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Pinglay S, Lalanne JB, Daza RM, Koeppel J, Li X, Lee DS, Shendure J. Multiplex generation and single cell analysis of structural variants in a mammalian genome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.22.576756. [PMID: 38405830 PMCID: PMC10888807 DOI: 10.1101/2024.01.22.576756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
The functional consequences of structural variants (SVs) in mammalian genomes are challenging to study. This is due to several factors, including: 1) their numerical paucity relative to other forms of standing genetic variation such as single nucleotide variants (SNVs) and short insertions or deletions (indels); 2) the fact that a single SV can involve and potentially impact the function of more than one gene and/or cis regulatory element; and 3) the relative immaturity of methods to generate and map SVs, either randomly or in targeted fashion, in in vitro or in vivo model systems. Towards addressing these challenges, we developed Genome-Shuffle-seq, a straightforward method that enables the multiplex generation and mapping of several major forms of SVs (deletions, inversions, translocations) throughout a mammalian genome. Genome-Shuffle-seq is based on the integration of "shuffle cassettes" to the genome, wherein each shuffle cassette contains components that facilitate its site-specific recombination (SSR) with other integrated shuffle cassettes (via Cre-loxP), its mapping to a specific genomic location (via T7-mediated in vitro transcription or IVT), and its identification in single-cell RNA-seq (scRNA-seq) data (via T7-mediated in situ transcription or IST). In this proof-of-concept, we apply Genome-Shuffle-seq to induce and map thousands of genomic SVs in mouse embryonic stem cells (mESCs) in a single experiment. Induced SVs are rapidly depleted from the cellular population over time, possibly due to Cre-mediated toxicity and/or negative selection on the rearrangements themselves. Leveraging T7 IST of barcodes whose positions are already mapped, we further demonstrate that we can efficiently genotype which SVs are present in association with each of many single cell transcriptomes in scRNA-seq data. Finally, preliminary evidence suggests our method may be a powerful means of generating extrachromosomal circular DNAs (ecDNAs). Looking forward, we anticipate that Genome-Shuffle-seq may be broadly useful for the systematic exploration of the functional consequences of SVs on gene expression, the chromatin landscape, and 3D nuclear architecture. We further anticipate potential uses for in vitro modeling of ecDNAs, as well as in paving the path to a minimal mammalian genome.
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Affiliation(s)
- Sudarshan Pinglay
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Seattle Hub for Synthetic Biology, Seattle, WA, USA
| | | | - Riza M Daza
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Seattle Hub for Synthetic Biology, Seattle, WA, USA
| | | | - Xiaoyi Li
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - David S Lee
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Seattle Hub for Synthetic Biology, Seattle, WA, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
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2
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Yao F, Huang S, Liu J, Tan C, Xu M, Wang D, Huang M, Zhu Y, Huang X, He S. Deletion of ARGLU1 causes global defects in alternative splicing in vivo and mouse cortical malformations primarily via apoptosis. Cell Death Dis 2023; 14:543. [PMID: 37612280 PMCID: PMC10447433 DOI: 10.1038/s41419-023-06071-w] [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: 02/14/2023] [Revised: 08/01/2023] [Accepted: 08/15/2023] [Indexed: 08/25/2023]
Abstract
Haploinsufficient mutation in arginine and glutamine-rich protein 1 (Arglu1), a newly identified pre-mRNA splicing regulator, may be linked to neural developmental disorders associated with mental retardation and epilepsy in human patients, but the underlying causes remain elusive. Here we show that ablation of Arglu1 promotes radial glial cell (RG) detachment from the ventricular zone (VZ), leading to ectopic localized RGs in the mouse embryonic cortex. Although they remain proliferative, ectopic progenitors, as well as progenitors in the VZ, exhibit prolonged mitosis, p53 upregulation and cell apoptosis, leading to reduced neuron production, neuronal loss and microcephaly. RNA seq analysis reveals widespread changes in alternative splicing in the mutant mouse embryonic cortex, preferentially affecting genes involved in neuronal functions. Mdm2 and Mdm4 are found to be alternatively spliced at the exon 3 and exon 5 respectively, leading to absence of the p53-binding domain and nonsense-mediated mRNA decay (NMD) and thus relieve inhibition of p53. Removal of p53 largely rescues the microcephaly caused by deletion of Arglu1. Our findings provide mechanistic insights into cortical malformations of human patients with Arglu1 haploinsufficient mutation.
