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Sánchez Rivera FJ, Dow LE. How CRISPR Is Revolutionizing the Generation of New Models for Cancer Research. Cold Spring Harb Perspect Med 2024; 14:a041384. [PMID: 37487630 PMCID: PMC11065179 DOI: 10.1101/cshperspect.a041384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023]
Abstract
Cancers arise through acquisition of mutations in genes that regulate core biological processes like cell proliferation and cell death. Decades of cancer research have led to the identification of genes and mutations causally involved in disease development and evolution, yet defining their precise function across different cancer types and how they influence therapy responses has been challenging. Mouse models have helped define the in vivo function of cancer-associated alterations, and genome-editing approaches using CRISPR have dramatically accelerated the pace at which these models are developed and studied. Here, we highlight how CRISPR technologies have impacted the development and use of mouse models for cancer research and discuss the many ways in which these rapidly evolving platforms will continue to transform our understanding of this disease.
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Affiliation(s)
- Francisco J Sánchez Rivera
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Lukas E Dow
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, New York 10065, USA
- Department of Biochemistry, Weill Cornell Medicine, New York, New York 10065, USA
- Department of Medicine, Weill Cornell Medicine, New York, New York 10065, USA
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2
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Murphy KC, Ruscetti M. Advances in Making Cancer Mouse Models More Accessible and Informative through Non-Germline Genetic Engineering. Cold Spring Harb Perspect Med 2024; 14:a041348. [PMID: 37277206 PMCID: PMC10982712 DOI: 10.1101/cshperspect.a041348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Genetically engineered mouse models (GEMMs) allow for modeling of spontaneous tumorigenesis within its native microenvironment in mice and have provided invaluable insights into mechanisms of tumorigenesis and therapeutic strategies to treat human disease. However, as their generation requires germline manipulation and extensive animal breeding that is time-, labor-, and cost-intensive, traditional GEMMs are not accessible to most researchers, and fail to model the full breadth of cancer-associated genetic alterations and therapeutic targets. Recent advances in genome-editing technologies and their implementation in somatic tissues of mice have ushered in a new class of mouse models: non-germline GEMMs (nGEMMs). nGEMM approaches can be leveraged to generate somatic tumors de novo harboring virtually any individual or group of genetic alterations found in human cancer in a mouse through simple procedures that do not require breeding, greatly increasing the accessibility and speed and scale on which GEMMs can be produced. Here we describe the technologies and delivery systems used to create nGEMMs and highlight new biological insights derived from these models that have rapidly informed functional cancer genomics, precision medicine, and immune oncology.
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Affiliation(s)
- Katherine C Murphy
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, USA
| | - Marcus Ruscetti
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, USA;
- Immunology and Microbiology Program, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, USA
- Cancer Center, University of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, USA
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3
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Le Roux Ö, Everitt JI, Counter CM. p53 dosage can impede KrasG12D- and KrasQ61R-mediated tumorigenesis. PLoS One 2024; 19:e0292189. [PMID: 38547169 PMCID: PMC10977719 DOI: 10.1371/journal.pone.0292189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 01/03/2024] [Indexed: 04/02/2024] Open
Abstract
Mice engineered with a G12D versus Q61R mutation in Kras exhibited differences in tumorigenesis. Namely, the incidence or grade of oral or forestomach squamous epithelial lesions was more prevalent in the KrasG12D background while hematolymphopoietic disease was more prevalent in the KrasQ61R background. Loss of the Trp53 gene encoding the tumor suppressor p53 enhances the ability of oncogenic Kras to initiate tumorigenesis in carcinogen and genetic models of lung cancer. Conversley, an extra copy of Trp53 (Super p53) was recently shown to suppress Kras-induced tumorigenesis in a genetic model of this disease. Given this, we evaluated whether an extra copy of Trp53 would alter tumorigenesis upon global activation of a modified Kras allele engineered with either a G12D or Q61R mutation. We report that an increase in p53 dosage significantly reduced the incidence or grade of oral and forestomach squamous tumors induced by either G12D and Q61R-mutant Kras. The incidence of myeloproliferative disease was also significantly reduced with increased p53 dosage in the KrasQ61R background. Both the percentage of mice with lung tumors and total number of adenomas per animal were unchanged. However, the incidence and grade of peripheral atypical alveolar hyperplasia was significantly decreased in both backgrounds with increased p53 dosage. Finally, the number of foci of bronchioloalveolar hyperplasia per animal significantly increased with increased p53 dosage in the KrasG12D background. These results suggest that an extra copy of p53 can impede oncogenic Kras driven tumorigenesis in some tissues.
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Affiliation(s)
- Özgün Le Roux
- Department of Pharmacology & Cancer Biology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Jeffery I. Everitt
- Department of Pathology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Christopher M. Counter
- Department of Pharmacology & Cancer Biology, Duke University Medical Center, Durham, North Carolina, United States of America
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4
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Gould SI, Wuest AN, Dong K, Johnson GA, Hsu A, Narendra VK, Atwa O, Levine SS, Liu DR, Sánchez Rivera FJ. High-throughput evaluation of genetic variants with prime editing sensor libraries. Nat Biotechnol 2024:10.1038/s41587-024-02172-9. [PMID: 38472508 DOI: 10.1038/s41587-024-02172-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 02/09/2024] [Indexed: 03/14/2024]
Abstract
Tumor genomes often harbor a complex spectrum of single nucleotide alterations and chromosomal rearrangements that can perturb protein function. Prime editing has been applied to install and evaluate genetic variants, but previous approaches have been limited by the variable efficiency of prime editing guide RNAs. Here we present a high-throughput prime editing sensor strategy that couples prime editing guide RNAs with synthetic versions of their cognate target sites to quantitatively assess the functional impact of endogenous genetic variants. We screen over 1,000 endogenous cancer-associated variants of TP53-the most frequently mutated gene in cancer-to identify alleles that impact p53 function in mechanistically diverse ways. We find that certain endogenous TP53 variants, particularly those in the p53 oligomerization domain, display opposite phenotypes in exogenous overexpression systems. Our results emphasize the physiological importance of gene dosage in shaping native protein stoichiometry and protein-protein interactions, and establish a framework for studying genetic variants in their endogenous sequence context at scale.
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Affiliation(s)
- Samuel I Gould
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alexandra N Wuest
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kexin Dong
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- University of Chinese Academy of Sciences, Beijing, China
| | - Grace A Johnson
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alvin Hsu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Varun K Narendra
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ondine Atwa
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Stuart S Levine
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Francisco J Sánchez Rivera
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
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5
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Katti A, Vega-Pérez A, Foronda M, Zimmerman J, Zafra MP, Granowsky E, Goswami S, Gardner EE, Diaz BJ, Simon JM, Wuest A, Luan W, Fernandez MTC, Kadina AP, Walker JA, Holden K, Lowe SW, Sánchez Rivera FJ, Dow LE. Generation of precision preclinical cancer models using regulated in vivo base editing. Nat Biotechnol 2024; 42:437-447. [PMID: 37563300 PMCID: PMC11295146 DOI: 10.1038/s41587-023-01900-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 07/10/2023] [Indexed: 08/12/2023]
Abstract
Although single-nucleotide variants (SNVs) make up the majority of cancer-associated genetic changes and have been comprehensively catalogued, little is known about their impact on tumor initiation and progression. To enable the functional interrogation of cancer-associated SNVs, we developed a mouse system for temporal and regulatable in vivo base editing. The inducible base editing (iBE) mouse carries a single expression-optimized cytosine base editor transgene under the control of a tetracycline response element and enables robust, doxycycline-dependent expression across a broad range of tissues in vivo. Combined with plasmid-based or synthetic guide RNAs, iBE drives efficient engineering of individual or multiple SNVs in intestinal, lung and pancreatic organoids. Temporal regulation of base editor activity allows controlled sequential genome editing ex vivo and in vivo, and delivery of sgRNAs directly to target tissues facilitates generation of in situ preclinical cancer models.
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Affiliation(s)
- Alyna Katti
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Adrián Vega-Pérez
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Miguel Foronda
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jill Zimmerman
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Maria Paz Zafra
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Biosanitary Research Institute (IBS)-Granada, Granada, Spain
| | - Elizabeth Granowsky
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Sukanya Goswami
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Eric E Gardner
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Bianca J Diaz
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Janelle M Simon
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexandra Wuest
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wei Luan
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | | | | | - Scott W Lowe
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Francisco J Sánchez Rivera
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Lukas E Dow
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
- Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA.
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
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6
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Ely ZA, Mathey-Andrews N, Naranjo S, Gould SI, Mercer KL, Newby GA, Cabana CM, Rideout WM, Jaramillo GC, Khirallah JM, Holland K, Randolph PB, Freed-Pastor WA, Davis JR, Kulstad Z, Westcott PMK, Lin L, Anzalone AV, Horton BL, Pattada NB, Shanahan SL, Ye Z, Spranger S, Xu Q, Sánchez-Rivera FJ, Liu DR, Jacks T. A prime editor mouse to model a broad spectrum of somatic mutations in vivo. Nat Biotechnol 2024; 42:424-436. [PMID: 37169967 PMCID: PMC11120832 DOI: 10.1038/s41587-023-01783-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 04/05/2023] [Indexed: 05/13/2023]
Abstract
Genetically engineered mouse models only capture a small fraction of the genetic lesions that drive human cancer. Current CRISPR-Cas9 models can expand this fraction but are limited by their reliance on error-prone DNA repair. Here we develop a system for in vivo prime editing by encoding a Cre-inducible prime editor in the mouse germline. This model allows rapid, precise engineering of a wide range of mutations in cell lines and organoids derived from primary tissues, including a clinically relevant Kras mutation associated with drug resistance and Trp53 hotspot mutations commonly observed in pancreatic cancer. With this system, we demonstrate somatic prime editing in vivo using lipid nanoparticles, and we model lung and pancreatic cancer through viral delivery of prime editing guide RNAs or orthotopic transplantation of prime-edited organoids. We believe that this approach will accelerate functional studies of cancer-associated mutations and complex genetic combinations that are challenging to construct with traditional models.
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Affiliation(s)
- Zackery A Ely
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nicolas Mathey-Andrews
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Santiago Naranjo
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Samuel I Gould
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kim L Mercer
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Gregory A Newby
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Christina M Cabana
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - William M Rideout
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Grissel Cervantes Jaramillo
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Katie Holland
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Angelo State University, San Angelo, TX, USA
| | - Peyton B Randolph
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - William A Freed-Pastor
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jessie R Davis
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Zachary Kulstad
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Peter M K Westcott
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Cold Spring Harbor Laboratory, Huntington, NY, USA
| | - Lin Lin
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Andrew V Anzalone
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Brendan L Horton
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nimisha B Pattada
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sean-Luc Shanahan
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Zhongfeng Ye
- Department of Biomedical Engineering, Tufts University, Medford, MA, USA
| | - Stefani Spranger
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Qiaobing Xu
- Department of Biomedical Engineering, Tufts University, Medford, MA, USA
| | - Francisco J Sánchez-Rivera
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Tyler Jacks
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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7
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Khoshandam M, Soltaninejad H, Mousazadeh M, Hamidieh AA, Hosseinkhani S. Clinical applications of the CRISPR/Cas9 genome-editing system: Delivery options and challenges in precision medicine. Genes Dis 2024; 11:268-282. [PMID: 37588217 PMCID: PMC10425811 DOI: 10.1016/j.gendis.2023.02.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 02/08/2023] [Indexed: 03/29/2023] Open
Abstract
CRISPR/Cas9 is an effective gene editing tool with broad applications for the prevention or treatment of numerous diseases. It depends on CRISPR (clustered regularly interspaced short palindromic repeats) as a bacterial immune system and plays as a gene editing tool. Due to the higher specificity and efficiency of CRISPR/Cas9 compared to other editing approaches, it has been broadly investigated to treat numerous hereditary and acquired illnesses, including cancers, hemolytic diseases, immunodeficiency disorders, cardiovascular diseases, visual maladies, neurodegenerative conditions, and a few X-linked disorders. CRISPR/Cas9 system has been used to treat cancers through a variety of approaches, with stable gene editing techniques. Here, the applications and clinical trials of CRISPR/Cas9 in various illnesses are described. Due to its high precision and efficiency, CRISPR/Cas9 strategies may treat gene-related illnesses by deleting, inserting, modifying, or blocking the expression of specific genes. The most challenging barrier to the in vivo use of CRISPR/Cas9 like off-target effects will be discussed. The use of transfection vehicles for CRISPR/Cas9, including viral vectors (such as an Adeno-associated virus (AAV)), and the development of non-viral vectors is also considered.
