1
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Greig LC, Woodworth MB, Poulopoulos A, Lim S, Macklis JD. BEAM: A combinatorial recombinase toolbox for binary gene expression and mosaic genetic analysis. Cell Rep 2024; 43:114650. [PMID: 39159043 DOI: 10.1016/j.celrep.2024.114650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 05/25/2024] [Accepted: 08/01/2024] [Indexed: 08/21/2024] Open
Abstract
We describe a binary expression aleatory mosaic (BEAM) system, which relies on DNA delivery by transfection or viral transduction along with nested recombinase activity to generate two genetically distinct, non-overlapping populations of cells for comparative analysis. Control cells labeled with red fluorescent protein (RFP) can be directly compared with experimental cells manipulated by genetic gain or loss of function and labeled with GFP. Importantly, BEAM incorporates recombinase-dependent signal amplification and delayed reporter expression to enable sharper delineation of control and experimental cells and to improve reliability relative to existing methods. We applied BEAM to a variety of known phenotypes to illustrate its advantages for identifying temporally or spatially aberrant phenotypes, for revealing changes in cell proliferation or death, and for controlling for procedural variability. In addition, we used BEAM to test the cortical protomap hypothesis at the individual radial unit level, revealing that area identity is cell autonomously specified in adjacent radial units.
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Affiliation(s)
- Luciano C Greig
- Department of Stem Cell and Regenerative Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA.
| | - Mollie B Woodworth
- Department of Stem Cell and Regenerative Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Alexandros Poulopoulos
- Department of Stem Cell and Regenerative Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Stephanie Lim
- Department of Stem Cell and Regenerative Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Jeffrey D Macklis
- Department of Stem Cell and Regenerative Biology and Center for Brain Science, Harvard University, Cambridge, MA, USA; Harvard Medical School, Boston, MA, USA.
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2
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Garcia-Gonzalez I, Rocha SF, Hamidi A, Garcia-Ortega L, Regano A, Sanchez-Muñoz M, Lytvyn M, Garcia-Cabero A, Roig-Soucase S, Schoofs H, Castro M, Sabata H, Potente M, Graupera M, Makinen T, Benedito R. iSuRe-HadCre is an essential tool for effective conditional genetics. Nucleic Acids Res 2024; 52:e56. [PMID: 38850155 PMCID: PMC11260470 DOI: 10.1093/nar/gkae472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 05/04/2024] [Accepted: 06/05/2024] [Indexed: 06/10/2024] Open
Abstract
Methods for modifying gene function at high spatiotemporal resolution in mice have revolutionized biomedical research, with Cre-loxP being the most widely used technology. However, the Cre-loxP technology has several drawbacks, including weak activity, leakiness, toxicity, and low reliability of existing Cre-reporters. This is mainly because different genes flanked by loxP sites (floxed) vary widely in their sensitivity to Cre-mediated recombination. Here, we report the generation, validation, and utility of iSuRe-HadCre, a new dual Cre-reporter and deleter mouse line that avoids these drawbacks. iSuRe-HadCre achieves this through a novel inducible dual-recombinase genetic cascade that ensures that cells expressing a fluorescent reporter had only transient Cre activity, that is nonetheless sufficient to effectively delete floxed genes. iSuRe-HadCre worked reliably in all cell types and for the 13 floxed genes tested. This new tool will enable the precise, efficient, and trustworthy analysis of gene function in entire mouse tissues or in single cells.
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Affiliation(s)
- Irene Garcia-Gonzalez
- Molecular Genetics of Angiogenesis Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Susana F Rocha
- Molecular Genetics of Angiogenesis Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Anahita Hamidi
- Molecular Genetics of Angiogenesis Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Lourdes Garcia-Ortega
- Molecular Genetics of Angiogenesis Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Alvaro Regano
- Molecular Genetics of Angiogenesis Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Maria S Sanchez-Muñoz
- Molecular Genetics of Angiogenesis Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Mariya Lytvyn
- Molecular Genetics of Angiogenesis Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Aroa Garcia-Cabero
- Molecular Genetics of Angiogenesis Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Sergi Roig-Soucase
- Molecular Genetics of Angiogenesis Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Hans Schoofs
- Uppsala University, Department of Immunology, Genetics and Pathology, Dag Hammarskjölds väg 20, 751 85 Uppsala, Sweden
| | - Marco Castro
- Angiogenesis & Metabolism Laboratory, Center of Vascular Biomedicine, Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Helena Sabata
- Endothelial Pathobiology and Microenviroment Group, Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Barcelona, Catalonia, Spain
| | - Michael Potente
- Angiogenesis & Metabolism Laboratory, Center of Vascular Biomedicine, Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Mariona Graupera
- Endothelial Pathobiology and Microenviroment Group, Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Barcelona, Catalonia, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 5, 28029 Madrid, Spain
- ICREA, Institució Catalana de Recerca i Estudis Avançats, Pg. Lluís Companys 23, Barcelona, Spain
| | - Taija Makinen
- Uppsala University, Department of Immunology, Genetics and Pathology, Dag Hammarskjölds väg 20, 751 85 Uppsala, Sweden
- Translational Cancer Medicine Program, Research Programs Unit, Biomedicum Helsinki, University of Helsinki, Haartmaninkatu 8, 00014 Helsinki, Finland
- Wihuri Research Institute, Haartmaninkatu 8, 00290 Helsinki, Finland
| | - Rui Benedito
- Molecular Genetics of Angiogenesis Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
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3
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Wu SHS, Kim S, Lee H, Lee JH, Park SY, Bakonyi R, Teriyapirom I, Hallay N, Pilat-Carotta S, Theussl HC, Kim J, Lee JH, Simons BD, Kim JK, Colozza G, Koo BK. Red2Flpe-SCON: a versatile, multicolor strategy for generating mosaic conditional knockout mice. Nat Commun 2024; 15:4963. [PMID: 38862535 PMCID: PMC11166929 DOI: 10.1038/s41467-024-49382-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 06/04/2024] [Indexed: 06/13/2024] Open
Abstract
Image-based lineage tracing enables tissue turnover kinetics and lineage potentials of different adult cell populations to be investigated. Previously, we reported a genetic mouse model system, Red2Onco, which ectopically expressed mutated oncogenes together with red fluorescent proteins (RFP). This system enabled the expansion kinetics and neighboring effects of oncogenic clones to be dissected. We now report Red2Flpe-SCON: a mosaic knockout system that uses multicolor reporters to label both mutant and wild-type cells. We develop the Red2Flpe mouse line for red clone-specific Flpe expression, as well as the FRT-based SCON (Short Conditional IntrON) method to facilitate tunable conditional mosaic knockouts in mice. We use the Red2Flpe-SCON method to study Sox2 mutant clonal analysis in the esophageal epithelium of adult mice which reveal that the stem cell gene, Sox2, is less essential for adult stem cell maintenance itself, but rather for stem cell proliferation and differentiation.
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Affiliation(s)
- Szu-Hsien Sam Wu
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Somi Kim
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Heetak Lee
- Center for Genome Engineering, Institute for Basic Science, Expo-ro 55, Yuseong-gu, Daejeon, 34126, Republic of Korea
| | - Ji-Hyun Lee
- Center for Genome Engineering, Institute for Basic Science, Expo-ro 55, Yuseong-gu, Daejeon, 34126, Republic of Korea
| | - So-Yeon Park
- Center for Genome Engineering, Institute for Basic Science, Expo-ro 55, Yuseong-gu, Daejeon, 34126, Republic of Korea
| | - Réka Bakonyi
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Isaree Teriyapirom
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Natalia Hallay
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Sandra Pilat-Carotta
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | | | - Jihoon Kim
- Center for Genome Engineering, Institute for Basic Science, Expo-ro 55, Yuseong-gu, Daejeon, 34126, Republic of Korea
- Department of Medical and Biological Sciences, The Catholic University of Korea, Bucheon, 14662, South Korea
| | - Joo-Hyeon Lee
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Benjamin D Simons
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- The Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
- Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, Wilberforce Road, Cambridge, CB3 0WA, UK
| | - Jong Kyoung Kim
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Gabriele Colozza
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria.
| | - Bon-Kyoung Koo
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea.
- Center for Genome Engineering, Institute for Basic Science, Expo-ro 55, Yuseong-gu, Daejeon, 34126, Republic of Korea.
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4
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Zhu X, Yang Y, Feng D, Wang O, Chen J, Wang J, Wang B, Liu Y, Edenfield BH, Haddock AN, Wang Y, Patel T, Bi Y, Ji B. Albumin promoter-driven FlpO expression induces efficient genetic recombination in mouse liver. Am J Physiol Gastrointest Liver Physiol 2024; 326:G495-G503. [PMID: 38469630 DOI: 10.1152/ajpgi.00263.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 02/14/2024] [Accepted: 02/15/2024] [Indexed: 03/13/2024]
Abstract
Tissue-specific gene manipulations are widely used in genetically engineered mouse models. A single recombinase system, such as the one using Alb-Cre, has been commonly used for liver-specific genetic manipulations. However, most diseases are complex, involving multiple genetic changes and various cell types. A dual recombinase system is required for conditionally modifying different genes sequentially in the same cell or inducing genetic changes in different cell types within the same organism. A FlpO cDNA was inserted between the last exon and 3'-UTR of the mouse albumin gene in a bacterial artificial chromosome (BAC-Alb-FlpO). The founders were crossed with various reporter mice to examine the efficiency of recombination. Liver cancer tumorigenesis was investigated by crossing the FlpO mice with FSF-KrasG12D mice and p53frt mice (KPF mice). BAC-Alb-FlpO mice exhibited highly efficient recombination capability in both hepatocytes and intrahepatic cholangiocytes. No recombination was observed in the duodenum and pancreatic cells. BAC-Alb-FlpO-mediated liver-specific expression of mutant KrasG12D and conditional deletion of p53 gene caused the development of liver cancer. Remarkably, liver cancer in these KPF mice manifested a distinctive mixed hepatocellular carcinoma and cholangiocarcinoma phenotype. A highly efficient and liver-specific BAC-Alb-FlpO mouse model was developed. In combination with other Cre lines, different genes can be manipulated sequentially in the same cell, or distinct genetic changes can be induced in different cell types of the same organism.NEW & NOTEWORTHY A liver-specific Alb-FlpO mouse line was generated. By coupling it with other existing CreERT or Cre lines, the dual recombinase approach can enable sequential gene modifications within the same cell or across various cell types in an organism for liver research through temporal and spatial gene manipulations.
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Affiliation(s)
- Xiaohui Zhu
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States
| | - Yan Yang
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States
| | - Dongfeng Feng
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States
| | - Oliver Wang
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States
| | - Jiaxiang Chen
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States
| | - Jiale Wang
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States
| | - Bin Wang
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States
| | - Yang Liu
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States
| | - Brandy H Edenfield
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States
| | - Ashley N Haddock
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States
| | - Ying Wang
- Departments of Cardiovascular Diseases and Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, United States
| | - Tushar Patel
- Department of Transplantation, Mayo Clinic, Jacksonville, Florida, United States
| | - Yan Bi
- Department of Gastroenterology and Hepatology, Mayo Clinic, Jacksonville, Florida, United States
| | - Baoan Ji
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States
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5
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Yamada M, Keller RR, Gutierrez RL, Cameron D, Suzuki H, Sanghrajka R, Vaynshteyn J, Gerwin J, Maura F, Hooper W, Shah M, Robine N, Demarest P, Bayin NS, Zapater LJ, Reed C, Hébert S, Masilionis I, Chaligne R, Socci ND, Taylor MD, Kleinman CL, Joyner AL, Raju GP, Kentsis A. Childhood cancer mutagenesis caused by transposase-derived PGBD5. SCIENCE ADVANCES 2024; 10:eadn4649. [PMID: 38517960 PMCID: PMC10959420 DOI: 10.1126/sciadv.adn4649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 02/16/2024] [Indexed: 03/24/2024]
Abstract
Genomic rearrangements are a hallmark of most childhood tumors, including medulloblastoma, one of the most common brain tumors in children, but their causes remain largely unknown. Here, we show that PiggyBac transposable element derived 5 (Pgbd5) promotes tumor development in multiple developmentally accurate mouse models of Sonic Hedgehog (SHH) medulloblastoma. Most Pgbd5-deficient mice do not develop tumors, while maintaining normal cerebellar development. Ectopic activation of SHH signaling is sufficient to enforce cerebellar granule cell progenitor-like cell states, which exhibit Pgbd5-dependent expression of distinct DNA repair and neurodevelopmental factors. Mouse medulloblastomas expressing Pgbd5 have increased numbers of somatic structural DNA rearrangements, some of which carry PGBD5-specific sequences at their breakpoints. Similar sequence breakpoints recurrently affect somatic DNA rearrangements of known tumor suppressors and oncogenes in medulloblastomas in 329 children. This identifies PGBD5 as a medulloblastoma mutator and provides a genetic mechanism for the generation of oncogenic DNA rearrangements in childhood cancer.
