1
|
Martinez S, Wu S, Geuenich M, Malik A, Weber R, Woo T, Zhang A, Jang GH, Dervovic D, Al-Zahrani KN, Tsai R, Fodil N, Gros P, Gallinger S, Neely GG, Notta F, Sendoel A, Campbell K, Elling U, Schramek D. In vivo CRISPR screens reveal SCAF1 and USP15 as drivers of pancreatic cancer. Nat Commun 2024; 15:5266. [PMID: 38902237 PMCID: PMC11189927 DOI: 10.1038/s41467-024-49450-3] [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: 12/06/2022] [Accepted: 06/05/2024] [Indexed: 06/22/2024] Open
Abstract
Functionally characterizing the genetic alterations that drive pancreatic cancer is a prerequisite for precision medicine. Here, we perform somatic CRISPR/Cas9 mutagenesis screens to assess the transforming potential of 125 recurrently mutated pancreatic cancer genes, which revealed USP15 and SCAF1 as pancreatic tumor suppressors. Mechanistically, we find that USP15 functions in a haploinsufficient manner and that loss of USP15 or SCAF1 leads to reduced inflammatory TNFα, TGF-β and IL6 responses and increased sensitivity to PARP inhibition and Gemcitabine. Furthermore, we find that loss of SCAF1 leads to the formation of a truncated, inactive USP15 isoform at the expense of full-length USP15, functionally coupling SCAF1 and USP15. Notably, USP15 and SCAF1 alterations are observed in 31% of pancreatic cancer patients. Our results highlight the utility of in vivo CRISPR screens to integrate human cancer genomics and mouse modeling for the discovery of cancer driver genes with potential prognostic and therapeutic implications.
Collapse
Affiliation(s)
- Sebastien Martinez
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Shifei Wu
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Michael Geuenich
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Ahmad Malik
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Ramona Weber
- Institute for Regenerative Medicine (IREM), University of Zurich, Zurich, Switzerland
| | - Tristan Woo
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Amy Zhang
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Gun Ho Jang
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Dzana Dervovic
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Khalid N Al-Zahrani
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Ricky Tsai
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Nassima Fodil
- Department of Biochemistry, Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, QC, Canada
| | - Philippe Gros
- Department of Biochemistry, Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, QC, Canada
| | - Steven Gallinger
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - G Gregory Neely
- Dr. John and Anne Chong Lab for Functional Genomics, Charles Perkins Centre, and School of Life and Environmental Sciences, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Faiyaz Notta
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- PanCuRx Translational Research Initiative, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Ataman Sendoel
- Institute for Regenerative Medicine (IREM), University of Zurich, Zurich, Switzerland
| | - Kieran Campbell
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Ulrich Elling
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Dr. Bohr-Gasse 3, Vienna BioCenter (VBC), 1030, Vienna, Austria
| | - Daniel Schramek
- Centre for Molecular and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
| |
Collapse
|
2
|
Di Fede E, Grazioli P, Lettieri A, Parodi C, Castiglioni S, Taci E, Colombo EA, Ancona S, Priori A, Gervasini C, Massa V. Epigenetic disorders: Lessons from the animals–animal models in chromatinopathies. Front Cell Dev Biol 2022; 10:979512. [PMID: 36225316 PMCID: PMC9548571 DOI: 10.3389/fcell.2022.979512] [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: 06/27/2022] [Accepted: 09/05/2022] [Indexed: 11/13/2022] Open
Abstract
Chromatinopathies are defined as genetic disorders caused by mutations in genes coding for protein involved in the chromatin state balance. So far 82 human conditions have been described belonging to this group of congenital disorders, sharing some molecular features and clinical signs. For almost all of these conditions, no specific treatment is available. For better understanding the molecular cascade caused by chromatin imbalance and for envisaging possible therapeutic strategies it is fundamental to combine clinical and basic research studies. To this end, animal modelling systems represent an invaluable tool to study chromatinopathies. In this review, we focused on available data in the literature of animal models mimicking the human genetic conditions. Importantly, affected organs and abnormalities are shared in the different animal models and most of these abnormalities are reported as clinical manifestation, underlying the parallelism between clinics and translational research.
Collapse
Affiliation(s)
- Elisabetta Di Fede
- Department of Health Sciences, Università Degli Studi di Milano, Milan, Italy
| | - Paolo Grazioli
- Department of Health Sciences, Università Degli Studi di Milano, Milan, Italy
| | - Antonella Lettieri
- Department of Health Sciences, Università Degli Studi di Milano, Milan, Italy
| | - Chiara Parodi
- Department of Health Sciences, Università Degli Studi di Milano, Milan, Italy
| | - Silvia Castiglioni
- Department of Health Sciences, Università Degli Studi di Milano, Milan, Italy
| | - Esi Taci
- Department of Health Sciences, Università Degli Studi di Milano, Milan, Italy
| | - Elisa Adele Colombo
- Department of Health Sciences, Università Degli Studi di Milano, Milan, Italy
| | - Silvia Ancona
- Department of Health Sciences, Università Degli Studi di Milano, Milan, Italy
| | - Alberto Priori
- Department of Health Sciences, Università Degli Studi di Milano, Milan, Italy
- “Aldo Ravelli” Center for Neurotechnology and Experimental Brain Therapeutics, Università Degli Studi di Milano, Milan, Italy
| | - Cristina Gervasini
- Department of Health Sciences, Università Degli Studi di Milano, Milan, Italy
- “Aldo Ravelli” Center for Neurotechnology and Experimental Brain Therapeutics, Università Degli Studi di Milano, Milan, Italy
| | - Valentina Massa
- Department of Health Sciences, Università Degli Studi di Milano, Milan, Italy
- “Aldo Ravelli” Center for Neurotechnology and Experimental Brain Therapeutics, Università Degli Studi di Milano, Milan, Italy
- *Correspondence: Valentina Massa,
| |
Collapse
|
3
|
Li G, Li X, Zhuang S, Wang L, Zhu Y, Chen Y, Sun W, Wu Z, Zhou Z, Chen J, Huang X, Wang J, Li D, Li W, Wang H, Wei W. Gene editing and its applications in biomedicine. SCIENCE CHINA. LIFE SCIENCES 2022; 65:660-700. [PMID: 35235150 PMCID: PMC8889061 DOI: 10.1007/s11427-021-2057-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/06/2021] [Indexed: 02/06/2023]
Abstract
The steady progress in genome editing, especially genome editing based on the use of clustered regularly interspaced short palindromic repeats (CRISPR) and programmable nucleases to make precise modifications to genetic material, has provided enormous opportunities to advance biomedical research and promote human health. The application of these technologies in basic biomedical research has yielded significant advances in identifying and studying key molecular targets relevant to human diseases and their treatment. The clinical translation of genome editing techniques offers unprecedented biomedical engineering capabilities in the diagnosis, prevention, and treatment of disease or disability. Here, we provide a general summary of emerging biomedical applications of genome editing, including open challenges. We also summarize the tools of genome editing and the insights derived from their applications, hoping to accelerate new discoveries and therapies in biomedicine.
Collapse
Affiliation(s)
- Guanglei Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Xiangyang Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Songkuan Zhuang
- Department of Clinical Laboratory, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, 518035, China
| | - Liren Wang
- Shanghai Frontiers Science Research Base of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Yifan Zhu
- Shanghai Frontiers Science Research Base of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Yangcan Chen
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wen Sun
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zeguang Wu
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Zhuo Zhou
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Jia Chen
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Xingxu Huang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Jin Wang
- Department of Clinical Laboratory, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, 518035, China.
| | - Dali Li
- Shanghai Frontiers Science Research Base of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, 200241, China.
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, 100101, China.
- Bejing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
- HIT Center for Life Sciences, Harbin Institute of Technology, Harbin, 150001, China.
| | - Haoyi Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Wensheng Wei
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China.
| |
Collapse
|
4
|
Mahmoudian RA, Farshchian M, Abbaszadegan MR. Genetically engineered mouse models of esophageal cancer. Exp Cell Res 2021; 406:112757. [PMID: 34331909 DOI: 10.1016/j.yexcr.2021.112757] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 07/10/2021] [Accepted: 07/26/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND Esophageal cancer is the most common cause of cancer-related death worldwide with a diverse geographical distribution, poor prognosis, and diagnosis in advanced stages of the disease. Identification of the mechanisms involved in esophageal cancer development is evaluative to improve outcomes for patients. Genetically engineered mouse models (GEMMs) of cancer provide the physiologic, molecular, and histologic features of the human tumors to determine the pathogenesis and treatments for cancer, hence exhibiting a source of tremendous potential for oncology research. The advancement of cancer modeling in mice has improved to the extent that researchers can observe and manipulate the disease process in a specific manner. Despite the significant differences between mice and humans, mice can be great models for human oncology researches due to similarities between them at the molecular and physiological levels. Due to most of the existing esophageal cancer GEMMs do not propose an ideal system for pathogenesis of the disease, genetic risks, and microenvironment exposure, so identification of challenges in GEM modeling and well-developed technologies are required to obtain the most value for patients. In this review, we describe the biology of human and mouse, followed by the exciting esophageal cancer mouse models with a discussion of applicability and challenges of these models for generating new GEMMs in future studies.
Collapse
Affiliation(s)
| | - Moein Farshchian
- Stem Cell and Regenerative Medicine Research Group, Academic Center for Education, Culture and Research (ACECR), Khorasan Razavi, Mashhad, Iran.
| | | |
Collapse
|
5
|
|
6
|
Bok I, Vera O, Xu X, Jasani N, Nakamura K, Reff J, Nenci A, Gonzalez JG, Karreth FA. A Versatile ES Cell-Based Melanoma Mouse Modeling Platform. Cancer Res 2019; 80:912-921. [PMID: 31744817 DOI: 10.1158/0008-5472.can-19-2924] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 10/24/2019] [Accepted: 11/13/2019] [Indexed: 01/04/2023]
Abstract
The cumbersome and time-consuming process of generating new mouse strains and multiallelic experimental animals often hinders the use of genetically engineered mouse models (GEMM) in cancer research. Here, we describe the development and validation of an embryonic stem cell (ESC)-GEMM platform for rapid modeling of melanoma in mice. The platform incorporates 12 clinically relevant genotypes composed of combinations of four driver alleles (LSL-BrafV600E, LSL-NrasQ61R, PtenFlox, and Cdkn2aFlox) and regulatory alleles to spatiotemporally control the perturbation of genes of interest. The ESCs produce high-contribution chimeras, which recapitulate the melanoma phenotypes of conventionally bred mice. Using the ESC-GEMM platform to modulate Pten expression in melanocytes in vivo, we highlighted the utility and advantages of gene depletion by CRISPR-Cas9, RNAi, or conditional knockout for melanoma modeling. Moreover, complementary genetic methods demonstrated the impact of Pten restoration on the prevention and maintenance of Pten-deficient melanomas. Finally, we showed that chimera-derived melanoma cell lines retain regulatory allele competency and are a powerful resource to complement ESC-GEMM chimera experiments in vitro and in syngeneic grafts in vivo Thus, when combined with sophisticated genetic tools, the ESC-GEMM platform enables rapid, high-throughput, and versatile studies aimed at addressing outstanding questions in melanoma biology.Significance: This study presents a high-throughput and versatile ES cell-based mouse modeling platform that can be combined with state-of-the-art genetic tools to address unanswered questions in melanoma in vivo See related commentary by Thorkelsson et al., p. 655.