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Affiliation(s)
- Mohadeseh Khoshandam
- Department of Reproductive Biology, Academic Center for Education, Culture, and Research (ACECR), Qom Branch, Qom 3716986466, Iran
- National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran 14155-6463, Iran
| | - Hossein Soltaninejad
- Faculty of Interdisciplinary Science and Technology, Tarbiat Modares University, Tehran 14117-13116, Iran
- Pediatric Cell and Gene Therapy Research Center, Gene, Cell & Tissue Research Institute, Tehran University of Medical Sciences, Tehran 14155-6559, Iran
| | - Marziyeh Mousazadeh
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14117-13116, Iran
| | - Amir Ali Hamidieh
- Pediatric Cell and Gene Therapy Research Center, Gene, Cell & Tissue Research Institute, Tehran University of Medical Sciences, Tehran 14155-6559, Iran
| | - Saman Hosseinkhani
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14117-13116, Iran
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8
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Shan C, Liang Y, Wang K, Li P. Mesenchymal Stem Cell-Derived Extracellular Vesicles in Cancer Therapy Resistance: from Biology to Clinical Opportunity. Int J Biol Sci 2024; 20:347-366. [PMID: 38164177 PMCID: PMC10750277 DOI: 10.7150/ijbs.88500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 11/09/2023] [Indexed: 01/03/2024] Open
Abstract
Mesenchymal stem cells (MSCs) are a type of stromal cells characterized by their properties of self-renewal and multi-lineage differentiation, which make them prominent in regenerative medicine. MSCs have shown significant potential for the treatment of various diseases, primarily through the paracrine effects mediated by soluble factors, specifically extracellular vesicles (EVs). MSC-EVs play a crucial role in intercellular communication by transferring various bioactive substances, including proteins, RNA, DNA, and lipids, highlighting the contribution of MSC-EVs in regulating cancer development and progression. Remarkably, increasing evidence indicates the association between MSC-EVs and resistance to various types of cancer treatments, including radiotherapy, chemotherapy, targeted therapy, immunotherapy, and endocrinotherapy. In this review, we provide an overview of the recent advancements in the biogenesis, isolation, and characterization of MSC-EVs, with an emphasis on their functions in cancer therapy resistance. The clinical applications and future prospects of MSC-EVs for mitigating cancer therapy resistance and enhancing drug delivery are also discussed. Elucidating the role and mechanism of MSC-EVs in the development of treatment resistance in cancer, as well as evaluating the clinical significance of MSC-EVs, is crucial for advancing our understanding of tumor biology. Meanwhile, inform the development of effective treatment strategies for cancer patients in the future.
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Affiliation(s)
- Chan Shan
- Institute of Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Yan Liang
- Department of Pharmaceutics, School of Pharmacy, Qingdao University, Qingdao 266021, China
| | - Kun Wang
- Institute of Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Peifeng Li
- Institute of Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
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9
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Zeissig MN, Ashwood LM, Kondrashova O, Sutherland KD. Next batter up! Targeting cancers with KRAS-G12D mutations. Trends Cancer 2023; 9:955-967. [PMID: 37591766 DOI: 10.1016/j.trecan.2023.07.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 06/12/2023] [Accepted: 07/18/2023] [Indexed: 08/19/2023]
Abstract
KRAS is the most frequently mutated oncogene in cancer. Activating mutations in codon 12, especially G12D, have the highest prevalence across a range of carcinomas and adenocarcinomas. With inhibitors to KRAS-G12D now entering clinical trials, understanding the biology of KRAS-G12D cancers, and identifying biomarkers that predict therapeutic response is crucial. In this Review, we discuss the genomics and biology of KRAS-G12D adenocarcinomas, including histological features, transcriptional landscape, the immune microenvironment, and how these factors influence response to therapy. Moreover, we explore potential therapeutic strategies using novel G12D inhibitors, leveraging knowledge gained from clinical trials using G12C inhibitors.
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Affiliation(s)
- Mara N Zeissig
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, 3052, Australia
| | - Lauren M Ashwood
- QIMR Berghofer Medical Research Institute, Herston, 4006, Australia; The University of Queensland, Brisbane, 4072, Australia
| | - Olga Kondrashova
- QIMR Berghofer Medical Research Institute, Herston, 4006, Australia; The University of Queensland, Brisbane, 4072, Australia
| | - Kate D Sutherland
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, 3052, Australia.
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10
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Ravichandran M, Maddalo D. Applications of CRISPR-Cas9 for advancing precision medicine in oncology: from target discovery to disease modeling. Front Genet 2023; 14:1273994. [PMID: 37908590 PMCID: PMC10613999 DOI: 10.3389/fgene.2023.1273994] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 09/27/2023] [Indexed: 11/02/2023] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (Cas9) (CRISPR/Cas9) system is a powerful tool that enables precise and efficient gene manipulation. In a relatively short time, CRISPR has risen to become the preferred gene-editing system due to its high efficiency, simplicity, and programmability at low costs. Furthermore, in the recent years, the CRISPR toolkit has been rapidly expanding, and the emerging advancements have shown tremendous potential in uncovering molecular mechanisms and new therapeutic strategies for human diseases. In this review, we provide our perspectives on the recent advancements in CRISPR technology and its impact on precision medicine, ranging from target identification, disease modeling, and diagnostics. We also discuss the impact of novel approaches such as epigenome, base, and prime editing on preclinical cancer drug discovery.
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Affiliation(s)
- Mirunalini Ravichandran
- 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
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11
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Blair LM, Juan JM, Sebastian L, Tran VB, Nie W, Wall GD, Gerceker M, Lai IK, Apilado EA, Grenot G, Amar D, Foggetti G, Do Carmo M, Ugur Z, Deng D, Chenchik A, Paz Zafra M, Dow LE, Politi K, MacQuitty JJ, Petrov DA, Winslow MM, Rosen MJ, Winters IP. Oncogenic context shapes the fitness landscape of tumor suppression. Nat Commun 2023; 14:6422. [PMID: 37828026 PMCID: PMC10570323 DOI: 10.1038/s41467-023-42156-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 10/02/2023] [Indexed: 10/14/2023] Open
Abstract
Tumors acquire alterations in oncogenes and tumor suppressor genes in an adaptive walk through the fitness landscape of tumorigenesis. However, the interactions between oncogenes and tumor suppressor genes that shape this landscape remain poorly resolved and cannot be revealed by human cancer genomics alone. Here, we use a multiplexed, autochthonous mouse platform to model and quantify the initiation and growth of more than one hundred genotypes of lung tumors across four oncogenic contexts: KRAS G12D, KRAS G12C, BRAF V600E, and EGFR L858R. We show that the fitness landscape is rugged-the effect of tumor suppressor inactivation often switches between beneficial and deleterious depending on the oncogenic context-and shows no evidence of diminishing-returns epistasis within variants of the same oncogene. These findings argue against a simple linear signaling relationship amongst these three oncogenes and imply a critical role for off-axis signaling in determining the fitness effects of inactivating tumor suppressors.
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Affiliation(s)
| | | | | | - Vy B Tran
- D2G Oncology, Mountain View, CA, USA
| | | | | | | | - Ian K Lai
- D2G Oncology, Mountain View, CA, USA
| | | | | | - David Amar
- D2G Oncology, Mountain View, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
- Department of Cardiovascular Medicine and the Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Mariana Do Carmo
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Zeynep Ugur
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | | | | | - Maria Paz Zafra
- Sandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Excellence Research Unit "Modeling Nature" (MNat), University of Granada, E-18016, Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), E-18071, Granada, Spain
| | - Lukas E Dow
- Sandra and Edward Meyer Cancer Center, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Katerina Politi
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
- Section of Medical Oncology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | | | - Dmitri A Petrov
- Department of Biology, Stanford University, Stanford, CA, USA
- Chan Zuckerberg BioHub, San Francisco, CA, USA
| | - Monte M Winslow
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
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12
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Lue NZ, Liau BB. Base editor screens for in situ mutational scanning at scale. Mol Cell 2023; 83:2167-2187. [PMID: 37390819 PMCID: PMC10330937 DOI: 10.1016/j.molcel.2023.06.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/30/2023] [Accepted: 06/06/2023] [Indexed: 07/02/2023]
Abstract
A fundamental challenge in biology is understanding the molecular details of protein function. How mutations alter protein activity, regulation, and response to drugs is of critical importance to human health. Recent years have seen the emergence of pooled base editor screens for in situ mutational scanning: the interrogation of protein sequence-function relationships by directly perturbing endogenous proteins in live cells. These studies have revealed the effects of disease-associated mutations, discovered novel drug resistance mechanisms, and generated biochemical insights into protein function. Here, we discuss how this "base editor scanning" approach has been applied to diverse biological questions, compare it with alternative techniques, and describe the emerging challenges that must be addressed to maximize its utility. Given its broad applicability toward profiling mutations across the proteome, base editor scanning promises to revolutionize the investigation of proteins in their native contexts.
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Affiliation(s)
- Nicholas Z Lue
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Brian B Liau
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
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13
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Tang YJ, Shuldiner EG, Karmakar S, Winslow MM. High-Throughput Identification, Modeling, and Analysis of Cancer Driver Genes In Vivo. Cold Spring Harb Perspect Med 2023; 13:a041382. [PMID: 37277208 PMCID: PMC10317066 DOI: 10.1101/cshperspect.a041382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The vast number of genomic and molecular alterations in cancer pose a substantial challenge to uncovering the mechanisms of tumorigenesis and identifying therapeutic targets. High-throughput functional genomic methods in genetically engineered mouse models allow for rapid and systematic investigation of cancer driver genes. In this review, we discuss the basic concepts and tools for multiplexed investigation of functionally important cancer genes in vivo using autochthonous cancer models. Furthermore, we highlight emerging technical advances in the field, potential opportunities for future investigation, and outline a vision for integrating multiplexed genetic perturbations with detailed molecular analyses to advance our understanding of the genetic and molecular basis of cancer.
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Affiliation(s)
- Yuning J Tang
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Emily G Shuldiner
- Department of Biology, Stanford University, Stanford, California 94305, USA
| | - Saswati Karmakar
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Monte M Winslow
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA
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14
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Bu W, Creighton CJ, Heavener KS, Gutierrez C, Dou Y, Ku AT, Zhang Y, Jiang W, Urrutia J, Jiang W, Yue F, Jia L, Ibrahim AA, Zhang B, Huang S, Li Y. Efficient cancer modeling through CRISPR-Cas9/HDR-based somatic precision gene editing in mice. SCIENCE ADVANCES 2023; 9:eade0059. [PMID: 37172086 PMCID: PMC10181191 DOI: 10.1126/sciadv.ade0059] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 04/06/2023] [Indexed: 05/14/2023]
Abstract
CRISPR-Cas9 has been used successfully to introduce indels in somatic cells of rodents; however, precise editing of single nucleotides has been hampered by limitations of flexibility and efficiency. Here, we report technological modifications to the CRISPR-Cas9 vector system that now allows homology-directed repair-mediated precise editing of any proto-oncogene in murine somatic tissues to generate tumor models with high flexibility and efficiency. Somatic editing of either Kras or Pik3ca in both normal and hyperplastic mammary glands led to swift tumorigenesis. The resulting tumors shared some histological, transcriptome, and proteome features with tumors induced by lentivirus-mediated expression of the respective oncogenes, but they also exhibited some distinct characteristics, particularly showing less intertumor variation, thus potentially offering more consistent models for cancer studies and therapeutic development. Therefore, this technological advance fills a critical gap between the power of CRISPR technology and high-fidelity mouse models for studying human tumor evolution and preclinical drug testing.
