1
|
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.
Collapse
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
| |
Collapse
|
2
|
Vanoli F, Antonescu CR. Modeling sarcoma relevant translocations using CRISPR-Cas9 in human embryonic stem derived mesenchymal precursors. Genes Chromosomes Cancer 2023; 62:501-509. [PMID: 36965130 PMCID: PMC10725040 DOI: 10.1002/gcc.23141] [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: 01/24/2023] [Revised: 03/06/2023] [Accepted: 03/16/2023] [Indexed: 03/27/2023] Open
Abstract
The role of cancer relevant translocations in tumorigenesis has been historically hampered by the lack of faithful in vitro and in vivo models. The development of the latest genome editing tools (e.g., CRISPR-Cas9) allowed modeling of various chromosomal translocations with different effects on proliferation and transformation capacity depending on the cell line used and secondary genetic alterations. The cellular context is particularly relevant in the case of oncogenic fusions expressed in sarcomas whose histogenesis remain uncertain. Moreover, recent studies have emphasized the increased frequency of gene fusion promiscuity across different mesenchymal tumor entities, which are clinicopathologically unrelated. This review provides a summary of different strategies utilized to generate cancer models with a focus on fusion-driven mesenchymal neoplasia.
Collapse
Affiliation(s)
- Fabio Vanoli
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Cristina R Antonescu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| |
Collapse
|
3
|
Abstract
Undifferentiated small round cell sarcomas (SRCSs) of bone and soft tissue comprise a heterogeneous group of highly aggressive tumours associated with a poor prognosis, especially in metastatic disease. SRCS entities mainly occur in the third decade of life and can exhibit striking disparities regarding preferentially affected sex and tumour localization. SRCSs comprise new entities defined by specific genetic abnormalities, namely EWSR1-non-ETS fusions, CIC-rearrangements or BCOR genetic alterations, as well as EWSR1-ETS fusions in the prototypic SRCS Ewing sarcoma. These gene fusions mainly encode aberrant oncogenic transcription factors that massively rewire the transcriptome and epigenome of the as yet unknown cell or cells of origin. Additional mutations or copy number variants are rare at diagnosis and, depending on the tumour entity, may involve TP53, CDKN2A and others. Histologically, these lesions consist of small round cells expressing variable levels of CD99 and specific marker proteins, including cyclin B3, ETV4, WT1, NKX3-1 and aggrecan, depending on the entity. Besides locoregional treatment that should follow standard protocols for sarcoma management, (neo)adjuvant treatment is as yet ill-defined but generally follows that of Ewing sarcoma and is associated with adverse effects that might compromise quality of life. Emerging studies on the molecular mechanisms of SRCSs and the development of genetically engineered animal models hold promise for improvements in early detection, disease monitoring, treatment-related toxicity, overall survival and quality of life.
Collapse
|
4
|
Becklin KL, Draper GM, Madden RA, Kluesner MG, Koga T, Huang M, Weiss WA, Spector LG, Largaespada DA, Moriarity BS, Webber BR. Developing Bottom-Up Induced Pluripotent Stem Cell Derived Solid Tumor Models Using Precision Genome Editing Technologies. CRISPR J 2022; 5:517-535. [PMID: 35972367 PMCID: PMC9529369 DOI: 10.1089/crispr.2022.0032] [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] [Received: 03/10/2022] [Accepted: 07/29/2022] [Indexed: 11/13/2022] Open
Abstract
Advances in genome and tissue engineering have spurred significant progress and opportunity for innovation in cancer modeling. Human induced pluripotent stem cells (iPSCs) are an established and powerful tool to study cellular processes in the context of disease-specific genetic backgrounds; however, their application to cancer has been limited by the resistance of many transformed cells to undergo successful reprogramming. Here, we review the status of human iPSC modeling of solid tumors in the context of genetic engineering, including how base and prime editing can be incorporated into "bottom-up" cancer modeling, a term we coined for iPSC-based cancer models using genetic engineering to induce transformation. This approach circumvents the need to reprogram cancer cells while allowing for dissection of the genetic mechanisms underlying transformation, progression, and metastasis with a high degree of precision and control. We also discuss the strengths and limitations of respective engineering approaches and outline experimental considerations for establishing future models.