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Affiliation(s)
- Makiko Yamada
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA
| | - Ross R. Keller
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA
| | | | - Daniel Cameron
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA
| | - Hiromichi Suzuki
- Division of Brain Tumor Translational Research, National Cancer Center Research Institute, Tokyo, Japan
| | - Reeti Sanghrajka
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Jake Vaynshteyn
- Departments of Neurology and Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jeffrey Gerwin
- Departments of Neurology and Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Francesco Maura
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - William Hooper
- Computational Biology, New York Genome Center, New York, NY, USA
| | - Minita Shah
- Computational Biology, New York Genome Center, New York, NY, USA
| | - Nicolas Robine
- Computational Biology, New York Genome Center, New York, NY, USA
| | - Phillip Demarest
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA
| | - N. Sumru Bayin
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
- Wellcome Trust/Cancer Research UK Gurdon Institute, Cambridge University, Cambridge, UK
| | - Luz Jubierre Zapater
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA
| | - Casie Reed
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA
| | - Steven Hébert
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Ignas Masilionis
- Single-Cell Analytics Innovation Lab, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ronan Chaligne
- Single-Cell Analytics Innovation Lab, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nicholas D. Socci
- Bioinformatics Core, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael D. Taylor
- Department of Pediatrics—Hematology/Oncology and Neurosurgery, Baylor College of Medicine, Houston, TX, USA
- Hematology-Oncology Section, Texas Children’s Cancer Center, Houston, TX, USA
- The Arthur and Sonia Labatt Brain Tumour Research Centre and the Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Claudia L. Kleinman
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Alexandra L. Joyner
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
- Biochemistry, Cell and Molecular Biology Program and Neuroscience Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - G. Praveen Raju
- Departments of Neurology and Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alex Kentsis
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, USA
- Departments of Pediatrics, Pharmacology, and Physiology & Biophysics, Weill Medical College of Cornell University, New York, NY, USA
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6
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Deska-Gauthier D, Borowska-Fielding J, Jones C, Zhang H, MacKay CS, Michail R, Bennett LA, Bikoff JB, Zhang Y. Embryonic temporal-spatial delineation of excitatory spinal V3 interneuron diversity. Cell Rep 2024; 43:113635. [PMID: 38160393 PMCID: PMC10877927 DOI: 10.1016/j.celrep.2023.113635] [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: 05/09/2023] [Revised: 10/24/2023] [Accepted: 12/14/2023] [Indexed: 01/03/2024] Open
Abstract
Spinal neural circuits that execute movement are composed of cardinal classes of neurons that emerged from distinct progenitor lineages. Each cardinal class contains multiple neuronal subtypes characterized by distinct molecular, anatomical, and physiological characteristics. Through a focus on the excitatory V3 interneuron class, here we demonstrate that interneuron subtype diversity is delineated through a combination of neurogenesis timing and final laminar settling position. We have revealed that early-born and late-born embryonic V3 temporal classes further diversify into subclasses with spatially and molecularly discrete identities. While neurogenesis timing accounts for V3 morphological diversification, laminar settling position accounts for electrophysiological profiles distinguishing V3 subtypes within the same temporal classes. Furthermore, V3 interneuron subtypes display independent behavioral recruitment patterns demonstrating a functional modularity underlying V3 interneuron diversity. These studies provide a framework for how early embryonic temporal and spatial mechanisms combine to delineate spinal interneuron classes into molecularly, anatomically, and functionally relevant subtypes in adults.
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Affiliation(s)
- Dylan Deska-Gauthier
- Department of Medical Neuroscience, Faculty of Medicine, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Joanna Borowska-Fielding
- Department of Medical Neuroscience, Faculty of Medicine, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Chris Jones
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Han Zhang
- Department of Medical Neuroscience, Faculty of Medicine, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Colin S MacKay
- Department of Medical Neuroscience, Faculty of Medicine, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Ramez Michail
- Department of Medical Neuroscience, Faculty of Medicine, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Laura A Bennett
- Department of Medical Neuroscience, Faculty of Medicine, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Jay B Bikoff
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ying Zhang
- Department of Medical Neuroscience, Faculty of Medicine, Dalhousie University, Halifax, NS B3H 4R2, Canada.
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7
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LaFleur MW, Lemmen AM, Streeter ISL, Nguyen TH, Milling LE, Derosia NM, Hoffman ZM, Gillis JE, Tjokrosurjo Q, Markson SC, Huang AY, Anekal PV, Montero Llopis P, Haining WN, Doench JG, Sharpe AH. X-CHIME enables combinatorial, inducible, lineage-specific and sequential knockout of genes in the immune system. Nat Immunol 2024; 25:178-188. [PMID: 38012416 PMCID: PMC10881062 DOI: 10.1038/s41590-023-01689-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 10/20/2023] [Indexed: 11/29/2023]
Abstract
Annotation of immunologic gene function in vivo typically requires the generation of knockout mice, which is time consuming and low throughput. We previously developed CHimeric IMmune Editing (CHIME), a CRISPR-Cas9 bone marrow delivery system for constitutive, ubiquitous deletion of single genes. Here we describe X-CHIME, four new CHIME-based systems for modular and rapid interrogation of gene function combinatorially (C-CHIME), inducibly (I-CHIME), lineage-specifically (L-CHIME) or sequentially (S-CHIME). We use C-CHIME and S-CHIME to assess the consequences of combined deletion of Ptpn1 and Ptpn2, an embryonic lethal gene pair, in adult mice. We find that constitutive deletion of both PTPN1 and PTPN2 leads to bone marrow hypoplasia and lethality, while inducible deletion after immune development leads to enteritis and lethality. These findings demonstrate that X-CHIME can be used for rapid mechanistic evaluation of genes in distinct in vivo contexts and that PTPN1 and PTPN2 have some functional redundancy important for viability in adult mice.
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Affiliation(s)
- Martin W LaFleur
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Ashlyn M Lemmen
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Ivy S L Streeter
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Thao H Nguyen
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Lauren E Milling
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Nicole M Derosia
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Zachary M Hoffman
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Jacob E Gillis
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Qin Tjokrosurjo
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Samuel C Markson
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Amy Y Huang
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | | | - John G Doench
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Arlene H Sharpe
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
- Gene Lay Institute of Immunology and Inflammation, Brigham and Women's Hospital, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA.
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8
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Sanghrajka RM, Koche R, Medrano H, El Nagar S, Stephen DN, Lao Z, Bayin NS, Ge K, Joyner AL. KMT2D suppresses Sonic hedgehog-driven medulloblastoma progression and metastasis. iScience 2023; 26:107831. [PMID: 37822508 PMCID: PMC10562805 DOI: 10.1016/j.isci.2023.107831] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 03/29/2023] [Accepted: 09/01/2023] [Indexed: 10/13/2023] Open
Abstract
The major cause of treatment failure and mortality among medulloblastoma patients is metastasis intracranially or along the spinal cord. The molecular mechanisms driving tumor metastasis in Sonic hedgehog-driven medulloblastoma (SHH-MB) patients, however, remain largely unknown. In this study we define a tumor suppressive role of KMT2D (MLL2), a gene frequently mutated in the most metastatic β-subtype. Strikingly, genetic mouse models of SHH-MB demonstrate that heterozygous loss of Kmt2d in conjunction with activation of the SHH pathway causes highly penetrant disease with decreased survival, increased hindbrain invasion and spinal cord metastasis. Loss of Kmt2d attenuates neural differentiation and shifts the transcriptional/chromatin landscape of primary and metastatic tumors toward a decrease in differentiation genes and tumor suppressors and an increase in genes/pathways implicated in advanced stage cancer and metastasis (TGFβ, Notch, Atoh1, Sox2, and Myc). Thus, secondary heterozygous KMT2D mutations likely have prognostic value for identifying SHH-MB patients prone to develop metastasis.
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Affiliation(s)
- Reeti Mayur Sanghrajka
- Developmental Biology Program, Sloan Kettering Institute of Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Biochemistry, Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Richard Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hector Medrano
- Developmental Biology Program, Sloan Kettering Institute of Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Salsabiel El Nagar
- Developmental Biology Program, Sloan Kettering Institute of Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel N. Stephen
- Developmental Biology Program, Sloan Kettering Institute of Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zhimin Lao
- Developmental Biology Program, Sloan Kettering Institute of Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - N. Sumru Bayin
- Developmental Biology Program, Sloan Kettering Institute of Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kai Ge
- Adipocyte Biology and Gene Regulation Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Alexandra L. Joyner
- Developmental Biology Program, Sloan Kettering Institute of Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Biochemistry, Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
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9
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Freeburg NF, Peterson N, Ruiz DA, Gladstein AC, Feldser DM. Metastatic Competency and Tumor Spheroid Formation Are Independent Cell States Governed by RB in Lung Adenocarcinoma. CANCER RESEARCH COMMUNICATIONS 2023; 3:1992-2002. [PMID: 37728504 PMCID: PMC10545537 DOI: 10.1158/2767-9764.crc-23-0172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 08/08/2023] [Accepted: 09/06/2023] [Indexed: 09/21/2023]
Abstract
Inactivation of the retinoblastoma (RB) tumor suppressor in lung adenocarcinoma is associated with the rapid acquisition of metastatic ability and the loss of lung cell lineage commitment. We previously showed that restoration of RB in advanced lung adenocarcinomas in the mouse was correlated with a decreased frequency of lineage decommitted tumors and overt metastases. To identify a causal relationship for RB and its role in reprogramming lineage commitment and reducing metastatic competency in lung adenocarcinoma, we developed multiple tumor spheroid forming lines where RB restoration could be achieved after characterization of the degree of each spheroid's lineage commitment and metastatic ability. Surprisingly, we discovered that RB inactivation dramatically promoted tumor spheroid forming potential in tumors that arise in the KrasLSL-G12D/+; p53flox/flox lung adenocarcinoma model. However, RB reactivation had no effect on the maintenance of tumor spheroid lines once established. In addition, we show that RB-deficient tumor spheroid lines are not uniformly metastatically competent but are equally likely to be nonmetastatic. Interestingly, unlike tumor spheroid maintenance, RB restoration could functionally revert metastatic tumor spheroids to a nonmetastatic cell state. Thus, strategies to reinstate RB pathway activity in lung cancer may reverse metastatic ability and have therapeutic potential. Finally, the acquisition of tumor spheroid forming potential reflects underlying cell state plasticity, which is often predictive of, or even conflated with metastatic ability. Our data support that each is a discrete cell state restricted by RB and question the suitability of tumor spheroid models for their predictive potential of advanced metastatic tumor cell states. SIGNIFICANCE Members of the RB pathway are frequently mutated in lung adenocarcinoma. We show that RB regulates cell state plasticity, tumor spheroid formation, and metastatic competency. Our data indicate that these are independent states where spheroid formation is distinct from metastatic competency. Thus, we caution against conflating spheroid formation and other signs of cell state plasticity with advanced metastatic cell states. Nevertheless, our work supports clinical strategies to reactivate RB pathways.
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Affiliation(s)
- Nelson F. Freeburg
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, Pennsylvania
- Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Nia Peterson
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Dain A. Ruiz
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Amy C. Gladstein
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, Pennsylvania
- Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, Pennsylvania
| | - David M. Feldser
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, Pennsylvania
- Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, Pennsylvania
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, Pennsylvania
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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10
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Martelletti E, Ingham NJ, Steel KP. Reversal of an existing hearing loss by gene activation in Spns2 mutant mice. Proc Natl Acad Sci U S A 2023; 120:e2307355120. [PMID: 37552762 PMCID: PMC10450448 DOI: 10.1073/pnas.2307355120] [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: 05/02/2023] [Accepted: 07/06/2023] [Indexed: 08/10/2023] Open
Abstract
Hearing loss is highly heterogeneous, but one common form involves a failure to maintain the local ionic environment of the sensory hair cells reflected in a reduced endocochlear potential. We used a genetic approach to ask whether this type of pathology can be reversed, using the Spns2tm1a mouse mutant known to show this defect. By activating Spns2 gene transcription at different ages after the onset of hearing loss, we found that an existing auditory impairment can be reversed to give close to normal thresholds for an auditory brainstem response (ABR), at least at low to mid stimulus frequencies. Delaying the activation of Spns2 led to less effective recovery of ABR thresholds, suggesting that there is a critical period for intervention. Early activation of Spns2 not only led to improvement in auditory function but also to protection of sensory hair cells from secondary degeneration. The genetic approach we have used to establish that this type of hearing loss is in principle reversible could be extended to many other diseases using available mouse resources.
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Affiliation(s)
- Elisa Martelletti
- Wolfson Centre for Age-Related Diseases, King’s College London, Guy’s Campus, LondonSE1 1UL, United Kingdom
| | - Neil J. Ingham
- Wolfson Centre for Age-Related Diseases, King’s College London, Guy’s Campus, LondonSE1 1UL, United Kingdom
| | - Karen P. Steel
- Wolfson Centre for Age-Related Diseases, King’s College London, Guy’s Campus, LondonSE1 1UL, United Kingdom
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11
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Acosta J, Li Q, Freeburg NF, Murali N, Indeglia A, Grothusen GP, Cicchini M, Mai H, Gladstein AC, Adler KM, Doerig KR, Li J, Ruiz-Torres M, Manning KL, Stanger BZ, Busino L, Murphy M, Wan L, Feldser DM. p53 restoration in small cell lung cancer identifies a latent cyclophilin-dependent necrosis mechanism. Nat Commun 2023; 14:4403. [PMID: 37479684 PMCID: PMC10362054 DOI: 10.1038/s41467-023-40161-9] [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: 08/12/2022] [Accepted: 07/12/2023] [Indexed: 07/23/2023] Open
Abstract
The p53 tumor suppressor regulates multiple context-dependent tumor suppressive programs. Although p53 is mutated in ~90% of small cell lung cancer (SCLC) tumors, how p53 mediates tumor suppression in this context is unknown. Here, using a mouse model of SCLC in which endogenous p53 expression can be conditionally and temporally regulated, we show that SCLC tumors maintain a requirement for p53 inactivation. However, we identify tumor subtype heterogeneity between SCLC tumors such that p53 reactivation induces senescence in a subset of tumors, while in others, p53 induces necrosis. We pinpoint cyclophilins as critical determinants of a p53-induced transcriptional program that is specific to SCLC tumors and cell lines poised to undergo p53-mediated necrosis. Importantly, inhibition of cyclophilin isomerase activity, or genetic ablation of specific cyclophilin genes, suppresses p53-mediated necrosis by limiting p53 transcriptional output without impacting p53 chromatin binding. Our study demonstrates that intertumoral heterogeneity in SCLC influences the biological response to p53 restoration, describes a cyclophilin-dependent mechanism of p53-regulated cell death, and uncovers putative mechanisms for the treatment of this most-recalcitrant tumor type.