Collapse
Affiliation(s)
- Ilah Bok
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida.,Cancer Biology PhD Program, University of South Florida, Tampa, Florida
| | - Olga Vera
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Xiaonan Xu
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Neel Jasani
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida.,Cancer Biology PhD Program, University of South Florida, Tampa, Florida
| | - Koji Nakamura
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Jordan Reff
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Arianna Nenci
- Gene Targeting Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Jose G Gonzalez
- Gene Targeting Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Florian A Karreth
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida.
| |
Collapse
|
7
|
Soares MJ, Varberg KM, Iqbal K. Hemochorial placentation: development, function, and adaptations. Biol Reprod 2019; 99:196-211. [PMID: 29481584 DOI: 10.1093/biolre/ioy049] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 02/21/2018] [Indexed: 11/12/2022] Open
Abstract
Placentation is a reproductive adaptation that permits fetal growth and development within the protected confines of the female reproductive tract. Through this important role, the placenta also determines postnatal health and susceptibility to disease. The hemochorial placenta is a prominent feature in primate and rodent development. This manuscript provides an overview of the basics of hemochorial placental development and function, provides perspectives on major discoveries that have shaped placental research, and thoughts on strategies for future investigation.
Collapse
Affiliation(s)
- Michael J Soares
- Institute for Reproduction and Perinatal Research and the Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA.,Department of Pediatrics, University of Kansas Medical Center, Kansas City, Kansas, USA and the Center for Perinatal Research, Children΄s Research Institute, Children΄s Mercy, Kansas City, Missouri, USA
| | - Kaela M Varberg
- Institute for Reproduction and Perinatal Research and the Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Khursheed Iqbal
- Institute for Reproduction and Perinatal Research and the Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas, USA
| |
Collapse
|
8
|
O'Loughlin TA, Gilbert LA. Functional Genomics for Cancer Research: Applications In Vivo and In Vitro. ANNUAL REVIEW OF CANCER BIOLOGY 2019. [DOI: 10.1146/annurev-cancerbio-030518-055742] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Functional genomics holds great promise for the dissection of cancer biology. The elucidation of genetic cooperation and molecular details that govern oncogenesis, metastasis, and response to therapy is made possible by robust technologies for perturbing gene function coupled to quantitative analysis of cancer phenotypes resulting from genetic or epigenetic perturbations. Multiplexed genetic perturbations enable the dissection of cooperative genetic lesions as well as the identification of synthetic lethal gene pairs that hold particular promise for constructing innovative cancer therapies. Lastly, functional genomics strategies enable the highly multiplexed in vivo analysis of genes that govern tumorigenesis as well as of the complex multicellular biology of a tumor, such as immune response and metastasis phenotypes. In this review, we discuss both historical and emerging functional genomics approaches and their impact on the cancer research landscape.
Collapse
Affiliation(s)
- Thomas A. O'Loughlin
- Department of Urology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California 94158, USA
| | - Luke A. Gilbert
- Department of Urology and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California 94158, USA
- Innovative Genomics Institute, University of California, San Francisco, California 94158, USA
| |
Collapse
|
9
|
Goemann IM, Marczyk VR, Romitti M, Wajner SM, Maia AL. Current concepts and challenges to unravel the role of iodothyronine deiodinases in human neoplasias. Endocr Relat Cancer 2018; 25:R625-R645. [PMID: 30400023 DOI: 10.1530/erc-18-0097] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 07/10/2018] [Indexed: 12/20/2022]
Abstract
Thyroid hormones (THs) are essential for the regulation of several metabolic processes and the energy consumption of the organism. Their action is exerted primarily through interaction with nuclear receptors controlling the transcription of thyroid hormone-responsive genes. Proper regulation of TH levels in different tissues is extremely important for the equilibrium between normal cellular proliferation and differentiation. The iodothyronine deiodinases types 1, 2 and 3 are key enzymes that perform activation and inactivation of THs, thus controlling TH homeostasis in a cell-specific manner. As THs seem to exert their effects in all hallmarks of the neoplastic process, dysregulation of deiodinases in the tumoral context can be critical to the neoplastic development. Here, we aim at reviewing the deiodinases expression in different neoplasias and exploit the mechanisms by which they play an essential role in human carcinogenesis. TH modulation by deiodinases and other classical pathways may represent important targets with the potential to oppose the neoplastic process.
Collapse
Affiliation(s)
- Iuri Martin Goemann
- Thyroid Unit, Endocrine Division, Hospital de Clínicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Vicente Rodrigues Marczyk
- Thyroid Unit, Endocrine Division, Hospital de Clínicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Mirian Romitti
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire, Université Libre de Bruxelles, Brussels, Belgium
| | - Simone Magagnin Wajner
- Thyroid Unit, Endocrine Division, Hospital de Clínicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Ana Luiza Maia
- Thyroid Unit, Endocrine Division, Hospital de Clínicas de Porto Alegre, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| |
Collapse
|
10
|
Vimalraj S, Saravanan S, Anuradha D, Chatterjee S. Models to investigate intussusceptive angiogenesis: A special note on CRISPR/Cas9 based system in zebrafish. Int J Biol Macromol 2018; 123:1229-1240. [PMID: 30468812 DOI: 10.1016/j.ijbiomac.2018.11.164] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 11/08/2018] [Accepted: 11/17/2018] [Indexed: 01/05/2023]
Abstract
Angiogenesis is a distinct process which follows sprouting angiogenesis (SA) and intussusceptive angiogenesis (IA) forming the basis for various physiological and pathological scenarios. Angiogenesis is a double edged sword exerting both desirable and discernible effects owing to the referred microenvironment. Therapeutic interventions to promote angiogenesis in regenerative medicine is essential to achieve functional syncytium of tissue constructs while, angiogenic inhibition is a key therapeutic target to suppress tumor growth. In the recent years, clustered regularly interspaced short palindromic repeats associated 9 (CRISPR-Cas9) based gene editing approaches have been gaining considerable attention in the field of biomedical research owing to its ease in tailoring targeted genome in living organisms. The Zebrafish model, with adequately high-throughput fitness, is a likely option for genome editing and angiogenesis research. In this review, we focus on the implication of Zebrafish as a model to study IA and furthermore enumerate CRISPR/Cas9 based genome editing in Zebrafish as a candidate for modeling different types of angiogenesis and support its candidature as a model organism.
Collapse
Affiliation(s)
- Selvaraj Vimalraj
- Centre for Biotechnology, Anna University, Chennai 600 044, Tamil Nadu, India.
| | - Sekaran Saravanan
- Centre for Nanotechnology & Advanced Biomaterials (CeNTAB), Department of Bioengineering, School of Chemical and Biotechnology, SASTRA University, Thanjavur 613 401, Tamil Nadu, India.
| | | | - Suvro Chatterjee
- Centre for Biotechnology, Anna University, Chennai 600 044, Tamil Nadu, India
| |
Collapse
|
11
|
Adamson KI, Sheridan E, Grierson AJ. Use of zebrafish models to investigate rare human disease. J Med Genet 2018; 55:641-649. [PMID: 30065072 DOI: 10.1136/jmedgenet-2018-105358] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 07/02/2018] [Accepted: 07/04/2018] [Indexed: 01/07/2023]
Abstract
Rare diseases are collectively common and often extremely debilitating. Following the emergence of next-generation sequencing (NGS) technologies, the variants underpinning rare genetic disorders are being unearthed at an accelerating rate. However, many rare conditions lack effective treatments due to their poorly understood pathophysiology. There is therefore a growing demand for the development of novel experimental models of rare genetic diseases, so that potentially causative variants can be validated, pathogenic mechanisms can be investigated and therapeutic targets can be identified. Animal models of rare diseases need to be genetically and physiologically similar to humans, and well-suited to large-scale experimental manipulation, considering the vast number of novel variants that are being identified through NGS. The zebrafish has emerged as a popular model system for investigating these variants, combining conserved vertebrate characteristics with a capacity for large-scale phenotypic and therapeutic screening. In this review, we aim to highlight the unique advantages of the zebrafish over other in vivo model systems for the large-scale study of rare genetic variants. We will also consider the generation of zebrafish disease models from a practical standpoint, by discussing how genome editing technologies, particularly the recently developed clustered regularly interspaced repeat (CRISPR)/CRISPR-associated protein 9 system, can be used to model rare pathogenic variants in zebrafish. Finally, we will review examples in the literature where zebrafish models have played a pivotal role in confirming variant causality and revealing the underlying mechanisms of rare diseases, often with wider implications for our understanding of human biology.
Collapse
Affiliation(s)
- Kathryn Isabel Adamson
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | | | - Andrew James Grierson
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK.,Department of Neuroscience, University of Sheffield, Sheffield, UK
| |
Collapse
|
12
|
Lampreht Tratar U, Horvat S, Cemazar M. Transgenic Mouse Models in Cancer Research. Front Oncol 2018; 8:268. [PMID: 30079312 PMCID: PMC6062593 DOI: 10.3389/fonc.2018.00268] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 06/29/2018] [Indexed: 12/26/2022] Open
Abstract
The use of existing mouse models in cancer research is of utmost importance as they aim to explore the casual link between candidate cancer genes and carcinogenesis as well as to provide models to develop and test new therapies. However, faster progress in translating mouse cancer model research into the clinic has been hampered due to the limitations of these models to better reflect the complexities of human tumors. Traditionally, immunocompetent and immunodeficient mice with syngeneic and xenografted tumors transplanted subcutaneously or orthotopically have been used. These models are still being widely employed for many different types of studies, in part due to their widespread availability and low cost. Other types of mouse models used in cancer research comprise transgenic mice in which oncogenes can be constitutively or conditionally expressed and tumor-suppressor genes silenced using conventional methods, such as retroviral infection, microinjection of DNA constructs, and the so-called "gene-targeted transgene" approach. These traditional transgenic models have been very important in studies of carcinogenesis and tumor pathogenesis, as well as in studies evaluating the development of resistance to therapy. Recently, the clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editing approach has revolutionized the field of mouse cancer models and has had a profound and rapid impact on the development of more effective systems to study human cancers. The CRISPR/Cas9-based transgenic models have the capacity to engineer a wide spectrum of mutations found in human cancers and provide solutions to problems that were previously unsolvable. Recently, humanized mouse xenograft models that accept patient-derived xenografts and CD34+ cells were developed to better mimic tumor heterogeneity, the tumor microenvironment, and cross-talk between the tumor and stromal/immune cells. These features make them extremely valuable models for the evaluation of investigational cancer therapies, specifically new immunotherapies. Taken together, improvements in both the CRISPR/Cas9 system producing more valid mouse models and in the humanized mouse xenograft models resembling complex interactions between the tumor and its environment might represent one of the successful pathways to precise individualized cancer therapy, leading to improved cancer patient survival and quality of life.
