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Lattanzi A, Maddalo D. The CRISPR Revolution in the Drug Discovery Workflow: An Industry Perspective. CRISPR J 2022; 5:634-641. [PMID: 35917561 DOI: 10.1089/crispr.2022.0002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
In a relatively short time, the pharmaceutical industry has witnessed a rapid integration of the CRISPR technology in multiple areas of research, development, therapy, and diagnostics. A unique feature to this system compared with other technologies is the exceptional versatility in adapting to the broad range of needs across the drug discovery pipeline, such as target identification, cell engineering, and in vivo modeling. As a consequence, the CRISPR toolbox has been evolving to address key questions around preclinical and clinical drug development. In this review, we provide a high-level perspective of how CRISPR has impacted several aspects of the drug discovery workflow and the future ahead for this exciting technology.
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Affiliation(s)
- Annalisa Lattanzi
- Department of Molecular Biology and Genentech, Inc., South San Francisco, California, USA
| | - Danilo Maddalo
- Department of Translational Oncology, Genentech, Inc., South San Francisco, California, USA
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2
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Abstract
Over the past decade, CRISPR has become as much a verb as it is an acronym, transforming biomedical research and providing entirely new approaches for dissecting all facets of cell biology. In cancer research, CRISPR and related tools have offered a window into previously intractable problems in our understanding of cancer genetics, the noncoding genome and tumour heterogeneity, and provided new insights into therapeutic vulnerabilities. Here, we review the progress made in the development of CRISPR systems as a tool to study cancer, and the emerging adaptation of these technologies to improve diagnosis and treatment.
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Affiliation(s)
- Alyna Katti
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Weill Cornell Graduate School of Medical Science, Weill Cornell Medicine, New York, NY, USA
| | - Bianca J Diaz
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Weill Cornell Graduate School of Medical Science, Weill Cornell Medicine, New York, NY, USA
| | - Christina M Caragine
- Department of Biology, New York University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Neville E Sanjana
- Department of Biology, New York University, New York, NY, USA.
- New York Genome Center, New York, NY, USA.
| | - Lukas E Dow
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
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Lima A, Maddalo D. SEMMs: Somatically Engineered Mouse Models. A New Tool for In Vivo Disease Modeling for Basic and Translational Research. Front Oncol 2021; 11:667189. [PMID: 33968774 PMCID: PMC8103029 DOI: 10.3389/fonc.2021.667189] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 03/23/2021] [Indexed: 12/13/2022] Open
Abstract
Most experimental oncology therapies fail during clinical development despite years of preclinical testing rationalizing their use. This begs the question of whether the current preclinical models used for evaluating oncology therapies adequately capture patient heterogeneity and response to therapy. Most of the preclinical work is based on xenograft models where tumor mis-location and the lack of the immune system represent a major limitation for the translatability of many observations from preclinical models to patients. Genetically engineered mouse models (GEMMs) hold great potential to recapitulate more accurately disease models but their cost and complexity have stymied their widespread adoption in discovery, early or late drug screening programs. Recent advancements in genome editing technology made possible by the discovery and development of the CRISPR/Cas9 system has opened the opportunity of generating disease-relevant animal models by direct mutation of somatic cell genomes in an organ or tissue compartment of interest. The advent of CRISPR/Cas9 has not only aided in the production of conventional GEMMs but has also enabled the bypassing of the construction of these costly strains. In this review, we describe the Somatically Engineered Mouse Models (SEMMs) as a new category of models where a specific oncogenic signature is introduced in somatic cells of an intended organ in a post-natal animal. In addition, SEMMs represent a novel platform to perform in vivo functional genomics studies, here defined as DIVoS (Direct In Vivo Screening).
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Affiliation(s)
- Anthony Lima
- Department of Translational Oncology, Genentech, Inc., South San Francisco, CA, United States
| | - Danilo Maddalo
- Department of Translational Oncology, Genentech, Inc., South San Francisco, CA, United States
- Roche Pharmaceuticals, Basel, Switzerland
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5
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Cook PJ, Thomas R, Kannan R, de Leon ES, Drilon A, Rosenblum MK, Scaltriti M, Benezra R, Ventura A. Somatic chromosomal engineering identifies BCAN-NTRK1 as a potent glioma driver and therapeutic target. Nat Commun 2017; 8:15987. [PMID: 28695888 PMCID: PMC5508201 DOI: 10.1038/ncomms15987] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 05/19/2017] [Indexed: 12/12/2022] Open
Abstract
The widespread application of high-throughput sequencing methods is resulting in the identification of a rapidly growing number of novel gene fusions caused by tumour-specific chromosomal rearrangements, whose oncogenic potential remains unknown. Here we describe a strategy that builds upon recent advances in genome editing and combines ex vivo and in vivo chromosomal engineering to rapidly and effectively interrogate the oncogenic potential of genomic rearrangements identified in human brain cancers. We show that one such rearrangement, an microdeletion resulting in a fusion between Brevican (BCAN) and Neurotrophic Receptor Tyrosine Kinase 1 (NTRK1), is a potent oncogenic driver of high-grade gliomas and confers sensitivity to the experimental TRK inhibitor entrectinib. This work demonstrates that BCAN-NTRK1 is a bona fide human glioma driver and describes a general strategy to define the oncogenic potential of novel glioma-associated genomic rearrangements and to generate accurate preclinical models of this lethal human cancer.