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Affiliation(s)
- Wen Bu
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Chad J. Creighton
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Kelsey S. Heavener
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA
| | - Carolina Gutierrez
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA
| | - Yongchao Dou
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Amy T. Ku
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA
| | - Yiqun Zhang
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Weiyu Jiang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA
| | - Jazmin Urrutia
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA
| | - Wen Jiang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Fei Yue
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Luyu Jia
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA
| | - Ahmed Atef Ibrahim
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Shixia Huang
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Department of Education, Innovation, and Technology, Baylor College of Medicine, Houston, TX, USA
| | - Yi Li
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
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15
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Sevrin T, Strasser L, Ternet C, Junk P, Caffarini M, Prins S, D’Arcy C, Catozzi S, Oliviero G, Wynne K, Kiel C, Luthert PJ. Whole-cell energy modeling reveals quantitative changes of predicted energy flows in RAS mutant cancer cell lines. iScience 2023; 26:105931. [PMID: 36711246 PMCID: PMC9874014 DOI: 10.1016/j.isci.2023.105931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 10/27/2022] [Accepted: 01/03/2023] [Indexed: 01/06/2023] Open
Abstract
Cellular utilization of available energy flows to drive a multitude of forms of cellular "work" is a major biological constraint. Cells steer metabolism to address changing phenotypic states but little is known as to how bioenergetics couples to the richness of processes in a cell as a whole. Here, we outline a whole-cell energy framework that is informed by proteomic analysis and an energetics-based gene ontology. We separate analysis of metabolic supply and the capacity to generate high-energy phosphates from a representation of demand that is built on the relative abundance of ATPases and GTPases that deliver cellular work. We employed mouse embryonic fibroblast cell lines that express wild-type KRAS or oncogenic mutations and with distinct phenotypes. We observe shifts between energy-requiring processes. Calibrating against Seahorse analysis, we have created a whole-cell energy budget with apparent predictive power, for instance in relation to protein synthesis.
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Affiliation(s)
- Thomas Sevrin
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield Dublin 4, Ireland
- UCD Charles Institute of Dermatology, School of Medicine, University College Dublin, Belfield Dublin 4, Ireland
| | - Lisa Strasser
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield Dublin 4, Ireland
- UCD Charles Institute of Dermatology, School of Medicine, University College Dublin, Belfield Dublin 4, Ireland
| | - Camille Ternet
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield Dublin 4, Ireland
- UCD Charles Institute of Dermatology, School of Medicine, University College Dublin, Belfield Dublin 4, Ireland
| | - Philipp Junk
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield Dublin 4, Ireland
- UCD Charles Institute of Dermatology, School of Medicine, University College Dublin, Belfield Dublin 4, Ireland
| | - Miriam Caffarini
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield Dublin 4, Ireland
- UCD Charles Institute of Dermatology, School of Medicine, University College Dublin, Belfield Dublin 4, Ireland
| | - Stella Prins
- UCL Institute of Ophthalmology, University College London, 11-43 Bath Street, London EC1V 9EL, UK
| | - Cian D’Arcy
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield Dublin 4, Ireland
- UCD Charles Institute of Dermatology, School of Medicine, University College Dublin, Belfield Dublin 4, Ireland
| | - Simona Catozzi
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield Dublin 4, Ireland
- UCD Charles Institute of Dermatology, School of Medicine, University College Dublin, Belfield Dublin 4, Ireland
| | - Giorgio Oliviero
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield Dublin 4, Ireland
| | - Kieran Wynne
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield Dublin 4, Ireland
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin 4, Ireland
| | - Christina Kiel
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield Dublin 4, Ireland
- UCD Charles Institute of Dermatology, School of Medicine, University College Dublin, Belfield Dublin 4, Ireland
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Corresponding author
| | - Philip J. Luthert
- UCL Institute of Ophthalmology, University College London, 11-43 Bath Street, London EC1V 9EL, UK
- NIHR Moorfields Biomedical Research Centre, University College London, 11-43 Bath Street, London EC1V 9EL, UK
- Corresponding author
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16
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The dynamicity of mutant KRAS β2 strand modulates its downstream activation and predicts anticancer KRAS inhibition. Life Sci 2022; 310:121053. [DOI: 10.1016/j.lfs.2022.121053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 10/03/2022] [Accepted: 10/05/2022] [Indexed: 11/05/2022]
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17
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Scharpf RB, Balan A, Ricciuti B, Fiksel J, Cherry C, Wang C, Lenoue-Newton ML, Rizvi HA, White JR, Baras AS, Anaya J, Landon BV, Majcherska-Agrawal M, Ghanem P, Lee J, Raskin L, Park AS, Tu H, Hsu H, Arbour KC, Awad MM, Riely GJ, Lovly CM, Anagnostou V. Genomic Landscapes and Hallmarks of Mutant RAS in Human Cancers. Cancer Res 2022; 82:4058-4078. [PMID: 36074020 PMCID: PMC9627127 DOI: 10.1158/0008-5472.can-22-1731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 08/12/2022] [Accepted: 09/01/2022] [Indexed: 01/07/2023]
Abstract
The RAS family of small GTPases represents the most commonly activated oncogenes in human cancers. To better understand the prevalence of somatic RAS mutations and the compendium of genes that are coaltered in RAS-mutant tumors, we analyzed targeted next-generation sequencing data of 607,863 mutations from 66,372 tumors in 51 cancer types in the AACR Project GENIE Registry. Bayesian hierarchical models were implemented to estimate the cancer-specific prevalence of RAS and non-RAS somatic mutations, to evaluate co-occurrence and mutual exclusivity, and to model the effects of tumor mutation burden and mutational signatures on comutation patterns. These analyses revealed differential RAS prevalence and comutations with non-RAS genes in a cancer lineage-dependent and context-dependent manner, with differences across age, sex, and ethnic groups. Allele-specific RAS co-mutational patterns included an enrichment in NTRK3 and chromatin-regulating gene mutations in KRAS G12C-mutant non-small cell lung cancer. Integrated multiomic analyses of 10,217 tumors from The Cancer Genome Atlas (TCGA) revealed distinct genotype-driven gene expression programs pointing to differential recruitment of cancer hallmarks as well as phenotypic differences and immune surveillance states in the tumor microenvironment of RAS-mutant tumors. The distinct genomic tracks discovered in RAS-mutant tumors reflected differential clinical outcomes in TCGA cohort and in an independent cohort of patients with KRAS G12C-mutant non-small cell lung cancer that received immunotherapy-containing regimens. The RAS genetic architecture points to cancer lineage-specific therapeutic vulnerabilities that can be leveraged for rationally combining RAS-mutant allele-directed therapies with targeted therapies and immunotherapy. SIGNIFICANCE The complex genomic landscape of RAS-mutant tumors is reflective of selection processes in a cancer lineage-specific and context-dependent manner, highlighting differential therapeutic vulnerabilities that can be clinically translated.
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Affiliation(s)
- Robert B. Scharpf
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Archana Balan
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Biagio Ricciuti
- Department of Medicine, Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jacob Fiksel
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Christopher Cherry
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Chenguang Wang
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Michele L. Lenoue-Newton
- Division of Hematology-Oncology, Department of Medicine, Vanderbilt University Medical Center and Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
| | - Hira A. Rizvi
- Department of Medicine, Collaborative Research Centers, Memorial Sloan Kettering Cancer Center, New York, New York
| | - James R. White
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Alexander S. Baras
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jordan Anaya
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Blair V. Landon
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Marta Majcherska-Agrawal
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Paola Ghanem
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jocelyn Lee
- AACR Project GENIE, American Association for Cancer Research, Pennsylvania
| | - Leon Raskin
- Center for Observational Research, Amgen Inc., Thousand Oaks, California
| | - Andrew S. Park
- Center for Observational Research, Amgen Inc., Thousand Oaks, California
| | - Huakang Tu
- Center for Observational Research, Amgen Inc., Thousand Oaks, California
| | - Hil Hsu
- Center for Observational Research, Amgen Inc., Thousand Oaks, California
| | - Kathryn C. Arbour
- Department of Medicine, Division of Clinical Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mark M. Awad
- Department of Medicine, Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Gregory J. Riely
- Department of Medicine, Division of Clinical Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Christine M. Lovly
- Division of Hematology-Oncology, Department of Medicine, Vanderbilt University Medical Center and Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
| | - Valsamo Anagnostou
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
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18
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Shi H, Seegobin K, Heng F, Zhou K, Chen R, Qin H, Manochakian R, Zhao Y, Lou Y. Genomic landscape of lung adenocarcinomas in different races. Front Oncol 2022; 12:946625. [PMID: 36248982 PMCID: PMC9557241 DOI: 10.3389/fonc.2022.946625] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 09/05/2022] [Indexed: 11/26/2022] Open
Abstract
Background Lung adenocarcinoma is a molecularly heterogeneous disease. Several studies, including The Cancer Genome Atlas Research Network (TCGA) and Lung Cancer Mutation Consortium (LCMC), explored the genetic alterations among different ethnic groups. However, minority groups are often under-represented in these relevant studies and the genomic alterations among racial groups are not fully understood. Methods We analyze genomic characteristics among racial groups to understand the diversities and their impact on clinical outcomes. Results Native Americans had significantly higher rates of insertions and deletions than other races (P<0.001). Among patients with lung adenocarcinomas, EGFR and KRAS were the highest discrepancy genes in the different racial groups (P<0.001). The EGFR exon 21 L858R point mutation was three times higher in Asians than in all other races (P<0.001). Asians, Whites, and Blacks had 4.7%, 3.1%, and 1.8% ALK rearrangement, respectively (P<0.001). White patients had the highest rates of reported KRAS G12C (15.51%) than other races (P<0.001). Whites (17.2%), Blacks (15.1%), and Other (15.7%) had higher rates of STK11 mutation than Asians (3.94%) (P<0.001). RET rearrangement and ERBB2 amplification were more common in Asian patients than in Other racial groups. Apart from point mutations, structural variations, and fusion genes, we identified a significant amount of copy number alterations in each race. Conclusions The tumor genomic landscape is significantly distinct in different races. This data would shed light on the understanding of molecular alterations and their impacts on clinical management in different lung cancer patients.
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Affiliation(s)
- Huashan Shi
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, United States
| | - Karan Seegobin
- Department of Hematology and Oncology, Mayo Clinic, Jacksonville, FL, United States
| | - Fei Heng
- Department of Mathematics and Statistics, University of North Florida, Jacksonville, FL, United States
| | - Kexun Zhou
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL, United States
| | - Ruqin Chen
- Department of Hematology and Oncology, Mayo Clinic, Jacksonville, FL, United States
| | - Hong Qin
- Department of Hematology and Oncology, Mayo Clinic, Jacksonville, FL, United States
| | - Rami Manochakian
- Department of Hematology and Oncology, Mayo Clinic, Jacksonville, FL, United States
| | - Yujie Zhao
- Department of Hematology and Oncology, Mayo Clinic, Jacksonville, FL, United States
| | - Yanyan Lou
- Department of Hematology and Oncology, Mayo Clinic, Jacksonville, FL, United States
- *Correspondence: Yanyan Lou,
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19
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Le Roux Ö, Pershing NLK, Kaltenbrun E, Newman NJ, Everitt JI, Baldelli E, Pierobon M, Petricoin EF, Counter CM. Genetically manipulating endogenous Kras levels and oncogenic mutations in vivo influences tissue patterning of murine tumorigenesis. eLife 2022; 11:e75715. [PMID: 36069770 PMCID: PMC9451540 DOI: 10.7554/elife.75715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 08/02/2022] [Indexed: 12/04/2022] Open
Abstract
Despite multiple possible oncogenic mutations in the proto-oncogene KRAS, unique subsets of these mutations are detected in different cancer types. As KRAS mutations occur early, if not being the initiating event, these mutational biases are ostensibly a product of how normal cells respond to the encoded oncoprotein. Oncogenic mutations can impact not only the level of active oncoprotein, but also engagement with proteins. To attempt to separate these two effects, we generated four novel Cre-inducible (LSL) Kras alleles in mice with the biochemically distinct G12D or Q61R mutations and encoded by native (nat) rare or common (com) codons to produce low or high protein levels. While there were similarities, each allele also induced a distinct transcriptional response shortly after activation in vivo. At one end of the spectrum, activating the KrasLSL-natG12D allele induced transcriptional hallmarks suggestive of an expansion of multipotent cells, while at the other end, activating the KrasLSL-comQ61R allele led to hallmarks of hyperproliferation and oncogenic stress. Evidence suggests that these changes may be a product of signaling differences due to increased protein expression as well as the specific mutation. To determine the impact of these distinct responses on RAS mutational patterning in vivo, all four alleles were globally activated, revealing that hematolymphopoietic lesions were permissive to the level of active oncoprotein, squamous tumors were permissive to the G12D mutant, while carcinomas were permissive to both these features. We suggest that different KRAS mutations impart unique signaling properties that are preferentially capable of inducing tumor initiation in a distinct cell-specific manner.