Collapse
Affiliation(s)
- Ursa Lampreht Tratar
- Department of Experimental Oncology, Institute of Oncology Ljubljana, Ljubljana, Slovenia
| | - Simon Horvat
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Maja Cemazar
- Department of Experimental Oncology, Institute of Oncology Ljubljana, Ljubljana, Slovenia.,Faculty of Health Sciences, University of Primorska, Isola, Slovenia
| |
Collapse
|
13
|
Vazquez-Martin A, Anatskaya OV, Giuliani A, Erenpreisa J, Huang S, Salmina K, Inashkina I, Huna A, Nikolsky NN, Vinogradov AE. Somatic polyploidy is associated with the upregulation of c-MYC interacting genes and EMT-like signature. Oncotarget 2018; 7:75235-75260. [PMID: 27655693 PMCID: PMC5342737 DOI: 10.18632/oncotarget.12118] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 09/05/2016] [Indexed: 12/30/2022] Open
Abstract
The dependence of cancer on overexpressed c-MYC and its predisposition for polyploidy represents a double puzzle. We address this conundrum by cross-species transcription analysis of c-MYC interacting genes in polyploid vs. diploid tissues and cells, including human vs. mouse heart, mouse vs. human liver and purified 4n vs. 2n mouse decidua cells. Gene-by-gene transcriptome comparison and principal component analysis indicated that c-MYC interactants are significantly overrepresented among ploidy-associated genes. Protein interaction networks and gene module analysis revealed that the most upregulated genes relate to growth, stress response, proliferation, stemness and unicellularity, as well as to the pathways of cancer supported by MAPK and RAS coordinated pathways. A surprising feature was the up-regulation of epithelial-mesenchymal transition (EMT) modules embodied by the N-cadherin pathway and EMT regulators from SNAIL and TWIST families. Metabolic pathway analysis also revealed the EMT-linked features, such as global proteome remodeling, oxidative stress, DNA repair and Warburg-like energy metabolism. Genes associated with apoptosis, immunity, energy demand and tumour suppression were mostly down-regulated. Noteworthy, despite the association between polyploidy and ample features of cancer, polyploidy does not trigger it. Possibly it occurs because normal polyploidy does not go that far in embryonalisation and linked genome destabilisation. In general, the analysis of polyploid transcriptome explained the evolutionary relation of c-MYC and polyploidy to cancer.
Collapse
Affiliation(s)
| | - Olga V Anatskaya
- Institute of Cytology, St-Petersburg, Russian Federation, Russia
| | | | | | - Sui Huang
- Systems Biology Institute, Seattle, USA
| | | | - Inna Inashkina
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Anda Huna
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | | | | |
Collapse
|
14
|
Imran A, Qamar HY, Ali Q, Naeem H, Riaz M, Amin S, Kanwal N, Ali F, Sabar MF, Nasir IA. Role of Molecular Biology in Cancer Treatment: A Review Article. IRANIAN JOURNAL OF PUBLIC HEALTH 2017; 46:1475-1485. [PMID: 29167765 PMCID: PMC5696686 DOI: pmid/29167765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Background: Cancer is a genetic disease and mainly arises due to a number of reasons include activation of onco-genes, malfunction of tumor suppressor genes or mutagenesis due to external factors. Methods: This article was written from the data collected from PubMed, Nature, Science Direct, Springer and Elsevier groups of journals. Results: Oncogenes are deregulated form of normal proto-oncogenes required for cell division, differentiation and regulation. The conversion of proto-oncogene to oncogene is caused due to translocation, rearrangement of chromosomes or mutation in gene due to addition, deletion, duplication or viral infection. These oncogenes are targeted by drugs or RNAi system to prevent proliferation of cancerous cells. There have been developed different techniques of molecular biology used to diagnose and treat cancer, including retroviral therapy, silencing of oncogenes and mutations in tumor suppressor genes. Conclusion: Among all the techniques used, RNAi, zinc finger nucleases and CRISPR hold a brighter future towards creating a Cancer Free World.
Collapse
Affiliation(s)
- Aman Imran
- Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Hafiza Yasara Qamar
- Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Qurban Ali
- Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan.,Institute of Molecular Biology and Biotechnology, University of Lahore, Lahore, Pakistan
| | - Hafsa Naeem
- Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Mariam Riaz
- Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Saima Amin
- Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Naila Kanwal
- Dept. of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan
| | - Fawad Ali
- Dept. of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan.,Southern Cross Plant Science, Southern Cross University, Lismore, Australia
| | | | - Idrees Ahmad Nasir
- Center of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| |
Collapse
|
15
|
Fu DJ, Miller AD, Southard TL, Flesken-Nikitin A, Ellenson LH, Nikitin AY. Stem Cell Pathology. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2017; 13:71-92. [PMID: 29059010 DOI: 10.1146/annurev-pathol-020117-043935] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Rapid advances in stem cell biology and regenerative medicine have opened new opportunities for better understanding disease pathogenesis and the development of new diagnostic, prognostic, and treatment approaches. Many stem cell niches are well defined anatomically, thereby allowing their routine pathological evaluation during disease initiation and progression. Evaluation of the consequences of genetic manipulations in stem cells and investigation of the roles of stem cells in regenerative medicine and pathogenesis of various diseases such as cancer require significant expertise in pathology for accurate interpretation of novel findings. Therefore, there is an urgent need for developing stem cell pathology as a discipline to facilitate stem cell research and regenerative medicine. This review provides examples of anatomically defined niches suitable for evaluation by diagnostic pathologists, describes neoplastic lesions associated with them, and discusses further directions of stem cell pathology.
Collapse
Affiliation(s)
- Dah-Jiun Fu
- Department of Biomedical Sciences and Cornell Stem Cell Program, Cornell University, Ithaca, New York 14853, USA;
| | - Andrew D Miller
- Department of Biomedical Sciences and Cornell Stem Cell Program, Cornell University, Ithaca, New York 14853, USA;
| | - Teresa L Southard
- Department of Biomedical Sciences and Cornell Stem Cell Program, Cornell University, Ithaca, New York 14853, USA;
| | - Andrea Flesken-Nikitin
- Department of Biomedical Sciences and Cornell Stem Cell Program, Cornell University, Ithaca, New York 14853, USA;
| | - Lora H Ellenson
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Alexander Yu Nikitin
- Department of Biomedical Sciences and Cornell Stem Cell Program, Cornell University, Ithaca, New York 14853, USA;
| |
Collapse
|
16
|
Skin-derived precursors from human subjects with Type 2 diabetes yield dysfunctional vascular smooth muscle cells. Clin Sci (Lond) 2017; 131:1801-1814. [PMID: 28424290 DOI: 10.1042/cs20170239] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Revised: 04/16/2017] [Accepted: 04/19/2017] [Indexed: 01/04/2023]
Abstract
Objective: Few methods enable molecular and cellular studies of vascular aging or Type 2 diabetes (T2D). Here, we report a new approach to studying human vascular smooth muscle cell (VSMC) pathophysiology by examining VSMCs differentiated from progenitors found in skin. Approach and results: Skin-derived precursors (SKPs) were cultured from biopsies (N=164, ∼1 cm2) taken from the edges of surgical incisions of older adults (N=158; males 72%; mean age 62.7 ± 13 years) undergoing cardiothoracic surgery, and differentiated into VSMCs at high efficiency (>80% yield). The number of SKPs isolated from subjects with T2D was ∼50% lower than those without T2D (cells/g: 0.18 ± 0.03, N=58 versus 0.40 ± 0.05, N=100, P<0.05). Importantly, SKP-derived VSMCs from subjects with T2D had higher Fluo-5F-determined baseline cytosolic Ca2+ concentrations (AU: 1,968 ± 160, N=7 versus 1,386 ± 170, N=13, P<0.05), and a trend toward greater Ca2+ cycling responses to norepinephrine (NE) (AUC: 177,207 ± 24,669, N=7 versus 101,537 ± 15,881, N=20, P<0.08) despite a reduced frequency of Ca2+ cycling (events s-1 cell-1: 0.011 ± 0.004, N=8 versus 0.021 ± 0.003, N=19, P<0.05) than those without T2D. SKP-derived VSMCs from subjects with T2D also manifest enhanced sensitivity to phenylephrine (PE) in an impedance-based assay (EC50 nM: 72.3 ± 63.6, N=5 versus 3,684 ± 3,122, N=9, P<0.05), and impaired wound closure in vitro (% closure: 21.9 ± 3.6, N=4 versus 67.0 ± 10.3, N=4, P<0.05). Compared with aortic- and saphenous vein-derived primary VSMCs, SKP-derived VSMCs are functionally distinct, but mirror defects of T2D also exhibited by primary VSMCs. CONCLUSION Skin biopsies from older adults yield sufficient SKPs to differentiate VSMCs, which reveal abnormal phenotypes of T2D that survive differentiation and persist even after long-term normoglycemic culture.
Collapse
|
17
|
Rumi MAK, Singh P, Roby KF, Zhao X, Iqbal K, Ratri A, Lei T, Cui W, Borosha S, Dhakal P, Kubota K, Chakraborty D, Vivian JL, Wolfe MW, Soares MJ. Defining the Role of Estrogen Receptor β in the Regulation of Female Fertility. Endocrinology 2017; 158:2330-2343. [PMID: 28520870 PMCID: PMC5505218 DOI: 10.1210/en.2016-1916] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 05/11/2017] [Indexed: 01/23/2023]
Abstract
Estrogens are essential hormones for the regulation of fertility. Cellular responses to estrogens are mediated by estrogen receptor α (ESR1) and estrogen receptor β (ESR2). In mouse and rat models, disruption of Esr1 causes infertility in both males and females. However, the role of ESR2 in reproductive function remains undecided because of a wide variation in phenotypic observations among Esr2-mutant mouse strains. Regulatory pathways independent of ESR2 binding to its cognate DNA response element have also been implicated in ESR2 signaling. To clarify the regulatory roles of ESR2, we generated two mutant rat models: one with a null mutation (exon 3 deletion, Esr2ΔE3) and the other with an inframe deletion selectively disrupting the DNA binding domain (exon 4 deletion, Esr2ΔE4). In both models, we observed that ESR2-mutant males were fertile. ESR2-mutant females exhibited regular estrous cycles and could be inseminated by wild-type (WT) males but did not become pregnant or pseudopregnant. Esr2-mutant ovaries were small and differed from WT ovaries by their absence of corpora lutea, despite the presence of follicles at various stages of development. Esr2ΔE3- and Esr2ΔE4-mutant females exhibited attenuated preovulatory gonadotropin surges and did not ovulate in response to a gonadotropin regimen effective in WT rats. Similarities of reproductive deficits in Esr2ΔE3 and Esr2ΔE4 mutants suggest that DNA binding-dependent transcriptional function of ESR2 is critical for preovulatory follicle maturation and ovulation. Overall, the findings indicate that neuroendocrine and ovarian deficits are linked to infertility observed in Esr2-mutant rats.