Collapse
Affiliation(s)
- Kelsie L. Becklin
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
| | - Garrett M. Draper
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
| | - Rebecca A. Madden
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
| | - Mitchell G. Kluesner
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
| | - Tomoyuki Koga
- Ludwig Cancer Research San Diego Branch, La Jolla, California, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Department of Neurosurgery, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
| | - Miller Huang
- Department of Pediatrics, University of Southern California, Los Angeles, California, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Cancer and Blood Disease Institute, Children's Hospital Los Angeles and The Saban Research Institute, Los Angeles, California, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
| | - William A. Weiss
- Departments of Neurology, Pediatrics, Neurosurgery, Brain Tumor Research Center, and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California, USA; and Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Departments of Pediatrics, Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
| | - Logan G. Spector
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
| | - David A. Largaespada
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
| | - Branden S. Moriarity
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
| | - Beau R. Webber
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA; Neurosurgery and Brain Tumor Research Center, University of California, San Francisco, San Francisco, California, USA
| |
Collapse
|
5
|
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.
Collapse
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.
| |
Collapse
|
6
|
CIC-mediated modulation of MAPK signaling opposes receptor tyrosine kinase inhibitor response in kinase-addicted sarcoma. Cancer Res 2022; 82:1110-1127. [DOI: 10.1158/0008-5472.can-21-1397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 09/15/2021] [Accepted: 01/20/2022] [Indexed: 11/16/2022]
|
7
|
McEachron TA, Helman LJ. Recent Advances in Pediatric Cancer Research. Cancer Res 2021; 81:5783-5799. [PMID: 34561271 DOI: 10.1158/0008-5472.can-21-1191] [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] [Received: 04/15/2021] [Revised: 09/05/2021] [Accepted: 09/22/2021] [Indexed: 11/16/2022]
Abstract
Over the past few years, the field of pediatric cancer has experienced a shift in momentum, and this has led to new and exciting findings that have relevance beyond pediatric malignancies. Here we present the current status of key aspects of pediatric cancer research. We have focused on genetic and epigenetic drivers of disease, cellular origins of different pediatric cancers, disease models, the tumor microenvironment, and cellular immunotherapies.
Collapse
Affiliation(s)
| | - Lee J Helman
- Osteosarcoma Institute, Dallas, Texas
- Cancer and Blood Disease Institute, Children's Hospital Los Angeles, Los Angeles, California
| |
Collapse
|
8
|
Liu W, Wang S, Lin B, Zhang W, Ji G. Applications of CRISPR/Cas9 in the research of malignant musculoskeletal tumors. BMC Musculoskelet Disord 2021; 22:149. [PMID: 33546657 PMCID: PMC7866880 DOI: 10.1186/s12891-021-04020-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 01/26/2021] [Indexed: 12/05/2022] Open
Abstract
Background Malignant tumors of the musculoskeletal system, especially osteosarcoma, Ewing sarcoma and rhabdomyosarcoma, pose a major threat to the lives and health of adolescents and children. Current treatments for musculoskeletal tumors mainly include surgery, chemotherapy, and radiotherapy. The problems of chemotherapy resistance, poor long-term outcome of radiotherapy, and the inherent toxicity and side effects of chemical drugs make it extremely urgent to seek new treatment strategies. Main text As a potent gene editing tool, the rapid development of CRISPR/Cas9 technology in recent years has prompted scientists to apply it to the study of musculoskeletal tumors. This review summarizes the application of CRISPR/Cas9 technology for the treatment of malignant musculoskeletal tumors, focusing on its essential role in the field of basic research. Conclusion CRISPR, has demonstrated strong efficacy in targeting tumor-related genes, and its future application in the clinical treatment of musculoskeletal tumors is promising.
Collapse
Affiliation(s)
- Wei Liu
- Department of Orthopaedics, Xiang'an Hospital, School of Medicine, Xiamen University, No. 2000 East Xiang'an Road, Xiang'an District, Xiamen, 361102, China
| | - Shubin Wang
- Department of Orthopaedics, Xiang'an Hospital, School of Medicine, Xiamen University, No. 2000 East Xiang'an Road, Xiang'an District, Xiamen, 361102, China
| | - Binhui Lin
- Department of Orthopaedics, Xiang'an Hospital, School of Medicine, Xiamen University, No. 2000 East Xiang'an Road, Xiang'an District, Xiamen, 361102, China
| | - Wei Zhang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Guangrong Ji
- Department of Orthopaedics, Xiang'an Hospital, School of Medicine, Xiamen University, No. 2000 East Xiang'an Road, Xiang'an District, Xiamen, 361102, China.
