledge Graph (SLKG), presenting the tumor therapy landscape of synthetic lethality (SL) and synthetic dosage lethality (SDL). SLKG integrates the large-scale entity of different tumors, drugs and drug targets by exploring a comprehensive set of SL and SDL pairs. The overall therapy landscape is prioritized to identify the best repurposable drug candidates and drug combinations with literature supports, in vitro pharmacologic evidence or clinical trial records. Finally, cladribine, an FDA-approved multiple sclerosis treatment drug, is selected and identified as a repurposable drug for treating melanoma with CDKN2A mutation by in vitro validation, serving as a demonstrating SLKG utility example for novel tumor therapy discovery. Collectively, SLKG forms the computational basis to uncover cancer-specific susceptibilities and therapy strategies based on the principle of synthetic lethality. Various methods have been proposed to identify synthetic lethality interactions, but selective treatment opportunities for various tumors have not yet been explored. Here, the authors develop the Synthetic Lethality Knowledge Graph webserver (SLKG, http://www.slkg.net) to explore the comprehensive tumor therapy landscape and uncover cancer-specific susceptibilities based on the principle of synthetic lethality.
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183
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Siddiqui FA, Parkkola H, Vukic V, Oetken-Lindholm C, Jaiswal A, Kiriazis A, Pavic K, Aittokallio T, Salminen TA, Abankwa D. Novel Small Molecule Hsp90/Cdc37 Interface Inhibitors Indirectly Target K-Ras-Signaling. Cancers (Basel) 2021; 13:927. [PMID: 33672199 PMCID: PMC7927014 DOI: 10.3390/cancers13040927] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/12/2021] [Accepted: 02/17/2021] [Indexed: 12/23/2022] Open
Abstract
The ATP-competitive inhibitors of Hsp90 have been tested predominantly in kinase addicted cancers; however, they have had limited success. A mechanistic connection between Hsp90 and oncogenic K-Ras is not known. Here, we show that K-Ras selectivity is enabled by the loss of the K-Ras membrane nanocluster modulator galectin-3 downstream of the Hsp90 client HIF-1α. This mechanism suggests a higher drug sensitivity in the context of KRAS mutant, HIF-1α-high and/or Gal3-high cancer cells, such as those found, in particular, in pancreatic adenocarcinoma. The low toxicity of conglobatin further indicates a beneficial on-target toxicity profile for Hsp90/Cdc37 interface inhibitors. We therefore computationally screened >7 M compounds, and identified four novel small molecules with activities of 4 μM-44 μM in vitro. All of the compounds were K-Ras selective, and potently decreased the Hsp90 client protein levels without inducing the heat shock response. Moreover, they all inhibited the 2D proliferation of breast, pancreatic, and lung cancer cell lines. The most active compounds from each scaffold, furthermore, significantly blocked 3D spheroids and the growth of K-Ras-dependent microtumors. We foresee new opportunities for improved Hsp90/Cdc37 interface inhibitors in cancer and other aging-associated diseases.
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Affiliation(s)
- Farid Ahmad Siddiqui
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland; (F.A.S.); (H.P.); (V.V.); (C.O.-L.); (A.K.)
| | - Hanna Parkkola
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland; (F.A.S.); (H.P.); (V.V.); (C.O.-L.); (A.K.)
| | - Vladimir Vukic
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland; (F.A.S.); (H.P.); (V.V.); (C.O.-L.); (A.K.)
- Faculty of Technology, University of Novi Sad, 21000 Novi Sad, Serbia
| | - Christina Oetken-Lindholm
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland; (F.A.S.); (H.P.); (V.V.); (C.O.-L.); (A.K.)
| | - Alok Jaiswal
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 00014 Helsinki, Finland; (A.J.); (T.A.)
| | - Alexandros Kiriazis
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland; (F.A.S.); (H.P.); (V.V.); (C.O.-L.); (A.K.)
| | - Karolina Pavic
- Cancer Cell Biology and Drug Discovery Group, Department of Life Sciences and Medicine, University of Luxembourg, 4362 Esch-sur-Alzette, Luxembourg;
| | - Tero Aittokallio
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 00014 Helsinki, Finland; (A.J.); (T.A.)
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, N-0310 Oslo, Norway
- Centre for Biostatistics and Epidemiology (OCBE), Faculty of Medicine, University of Oslo, N-0372 Oslo, Norway
| | - Tiina A. Salminen
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland;
| | - Daniel Abankwa
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, 20520 Turku, Finland; (F.A.S.); (H.P.); (V.V.); (C.O.-L.); (A.K.)
- Cancer Cell Biology and Drug Discovery Group, Department of Life Sciences and Medicine, University of Luxembourg, 4362 Esch-sur-Alzette, Luxembourg;
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184
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Towards the routine use of in silico screenings for drug discovery using metabolic modelling. Biochem Soc Trans 2021; 48:955-969. [PMID: 32369553 PMCID: PMC7329353 DOI: 10.1042/bst20190867] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 04/01/2020] [Accepted: 04/06/2020] [Indexed: 12/12/2022]
Abstract
Currently, the development of new effective drugs for cancer therapy is not only hindered by development costs, drug efficacy, and drug safety but also by the rapid occurrence of drug resistance in cancer. Hence, new tools are needed to study the underlying mechanisms in cancer. Here, we discuss the current use of metabolic modelling approaches to identify cancer-specific metabolism and find possible new drug targets and drugs for repurposing. Furthermore, we list valuable resources that are needed for the reconstruction of cancer-specific models by integrating various available datasets with genome-scale metabolic reconstructions using model-building algorithms. We also discuss how new drug targets can be determined by using gene essentiality analysis, an in silico method to predict essential genes in a given condition such as cancer and how synthetic lethality studies could greatly benefit cancer patients by suggesting drug combinations with reduced side effects.