Collapse
Affiliation(s)
- M. A. Karim Rumi
- Institute for Reproductive Health and Regenerative Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160
| | - Prabhakar Singh
- Institute for Reproductive Health and Regenerative Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160
| | - Katherine F. Roby
- Institute for Reproductive Health and Regenerative Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, Kansas 66160
| | - Xiao Zhao
- Institute for Reproductive Health and Regenerative Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160
| | - Khursheed Iqbal
- Institute for Reproductive Health and Regenerative Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160
| | - Anamika Ratri
- Institute for Reproductive Health and Regenerative Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160
| | - Tianhua Lei
- Institute for Reproductive Health and Regenerative Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160
| | - Wei Cui
- Institute for Reproductive Health and Regenerative Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, Kansas 66160
| | - Shaon Borosha
- Institute for Reproductive Health and Regenerative Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, Kansas 66160
| | - Pramod Dhakal
- Institute for Reproductive Health and Regenerative Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160
| | - Kaiyu Kubota
- Institute for Reproductive Health and Regenerative Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160
| | - Damayanti Chakraborty
- Institute for Reproductive Health and Regenerative Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160
| | - Jay L. Vivian
- Institute for Reproductive Health and Regenerative Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160
| | - Michael W. Wolfe
- Institute for Reproductive Health and Regenerative Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, Kansas 66160
| | - Michael J. Soares
- Institute for Reproductive Health and Regenerative Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160
- Department of Pediatrics, University of Kansas Medical Center, Kansas City, Kansas 66160
| |
Collapse
|
18
|
Abstract
How can we treat cancer more effectively? Traditionally, tumours from the same anatomical site are treated as one tumour entity. This concept has been challenged by recent breakthroughs in cancer genomics and translational research that have enabled molecular tumour profiling. The identification and validation of cancer drivers that are shared between different tumour types, spurred the new paradigm to target driver pathways across anatomical sites by off-label drug use, or within so-called basket or umbrella trials which are designed to test whether molecular alterations in one tumour entity can be extrapolated to all others. However, recent clinical and preclinical studies suggest that there are tissue- and cell type-specific differences in tumorigenesis and the organization of oncogenic signalling pathways. In this Opinion article, we focus on the molecular, cellular, systemic and environmental determinants of organ-specific tumorigenesis and the mechanisms of context-specific oncogenic signalling outputs. Investigation, recognition and in-depth biological understanding of these differences will be vital for the design of next-generation clinical trials and the implementation of molecularly guided cancer therapies in the future.
Collapse
Affiliation(s)
- Günter Schneider
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Ismaningerstr. 22, 81675 München, Germany
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Marc Schmidt-Supprian
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
- Department of Medicine III, Klinikum rechts der Isar, Technische Universität München, Ismaningerstr. 22, 81675 München, Germany
| | - Roland Rad
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Ismaningerstr. 22, 81675 München, Germany
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Dieter Saur
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Ismaningerstr. 22, 81675 München, Germany
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| |
Collapse
|
19
|
Fremont R, Tewari A, Angueyra C, Khodakhah K. A role for cerebellum in the hereditary dystonia DYT1. eLife 2017; 6. [PMID: 28198698 PMCID: PMC5340526 DOI: 10.7554/elife.22775] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 02/14/2017] [Indexed: 02/06/2023] Open
Abstract
DYT1 is a debilitating movement disorder caused by loss-of-function mutations in torsinA. How these mutations cause dystonia remains unknown. Mouse models which have embryonically targeted torsinA have failed to recapitulate the dystonia seen in patients, possibly due to differential developmental compensation between rodents and humans. To address this issue, torsinA was acutely knocked down in select brain regions of adult mice using shRNAs. TorsinA knockdown in the cerebellum, but not in the basal ganglia, was sufficient to induce dystonia. In agreement with a potential developmental compensation for loss of torsinA in rodents, torsinA knockdown in the immature cerebellum failed to produce dystonia. Abnormal motor symptoms in knockdown animals were associated with irregular cerebellar output caused by changes in the intrinsic activity of both Purkinje cells and neurons of the deep cerebellar nuclei. These data identify the cerebellum as the main site of dysfunction in DYT1, and offer new therapeutic targets. DOI:http://dx.doi.org/10.7554/eLife.22775.001 Dystonia is the third most common type of movement disorder after Parkinson’s disease and tremor. Patients with dystonia experience prolonged involuntary contractions of their muscles, often causing uncontrollable postures or repetitive movements. Almost thirty years ago, genetic studies revealed that a mutation in the gene that encodes a protein called torsinA causes the most common type of dystonia, called DYT1. Exactly how mutations that affect the torsinA protein give rise to DYT1 remains unclear, and there are still no effective treatments for the disorder. Part of the problem is that we do not fully understand how torsinA works, or which of its many proposed functions is relevant to dystonia. Moreover, attempts to study DYT1 using genetically modified mice have proved largely unsuccessful. This is because mice that simply express the same genetic mutations that cause dystonia in humans do not show the overt symptoms of dystonia. Fremont, Tewari et al. have now generated a mouse ‘model’ that does show symptoms of dystonia, and used these model mice to investigate the role of torsinA in the disorder. Acutely reducing the amount of torsinA protein in a region of the brain called the cerebellum induced the symptoms of dystonia in the mice. Conversely, reducing the amount of torsinA in a different brain area known as the basal ganglia had no such effect, even though both the cerebellum and the basal ganglia contribute to movement. Furthermore, neither manipulation had any effect in juvenile mice, which suggests that, in contrast to humans, young mice can compensate for the loss of torsinA. Fremont, Tewari et al. also found that the loss of torsinA causes the cerebellum to generate incorrect output signals, which in turn trigger the abnormal movements seen in dystonia. In the future, further studies of the model mice could identify the exact changes that occur in neurons following the loss of torsinA from the cerebellum. Understanding these changes could potentially pave the way for developing effective treatments for DYT1 and other dystonias. DOI:http://dx.doi.org/10.7554/eLife.22775.002
Collapse
Affiliation(s)
- Rachel Fremont
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, New York, United States
| | - Ambika Tewari
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, New York, United States
| | - Chantal Angueyra
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, New York, United States
| | - Kamran Khodakhah
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, New York, United States
| |
Collapse
|
20
|
Application of CRISPR-mediated genome engineering in cancer research. Cancer Lett 2017; 387:10-17. [DOI: 10.1016/j.canlet.2016.03.029] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Revised: 03/12/2016] [Accepted: 03/14/2016] [Indexed: 12/21/2022]
|
21
|
Liu J, Zhou Y, Qi X, Chen J, Chen W, Qiu G, Wu Z, Wu N. CRISPR/Cas9 in zebrafish: an efficient combination for human genetic diseases modeling. Hum Genet 2016; 136:1-12. [PMID: 27807677 PMCID: PMC5214880 DOI: 10.1007/s00439-016-1739-6] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 10/17/2016] [Indexed: 12/26/2022]
Abstract
The next-generation sequencing identifies a growing number of candidate genes associated with human genetic diseases, which inevitably requires efficient methods to validate the causal links between genotype and phenotype. Recently, zebrafish, with sufficiently high-throughput capabilities, has become a favored option to study human pathogenesis. In addition, CRISPR/Cas9-based approaches have radically reduced the efforts to introduce targeted genome engineering in various organisms. Here, we systemically review the basic considerations in the design of gene editing in zebrafish with CRISPR/Cas9, and explore the potential of the combination of these two to support efficient functional analysis of human genetic variants.
Collapse
Affiliation(s)
- Jiaqi Liu
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Beijing, 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Department of Breast Surgical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yangzhong Zhou
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopaedics, Chinese Academy of Medical Sciences, Beijing, China.,Tsinghua University Medical School, Beijing, China
| | - Xiaolong Qi
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jia Chen
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Beijing, 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopaedics, Chinese Academy of Medical Sciences, Beijing, China
| | - Weisheng Chen
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Beijing, 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopaedics, Chinese Academy of Medical Sciences, Beijing, China
| | - Guixing Qiu
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Beijing, 100730, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopaedics, Chinese Academy of Medical Sciences, Beijing, China
| | - Zhihong Wu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China. .,Medical Research Center of Orthopaedics, Chinese Academy of Medical Sciences, Beijing, China. .,Department of Central Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Beijing, 100730, China.
| | - Nan Wu
- Department of Orthopaedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, No. 1 Shuaifuyuan, Beijing, 100730, China. .,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China. .,Medical Research Center of Orthopaedics, Chinese Academy of Medical Sciences, Beijing, China.
| |
Collapse
|
22
|
Dow LE. Modeling Disease In Vivo With CRISPR/Cas9. Trends Mol Med 2016; 21:609-621. [PMID: 26432018 DOI: 10.1016/j.molmed.2015.07.006] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 07/26/2015] [Accepted: 07/31/2015] [Indexed: 01/11/2023]
Abstract
The recent advent of CRISPR/Cas9-mediated genome editing has created a wave of excitement across the scientific research community, carrying the promise of simple and effective genomic manipulation of nearly any cell type. CRISPR has quickly become the preferred tool for genetic manipulation, and shows incredible promise as a platform for studying gene function in vivo. I discuss the current application of CRISPR technology to create new in vivo disease models, with a particular focus on how these tools, derived from an adaptive bacterial immune system, are helping us to better model the complexity of human cancer.
Collapse
Affiliation(s)
- Lukas E Dow
- Department of Medicine, Hematology and Medical Oncology, Weill Cornell Medical College, New York, NY 10021, USA.
| |
Collapse
|
23
|
Tschaharganeh DF, Lowe SW, Garippa RJ, Livshits G. Using CRISPR/Cas to study gene function and model disease in vivo. FEBS J 2016; 283:3194-203. [PMID: 27149548 DOI: 10.1111/febs.13750] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 04/14/2016] [Accepted: 05/03/2016] [Indexed: 12/23/2022]
Abstract
The recent discovery of the CRISPR/Cas system and repurposing of this technology to edit a variety of different genomes have revolutionized an array of scientific fields, from genetics and translational research, to agriculture and bioproduction. In particular, the prospect of rapid and precise genome editing in laboratory animals by CRISPR/Cas has generated an immense interest in the scientific community. Here we review current in vivo applications of CRISPR/Cas and how this technology can improve our knowledge of gene function and our understanding of biological processes in animal models.