| |
Collapse
|
9
|
Erdogan M, Fabritius A, Basquin J, Griesbeck O. Targeted In Situ Protein Diversification and Intra-organelle Validation in Mammalian Cells. Cell Chem Biol 2020; 27:610-621.e5. [PMID: 32142629 DOI: 10.1016/j.chembiol.2020.02.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 12/22/2019] [Accepted: 02/14/2020] [Indexed: 02/08/2023]
Abstract
Engineered proteins must be phenotypically selected for function in the appropriate physiological context. Here, we present a versatile approach that allows generating panels of mammalian cells that express diversified heterologous protein libraries in the cytosol or subcellular compartments under stable conditions and in a single-variant-per-cell manner. To this end we adapt CRISPR/Cas9 editing technology to diversify targeted stretches of a protein of interest in situ. We demonstrate the utility of the approach by in situ engineering and intra-lysosome specific selection of an extremely pH-resistant long Stokes shift red fluorescent protein variant. Tailoring properties to specific conditions of cellular sub-compartments or organelles of mammalian cells can be an important asset to optimize various proteins, protein-based tools, and biosensors for distinct functions.
Collapse
Affiliation(s)
- Mutlu Erdogan
- Tools for Bio-Imaging, Max-Planck-Institut für Neurobiologie, Am Klopferspitz 18, Martinsried 82152, Germany
| | - Arne Fabritius
- Tools for Bio-Imaging, Max-Planck-Institut für Neurobiologie, Am Klopferspitz 18, Martinsried 82152, Germany
| | - Jérome Basquin
- Structural Cell Biology, Max-Planck-Institut für Biochemie, Am Klopferspitz 18, Martinsried 82152, Germany
| | - Oliver Griesbeck
- Tools for Bio-Imaging, Max-Planck-Institut für Neurobiologie, Am Klopferspitz 18, Martinsried 82152, Germany.
| |
Collapse
|
10
|
Pomella S, Rota R. The CRISP(Y) Future of Pediatric Soft Tissue Sarcomas. Front Chem 2020; 8:178. [PMID: 32232030 PMCID: PMC7083251 DOI: 10.3389/fchem.2020.00178] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 02/26/2020] [Indexed: 12/14/2022] Open
Abstract
The RNA-guided clustered regularly interspaced palindromic repeats (CRISPR)/associated nuclease 9 (Cas9)-based genome editing technology has increasingly become a recognized method for translational research. In oncology, the ease and versatility of CRISPR/Cas9 has made it possible to obtain many results in the identification of new target genes and in unravel mechanisms of resistance to therapy. The majority of the studies have been made on adult tumors so far. In this mini review we present an overview on the major aspects of CRISPR/Cas9 technology with a focus on a group of rare pediatric malignancies, soft tissue sarcomas, on which this approach is having promising results.
Collapse
Affiliation(s)
| | - Rossella Rota
- Department of Oncohematology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| |
Collapse
|
11
|
Lee J, Nguyen PT, Shim HS, Hyeon SJ, Im H, Choi MH, Chung S, Kowall NW, Lee SB, Ryu H. EWSR1, a multifunctional protein, regulates cellular function and aging via genetic and epigenetic pathways. Biochim Biophys Acta Mol Basis Dis 2019; 1865:1938-1945. [PMID: 30481590 PMCID: PMC6527469 DOI: 10.1016/j.bbadis.2018.10.042] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 10/05/2018] [Accepted: 10/15/2018] [Indexed: 12/13/2022]
Abstract
Ewing's sarcoma (EWS) is a bone cancer arising predominantly in young children. EWSR1 (Ewing Sarcoma breakpoint region 1/EWS RNA binding protein 1) gene is ubiquitously expressed in most cell types, indicating it has diverse roles in various cellular processes and organ development. Recently, several studies have shown that missense mutations of EWSR1 genes are known to be associated with central nervous system disorders such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Otherwise, EWSR1 plays epigenetic roles in gene expression, RNA processing, and cellular signal transduction. Interestingly, EWSR1 controls micro RNA (miRNA) levels via Drosha, leading to autophagy dysfunction and impaired dermal development. Ewsr1 deficiency also leads to premature senescence of blood cells and gamete cells with a high rate of apoptosis due to the abnormal meiosis. Despite these roles of EWSR1 in various cellular functions, the exact mechanisms are not yet understood. In this context, the current review overviews a large body of evidence and discusses on what EWSR1 genetic mutations are associated with brain diseases and on how EWSR1 modulates cellular function via the epigenetic pathway. This will provide a better understanding of bona fide roles of EWSR1 in aging and its association with brain disorders.