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Affiliation(s)
- Jonuelle Acosta
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Qinglan Li
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Nelson F Freeburg
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Nivitha Murali
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alexandra Indeglia
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Grant P Grothusen
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Michelle Cicchini
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hung Mai
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Amy C Gladstein
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Keren M Adler
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Katherine R Doerig
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jinyang Li
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Miguel Ruiz-Torres
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kimberly L Manning
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ben Z Stanger
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Luca Busino
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Maureen Murphy
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Program in Molecular and Cellular Oncogenesis, The Wistar Institute, Philadelphia, PA, USA
| | - Liling Wan
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - David M Feldser
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA, USA.
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12
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Li H, Weng W, Zhou B. Perfect duet: Dual recombinases improve genetic resolution. Cell Prolif 2023; 56:e13446. [PMID: 37060165 PMCID: PMC10212704 DOI: 10.1111/cpr.13446] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 02/25/2023] [Accepted: 03/01/2023] [Indexed: 04/16/2023] Open
Abstract
As a powerful genetic tool, site-specific recombinases (SSRs) have been widely used in genomic manipulation to elucidate cell fate plasticity in vivo, advancing research in stem cell and regeneration medicine. However, the low resolution of conventional single-recombinase-mediated lineage tracing strategies, which rely heavily on the specificity of one marker gene, has led to controversial conclusions in many scientific questions. Therefore, different SSRs systems are combined to improve the accuracy of lineage tracing. Here we review the recent advances in dual-recombinase-mediated genetic approaches, including the development of novel genetic recombination technologies and their applications in cell differentiation, proliferation, and genetic manipulation. In comparison with the single-recombinase system, we also discuss the advantages of dual-genetic strategies in solving scientific issues as well as their technical limitations.
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Affiliation(s)
- Hongxin Li
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesUniversity of Chinese Academy of SciencesShanghaiChina
| | - Wendong Weng
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesUniversity of Chinese Academy of SciencesShanghaiChina
| | - Bin Zhou
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of SciencesUniversity of Chinese Academy of SciencesShanghaiChina
- Key Laboratory of Systems Health Science of Zhejiang ProvinceSchool of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of SciencesHangzhouChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
- New Cornerstone Science LaboratoryShenzhenChina
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13
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Greig LC, Woodworth MB, Poulopoulos A, Lim S, Macklis JD. BEAM: a combinatorial recombinase toolbox for binary gene expression and mosaic analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.16.528875. [PMID: 36824714 PMCID: PMC9949094 DOI: 10.1101/2023.02.16.528875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
Genetic mosaic analysis, in which mutant cells reside intermingled with wild-type cells, is a powerful experimental approach, but has not been widely used in mice because existing genome-based strategies require complicated and protracted breeding schemes. We have developed an alternative approach termed BEAM (for Binary Expression Aleatory Mosaic) that relies on sparse recombinase activation to generate two genetically distinct, non-overlapping populations of cells for comparative analysis. Following delivery of DNA constructs by transfection or viral transduction, combinatorial recombinase activity generates two distinct populations of cells labeled with either green or red fluorescent protein. Any gene of interest can be mis-expressed or deleted in one population for comparison with intermingled control cells. We have extensively optimized and characterized this system both in vitro and in vivo , and demonstrate its power for investigating cell autonomy, identifying temporally or spatially aberrant phenotypes, revealing changes in cell proliferation or death, and controlling for procedural variability.
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14
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Brownfield DG, de Arce AD, Ghelfi E, Gillich A, Desai TJ, Krasnow MA. Alveolar cell fate selection and lifelong maintenance of AT2 cells by FGF signaling. Nat Commun 2022; 13:7137. [PMID: 36414616 PMCID: PMC9681748 DOI: 10.1038/s41467-022-34059-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 10/12/2022] [Indexed: 11/24/2022] Open
Abstract
The lung's gas exchange surface is comprised of alveolar AT1 and AT2 cells that are corrupted in several common and deadly diseases. They arise from a bipotent progenitor whose differentiation is thought to be dictated by differential mechanical forces. Here we show the critical determinant is FGF signaling. Fgfr2 is expressed in the developing progenitors in mouse then restricts to nascent AT2 cells and remains on throughout life. Its ligands are expressed in surrounding mesenchyme and can, in the absence of exogenous mechanical cues, induce progenitors to form alveolospheres with intermingled AT2 and AT1 cells. FGF signaling directly and cell autonomously specifies AT2 fate; progenitors lacking Fgfr2 in vitro and in vivo exclusively acquire AT1 fate. Fgfr2 loss in AT2 cells perinatally results in reprogramming to AT1 identity, whereas loss or inhibition later in life triggers AT2 apoptosis and compensatory regeneration. We propose that Fgfr2 signaling selects AT2 fate during development, induces a cell non-autonomous AT1 differentiation signal, then continuously maintains AT2 identity and survival throughout life.
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Affiliation(s)
- Douglas G Brownfield
- Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, 94305-5307, USA.
- Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Division of Pulmonary and Critical Care Medicine, Departments of Physiology and Biomedical Engineering and of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine and Science, Rochester, MN, 55905, USA.
| | - Alex Diaz de Arce
- Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, 94305-5307, USA
| | - Elisa Ghelfi
- Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Astrid Gillich
- Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, 94305-5307, USA
| | - Tushar J Desai
- Department of Internal Medicine and Stem Cell Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| | - Mark A Krasnow
- Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, 94305-5307, USA.
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15
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Joyner AL, Bayin NS. Cerebellum lineage allocation, morphogenesis and repair: impact of interplay amongst cells. Development 2022; 149:dev185587. [PMID: 36172987 PMCID: PMC9641654 DOI: 10.1242/dev.185587] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The cerebellum has a simple cytoarchitecture consisting of a folded cortex with three cell layers that surrounds a nuclear structure housing the output neurons. The excitatory neurons are generated from a unique progenitor zone, the rhombic lip, whereas the inhibitory neurons and astrocytes are generated from the ventricular zone. The growth phase of the cerebellum is driven by lineage-restricted progenitor populations derived from each zone. Research during the past decade has uncovered the importance of cell-to-cell communication between the lineages through largely unknown signaling mechanisms for regulating the scaling of cell numbers and cell plasticity during mouse development and following injury in the neonatal (P0-P14) cerebellum. This Review focuses on how the interplay between cell types is key to morphogenesis, production of robust neural circuits and replenishment of cells after injury, and ends with a discussion of the implications of the greater complexity of the human cerebellar progenitor zones for development and disease.
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Affiliation(s)
- Alexandra L. Joyner
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Biochemistry Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY 10065, USA
| | - N. Sumru Bayin
- Wellcome Trust/Cancer Research UK Gurdon Institute, Cambridge University, Cambridge CB2 1NQ, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3DY, UK
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16
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LKB1 drives stasis and C/EBP-mediated reprogramming to an alveolar type II fate in lung cancer. Nat Commun 2022; 13:1090. [PMID: 35228570 PMCID: PMC8885825 DOI: 10.1038/s41467-022-28619-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 02/01/2022] [Indexed: 02/07/2023] Open
Abstract
LKB1 is among the most frequently altered tumor suppressors in lung adenocarcinoma. Inactivation of Lkb1 accelerates the growth and progression of oncogenic KRAS-driven lung tumors in mouse models. However, the molecular mechanisms by which LKB1 constrains lung tumorigenesis and whether the cancer state that stems from Lkb1 deficiency can be reverted remains unknown. To identify the processes governed by LKB1 in vivo, we generated an allele which enables Lkb1 inactivation at tumor initiation and subsequent Lkb1 restoration in established tumors. Restoration of Lkb1 in oncogenic KRAS-driven lung tumors suppressed proliferation and led to tumor stasis. Lkb1 restoration activated targets of C/EBP transcription factors and drove neoplastic cells from a progenitor-like state to a less proliferative alveolar type II cell-like state. We show that C/EBP transcription factors govern a subset of genes that are induced by LKB1 and depend upon NKX2-1. We also demonstrate that a defining factor of the alveolar type II lineage, C/EBPα, constrains oncogenic KRAS-driven lung tumor growth in vivo. Thus, this key tumor suppressor regulates lineage-specific transcription factors, thereby constraining lung tumor development through enforced differentiation.
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17
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Emerging strategies for the genetic dissection of gene functions, cell types, and neural circuits in the mammalian brain. Mol Psychiatry 2022; 27:422-435. [PMID: 34561609 DOI: 10.1038/s41380-021-01292-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 08/17/2021] [Accepted: 09/08/2021] [Indexed: 02/08/2023]
Abstract
The mammalian brain is composed of a large number of highly diverse cell types with different molecular, anatomical, and functional features. Distinct cellular identities are generated during development under the regulation of intricate genetic programs and manifested through unique combinations of gene expression. Recent advancements in our understanding of the molecular and cellular mechanisms underlying the assembly, function, and pathology of the brain circuitry depend on the invention and application of genetic strategies that engage intrinsic gene regulatory mechanisms. Here we review the strategies for gene regulation on DNA, RNA, and protein levels and their applications in cell type targeting and neural circuit dissection. We highlight newly emerged strategies and emphasize the importance of combinatorial approaches. We also discuss the potential caveats and pitfalls in current methods and suggest future prospects to improve their comprehensiveness and versatility.
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18
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Dong K, Zhang C, Tian X, Coman D, Hyder F, Ma M, Somlo S. Renal plasticity revealed through reversal of polycystic kidney disease in mice. Nat Genet 2021; 53:1649-1663. [PMID: 34635846 PMCID: PMC9278957 DOI: 10.1038/s41588-021-00946-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 08/30/2021] [Indexed: 02/07/2023]
Abstract
Initiation of cyst formation in autosomal dominant polycystic kidney disease (ADPKD) occurs when kidney tubule cells are rendered null for either PKD1 or PKD2 by somatic 'second hit' mutations. Subsequent cyst progression remodels the organ through changes in tubule cell shape, proliferation and secretion. The kidney develops inflammation and fibrosis. We constructed a mouse model in which adult inactivation of either Pkd gene can be followed by reactivation of the gene at a later time. Using this model, we show that re-expression of Pkd genes in cystic kidneys results in rapid reversal of ADPKD. Cyst cell proliferation is reduced, autophagy is activated and cystic tubules with expanded lumina lined by squamoid cells revert to normal lumina lined by cuboidal cells. Increases in inflammation, extracellular matrix deposition and myofibroblast activation are reversed, and the kidneys become smaller. We conclude that phenotypic features of ADPKD are reversible and that the kidney has an unexpected capacity for plasticity controlled at least in part by ADPKD gene function.
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Affiliation(s)
- Ke Dong
- Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Chao Zhang
- Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Xin Tian
- Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Daniel Coman
- Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, Connecticut, USA
| | - Fahmeed Hyder
- Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, Connecticut, USA,Department of Biomedical Engineering, Yale School of Medicine, New Haven, Connecticut, USA
| | - Ming Ma
- Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Stefan Somlo
- Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, USA,Department of Genetics, Yale School of Medicine, New Haven, Connecticut, USA.,
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19
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Datta P, Ruffcorn A, Seo S. Limited time window for retinal gene therapy in a preclinical model of ciliopathy. Hum Mol Genet 2021; 29:2337-2352. [PMID: 32568387 DOI: 10.1093/hmg/ddaa124] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 05/04/2020] [Accepted: 06/15/2020] [Indexed: 12/15/2022] Open
Abstract
Retinal degeneration is a common clinical feature of ciliopathies, a group of genetic diseases linked to ciliary dysfunction, and gene therapy is an attractive treatment option to prevent vision loss. Although the efficacy of retinal gene therapy is well established by multiple proof-of-concept preclinical studies, its long-term effect, particularly when treatments are given at advanced disease stages, is controversial. Incomplete treatment and intrinsic variability of gene delivery methods may contribute to the variable outcomes. Here, we used a genetic rescue approach to 'optimally' treat retinal degeneration at various disease stages and examined the long-term efficacy of gene therapy in a mouse model of ciliopathy. We used a Bardet-Biedl syndrome type 17 (BBS17) mouse model, in which the gene-trap that suppresses Bbs17 (also known as Lztfl1) expression can be removed by tamoxifen administration, restoring normal gene expression systemically. Our data indicate that therapeutic effects of retinal gene therapy decrease gradually as treatments are given at later stages. These results suggest the presence of limited time window for successful gene therapy in certain retinal degenerations. Our study also implies that the long-term efficacy of retinal gene therapy may depend on not only the timing of treatment but also other factors such as the function of mutated genes and residual activities of mutant alleles.