Collapse
Affiliation(s)
- Darjus F Tschaharganeh
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Scott W Lowe
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Howard Hughes Medical Institute, New York, NY, USA
| | - Ralph J Garippa
- RNAi Core Facility, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Geulah Livshits
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| |
Collapse
|
24
|
Abstract
Loss of the tumor suppressor gene PTEN is implicated in breast cancer progression and resistance to targeted therapies, and is thought to promote tumorigenesis by activating PI3K signaling. In a transgenic model of breast cancer, Pten suppression using a tetracycline-regulatable short hairpin (sh)RNA cooperates with human epidermal growth factor receptor 2 (HER2/neu), leading to aggressive and metastatic disease with elevated signaling through PI3K and, surprisingly, the mitogen-activated protein kinase (MAPK) pathway. Restoring Pten function is sufficient to down-regulate both PI3K and MAPK signaling and triggers dramatic tumor regression. Pharmacologic inhibition of MAPK signaling produces similar effects to Pten restoration, suggesting that the MAPK pathway contributes to the maintenance of advanced breast cancers harboring Pten loss.
Collapse
|
25
|
Kang Y, Zheng B, Shen B, Chen Y, Wang L, Wang J, Niu Y, Cui Y, Zhou J, Wang H, Guo X, Hu B, Zhou Q, Sha J, Ji W, Huang X. CRISPR/Cas9-mediatedDax1knockout in the monkey recapitulates human AHC-HH. Hum Mol Genet 2015; 24:7255-64. [DOI: 10.1093/hmg/ddv425] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Accepted: 10/05/2015] [Indexed: 12/11/2022] Open
|
26
|
Garcia-Bloj B, Moses C, Blancafort P. The CRISPR road: from bench to bedside on an RNA-guided path. ANNALS OF TRANSLATIONAL MEDICINE 2015; 3:174. [PMID: 26366391 DOI: 10.3978/j.issn.2305-5839.2015.07.20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 07/14/2015] [Indexed: 11/14/2022]
Affiliation(s)
- Benjamin Garcia-Bloj
- 1 Cancer Epigenetics Group, Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia ; 2 School of Medicine, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile ; 3 School of Anatomy, Physiology and Human Biology, Faculty of Life and Physical Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Colette Moses
- 1 Cancer Epigenetics Group, Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia ; 2 School of Medicine, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile ; 3 School of Anatomy, Physiology and Human Biology, Faculty of Life and Physical Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Pilar Blancafort
- 1 Cancer Epigenetics Group, Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia ; 2 School of Medicine, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile ; 3 School of Anatomy, Physiology and Human Biology, Faculty of Life and Physical Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
| |
Collapse
|
27
|
Abstract
The prokaryotic type II CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats-CRISPR-associated 9) system is rapidly revolutionizing the field of genetic engineering, allowing researchers to alter the genomes of a large range of organisms with relative ease. Experimental approaches based on this versatile technology have the potential to transform the field of cancer genetics. Here, we review current approaches for functional studies of cancer genes that are based on CRISPR-Cas, with emphasis on their applicability for the development of next-generation models of human cancer.
Collapse
Affiliation(s)
- Francisco J. Sánchez-Rivera
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142
| | - Tyler Jacks
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
- Corresponding author. Communication can be sent to
| |
Collapse
|
28
|
Mou H, Kennedy Z, Anderson DG, Yin H, Xue W. Precision cancer mouse models through genome editing with CRISPR-Cas9. Genome Med 2015; 7:53. [PMID: 26060510 PMCID: PMC4460969 DOI: 10.1186/s13073-015-0178-7] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The cancer genome is highly complex, with hundreds of point mutations, translocations, and chromosome gains and losses per tumor. To understand the effects of these alterations, precise models are needed. Traditional approaches to the construction of mouse models are time-consuming and laborious, requiring manipulation of embryonic stem cells and multiple steps. The recent development of the clustered regularly interspersed short palindromic repeats (CRISPR)-Cas9 system, a powerful genome-editing tool for efficient and precise genome engineering in cultured mammalian cells and animals, is transforming mouse-model generation. Here, we review how CRISPR-Cas9 has been used to create germline and somatic mouse models with point mutations, deletions and complex chromosomal rearrangements. We highlight the progress and challenges of such approaches, and how these models can be used to understand the evolution and progression of individual tumors and identify new strategies for cancer treatment. The generation of precision cancer mouse models through genome editing will provide a rapid avenue for functional cancer genomics and pave the way for precision cancer medicine.
Collapse
Affiliation(s)
- Haiwei Mou
- RNA Therapeutics Institute and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605 USA
| | - Zachary Kennedy
- RNA Therapeutics Institute and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605 USA
| | - Daniel G Anderson
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142 USA ; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142 USA ; Harvard-MIT Division of Health Sciences & Technology, Cambridge, MA 02139 USA ; Institute of Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02142 USA
| | - Hao Yin
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142 USA
| | - Wen Xue
- RNA Therapeutics Institute and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605 USA
| |
Collapse
|
29
|
Preclinical Murine Models for Lung Cancer: Clinical Trial Applications. BIOMED RESEARCH INTERNATIONAL 2015; 2015:621324. [PMID: 26064932 PMCID: PMC4433653 DOI: 10.1155/2015/621324] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 11/24/2014] [Indexed: 12/18/2022]
Abstract
Murine models for the study of lung cancer have historically been the backbone of preliminary preclinical data to support early human clinical trials. However, the availability of multiple experimental systems leads to debate concerning which model, if any, is best suited for a particular therapeutic strategy. It is imperative that these models accurately predict clinical benefit of therapy. This review provides an overview of the current murine models used to study lung cancer and the advantages and limitations of each model, as well as a retrospective evaluation of the uses of each model with respect to accuracy in predicting clinical benefit of therapy. A better understanding of murine models and their uses, as well as their limitations may aid future research concerning the development and implementation of new targeted therapies and chemotherapeutic agents for lung cancer.
Collapse
|
30
|
Albers J, Danzer C, Rechsteiner M, Lehmann H, Brandt LP, Hejhal T, Catalano A, Busenhart P, Gonçalves AF, Brandt S, Bode PK, Bode-Lesniewska B, Wild PJ, Frew IJ. A versatile modular vector system for rapid combinatorial mammalian genetics. J Clin Invest 2015; 125:1603-19. [PMID: 25751063 PMCID: PMC4396471 DOI: 10.1172/jci79743] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 01/20/2015] [Indexed: 01/29/2023] Open
Abstract
Here, we describe the multiple lentiviral expression (MuLE) system that allows multiple genetic alterations to be introduced simultaneously into mammalian cells. We created a toolbox of MuLE vectors that constitute a flexible, modular system for the rapid engineering of complex polycistronic lentiviruses, allowing combinatorial gene overexpression, gene knockdown, Cre-mediated gene deletion, or CRISPR/Cas9-mediated (where CRISPR indicates clustered regularly interspaced short palindromic repeats) gene mutation, together with expression of fluorescent or enzymatic reporters for cellular assays and animal imaging. Examples of tumor engineering were used to illustrate the speed and versatility of performing combinatorial genetics using the MuLE system. By transducing cultured primary mouse cells with single MuLE lentiviruses, we engineered tumors containing up to 5 different genetic alterations, identified genetic dependencies of molecularly defined tumors, conducted genetic interaction screens, and induced the simultaneous CRISPR/Cas9-mediated knockout of 3 tumor-suppressor genes. Intramuscular injection of MuLE viruses expressing oncogenic H-RasG12V together with combinations of knockdowns of the tumor suppressors cyclin-dependent kinase inhibitor 2A (Cdkn2a), transformation-related protein 53 (Trp53), and phosphatase and tensin homolog (Pten) allowed the generation of 3 murine sarcoma models, demonstrating that genetically defined autochthonous tumors can be rapidly generated and quantitatively monitored via direct injection of polycistronic MuLE lentiviruses into mouse tissues. Together, our results demonstrate that the MuLE system provides genetic power for the systematic investigation of the molecular mechanisms that underlie human diseases.
Collapse
|
31
|
Kasparek P, Krausova M, Haneckova R, Kriz V, Zbodakova O, Korinek V, Sedlacek R. Efficient gene targeting of the Rosa26 locus in mouse zygotes using TALE nucleases. FEBS Lett 2014; 588:3982-8. [PMID: 25241166 DOI: 10.1016/j.febslet.2014.09.014] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 08/27/2014] [Accepted: 09/03/2014] [Indexed: 01/06/2023]
Abstract
Gene targeting in mice mainly employs homologous recombination (HR) in embryonic stem (ES) cells. Although it is a standard way for production of genetically modified mice, the procedure is laborious and time-consuming. This study describes targeting of the mouse Rosa26 locus by transcription activator-like effector nucleases (TALENs). We employed TALEN-assisted HR in zygotes to introduce constructs encoding TurboRFP and TagBFP fluorescent proteins into the first intron of the Rosa26 gene, and in this way generated two transgenic mice. We also demonstrated that these Rosa26-specific TALENs exhibit high targeting efficiency superior to that of zinc-finger nucleases (ZFNs) specific for the same targeting sequence. Moreover, we devised a reporter assay to assess TALENs activity and specificity to improve the quality of TALEN-assisted targeting.
Collapse
Affiliation(s)
- Petr Kasparek
- Institute of Molecular Genetics of the AS CR, v.v.i., Videnska 1083, 142 20, Czech Republic
| | - Michaela Krausova
- Institute of Molecular Genetics of the AS CR, v.v.i., Videnska 1083, 142 20, Czech Republic
| | - Radka Haneckova
- Institute of Molecular Genetics of the AS CR, v.v.i., Videnska 1083, 142 20, Czech Republic
| | - Vitezslav Kriz
- Institute of Molecular Genetics of the AS CR, v.v.i., Videnska 1083, 142 20, Czech Republic
| | - Olga Zbodakova
- Institute of Molecular Genetics of the AS CR, v.v.i., Videnska 1083, 142 20, Czech Republic
| | - Vladimir Korinek
- Institute of Molecular Genetics of the AS CR, v.v.i., Videnska 1083, 142 20, Czech Republic.
| | - Radislav Sedlacek
- Institute of Molecular Genetics of the AS CR, v.v.i., Videnska 1083, 142 20, Czech Republic.
| |
Collapse
|
32
|
Abstract
Non-small-cell lung cancers (NSCLCs), the most common lung cancers, are known to have diverse pathological features. During the past decade, in-depth analyses of lung cancer genomes and signalling pathways have further defined NSCLCs as a group of distinct diseases with genetic and cellular heterogeneity. Consequently, an impressive list of potential therapeutic targets was unveiled, drastically altering the clinical evaluation and treatment of patients. Many targeted therapies have been developed with compelling clinical proofs of concept; however, treatment responses are typically short-lived. Further studies of the tumour microenvironment have uncovered new possible avenues to control this deadly disease, including immunotherapy.