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185
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Taha-Mehlitz S, Bianco G, Coto-Llerena M, Kancherla V, Bantug GR, Gallon J, Ercan C, Panebianco F, Eppenberger-Castori S, von Strauss M, Staubli S, Bolli M, Peterli R, Matter MS, Terracciano LM, von Flüe M, Ng CK, Soysal SD, Kollmar O, Piscuoglio S. Adenylosuccinate lyase is oncogenic in colorectal cancer by causing mitochondrial dysfunction and independent activation of NRF2 and mTOR-MYC-axis. Am J Cancer Res 2021; 11:4011-4029. [PMID: 33754045 PMCID: PMC7977451 DOI: 10.7150/thno.50051] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 01/12/2021] [Indexed: 12/11/2022] Open
Abstract
Rationale: Adenylosuccinate lyase (ADSL) is an essential enzyme for de novo purine biosynthesis. Here we sought to investigate the putative role of ADSL in colorectal carcinoma (CRC) carcinogenesis and response to antimetabolites. Methods: ADSL expression levels were assessed by immunohistochemistry or retrieved from The Cancer Genome Atlas (TCGA) dataset. The effects of ADSL silencing or overexpression were evaluated on CRC cell proliferation, cell migration and cell-cycle. In vivo tumor growth was assessed by the chicken chorioallantoic membrane (CAM). Transfected cell lines or patient-derived organoids (PDO) were treated with 5-fluorouracil (5-FU) and 6-mercaptopurine (6-MP) and drug response was correlated with ADSL expression levels. Metabolomic and transcriptomic profiling were performed to identify dysregulated pathways and ADSL downstream effectors. Mitochondrial respiration and glycolytic capacity were measured using Seahorse; mitochondrial membrane potential and the accumulation of ROS were measured by FACS using MitoTracker Red and MitoSOX staining, respectively. Activation of canonical pathways was assessed by immunohistochemistry and immunoblotting. Results: ADSL expression is significantly increased in CRC tumors compared to non-tumor tissue. ADSL-high CRCs show upregulation of genes involved in DNA synthesis, DNA repair and cell cycle. Accordingly, ADSL overexpression accelerated progression through the cell cycle and significantly increased proliferation and migration in CRC cell lines. Additionally, ADSL expression increased tumor growth in vivo and sensitized CRCs to 6-MP in vitro, ex vivo (PDOs) and in vivo (CAM model). ADSL exerts its oncogenic function by affecting mitochondrial function via alteration of the TCA cycle and impairment of mitochondrial respiration. The KEAP1-NRF2 and mTORC1-cMyc axis are independently activated upon ADSL overexpression and may favor the survival and proliferation of ROS-accumulating cells, favoring DNA damage and tumorigenesis. Conclusions: Our results suggest that ADSL is a novel oncogene in CRC, modulating mitochondrial function, metabolism and oxidative stress, thus promoting cell cycle progression, proliferation and migration. Our results also suggest that ADSL is a predictive biomarker of response to 6-mercaptopurine in the pre-clinical setting.
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186
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Apfel V, Begue D, Cordo' V, Holzer L, Martinuzzi L, Buhles A, Kerr G, Barbosa I, Naumann U, Piquet M, Ruddy D, Weiss A, Ferretti S, Almeida R, Bonenfant D, Tordella L, Galli GG. Therapeutic Assessment of Targeting ASNS Combined with l-Asparaginase Treatment in Solid Tumors and Investigation of Resistance Mechanisms. ACS Pharmacol Transl Sci 2021; 4:327-337. [PMID: 33615182 DOI: 10.1021/acsptsci.0c00196] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Indexed: 11/29/2022]
Abstract
Asparagine deprivation by l-asparaginase (L-ASNase) is an effective therapeutic strategy in acute lymphoblastic leukemia, with resistance occurring due to upregulation of ASNS, the only human enzyme synthetizing asparagine (Annu. Rev. Biochem. 2006, 75 (1), 629-654). l-Asparaginase efficacy in solid tumors is limited by dose-related toxicities (OncoTargets and Therapy 2017, pp 1413-1422). Large-scale loss of function genetic in vitro screens identified ASNS as a cancer dependency in several solid malignancies (Cell 2017, 170 (3), 564-576.e16. Cell 2017, 170 (3), 577-592.e10). Here we evaluate the therapeutic potential of targeting ASNS in melanoma cells. While we confirm in vitro dependency on ASNS silencing, this is largely dispensable for in vivo tumor growth, even in the face of asparagine deprivation, prompting us to characterize such a resistance mechanism to devise novel therapeutic strategies. Using ex vivo quantitative proteome and transcriptome profiling, we characterize the compensatory mechanism elicited by ASNS knockout melanoma cells allowing their survival. Mechanistically, a genome-wide CRISPR screen revealed that such a resistance mechanism is elicited by a dual axis: GCN2-ATF4 aimed at restoring amino acid levels and MAPK-BCLXL to promote survival. Importantly, pharmacological inhibition of such nodes synergizes with l-asparaginase-mediated asparagine deprivation in ASNS deficient cells suggesting novel potential therapeutic combinations in melanoma.