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Affiliation(s)
- Poppy Datta
- Department of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA.,Institute for Vision Research, The University of Iowa, Iowa City, IA 52242, USA
| | - Avri Ruffcorn
- Department of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA.,Institute for Vision Research, The University of Iowa, Iowa City, IA 52242, USA
| | - Seongjin Seo
- Department of Ophthalmology and Visual Sciences, The University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA.,Institute for Vision Research, The University of Iowa, Iowa City, IA 52242, USA
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20
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Contreras X, Amberg N, Davaatseren A, Hansen AH, Sonntag J, Andersen L, Bernthaler T, Streicher C, Heger A, Johnson RL, Schwarz LA, Luo L, Rülicke T, Hippenmeyer S. A genome-wide library of MADM mice for single-cell genetic mosaic analysis. Cell Rep 2021; 35:109274. [PMID: 34161767 PMCID: PMC8317686 DOI: 10.1016/j.celrep.2021.109274] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 04/14/2021] [Accepted: 05/28/2021] [Indexed: 10/21/2022] Open
Abstract
Mosaic analysis with double markers (MADM) offers one approach to visualize and concomitantly manipulate genetically defined cells in mice with single-cell resolution. MADM applications include the analysis of lineage, single-cell morphology and physiology, genomic imprinting phenotypes, and dissection of cell-autonomous gene functions in vivo in health and disease. Yet, MADM can only be applied to <25% of all mouse genes on select chromosomes to date. To overcome this limitation, we generate transgenic mice with knocked-in MADM cassettes near the centromeres of all 19 autosomes and validate their use across organs. With this resource, >96% of the entire mouse genome can now be subjected to single-cell genetic mosaic analysis. Beyond a proof of principle, we apply our MADM library to systematically trace sister chromatid segregation in distinct mitotic cell lineages. We find striking chromosome-specific biases in segregation patterns, reflecting a putative mechanism for the asymmetric segregation of genetic determinants in somatic stem cell division.
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Affiliation(s)
- Ximena Contreras
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Nicole Amberg
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | | | - Andi H Hansen
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Johanna Sonntag
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Lill Andersen
- Institute of Laboratory Animal Science, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
| | - Tina Bernthaler
- Institute of Laboratory Animal Science, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
| | - Carmen Streicher
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Anna Heger
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - Randy L Johnson
- Department of Biochemistry and Molecular Biology, University of Texas, Houston, TX 77030, USA
| | - Lindsay A Schwarz
- HHMI and Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Liqun Luo
- HHMI and Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Thomas Rülicke
- Institute of Laboratory Animal Science, University of Veterinary Medicine Vienna, 1210 Vienna, Austria
| | - Simon Hippenmeyer
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria.
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21
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Abstract
PURPOSE OF REVIEW Conditional or inducible recombinase-based genetics is still the gold standard to analyse gene function, given its high specificity, temporal control, limited toxicity and the many available genetic tools. However, it is based on methods that have inherent limitations and shortcomings. The purpose of this review is to summarize and contrast the different available methods used to perform conditional gene function analysis to better inform the community about their particularities and the need to use better methods. RECENT FINDINGS As any other biomedical field, the vascular biology field has moved from using and analysing standard gene knockout (KO) mice, to use conditional genetics to delete a given gene only at a given time point, cell-type or organ of interest. This is the only way to accurately understand a gene function and avoid other confounding factors. Therefore, nowadays the majority of laboratories working with mice use CreERT2-tamoxifen-inducible genetics. However, this necessary transition from the relatively simple KO genetics to the more sophisticated conditional genetics brought a series of additional methodological issues that are often overlooked or unappreciated. Recent findings from several laboratories have shown how important is to know what to expect from and control for in conditional genetics. Without this a priori knowledge, the quality, robustness, time and costs of conditional genetic experiments can be significantly compromised. SUMMARY We start this review by discussing the intricacies of the most simple and widely used methods to perform conditional genetics and then extend on the need of novel and more advanced methods to increase the ease, efficiency and reliability of conditional mutagenesis and gene function analysis.
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Affiliation(s)
- Irene Garcia-Gonzalez
- Molecular Genetics of Angiogenesis Laboratory, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
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22
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Mizrak D, Bayin NS, Yuan J, Liu Z, Suciu RM, Niphakis MJ, Ngo N, Lum KM, Cravatt BF, Joyner AL, Sims PA. Single-Cell Profiling and SCOPE-Seq Reveal Lineage Dynamics of Adult Ventricular-Subventricular Zone Neurogenesis and NOTUM as a Key Regulator. Cell Rep 2021; 31:107805. [PMID: 32579931 PMCID: PMC7396151 DOI: 10.1016/j.celrep.2020.107805] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 05/13/2020] [Accepted: 06/02/2020] [Indexed: 12/14/2022] Open
Abstract
In the adult ventricular-subventricular zone (V-SVZ), neural stem cells (NSCs) generate new olfactory bulb (OB) neurons and glia throughout life. To map adult neuronal lineage progression, we profiled >56,000 V-SVZ and OB cells by single-cell RNA sequencing (scRNA-seq). Our analyses reveal the molecular diversity of OB neurons, including fate-mapped neurons, lineage progression dynamics, and an NSC intermediate enriched for Notum, which encodes a secreted WNT antagonist. SCOPE-seq technology, which links live-cell imaging with scRNA-seq, uncovers cell-size transitions during NSC differentiation and preferential NOTUM binding to proliferating neuronal precursors. Consistently, application of NOTUM protein in slice cultures and pharmacological inhibition of NOTUM in slice cultures and in vivo demonstrated that NOTUM negatively regulates V-SVZ proliferation. Timely, context-dependent neurogenesis demands adaptive signaling among neighboring progenitors. Our findings highlight a critical regulatory state during NSC activation marked by NOTUM, which attenuates WNT-stimulated proliferation in NSC progeny.
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Affiliation(s)
- Dogukan Mizrak
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - N Sumru Bayin
- Developmental Biology Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Jinzhou Yuan
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Zhouzerui Liu
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Radu M Suciu
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Micah J Niphakis
- Lundbeck La Jolla Research Center, Inc., 10835 Road to the Cure, Suite 250, San Diego, CA 92121, USA
| | - Nhi Ngo
- Lundbeck La Jolla Research Center, Inc., 10835 Road to the Cure, Suite 250, San Diego, CA 92121, USA
| | - Kenneth M Lum
- Lundbeck La Jolla Research Center, Inc., 10835 Road to the Cure, Suite 250, San Diego, CA 92121, USA
| | - Benjamin F Cravatt
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Alexandra L Joyner
- Developmental Biology Program, Sloan Kettering Institute, New York, NY 10065, USA; Biochemistry, Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA
| | - Peter A Sims
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Biochemistry & Molecular Biophysics, Columbia University Irving Medical Center, New York, NY 10032, USA.
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23
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A MASCOT for mosaic analysis. Proc Natl Acad Sci U S A 2020; 117:30876-30878. [PMID: 33199634 DOI: 10.1073/pnas.2021382117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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24
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Trovato F, Parra R, Pracucci E, Landi S, Cozzolino O, Nardi G, Cruciani F, Pillai V, Mosti L, Cwetsch AW, Cancedda L, Gritti L, Sala C, Verpelli C, Maset A, Lodovichi C, Ratto GM. Modelling genetic mosaicism of neurodevelopmental disorders in vivo by a Cre-amplifying fluorescent reporter. Nat Commun 2020; 11:6194. [PMID: 33273479 PMCID: PMC7713426 DOI: 10.1038/s41467-020-19864-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 10/27/2020] [Indexed: 12/20/2022] Open
Abstract
Genetic mosaicism, a condition in which an organ includes cells with different genotypes, is frequently present in monogenic diseases of the central nervous system caused by the random inactivation of the X-chromosome, in the case of X-linked pathologies, or by somatic mutations affecting a subset of neurons. The comprehension of the mechanisms of these diseases and of the cell-autonomous effects of specific mutations requires the generation of sparse mosaic models, in which the genotype of each neuron is univocally identified by the expression of a fluorescent protein in vivo. Here, we show a dual-color reporter system that, when expressed in a floxed mouse line for a target gene, leads to the creation of mosaics with tunable degree. We demonstrate the generation of a knockout mosaic of the autism/epilepsy related gene PTEN in which the genotype of each neuron is reliably identified, and the neuronal phenotype is accurately characterized by two-photon microscopy.
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Affiliation(s)
- Francesco Trovato
- National Enterprise for Nanoscience and Nanotechnology (NEST), Istituto Nanoscienze Consiglio Nazionale delle Ricerche (CNR) and Scuola Normale Superiore Pisa, 56127, Pisa, Italy.
| | - Riccardo Parra
- National Enterprise for Nanoscience and Nanotechnology (NEST), Istituto Nanoscienze Consiglio Nazionale delle Ricerche (CNR) and Scuola Normale Superiore Pisa, 56127, Pisa, Italy
| | - Enrico Pracucci
- National Enterprise for Nanoscience and Nanotechnology (NEST), Istituto Nanoscienze Consiglio Nazionale delle Ricerche (CNR) and Scuola Normale Superiore Pisa, 56127, Pisa, Italy
| | - Silvia Landi
- National Enterprise for Nanoscience and Nanotechnology (NEST), Istituto Nanoscienze Consiglio Nazionale delle Ricerche (CNR) and Scuola Normale Superiore Pisa, 56127, Pisa, Italy
- Institute of Neuroscience CNR, Pisa, Italy
| | - Olga Cozzolino
- National Enterprise for Nanoscience and Nanotechnology (NEST), Istituto Nanoscienze Consiglio Nazionale delle Ricerche (CNR) and Scuola Normale Superiore Pisa, 56127, Pisa, Italy
| | - Gabriele Nardi
- National Enterprise for Nanoscience and Nanotechnology (NEST), Istituto Nanoscienze Consiglio Nazionale delle Ricerche (CNR) and Scuola Normale Superiore Pisa, 56127, Pisa, Italy
| | - Federica Cruciani
- National Enterprise for Nanoscience and Nanotechnology (NEST), Istituto Nanoscienze Consiglio Nazionale delle Ricerche (CNR) and Scuola Normale Superiore Pisa, 56127, Pisa, Italy
| | - Vinoshene Pillai
- National Enterprise for Nanoscience and Nanotechnology (NEST), Istituto Nanoscienze Consiglio Nazionale delle Ricerche (CNR) and Scuola Normale Superiore Pisa, 56127, Pisa, Italy
| | - Laura Mosti
- National Enterprise for Nanoscience and Nanotechnology (NEST), Istituto Nanoscienze Consiglio Nazionale delle Ricerche (CNR) and Scuola Normale Superiore Pisa, 56127, Pisa, Italy
| | - Andrzej W Cwetsch
- Istituto Italiano di Tecnologia, Genoa, Italy
- Università degli studi di Genova, Genoa, Italy
| | - Laura Cancedda
- Istituto Italiano di Tecnologia, Genoa, Italy
- Istituto Telethon Dulbecco, Rome, Italy
| | | | - Carlo Sala
- Institute of Neuroscience CNR, Milan, Italy
| | | | - Andrea Maset
- Veneto Institute of Molecular Medicine, Padua, Italy
- Padova Neuroscience Center, Padova Università di Padova, Padua, Italy
| | - Claudia Lodovichi
- Veneto Institute of Molecular Medicine, Padua, Italy
- Padova Neuroscience Center, Padova Università di Padova, Padua, Italy
- Institute of Neuroscience CNR, Padua, Italy
| | - Gian Michele Ratto
- National Enterprise for Nanoscience and Nanotechnology (NEST), Istituto Nanoscienze Consiglio Nazionale delle Ricerche (CNR) and Scuola Normale Superiore Pisa, 56127, Pisa, Italy.
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25
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Abstract
Somatic mutations are the driving force of many age-related diseases such as cancer and hematopoietic failure. A challenge in the field is to evaluate health impact of somatic mutations prior to the appearance of disease symptoms. We describe a genetic tool named MASCOT (mosaic analysis system with Cre or Tomato) for mosaic analysis of somatic mutations that drive clonal hematopoiesis and lymphomagenesis. MASCOT can be applied to mosaic analysis of broad tissue types, and thus provides a valuable tool to aid functional dissection of somatic mutations in studies of development and disease. Somatic mutations are major genetic contributors to cancers and many other age-related diseases. Many disease-causing somatic mutations can initiate clonal growth prior to the appearance of any disease symptoms, yet experimental models that can be used to examine clonal abnormalities are limited. We describe a mosaic analysis system with Cre or Tomato (MASCOT) for tracking mutant cells and demonstrate its utility for modeling clonal hematopoiesis. MASCOT can be induced to constitutively express either Cre-GFP or Tomato for lineage tracing of a mutant and a reference group of cells simultaneously. We conducted mosaic analysis to assess functions of the Id3 and/or Tet2 gene in hematopoietic cell development and clonal hematopoiesis. Using Tomato-positive cells as a reference population, we demonstrated the high sensitivity of this system for detecting cell-intrinsic phenotypes during short-term or long-term tracking of hematopoietic cells. Long-term tracking of Tet2 mutant or Tet2/Id3 double-mutant cells in our MASCOT model revealed a dynamic shift from myeloid expansion to lymphoid expansion and subsequent development of lymphoma. This work demonstrates the utility of the MASCOT method in mosaic analysis of single or combined mutations, making the system suitable for modeling somatic mutations identified in humans.
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26
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Abstract
The mouse is one of the most widely used model organisms for genetic study. The tools available to alter the mouse genome have developed over the preceding decades from forward screens to gene targeting in stem cells to the recent influx of CRISPR approaches. In this review, we first consider the history of mice in genetic study, the development of classic approaches to genome modification, and how such approaches have been used and improved in recent years. We then turn to the recent surge of nuclease-mediated techniques and how they are changing the field of mouse genetics. Finally, we survey common classes of alleles used in mice and discuss how they might be engineered using different methods.