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Affiliation(s)
- Özgün Le Roux
- Department of Pharmacology & Cancer Biology, Duke University Medical CenterDurhamUnited States
| | - Nicole LK Pershing
- Department of Pharmacology & Cancer Biology, Duke University Medical CenterDurhamUnited States
| | - Erin Kaltenbrun
- Department of Pharmacology & Cancer Biology, Duke University Medical CenterDurhamUnited States
| | - Nicole J Newman
- Department of Pharmacology & Cancer Biology, Duke University Medical CenterDurhamUnited States
| | - Jeffrey I Everitt
- Department of Pathology, Duke University Medical CenterDurhamUnited States
| | - Elisa Baldelli
- Center for Applied Proteomics and Molecular Medicine, School of Systems Biology, George Mason UniversityManassasUnited States
| | - Mariaelena Pierobon
- Center for Applied Proteomics and Molecular Medicine, School of Systems Biology, George Mason UniversityManassasUnited States
| | - Emanuel F Petricoin
- Center for Applied Proteomics and Molecular Medicine, School of Systems Biology, George Mason UniversityManassasUnited States
| | - Christopher M Counter
- Department of Pharmacology & Cancer Biology, Duke University Medical CenterDurhamUnited States
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20
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DNA Polymerase Theta Plays a Critical Role in Pancreatic Cancer Development and Metastasis. Cancers (Basel) 2022; 14:cancers14174077. [PMID: 36077614 PMCID: PMC9454495 DOI: 10.3390/cancers14174077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/12/2022] [Accepted: 08/16/2022] [Indexed: 11/16/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC), due to its genomic heterogeneity and lack of effective treatment, despite decades of intensive research, will become the second leading cause of cancer-related deaths by 2030. Step-wise acquisition of mutations, due to genomic instability, is considered to drive the development of PDAC; the KRAS mutation occurs in 95 to 100% of human PDAC, and is already detectable in early premalignant lesions designated as pancreatic intraepithelial neoplasia (PanIN). This mutation is possibly the key event leading to genomic instability and PDAC development. Our study aimed to investigate the role of the error-prone DNA double-strand breaks (DSBs) repair pathway, alt-EJ, in the presence of the KRAS G12D mutation in pancreatic cancer development. Our findings show that oncogenic KRAS contributes to increasing the expression of Polθ, Lig3, and Mre11, key components of alt-EJ in both mouse and human PDAC models. We further confirm increased catalytic activity of alt-EJ in a mouse and human model of PDAC bearing the KRAS G12D mutation. Subsequently, we focused on estimating the impact of alt-EJ inactivation by polymerase theta (Polθ) deletion on pancreatic cancer development, and survival in genetically engineered mouse models (GEMMs) and cancer patients. Here, we show that even though Polθ deficiency does not fully prevent the development of pancreatic cancer, it significantly delays the onset of PanIN formation, prolongs the overall survival of experimental mice, and correlates with the overall survival of pancreatic cancer patients in the TCGA database. Our study clearly demonstrates the role of alt-EJ in the development of PDAC, and alt-EJ may be an attractive therapeutic target for pancreatic cancer patients.
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21
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Huynh MV, Hobbs GA, Schaefer A, Pierobon M, Carey LM, Diehl JN, DeLiberty JM, Thurman RD, Cooke AR, Goodwin CM, Cook JH, Lin L, Waters AM, Rashid NU, Petricoin EF, Campbell SL, Haigis KM, Simeone DM, Lyssiotis CA, Cox AD, Der CJ. Functional and biological heterogeneity of KRAS Q61 mutations. Sci Signal 2022; 15:eabn2694. [PMID: 35944066 PMCID: PMC9534304 DOI: 10.1126/scisignal.abn2694] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Missense mutations at the three hotspots in the guanosine triphosphatase (GTPase) RAS-Gly12, Gly13, and Gln61 (commonly known as G12, G13, and Q61, respectively)-occur differentially among the three RAS isoforms. Q61 mutations in KRAS are infrequent and differ markedly in occurrence. Q61H is the predominant mutant (at 57%), followed by Q61R/L/K (collectively 40%), and Q61P and Q61E are the rarest (2 and 1%, respectively). Probability analysis suggested that mutational susceptibility to different DNA base changes cannot account for this distribution. Therefore, we investigated whether these frequencies might be explained by differences in the biochemical, structural, and biological properties of KRASQ61 mutants. Expression of KRASQ61 mutants in NIH 3T3 fibroblasts and RIE-1 epithelial cells caused various alterations in morphology, growth transformation, effector signaling, and metabolism. The relatively rare KRASQ61E mutant stimulated actin stress fiber formation, a phenotype distinct from that of KRASQ61H/R/L/P, which disrupted actin cytoskeletal organization. The crystal structure of KRASQ61E was unexpectedly similar to that of wild-type KRAS, a potential basis for its weak oncogenicity. KRASQ61H/L/R-mutant pancreatic ductal adenocarcinoma (PDAC) cell lines exhibited KRAS-dependent growth and, as observed with KRASG12-mutant PDAC, were susceptible to concurrent inhibition of ERK-MAPK signaling and of autophagy. Our results uncover phenotypic heterogeneity among KRASQ61 mutants and support the potential utility of therapeutic strategies that target KRASQ61 mutant-specific signaling and cellular output.
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Affiliation(s)
- Minh V. Huynh
- Department of Biochemistry & Biophysics, University of
North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - G. Aaron Hobbs
- Department of Pharmacology, University of North Carolina at
Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North
Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Antje Schaefer
- Department of Pharmacology, University of North Carolina at
Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North
Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Mariaelena Pierobon
- Center for Applied Proteomics and Molecular Medicine,
George Mason University, Manassas, VA 20110, USA
| | - Leiah M. Carey
- Department of Biochemistry & Biophysics, University of
North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North
Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - J. Nathaniel Diehl
- Curriculum in Genetics and Molecular Biology, University of
North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jonathan M. DeLiberty
- Department of Pharmacology, University of North Carolina at
Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ryan D. Thurman
- Department of Biochemistry & Biophysics, University of
North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Adelaide R. Cooke
- Lineberger Comprehensive Cancer Center, University of North
Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Craig M. Goodwin
- Lineberger Comprehensive Cancer Center, University of North
Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Joshua H. Cook
- Department of Cancer Biology, Dana-Farber Cancer Institute,
Boston, MA 02215, USA
- Department of Medicine, Brigham & Women's
Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Biomedical Informatics, Harvard Medical
School, Boston, MA 02115, USA
| | - Lin Lin
- Department of Molecular and Integrative Physiology,
University of Michigan Health System, Ann Arbor, MI 48109, USA
| | - Andrew M. Waters
- Department of Pharmacology, University of North Carolina at
Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North
Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Naim U. Rashid
- Department of Biostatistics, University of North Carolina
at Chapel Hill, NC 27955, USA
| | - Emanuel F. Petricoin
- Center for Applied Proteomics and Molecular Medicine,
George Mason University, Manassas, VA 20110, USA
| | - Sharon L. Campbell
- Department of Biochemistry & Biophysics, University of
North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North
Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kevin M. Haigis
- Department of Cancer Biology, Dana-Farber Cancer Institute,
Boston, MA 02215, USA
- Department of Medicine, Brigham & Women's
Hospital, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute, Cambridge, MA 02142, USA
- Harvard Digestive Disease Center, Harvard Medical School,
Boston, MA 02115, USA
| | - Diane M. Simeone
- Perlmutter Cancer Center, New York University, New York,
NY10016, USA
| | - Costas A. Lyssiotis
- Department of Molecular and Integrative Physiology,
University of Michigan Health System, Ann Arbor, MI 48109, USA
- Department of Internal Medicine, Division of
Gastroenterology, University of Michigan, Ann Arbor, MI 48198, USA
- University of Michigan Comprehensive Cancer Center, Ann
Arbor, MI 48109, USA
| | - Adrienne D. Cox
- Department of Pharmacology, University of North Carolina at
Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North
Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Radiation Oncology, University of North
Carolina at Chapel Hill, Chapel Hill, NC 2799, USA
| | - Channing J. Der
- Department of Pharmacology, University of North Carolina at
Chapel Hill, Chapel Hill, NC 27599, USA
- Lineberger Comprehensive Cancer Center, University of North
Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Curriculum in Genetics and Molecular Biology, University of
North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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22
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Du PP, Liu K, Bassik MC, Hess GT. Pathogenic or benign? Nat Biotechnol 2022; 40:834-836. [PMID: 35578021 DOI: 10.1038/s41587-022-01333-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Peter P Du
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Katherine Liu
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael C Bassik
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA.,Program in Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA, USA
| | - Gaelen T Hess
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA. .,Center for Human Genomics and Precision Medicine, University of Wisconsin-Madison, Madison, WI, USA.
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23
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Schaefer A, Der CJ. RHOA takes the RHOad less traveled to cancer. Trends Cancer 2022; 8:655-669. [PMID: 35568648 DOI: 10.1016/j.trecan.2022.04.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/08/2022] [Accepted: 04/14/2022] [Indexed: 10/18/2022]
Abstract
RAS and RHO GTPases function as signaling nodes that regulate diverse cellular processes. Whereas RAS mutations were identified in human cancers nearly four decades ago, only recently have mutations in two RHO GTPases, RAC1 and RHOA, been identified in cancer. RAS mutations are found in a diverse spectrum of human cancer types. By contrast, RAC1 and RHOA mutations are associated with distinct and restricted cancer types. Despite a conservation of RAS and RAC1 residues that comprise mutational hotspots, RHOA mutations comprise highly divergent hotspots. Whereas RAS and RAC1 act as oncogenes, RHOA may act as both an oncogene and a tumor suppressor. Thus, while RAS and RHO each take different mutational paths, they arrive at the same biological destination as cancer drivers.
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Affiliation(s)
- Antje Schaefer
- University of North Carolina at Chapel Hill, Lineberger Comprehensive Cancer Center, Department of Pharmacology, Chapel Hill, NC 27599, USA
| | - Channing J Der
- University of North Carolina at Chapel Hill, Lineberger Comprehensive Cancer Center, Department of Pharmacology, Chapel Hill, NC 27599, USA.
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24
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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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25
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Yousefi M, Boross G, Weiss C, Murray CW, Hebert JD, Cai H, Ashkin EL, Karmakar S, Andrejka L, Chen L, Wang M, Tsai MK, Lin WY, Li C, Yakhchalian P, Colón CI, Chew SK, Chu P, Swanton C, Kunder CA, Petrov DA, Winslow MM. Combinatorial Inactivation of Tumor Suppressors Efficiently Initiates Lung Adenocarcinoma with Therapeutic Vulnerabilities. Cancer Res 2022; 82:1589-1602. [PMID: 35425962 PMCID: PMC9022333 DOI: 10.1158/0008-5472.can-22-0059] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/07/2022] [Accepted: 02/09/2022] [Indexed: 11/16/2022]
Abstract
Lung cancer is the leading cause of cancer death worldwide, with lung adenocarcinoma being the most common subtype. Many oncogenes and tumor suppressor genes are altered in this cancer type, and the discovery of oncogene mutations has led to the development of targeted therapies that have improved clinical outcomes. However, a large fraction of lung adenocarcinomas lacks mutations in known oncogenes, and the genesis and treatment of these oncogene-negative tumors remain enigmatic. Here, we perform iterative in vivo functional screens using quantitative autochthonous mouse model systems to uncover the genetic and biochemical changes that enable efficient lung tumor initiation in the absence of oncogene alterations. Generation of hundreds of diverse combinations of tumor suppressor alterations demonstrates that inactivation of suppressors of the RAS and PI3K pathways drives the development of oncogene-negative lung adenocarcinoma. Human genomic data and histology identified RAS/MAPK and PI3K pathway activation as a common feature of an event in oncogene-negative human lung adenocarcinomas. These Onc-negativeRAS/PI3K tumors and related cell lines are vulnerable to pharmacologic inhibition of these signaling axes. These results transform our understanding of this prevalent yet understudied subtype of lung adenocarcinoma. SIGNIFICANCE To address the large fraction of lung adenocarcinomas lacking mutations in proto-oncogenes for which targeted therapies are unavailable, this work uncovers driver pathways of oncogene-negative lung adenocarcinomas and demonstrates their therapeutic vulnerabilities.