Collapse
Affiliation(s)
- Junghee Lee
- Boston University Alzheimer's Disease Center and Departments of Neurology, Boston University School of Medicine, Boston, MA 02118, United States of America; Veteran's Affairs Boston Healthcare System, Boston, MA 02130, USA
| | - Phuong T Nguyen
- Centers for Neuromedicine and Neuroscience, Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, South Korea
| | - Hyun Soo Shim
- Centers for Neuromedicine and Neuroscience, Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, South Korea
| | - Seung Jae Hyeon
- Centers for Neuromedicine and Neuroscience, Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, South Korea
| | - Hyeonjoo Im
- Centers for Neuromedicine and Neuroscience, Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, South Korea
| | - Mi-Hyun Choi
- Centers for Neuromedicine and Neuroscience, Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, South Korea
| | - Sooyoung Chung
- Centers for Neuromedicine and Neuroscience, Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, South Korea
| | - Neil W Kowall
- Boston University Alzheimer's Disease Center and Departments of Neurology, Boston University School of Medicine, Boston, MA 02118, United States of America; Veteran's Affairs Boston Healthcare System, Boston, MA 02130, USA
| | - Sean Bong Lee
- Department of Pathology & Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA 70112, USA.
| | - Hoon Ryu
- Boston University Alzheimer's Disease Center and Departments of Neurology, Boston University School of Medicine, Boston, MA 02118, United States of America; Veteran's Affairs Boston Healthcare System, Boston, MA 02130, USA; Centers for Neuromedicine and Neuroscience, Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, South Korea.
| |
Collapse
|
12
|
Ahmadzadeh V, Farajnia S, Baghban R, Rahbarnia L, Zarredar H. CRISPR-Cas system: Toward a more efficient technology for genome editing and beyond. J Cell Biochem 2019; 120:16379-16392. [PMID: 31219653 DOI: 10.1002/jcb.29140] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 05/07/2019] [Indexed: 12/26/2022]
Abstract
Genome engineering technology is of great interest for biomedical research that enables scientists to make specific manipulation in the DNA sequence. Early methods for introducing double-stranded DNA breaks relies on protein-based systems. These platforms have enabled fascinating advances, but all are costly and time-consuming to engineer, preventing these from gaining high-throughput applications. The CRISPR-Cas9 system, co-opted from bacteria, has generated considerable excitement in gene targeting. In this review, we describe gene targeting techniques with an emphasis on recent strategies to improve the specificities of CRISPR-Cas systems for nuclease and non-nuclease applications.
Collapse
Affiliation(s)
- Vahideh Ahmadzadeh
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Safar Farajnia
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Roghayyeh Baghban
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Leila Rahbarnia
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Habib Zarredar
- Tuberculosis and Lung Disease Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| |
Collapse
|
13
|
Therapeutic application of the CRISPR system: current issues and new prospects. Hum Genet 2019; 138:563-590. [DOI: 10.1007/s00439-019-02028-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Accepted: 05/13/2019] [Indexed: 12/23/2022]
|
14
|
Tsuyama N, Abe Y, Yanagi A, Yanai Y, Sugai M, Katafuchi A, Kawamura F, Kamiya K, Sakai A. Induction of t(11;14) IgH enhancer/promoter- cyclin D1 gene translocation using CRISPR/Cas9. Oncol Lett 2019; 18:275-282. [PMID: 31289497 PMCID: PMC6539856 DOI: 10.3892/ol.2019.10303] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 04/18/2019] [Indexed: 12/13/2022] Open
Abstract
Chromosomal translocation is a key process in the oncogenic transformation of somatic cells. Previously, artificial induction of chromosomal translocation was performed using homologous recombination-mediated loxP labeling of target regions followed by Cre-mediated recombination. Recent progress in genome editing techniques has facilitated the easier induction of artificial translocation by cutting two targeted genome sequences from different chromosomes. The present study established a system to induce t(11;14)(q13;q32), which is observed primarily in multiple myeloma (MM) and involves the repositioning of the cyclin D1 (CCND1) gene downstream of the immunoglobulin heavy chain (IgH) constant region enhancers by translocation. The placing of tandem gRNAs designed to cut both the IgH Eµ and CCND1 15-kb upstream regions in lentiCRISPRv2 enabled the induction of chromosomal translocation in 293T cells, with confirmation by translocation-specific PCR and fluorescence in situ hybridization probing with IgH and CCND1. At the translocation junctions, small deletions and the addition of DNA sequences (indels) were observed in several clones. Cloned cells with t(11;14) exhibited slower growth and lower CCND1 mRNA expression compared to the parent cells, presenting the opposite phenomena induced by t(11;14) in MM cells, indicating that the silent IgH gene juxtaposed to CCND1 may negatively affect CCND1 gene expression and cell proliferation in the non-B lymphocyte lineage. Therefore, the present study achieved the induction of silent promoter/enhancer translocation in t(11;14)(q13;q32) as a preparatory experiment to study the role of IgH constant region enhancer-driven CCND1 overexpression in oncogenic transformation processes in B lymphocytes.