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Affiliation(s)
- James F Clark
- Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mt. Sinai, New York, New York 10029, USA
| | - Colin J Dinsmore
- Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mt. Sinai, New York, New York 10029, USA
| | - Philippe Soriano
- Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mt. Sinai, New York, New York 10029, USA
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27
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Garcia-Gonzalez I, Mühleder S, Fernández-Chacón M, Benedito R. Genetic Tools to Study Cardiovascular Biology. Front Physiol 2020; 11:1084. [PMID: 33071802 PMCID: PMC7541935 DOI: 10.3389/fphys.2020.01084] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 08/06/2020] [Indexed: 12/22/2022] Open
Abstract
Progress in biomedical science is tightly associated with the improvement of methods and genetic tools to manipulate and analyze gene function in mice, the most widely used model organism in biomedical research. The joint effort of numerous individual laboratories and consortiums has contributed to the creation of a large genetic resource that enables scientists to image cells, probe signaling pathways activities, or modify a gene function in any desired cell type or time point, à la carte. However, as these tools significantly increase in number and become more sophisticated, it is more difficult to keep track of each tool's possibilities and understand their advantages and disadvantages. Knowing the best currently available genetic technology to answer a particular biological question is key to reach a higher standard in biomedical research. In this review, we list and discuss the main advantages and disadvantages of available mammalian genetic technology to analyze cardiovascular cell biology at higher cellular and molecular resolution. We start with the most simple and classical genetic approaches and end with the most advanced technology available to fluorescently label cells, conditionally target their genes, image their clonal expansion, and decode their lineages.
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Affiliation(s)
| | | | | | - Rui Benedito
- Molecular Genetics of Angiogenesis Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
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28
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Fenno LE, Ramakrishnan C, Kim YS, Evans KE, Lo M, Vesuna S, Inoue M, Cheung KYM, Yuen E, Pichamoorthy N, Hong ASO, Deisseroth K. Comprehensive Dual- and Triple-Feature Intersectional Single-Vector Delivery of Diverse Functional Payloads to Cells of Behaving Mammals. Neuron 2020; 107:836-853.e11. [PMID: 32574559 PMCID: PMC7687746 DOI: 10.1016/j.neuron.2020.06.003] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 05/08/2020] [Accepted: 05/29/2020] [Indexed: 01/12/2023]
Abstract
The resolution and dimensionality with which biologists can characterize cell types have expanded dramatically in recent years, and intersectional consideration of such features (e.g., multiple gene expression and anatomical parameters) is increasingly understood to be essential. At the same time, genetically targeted technology for writing in and reading out activity patterns for cells in living organisms has enabled causal investigation in physiology and behavior; however, cell-type-specific delivery of these tools (including microbial opsins for optogenetics and genetically encoded Ca2+ indicators) has thus far fallen short of versatile targeting to cells jointly defined by many individually selected features. Here, we develop a comprehensive intersectional targeting toolbox including 39 novel vectors for joint-feature-targeted delivery of 13 molecular payloads (including opsins, indicators, and fluorophores), systematic approaches for development and optimization of new intersectional tools, hardware for in vivo monitoring of expression dynamics, and the first versatile single-virus tools (Triplesect) that enable targeting of triply defined cell types.
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Affiliation(s)
- Lief E Fenno
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Charu Ramakrishnan
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Yoon Seok Kim
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Kathryn E Evans
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Maisie Lo
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Sam Vesuna
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Masatoshi Inoue
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Kathy Y M Cheung
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Elle Yuen
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | | | - Alice S O Hong
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Karl Deisseroth
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
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29
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Kohara K, Inoue A, Nakano Y, Hirai H, Kobayashi T, Maruyama M, Baba R, Kawashima C. BATTLE: Genetically Engineered Strategies for Split-Tunable Allocation of Multiple Transgenes in the Nervous System. iScience 2020; 23:101248. [PMID: 32629613 PMCID: PMC7322263 DOI: 10.1016/j.isci.2020.101248] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/02/2019] [Accepted: 06/04/2020] [Indexed: 11/26/2022] Open
Abstract
Elucidating fine architectures and functions of cellular and synaptic connections requires development of new flexible methods. Here, we created a concept called the “battle of transgenes,” based on which we generated strategies using genetically engineered battles of multiple recombinases. The strategies enabled split-tunable allocation of multiple transgenes. We demonstrated the versatility of these strategies and technologies in inducing strong and multi-sparse allocations of multiple transgenes. Furthermore, the combination of our transgenic strategy and expansion microscopy enabled three-dimensional high-resolution imaging of whole synaptic structures in the hippocampus with simultaneous visualizations of endogenous synaptic proteins. These strategies and technologies based on the battle of genes may accelerate the analysis of whole synaptic and cellular connections in diverse life science fields. Generation of BATTLE-recombinase systems for allocation of multiple transgenes Split-tunable allocation in BATTLE-1 and multi-sparse allocation in BATTLE-2 Clear and strong labeling of dendrites and axons using BATTLE-2 3D high-resolution imaging of whole synapses in hippocampus in BATTLE-1EX
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Affiliation(s)
- Keigo Kohara
- Department of Cellular and Functional Biology, Institute of Biomedical Science, Kansai Medical University, Hirakata, Osaka 573-1010, Japan.
| | - Akitoshi Inoue
- Department of Medical Chemistry, Kansai Medical University, Graduate School of Medicine, Hirakata, Osaka 573-1010, Japan
| | - Yousuke Nakano
- Department of Anatomy, Kansai Medical University, Graduate School of Medicine, Hirakata, Osaka 573-1010, Japan
| | - Hirokazu Hirai
- Department of Neurophysiology and Neural Repair, Gunma University Graduate School of Medicine, Maebashi, Gunma 371-8511, Japan; Research Program for Neural Signalling, Division of Endocrinology, Metabolism and Signal Research, Gunma University Initiative for Advanced Research, Maebashi, Gunma 371-8512, Japan
| | - Takuya Kobayashi
- Department of Medical Chemistry, Kansai Medical University, Graduate School of Medicine, Hirakata, Osaka 573-1010, Japan; Japan Agency for Medical Research and Development (AMED), Core Research for Evolutional Science and Technology (CREST), 2-5-1 Shinmachi, Hirakata, Osaka 573-1010, Japan
| | - Masato Maruyama
- Department of Anatomy, Kansai Medical University, Graduate School of Medicine, Hirakata, Osaka 573-1010, Japan; Faculty of Pharmaceutical Sciences, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
| | - Ryosuke Baba
- Department of Cellular and Functional Biology, Institute of Biomedical Science, Kansai Medical University, Hirakata, Osaka 573-1010, Japan
| | - Chiho Kawashima
- Department of Cellular and Functional Biology, Institute of Biomedical Science, Kansai Medical University, Hirakata, Osaka 573-1010, Japan; Department of Bioscience, Osaka College of High Technology, Osaka 532-003, Japan
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30
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In situ conversion of defective Treg into SuperTreg cells to treat advanced IPEX-like disorders in mice. Nat Commun 2020; 11:2781. [PMID: 32493900 PMCID: PMC7271236 DOI: 10.1038/s41467-020-15836-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 03/24/2020] [Indexed: 12/20/2022] Open
Abstract
Mutations disrupting regulatory T (Treg) cell function can cause IPEX and IPEX-related disorders, but whether established disease can be reversed by correcting these mutations is unclear. Treg-specific deletion of the chromatin remodeling factor Brg1 impairs Treg cell activation and causes fatal autoimmunity in mice. Here, we show with a reversible knockout model that re-expression of Brg1, in conjunction with the severe endogenous proinflammatory environment, can convert defective Treg cells into powerful, super-activated Treg cells (SuperTreg cells) that can resolve advanced autoimmunity, with Brg1 re-expression in a minor fraction of Treg cells sufficient for the resolution in some cases. SuperTreg cells have enhanced trafficking and regulatory capabilities, but become deactivated as the inflammation subsides, thus avoiding excessive immune suppression. We propose a simple, robust yet safe gene-editing-based therapy for IPEX and IPEX-related disorders that exploits the defective Treg cells and the inflammatory environment pre-existing in the patients. Mutations that affect Treg cell function can cause lethal autoimmunity, but whether correcting these mutations can reverse established disease is unclear. Here, the authors correct Treg cell-specific Brg1 mutation in a minor fraction of Treg cells, which supercharges these cells to rescue mice from otherwise fatal IPEX-like autoimmunity.
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31
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Sun C, Sakashita H, Kim J, Tang Z, Upchurch GM, Yao L, Berry WL, Griffin TM, Olson LE. Mosaic Mutant Analysis Identifies PDGFRα/PDGFRβ as Negative Regulators of Adipogenesis. Cell Stem Cell 2020; 26:707-721.e5. [PMID: 32229310 DOI: 10.1016/j.stem.2020.03.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 11/26/2019] [Accepted: 03/06/2020] [Indexed: 01/01/2023]
Abstract
Adipocyte progenitors (APs) express platelet-derived growth factor receptors (PDGFRs), PDGFRα and PDGFRβ. Elevated PDGFRα signaling inhibits adipogenesis and promotes fibrosis; however, the function of PDGFRs in APs remains unclear. We combined lineage tracing and functional analyses in a sequential dual-recombinase approach that creates mosaic Pdgfr mutant cells by Cre/lox recombination with a linked Flp/frt reporter to track individual cell fates. Using mosaic lineage labeling, we show that adipocytes are derived from the Pdgfra lineage during postnatal growth and adulthood. In contrast, adipocytes are only derived from the mosaic Pdgfrb lineage during postnatal growth. Functionally, postnatal mosaic deletion of PDGFRα enhances adipogenesis and adult deletion enhances β3-adrenergic-receptor-induced beige adipocyte formation. Mosaic deletion of PDGFRβ also enhances white, brown, and beige adipogenesis. These data show that both PDGFRs are cell-autonomous inhibitors of adipocyte differentiation and implicate downregulation of PDGF signaling as a critical event in the transition from AP to adipocyte.
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Affiliation(s)
- Chengyi Sun
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA; Division of Molecular Cardiovascular Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Hiromi Sakashita
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Jang Kim
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Zifeng Tang
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - G Michael Upchurch
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Longbiao Yao
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - William L Berry
- Department of Surgery, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Timothy M Griffin
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Lorin E Olson
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA.
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32
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Cardot-Ruffino V, Chauvet V, Caligaris C, Bertrand-Chapel A, Chuvin N, Pommier RM, Valcourt U, Vincent D, Martel S, Aires S, Kaniewski B, Dubus P, Cassier P, Sentis S, Bartholin L. Generation of an Fsp1 (fibroblast-specific protein 1)-Flpo transgenic mouse strain. Genesis 2020; 58:e23359. [PMID: 32191380 PMCID: PMC7317532 DOI: 10.1002/dvg.23359] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 03/06/2020] [Accepted: 03/06/2020] [Indexed: 12/12/2022]
Abstract
Recombination systems represent a major breakthrough in the field of genetic model engineering. The Flp recombinases (Flp, Flpe, and Flpo) bind and cleave DNA Frt sites. We created a transgenic mouse strain ([Fsp1‐Flpo]) expressing the Flpo recombinase in fibroblasts. This strain was obtained by random insertion inside mouse zygotes after pronuclear injection. Flpo expression was placed under the control of the promoter of Fsp1 (fibroblast‐specific protein 1) gene, whose expression starts after gastrulation at Day 8.5 in cells of mesenchymal origin. We verified the correct expression and function of the Flpo enzyme by several ex vivo and in vivo approaches. The [Fsp1‐Flpo] strain represents a genuine tool to further target the recombination of transgenes with Frt sites specifically in cells of mesenchymal origin or with a fibroblastic phenotype.