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Affiliation(s)
- Fenyong Yao
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Pudong New District, 201210, Shanghai, China
| | - Shisheng Huang
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Pudong New District, 201210, Shanghai, China
- Institute of Neuroscience, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jiahui Liu
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Pudong New District, 201210, Shanghai, China
| | - Chunhua Tan
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Pudong New District, 201210, Shanghai, China
| | - Mengqi Xu
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Pudong New District, 201210, Shanghai, China
| | - Dengkui Wang
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Pudong New District, 201210, Shanghai, China
| | - Maoqing Huang
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Pudong New District, 201210, Shanghai, China
| | - Yiyao Zhu
- School of Information Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Pudong New District, 201210, Shanghai, China
| | - Xingxu Huang
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Pudong New District, 201210, Shanghai, China.
| | - Shuijin He
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Pudong New District, 201210, Shanghai, China.
- Shanghai Clinical Research and Trial Center, 201210, Shanghai, China.
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3
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Rashbrook VS, Brash JT, Ruhrberg C. Cre toxicity in mouse models of cardiovascular physiology and disease. NATURE CARDIOVASCULAR RESEARCH 2022; 1:806-816. [PMID: 37692772 PMCID: PMC7615056 DOI: 10.1038/s44161-022-00125-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 07/27/2022] [Indexed: 09/12/2023]
Abstract
The Cre-LoxP system provides a widely used method for studying gene requirements in the mouse as the main mammalian genetic model organism. To define the molecular and cellular mechanisms that underlie cardiovascular development, function and disease, various mouse strains have been engineered that allow Cre-LoxP-mediated gene targeting within specific cell types of the cardiovascular system. Despite the usefulness of this system, evidence is accumulating that Cre activity can have toxic effects in cells, independently of its ability to recombine pairs of engineered LoxP sites in target genes. Here, we have gathered published evidence for Cre toxicity in cells and tissues relevant to cardiovascular biology and provide an overview of mechanisms proposed to underlie Cre toxicity. Based on this knowledge, we propose that each study utilising the Cre-LoxP system to investigate gene function in the cardiovascular system should incorporate appropriate controls to account for Cre toxicity.
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Affiliation(s)
- Victoria S. Rashbrook
- UCL Institute of Ophthalmology, University College London, 11-43 Bath Street, London EC1V 9EL, UK
| | - James T. Brash
- UCL Institute of Ophthalmology, University College London, 11-43 Bath Street, London EC1V 9EL, UK
| | - Christiana Ruhrberg
- UCL Institute of Ophthalmology, University College London, 11-43 Bath Street, London EC1V 9EL, UK
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4
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Erben L, Welday JP, Murphy R, Buonanno A. Toxic and Phenotypic Effects of AAV_Cre Used to Transduce Mesencephalic Dopaminergic Neurons. Int J Mol Sci 2022; 23:9462. [PMID: 36012727 PMCID: PMC9408874 DOI: 10.3390/ijms23169462] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/12/2022] [Accepted: 08/15/2022] [Indexed: 11/16/2022] Open
Abstract
A popular approach to spatiotemporally target genes using the loxP/Cre recombination system is stereotaxic microinjection of adeno-associated virus (AAV) expressing Cre recombinase (AAV_Cre) in specific neuronal structures. Here, we report that AAV_Cre microinjection in the ventral tegmental area (VTA) of ErbB4 Cyt-1-floxed (ErbB4 Cyt-1fl/fl) mice at titers commonly used in the literature (~1012-1013 GC/mL) can have neurotoxic effects on dopaminergic neurons and elicit behavioral abnormalities. However, these effects of AAV_Cre microinjection are independent of ErbB4 Cyt-1 recombination because they are also observed in microinjected wild-type (WT) controls. Mice microinjected with AAV_Cre (1012-1013 GC/mL) exhibit reductions of tyrosine hydroxylase (TH) and dopamine transporter (DAT) expression, loss of dopaminergic neurons, and they behaviorally become hyperactive, fail to habituate in the open field and exhibit sensorimotor gating deficits compared to controls microinjected with AAV_GFP. Importantly, these AAV_Cre non-specific effects are: (1) independent of serotype, (2) occur with vectors expressing either Cre or Cre-GFP fusion protein and (3) preventable by reducing viral titers by 1000-fold (1010 GC/mL), which retains sufficient recombination activity to target floxed genes. Our studies emphasize the importance of including AAV_Cre-injected WT controls in experiments because recombination-independent effects on gene expression, neurotoxicity and behaviors could be erroneously attributed to consequences of gene ablation.