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Affiliation(s)
- Verena Apfel
- Disease area Oncology, Novartis Institute for Biomedical Research, Basel, Switzerland
| | - Damien Begue
- Analytical Sciences and Imaging, Novartis Institutes for Biomedical Research, CH-4002 Basel, Switzerland
| | - Valentina Cordo'
- Disease area Oncology, Novartis Institute for Biomedical Research, Basel, Switzerland
| | - Laura Holzer
- Disease area Oncology, Novartis Institute for Biomedical Research, Basel, Switzerland
| | - Laetitia Martinuzzi
- Disease area Oncology, Novartis Institute for Biomedical Research, Basel, Switzerland
| | - Alexandra Buhles
- Disease area Oncology, Novartis Institute for Biomedical Research, Basel, Switzerland
| | - Grainne Kerr
- Disease area Oncology, Novartis Institute for Biomedical Research, Basel, Switzerland
| | - Ines Barbosa
- Disease area Oncology, Novartis Institute for Biomedical Research, Basel, Switzerland
| | - Ulrike Naumann
- Analytical Sciences and Imaging, Novartis Institutes for Biomedical Research, CH-4002 Basel, Switzerland
| | - Michelle Piquet
- Disease area Oncology, Novartis Institute for Biomedical Research, Cambridge, Massachusetts 02139United States
| | - David Ruddy
- Disease area Oncology, Novartis Institute for Biomedical Research, Cambridge, Massachusetts 02139United States
| | - Andreas Weiss
- Disease area Oncology, Novartis Institute for Biomedical Research, Basel, Switzerland
| | - Stephane Ferretti
- Disease area Oncology, Novartis Institute for Biomedical Research, Basel, Switzerland
| | - Reinaldo Almeida
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, CH-4002 Basel, Switzerland
| | - Debora Bonenfant
- Analytical Sciences and Imaging, Novartis Institutes for Biomedical Research, CH-4002 Basel, Switzerland
| | - Luca Tordella
- Disease area Oncology, Novartis Institute for Biomedical Research, Basel, Switzerland
| | - Giorgio G Galli
- Disease area Oncology, Novartis Institute for Biomedical Research, Basel, Switzerland
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187
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Fuchs A, Riegler S, Ayatollahi Z, Cavallari N, Giono LE, Nimeth BA, Mutanwad KV, Schweighofer A, Lucyshyn D, Barta A, Petrillo E, Kalyna M. Targeting alternative splicing by RNAi: from the differential impact on splice variants to triggering artificial pre-mRNA splicing. Nucleic Acids Res 2021; 49:1133-1151. [PMID: 33406240 PMCID: PMC7826280 DOI: 10.1093/nar/gkaa1260] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 12/08/2020] [Accepted: 12/17/2020] [Indexed: 12/25/2022] Open
Abstract
Alternative splicing generates multiple transcript and protein isoforms from a single gene and controls transcript intracellular localization and stability by coupling to mRNA export and nonsense-mediated mRNA decay (NMD). RNA interference (RNAi) is a potent mechanism to modulate gene expression. However, its interactions with alternative splicing are poorly understood. We used artificial microRNAs (amiRNAs, also termed shRNAmiR) to knockdown all splice variants of selected target genes in Arabidopsis thaliana. We found that splice variants, which vary by their protein-coding capacity, subcellular localization and sensitivity to NMD, are affected differentially by an amiRNA, although all of them contain the target site. Particular transcript isoforms escape amiRNA-mediated degradation due to their nuclear localization. The nuclear and NMD-sensitive isoforms mask RNAi action in alternatively spliced genes. Interestingly, Arabidopsis SPL genes, which undergo alternative splicing and are targets of miR156, are regulated in the same manner. Moreover, similar results were obtained in mammalian cells using siRNAs, indicating cross-kingdom conservation of these interactions among RNAi and splicing isoforms. Furthermore, we report that amiRNA can trigger artificial alternative splicing, thus expanding the RNAi functional repertoire. Our findings unveil novel interactions between different post-transcriptional processes in defining transcript fates and regulating gene expression.
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Affiliation(s)
- Armin Fuchs
- Max Perutz Labs, Medical University of Vienna, Vienna 1030, Austria
| | - Stefan Riegler
- Max Perutz Labs, Medical University of Vienna, Vienna 1030, Austria.,Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences Vienna, Vienna 1190, Austria
| | - Zahra Ayatollahi
- Max Perutz Labs, Medical University of Vienna, Vienna 1030, Austria
| | - Nicola Cavallari
- Max Perutz Labs, Medical University of Vienna, Vienna 1030, Austria
| | - Luciana E Giono
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-Universidad de Buenos Aires, C1428EHA, Buenos Aires, Argentina
| | - Barbara A Nimeth
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences Vienna, Vienna 1190, Austria
| | - Krishna V Mutanwad
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences Vienna, Vienna 1190, Austria
| | | | - Doris Lucyshyn
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences Vienna, Vienna 1190, Austria
| | - Andrea Barta
- Max Perutz Labs, Medical University of Vienna, Vienna 1030, Austria
| | - Ezequiel Petrillo
- Max Perutz Labs, Medical University of Vienna, Vienna 1030, Austria.,Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-Universidad de Buenos Aires, C1428EHA, Buenos Aires, Argentina
| | - Maria Kalyna
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences Vienna, Vienna 1190, Austria
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188
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Broyde J, Simpson DR, Murray D, Paull EO, Chu BW, Tagore S, Jones SJ, Griffin AT, Giorgi FM, Lachmann A, Jackson P, Sweet-Cordero EA, Honig B, Califano A. Oncoprotein-specific molecular interaction maps (SigMaps) for cancer network analyses. Nat Biotechnol 2021; 39:215-224. [PMID: 32929263 PMCID: PMC7878435 DOI: 10.1038/s41587-020-0652-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 07/23/2020] [Indexed: 02/08/2023]
Abstract
Tumor-specific elucidation of physical and functional oncoprotein interactions could improve tumorigenic mechanism characterization and therapeutic response prediction. Current interaction models and pathways, however, lack context specificity and are not oncoprotein specific. We introduce SigMaps as context-specific networks, comprising modulators, effectors and cognate binding-partners of a specific oncoprotein. SigMaps are reconstructed de novo by integrating diverse evidence sources-including protein structure, gene expression and mutational profiles-via the OncoSig machine learning framework. We first generated a KRAS-specific SigMap for lung adenocarcinoma, which recapitulated published KRAS biology, identified novel synthetic lethal proteins that were experimentally validated in three-dimensional spheroid models and established uncharacterized crosstalk with RAB/RHO. To show that OncoSig is generalizable, we first inferred SigMaps for the ten most mutated human oncoproteins and then for the full repertoire of 715 proteins in the COSMIC Cancer Gene Census. Taken together, these SigMaps show that the cell's regulatory and signaling architecture is highly tissue specific.