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Affiliation(s)
- Peter J Cook
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Rozario Thomas
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.,Department of Molecular Biology, Weill Cornell Graduate School of Medical Sciences of Cornell University, New York, New York 10065, USA
| | - Ram Kannan
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Esther Sanchez de Leon
- Department of Molecular Biology, Weill Cornell Graduate School of Medical Sciences of Cornell University, New York, New York 10065, USA
| | - Alexander Drilon
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Marc K Rosenblum
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Maurizio Scaltriti
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Robert Benezra
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Andrea Ventura
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
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Roper J, Tammela T, Cetinbas NM, Akkad A, Roghanian A, Rickelt S, Almeqdadi M, Wu K, Oberli MA, Sánchez-Rivera FJ, Park YK, Liang X, Eng G, Taylor MS, Azimi R, Kedrin D, Neupane R, Beyaz S, Sicinska ET, Suarez Y, Yoo J, Chen L, Zukerberg L, Katajisto P, Deshpande V, Bass AJ, Tsichlis PN, Lees J, Langer R, Hynes RO, Chen J, Bhutkar A, Jacks T, Yilmaz ÖH. In vivo genome editing and organoid transplantation models of colorectal cancer and metastasis. Nat Biotechnol 2017; 35:569-576. [PMID: 28459449 PMCID: PMC5462879 DOI: 10.1038/nbt.3836] [Citation(s) in RCA: 237] [Impact Index Per Article: 33.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 03/01/2017] [Indexed: 02/07/2023]
Abstract
In vivo interrogation of the function of genes implicated in tumorigenesis is limited by the need to generate and cross germline mutant mice. Here we describe approaches to model colorectal cancer (CRC) and metastasis, which rely on in situ gene editing and orthotopic organoid transplantation in mice without cancer-predisposing mutations. Autochthonous tumor formation is induced by CRISPR-Cas9-based editing of the Apc and Trp53 tumor suppressor genes in colon epithelial cells and by orthotopic transplantation of Apc-edited colon organoids. ApcΔ/Δ;KrasG12D/+;Trp53Δ/Δ (AKP) mouse colon organoids and human CRC organoids engraft in the distal colon and metastasize to the liver. Finally, we apply the orthotopic transplantation model to characterize the clonal dynamics of Lgr5+ stem cells and demonstrate sequential activation of an oncogene in established colon adenomas. These experimental systems enable rapid in vivo characterization of cancer-associated genes and reproduce the entire spectrum of tumor progression and metastasis.
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Affiliation(s)
- Jatin Roper
- The David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, Massachusetts, USA
- Division of Gastroenterology, Tufts Medical Center, Boston, Massachusetts, USA
- Molecular Oncology Research Institute, Tufts Medical Center, Boston, Massachusetts, USA
| | - Tuomas Tammela
- The David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, Massachusetts, USA
| | - Naniye Malli Cetinbas
- The David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, Massachusetts, USA
| | - Adam Akkad
- The David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, Massachusetts, USA
| | - Ali Roghanian
- The David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, Massachusetts, USA
- Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, United Kingdom
| | - Steffen Rickelt
- The David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, Massachusetts, USA
| | - Mohammad Almeqdadi
- The David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, Massachusetts, USA
| | - Katherine Wu
- The David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, Massachusetts, USA
| | - Matthias A Oberli
- The David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, Massachusetts, USA
| | | | - Yoona K Park
- The David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, Massachusetts, USA
| | - Xu Liang
- The David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, Massachusetts, USA
| | - George Eng
- The David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, Massachusetts, USA
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Martin S Taylor
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Roxana Azimi
- The David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, Massachusetts, USA
| | - Dmitriy Kedrin
- The David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, Massachusetts, USA
| | - Rachit Neupane
- The David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, Massachusetts, USA
| | - Semir Beyaz
- The David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, Massachusetts, USA
| | - Ewa T Sicinska
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Yvelisse Suarez
- Department of Pathology, Tufts Medical Center, Boston, Massachusetts, USA
| | - James Yoo
- Molecular Oncology Research Institute, Tufts Medical Center, Boston, Massachusetts, USA
- Department of Surgery, Tufts Medical Center, Boston, Massachusetts, USA
| | - Lillian Chen
- Department of Surgery, Tufts Medical Center, Boston, Massachusetts, USA
| | - Lawrence Zukerberg
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Pekka Katajisto
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Vikram Deshpande
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Adam J Bass
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts, USA
| | - Philip N Tsichlis
- Molecular Oncology Research Institute, Tufts Medical Center, Boston, Massachusetts, USA
| | - Jacqueline Lees
- The David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, Massachusetts, USA
| | - Robert Langer
- The David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, Massachusetts, USA
| | - Richard O Hynes
- The David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, Massachusetts, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jianzhu Chen
- The David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, Massachusetts, USA
| | - Arjun Bhutkar
- The David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, Massachusetts, USA
| | - Tyler Jacks
- The David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, Massachusetts, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Ömer H Yilmaz
- The David H. Koch Institute for Integrative Cancer Research at MIT, Cambridge, Massachusetts, USA
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
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