Collapse
Affiliation(s)
- Naohiro Tsuyama
- Department of Radiation Life Sciences, Fukushima Medical University, Fukushima 960-1295, Japan
| | - Yu Abe
- Department of Radiation Life Sciences, Fukushima Medical University, Fukushima 960-1295, Japan
| | - Aki Yanagi
- Department of Radiation Life Sciences, Fukushima Medical University, Fukushima 960-1295, Japan
| | - Yukari Yanai
- Department of Radiation Life Sciences, Fukushima Medical University, Fukushima 960-1295, Japan
| | - Misaki Sugai
- Department of Radiation Life Sciences, Fukushima Medical University, Fukushima 960-1295, Japan
| | - Atsushi Katafuchi
- Department of Radiation Life Sciences, Fukushima Medical University, Fukushima 960-1295, Japan
| | - Fumihiko Kawamura
- Department of Radiation Life Sciences, Fukushima Medical University, Fukushima 960-1295, Japan
| | - Kenji Kamiya
- Department of Experimental Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Minami-ku, Hiroshima 734-8553, Japan
| | - Akira Sakai
- Department of Radiation Life Sciences, Fukushima Medical University, Fukushima 960-1295, Japan
| |
Collapse
|
15
|
Vojnic M, Kubota D, Kurzatkowski C, Offin M, Suzawa K, Benayed R, Schoenfeld AJ, Plodkowski AJ, Poirier JT, Rudin CM, Kris MG, Rosen NX, Yu HA, Riely GJ, Arcila ME, Somwar R, Ladanyi M. Acquired BRAF Rearrangements Induce Secondary Resistance to EGFR therapy in EGFR-Mutated Lung Cancers. J Thorac Oncol 2019; 14:802-815. [PMID: 30831205 PMCID: PMC6486868 DOI: 10.1016/j.jtho.2018.12.038] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 10/23/2018] [Accepted: 12/27/2018] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Multiple genetic mechanisms have been identified in EGFR-mutant lung cancers as mediators of acquired resistance (AR) to EGFR tyrosine kinase inhibitors (TKIs), but many cases still lack a known mechanism. METHODS To identify novel mechanisms of AR, we performed targeted large panel sequencing of samples from 374 consecutive patients with metastatic EGFR-mutant lung cancer, including 174 post-TKI samples, of which 38 also had a matched pre-TKI sample. Alterations hypothesized to confer AR were introduced into drug-sensitive EGFR-mutant lung cancer cell lines (H1975, HCC827, and PC9) by using clustered regularly interspaced short palindromic repeats/Cas9 genome editing. MSK-LX138cl, a cell line with EGFR exon 19 deletion (ex19del) and praja ring finger ubiquitin ligase 2 gene (PJA2)/BRAF fusion, was generated from an EGFR TKI-resistant patient sample. RESULTS We identified four patients (2.3%) with a BRAF fusion (three with acylglycerol kinase gene (AGK)/BRAF and one with PJA2/BRAF) in samples obtained at AR to EGFR TKI therapy (two posterlotinib samples and two posterlotinib and postosimertinib samples). Pre-TKI samples were available for two of four patients and both were negative for BRAF fusion. Induction of AGK/BRAF fusion in H1975 (L858R + T790M), PC9 (ex19del) and HCC827 (ex19del) cells increased phosphorylation of BRAF, MEK1/2, ERK1/2, and signal transducer and activator of transcription 3 and conferred resistance to growth inhibition by osimertinib. MEK inhibition with trametinib synergized with osimertinib to block growth. Alternately, a pan-RAF inhibitor as a single agent blocked growth of all cell lines with mutant EGFR and BRAF fusion. CONCLUSION BRAF fusion is a mechanism of AR to EGFR TKI therapy in approximately 2% of patients. Combined inhibition of EGFR and MEK (with osimertinib and trametinib) or BRAF (with a pan-RAF inhibitor) are potential therapeutic strategies that should be explored.