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Affiliation(s)
- Joshua Broyde
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - David R Simpson
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, UCSF Benioff Children's Hospital, San Francisco, CA, USA
| | - Diana Murray
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Evan O Paull
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Brennan W Chu
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Somnath Tagore
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Sunny J Jones
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Aaron T Griffin
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Federico M Giorgi
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Alexander Lachmann
- Mount Sinai Center for Bioinformatics; Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Peter Jackson
- Baxter Laboratory, Department of Microbiology & Immunology, Stanford University, Palo Alto, CA, USA
- Department of Pathology, Stanford University, Palo Alto, CA, USA
| | - E Alejandro Sweet-Cordero
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, UCSF Benioff Children's Hospital, San Francisco, CA, USA.
| | - Barry Honig
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
- Department of Medicine, Columbia University, New York, NY, USA.
- Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY, USA.
| | - Andrea Califano
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
- Department of Medicine, Columbia University, New York, NY, USA.
- JP Sulzberger Columbia Genome Center, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Biomedical Informatics, Columbia University, New York, NY, USA.
- Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA.
- Motor Neuron Center and Columbia Initiative in Stem Cells, Columbia University, New York, NY, USA.
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189
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Amici DR, Jackson JM, Truica MI, Smith RS, Abdulkadir SA, Mendillo ML. FIREWORKS: a bottom-up approach to integrative coessentiality network analysis. Life Sci Alliance 2021; 4:e202000882. [PMID: 33328249 PMCID: PMC7756899 DOI: 10.26508/lsa.202000882] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 12/01/2020] [Accepted: 12/02/2020] [Indexed: 12/11/2022] Open
Abstract
Genetic coessentiality analysis, a computational approach which identifies genes sharing a common effect on cell fitness across large-scale screening datasets, has emerged as a powerful tool to identify functional relationships between human genes. However, widespread implementation of coessentiality to study individual genes and pathways is limited by systematic biases in existing coessentiality approaches and accessibility barriers for investigators without computational expertise. We created FIREWORKS, a method and interactive tool for the construction and statistical analysis of coessentiality networks centered around gene(s) provided by the user. FIREWORKS incorporates a novel bias reduction approach to reduce false discoveries, enables restriction of coessentiality analyses to custom subsets of cell lines, and integrates multiomic and drug-gene interaction datasets to investigate and target contextual gene essentiality. We demonstrate the broad utility of FIREWORKS through case vignettes investigating gene function and specialization, indirect therapeutic targeting of "undruggable" proteins, and context-specific rewiring of genetic networks.
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Affiliation(s)
- David R Amici
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL, USA
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Robert H Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Jasen M Jackson
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL, USA
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Robert H Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Mihai I Truica
- Robert H Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Roger S Smith
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL, USA
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Robert H Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Medical Scientist Training Program, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Sarki A Abdulkadir
- Robert H Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Department of Urology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Marc L Mendillo
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL, USA
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Robert H Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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190
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Parkhitko AA, Singh A, Hsieh S, Hu Y, Binari R, Lord CJ, Hannenhalli S, Ryan CJ, Perrimon N. Cross-species identification of PIP5K1-, splicing- and ubiquitin-related pathways as potential targets for RB1-deficient cells. PLoS Genet 2021; 17:e1009354. [PMID: 33591981 PMCID: PMC7909629 DOI: 10.1371/journal.pgen.1009354] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 02/26/2021] [Accepted: 01/11/2021] [Indexed: 01/02/2023] Open
Abstract
The RB1 tumor suppressor is recurrently mutated in a variety of cancers including retinoblastomas, small cell lung cancers, triple-negative breast cancers, prostate cancers, and osteosarcomas. Finding new synthetic lethal (SL) interactions with RB1 could lead to new approaches to treating cancers with inactivated RB1. We identified 95 SL partners of RB1 based on a Drosophila screen for genetic modifiers of the eye phenotype caused by defects in the RB1 ortholog, Rbf1. We validated 38 mammalian orthologs of Rbf1 modifiers as RB1 SL partners in human cancer cell lines with defective RB1 alleles. We further show that for many of the RB1 SL genes validated in human cancer cell lines, low activity of the SL gene in human tumors, when concurrent with low levels of RB1 was associated with improved patient survival. We investigated higher order combinatorial gene interactions by creating a novel Drosophila cancer model with co-occurring Rbf1, Pten and Ras mutations, and found that targeting RB1 SL genes in this background suppressed the dramatic tumor growth and rescued fly survival whilst having minimal effects on wild-type cells. Finally, we found that drugs targeting the identified RB1 interacting genes/pathways, such as UNC3230, PYR-41, TAK-243, isoginkgetin, madrasin, and celastrol also elicit SL in human cancer cell lines. In summary, we identified several high confidence, evolutionarily conserved, novel targets for RB1-deficient cells that may be further adapted for the treatment of human cancer.
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Affiliation(s)
- Andrey A. Parkhitko
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Aging Institute of UPMC and the University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Arashdeep Singh
- Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Sharon Hsieh
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
| | - Yanhui Hu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Richard Binari
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Boston, Massachusetts, United States of America
| | - Christopher J. Lord
- CRUK Gene Function Laboratory, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Sridhar Hannenhalli
- Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Colm J. Ryan
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
- School of Computer Science, University College Dublin, Dublin, Ireland
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Boston, Massachusetts, United States of America
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191
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Serresi M, Kertalli S, Li L, Schmitt MJ, Dramaretska Y, Wierikx J, Hulsman D, Gargiulo G. Functional antagonism of chromatin modulators regulates epithelial-mesenchymal transition. SCIENCE ADVANCES 2021; 7:7/9/eabd7974. [PMID: 33627422 PMCID: PMC7904264 DOI: 10.1126/sciadv.abd7974] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 01/06/2021] [Indexed: 05/27/2023]
Abstract
Epithelial-mesenchymal transition (EMT) is a developmental process hijacked by cancer cells to modulate proliferation, migration, and stress response. Whereas kinase signaling is believed to be an EMT driver, the molecular mechanisms underlying epithelial-mesenchymal interconversion are incompletely understood. Here, we show that the impact of chromatin regulators on EMT interconversion is broader than that of kinases. By combining pharmacological modulation of EMT, synthetic genetic tracing, and CRISPR interference screens, we uncovered a minority of kinases and several chromatin remodelers, writers, and readers governing homeostatic EMT in lung cancer cells. Loss of ARID1A, DOT1L, BRD2, and ZMYND8 had nondeterministic and sometimes opposite consequences on epithelial-mesenchymal interconversion. Together with RNAPII and AP-1, these antagonistic gatekeepers control chromatin of active enhancers, including pan-cancer-EMT signature genes enabling supraclassification of anatomically diverse tumors. Thus, our data uncover general principles underlying transcriptional control of cancer cell plasticity and offer a platform to systematically explore chromatin regulators in tumor-state-specific therapy.