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Affiliation(s)
- Maryam Yousefi
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- These authors contributed equally
| | - Gábor Boross
- Department of Biology, Stanford University, Stanford, CA, USA
- These authors contributed equally
| | - Carly Weiss
- Department of Biology, Stanford University, Stanford, CA, USA
| | | | - Jess D. Hebert
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Hongchen Cai
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Emily L. Ashkin
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Saswati Karmakar
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Laura Andrejka
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Leo Chen
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Minwei Wang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Min K. Tsai
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Wen-Yang Lin
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Chuan Li
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Pegah Yakhchalian
- Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA, USA
| | - Caterina I. Colón
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Su-Kit Chew
- Cancer Evolution and Genome Instability Laboratory, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Pauline Chu
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Christian A. Kunder
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Dmitri A. Petrov
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Monte M. Winslow
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
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26
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Ricciuti B, Son J, Okoro JJ, Mira A, Patrucco E, Eum Y, Wang X, Paranal R, Wang H, Lin M, Haikala HM, Li J, Xu Y, Alessi JV, Chhoeu C, Redig AJ, Köhler J, Dholakia KH, Chen Y, Richard E, Nokin MJ, Santamaria D, Gokhale PC, Awad MM, Jänne PA, Ambrogio C. Comparative Analysis and Isoform-Specific Therapeutic Vulnerabilities of KRAS Mutations in Non-Small Cell Lung Cancer. Clin Cancer Res 2022; 28:1640-1650. [PMID: 35091439 PMCID: PMC10979418 DOI: 10.1158/1078-0432.ccr-21-2719] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 12/21/2021] [Accepted: 01/25/2022] [Indexed: 11/16/2022]
Abstract
PURPOSE Activating missense mutations of KRAS are the most frequent oncogenic driver events in lung adenocarcinoma (LUAD). However, KRAS isoforms are highly heterogeneous, and data on the potential isoform-dependent therapeutic vulnerabilities are still lacking. EXPERIMENTAL DESIGN We developed an isogenic cell-based platform to compare the oncogenic properties and specific therapeutic actionability of KRAS-mutant isoforms. In parallel, we analyzed clinicopathologic and genomic data from 3,560 patients with non-small cell lung cancer (NSCLC) to survey allele-specific features associated with oncogenic KRAS mutations. RESULTS In isogenic cell lines expressing different mutant KRAS isoforms, we identified isoform-specific biochemical, biological, and oncogenic properties both in vitro and in vivo. These exclusive features correlated with different therapeutic responses to MEK inhibitors, with KRAS G12C and Q61H mutants being more sensitive compared with other isoforms. In vivo, combined KRAS G12C and MEK inhibition was more effective than either drug alone. Among patients with NSCLCs that underwent comprehensive tumor genomic profiling, STK11 and ATM mutations were significantly enriched among tumors harboring KRAS G12C, G12A, and G12V mutations. KEAP1 mutation was significantly enriched among KRAS G12C and KRAS G13X LUADs. KRAS G13X-mutated tumors had the highest frequency of concurrent STK11 and KEAP1 mutations. Transcriptomic profiling revealed unique patterns of gene expression in each KRAS isoform, compared with KRAS wild-type tumors. CONCLUSIONS This study demonstrates that KRAS isoforms are highly heterogeneous in terms of concurrent genomic alterations and gene-expression profiles, and that stratification based on KRAS alleles should be considered in the design of future clinical trials.
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Affiliation(s)
- Biagio Ricciuti
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, USA
| | - Jieun Son
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, USA
| | - Jeffrey J. Okoro
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, USA
| | - Alessia Mira
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center, University of Torino, Torino, Italy
| | - Enrico Patrucco
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center, University of Torino, Torino, Italy
| | - Yoonji Eum
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, USA
| | - Xinan Wang
- Harvard Graduate School of Arts and Sciences, Harvard University, Cambridge, USA
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard University, Boston, USA
| | - Raymond Paranal
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, USA
| | - Haiyun Wang
- School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Mika Lin
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, USA
| | - Heidi M. Haikala
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, USA
| | - Jiaqi Li
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, USA
| | - Yue Xu
- School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Joao Victor Alessi
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, USA
| | - Chhayheng Chhoeu
- Experimental Therapeutics Core and Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, USA
| | - Amanda J. Redig
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, USA
| | - Jens Köhler
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, USA
| | - Kshiti H. Dholakia
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, USA
| | - Yunhan Chen
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, USA
| | - Elodie Richard
- Institut Bergonié, INSERM U1218, ACTION Laboratory, Bordeaux, France
| | - Marie-Julie Nokin
- University of Bordeaux, INSERM U1218, ACTION Laboratory, IECB, Pessac, France
| | - David Santamaria
- University of Bordeaux, INSERM U1218, ACTION Laboratory, IECB, Pessac, France
| | - Prafulla C. Gokhale
- Experimental Therapeutics Core and Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, USA
| | - Mark M. Awad
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, USA
| | - Pasi A. Jänne
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, USA
| | - Chiara Ambrogio
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, USA
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center, University of Torino, Torino, Italy
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27
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Kaltenbacher T, Löprich J, Maresch R, Weber J, Müller S, Oellinger R, Groß N, Griger J, de Andrade Krätzig N, Avramopoulos P, Ramanujam D, Brummer S, Widholz SA, Bärthel S, Falcomatà C, Pfaus A, Alnatsha A, Mayerle J, Schmidt-Supprian M, Reichert M, Schneider G, Ehmer U, Braun CJ, Saur D, Engelhardt S, Rad R. CRISPR somatic genome engineering and cancer modeling in the mouse pancreas and liver. Nat Protoc 2022; 17:1142-1188. [PMID: 35288718 DOI: 10.1038/s41596-021-00677-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 12/07/2021] [Indexed: 12/23/2022]
Abstract
Genetically engineered mouse models (GEMMs) transformed the study of organismal disease phenotypes but are limited by their lengthy generation in embryonic stem cells. Here, we describe methods for rapid and scalable genome engineering in somatic cells of the liver and pancreas through delivery of CRISPR components into living mice. We introduce the spectrum of genetic tools, delineate viral and nonviral CRISPR delivery strategies and describe a series of applications, ranging from gene editing and cancer modeling to chromosome engineering or CRISPR multiplexing and its spatio-temporal control. Beyond experimental design and execution, the protocol describes quantification of genetic and functional editing outcomes, including sequencing approaches, data analysis and interpretation. Compared to traditional knockout mice, somatic GEMMs face an increased risk for mouse-to-mouse variability because of the higher experimental demands of the procedures. The robust protocols described here will help unleash the full potential of somatic genome manipulation. Depending on the delivery method and envisaged application, the protocol takes 3-5 weeks.
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Affiliation(s)
- Thorsten Kaltenbacher
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Jessica Löprich
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Roman Maresch
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Julia Weber
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Sebastian Müller
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Rupert Oellinger
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Nina Groß
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Joscha Griger
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Niklas de Andrade Krätzig
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Petros Avramopoulos
- Institute of Pharmacology and Toxicology, Technical University of Munich, Munich, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
| | - Deepak Ramanujam
- Institute of Pharmacology and Toxicology, Technical University of Munich, Munich, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
| | - Sabine Brummer
- Institute of Pharmacology and Toxicology, Technical University of Munich, Munich, Germany
| | - Sebastian A Widholz
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Stefanie Bärthel
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany.,Institute of Experimental Cancer Therapy, Technical University of Munich, Munich, Germany
| | - Chiara Falcomatà
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany.,Institute of Experimental Cancer Therapy, Technical University of Munich, Munich, Germany
| | - Anja Pfaus
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany
| | - Ahmed Alnatsha
- Department of Medicine II, University Hospital, LMU Munich, Munich, Germany
| | - Julia Mayerle
- Department of Medicine II, University Hospital, LMU Munich, Munich, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marc Schmidt-Supprian
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Experimental Hematology, School of Medicine, Technical University of Munich, Munich, Germany
| | - Maximilian Reichert
- Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Günter Schneider
- Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Ursula Ehmer
- Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Christian J Braun
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany.,Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany.,Hopp Children's Cancer Center Heidelberg (KiTZ), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dieter Saur
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany.,Institute of Experimental Cancer Therapy, Technical University of Munich, Munich, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Stefan Engelhardt
- Institute of Pharmacology and Toxicology, Technical University of Munich, Munich, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany. .,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Munich, Germany. .,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany. .,Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany.
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28
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Wang SW, Gao C, Zheng YM, Yi L, Lu JC, Huang XY, Cai JB, Zhang PF, Cui YH, Ke AW. Current applications and future perspective of CRISPR/Cas9 gene editing in cancer. Mol Cancer 2022; 21:57. [PMID: 35189910 PMCID: PMC8862238 DOI: 10.1186/s12943-022-01518-8] [Citation(s) in RCA: 92] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 01/24/2022] [Indexed: 02/08/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) system provides adaptive immunity against plasmids and phages in prokaryotes. This system inspires the development of a powerful genome engineering tool, the CRISPR/CRISPR-associated nuclease 9 (CRISPR/Cas9) genome editing system. Due to its high efficiency and precision, the CRISPR/Cas9 technique has been employed to explore the functions of cancer-related genes, establish tumor-bearing animal models and probe drug targets, vastly increasing our understanding of cancer genomics. Here, we review current status of CRISPR/Cas9 gene editing technology in oncological research. We first explain the basic principles of CRISPR/Cas9 gene editing and introduce several new CRISPR-based gene editing modes. We next detail the rapid progress of CRISPR screening in revealing tumorigenesis, metastasis, and drug resistance mechanisms. In addition, we introduce CRISPR/Cas9 system delivery vectors and finally demonstrate the potential of CRISPR/Cas9 engineering to enhance the effect of adoptive T cell therapy (ACT) and reduce adverse reactions.
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Burge RA, Hobbs GA. Not all RAS mutations are equal: A detailed review of the functional diversity of RAS hot spot mutations. Adv Cancer Res 2022; 153:29-61. [PMID: 35101234 DOI: 10.1016/bs.acr.2021.07.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The RAS family of small GTPases are among the most frequently mutated oncogenes in human cancer. Approximately 20% of cancers harbor a RAS mutation, and >150 different missense mutations have been detected. Many of these mutations have mutant-specific biochemical defects that alter nucleotide binding and hydrolysis, effector interactions and cell signaling, prompting renewed efforts in the development of anti-RAS therapies, including the mutation-specific strategies. Previously viewed as undruggable, the recent FDA approval of a KRASG12C-selective inhibitor has offered real promise to the development of allele-specific RAS therapies. A broader understanding of the mutational consequences on RAS function must be developed to exploit additional allele-specific vulnerabilities. Approximately 94% of RAS mutations occur at one of three mutational "hot spots" at Gly12, Gly13 and Gln61. Further, the single-nucleotide substitutions represent >99% of these mutations. Within this scope, we discuss the mutational frequencies of RAS isoforms in cancer, mutant-specific effector interactions and biochemical properties. By limiting our analysis to this mutational subset, we simplify the analysis while only excluding a small percentage of total mutations. Combined, these data suggest that the presence or absence of select RAS mutations in human cancers can be linked to their biochemical properties. Continuing to examine the biochemical differences in each RAS-mutant protein will continue to provide additional breakthroughs in allele-specific therapeutic strategies.
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Affiliation(s)
- Rachel A Burge
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, United States
| | - G Aaron Hobbs
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, United States; Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, United States.
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Diffusion kernel-based predictive modeling of KRAS dependency in KRAS wild type cancer cell lines. NPJ Syst Biol Appl 2022; 8:2. [PMID: 35046405 PMCID: PMC8770632 DOI: 10.1038/s41540-021-00211-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 12/16/2021] [Indexed: 11/19/2022] Open
Abstract
Recent progress in clinical development of KRAS inhibitors has raised interest in predicting the tumor dependency on frequently mutated RAS-pathway oncogenes. However, even without such activating mutations, RAS proteins represent core components in signal integration of several membrane-bound kinases. This raises the question of applications of specific inhibitors independent from the mutational status. Here, we examined CRISPR/RNAi data from over 700 cancer cell lines and identified a subset of cell lines without KRAS gain-of-function mutations (KRASwt) which are dependent on KRAS expression. Combining machine learning-based modeling and whole transcriptome data with prior variable selection through protein-protein interaction network analysis by a diffusion kernel successfully predicted KRAS dependency in the KRASwt subgroup and in all investigated cancer cell lines. In contrast, modeling by RAS activating events (RAE) or previously published RAS RNA-signatures did not provide reliable results, highlighting the heterogeneous distribution of RAE in KRASwt cell lines and the importance of methodological references for expression signature modeling. Furthermore, we show that predictors of KRASwt models contain non-substitutable information signals, indicating a KRAS dependency phenotype in the KRASwt subgroup. Our data suggest that KRAS dependent cancers harboring KRAS wild type status could be targeted by directed therapeutic approaches. RNA-based machine learning models could help in identifying responsive and non-responsive tumors.