Collapse
Affiliation(s)
- Morana Vojnic
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Daisuke Kubota
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Michael Offin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ken Suzawa
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Adam J Schoenfeld
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Andrew J Plodkowski
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - John T Poirier
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Charles M Rudin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Weill Cornell Medical College, New York, New York
| | - Mark G Kris
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Weill Cornell Medical College, New York, New York
| | - Neal X Rosen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Helena A Yu
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Weill Cornell Medical College, New York, New York
| | - Gregory J Riely
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Weill Cornell Medical College, New York, New York
| | - Maria E Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Romel Somwar
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York.
| |
Collapse
|
16
|
Nakano K, Takahashi S. Translocation-Related Sarcomas. Int J Mol Sci 2018; 19:ijms19123784. [PMID: 30487384 PMCID: PMC6320865 DOI: 10.3390/ijms19123784] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 11/20/2018] [Accepted: 11/27/2018] [Indexed: 12/13/2022] Open
Abstract
Chromosomal translocations are observed in approximately 20% of soft tissue sarcomas (STS). With the advances in pathological examination technology, the identification of translocations has enabled precise diagnoses and classifications of STS, and it has been suggested that the presence of and differences in translocations could be prognostic factors in some translocation-related sarcomas. Most of the translocations in STS were not regarded as targets of molecular therapies until recently. However, trabectedin, an alkylating agent, has shown clinical benefits against translocation-related sarcoma based on a modulation of the transcription of the tumor's oncogenic fusion proteins. Many molecular-targeted drugs that are specific to translocations (e.g., anaplastic lymphoma kinase and tropomyosin kinase related fusion proteins) have emerged. The progress in gene technologies has allowed researchers to identify and even induce new translocations and fusion proteins, which might become targets of molecular-targeted therapies. In this review, we discuss the clinical significance of translocation-related sarcomas, including their diagnoses and targeted therapies.
Collapse
Affiliation(s)
- Kenji Nakano
- Department of Medical Oncology, Cancer Institute Hospital of the Japanese Foundation for Cancer Research, Tokyo 135-0063, Japan.
| | - Shunji Takahashi
- Department of Medical Oncology, Cancer Institute Hospital of the Japanese Foundation for Cancer Research, Tokyo 135-0063, Japan.
| |
Collapse
|
17
|
Wang D, Li J, Song CQ, Tran K, Mou H, Wu PH, Tai PWL, Mendonca CA, Ren L, Wang BY, Su Q, Gessler DJ, Zamore PD, Xue W, Gao G. Cas9-mediated allelic exchange repairs compound heterozygous recessive mutations in mice. Nat Biotechnol 2018; 36:839-842. [PMID: 30102296 PMCID: PMC6126964 DOI: 10.1038/nbt.4219] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 06/01/2018] [Indexed: 02/05/2023]
Abstract
We report a genome-editing strategy to correct compound heterozygous mutations, a common genotype in patients with recessive genetic disorders. Adeno-associated viral vector delivery of Cas9 and guide RNA induces allelic exchange and rescues the disease phenotype in mouse models of hereditary tyrosinemia type I and mucopolysaccharidosis type I. This approach recombines non-mutated genetic information present in two heterozygous alleles into one functional allele without using donor DNA templates.
Collapse
Affiliation(s)
- Dan Wang
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Jia Li
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Chun-Qing Song
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Karen Tran
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Haiwei Mou
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Pei-Hsuan Wu
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Phillip W L Tai
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Craig A Mendonca
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Lingzhi Ren
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Blake Y Wang
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Qin Su
- Viral Vector Core, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Dominic J Gessler
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Phillip D Zamore
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Wen Xue
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Program in Molecular Medicine and Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Guangping Gao
- Horae Gene Therapy Center, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Li Weibo Institute for Rare Diseases Research, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| |
Collapse
|
18
|
Xu H, Wu X, Sun D, Li S, Zhang S, Teng M, Bu J, Zhang X, Meng B, Wang W, Tian G, Lin H, Yuan D, Lang J, Xu S. SEGF: A Novel Method for Gene Fusion Detection from Single-End Next-Generation Sequencing Data. Genes (Basel) 2018; 9:genes9070331. [PMID: 30004447 PMCID: PMC6070977 DOI: 10.3390/genes9070331] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 06/21/2018] [Accepted: 06/27/2018] [Indexed: 11/23/2022] Open
Abstract
With the development and application of next-generation sequencing (NGS) and target capture technology, the demand for an effective analysis method to accurately detect gene fusion from high-throughput data is growing. Hence, we developed a novel fusion gene analyzing method called single-end gene fusion (SEGF) by starting with single-end DNA-seq data. This approach takes raw sequencing data as input, and integrates the commonly used alignment approach basic local alignment search tool (BLAST) and short oligonucleotide analysis package (SOAP) with stringent passing filters to achieve successful fusion gene detection. To evaluate SEGF, we compared it with four other fusion gene discovery analysis methods by analyzing sequencing results of 23 standard DNA samples and DNA extracted from 286 lung cancer formalin fixed paraffin embedded (FFPE) samples. The results generated by SEGF indicated that it not only detected the fusion genes from standard samples and clinical samples, but also had the highest accuracy and sensitivity among the five compared methods. In addition, SEGF was capable of detecting complex gene fusion types from single-end NGS sequencing data compared with other methods. By using SEGF to acquire gene fusion information at DNA level, more useful information can be retrieved from the DNA panel or other DNA sequencing methods without generating RNA sequencing information to benefit clinical diagnosis or medication instruction. It was a timely and cost-effective measure with regard to research or diagnosis. Considering all the above, SEGF is a straightforward method without manipulating complicated arguments, providing a useful approach for the precise detection of gene fusion variation.