Collapse
Affiliation(s)
- Zhao Chen
- 1] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA. [2]
| | - Christine M Fillmore
- 1] Stem Cell Program, Boston Children's Hospital, Boston, Massachusetts 02115, USA. [2] Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA. [3] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. [4]
| | - Peter S Hammerman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Carla F Kim
- 1] Stem Cell Program, Boston Children's Hospital, Boston, Massachusetts 02115, USA. [2] Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA. [3] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Kwok-Kin Wong
- 1] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA. [2] Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, USA. [3] Belfer Institute for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
| |
Collapse
|
33
|
Chen Z, Fillmore CM, Hammerman PS, Kim CF, Wong KK. Non-small-cell lung cancers: a heterogeneous set of diseases. Nat Rev Cancer 2014; 14:535-46. [PMID: 25056707 PMCID: PMC5712844 DOI: 10.1038/nrc3775] [Citation(s) in RCA: 1220] [Impact Index Per Article: 122.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Non-small-cell lung cancers (NSCLCs), the most common lung cancers, are known to have diverse pathological features. During the past decade, in-depth analyses of lung cancer genomes and signalling pathways have further defined NSCLCs as a group of distinct diseases with genetic and cellular heterogeneity. Consequently, an impressive list of potential therapeutic targets was unveiled, drastically altering the clinical evaluation and treatment of patients. Many targeted therapies have been developed with compelling clinical proofs of concept; however, treatment responses are typically short-lived. Further studies of the tumour microenvironment have uncovered new possible avenues to control this deadly disease, including immunotherapy.
Collapse
Affiliation(s)
- Zhao Chen
- 1] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA. [2]
| | - Christine M Fillmore
- 1] Stem Cell Program, Boston Children's Hospital, Boston, Massachusetts 02115, USA. [2] Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA. [3] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. [4]
| | - Peter S Hammerman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Carla F Kim
- 1] Stem Cell Program, Boston Children's Hospital, Boston, Massachusetts 02115, USA. [2] Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA. [3] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Kwok-Kin Wong
- 1] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA. [2] Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, USA. [3] Belfer Institute for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
| |
Collapse
|
34
|
Remy S, Tesson L, Menoret S, Usal C, De Cian A, Thepenier V, Thinard R, Baron D, Charpentier M, Renaud JB, Buelow R, Cost GJ, Giovannangeli C, Fraichard A, Concordet JP, Anegon I. Efficient gene targeting by homology-directed repair in rat zygotes using TALE nucleases. Genome Res 2014; 24:1371-83. [PMID: 24989021 PMCID: PMC4120090 DOI: 10.1101/gr.171538.113] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The generation of genetically modified animals is important for both research and commercial purposes. The rat is an important model organism that until recently lacked efficient genetic engineering tools. Sequence-specific nucleases, such as ZFNs, TALE nucleases, and CRISPR/Cas9 have allowed the creation of rat knockout models. Genetic engineering by homology-directed repair (HDR) is utilized to create animals expressing transgenes in a controlled way and to introduce precise genetic modifications. We applied TALE nucleases and donor DNA microinjection into zygotes to generate HDR-modified rats with large new sequences introduced into three different loci with high efficiency (0.62%–5.13% of microinjected zygotes). Two of these loci (Rosa26 and Hprt1) are known to allow robust and reproducible transgene expression and were targeted for integration of a GFP expression cassette driven by the CAG promoter. GFP-expressing embryos and four Rosa26 GFP rat lines analyzed showed strong and widespread GFP expression in most cells of all analyzed tissues. The third targeted locus was Ighm, where we performed successful exon exchange of rat exon 2 for the human one. At all three loci we observed HDR only when using linear and not circular donor DNA. Mild hypothermic (30°C) culture of zygotes after microinjection increased HDR efficiency for some loci. Our study demonstrates that TALE nuclease and donor DNA microinjection into rat zygotes results in efficient and reproducible targeted donor integration by HDR. This allowed creation of genetically modified rats in a work-, cost-, and time-effective manner.
Collapse
Affiliation(s)
- Séverine Remy
- INSERM UMR 1064-ITUN, CHU de Nantes, Nantes F44093, France; Platform Rat Transgenesis, Nantes F44093, France
| | - Laurent Tesson
- INSERM UMR 1064-ITUN, CHU de Nantes, Nantes F44093, France; Platform Rat Transgenesis, Nantes F44093, France
| | - Séverine Menoret
- INSERM UMR 1064-ITUN, CHU de Nantes, Nantes F44093, France; Platform Rat Transgenesis, Nantes F44093, France
| | - Claire Usal
- INSERM UMR 1064-ITUN, CHU de Nantes, Nantes F44093, France; Platform Rat Transgenesis, Nantes F44093, France
| | - Anne De Cian
- INSERM U565, CNRS UMR7196, Museum National d'Histoire Naturelle, F75005 Paris, France
| | - Virginie Thepenier
- INSERM UMR 1064-ITUN, CHU de Nantes, Nantes F44093, France; Platform Rat Transgenesis, Nantes F44093, France
| | - Reynald Thinard
- INSERM UMR 1064-ITUN, CHU de Nantes, Nantes F44093, France; Platform Rat Transgenesis, Nantes F44093, France
| | - Daniel Baron
- INSERM UMR 1064-ITUN, CHU de Nantes, Nantes F44093, France
| | - Marine Charpentier
- INSERM U565, CNRS UMR7196, Museum National d'Histoire Naturelle, F75005 Paris, France
| | - Jean-Baptiste Renaud
- INSERM U565, CNRS UMR7196, Museum National d'Histoire Naturelle, F75005 Paris, France
| | - Roland Buelow
- Open Monoclonal Technologies, Palo Alto, California 94303, USA
| | | | - Carine Giovannangeli
- INSERM U565, CNRS UMR7196, Museum National d'Histoire Naturelle, F75005 Paris, France
| | | | - Jean-Paul Concordet
- INSERM U565, CNRS UMR7196, Museum National d'Histoire Naturelle, F75005 Paris, France
| | - Ignacio Anegon
- INSERM UMR 1064-ITUN, CHU de Nantes, Nantes F44093, France; Platform Rat Transgenesis, Nantes F44093, France
| |
Collapse
|
35
|
Rumi MAK, Dhakal P, Kubota K, Chakraborty D, Lei T, Larson MA, Wolfe MW, Roby KF, Vivian JL, Soares MJ. Generation of Esr1-knockout rats using zinc finger nuclease-mediated genome editing. Endocrinology 2014; 155:1991-9. [PMID: 24506075 PMCID: PMC3990838 DOI: 10.1210/en.2013-2150] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Estrogens play pivotal roles in development and function of many organ systems, including the reproductive system. We have generated estrogen receptor 1 (Esr1)-knockout rats using zinc finger nuclease (ZFN) genome targeting. mRNAs encoding ZFNs targeted to exon 3 of Esr1 were microinjected into single-cell rat embryos and transferred to pseudopregnant recipients. Of 17 live births, 5 had biallelic and 1 had monoallelic Esr1 mutations. A founder with monoallelic mutations was backcrossed to a wild-type rat. Offspring possessed only wild-type Esr1 alleles or wild-type alleles and Esr1 alleles containing either 482 bp (Δ482) or 223 bp (Δ223) deletions, indicating mosaicism in the founder. These heterozygous mutants were bred for colony expansion, generation of homozygous mutants, and phenotypic characterization. The Δ482 Esr1 allele yielded altered transcript processing, including the absence of exon 3, aberrant splicing of exon 2 and 4, and a frameshift that generated premature stop codons located immediately after the codon for Thr157. ESR1 protein was not detected in homozygous Δ482 mutant uteri. ESR1 disruption affected sexually dimorphic postnatal growth patterns and serum levels of gonadotropins and sex steroid hormones. Both male and female Esr1-null rats were infertile. Esr1-null males had small testes with distended and dysplastic seminiferous tubules, whereas Esr1-null females possessed large polycystic ovaries, thread-like uteri, and poorly developed mammary glands. In addition, uteri of Esr1-null rats did not effectively respond to 17β-estradiol treatment, further demonstrating that the Δ482 Esr1 mutation created a null allele. This rat model provides a new experimental tool for investigating the pathophysiology of estrogen action.
Collapse
MESH Headings
- Animals
- Codon, Nonsense
- Crosses, Genetic
- Deoxyribonucleases/chemistry
- Deoxyribonucleases/genetics
- Deoxyribonucleases/metabolism
- Estrogen Receptor alpha/chemistry
- Estrogen Receptor alpha/genetics
- Estrogen Receptor alpha/metabolism
- Exons
- Female
- Gene Knockout Techniques
- Infertility, Female/blood
- Infertility, Female/metabolism
- Infertility, Female/pathology
- Infertility, Male/blood
- Infertility, Male/metabolism
- Infertility, Male/pathology
- Male
- Microinjections
- Protein Engineering
- RNA, Messenger/metabolism
- Rats
- Rats, Mutant Strains
- Rats, Sprague-Dawley
- Rats, Transgenic
- Zinc Fingers
- Zygote/metabolism
Collapse
Affiliation(s)
- M A Karim Rumi
- Institute for Reproductive Health and Regenerative Medicine; Departments of Pathology and Laboratory Medicine (M.A.K.R., P.D., K.K., D.C., T.L., J.L.V., M.J.S.), Molecular and Integrative Physiology (M.A.L., M.W.W.), and Anatomy and Cell Biology (K.F.R.), University of Kansas Medical Center, Kansas City, Kansas 66160
| | | | | | | | | | | | | | | | | | | |
Collapse
|
36
|
Dow LE, Nasr Z, Saborowski M, Ebbesen SH, Manchado E, Tasdemir N, Lee T, Pelletier J, Lowe SW. Conditional reverse tet-transactivator mouse strains for the efficient induction of TRE-regulated transgenes in mice. PLoS One 2014; 9:e95236. [PMID: 24743474 PMCID: PMC3990578 DOI: 10.1371/journal.pone.0095236] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Accepted: 03/24/2014] [Indexed: 01/13/2023] Open
Abstract
Tetracycline or doxycycline (dox)-regulated control of genetic elements allows inducible, reversible and tissue specific regulation of gene expression in mice. This approach provides a means to investigate protein function in specific cell lineages and at defined periods of development and disease. Efficient and stable regulation of cDNAs or non-coding elements (e.g. shRNAs) downstream of the tetracycline-regulated element (TRE) requires the robust expression of a tet-transactivator protein, commonly the reverse tet-transactivator, rtTA. Most rtTA strains rely on tissue specific promoters that often do not provide sufficient rtTA levels for optimal inducible expression. Here we describe the generation of two mouse strains that enable Cre-dependent, robust expression of rtTA3, providing tissue-restricted and consistent induction of TRE-controlled transgenes. We show that these transgenic strains can be effectively combined with established mouse models of disease, including both Cre/LoxP-based approaches and non Cre-dependent disease models. The integration of these new tools with established mouse models promises the development of more flexible genetic systems to uncover the mechanisms of development and disease pathogenesis.