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31
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Arnal-Estapé A, Foggetti G, Starrett JH, Nguyen DX, Politi K. Preclinical Models for the Study of Lung Cancer Pathogenesis and Therapy Development. Cold Spring Harb Perspect Med 2021; 11:a037820. [PMID: 34518338 PMCID: PMC8634791 DOI: 10.1101/cshperspect.a037820] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Experimental preclinical models have been a cornerstone of lung cancer translational research. Work in these model systems has provided insights into the biology of lung cancer subtypes and their origins, contributed to our understanding of the mechanisms that underlie tumor progression, and revealed new therapeutic vulnerabilities. Initially patient-derived lung cancer cell lines were the main preclinical models available. The landscape is very different now with numerous preclinical models for research each with unique characteristics. These include genetically engineered mouse models (GEMMs), patient-derived xenografts (PDXs) and three-dimensional culture systems ("organoid" cultures). Here we review the development and applications of these models and describe their contributions to lung cancer research.
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Affiliation(s)
- Anna Arnal-Estapé
- Department of Pathology
- Yale Cancer Center, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | | | | | - Don X Nguyen
- Department of Pathology
- Department of Internal Medicine (Section of Medical Oncology)
- Yale Cancer Center, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Katerina Politi
- Department of Pathology
- Department of Internal Medicine (Section of Medical Oncology)
- Yale Cancer Center, Yale University School of Medicine, New Haven, Connecticut 06510, USA
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32
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Long JE, Jankovic M, Maddalo D. Drug discovery oncology in a mouse: concepts, models and limitations. Future Sci OA 2021; 7:FSO737. [PMID: 34295539 PMCID: PMC8288236 DOI: 10.2144/fsoa-2021-0019] [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: 02/09/2021] [Accepted: 05/27/2021] [Indexed: 02/08/2023] Open
Abstract
The utilization of suitable mouse models is a critical step in the drug discovery oncology workflow as their generation and use are important for target identification and validation as well as toxicity and efficacy assessments. Current murine models have been instrumental in furthering insights into the mode of action of drugs before transitioning into the clinic. Recent advancements in genome editing with the development of the CRISPR/Cas9 system and the possibility of applying such technology directly in vivo have expanded the toolkit of preclinical models available. In this review, a brief presentation of the current models used in drug discovery will be provided with a particular emphasis on the novel CRISPR/Cas9 models.
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Affiliation(s)
- Jason E Long
- Department of Translational Oncology, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Maja Jankovic
- Department of Medicine, Division of Experimental Medicine, McGill University, Montréal, QC, H4A 3J1, Canada
- Lady Davis Institute for Medical Research, Montréal, QC, H4A 3J1, Canada
| | - Danilo Maddalo
- Department of Translational Oncology, Genentech, Inc., South San Francisco, CA 94080, USA
- Pharmaceutical Research & Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, 4070, Switzerland
- Author for correspondence:
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Loree JM, Wang Y, Syed MA, Sorokin AV, Coker O, Xiu J, Weinberg BA, Vanderwalde AM, Tesfaye A, Raymond VM, Miron B, Tarcic G, Zelichov O, Broaddus RR, Ng PKS, Jeong KJ, Tsang YH, Mills GB, Overman MJ, Grothey A, Marshall JL, Kopetz S. Clinical and Functional Characterization of Atypical KRAS/ NRAS Mutations in Metastatic Colorectal Cancer. Clin Cancer Res 2021; 27:4587-4598. [PMID: 34117033 PMCID: PMC8364867 DOI: 10.1158/1078-0432.ccr-21-0180] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 04/29/2021] [Accepted: 06/09/2021] [Indexed: 01/13/2023]
Abstract
PURPOSE Mutations in KRAS/NRAS (RAS) predict lack of anti-EGFR efficacy in metastatic colorectal cancer (mCRC). However, it is unclear if all RAS mutations have similar impact, and atypical mutations beyond those in standard guidelines exist. EXPERIMENTAL DESIGN We reviewed 7 tissue and 1 cell-free DNA cohorts of 9,485 patients to characterize atypical RAS variants. Using an in vitro cell-based assay (functional annotation for cancer treatment), Ba/F3 transformation, and in vivo xenograft models of transduced isogenic clones, we assessed signaling changes across mutations. RESULTS KRAS exon 2, extended RAS, and atypical RAS mutations were noted in 37.8%, 9.5%, and 1.2% of patients, respectively. Among atypical variants, KRAS L19F, Q22K, and D33E occurred at prevalence ≥0.1%, whereas no NRAS codon 117/146 and only one NRAS codon 59 mutation was noted. Atypical RAS mutations had worse overall survival than RAS/BRAF wild-type mCRC (HR, 2.90; 95% confidence interval, 1.24-6.80; P = 0.014). We functionally characterized 114 variants with the FACT assay. All KRAS exon 2 and extended RAS mutations appeared activating. Of 57 atypical RAS variants characterized, 18 (31.6%) had signaling below wild-type, 23 (40.4%) had signaling between wild-type and activating control, and 16 (28.1%) were hyperactive beyond the activating control. Ba/F3 transformation (17/18 variants) and xenograft model (7/8 variants) validation was highly concordant with FACT results, and activating atypical variants were those that occurred at highest prevalence in clinical cohorts. CONCLUSIONS We provide best available evidence to guide treatment when atypical RAS variants are identified. KRAS L19F, Q22K, D33E, and T50I are more prevalent than many guideline-included RAS variants and functionally relevant.
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Affiliation(s)
| | | | - Muddassir A Syed
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Alexey V Sorokin
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Oluwadara Coker
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Benjamin A Weinberg
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC
| | | | | | | | | | | | | | | | | | - Kang Jin Jeong
- Oregon Health Sciences University Knight Cancer Institute, Portland, Oregon
| | - Yiu Huen Tsang
- Oregon Health Sciences University Knight Cancer Institute, Portland, Oregon
| | - Gordon B Mills
- Oregon Health Sciences University Knight Cancer Institute, Portland, Oregon
| | | | | | | | - Scott Kopetz
- The University of Texas MD Anderson Cancer Center, Houston, Texas.
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34
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Foggetti G, Li C, Cai H, Hellyer JA, Lin WY, Ayeni D, Hastings K, Choi J, Wurtz A, Andrejka L, Maghini DG, Rashleigh N, Levy S, Homer R, Gettinger SN, Diehn M, Wakelee HA, Petrov DA, Winslow MM, Politi K. Genetic Determinants of EGFR-Driven Lung Cancer Growth and Therapeutic Response In Vivo. Cancer Discov 2021; 11:1736-1753. [PMID: 33707235 PMCID: PMC8530463 DOI: 10.1158/2159-8290.cd-20-1385] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 12/23/2020] [Accepted: 02/11/2021] [Indexed: 11/16/2022]
Abstract
In lung adenocarcinoma, oncogenic EGFR mutations co-occur with many tumor suppressor gene alterations; however, the extent to which these contribute to tumor growth and response to therapy in vivo remains largely unknown. By quantifying the effects of inactivating 10 putative tumor suppressor genes in a mouse model of EGFR-driven Trp53-deficient lung adenocarcinoma, we found that Apc, Rb1, or Rbm10 inactivation strongly promoted tumor growth. Unexpectedly, inactivation of Lkb1 or Setd2-the strongest drivers of growth in a KRAS-driven model-reduced EGFR-driven tumor growth. These results are consistent with mutational frequencies in human EGFR- and KRAS-driven lung adenocarcinomas. Furthermore, KEAP1 inactivation reduced the sensitivity of EGFR-driven tumors to the EGFR inhibitor osimertinib, and mutations in genes in the KEAP1 pathway were associated with decreased time on tyrosine kinase inhibitor treatment in patients. Our study highlights how the impact of genetic alterations differs across oncogenic contexts and that the fitness landscape shifts upon treatment. SIGNIFICANCE: By modeling complex genotypes in vivo, this study reveals key tumor suppressors that constrain the growth of EGFR-mutant tumors. Furthermore, we uncovered that KEAP1 inactivation reduces the sensitivity of these tumors to tyrosine kinase inhibitors. Thus, our approach identifies genotypes of biological and therapeutic importance in this disease.This article is highlighted in the In This Issue feature, p. 1601.
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Affiliation(s)
- Giorgia Foggetti
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
| | - Chuan Li
- Department of Biology, Stanford University, Stanford, California
| | - Hongchen Cai
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Jessica A Hellyer
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, California
| | - Wen-Yang Lin
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Deborah Ayeni
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut
| | | | - Jungmin Choi
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Korea
| | - Anna Wurtz
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
| | - Laura Andrejka
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Dylan G Maghini
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | | | - Stellar Levy
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
| | - Robert Homer
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut
- VA Connecticut Healthcare System, Pathology and Laboratory Medicine Service, West Haven, Connecticut
| | - Scott N Gettinger
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
- Section of Medical Oncology, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut
| | - Maximilian Diehn
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California
| | - Heather A Wakelee
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, California
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California
| | - Dmitri A Petrov
- Department of Biology, Stanford University, Stanford, California
| | - Monte M Winslow
- Department of Genetics, Stanford University School of Medicine, Stanford, California.
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, California
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Katerina Politi
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut.
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut
- Section of Medical Oncology, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut
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35
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Cai H, Chew SK, Li C, Tsai MK, Andrejka L, Murray CW, Hughes NW, Shuldiner EG, Ashkin EL, Tang R, Hung KL, Chen LC, Lee SYC, Yousefi M, Lin WY, Kunder CA, Cong L, McFarland CD, Petrov DA, Swanton C, Winslow MM. A Functional Taxonomy of Tumor Suppression in Oncogenic KRAS-Driven Lung Cancer. Cancer Discov 2021; 11:1754-1773. [PMID: 33608386 PMCID: PMC8292166 DOI: 10.1158/2159-8290.cd-20-1325] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 12/25/2020] [Accepted: 02/12/2021] [Indexed: 12/13/2022]
Abstract
Cancer genotyping has identified a large number of putative tumor suppressor genes. Carcinogenesis is a multistep process, but the importance and specific roles of many of these genes during tumor initiation, growth, and progression remain unknown. Here we use a multiplexed mouse model of oncogenic KRAS-driven lung cancer to quantify the impact of 48 known and putative tumor suppressor genes on diverse aspects of carcinogenesis at an unprecedented scale and resolution. We uncover many previously understudied functional tumor suppressors that constrain cancer in vivo. Inactivation of some genes substantially increased growth, whereas the inactivation of others increases tumor initiation and/or the emergence of exceptionally large tumors. These functional in vivo analyses revealed an unexpectedly complex landscape of tumor suppression that has implications for understanding cancer evolution, interpreting clinical cancer genome sequencing data, and directing approaches to limit tumor initiation and progression. SIGNIFICANCE: Our high-throughput and high-resolution analysis of tumor suppression uncovered novel genetic determinants of oncogenic KRAS-driven lung cancer initiation, overall growth, and exceptional growth. This taxonomy is consistent with changing constraints during the life history of cancer and highlights the value of quantitative in vivo genetic analyses in autochthonous cancer models.This article is highlighted in the In This Issue feature, p. 1601.
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Affiliation(s)
- Hongchen Cai
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Su Kit Chew
- Cancer Evolution and Genome Instability Laboratory, University College London Cancer Institute, London, United Kingdom
| | - Chuan Li
- Department of Biology, Stanford University, Stanford, California
| | - Min K Tsai
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Laura Andrejka
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Christopher W Murray
- Cancer Biology Program, Stanford University School of Medicine, Stanford, California
| | - Nicholas W Hughes
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | | | - Emily L Ashkin
- Cancer Biology Program, Stanford University School of Medicine, Stanford, California
| | - Rui Tang
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - King L Hung
- Cancer Biology Program, Stanford University School of Medicine, Stanford, California
| | - Leo C Chen
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Shi Ya C Lee
- Cancer Evolution and Genome Instability Laboratory, University College London Cancer Institute, London, United Kingdom
| | - Maryam Yousefi
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Wen-Yang Lin
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Christian A Kunder
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Le Cong
- Department of Genetics, Stanford University School of Medicine, Stanford, California
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | | | - Dmitri A Petrov
- Department of Biology, Stanford University, Stanford, California.
- Cancer Biology Program, Stanford University School of Medicine, Stanford, California
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, University College London Cancer Institute, London, United Kingdom.
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Monte M Winslow
- Department of Genetics, Stanford University School of Medicine, Stanford, California.