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Affiliation(s)
- Victoire Cardot-Ruffino
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,Université de Lyon, Lyon, France.,Université Lyon 1, Lyon, France.,Centre Léon Bérard, Lyon, France
| | - Véronique Chauvet
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,Université de Lyon, Lyon, France.,Université Lyon 1, Lyon, France.,Centre Léon Bérard, Lyon, France
| | - Cassandre Caligaris
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,Université de Lyon, Lyon, France.,Université Lyon 1, Lyon, France.,Centre Léon Bérard, Lyon, France
| | - Adrien Bertrand-Chapel
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,Université de Lyon, Lyon, France.,Université Lyon 1, Lyon, France.,Centre Léon Bérard, Lyon, France
| | - Nicolas Chuvin
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,Université de Lyon, Lyon, France.,Université Lyon 1, Lyon, France.,Centre Léon Bérard, Lyon, France
| | - Roxane M Pommier
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,Université de Lyon, Lyon, France.,Université Lyon 1, Lyon, France.,Centre Léon Bérard, Lyon, France
| | - Ulrich Valcourt
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,Université de Lyon, Lyon, France.,Université Lyon 1, Lyon, France.,Centre Léon Bérard, Lyon, France
| | - David Vincent
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,Université de Lyon, Lyon, France.,Université Lyon 1, Lyon, France.,Centre Léon Bérard, Lyon, France.,Beatson Institute for Cancer Research, Glasgow, UK
| | - Sylvie Martel
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,Université de Lyon, Lyon, France.,Université Lyon 1, Lyon, France.,Centre Léon Bérard, Lyon, France
| | - Sophie Aires
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,Université de Lyon, Lyon, France.,Université Lyon 1, Lyon, France.,Centre Léon Bérard, Lyon, France
| | - Bastien Kaniewski
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,Université de Lyon, Lyon, France.,Université Lyon 1, Lyon, France.,Centre Léon Bérard, Lyon, France
| | - Pierre Dubus
- INSERM, Univ Bordeaux UMR1053 Bordeaux Research in Translational Oncology, Bordeaux, France.,CHU de Bordeaux, Bordeaux, France
| | - Philippe Cassier
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,Université de Lyon, Lyon, France.,Université Lyon 1, Lyon, France.,Centre Léon Bérard, Lyon, France.,Departement d'Oncologie Médicale, Centre Léon Bérard, Lyon, France
| | - Stéphanie Sentis
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,Université de Lyon, Lyon, France.,Université Lyon 1, Lyon, France.,Centre Léon Bérard, Lyon, France
| | - Laurent Bartholin
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,Université de Lyon, Lyon, France.,Université Lyon 1, Lyon, France.,Centre Léon Bérard, Lyon, France
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Zhao H, Zhou B. Dual genetic approaches for deciphering cell fate plasticity in vivo: more than double. Curr Opin Cell Biol 2019; 61:101-109. [DOI: 10.1016/j.ceb.2019.07.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 07/01/2019] [Accepted: 07/04/2019] [Indexed: 12/16/2022]
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34
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Mukai J, Cannavò E, Crabtree GW, Sun Z, Diamantopoulou A, Thakur P, Chang CY, Cai Y, Lomvardas S, Takata A, Xu B, Gogos JA. Recapitulation and Reversal of Schizophrenia-Related Phenotypes in Setd1a-Deficient Mice. Neuron 2019; 104:471-487.e12. [PMID: 31606247 DOI: 10.1016/j.neuron.2019.09.014] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 07/28/2019] [Accepted: 09/10/2019] [Indexed: 12/15/2022]
Abstract
SETD1A, a lysine-methyltransferase, is a key schizophrenia susceptibility gene. Mice carrying a heterozygous loss-of-function mutation of the orthologous gene exhibit alterations in axonal branching and cortical synaptic dynamics accompanied by working memory deficits. We show that Setd1a binds both promoters and enhancers with a striking overlap between Setd1a and Mef2 on enhancers. Setd1a targets are highly expressed in pyramidal neurons and display a complex pattern of transcriptional up- and downregulations shaped by presumed opposing functions of Setd1a on promoters and Mef2-bound enhancers. Notably, evolutionarily conserved Setd1a targets are associated with neuropsychiatric genetic risk burden. Reinstating Setd1a expression in adulthood rescues cognitive deficits. Finally, we identify LSD1 as a major counteracting demethylase for Setd1a and show that its pharmacological antagonism results in a full rescue of the behavioral and morphological deficits in Setd1a-deficient mice. Our findings advance understanding of how SETD1A mutations predispose to schizophrenia (SCZ) and point to novel therapeutic interventions.
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Affiliation(s)
- Jun Mukai
- Department of Physiology and Cellular Biophysics, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA; Mortimer B. Zuckerman Mind Brain and Behavior Institute Columbia University, New York, NY 10027, USA
| | - Enrico Cannavò
- Mortimer B. Zuckerman Mind Brain and Behavior Institute Columbia University, New York, NY 10027, USA
| | - Gregg W Crabtree
- Department of Physiology and Cellular Biophysics, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA; Mortimer B. Zuckerman Mind Brain and Behavior Institute Columbia University, New York, NY 10027, USA
| | - Ziyi Sun
- Department of Physiology and Cellular Biophysics, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Anastasia Diamantopoulou
- Department of Physiology and Cellular Biophysics, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Pratibha Thakur
- Department of Physiology and Cellular Biophysics, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA; Mortimer B. Zuckerman Mind Brain and Behavior Institute Columbia University, New York, NY 10027, USA
| | - Chia-Yuan Chang
- Department of Physiology and Cellular Biophysics, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Yifei Cai
- Department of Physiology and Cellular Biophysics, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Stavros Lomvardas
- Mortimer B. Zuckerman Mind Brain and Behavior Institute Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA; Department of Neuroscience, Columbia University, New York, NY 10032, USA
| | - Atsushi Takata
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Fukuura 3-9, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Bin Xu
- Department of Psychiatry, Columbia University Medical Center, New York, NY 10032, USA
| | - Joseph A Gogos
- Department of Physiology and Cellular Biophysics, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA; Mortimer B. Zuckerman Mind Brain and Behavior Institute Columbia University, New York, NY 10027, USA; Department of Neuroscience, Columbia University, New York, NY 10032, USA.
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35
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Chakravarti D, Caraballo LD, Weinberg BH, Wong WW. Inducible Gene Switches with Memory in Human T Cells for Cellular Immunotherapy. ACS Synth Biol 2019; 8:1744-1754. [PMID: 31268301 PMCID: PMC6703182 DOI: 10.1021/acssynbio.8b00512] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
![]()
Cell-based therapies that employ
engineered T cells—including
those modified to express chimeric antigen receptors (CARs)—to
target cancer cells have demonstrated promising responses in clinical
trials. However, engineered T cell responses must be regulated to
prevent severe side effects such as cytokine storms and off-target
responses. Here we present a class of recombinase-based gene circuits
that will enable inducible, one-time state switching in adoptive T
cell therapy using an FDA-approved drug, creating a generalizable
platform that can be used to control when and how strongly a gene
is expressed. These circuits exhibit memory such that induced T cells
will maintain any changes made even when the drug inducer is removed.
This memory feature avoids prolonged drug inducer exposure, thus reducing
the complexity and potential side effect associated with the drug
inducer. We have utilized these circuits to control the expression
of an anti-Her2-CAR, demonstrating the ability of these circuits to
regulate CAR expression and T cell activity. We envision this platform
can be extended to regulate other genes involved in T cell behavior
for applications in various adoptive T cell therapies.
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Affiliation(s)
- Deboki Chakravarti
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
- Biological Design Center, Boston University, Boston, Massachusetts 02215, United States
| | - Leidy D. Caraballo
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
- Biological Design Center, Boston University, Boston, Massachusetts 02215, United States
| | - Benjamin H. Weinberg
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
- Biological Design Center, Boston University, Boston, Massachusetts 02215, United States
| | - Wilson W. Wong
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
- Biological Design Center, Boston University, Boston, Massachusetts 02215, United States
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36
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Yang Z, Joyner AL. YAP1 is involved in replenishment of granule cell precursors following injury to the neonatal cerebellum. Dev Biol 2019; 455:458-472. [PMID: 31376393 DOI: 10.1016/j.ydbio.2019.07.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 07/30/2019] [Accepted: 07/30/2019] [Indexed: 01/08/2023]
Abstract
The cerebellum undergoes major rapid growth during the third trimester and early neonatal stage in humans, making it vulnerable to injuries in pre-term babies. Experiments in mice have revealed a remarkable ability of the neonatal cerebellum to recover from injuries around birth. In particular, recovery following irradiation-induced ablation of granule cell precursors (GCPs) involves adaptive reprogramming of Nestin-expressing glial progenitors (NEPs). Sonic hedgehog signaling is required for the initial step in NEP reprogramming; however, the full spectrum of developmental signaling pathways that promote NEP-driven regeneration is not known. Since the growth regulatory Hippo pathway has been implicated in the repair of several tissue types, we tested whether Hippo signaling is involved in regeneration of the cerebellum. Using mouse models, we found that the Hippo pathway transcriptional co-activator YAP1 (Yes-associated protein 1) but not TAZ (transcriptional coactivator with PDZ binding motif, or WWTR1) is required in NEPs for full recovery of cerebellar growth following irradiation one day after birth. Although Yap1 plays only a minor role during normal development in differentiation of NEPs or GCPs, the size of the cerebellum, and in particular the internal granule cell layer produced by GCPs, is significantly reduced in Yap1 mutants after irradiation, and the organization of Purkinje cells and Bergmann glial fibers is disrupted. The initial proliferative response of Yap1 mutant NEPs to irradiation is normal and the cells migrate to the GCP niche, but subsequently there is increased cell death of GCPs and altered migration of granule cells, possibly due to defects in Bergmann glia. Moreover, loss of Taz along with Yap1 in NEPs does not abrogate regeneration or alter development of the cerebellum. Our study provides new insights into the molecular signaling underlying postnatal cerebellar development and regeneration.
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Affiliation(s)
- Zhaohui Yang
- Biochemistry, Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, 10065, United States; Developmental Biology Program, Sloan Kettering Institute, New York, NY, 10065, United States
| | - Alexandra L Joyner
- Biochemistry, Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, 10065, United States; Developmental Biology Program, Sloan Kettering Institute, New York, NY, 10065, United States.
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37
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Abstract
For studies of gene function during development, it can be very useful to generate mosaic embryos in which a small subset of cells in a given cell lineage lacks a gene of interest and carries a marker that allows the mutant cells to be specifically visualized and compared to wild-type cells. Several methods have been used to generate genetically mosaic mouse kidneys for such studies. These include (1) chimeric embryos generated using embryonic stem cells, (2) chimeric renal organoids generated by dissociation and reaggregation of the fetal kidneys, (3) generation of a knockout allele with a built-in reporter gene, (4) mosaic analysis with double markers (MADM), and (5) mosaic mutant analysis with spatial and temporal control of recombination (MASTR). In this chapter, these five methods are described, and their advantages and disadvantages are discussed.
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38
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Fernández-Chacón M, Casquero-García V, Luo W, Francesca Lunella F, Ferreira Rocha S, Del Olmo-Cabrera S, Benedito R. iSuRe-Cre is a genetic tool to reliably induce and report Cre-dependent genetic modifications. Nat Commun 2019; 10:2262. [PMID: 31118412 PMCID: PMC6531465 DOI: 10.1038/s41467-019-10239-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 04/23/2019] [Indexed: 01/09/2023] Open
Abstract
Most biomedical research aimed at understanding gene function uses the Cre-Lox system, which consists of the Cre recombinase-dependent deletion of genes containing LoxP sites. This system enables conditional genetic modifications because the expression and activity of the recombinase Cre/CreERT2 can be regulated in space by tissue-specific promoters and in time by the ligand tamoxifen. Since the precise Cre-Lox recombination event is invisible, methods were developed to report Cre activity and are widely used. However, numerous studies have shown that expression of a given Cre activity reporter cannot be assumed to indicate deletion of other LoxP-flanked genes of interest. Here, we report the generation of an inducible dual reporter-Cre mouse allele, iSuRe-Cre. By significantly increasing Cre activity in reporter-expressing cells, iSuRe-Cre provides certainty that these cells have completely recombined floxed alleles. This genetic tool increases the ease, efficiency, and reliability of conditional mutagenesis and gene function analysis.
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Affiliation(s)
- Macarena Fernández-Chacón
- Molecular Genetics of Angiogenesis Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, E28029, Spain
| | - Verónica Casquero-García
- Molecular Genetics of Angiogenesis Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, E28029, Spain
| | - Wen Luo
- Molecular Genetics of Angiogenesis Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, E28029, Spain
| | - Federica Francesca Lunella
- Molecular Genetics of Angiogenesis Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, E28029, Spain
| | - Susana Ferreira Rocha
- Molecular Genetics of Angiogenesis Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, E28029, Spain
| | - Sergio Del Olmo-Cabrera
- Molecular Genetics of Angiogenesis Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, E28029, Spain
| | - Rui Benedito
- Molecular Genetics of Angiogenesis Group, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, E28029, Spain.
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Walter DM, Yates TJ, Ruiz-Torres M, Kim-Kiselak C, Gudiel AA, Deshpande C, Wang WZ, Cicchini M, Stokes KL, Tobias JW, Buza E, Feldser DM. RB constrains lineage fidelity and multiple stages of tumour progression and metastasis. Nature 2019; 569:423-427. [PMID: 31043741 PMCID: PMC6522292 DOI: 10.1038/s41586-019-1172-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 04/03/2019] [Indexed: 12/11/2022]
Abstract
Mutations in the Retinoblastoma (RB) tumour suppressor pathway are a hallmark of cancer and a prevalent feature of lung adenocarcinoma1,2,3. Despite being the first tumour suppressor to be identified, the molecular and cellular basis underlying selection for persistent RB loss in cancer remains unclear4–6. Methods that reactivate the RB pathway using inhibitors of cyclin-dependent kinases CDK4 and CDK6 are effective in some cancer types and currently under evaluation in lung adenocarcinoma7–9. Whether RB pathway reactivation will have therapeutic effects and if targeting CDK4/6 is sufficient to reactivate RB pathway activity in lung cancer is unknown. Here, we model RB loss during lung adenocarcinoma progression and pathway reactivation in established oncogenic KRAS-driven tumours in the mouse. We show that RB loss enables cancer cells to bypass two distinct barriers during tumour progression. First, RB loss abrogates the requirement for MAPK signal amplification during malignant progression. We identify CDK2-dependent phosphorylation of RB as an effector of MAPK signalling and critical mediator of resistance to CDK4/6 inhibition. Second, RB inactivation deregulates expression of cell state-determining factors, facilitates lineage infidelity, and accelerates the acquisition of metastatic competency. In contrast, reactivation of RB reprograms advanced tumours toward a less metastatic cell state, but is nevertheless unable to halt cancer cell proliferation and tumour growth due to adaptive rewiring of MAPK pathway signalling, which restores a CDK-dependent suppression of RB. Our study demonstrates the power of reversible gene perturbation approaches to identify molecular mechanisms of tumour progression, causal relationships between genes and the tumour suppressive programs they control, and critical determinants of successful therapy.