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Affiliation(s)
| | | | | | - Andres Buonanno
- Section on Molecular Neurobiology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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5
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Chemogenetics as a neuromodulatory approach to treating neuropsychiatric diseases and disorders. Mol Ther 2022; 30:990-1005. [PMID: 34861415 PMCID: PMC8899595 DOI: 10.1016/j.ymthe.2021.11.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 11/12/2021] [Accepted: 11/29/2021] [Indexed: 01/01/2023] Open
Abstract
Chemogenetics enables precise, non-invasive, and reversible modulation of neural activity via the activation of engineered receptors that are pharmacologically selective to endogenous or exogenous ligands. With recent advances in therapeutic gene delivery, chemogenetics is poised to support novel interventions against neuropsychiatric diseases and disorders. To evaluate its translational potential, we performed a scoping review of applications of chemogenetics that led to the reversal of molecular and behavioral deficits in studies relevant to neuropsychiatric diseases and disorders. In this review, we present these findings and discuss the potential and challenges for using chemogenetics as a precision medicine-based neuromodulation strategy.
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6
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Site-Specific Recombination with Inverted Target Sites: A Cautionary Tale of Dicentric and Acentric Chromosomes. Genetics 2020; 215:923-930. [PMID: 32586890 DOI: 10.1534/genetics.120.303394] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 06/22/2020] [Indexed: 11/18/2022] Open
Abstract
Site-specific recombinases are widely used tools for analysis of genetics, development, and cell biology, and many schemes have been devised to alter gene expression by recombinase-mediated DNA rearrangements. Because the FRT and lox target sites for the commonly used FLP and Cre recombinases are asymmetrical, and must pair in the same direction to recombine, construct design must take into account orientation of the target sites. Both direct and inverted configurations have been used. However, the outcome of recombination between target sites on sister chromatids is frequently overlooked. This is especially consequential with inverted target sites, where exchange between oppositely oriented target sites on sisters will produce dicentric and acentric chromosomes. By using constructs that have inverted target sites in Drosophila melanogaster and in mice, we show here that dicentric chromosomes are produced in the presence of recombinase, and that the frequency of this event is quite high. The negative effects on cell viability and behavior can be significant, and should be considered when using such constructs.