Collapse
Affiliation(s)
- Lukas E. Dow
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Zeina Nasr
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Michael Saborowski
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Saya H. Ebbesen
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Eusebio Manchado
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Nilgun Tasdemir
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Teresa Lee
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Jerry Pelletier
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- The Rosalind and Morris Goodman Cancer Research Center, McGill University, Montreal, Quebec, Canada
- * E-mail: (JP); (SWL)
| | - Scott W. Lowe
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- * E-mail: (JP); (SWL)
| |
Collapse
|
37
|
Abstract
RNA interference has become an indispensable tool for loss-of-function studies across eukaryotes. By enabling stable and reversible gene silencing, shRNAs provide a means to study long-term phenotypes, perform pool-based forward genetic screens and examine the consequences of temporary target inhibition in vivo. However, efficient implementation in vertebrate systems has been hindered by technical difficulties affecting potency and specificity. Focusing on these issues, we analyse current strategies to obtain maximal knockdown with minimal off-target effects.
Collapse
|
38
|
Abstract
Saborowski et al. developed a flexible embryonic stem cell (ESC)-based mouse model for pancreatic cancer. The ESCs harbor a latent Kras mutant, a homing cassette, and other genetic elements needed for rapid insertion and conditional expression of tetracycline-controlled transgenes, including fluorescence-coupled shRNAs. This model produces a disease that follows the progression of human pancreatic cancer, and they used it to dissect temporal roles for Pten and c-Myc in pancreatic cancer development and maintenance. Genetically engineered mouse models (GEMMs) have greatly expanded our knowledge of pancreatic ductal adenocarcinoma (PDAC) and serve as a critical tool to identify and evaluate new treatment strategies. However, the cost and time required to generate conventional pancreatic cancer GEMMs limits their use for investigating novel genetic interactions in tumor development and maintenance. To address this problem, we developed flexible embryonic stem cell (ESC)-based GEMMs that facilitate the rapid generation of genetically defined multiallelic chimeric mice without further strain intercrossing. The ESCs harbor a latent Kras mutant (a nearly ubiquitous feature of pancreatic cancer), a homing cassette, and other genetic elements needed for rapid insertion and conditional expression of tetracycline-controlled transgenes, including fluorescence-coupled shRNAs capable of efficiently silencing gene function by RNAi. This system produces a disease that recapitulates the progression of pancreatic cancer in human patients and enables the study and visualization of the impact of gene perturbation at any stage of pancreas cancer progression. We describe the use of this approach to dissect temporal roles for the tumor suppressor Pten and the oncogene c-Myc in pancreatic cancer development and maintenance.
Collapse
|
39
|
Malina A, Mills JR, Cencic R, Yan Y, Fraser J, Schippers LM, Paquet M, Dostie J, Pelletier J. Repurposing CRISPR/Cas9 for in situ functional assays. Genes Dev 2014; 27:2602-14. [PMID: 24298059 PMCID: PMC3861673 DOI: 10.1101/gad.227132.113] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Malina et al. readapted the CRISPR/Cas9 genome-editing system for targeted gene disruption positive selection assays. They generated “all-in-one” lentiviral and retroviral delivery vectors heterologously expressing both a codon-optimized Cas9 and its synthetic guide RNA (sgRNA) and linked Cas9 expression to GFP fluorescence for in vivo applications. These results establish Cas9 genome editing as a powerful and practical approach for positive in situ genetic screens. RNAi combined with next-generation sequencing has proven to be a powerful and cost-effective genetic screening platform in mammalian cells. Still, this technology has its limitations and is incompatible with in situ mutagenesis screens on a genome-wide scale. Using p53 as a proof-of-principle target, we readapted the CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 (CRISPR associated 9) genome-editing system to demonstrate the feasibility of this methodology for targeted gene disruption positive selection assays. By using novel “all-in-one” lentiviral and retroviral delivery vectors heterologously expressing both a codon-optimized Cas9 and its synthetic guide RNA (sgRNA), we show robust selection for the CRISPR-modified Trp53 locus following drug treatment. Furthermore, by linking Cas9 expression to GFP fluorescence, we use an “all-in-one” system to track disrupted Trp53 in chemoresistant lymphomas in the Eμ-myc mouse model. Deep sequencing analysis of the tumor-derived endogenous Cas9-modified Trp53 locus revealed a wide spectrum of mutants that were enriched with seemingly limited off-target effects. Taken together, these results establish Cas9 genome editing as a powerful and practical approach for positive in situ genetic screens.
Collapse
Affiliation(s)
- Abba Malina
- Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6 Canada,
| | | | | | | | | | | | | | | | | |
Collapse
|
40
|
Zhou J, Shen B, Zhang W, Wang J, Yang J, Chen L, Zhang N, Zhu K, Xu J, Hu B, Leng Q, Huang X. One-step generation of different immunodeficient mice with multiple gene modifications by CRISPR/Cas9 mediated genome engineering. Int J Biochem Cell Biol 2014; 46:49-55. [PMID: 24269190 DOI: 10.1016/j.biocel.2013.10.010] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Revised: 10/20/2013] [Accepted: 10/22/2013] [Indexed: 01/26/2023]
Abstract
Taking advantage of the multiplexable genome engineering feature of the CRISPR/Cas9 system, we sought to generate different kinds of immunodeficient mouse strains by embryo co-microinjection of Cas9 mRNA and multiple sgRNAs targeting mouse B2m, Il2rg, Prf1, Prkdc, and Rag1. We successfully achieved multiple gene modifications, fragment deletion, double knockout of genes localizing on the same chromosome, and got different kinds of immunodeficient mouse models with different heritable genetic modifications at once, providing a one-step strategy for generating different immunodeficient mice which represents significant time-, labor-, and money-saving advantages over traditional approaches. Meanwhile, we improved the technology by optimizing the concentration of Cas9 and sgRNAs and designing two adjacent sgRNAs targeting one exon for each gene, which greatly increased the targeting efficiency and bi-allelic mutations.
Collapse
Affiliation(s)
- Jiankui Zhou
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center of Nanjing University, National Resource Center for Mutant Mice, Nanjing 210061, China
| | - Bin Shen
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center of Nanjing University, National Resource Center for Mutant Mice, Nanjing 210061, China
| | - Wensheng Zhang
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Jianying Wang
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center of Nanjing University, National Resource Center for Mutant Mice, Nanjing 210061, China
| | - Jing Yang
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center of Nanjing University, National Resource Center for Mutant Mice, Nanjing 210061, China
| | - Li Chen
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center of Nanjing University, National Resource Center for Mutant Mice, Nanjing 210061, China
| | - Na Zhang
- Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 225 South Chongqing Road, Shanghai, China
| | - Kai Zhu
- Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 225 South Chongqing Road, Shanghai, China
| | - Juan Xu
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center of Nanjing University, National Resource Center for Mutant Mice, Nanjing 210061, China
| | - Bian Hu
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center of Nanjing University, National Resource Center for Mutant Mice, Nanjing 210061, China
| | - Qibin Leng
- Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 225 South Chongqing Road, Shanghai, China.
| | - Xingxu Huang
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center of Nanjing University, National Resource Center for Mutant Mice, Nanjing 210061, China.
| |
Collapse
|
41
|
Sun N, Bao Z, Xiong X, Zhao H. SunnyTALEN: A second-generation TALEN system for human genome editing. Biotechnol Bioeng 2013; 111:683-91. [DOI: 10.1002/bit.25154] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Revised: 10/17/2013] [Accepted: 11/14/2013] [Indexed: 12/18/2022]
Affiliation(s)
- Ning Sun
- Department of Biochemistry; University of Illinois at Urbana-Champaign; 600 South Mathews Avenue Urbana Illinois 61801
| | - Zehua Bao
- Department of Biochemistry; University of Illinois at Urbana-Champaign; 600 South Mathews Avenue Urbana Illinois 61801
| | - Xiong Xiong
- Department of Chemical and Biomolecular Engineering; University of Illinois at Urbana-Champaign; 600 South Mathews Avenue Urbana Illinois 61801
| | - Huimin Zhao
- Department of Biochemistry; University of Illinois at Urbana-Champaign; 600 South Mathews Avenue Urbana Illinois 61801
- Department of Chemical and Biomolecular Engineering; University of Illinois at Urbana-Champaign; 600 South Mathews Avenue Urbana Illinois 61801
- Department of Bioengineering, Department of Chemistry; Center for Biophysics and Computational Biology and Institute for Genomic Biology; University of Illinois at Urbana-Champaign; 600 South Mathews Avenue Urbana Illinois 61801
| |
Collapse
|
42
|
Shen B, Zhang X, Du Y, Wang J, Gong J, Zhang X, Tate PH, Li H, Huang X, Zhang W. Efficient knockin mouse generation by ssDNA oligonucleotides and zinc-finger nuclease assisted homologous recombination in zygotes. PLoS One 2013; 8:e77696. [PMID: 24167580 PMCID: PMC3805579 DOI: 10.1371/journal.pone.0077696] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 09/03/2013] [Indexed: 11/19/2022] Open
Abstract
The generation of specific mutant animal models is critical for functional analysis of human genes. The conventional gene targeting approach in embryonic stem cells (ESCs) by homologous recombination is however laborious, slow, expensive, and limited to species with functional ESCs. It is therefore a long-sought goal to develop an efficient and simple alternative gene targeting strategy. Here we demonstrate that, by combining an efficient ZFN pair and ssODN, a restriction site and a loxP site were successfully introduced into a specific genomic locus. A targeting efficiency up to 22.22% was achieved by coinciding the insertion site and the ZFN cleavage site isogenic and keeping the length of the homology arms equal and isogenic to the endogenous target locus. Furthermore, we determine that ZFN and ssODN-assisted HR is ssODN homology arm length dependent. We further show that mutant alleles generated by ZFN and ssODN-assisted HR can be transmitted through the germline successfully. This study establishes an efficient gene targeting strategy by ZFN and ssODN-assisted HR in mouse zygotes, and provides a potential avenue for genome engineering in animal species without functional ES cell lines.