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Affiliation(s)
- Michela Serresi
- Max-Delbrück-Center for Molecular Medicine (MDC), Robert-Rössle-Str. 10, 13092 Berlin, Germany.
| | - Sonia Kertalli
- Max-Delbrück-Center for Molecular Medicine (MDC), Robert-Rössle-Str. 10, 13092 Berlin, Germany
| | - Lifei Li
- Max-Delbrück-Center for Molecular Medicine (MDC), Robert-Rössle-Str. 10, 13092 Berlin, Germany
| | - Matthias Jürgen Schmitt
- Max-Delbrück-Center for Molecular Medicine (MDC), Robert-Rössle-Str. 10, 13092 Berlin, Germany
| | - Yuliia Dramaretska
- Max-Delbrück-Center for Molecular Medicine (MDC), Robert-Rössle-Str. 10, 13092 Berlin, Germany
| | - Jikke Wierikx
- Max-Delbrück-Center for Molecular Medicine (MDC), Robert-Rössle-Str. 10, 13092 Berlin, Germany
| | - Danielle Hulsman
- Division of Molecular Genetics, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066 CX, Netherlands
| | - Gaetano Gargiulo
- Max-Delbrück-Center for Molecular Medicine (MDC), Robert-Rössle-Str. 10, 13092 Berlin, Germany.
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192
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Cohen-Sharir Y, McFarland JM, Abdusamad M, Marquis C, Bernhard SV, Kazachkova M, Tang H, Ippolito MR, Laue K, Zerbib J, Malaby HLH, Jones A, Stautmeister LM, Bockaj I, Wardenaar R, Lyons N, Nagaraja A, Bass AJ, Spierings DCJ, Foijer F, Beroukhim R, Santaguida S, Golub TR, Stumpff J, Storchová Z, Ben-David U. Aneuploidy renders cancer cells vulnerable to mitotic checkpoint inhibition. Nature 2021; 590:486-491. [PMID: 33505028 PMCID: PMC8262644 DOI: 10.1038/s41586-020-03114-6] [Citation(s) in RCA: 112] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 11/19/2020] [Indexed: 01/30/2023]
Abstract
Selective targeting of aneuploid cells is an attractive strategy for cancer treatment1. However, it is unclear whether aneuploidy generates any clinically relevant vulnerabilities in cancer cells. Here we mapped the aneuploidy landscapes of about 1,000 human cancer cell lines, and analysed genetic and chemical perturbation screens2-9 to identify cellular vulnerabilities associated with aneuploidy. We found that aneuploid cancer cells show increased sensitivity to genetic perturbation of core components of the spindle assembly checkpoint (SAC), which ensures the proper segregation of chromosomes during mitosis10. Unexpectedly, we also found that aneuploid cancer cells were less sensitive than diploid cells to short-term exposure to multiple SAC inhibitors. Indeed, aneuploid cancer cells became increasingly sensitive to inhibition of SAC over time. Aneuploid cells exhibited aberrant spindle geometry and dynamics, and kept dividing when the SAC was inhibited, resulting in the accumulation of mitotic defects, and in unstable and less-fit karyotypes. Therefore, although aneuploid cancer cells could overcome inhibition of SAC more readily than diploid cells, their long-term proliferation was jeopardized. We identified a specific mitotic kinesin, KIF18A, whose activity was perturbed in aneuploid cancer cells. Aneuploid cancer cells were particularly vulnerable to depletion of KIF18A, and KIF18A overexpression restored their response to SAC inhibition. Our results identify a therapeutically relevant, synthetic lethal interaction between aneuploidy and the SAC.
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Affiliation(s)
- Yael Cohen-Sharir
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - James M McFarland
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mai Abdusamad
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Carolyn Marquis
- Department of Molecular Physiology and Biophysics, University of Vermont, Burlington, VT, USA
| | - Sara V Bernhard
- Department of Molecular Genetics, TU Kaiserlautern, Kaiserlautern, Germany
| | - Mariya Kazachkova
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Helen Tang
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Marica R Ippolito
- Department of Experimental Oncology at IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Kathrin Laue
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Johanna Zerbib
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Heidi L H Malaby
- Department of Molecular Physiology and Biophysics, University of Vermont, Burlington, VT, USA
| | - Andrew Jones
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Irena Bockaj
- European Research Institute for the Biology of Aging (ERIBA), University of Groningen, Groningen, The Netherlands
| | - René Wardenaar
- European Research Institute for the Biology of Aging (ERIBA), University of Groningen, Groningen, The Netherlands
| | - Nicholas Lyons
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ankur Nagaraja
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Dana Farber Cancer Institute, Boston, MA, USA
| | - Adam J Bass
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Dana Farber Cancer Institute, Boston, MA, USA
| | - Diana C J Spierings
- European Research Institute for the Biology of Aging (ERIBA), University of Groningen, Groningen, The Netherlands
| | - Floris Foijer
- European Research Institute for the Biology of Aging (ERIBA), University of Groningen, Groningen, The Netherlands
| | - Rameen Beroukhim
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Dana Farber Cancer Institute, Boston, MA, USA
| | - Stefano Santaguida
- Department of Experimental Oncology at IEO, European Institute of Oncology IRCCS, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Todd R Golub
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Dana Farber Cancer Institute, Boston, MA, USA
| | - Jason Stumpff
- Department of Molecular Physiology and Biophysics, University of Vermont, Burlington, VT, USA
| | - Zuzana Storchová
- Department of Molecular Genetics, TU Kaiserlautern, Kaiserlautern, Germany
| | - Uri Ben-David
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
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193