- Cancer Biology Program, Stanford University School of Medicine, Stanford, California
- Department of Pathology, Stanford University School of Medicine, Stanford, California
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36
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Ras Variant Biology and Contributions to Human Disease. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2262:3-18. [PMID: 33977468 DOI: 10.1007/978-1-0716-1190-6_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Analysis of cancer and RASopathy genetic databases reveals that ~19% of all cancer cases and ~4% of developmental disorders contain Ras mutations. Ras isoform and mutation variants differentially contribute to these diseases and provide an opportunity for deeper understanding of Ras function. The putative mechanisms underpinning these differences, new approaches that are being applied, and some of the key questions and challenges that remain are discussed.
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37
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Li S, Counter CM. Signaling levels mold the RAS mutation tropism of urethane. eLife 2021; 10:67172. [PMID: 33998997 PMCID: PMC8128437 DOI: 10.7554/elife.67172] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 04/01/2021] [Indexed: 12/29/2022] Open
Abstract
RAS genes are commonly mutated in human cancer. Despite many possible mutations, individual cancer types often have a 'tropism' towards a specific subset of RAS mutations. As driver mutations, these patterns ostensibly originate from normal cells. High oncogenic RAS activity causes oncogenic stress and different oncogenic mutations can impart different levels of activity, suggesting a relationship between oncoprotein activity and RAS mutation tropism. Here, we show that changing rare codons to common in the murine Kras gene to increase protein expression shifts tumors induced by the carcinogen urethane from arising from canonical Q61 to biochemically less active G12 Kras driver mutations, despite the carcinogen still being biased towards generating Q61 mutations. Conversely, inactivating the tumor suppressor p53 to blunt oncogenic stress partially reversed this effect, restoring Q61 mutations. One interpretation of these findings is that the RAS mutation tropism of urethane arises from selection in normal cells for specific mutations that impart a narrow window of signaling that promotes proliferation without causing oncogenic stress.
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Affiliation(s)
- Siqi Li
- Pharmacology and Cancer Biology, Duke University, Durham, United States
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38
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Abstract
What level of Ras genes activity leads to the development of cancer?
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Affiliation(s)
- Zohra Butt
- Department of Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative Biology, University of LiverpoolLiverpoolUnited Kingdom
| | - Ian Prior
- Department of Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative Biology, University of LiverpoolLiverpoolUnited Kingdom
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39
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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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40
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Spector LP, Tiffany M, Ferraro NM, Abell NS, Montgomery SB, Kay MA. Evaluating the Genomic Parameters Governing rAAV-Mediated Homologous Recombination. Mol Ther 2021; 29:1028-1046. [PMID: 33248247 PMCID: PMC7934627 DOI: 10.1016/j.ymthe.2020.11.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 10/16/2020] [Accepted: 11/18/2020] [Indexed: 12/26/2022] Open
Abstract
Recombinant adeno-associated virus (rAAV) vectors have the unique ability to promote targeted integration of transgenes via homologous recombination at specified genomic sites, reaching frequencies of 0.1%-1%. We studied genomic parameters that influence targeting efficiencies on a large scale. To do this, we generated more than 1,000 engineered, doxycycline-inducible target sites in the human HAP1 cell line and infected this polyclonal population with a library of AAV-DJ targeting vectors, with each carrying a unique barcode. The heterogeneity of barcode integration at each target site provided an assessment of targeting efficiency at that locus. We compared targeting efficiency with and without target site transcription for identical chromosomal positions. Targeting efficiency was enhanced by target site transcription, while chromatin accessibility was associated with an increased likelihood of targeting. ChromHMM chromatin states characterizing transcription and enhancers in wild-type K562 cells were also associated with increased AAV-HR efficiency with and without target site transcription, respectively. Furthermore, the amenability of a site to targeting was influenced by the endogenous transcriptional level of intersecting genes. These results define important parameters that may not only assist in designing optimal targeting vectors for genome editing, but also provide new insights into the mechanism of AAV-mediated homologous recombination.
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Affiliation(s)
- Laura P Spector
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Matthew Tiffany
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA; Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Nicole M Ferraro
- Biomedical Informatics Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Nathan S Abell
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Stephen B Montgomery
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Mark A Kay
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA; Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
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41
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Lim S, Khoo R, Juang YC, Gopal P, Zhang H, Yeo C, Peh KM, Teo J, Ng S, Henry B, Partridge AW. Exquisitely Specific anti-KRAS Biodegraders Inform on the Cellular Prevalence of Nucleotide-Loaded States. ACS CENTRAL SCIENCE 2021; 7:274-291. [PMID: 33655066 PMCID: PMC7908030 DOI: 10.1021/acscentsci.0c01337] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Indexed: 05/05/2023]
Abstract
Mutations to RAS proteins (H-, N-, and K-RAS) are among the most common oncogenic drivers, and tumors harboring these lesions are some of the most difficult to treat. Although covalent small molecules against KRASG12C have shown promising efficacy against lung cancers, traditional barriers remain for drugging the more prevalent KRASG12D and KRASG12V mutants. Targeted degradation has emerged as an attractive alternative approach, but for KRAS, identification of the required high-affinity ligands continues to be a challenge. Another significant hurdle is the discovery of a hybrid molecule that appends an E3 ligase-recruiting moiety in a manner that satisfies the precise geometries required for productive polyubiquitin transfer while maintaining favorable druglike properties. To gain insights into the advantages and feasibility of KRAS targeted degradation, we applied a protein-based degrader (biodegrader) approach. This workflow centers on the intracellular expression of a chimeric protein consisting of a high-affinity target-binding domain fused to an engineered E3 ligase adapter. A series of anti-RAS biodegraders spanning different RAS isoform/nucleotide-state specificities and leveraging different E3 ligases provided definitive evidence for RAS degradability. Further, these established that the functional consequences of KRAS degradation are context dependent. Of broader significance, using the exquisite degradation specificity that biodegraders can possess, we demonstrated how this technology can be applied to answer questions that other approaches cannot. Specifically, application of the GDP-state specific degrader uncovered the relative prevalence of the "off-state" of WT and various KRAS mutants in the cellular context. Finally, if delivery challenges can be addressed, anti-RAS biodegraders will be exciting candidates for clinical development.
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Aversive Stress Reduces Mu Opioid Receptor Expression in the Intercalated Nuclei of the Rat Amygdala. Cell Mol Neurobiol 2021; 41:1119-1129. [PMID: 33400082 DOI: 10.1007/s10571-020-01026-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 12/03/2020] [Indexed: 02/07/2023]
Abstract
The amygdala plays an important role in the integration of responses to noxious and fearful stimuli. Sensory information from many systems is integrated in the lateral and basolateral amygdala and transmitted to the central amygdala, the major output nucleus of the amygdala regulating both motor and emotional responses. The network of intercalated cells (ITC) which surrounds the lateral and basolateral amygdala and serves to modulate information flow from the lateral amygdala to the central nucleus, express a very high local concentration of mu-type opioid receptors. Loss of the ITC neurons impairs fear extinction. We demonstrate here that exposure of rats to a severe stress experience resulted in a marked downregulation of the level of expression of mu opioid receptors in the ITC nuclei over a period of at least 24 h after the end of the stress exposure. The endogenous opioid dynorphin is also expressed in the central and ITC nuclei of the amygdala. Following stress exposure, we also observed an increase in the expression in the more lateral regions of the central amygdala of pro-dynorphin mRNA and a peptide product of pro-dynorphin with known affinity for mu opioid receptors. It is possible that the downregulation of mu receptors in ITC neurons after stress may result from sustained activation and internalization of mu receptors following a stress-induced increase in the release of endogenous opioid peptides.
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Abstract
Molecular dynamics (MD) simulations have become increasingly useful in the modern drug development process. In this review, we give a broad overview of the current application possibilities of MD in drug discovery and pharmaceutical development. Starting from the target validation step of the drug development process, we give several examples of how MD studies can give important insights into the dynamics and function of identified drug targets such as sirtuins, RAS proteins, or intrinsically disordered proteins. The role of MD in antibody design is also reviewed. In the lead discovery and lead optimization phases, MD facilitates the evaluation of the binding energetics and kinetics of the ligand-receptor interactions, therefore guiding the choice of the best candidate molecules for further development. The importance of considering the biological lipid bilayer environment in the MD simulations of membrane proteins is also discussed, using G-protein coupled receptors and ion channels as well as the drug-metabolizing cytochrome P450 enzymes as relevant examples. Lastly, we discuss the emerging role of MD simulations in facilitating the pharmaceutical formulation development of drugs and candidate drugs. Specifically, we look at how MD can be used in studying the crystalline and amorphous solids, the stability of amorphous drug or drug-polymer formulations, and drug solubility. Moreover, since nanoparticle drug formulations are of great interest in the field of drug delivery research, different applications of nano-particle simulations are also briefly summarized using multiple recent studies as examples. In the future, the role of MD simulations in facilitating the drug development process is likely to grow substantially with the increasing computer power and advancements in the development of force fields and enhanced MD methodologies.
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Chang WC, Zhang YZ, Wolf JL, Hermelijn SM, Schnater JM, von der Thüsen JH, Rice A, Lantuejoul S, Mastroianni B, Farver C, Black F, Popat S, Nicholson AG. Mucinous adenocarcinoma arising in congenital pulmonary airway malformation: clinicopathological analysis of 37 cases. Histopathology 2020; 78:434-444. [PMID: 32810914 DOI: 10.1111/his.14239] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 08/11/2020] [Accepted: 08/16/2020] [Indexed: 11/29/2022]
Abstract
AIMS Mucinous adenocarcinoma arising in congenital pulmonary airway malformation (CPAM) is a rare complication, with little being known about its natural course. The aims of this article are to describe a series of mucinous adenocarcinomas arising from CPAMs, and present their clinicopathological features, genetics, and clinical outcome. METHODS AND RESULTS Thirty-seven cases were collected within a 34-year period, and the subtype of adenocarcinoma and CPAM, tumour location, stage, growth patterns, molecular data and follow-up were recorded. The cohort comprised CPAM type 1 (n = 33) and CPAM type 2 (n = 4). Morphologically, 34 cases were mucinous adenocarcinomas (21 in situ; 13 invasive), and three were mixed mucinous and non-mucinous adenocarcinoma. Seventeen cases showed purely extracystic (intra-alveolar) adenocarcinoma, 15 were mixed intracystic and extracystic, and five showed purely intracystic proliferation. Genetically, nine of 10 cases tested positive for KRAS mutations, four with exon 2 G12V mutation and five with exon 2 G12D mutation. Residual disease on completion lobectomy was observed in two cases, and three cases recurred 7, 15 and 32 years after the original diagnosis. Two patients died of metastatic invasive mucinous adenocarcinoma. CONCLUSIONS Most adenocarcinoma that arise in type 1 CPAMs, are purely mucinous, and are early-stage disease. Intracystic proliferation is associated with lepidic growth, an absence of invasion, and indolent behaviour, whereas extracystic proliferation may be associated with more aggressive behaviour and advanced stage. Most cases are cured by lobectomy, and recurrence/residual disease seems to be associated with limited surgery. Long-term follow-up is needed, as recurrence can occur decades later.
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Affiliation(s)
- Wei-Chin Chang
- Department of Histopathology, Royal Brompton and Harefield NHS Foundation Trust, London, UK.,Department of Pathology, MacKay Memorial Hospital, Taipei, Taiwan.,Department of Medicine, MacKay Medical College, New Taipei City, Taipei, Taiwan.,Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Yu Zhi Zhang
- Department of Histopathology, Royal Brompton and Harefield NHS Foundation Trust, London, UK.,National Heart and Lung Institute, Imperial College, London, UK
| | - Janina L Wolf
- Department of Pathology, Erasmus Medical Centre, Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Sergei M Hermelijn
- Department of Paediatric Surgery, Erasmus Medical Centre, Sophia Children's Hospital, Rotterdam, The Netherlands
| | - J Marco Schnater
- Department of Paediatric Surgery, Erasmus Medical Centre, Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Jan H von der Thüsen
- Department of Pathology, Erasmus Medical Centre, Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Alexandra Rice
- Department of Histopathology, Royal Brompton and Harefield NHS Foundation Trust, London, UK.,National Heart and Lung Institute, Imperial College, London, UK
| | - Sylvie Lantuejoul
- Department of Biopathology, Cancer Centre of Léon Bérard, Lyon, France.,Grenoble Alpes University, Grenoble, France
| | | | - Carol Farver
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Fiona Black
- Department of Cellular Pathology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Sanjay Popat
- National Heart and Lung Institute, Imperial College, London, UK.,Department of Medicine, Royal Marsden Hospital NHS Foundation Trust, London, UK.,Institute of Cancer Research, London, UK
| | - Andrew G Nicholson
- Department of Histopathology, Royal Brompton and Harefield NHS Foundation Trust, London, UK.,National Heart and Lung Institute, Imperial College, London, UK
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45
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Lundin A, Porritt MJ, Jaiswal H, Seeliger F, Johansson C, Bidar AW, Badertscher L, Wimberger S, Davies EJ, Hardaker E, Martins CP, James E, Admyre T, Taheri-Ghahfarokhi A, Bradley J, Schantz A, Alaeimahabadi B, Clausen M, Xu X, Mayr LM, Nitsch R, Bohlooly-Y M, Barry ST, Maresca M. Development of an ObLiGaRe Doxycycline Inducible Cas9 system for pre-clinical cancer drug discovery. Nat Commun 2020; 11:4903. [PMID: 32994412 PMCID: PMC7525522 DOI: 10.1038/s41467-020-18548-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 08/26/2020] [Indexed: 12/28/2022] Open
Abstract
The CRISPR-Cas9 system has increased the speed and precision of genetic editing in cells and animals. However, model generation for drug development is still expensive and time-consuming, demanding more target flexibility and faster turnaround times with high reproducibility. The generation of a tightly controlled ObLiGaRe doxycycline inducible SpCas9 (ODInCas9) transgene and its use in targeted ObLiGaRe results in functional integration into both human and mouse cells culminating in the generation of the ODInCas9 mouse. Genomic editing can be performed in cells of various tissue origins without any detectable gene editing in the absence of doxycycline. Somatic in vivo editing can model non-small cell lung cancer (NSCLC) adenocarcinomas, enabling treatment studies to validate the efficacy of candidate drugs. The ODInCas9 mouse allows robust and tunable genome editing granting flexibility, speed and uniformity at less cost, leading to high throughput and practical preclinical in vivo therapeutic testing.