Collapse
Affiliation(s)
- Hai Xu
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, Harbin 150049, China.
| | - Xiaojin Wu
- Department of Radiation Oncology, The First People's Hospital of Xuzhou, Xuzhou 221002, China.
| | - Dawei Sun
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, Harbin 150049, China.
| | - Shijun Li
- Department of Pathology, Chifeng Municiple Hospital, Chifeng 024000, China.
| | - Siwen Zhang
- Geneis Beijing Co., Ltd., Beijing 100102, China.
| | - Miao Teng
- Geneis Beijing Co., Ltd., Beijing 100102, China.
| | - Jianlong Bu
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, Harbin 150049, China.
| | - Xizhe Zhang
- Department of Anesthesiology, Chifeng Municiple Hospital, Chifeng 024000, China.
| | - Bo Meng
- Geneis Beijing Co., Ltd., Beijing 100102, China.
| | - Weitao Wang
- Geneis Beijing Co., Ltd., Beijing 100102, China.
| | - Geng Tian
- Geneis Beijing Co., Ltd., Beijing 100102, China.
| | - Huixin Lin
- Geneis Beijing Co., Ltd., Beijing 100102, China.
| | - Dawei Yuan
- Geneis Beijing Co., Ltd., Beijing 100102, China.
| | - Jidong Lang
- Geneis Beijing Co., Ltd., Beijing 100102, China.
| | - Shidong Xu
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, Harbin 150049, China.
| |
Collapse
|
19
|
Affiliation(s)
- Andrea Ventura
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Lukas E. Dow
- Department of Medicine, Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY 10021, USA
| |
Collapse
|
20
|
Brunet E, Jasin M. Induction of Chromosomal Translocations with CRISPR-Cas9 and Other Nucleases: Understanding the Repair Mechanisms That Give Rise to Translocations. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1044:15-25. [PMID: 29956288 DOI: 10.1007/978-981-13-0593-1_2] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Chromosomal translocations are associated with several tumor types, including hematopoietic malignancies, sarcomas, and solid tumors of epithelial origin, due to their activation of a proto-oncogene or generation of a novel fusion protein with oncogenic potential. In many cases, the availability of suitable human models has been lacking because of the difficulty in recapitulating precise expression of the fusion protein or other reasons. Further, understanding how translocations form mechanistically has been a goal, as it may suggest ways to prevent their occurrence. Chromosomal translocations arise when DNA ends from double-strand breaks (DSBs) on two heterologous chromosomes are improperly joined. This review provides a summary of DSB repair mechanisms and their contribution to translocation formation, the various programmable nuclease platforms that have been used to generate translocations, and the successes that have been achieved in this area.
Collapse
Affiliation(s)
- Erika Brunet
- Genome Dynamics in the Immune System Laboratory, Institut Imagine, INSERM UMR 1163, Université Paris Descartes, Sorbonne Paris Cité, Paris, France.
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| |
Collapse
|
21
|
Advances in chromosomal translocations and fusion genes in sarcomas and potential therapeutic applications. Cancer Treat Rev 2017; 63:61-70. [PMID: 29247978 DOI: 10.1016/j.ctrv.2017.12.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 12/01/2017] [Indexed: 12/12/2022]
Abstract
Chromosomal translocations and fusion genes are very common in human cancer especially in subtypes of sarcomas, such as rhabdomyosarcoma, Ewing's sarcoma, synovial sarcoma and liposarcoma. The discovery of novel chromosomal translocations and fusion genes in different tumors are due to the advancement of next-generation sequencing (NGS) technologies such as whole genome sequencing. Recently, many novel chromosomal translocations and gene fusions have been identified in different types of sarcoma through NGS approaches. In addition to previously known sarcoma fusion genes, these novel specific fusion genes and associated molecular events represent important targets for novel therapeutic approaches in the treatment of sarcomas. This review focuses on recent advances in chromosomal translocations and fusion genes in sarcomas and their potential therapeutic applications in the treatment of sarcomas.