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7
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Altamura S, Vegi NM, Hoppe PS, Schroeder T, Aichler M, Walch A, Okreglicka K, Hültner L, Schneider M, Ladinig C, Kuklik-Roos C, Mysliwietz J, Janik D, Neff F, Rathkolb B, de Angelis MTH, Buske C, Silva ARD, Muedder K, Conrad M, Ganz T, Kopf M, Muckenthaler MU, Bornkamm GW. Glutathione peroxidase 4 and vitamin E control reticulocyte maturation, stress erythropoiesis and iron homeostasis. Haematologica 2019; 105:937-950. [PMID: 31248967 PMCID: PMC7109755 DOI: 10.3324/haematol.2018.212977] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Accepted: 06/20/2019] [Indexed: 12/27/2022] Open
Abstract
Glutathione peroxidase 4 (GPX4) is unique as it is the only enzyme that can prevent detrimental lipid peroxidation in vivo by reducing lipid peroxides to the respective alcohols thereby stabilizing oxidation products of unsaturated fatty acids. During reticulocyte maturation, lipid peroxidation mediated by 15-lipoxygenase in humans and rabbits and by 12/15-lipoxygenase (ALOX15) in mice was considered the initiating event for the elimination of mitochondria but is now known to occur through mitophagy. Yet, genetic ablation of the Alox15 gene in mice failed to provide evidence for this hypothesis. We designed a different genetic approach to tackle this open conundrum. Since either other lipoxygenases or non-enzymatic autooxidative mechanisms may compensate for the loss of Alox15, we asked whether ablation of Gpx4 in the hematopoietic system would result in the perturbation of reticulocyte maturation. Quantitative assessment of erythropoiesis indices in the blood, bone marrow (BM) and spleen of chimeric mice with Gpx4 ablated in hematopoietic cells revealed anemia with an increase in the fraction of erythroid precursor cells and reticulocytes. Additional dietary vitamin E depletion strongly aggravated the anemic phenotype. Despite strong extramedullary erythropoiesis reticulocytes failed to mature and accumulated large autophagosomes with engulfed mitochondria. Gpx4-deficiency in hematopoietic cells led to systemic hepatic iron overload and simultaneous severe iron demand in the erythroid system. Despite extremely high erythropoietin and erythroferrone levels in the plasma, hepcidin expression remained unchanged. Conclusively, perturbed reticulocyte maturation in response to Gpx4 loss in hematopoietic cells thus causes ineffective erythropoiesis, a phenotype partially masked by dietary vitamin E supplementation.
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Affiliation(s)
- Sandro Altamura
- Department of Pediatric Hematology, Oncology and Immunology - University of Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit, Heidelberg, Germany
| | - Naidu M Vegi
- Institute of Experimental Cancer Research, Universitätsklinikum Ulm, Ulm, Germany
| | - Philipp S Hoppe
- Department of Biosystems Bioscience and Engineering, ETH Zürich, Basel, Switzerland
| | - Timm Schroeder
- Department of Biosystems Bioscience and Engineering, ETH Zürich, Basel, Switzerland
| | - Michaela Aichler
- Research Unit Analytical Pathology, Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
| | - Axel Walch
- Research Unit Analytical Pathology, Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
| | | | - Lothar Hültner
- Institute of Clinical Molecular Biology and Tumor Genetics, Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), München, Germany
| | - Manuela Schneider
- Institute for Stroke and Dementia Research (ISD), Klinikum der Universität München, München, Germany
| | - Camilla Ladinig
- Institute of Clinical Molecular Biology and Tumor Genetics, Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), München, Germany
| | - Cornelia Kuklik-Roos
- Institute of Clinical Molecular Biology and Tumor Genetics, Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), München, Germany
| | - Josef Mysliwietz
- Institute of Molecular Immunology, Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), München, Germany
| | - Dirk Janik
- Research Unit Analytical Pathology, Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
| | - Frauke Neff
- Research Unit Analytical Pathology, Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
| | - Birgit Rathkolb
- Institute of Molecular Animal Breeding and Biotechnology, Ludwig-Maximilians-Universität München, Genzentum, München, Germany.,Institute of Experimental Genetics, Geman Mouse Clinic (GMC), Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany.,German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Mar Tin Hrabé de Angelis
- Institute of Experimental Genetics, Geman Mouse Clinic (GMC), Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany.,German Center for Diabetes Research (DZD), Neuherberg, Germany.,Chair of Experimental Genetics, School of Life Science Weihenstephan, Technische Universität München, Freising, Germany
| | - Christian Buske
- Institute of Experimental Cancer Research, Universitätsklinikum Ulm, Ulm, Germany
| | - Ana Rita da Silva
- Department of Pediatric Hematology, Oncology and Immunology - University of Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit, Heidelberg, Germany
| | - Katja Muedder
- Department of Pediatric Hematology, Oncology and Immunology - University of Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit, Heidelberg, Germany
| | - Marcus Conrad
- Institute of Developmental Genetics, Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
| | - Tomas Ganz
- Departments of Medicine and Pathology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Manfred Kopf