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Affiliation(s)
- David M Walter
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Cell and Molecular Biology Graduate Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Travis J Yates
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Miguel Ruiz-Torres
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Caroline Kim-Kiselak
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - A Andrea Gudiel
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Charuhas Deshpande
- Department of Pathology & Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Abramson Cancer Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - Walter Z Wang
- Vagelos Scholars Program, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Michelle Cicchini
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kate L Stokes
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - John W Tobias
- Abramson Cancer Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA.,Penn Genomic Analysis Core, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Elizabeth Buza
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - David M Feldser
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. .,Cell and Molecular Biology Graduate Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. .,Abramson Cancer Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA. .,Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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40
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Wojcinski A, Morabito M, Lawton AK, Stephen DN, Joyner AL. Genetic deletion of genes in the cerebellar rhombic lip lineage can stimulate compensation through adaptive reprogramming of ventricular zone-derived progenitors. Neural Dev 2019; 14:4. [PMID: 30764875 PMCID: PMC6375182 DOI: 10.1186/s13064-019-0128-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 01/17/2019] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND The cerebellum is a foliated posterior brain structure involved in coordination of motor movements and cognition. The cerebellum undergoes rapid growth postnataly due to Sonic Hedgehog (SHH) signaling-dependent proliferation of ATOH1+ granule cell precursors (GCPs) in the external granule cell layer (EGL), a key step for generating cerebellar foliation and the correct number of granule cells. Due to its late development, the cerebellum is particularly vulnerable to injury from preterm birth and stress around birth. We recently uncovered an intrinsic capacity of the developing cerebellum to replenish ablated GCPs via adaptive reprogramming of Nestin-expressing progenitors (NEPs). However, whether this compensation mechanism occurs in mouse mutants affecting the developing cerebellum and could lead to mis-interpretation of phenotypes was not known. METHODS We used two different approaches to remove the main SHH signaling activator GLI2 in GCPs: 1) Our mosaic mutant analysis with spatial and temporal control of recombination (MASTR) technique to delete Gli2 in a small subset of GCPs; 2) An Atoh1-Cre transgene to delete Gli2 in most of the EGL. Genetic Inducible Fate Mapping (GIFM) and live imaging were used to analyze the behavior of NEPs after Gli2 deletion. RESULTS Mosaic analysis demonstrated that SHH-GLI2 signaling is critical for generating the correct pool of granule cells by maintaining GCPs in an undifferentiated proliferative state and promoting their survival. Despite this, inactivation of GLI2 in a large proportion of GCPs in the embryo did not lead to the expected dramatic reduction in the size of the adult cerebellum. GIFM uncovered that NEPs do indeed replenish GCPs in Gli2 conditional mutants, and then expand and partially restore the production of granule cells. Furthermore, the SHH signaling-dependent NEP compensation requires Gli2, demonstrating that the activator side of the pathway is involved. CONCLUSION We demonstrate that a mouse conditional mutation that results in loss of SHH signaling in GCPs is not sufficient to induce long term severe cerebellum hypoplasia. The ability of the neonatal cerebellum to regenerate after loss of cells via a response by NEPs must therefore be considered when interpreting the phenotypes of Atoh1-Cre conditional mutants affecting GCPs.
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Affiliation(s)
- Alexandre Wojcinski
- Developmental Biology Program, Sloan Kettering Institute, 1275 York Avenue, Box 511, New York, NY, 10065, USA
| | - Morgane Morabito
- Developmental Biology Program, Sloan Kettering Institute, 1275 York Avenue, Box 511, New York, NY, 10065, USA
| | - Andrew K Lawton
- Developmental Biology Program, Sloan Kettering Institute, 1275 York Avenue, Box 511, New York, NY, 10065, USA
| | - Daniel N Stephen
- Developmental Biology Program, Sloan Kettering Institute, 1275 York Avenue, Box 511, New York, NY, 10065, USA
| | - Alexandra L Joyner
- Developmental Biology Program, Sloan Kettering Institute, 1275 York Avenue, Box 511, New York, NY, 10065, USA.
- Biochemistry, Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, 10065, USA.
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41
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Carugo A, Minelli R, Sapio L, Soeung M, Carbone F, Robinson FS, Tepper J, Chen Z, Lovisa S, Svelto M, Amin S, Srinivasan S, Del Poggetto E, Loponte S, Puca F, Dey P, Malouf GG, Su X, Li L, Lopez-Terrada D, Rakheja D, Lazar AJ, Netto GJ, Rao P, Sgambato A, Maitra A, Tripathi DN, Walker CL, Karam JA, Heffernan TP, Viale A, Roberts CWM, Msaouel P, Tannir NM, Draetta GF, Genovese G. p53 Is a Master Regulator of Proteostasis in SMARCB1-Deficient Malignant Rhabdoid Tumors. Cancer Cell 2019; 35:204-220.e9. [PMID: 30753823 PMCID: PMC7876656 DOI: 10.1016/j.ccell.2019.01.006] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 10/12/2018] [Accepted: 01/09/2019] [Indexed: 12/11/2022]
Abstract
Alterations in chromatin remodeling genes have been increasingly implicated in human oncogenesis. Specifically, the biallelic inactivation of the SWI/SNF subunit SMARCB1 results in the emergence of extremely aggressive pediatric malignancies. Here, we developed embryonic mosaic mouse models of malignant rhabdoid tumors (MRTs) that faithfully recapitulate the clinical-pathological features of the human disease. We demonstrated that SMARCB1-deficient malignancies exhibit dramatic activation of the unfolded protein response (UPR) and ER stress response via a genetically intact MYC-p19ARF-p53 axis. As a consequence, these tumors display an exquisite sensitivity to agents inducing proteotoxic stress and inhibition of the autophagic machinery. In conclusion, our findings provide a rationale for drug repositioning trials investigating combinations of agents targeting the UPR and autophagy in SMARCB1-deficient MRTs.
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Affiliation(s)
- Alessandro Carugo
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Rosalba Minelli
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Luigi Sapio
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Melinda Soeung
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Federica Carbone
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Frederick S Robinson
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - James Tepper
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Ziheng Chen
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Sara Lovisa
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Maria Svelto
- Telethon Institute of Genetics and Medicine, Via Campi Flegrei 34, Pozzuoli 80078, Italy
| | - Samirkumar Amin
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032, USA
| | - Sanjana Srinivasan
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Edoardo Del Poggetto
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Sara Loponte
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Francesca Puca
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Prasenjit Dey
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Gabriel G Malouf
- Centre Hospitalier Régional et Universitaire Strasbourg, Hôpital Civil, 1 Place de L'Hôpital, Strasbourg 67091, France; Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS, INSERM, Université de Strasbourg, Illkirch 67400, France
| | - Xiaoping Su
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Liren Li
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangzhou 510060, China
| | - Dolores Lopez-Terrada
- Department of Pathology, Texas Children's Hospital, 6621 Fannin Street, Houston, TX 77030, USA
| | - Dinesh Rakheja
- Department of Pathology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Alexander J Lazar
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA; Department of Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - George J Netto
- Department of Pathology, Johns Hopkins University, 600 N. Wolfe Street/Carnegie 417, Baltimore, MD 21287, USA
| | - Priya Rao
- Department of Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Alessandro Sgambato
- Dipartimento di Patologia Generale, Policlinico Agostino Gemelli, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, Roma 00168, Italy
| | - Anirban Maitra
- Department of Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA; Sheikh Ahmed Bin Zayed Al Nahyan Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Durga N Tripathi
- Center for Precision Environmental Health, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Cheryl L Walker
- Center for Precision Environmental Health, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Jose A Karam
- Department of Urology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA; Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Timothy P Heffernan
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Andrea Viale
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Charles W M Roberts
- Department of Oncology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38120, USA
| | - Pavlos Msaouel
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Nizar M Tannir
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA.
| | - Giulio F Draetta
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA.
| | - Giannicola Genovese
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA; Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA; David H. Koch Center for Applied Research of Genitourinary Cancers, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA.
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Sequentially inducible mouse models reveal that Npm1 mutation causes malignant transformation of Dnmt3a-mutant clonal hematopoiesis. Leukemia 2019; 33:1635-1649. [PMID: 30692594 PMCID: PMC6609470 DOI: 10.1038/s41375-018-0368-6] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 11/27/2018] [Accepted: 12/13/2018] [Indexed: 12/21/2022]
Abstract
Clonal hematopoiesis (CH) is a common aging-associated condition with increased risk of hematologic malignancy. Knowledge of the mechanisms driving evolution from CH to overt malignancy has been hampered by a lack of in vivo models that orthogonally activate mutant alleles. Here, we develop independently regulatable mutations in DNA methyltransferase 3A (Dnmt3a) and nucleophosmin 1 (Npm1), observed in human CH and AML, respectively. We find Dnmt3a mutation expands hematopoietic stem and multipotent progenitor cells (HSC/MPPs), modeling CH. Induction of mutant Npm1 after development of Dnmt3a-mutant CH causes progression to myeloproliferative disorder (MPD), and more aggressive MPD is observed with longer latency between mutations. MPDs uniformly progress to acute myeloid leukemia (AML) following transplant, accompanied by a decrease in HSC/MPPs and an increase in myeloid-restricted progenitors, the latter of which propagate AML in tertiary recipient mice. At a molecular level, progression of CH to MPD is accompanied by selection for mutations activating Ras/Raf/MAPK signaling. Progression to AML is characterized by additional oncogenic signaling mutations (Ptpn11, Pik3r1, Flt3) and/or mutations in epigenetic regulators (Hdac1, Idh1, Arid1a). Together, our study demonstrates that Npm1 mutation drives evolution of Dnmt3a-mutant CH to AML and rate of disease progression is accelerated with longer latency of CH.
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Brodski C, Blaess S, Partanen J, Prakash N. Crosstalk of Intercellular Signaling Pathways in the Generation of Midbrain Dopaminergic Neurons In Vivo and from Stem Cells. J Dev Biol 2019; 7:jdb7010003. [PMID: 30650592 PMCID: PMC6473842 DOI: 10.3390/jdb7010003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/07/2019] [Accepted: 01/09/2019] [Indexed: 12/25/2022] Open
Abstract
Dopamine-synthesizing neurons located in the mammalian ventral midbrain are at the center stage of biomedical research due to their involvement in severe human neuropsychiatric and neurodegenerative disorders, most prominently Parkinson’s Disease (PD). The induction of midbrain dopaminergic (mDA) neurons depends on two important signaling centers of the mammalian embryo: the ventral midline or floor plate (FP) of the neural tube, and the isthmic organizer (IsO) at the mid-/hindbrain boundary (MHB). Cells located within and close to the FP secrete sonic hedgehog (SHH), and members of the wingless-type MMTV integration site family (WNT1/5A), as well as bone morphogenetic protein (BMP) family. The IsO cells secrete WNT1 and the fibroblast growth factor 8 (FGF8). Accordingly, the FGF8, SHH, WNT, and BMP signaling pathways play crucial roles during the development of the mDA neurons in the mammalian embryo. Moreover, these morphogens are essential for the generation of stem cell-derived mDA neurons, which are critical for the modeling, drug screening, and cell replacement therapy of PD. This review summarizes our current knowledge about the functions and crosstalk of these signaling pathways in mammalian mDA neuron development in vivo and their applications in stem cell-based paradigms for the efficient derivation of these neurons in vitro.
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Affiliation(s)
- Claude Brodski
- Department of Physiology and Cell Biology, Zlotowski Center for Neuroscience, Faculty of Health Sciences, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel.
| | - Sandra Blaess
- Institute of Reconstructive Neurobiology, University of Bonn Medical Center, 53127 Bonn, Germany.
| | - Juha Partanen
- Faculty of Biological and Environmental Sciences, FIN00014-University of Helsinki, P.O. Box 56, Viikinkaari 9, FIN-00014 Helsinki, Finland.
| | - Nilima Prakash
- Department Hamm 2, Hamm-Lippstadt University of Applied Sciences, 59063 Hamm, Germany.
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44
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Goodrich MM, Talhouk R, Zhang X, Goodrich DW. An approach for controlling the timing and order of engineered mutations in mice. Genesis 2018; 56:e23243. [PMID: 30113769 DOI: 10.1002/dvg.23243] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 07/24/2018] [Accepted: 07/25/2018] [Indexed: 11/09/2022]
Abstract
Significant advances in our understanding of normal development and disease have been facilitated by engineered mice in which genes can be altered in a spatially, temporally, or cell type restricted manner using site specific recombinase systems like Cre-loxP or Flp-frt. In many circumstances it is important to understand how interactions between multiple genes influence a given phenotype. Robust approaches for precisely controlling multiple genetic alterations independently are limited, however, thus the impact of mutation order and timing on phenotype is generally unknown. Here we describe and validate a novel Gt(ROSA)26Sor targeted transgene allowing precise control over the order and timing of multiple genetic mutations in the mouse. The transgene expresses an optimized, Flp-estrogen receptor fusion protein (Flpo-ERT2) under the control of a loxP-stop-loxP cassette. In this system, genes modified by loxP sites are altered first upon expression of Cre. Cre also eliminates the loxP-stop-loxP cassette, permitting widespread expression of Flpo-ERT2. Because of the estrogen receptor fusion, Flp activity remains inert until administration of tamoxifen, allowing genes modified by frt sites to be modified subsequently with controllable timing. This mouse transgene will be useful in a wide variety of applications where independent control of different mutations in the mouse is desirable.