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Wu S, Fukumoto T, Lin J, Nacarelli T, Wang Y, Ong D, Liu H, Fatkhutdinov N, Zundell JA, Karakashev S, Zhou W, Schwartz LE, Tang HY, Drapkin R, Liu Q, Huntsman DG, Kossenkov AV, Speicher DW, Schug ZT, Van Dang C, Zhang R. Targeting glutamine dependence through GLS1 inhibition suppresses ARID1A-inactivated clear cell ovarian carcinoma. NATURE CANCER 2021; 2:189-200. [PMID: 34085048 PMCID: PMC8168620 DOI: 10.1038/s43018-020-00160-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Alterations in components of the SWI/SNF chromatin-remodeling complex occur in ~20% of all human cancers. For example, ARID1A is mutated in up to 62% of clear cell ovarian carcinoma (OCCC), a disease currently lacking effective therapies. Here we show that ARID1A mutation creates a dependence on glutamine metabolism. SWI/SNF represses glutaminase (GLS1) and ARID1A inactivation upregulates GLS1. ARID1A inactivation increases glutamine utilization and metabolism through the tricarboxylic acid cycle to support aspartate synthesis. Indeed, glutaminase inhibitor CB-839 suppresses the growth of ARID1A mutant, but not wildtype, OCCCs in both orthotopic and patient-derived xenografts. In addition, glutaminase inhibitor CB-839 synergizes with immune checkpoint blockade anti-PDL1 antibody in a genetic OCCC mouse model driven by conditional Arid1a inactivation. Our data indicate that pharmacological inhibition of glutaminase alone or in combination with immune checkpoint blockade represents an effective therapeutic strategy for cancers involving alterations in the SWI/SNF complex such as ARID1A mutations.
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Affiliation(s)
- Shuai Wu
- Immunology, Microenvironment & Metastasis Program, The Wistar Institute, Philadelphia, PA, USA
| | - Takeshi Fukumoto
- Immunology, Microenvironment & Metastasis Program, The Wistar Institute, Philadelphia, PA, USA
| | - Jianhuang Lin
- Immunology, Microenvironment & Metastasis Program, The Wistar Institute, Philadelphia, PA, USA
| | - Timothy Nacarelli
- Immunology, Microenvironment & Metastasis Program, The Wistar Institute, Philadelphia, PA, USA
| | - Yemin Wang
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada,Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Dionzie Ong
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Heng Liu
- Immunology, Microenvironment & Metastasis Program, The Wistar Institute, Philadelphia, PA, USA
| | - Nail Fatkhutdinov
- Immunology, Microenvironment & Metastasis Program, The Wistar Institute, Philadelphia, PA, USA
| | - Joseph A. Zundell
- Immunology, Microenvironment & Metastasis Program, The Wistar Institute, Philadelphia, PA, USA
| | - Sergey Karakashev
- Immunology, Microenvironment & Metastasis Program, The Wistar Institute, Philadelphia, PA, USA
| | - Wei Zhou
- Immunology, Microenvironment & Metastasis Program, The Wistar Institute, Philadelphia, PA, USA
| | - Lauren E. Schwartz
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hsin-Yao Tang
- Proteomics and Metabolomics Facility, The Wistar Institute, Philadelphia, PA, USA
| | - Ronny Drapkin
- Department of Obstetrics and Gynecology, Penn Ovarian Cancer Research Center, University of Pennsylvania, Philadelphia, PA, USA
| | - Qin Liu
- Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA, USA
| | - David G. Huntsman
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Andrew V. Kossenkov
- Immunology, Microenvironment & Metastasis Program, The Wistar Institute, Philadelphia, PA, USA
| | - David W. Speicher
- Proteomics and Metabolomics Facility, The Wistar Institute, Philadelphia, PA, USA,Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA, USA
| | - Zachary T. Schug
- Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA, USA
| | - Chi Van Dang
- Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA, USA,Ludwig Institute for Cancer Research, New York, NY, USA
| | - Rugang Zhang
- Immunology, Microenvironment & Metastasis Program, The Wistar Institute, Philadelphia, PA, USA.
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194
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Li Y, Dong YP, Qian YW, Yu LX, Wen W, Cui XL, Wang HY. Identification of important genes and drug repurposing based on clinical-centered analysis across human cancers. Acta Pharmacol Sin 2021; 42:282-289. [PMID: 32555508 DOI: 10.1038/s41401-020-0451-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 05/30/2020] [Indexed: 01/19/2023] Open
Abstract
Identification of the functional impact of mutated and altered genes in cancer is critical for implementing precision oncology and drug repurposing. In recent years, the emergence of multiomics data from large, well-characterized patient cohorts has provided us with an unprecedented opportunity to address this problem. In this study, we investigated survival-associated genes across 26 cancer types and found that these genes tended to be hub genes and had higher K-core values in biological networks. Moreover, the genes associated with adverse outcomes were mainly enriched in pathways related to genetic information processing and cellular processes, while the genes with favorable outcomes were enriched in metabolism and immune regulation pathways. We proposed using the number of survival-related neighbors to assess the impact of mutations. In addition, by integrating other databases including the Human Protein Atlas and the DrugBank database, we predicted novel targets and anticancer drugs using the drug repurposing strategy. Our results illustrated the significance of multidimensional analysis of clinical data in important gene identification and drug development.
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195
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Abstract
Pancreatic cancer is a recalcitrant cancer with one of the lowest 5-year survival rates. A hallmark of pancreatic cancer is the prevalence of oncogenic mutation in the KRAS gene. The KRAS oncogene plays a critical role in the initiation and maintenance of pancreatic tumors and its signaling network represents a major target for therapeutic intervention. A number of inhibitors have been developed against kinase effectors in various Ras signaling pathways. Their clinical activity, however, has been disappointing thus far. More recently, covalent inhibitors targeting the KRASG12C oncoprotein have been developed. These inhibitors showed promising activity in KRASG12C mutant pancreatic cancer in early clinical trials. This review will present an updated summary of our understanding of mutant KRAS function in pancreatic cancer and discuss therapeutic strategies that target oncogenic KRAS signaling in this disease.