- Institute of Molecular Health Sciences, ETH Zurich, Zürich, Switzerland
| | - Martina U Muckenthaler
- Department of Pediatric Hematology, Oncology and Immunology - University of Heidelberg, Heidelberg, Germany.,Molecular Medicine Partnership Unit, Heidelberg, Germany
| | - Georg W Bornkamm
- Institute of Clinical Molecular Biology and Tumor Genetics, Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), München, Germany
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8
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Rezai Amin S, Gruszczynski C, Guiard BP, Callebert J, Launay JM, Louis F, Betancur C, Vialou V, Gautron S. Viral vector-mediated Cre recombinase expression in substantia nigra induces lesions of the nigrostriatal pathway associated with perturbations of dopamine-related behaviors and hallmarks of programmed cell death. J Neurochem 2019; 150:330-340. [PMID: 30748001 DOI: 10.1111/jnc.14684] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 02/04/2019] [Accepted: 02/06/2019] [Indexed: 02/03/2023]
Abstract
Cre/loxP recombination is a widely used approach to study gene function in vivo, using mice models expressing the Cre recombinase under the control of specific promoters or through viral delivery of Cre-expressing constructs. A profuse literature on transgenic mouse lines points out the deleterious effects of Cre expression in various cell types and tissues, presumably by acting on illegitimate loxP-like sites present in the genome. However, most studies reporting the consequences of Cre-lox gene invalidation often omit adequate controls to exclude the potential toxic effects of Cre, compromising the interpretation of data. In this study, we report the anatomical, neurochemical, and behavioral consequences in mice of adeno-associated virus (AAV)-mediated Cre expression in the dopaminergic nuclei substantia nigra, at commonly used viral titers (3 × 109 genome copies/0.3 μL or 2 × 109 genome copies/0.6 μL). We found that injecting AAV-eGFP-Cre into the SN engendered drastic and reproducible modifications of behavior, with increased basal locomotor activity as well as impaired locomotor response to cocaine compared to AAV-eGFP-injected controls. Cre expression in the SN induced a massive decrease in neuronal populations of both pars compacta and pars reticulata and dopamine depletion in the nigrostriatal pathway. This anatomical injury was associated with typical features of programmed cell death, including an increase in DNA break markers, evidence of apoptosis, and disrupted macroautophagy. These observations underscore the need for careful control of Cre toxicity in the brain and the reassessment of previous studies. In addition, our findings suggest that Cre-mediated ablation may constitute an efficient tool to explore the function of specific cell populations and areas in the brain, and the impact of neurodegeneration in these populations.
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Affiliation(s)
- Sara Rezai Amin
- Sorbonne Université, INSERM, CNRS, Neuroscience Paris Seine, Institut de Biologie Paris Seine, Paris, France
| | - Carole Gruszczynski
- Sorbonne Université, INSERM, CNRS, Neuroscience Paris Seine, Institut de Biologie Paris Seine, Paris, France
| | - Bruno P Guiard
- Université de Toulouse, CNRS, Centre de Recherches sur la Cognition Animale, Centre de Biologie Intégrative, Toulouse, France
| | - Jacques Callebert
- INSERM U942, Hôpital Lariboisière, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Jean-Marie Launay
- INSERM U942, Hôpital Lariboisière, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Franck Louis
- Sorbonne Université, INSERM, CNRS, Neuroscience Paris Seine, Institut de Biologie Paris Seine, Paris, France
| | - Catalina Betancur
- Sorbonne Université, INSERM, CNRS, Neuroscience Paris Seine, Institut de Biologie Paris Seine, Paris, France
| | - Vincent Vialou
- Sorbonne Université, INSERM, CNRS, Neuroscience Paris Seine, Institut de Biologie Paris Seine, Paris, France
| | - Sophie Gautron
- Sorbonne Université, INSERM, CNRS, Neuroscience Paris Seine, Institut de Biologie Paris Seine, Paris, France
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9
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Chen Y, Anastassiadis K, Kranz A, Stewart AF, Arndt K, Waskow C, Yokoyama A, Jones K, Neff T, Lee Y, Ernst P. MLL2, Not MLL1, Plays a Major Role in Sustaining MLL-Rearranged Acute Myeloid Leukemia. Cancer Cell 2017; 31:755-770.e6. [PMID: 28609655 PMCID: PMC5598468 DOI: 10.1016/j.ccell.2017.05.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Revised: 03/09/2017] [Accepted: 05/05/2017] [Indexed: 01/11/2023]
Abstract
The MLL1 histone methyltransferase gene undergoes many distinct chromosomal rearrangements to yield poor-prognosis leukemia. The remaining wild-type allele is most commonly, but not always, retained. To what extent the wild-type allele contributes to leukemogenesis is unclear. Here we show, using rigorous, independent animal models, that endogenous MLL1 is dispensable for MLL-rearranged leukemia. Potential redundancy was addressed by co-deleting the closest paralog, Mll2. Surprisingly, Mll2 deletion alone had a significant impact on survival of MLL-AF9-transformed cells, and additional Mll1 loss further reduced viability and proliferation. We show that MLL1/MLL2 collaboration is not through redundancy, but regulation of distinct pathways. These findings highlight the relevance of MLL2 as a drug target in MLL-rearranged leukemia and suggest its broader significance in AML.