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Affiliation(s)
- Maxwell M Goodrich
- Department of Pharmacology & Therapeutics, Roswell Park Cancer Institute, Buffalo, New York
| | - Ramzi Talhouk
- Department of Pharmacology & Therapeutics, Roswell Park Cancer Institute, Buffalo, New York
| | - Xiaojing Zhang
- Department of Pharmacology & Therapeutics, Roswell Park Cancer Institute, Buffalo, New York
| | - David W Goodrich
- Department of Pharmacology & Therapeutics, Roswell Park Cancer Institute, Buffalo, New York
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45
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Ma J, Shen Z, Yu YC, Shi SH. Neural lineage tracing in the mammalian brain. Curr Opin Neurobiol 2018; 50:7-16. [PMID: 29125960 PMCID: PMC5938148 DOI: 10.1016/j.conb.2017.10.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Revised: 10/08/2017] [Accepted: 10/17/2017] [Indexed: 01/05/2023]
Abstract
Delineating the lineage of neural cells that captures the progressive steps in their specification is fundamental to understanding brain development, organization, and function. Since the earliest days of embryology, lineage questions have been addressed with methods of increasing specificity, capacity, and resolution. Yet, a full realization of individual cell lineages remains challenging for complex systems. A recent explosion of technical advances in genome-editing and single-cell sequencing has enabled lineage analysis in an unprecedented scale, speed, and depth across different species. In this review, we discuss the application of available as well as future genetic labeling techniques for tracking neural lineages in vivo in the mammalian nervous system.
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Affiliation(s)
- Jian Ma
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhongfu Shen
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yong-Chun Yu
- Institute of Brain Science, State Key Laboratory of Medical Neurobiology and Collaborative Innovation Center for Brain Science, Fudan University, Shanghai 200032, China
| | - Song-Hai Shi
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, U.S.A
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46
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Intersectional gene inactivation: there is more to conditional mutagenesis than Cre. SCIENCE CHINA-LIFE SCIENCES 2018; 61:1115-1117. [PMID: 29785571 DOI: 10.1007/s11427-018-9291-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 03/15/2018] [Indexed: 10/16/2022]
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47
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Pu W, He L, Han X, Tian X, Li Y, Zhang H, Liu Q, Huang X, Zhang L, Wang QD, Yu Z, Yang X, Smart N, Zhou B. Genetic Targeting of Organ-Specific Blood Vessels. Circ Res 2018; 123:86-99. [PMID: 29764841 DOI: 10.1161/circresaha.118.312981] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 05/10/2018] [Accepted: 05/14/2018] [Indexed: 01/20/2023]
Abstract
RATIONALE Organs of the body require vascular networks to supply oxygen and nutrients and maintain physiological function. The blood vessels of different organs are structurally and functionally heterogeneous in nature. To more precisely dissect their distinct in vivo function in individual organs, without potential interference from off-site targets, it is necessary to genetically target them in an organ-specific manner. OBJECTIVE The objective of this study was to generate a genetic system that targets vascular endothelial cells in an organ- or tissue-specific manner and to exemplify the potential application of intersectional genetics for precise, target-specific gene manipulation in vivo. METHODS AND RESULTS We took advantage of 2 orthogonal recombination systems, Dre-rox and Cre-loxP, to create a genetic targeting system based on intersectional genetics. Using this approach, Cre activity was only detectable in cells that had expressed both Dre and Cre. Applying this new system, we generated a coronary endothelial cell-specific Cre (CoEC-Cre) and a brain endothelial cell-specific Cre (BEC-Cre). Through lineage tracing, gene knockout and overexpression experiments, we demonstrated that CoEC-Cre and BEC-Cre efficiently and specifically target blood vessels in the heart and brain, respectively. By deletion of vascular endothelial growth factor receptor 2 using BEC-Cre, we showed that vascular endothelial growth factor signaling regulates angiogenesis in the central nervous system and also controls the integrity of the blood-brain barrier. CONCLUSIONS We provide 2 examples to illustrate the use of intersectional genetics for more precise gene targeting in vivo, namely manipulation of genes in blood vessels of the heart and brain. More broadly, this system provides a valuable strategy for tissue-specific gene manipulation that can be widely applied to other fields of biomedical research.
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Affiliation(s)
- Wenjuan Pu
- From the State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences (W.P., L.H., X.T., Y.L., H.Z., Q.L., X. Huang, L.Z., B.Z.).,Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences (W.P., L.H., X.T., Y.L., Q.L., X. Huang, L.Z., B.Z.)
| | - Lingjuan He
- From the State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences (W.P., L.H., X.T., Y.L., H.Z., Q.L., X. Huang, L.Z., B.Z.).,Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences (W.P., L.H., X.T., Y.L., Q.L., X. Huang, L.Z., B.Z.)
| | - Ximeng Han
- Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; School of Life Science and Technology, Shanghai Tech University, China (X. Han, H.Z., B.Z.)
| | - Xueying Tian
- From the State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences (W.P., L.H., X.T., Y.L., H.Z., Q.L., X. Huang, L.Z., B.Z.).,Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences (W.P., L.H., X.T., Y.L., Q.L., X. Huang, L.Z., B.Z.)
| | - Yan Li
- From the State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences (W.P., L.H., X.T., Y.L., H.Z., Q.L., X. Huang, L.Z., B.Z.).,Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences (W.P., L.H., X.T., Y.L., Q.L., X. Huang, L.Z., B.Z.)
| | - Hui Zhang
- From the State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences (W.P., L.H., X.T., Y.L., H.Z., Q.L., X. Huang, L.Z., B.Z.).,Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; School of Life Science and Technology, Shanghai Tech University, China (X. Han, H.Z., B.Z.)
| | - Qiaozhen Liu
- From the State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences (W.P., L.H., X.T., Y.L., H.Z., Q.L., X. Huang, L.Z., B.Z.).,Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences (W.P., L.H., X.T., Y.L., Q.L., X. Huang, L.Z., B.Z.)
| | - Xiuzhen Huang
- From the State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences (W.P., L.H., X.T., Y.L., H.Z., Q.L., X. Huang, L.Z., B.Z.).,Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences (W.P., L.H., X.T., Y.L., Q.L., X. Huang, L.Z., B.Z.)
| | - Libo Zhang
- From the State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences (W.P., L.H., X.T., Y.L., H.Z., Q.L., X. Huang, L.Z., B.Z.).,Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences (W.P., L.H., X.T., Y.L., Q.L., X. Huang, L.Z., B.Z.)
| | - Qing-Dong Wang
- Bioscience Heart Failure, Cardiovascular and Metabolic Diseases, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden (Q.-D.W.)
| | - Zhenyang Yu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Laboratory of Proteomics, Institute of Biotechnology, China (Z.Y., X.Y.)
| | - Xiao Yang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Laboratory of Proteomics, Institute of Biotechnology, China (Z.Y., X.Y.)
| | - Nicola Smart
- British Heart Foundation Centre of Regenerative Medicine, Department of Physiology, Anatomy and Genetics, University of Oxford, United Kingdom (N.S.)
| | - Bin Zhou
- From the State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences (W.P., L.H., X.T., Y.L., H.Z., Q.L., X. Huang, L.Z., B.Z.) .,Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences (W.P., L.H., X.T., Y.L., Q.L., X. Huang, L.Z., B.Z.).,Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences; School of Life Science and Technology, Shanghai Tech University, China (X. Han, H.Z., B.Z.).,Key Laboratory of Regenerative Medicine of Ministry of Education, Institute of Aging and Regenerative Medicine, Jinan University, Guangzhou, China (B.Z.)
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Abstract
Tumor suppressor genes play critical roles orchestrating anti-cancer programs that are both context dependent and mechanistically diverse. Beyond canonical tumor suppressive programs that control cell division, cell death, and genome stability, unexpected tumor suppressor gene activities that regulate metabolism, immune surveillance, the epigenetic landscape, and others have recently emerged. This diversity underscores the important roles these genes play in maintaining cellular homeostasis to suppress cancer initiation and progression, but also highlights a tremendous challenge in discerning precise context-specific programs of tumor suppression controlled by a given tumor suppressor. Fortunately, the rapid sophistication of genetically engineered mouse models of cancer has begun to shed light on these context-dependent tumor suppressor activities. By using techniques that not only toggle "off" tumor suppressor genes in nascent tumors, but also facilitate the timely restoration of gene function "back-on again" in disease specific contexts, precise mechanisms of tumor suppression can be revealed in an unbiased manner. This review discusses the development and implementation of genetic systems designed to toggle tumor suppressor genes off and back-on again and their potential to uncover the tumor suppressor's tale.
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Affiliation(s)
- Jonuelle Acosta
- Biomedical Graduate Studies Program in Cellular and Molecular Biology, Perelman School of Medicine, University of Pennsylvania, 421 Curie Blvd., 751 BRB II/III, Philadelphia, PA, 19104-6160, USA
| | - Walter Wang
- Vagelos Scholars Program, School of Arts and Sciences, University of Pennsylvania, 421 Curie Blvd., 751 BRB II/III, Philadelphia, PA, 19104-6160, USA
| | - David M Feldser
- Biomedical Graduate Studies Program in Cellular and Molecular Biology, Perelman School of Medicine, University of Pennsylvania, 421 Curie Blvd., 751 BRB II/III, Philadelphia, PA, 19104-6160, USA. .,Department of Cancer Biology, University of Pennsylvania, 421 Curie Blvd., 751 BRB II/III, Philadelphia, PA, 19104-6160, USA. .,Abramson Family Cancer Research Institute, University of Pennsylvania, 421 Curie Blvd., 751 BRB II/III, Philadelphia, PA, 19104-6160, USA.
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49
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Lateral cerebellum is preferentially sensitive to high sonic hedgehog signaling and medulloblastoma formation. Proc Natl Acad Sci U S A 2018. [PMID: 29531057 DOI: 10.1073/pnas.1717815115] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The main cell of origin of the Sonic hedgehog (SHH) subgroup of medulloblastoma (MB) is granule cell precursors (GCPs), a SHH-dependent transient amplifying population in the developing cerebellum. SHH-MBs can be further subdivided based on molecular and clinical parameters, as well as location because SHH-MBs occur preferentially in the lateral cerebellum (hemispheres). Our analysis of adult patient data suggests that tumors with Smoothened (SMO) mutations form more specifically in the hemispheres than those with Patched 1 (PTCH1) mutations. Using sporadic mouse models of SHH-MB with the two mutations commonly seen in adult MB, constitutive activation of Smo (SmoM2) or loss-of-Ptch1, we found that regardless of timing of induction or type of mutation, tumors developed primarily in the hemispheres, with SmoM2-mutants indeed showing a stronger specificity. We further uncovered that GCPs in the hemispheres are more susceptible to high-level SHH signaling compared with GCPs in the medial cerebellum (vermis), as more SmoM2 or Ptch1-mutant hemisphere cells remain undifferentiated and show increased tumorigenicity when transplanted. Finally, we identified location-specific GCP gene-expression profiles, and found that deletion of the genes most highly expressed in the hemispheres (Nr2f2) or vermis (Engrailed1) showed opposing effects on GCP differentiation. Our studies thus provide insights into intrinsic differences within GCPs that impact on SHH-MB progression.
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50
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González-Rosa JM, Sharpe M, Field D, Soonpaa MH, Field LJ, Burns CE, Burns CG. Myocardial Polyploidization Creates a Barrier to Heart Regeneration in Zebrafish. Dev Cell 2018; 44:433-446.e7. [PMID: 29486195 PMCID: PMC5830170 DOI: 10.1016/j.devcel.2018.01.021] [Citation(s) in RCA: 174] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 12/11/2017] [Accepted: 01/26/2018] [Indexed: 01/07/2023]
Abstract
Correlative evidence suggests that polyploidization of heart muscle, which occurs naturally in post-natal mammals, creates a barrier to heart regeneration. Here, we move beyond a correlation by demonstrating that experimental polyploidization of zebrafish cardiomyocytes is sufficient to suppress their proliferative potential during regeneration. Initially, we determined that zebrafish myocardium becomes susceptible to polyploidization upon transient cytokinesis inhibition mediated by dominant-negative Ect2. Using a transgenic strategy, we generated adult animals containing mosaic hearts composed of differentially labeled diploid and polyploid-enriched cardiomyocyte populations. Diploid cardiomyocytes outcompeted their polyploid neighbors in producing regenerated heart muscle. Moreover, hearts composed of equivalent proportions of diploid and polyploid cardiomyocytes failed to regenerate altogether, demonstrating that a critical percentage of diploid cardiomyocytes is required to achieve heart regeneration. Our data identify cardiomyocyte polyploidization as a barrier to heart regeneration and suggest that mobilizing rare diploid cardiomyocytes in the human heart will improve its regenerative capacity.
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Affiliation(s)
- Juan Manuel González-Rosa
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA 02129, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Michka Sharpe
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA 02129, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Dorothy Field
- The Krannert Institute of Cardiology, the Wells Center for Pediatric Research, and Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Mark H Soonpaa
- The Krannert Institute of Cardiology, the Wells Center for Pediatric Research, and Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Loren J Field
- The Krannert Institute of Cardiology, the Wells Center for Pediatric Research, and Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Caroline E Burns
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA 02129, USA; Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
| | - C Geoffrey Burns
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA 02129, USA; Harvard Medical School, Boston, MA 02115, USA.
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