Collapse
Affiliation(s)
- Bin Shen
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center of Nanjing University, National Resource Center for Mutant Mice, Nanjing, China
| | - Xin Zhang
- College of Life Sciences, Wuhan University, Wuhan, China
| | - Yinan Du
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center of Nanjing University, National Resource Center for Mutant Mice, Nanjing, China
| | - Jianying Wang
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center of Nanjing University, National Resource Center for Mutant Mice, Nanjing, China
| | - Jun Gong
- College of Life Sciences, Wuhan University, Wuhan, China
| | - Xiaodong Zhang
- College of Life Sciences, Wuhan University, Wuhan, China
| | - Peri H. Tate
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Hongliang Li
- College of Life Sciences, Wuhan University, Wuhan, China
| | - Xingxu Huang
- MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center of Nanjing University, National Resource Center for Mutant Mice, Nanjing, China
- * E-mail: (WZ); (XH)
| | - Wensheng Zhang
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- * E-mail: (WZ); (XH)
| |
Collapse
|
43
|
Abstract
PURPOSE OF REVIEW Sudden cardiac death (SCD) affects a significant percentage of young individuals. SCDs are due to genetic heart disorders, such as cardiomyopathies and channelopathies. In the present review, we will describe the recent advancements in understanding the genetic and molecular basis of hereditary cardiac diseases. RECENT FINDINGS Considerable progress has been made in identification of new genes associated with monogenic familial arrhythmogenic syndromes, giving the opportunity to delineate their molecular pathogenesis and identify potential targets for therapeutic intervention. Research discoveries and rapidly dropping costs of DNA sequencing technologies have resulted in availability of genetic testing panels. SUMMARY Advances in genetic sequencing technology are expected to significantly impact the clinical practice in the near future. Genetic testing represents a powerful tool for cause determination of arrhythmogenic cardiac diseases, efficient screening of family members, possible risk stratification and treatment choices. However, specific expertise is required for rational ordering and correct interpretation of the genetic screening results.
Collapse
|
44
|
Targeting versus tinkering: Explaining why the clinic is frustrated with molecular mapping of disease mechanisms. Med Hypotheses 2013; 81:553-6. [DOI: 10.1016/j.mehy.2013.06.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 06/22/2013] [Indexed: 12/17/2022]
|
45
|
Bertotti A, Trusolino L. From bench to bedside: does preclinical practice in translational oncology need some rebuilding? J Natl Cancer Inst 2013; 105:1426-7. [PMID: 24052623 DOI: 10.1093/jnci/djt253] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Andrea Bertotti
- Affiliations of authors: Department of Oncology, University of Torino Medical School (AB, LT); Laboratory of Molecular Pharmacology, Institute for Cancer Research and Treatment (AB, LT), Candiolo, Torino, Italy
| | | |
Collapse
|
46
|
Characterization of drug-induced transcriptional modules: towards drug repositioning and functional understanding. Mol Syst Biol 2013; 9:662. [PMID: 23632384 PMCID: PMC3658274 DOI: 10.1038/msb.2013.20] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Accepted: 03/28/2013] [Indexed: 12/14/2022] Open
Abstract
Drug-induced transcriptional modules (biclusters) were identified and annotated in three human cell lines and rat liver. These were used to assess conservation across systems and to infer and experimentally validate novel drug effects and gene functions. ![]()
Biclustering of drug-induced gene expression profiles resulted in modules of drugs and genes, which were enriched in both drug and gene annotations. Identifying drug-induced transcriptional modules separately in three human cell lines and rat liver allows assessment of their conservation across model systems. About 70% of modules are conserved across cell lines, a lower bound of 15% was estimated for their conservation across organisms, and between the in vitro and in vivo systems. Drug-induced transcriptional modules can predict novel gene functions. A conserved module associated with (chole)sterol metabolism revealed novel regulators of cellular cholesterol homeostasis; 10 of them were validated in functional imaging assays. Analysis of drugs clustered into modules can give new insights into their mechanisms of action and provide leads for drug repositioning. We predicted and experimentally validated novel cell cycle inhibitors and modulators of PPARγ, estrogen and adrenergic receptors, with potential for developing new therapies against diabetes and cancer.
In pharmacology, it is crucial to understand the complex biological responses that drugs elicit in the human organism and how well they can be inferred from model organisms. We therefore identified a large set of drug-induced transcriptional modules from genome-wide microarray data of drug-treated human cell lines and rat liver, and first characterized their conservation. Over 70% of these modules were common for multiple cell lines and 15% were conserved between the human in vitro and the rat in vivo system. We then illustrate the utility of conserved and cell-type-specific drug-induced modules by predicting and experimentally validating (i) gene functions, e.g., 10 novel regulators of cellular cholesterol homeostasis and (ii) new mechanisms of action for existing drugs, thereby providing a starting point for drug repositioning, e.g., novel cell cycle inhibitors and new modulators of α-adrenergic receptor, peroxisome proliferator-activated receptor and estrogen receptor. Taken together, the identified modules reveal the conservation of transcriptional responses towards drugs across cell types and organisms, and improve our understanding of both the molecular basis of drug action and human biology.
Collapse
|
47
|
Perdomini M, Hick A, Puccio H, Pook MA. Animal and cellular models of Friedreich ataxia. J Neurochem 2013; 126 Suppl 1:65-79. [PMID: 23859342 DOI: 10.1111/jnc.12219] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 02/01/2013] [Accepted: 02/04/2013] [Indexed: 11/30/2022]
Abstract
The development and use of animal and cellular models of Friedreich ataxia (FRDA) are essential requirements for the understanding of FRDA disease mechanisms and the investigation of potential FRDA therapeutic strategies. Although animal and cellular models of lower organisms have provided valuable information on certain aspects of FRDA disease and therapy, it is intuitive that the most useful models are those of mammals and mammalian cells, which are the closest in physiological terms to FRDA patients. To date, there have been considerable efforts put into the development of several different FRDA mouse models and relevant FRDA mouse and human cell line systems. We summarize the principal mammalian FRDA models, discuss the pros and cons of each system, and describe the ways in which such models have been used to address two of the fundamental, as yet unanswered, questions regarding FRDA. Namely, what is the exact pathophysiology of FRDA and what is the detailed genetic and epigenetic basis of FRDA?
Collapse
Affiliation(s)
- Morgane Perdomini
- Translational Medecine and Neurogenetics, IGBMC-Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
| | | | | | | |
Collapse
|
48
|
Li L, Blankenstein T. Generation of transgenic mice with megabase-sized human yeast artificial chromosomes by yeast spheroplast-embryonic stem cell fusion. Nat Protoc 2013; 8:1567-82. [PMID: 23868074 DOI: 10.1038/nprot.2013.093] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Introducing human genes into mice offers the opportunity to analyze their in vivo function or to obtain therapeutic molecules. For proper gene regulation, or in case of multigene families, megabase (Mb)-sized DNA fragments often have to be used. Yeast artificial chromosome (YAC)-mediated transgenesis is irreplaceable for this purpose, because alternative methods such as the use of bacterial artificial chromosomes (BACs) cannot introduce DNA fragments larger than 500 kb into the mouse germ line. However, YAC libraries often contain only partial gene loci. Time-consuming reconstruction of YACs, genetic instability and the difficulty in obtaining intact YAC DNA above a certain size impede the generation of humanized mice. Here we describe how to reconstruct YACs containing Mb-sized human DNA, such as the T cell receptor-α (TRA) gene locus, thus facilitating the introduction of large DNA fragments into the mouse germ line. Fusion of YAC-containing yeast and embryonic stem (ES) cells avoids the need for YAC DNA purification. These ES cells are then used to stably introduce the functional TRA gene locus into the mouse germ line. The protocol takes ∼1 year to complete, from reconstruction of the entire TRA gene locus from YACs containing partial but overlapping TRA regions to germline transmission of the YAC.
Collapse
Affiliation(s)
- Liangping Li
- Max Delbrück Center for Molecular Medicine, Berlin, Germany.
| | | |
Collapse
|
49
|
Kwon MC, Berns A. Mouse models for lung cancer. Mol Oncol 2013; 7:165-77. [PMID: 23481268 DOI: 10.1016/j.molonc.2013.02.010] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Accepted: 02/06/2013] [Indexed: 01/24/2023] Open
Abstract
Lung cancer is a devastating disease and a major therapeutic burden with poor survival rates. It is responsible for 30% of all cancer deaths. Lung cancer is strongly associated with smoking, although some subtypes are also seen in non-smokers. Tumors in the latter group are mostly adenocarcinomas with many carrying mutations in the epidermal growth factor receptor (EGFR). Survival statistics of lung cancer are grim because of its late detection and frequent local and distal metastases. Although DNA sequence information from tumors has revealed a number of frequently occurring mutations, affecting well-known tumor suppressor genes and proto-oncogenes, many of the driver mutations remain ill defined. This is likely due to the involvement of numerous rather infrequently occurring driver mutations that are difficult to distinguish from the very large number of passenger mutations detected in smoking-related lung cancers. Therefore, experimental model systems are indispensable to validate putative driver lesions and to gain insight into their mechanisms of action. Whereas a large fraction of these analyzes can be performed in cell cultures in vitro, in many cases the consequences of the mutations have to be assessed in the context of an intact organism, as this is the context in which the Mendelian selection process of the tumorigenic process took place and the advantages of particular mutations become apparent. Current mouse models for cancer are very suitable for this as they permit mimicking many of the salient features of human tumors. The capacity to swiftly re-engineer complex sets of lesions found in human tumors in mice enables us to assess the contribution of defined combinations of lesions to distinct tumor characteristics such as metastatic behavior and response to therapy. In this review we will describe mouse models of lung cancer and how they are used to better understand the disease and how they are exploited to develop better intervention strategies.
Collapse
Affiliation(s)
- Min-chul Kwon
- Division of Molecular Genetics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | | |
Collapse
|
50
|
Klarenbeek S, van Miltenburg MH, Jonkers J. Genetically engineered mouse models of PI3K signaling in breast cancer. Mol Oncol 2013; 7:146-64. [PMID: 23478237 DOI: 10.1016/j.molonc.2013.02.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 02/11/2013] [Indexed: 12/12/2022] Open
Abstract
Breast cancer is the most common type of cancer in women. A substantial fraction of breast cancers have acquired mutations that lead to activation of the phosphoinositide 3-kinase (PI3K) signaling pathway, which plays a central role in cellular processes that are essential in cancer, such as cell survival, growth, division and motility. Oncogenic mutations in the PI3K pathway generally involve either activating mutation of the gene encoding PI3K (PIK3CA) or AKT (AKT1), or loss or reduced expression of PTEN. Several kinases involved in PI3K signaling are being explored as a therapeutic targets for pharmacological inhibition. Despite the availability of a range of inhibitors, acquired resistance may limit the efficacy of single-agent therapy. In this review we discuss the role of PI3K pathway mutations in human breast cancer and relevant genetically engineered mouse models (GEMMs), with special attention to the role of PI3K signaling in oncogenesis, in therapeutic response, and in resistance to therapy. Several sophisticated GEMMs have revealed the cause-and-effect relationships between PI3K pathway mutations and mammary oncogenesis. These GEMMs enable us to study the biology of tumors induced by activated PI3K signaling, as well as preclinical response and resistance to PI3K pathway inhibitors.
Collapse
Affiliation(s)
- Sjoerd Klarenbeek
- Division of Molecular Pathology, Cancer Genomics Centre Netherlands and Cancer Systems Biology Center, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | | | | |
Collapse
|