Collapse
|
22
|
Torres-Ruiz R, Rodriguez-Perales S, Bueno C, Menendez P. Modeling mixed-lineage-rearranged leukemia initiation in CD34 + cells: a "CRISPR" solution. Haematologica 2017; 102:1467-1468. [PMID: 28860233 DOI: 10.3324/haematol.2017.173740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Affiliation(s)
- Raúl Torres-Ruiz
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain .,Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain
| | - Sandra Rodriguez-Perales
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
| | - Clara Bueno
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBER-ONC), ISCIII, Barcelona, Spain
| | - Pablo Menendez
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain .,Centro de Investigación Biomédica en Red de Cáncer (CIBER-ONC), ISCIII, Barcelona, Spain.,Instituciò Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluis Companys, Barcelona, Spain
| |
Collapse
|
23
|
Vanoli F, Jasin M. Generation of chromosomal translocations that lead to conditional fusion protein expression using CRISPR-Cas9 and homology-directed repair. Methods 2017; 121-122:138-145. [PMID: 28522325 PMCID: PMC5531069 DOI: 10.1016/j.ymeth.2017.05.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 04/24/2017] [Accepted: 05/10/2017] [Indexed: 10/19/2022] Open
Abstract
Recurrent chromosomal translocations often lead to expression of fusion proteins associated with oncogenic transformation. To study translocations and downstream events, genome editing techniques have been developed to generate chromosomal translocations through non-homologous end joining of DNA double-strand breaks introduced at the two participating endogenous loci. However, the frequencies at which these events occur is usually too low to efficiently clone cells carrying the translocation. This article provides a detailed method using CRISPR-Cas9 technology and homology-directed repair to efficiently isolate cells harboring a chromosomal translocation. For an additional level of control, the resulting fusion protein is conditionally expressed to allow early events in oncogenic transformation to be studied. We focus on the generation of the EWSR1-WT1 fusion using human mesenchymal cells, which is associated with the translocation found in desmoplastic small round cell tumors.
Collapse
MESH Headings
- Abdominal Neoplasms/genetics
- Abdominal Neoplasms/metabolism
- Abdominal Neoplasms/pathology
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- CRISPR-Associated Protein 9
- CRISPR-Cas Systems
- Cell Line
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/metabolism
- Cell Transformation, Neoplastic/pathology
- Chromosomes, Human, Pair 11
- Chromosomes, Human, Pair 22
- Clustered Regularly Interspaced Short Palindromic Repeats
- DNA Breaks, Double-Stranded
- Desmoplastic Small Round Cell Tumor/genetics
- Desmoplastic Small Round Cell Tumor/metabolism
- Desmoplastic Small Round Cell Tumor/pathology
- Endonucleases/genetics
- Endonucleases/metabolism
- Genome, Human
- Humans
- Mesenchymal Stem Cells/metabolism
- Mesenchymal Stem Cells/pathology
- Mutagenesis, Site-Directed/methods
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- RNA, Guide, CRISPR-Cas Systems/genetics
- RNA, Guide, CRISPR-Cas Systems/metabolism
- RNA-Binding Protein EWS/genetics
- RNA-Binding Protein EWS/metabolism
- Recombinational DNA Repair
- Translocation, Genetic
- WT1 Proteins/genetics
- WT1 Proteins/metabolism
Collapse
Affiliation(s)
- Fabio Vanoli
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA.
| |
Collapse
|
24
|
CRISPR-Cas9-guided oncogenic chromosomal translocations with conditional fusion protein expression in human mesenchymal cells. Proc Natl Acad Sci U S A 2017; 114:3696-3701. [PMID: 28325870 DOI: 10.1073/pnas.1700622114] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Gene editing techniques have been extensively used to attempt to model recurrent genomic rearrangements found in tumor cells. These methods involve the induction of double-strand breaks at endogenous loci followed by the identification of breakpoint junctions within a population, which typically arise by nonhomologous end joining. The low frequency of these events, however, has hindered the cloning of cells with the desired rearrangement before oncogenic transformation. Here we present a strategy combining CRISPR-Cas9 technology and homology-directed repair to allow for the selection of human mesenchymal stem cells harboring the oncogenic translocation EWSR1-WT1 found in the aggressive desmoplastic small round cell tumor. The expression of the fusion transcript is under the control of the endogenous EWSR1 promoter and, importantly, can be conditionally expressed using Cre recombinase. This method is easily adapted to generate any cancer-relevant rearrangement.
Collapse
|