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Affiliation(s)
- Anders Lundin
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Michelle J Porritt
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Himjyot Jaiswal
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
- Cellink AB, Gothenburg, Sweden
| | - Frank Seeliger
- Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Camilla Johansson
- Clinical Pharmacology and Safety Sciences, Sweden Imaging Hub, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Abdel Wahad Bidar
- Clinical Pharmacology and Safety Sciences, Sweden Imaging Hub, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Lukas Badertscher
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Sandra Wimberger
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Emma J Davies
- Early Oncology TDE, Oncology R&D, AstraZeneca, Li KaShing Centre, Cambridge, UK
- Healx, Cambridge, UK
| | - Elizabeth Hardaker
- Early Oncology TDE, Oncology R&D, AstraZeneca, Li KaShing Centre, Cambridge, UK
| | - Carla P Martins
- Early Oncology TDE, Oncology R&D, AstraZeneca, Li KaShing Centre, Cambridge, UK
| | - Emily James
- Early Oncology TDE, Oncology R&D, AstraZeneca, Li KaShing Centre, Cambridge, UK
| | - Therese Admyre
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Amir Taheri-Ghahfarokhi
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Jenna Bradley
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge Science Park, Cambridge, UK
| | - Anna Schantz
- Pharmaceutical Sciences, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Babak Alaeimahabadi
- Data Sciences and Quantitative Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Maryam Clausen
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Xiufeng Xu
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Lorenz M Mayr
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Roberto Nitsch
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Mohammad Bohlooly-Y
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Simon T Barry
- Early Oncology TDE, Oncology R&D, AstraZeneca, Li KaShing Centre, Cambridge, UK
| | - Marcello Maresca
- Translational Genomics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.
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46
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Noorani I, Bradley A, de la Rosa J. CRISPR and transposon in vivo screens for cancer drivers and therapeutic targets. Genome Biol 2020; 21:204. [PMID: 32811551 PMCID: PMC7437018 DOI: 10.1186/s13059-020-02118-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 07/23/2020] [Indexed: 02/07/2023] Open
Abstract
Human cancers harbor substantial genetic, epigenetic, and transcriptional changes, only some of which drive oncogenesis at certain times during cancer evolution. Identifying the cancer-driver alterations amongst the vast swathes of "passenger" changes still remains a major challenge. Transposon and CRISPR screens in vivo provide complementary methods for achieving this, and each platform has its own advantages. Here, we review recent major technological breakthroughs made with these two approaches and highlight future directions. We discuss how each genetic screening platform can provide unique insight into cancer evolution, including intra-tumoral heterogeneity, metastasis, and immune evasion, presenting transformative opportunities for targeted therapeutic intervention.
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Affiliation(s)
- Imran Noorani
- Department of Medicine, University of Cambridge School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK.
- Department of Neurosurgery, University of Cambridge, Cambridge, CB2 0QQ, UK.
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.
| | - Allan Bradley
- Department of Medicine, University of Cambridge School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Jorge de la Rosa
- Department of Medicine, University of Cambridge School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK.
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Zafra MP, Parsons MJ, Kim J, Alonso-Curbelo D, Goswami S, Schatoff EM, Han T, Katti A, Fernandez MTC, Wilkinson JE, Piskounova E, Dow LE. An In Vivo Kras Allelic Series Reveals Distinct Phenotypes of Common Oncogenic Variants. Cancer Discov 2020; 10:1654-1671. [PMID: 32792368 DOI: 10.1158/2159-8290.cd-20-0442] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 06/30/2020] [Accepted: 07/09/2020] [Indexed: 11/16/2022]
Abstract
KRAS is the most frequently mutated oncogene in cancer, yet there is little understanding of how specific KRAS amino acid changes affect tumor initiation, progression, or therapy response. Using high-fidelity CRISPR-based engineering, we created an allelic series of new LSL-Kras mutant mice, reflecting codon 12 and 13 mutations that are highly prevalent in lung (KRASG12C), pancreas (KRASG12R), and colon (KRASG13D) cancers. Induction of each allele in either the murine colon or pancreas revealed striking quantitative and qualitative differences between KRAS mutants in driving the early stages of transformation. Furthermore, using pancreatic organoid models, we show that KRASG13D mutants are sensitive to EGFR inhibition, whereas KRASG12C-mutant organoids are selectively responsive to covalent G12C inhibitors only when EGFR is suppressed. Together, these new mouse strains provide an ideal platform for investigating KRAS biology in vivo and for developing preclinical precision oncology models of KRAS-mutant pancreas, colon, and lung cancers. SIGNIFICANCE: KRAS is the most frequently mutated oncogene. Here, we describe new preclinical models that mimic tissue-selective KRAS mutations and show that each mutation has distinct cellular consequences in vivo and carries differential sensitivity to targeted therapeutic agents.See related commentary by Kostyrko and Sweet-Cordero, p. 1626.This article is highlighted in the In This Issue feature, p. 1611.
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Affiliation(s)
- Maria Paz Zafra
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, New York.
| | - Marie J Parsons
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, New York
| | - Jangkyung Kim
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, New York
| | - Direna Alonso-Curbelo
- Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sukanya Goswami
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, New York
| | - Emma M Schatoff
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, New York.,Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, New York
| | - Teng Han
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, New York.,Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, New York
| | - Alyna Katti
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, New York.,Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, New York
| | | | - John E Wilkinson
- Department of Pathology, University of Michigan, Ann Arbor, Michigan.,Department of Comparative Medicine, University of Washington, Seattle, Washington
| | - Elena Piskounova
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, New York.,Department of Dermatology, Weill Cornell Medicine, New York, New York.,Department of Biochemistry, Weill Cornell Medicine, New York, New York
| | - Lukas E Dow
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, New York. .,Department of Biochemistry, Weill Cornell Medicine, New York, New York.,Department of Medicine, Weill Cornell Medicine, New York, New York
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48
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Prior IA, Hood FE, Hartley JL. The Frequency of Ras Mutations in Cancer. Cancer Res 2020; 80:2969-2974. [PMID: 32209560 PMCID: PMC7367715 DOI: 10.1158/0008-5472.can-19-3682] [Citation(s) in RCA: 501] [Impact Index Per Article: 125.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 02/13/2020] [Accepted: 03/19/2020] [Indexed: 02/06/2023]
Abstract
Ras is frequently mutated in cancer, however, there is a lack of consensus in the literature regarding the cancer mutation frequency of Ras, with quoted values varying from 10%-30%. This variability is at least in part due to the selective aggregation of data from different databases and the dominant influence of particular cancer types and particular Ras isoforms within these datasets. To provide a more definitive figure for Ras mutation frequency in cancer, we cross-referenced the data in all major publicly accessible cancer mutation databases to determine reliable mutation frequency values for each Ras isoform in all major cancer types. These percentages were then applied to current U.S. cancer incidence statistics to estimate the number of new patients each year that have Ras-mutant cancers. We find that approximately 19% of patients with cancer harbor Ras mutations, equivalent to approximately 3.4 million new cases per year worldwide. We discuss the Ras isoform and mutation-specific trends evident within the datasets that are relevant to current Ras-targeted therapies.
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Affiliation(s)
- Ian A Prior
- Division of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom.
| | - Fiona E Hood
- Division of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - James L Hartley
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
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49
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Singh R, Das S, Datta S, Mazumdar A, Biswas NK, Maitra A, Majumder PP, Ghose S, Roy B. Study of Caspase 8 mutation in oral cancer and adjacent precancer tissues and implication in progression. PLoS One 2020; 15:e0233058. [PMID: 32492030 PMCID: PMC7269231 DOI: 10.1371/journal.pone.0233058] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 04/27/2020] [Indexed: 12/16/2022] Open
Abstract
It is hypothesized that same driver gene mutations should be present in both oral leukoplakia and cancer tissues. So, we attempted to find out mutations at one of the driver genes, CASP8, in cancer and adjacent leukoplakia tissues. Patients (n = 27), affected by both of cancer and adjacent leukoplakia, were recruited for the study. Blood and tissue DNA samples were used to identify somatic mutations at CASP8 by next generation sequencing method. In total, 56% (15 out of 27) cancer and 30% (8 out of 27) leukoplakia tissues had CASP8 somatic mutations. In 8 patients, both cancer and adjacent leukoplakia tissues, located within 2-5 cm of tumor sites, had identical somatic mutations. But, in 7 patients, cancer samples had somatic mutations but none of the leukoplakia tissues, located beyond 5cm of tumor sites, had somatic mutations. Mutated allele frequencies at CASP8 were found to be more in cancer compared to adjacent leukoplakia tissues. This study provides mutational evidence that oral cancer might have progressed from previously grown leukoplakia lesion. Leukoplakia tissues, located beyond 5cm of cancer sites, were free from mutation. The study implies that CASP8 mutation could be one of the signatures for some of the leukoplakia to progress to oral cancer.
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Affiliation(s)
- Richa Singh
- Human Genetics Unit, Indian Statistical Institute, Kolkata, India
| | - Shreya Das
- Dr. R. Ahmed Dental College and Hospital, Kolkata, India
| | - Sila Datta
- Dr. R. Ahmed Dental College and Hospital, Kolkata, India
| | | | - Nidhan K. Biswas
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | - Arindam Maitra
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | | | - Sandip Ghose
- Dr. R. Ahmed Dental College and Hospital, Kolkata, India
- * E-mail: (BR); (SG)
| | - Bidyut Roy
- Human Genetics Unit, Indian Statistical Institute, Kolkata, India
- * E-mail: (BR); (SG)
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50
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Li S, MacAlpine DM, Counter CM. Capturing the primordial Kras mutation initiating urethane carcinogenesis. Nat Commun 2020; 11:1800. [PMID: 32286309 PMCID: PMC7156420 DOI: 10.1038/s41467-020-15660-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 03/23/2020] [Indexed: 01/02/2023] Open
Abstract
The environmental carcinogen urethane exhibits a profound specificity for pulmonary tumors driven by an oncogenic Q61L/R mutation in the gene Kras. Similarly, the frequency, isoform, position, and substitution of oncogenic RAS mutations are often unique to human cancers. To elucidate the principles underlying this RAS mutation tropism of urethane, we adapted an error-corrected, high-throughput sequencing approach to detect mutations in murine Ras genes at great sensitivity. This analysis not only captured the initiating Kras mutation days after urethane exposure, but revealed that the sequence specificity of urethane mutagenesis, coupled with transcription and isoform locus, to be major influences on the extreme tropism of this carcinogen. Why the carcinogen urethane causes only lung tumours driven by a specific oncogenic mutation in just one Ras gene in mice is unclear. Here, the authors capture mutations immediately after urethane exposure and show that the sequence specificity of mutagenesis, transcriptional status, and Ras genetic loci may all contribute to this specificity.
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Affiliation(s)
- Siqi Li
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, 27710, USA
| | - David M MacAlpine
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Christopher M Counter
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, 27710, USA.
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