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Affiliation(s)
- Ji Luo
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD.
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196
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Cui Y, Cheng X, Chen Q, Song B, Chiu A, Gao Y, Dawson T, Chao L, Zhang W, Li D, Zeng Z, Yu J, Li Z, Fei T, Peng S, Li W. CRISP-view: a database of functional genetic screens spanning multiple phenotypes. Nucleic Acids Res 2021; 49:D848-D854. [PMID: 33010154 PMCID: PMC7778972 DOI: 10.1093/nar/gkaa809] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/12/2020] [Accepted: 09/30/2020] [Indexed: 12/21/2022] Open
Abstract
High-throughput genetic screening based on CRISPR/Cas9 or RNA-interference (RNAi) enables the exploration of genes associated with the phenotype of interest on a large scale. The rapid accumulation of public available genetic screening data provides a wealth of knowledge about genotype-to-phenotype relationships and a valuable resource for the systematic analysis of gene functions. Here we present CRISP-view, a comprehensive database of CRISPR/Cas9 and RNAi screening datasets that span multiple phenotypes, including in vitro and in vivo cell proliferation and viability, response to cancer immunotherapy, virus response, protein expression, etc. By 22 September 2020, CRISP-view has collected 10 321 human samples and 825 mouse samples from 167 papers. All the datasets have been curated, annotated, and processed by a standard MAGeCK-VISPR analysis pipeline with quality control (QC) metrics. We also developed a user-friendly webserver to visualize, explore, and search these datasets. The webserver is freely available at http://crispview.weililab.org.
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Affiliation(s)
- Yingbo Cui
- Sanyi Road, Changsha, Hunan Province, People's Republic of China
| | - Xiaolong Cheng
- Center for Genetic Medicine Research, Children's National Hospital. 111 Michigan Ave NW, Washington, DC 20010, USA
| | - Qing Chen
- Center for Genetic Medicine Research, Children's National Hospital. 111 Michigan Ave NW, Washington, DC 20010, USA
| | - Bicna Song
- Center for Genetic Medicine Research, Children's National Hospital. 111 Michigan Ave NW, Washington, DC 20010, USA
| | - Anthony Chiu
- Center for Genetic Medicine Research, Children's National Hospital. 111 Michigan Ave NW, Washington, DC 20010, USA.,School of Medicine and Health Sciences, George Washington University, 2300 I Street NW, Washington, DC 20037, USA
| | - Yuan Gao
- Center for Genetic Medicine Research, Children's National Hospital. 111 Michigan Ave NW, Washington, DC 20010, USA.,Department of Biochemistry and Molecular Biology, George Washington University, 2300 I Street NW, Washington, DC 20037, USA
| | - Tyson Dawson
- Center for Genetic Medicine Research, Children's National Hospital. 111 Michigan Ave NW, Washington, DC 20010, USA.,Institute for Biomedical Sciences, George Washington University, 2300 I Street NW, Washington, DC 20037, USA.,Computational Biology Institute, Milken Institute School of Public Health, George Washington University, 45085 University Drive, Ashburn, VA 20148, USA
| | - Lumen Chao
- Center for Genetic Medicine Research, Children's National Hospital. 111 Michigan Ave NW, Washington, DC 20010, USA
| | - Wubing Zhang
- Department of Data Sciences, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health. 450 Brookline Ave., Boston MA 02215, USA
| | - Dian Li
- Department of Data Sciences, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health. 450 Brookline Ave., Boston MA 02215, USA
| | - Zexiang Zeng
- Department of Data Sciences, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health. 450 Brookline Ave., Boston MA 02215, USA
| | - Jijun Yu
- Beijing Key Laboratory of Therapeutic Gene Engineering Antibody. Beijing, People's Republic of China
| | - Zexu Li
- College of Life and Health Sciences, Northeastern University. 110819 Shenyang, People's Republic of China
| | - Teng Fei
- College of Life and Health Sciences, Northeastern University. 110819 Shenyang, People's Republic of China
| | - Shaoliang Peng
- Lushan South Road, Changsha, Hunan Province, People's Republic of China
| | - Wei Li
- Center for Genetic Medicine Research, Children's National Hospital. 111 Michigan Ave NW, Washington, DC 20010, USA.,Department of Genomics and Precision Medicine, George Washington University. 111 Michigan Ave NW, Washington, DC 20010, USA
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197
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Cysteine and Folate Metabolism Are Targetable Vulnerabilities of Metastatic Colorectal Cancer. Cancers (Basel) 2021; 13:cancers13030425. [PMID: 33498690 PMCID: PMC7866204 DOI: 10.3390/cancers13030425] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 01/09/2021] [Accepted: 01/20/2021] [Indexed: 01/17/2023] Open
Abstract
Simple Summary In this work, we studied the metabolic reprogramming of same-patient-derived cell lines with increasing metastatic potential to develop new therapeutic approaches against metastatic colorectal cancer. Using a novel systems biology approach to integrate multiple layers of omics data, we predicted and validated that cystine uptake and folate metabolism, two key pathways related to redox metabolism, are potential targets against metastatic colorectal cancer. Our findings indicate that metastatic cell lines are selectively dependent on redox homeostasis, paving the way for new targeted therapies. Abstract With most cancer-related deaths resulting from metastasis, the development of new therapeutic approaches against metastatic colorectal cancer (mCRC) is essential to increasing patient survival. The metabolic adaptations that support mCRC remain undefined and their elucidation is crucial to identify potential therapeutic targets. Here, we employed a strategy for the rational identification of targetable metabolic vulnerabilities. This strategy involved first a thorough metabolic characterisation of same-patient-derived cell lines from primary colon adenocarcinoma (SW480), its lymph node metastasis (SW620) and a liver metastatic derivative (SW620-LiM2), and second, using a novel multi-omics integration workflow, identification of metabolic vulnerabilities specific to the metastatic cell lines. We discovered that the metastatic cell lines are selectively vulnerable to the inhibition of cystine import and folate metabolism, two key pathways in redox homeostasis. Specifically, we identified the system xCT and MTHFD1 genes as potential therapeutic targets, both individually and combined, for combating mCRC.
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198
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Kessler D, Mayer M, Zahn SK, Zeeb M, Wöhrle S, Bergner A, Bruchhaus J, Ciftci T, Dahmann G, Dettling M, Döbel S, Fuchs JE, Geist L, Hela W, Kofink C, Kousek R, Moser F, Puchner T, Rumpel K, Scharnweber M, Werni P, Wolkerstorfer B, Breitsprecher D, Baaske P, Pearson M, McConnell DB, Böttcher J. Getting a Grip on the Undrugged: Targeting β-Catenin with Fragment-Based Methods. ChemMedChem 2021; 16:1420-1424. [PMID: 33275320 PMCID: PMC8247886 DOI: 10.1002/cmdc.202000839] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Indexed: 12/20/2022]
Abstract
Aberrant WNT pathway activation, leading to nuclear accumulation of β‐catenin, is a key oncogenic driver event. Mutations in the tumor suppressor gene APC lead to impaired proteasomal degradation of β‐catenin and subsequent nuclear translocation. Restoring cellular degradation of β‐catenin represents a potential therapeutic strategy. Here, we report the fragment‐based discovery of a small molecule binder to β‐catenin, including the structural elucidation of the binding mode by X‐ray crystallography. The difficulty in drugging β‐catenin was confirmed as the primary screening campaigns identified only few and very weak hits. Iterative virtual and NMR screening techniques were required to discover a compound with sufficient potency to be able to obtain an X‐ray co‐crystal structure. The binding site is located between armadillo repeats two and three, adjacent to the BCL9 and TCF4 binding sites. Genetic studies show that it is unlikely to be useful for the development of protein–protein interaction inhibitors but structural information and established assays provide a solid basis for a prospective optimization towards β‐catenin proteolysis targeting chimeras (PROTACs) as alternative modality.
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Affiliation(s)
- Dirk Kessler
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Moriz Mayer
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Stephan K Zahn
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Markus Zeeb
- Boehringer Ingelheim Pharma GmbH & Co KG, Birkendorfer Straße 65, 88397, Biberach, Germany
| | - Simon Wöhrle
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Andreas Bergner
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Jens Bruchhaus
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Tuncay Ciftci
- Boehringer Ingelheim Pharma GmbH & Co KG, Birkendorfer Straße 65, 88397, Biberach, Germany
| | - Georg Dahmann
- Boehringer Ingelheim Pharma GmbH & Co KG, Birkendorfer Straße 65, 88397, Biberach, Germany
| | - Maike Dettling
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Sandra Döbel
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Julian E Fuchs
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Leonhard Geist
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Wolfgang Hela
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Christiane Kofink
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Roland Kousek
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Franziska Moser
- Boehringer Ingelheim Pharma GmbH & Co KG, Birkendorfer Straße 65, 88397, Biberach, Germany
| | - Teresa Puchner
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Klaus Rumpel
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | | | - Patrick Werni
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | | | - Dennis Breitsprecher
- NanoTemper Technologies GmbH, Floessergasse 4, 81369, Muenchen, Germany.,Leica Microsystems AG, Max Schmidheiny-Strasse 201, 9435, Heerbrugg, Switzerland
| | - Philipp Baaske
- NanoTemper Technologies GmbH, Floessergasse 4, 81369, Muenchen, Germany
| | - Mark Pearson
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Darryl B McConnell
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
| | - Jark Böttcher
- Boehringer Ingelheim RCV GmbH & Co KG, Dr.-Boehringer-Gasse 5-11, 1121, Vienna, Austria
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199
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Ultimate Precision: Targeting Cancer But Not Normal Self-Replication. Lung Cancer 2021. [DOI: 10.1007/978-3-030-74028-3_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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200
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Yuan B, Shen C, Luna A, Korkut A, Marks DS, Ingraham J, Sander C. CellBox: Interpretable Machine Learning for Perturbation Biology with Application to the Design of Cancer Combination Therapy. Cell Syst 2020; 12:128-140.e4. [PMID: 33373583 DOI: 10.1016/j.cels.2020.11.013] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 07/13/2020] [Accepted: 11/25/2020] [Indexed: 01/13/2023]
Abstract
Systematic perturbation of cells followed by comprehensive measurements of molecular and phenotypic responses provides informative data resources for constructing computational models of cell biology. Models that generalize well beyond training data can be used to identify combinatorial perturbations of potential therapeutic interest. Major challenges for machine learning on large biological datasets are to find global optima in a complex multidimensional space and mechanistically interpret the solutions. To address these challenges, we introduce a hybrid approach that combines explicit mathematical models of cell dynamics with a machine-learning framework, implemented in TensorFlow. We tested the modeling framework on a perturbation-response dataset of a melanoma cell line after drug treatments. The models can be efficiently trained to describe cellular behavior accurately. Even though completely data driven and independent of prior knowledge, the resulting de novo network models recapitulate some known interactions. The approach is readily applicable to various kinetic models of cell biology. A record of this paper's Transparent Peer Review process is included in the Supplemental Information.
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Affiliation(s)
- Bo Yuan
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA; cBio Center, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute, Cambridge, MA, USA.
| | - Ciyue Shen
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA; cBio Center, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute, Cambridge, MA, USA.
| | - Augustin Luna
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA; cBio Center, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute, Cambridge, MA, USA
| | - Anil Korkut
- Department of Bioinformatics & Computational Biology, the University of Texas M D Anderson Cancer Center, Houston, TX, USA
| | - Debora S Marks
- Broad Institute, Cambridge, MA, USA; Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - John Ingraham
- MIT Computer Science & Artificial Intelligence Laboratory, Boston, MA, USA
| | - Chris Sander
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA; cBio Center, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute, Cambridge, MA, USA.
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