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Affiliation(s)
- Yufei Chen
- Department of Pediatrics, Section of Hematology/Oncology/BMT, University of Colorado, Denver/Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Konstantinos Anastassiadis
- Genomics and Stem Cell Engineering, Biotechnology Center, Technische Universität Dresden, BioInnovations Zentrum, Tatzberg 47, Dresden 01307, Germany
| | - Andrea Kranz
- Genomics and Stem Cell Engineering, Biotechnology Center, Technische Universität Dresden, BioInnovations Zentrum, Tatzberg 47, Dresden 01307, Germany
| | - A Francis Stewart
- Genomics and Stem Cell Engineering, Biotechnology Center, Technische Universität Dresden, BioInnovations Zentrum, Tatzberg 47, Dresden 01307, Germany
| | - Kathrin Arndt
- Regeneration in Hematopoiesis and Animal Models in Hematopoiesis, Institute for Immunology, Medical Faculty, Technische Universität Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Claudia Waskow
- Regeneration in Hematopoiesis and Animal Models in Hematopoiesis, Institute for Immunology, Medical Faculty, Technische Universität Dresden, Fetscherstrasse 74, 01307 Dresden, Germany
| | - Akihiko Yokoyama
- Tsuruoka Metabolomics Laboratory, National Cancer Center, Mizukami 246-2, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan
| | - Kenneth Jones
- Department of Pediatrics, Section of Hematology/Oncology/BMT, University of Colorado, Denver/Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Tobias Neff
- Department of Pediatrics, Section of Hematology/Oncology/BMT, University of Colorado, Denver/Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Yoo Lee
- Department of Pediatrics, Section of Hematology/Oncology/BMT, University of Colorado, Denver/Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Patricia Ernst
- Department of Pediatrics, Section of Hematology/Oncology/BMT, University of Colorado, Denver/Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Pharmacology, University of Colorado, Denver/Anschutz Medical Campus, Aurora, CO 80045, USA.
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10
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Abstract
Technical advances in the development of organoid systems enable cell lines, primary adult cells, or stem or progenitor cells to develop into diverse, multicellular entities, which can self-renew, self-organize, and differentiate. These 3D organoid cultures have proven to be of value in increasing our understanding of the biology of disease and offer the potential of regenerative and genetic therapies. The successful application of 3D organoids derived from adult tissue into urological cancer research can further our understanding of these diseases and could also provide preclinical cancer models to realize the precision medicine paradigm by therapeutic screening of individual patient samples ex vivo. Kidney organoids derived from induced pluripotent stem cells provide personalized biomarkers, which can be correlated with genetic and clinical information. Organoid models can also improve our comprehension of aspects of particular diseases; for example, in prostate cancer, 3D organoids can aid in the identification of tumour-initiating cells from an epithelial cell lineage. Furthermore, kidney organoid differentiation from human pluripotent stem cells enables gene editing to model disease in kidney tubular epithelial cells. State-of-the-art human organoid cultures have potential as tools in basic and clinical research in renal, bladder, and prostatic diseases.
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Affiliation(s)
- Shangqian Wang
- Human Oncology and Pathogenesis Program, Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA.,Urology Department, the First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Dong Gao
- Human Oncology and Pathogenesis Program, Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA.,Key Laboratory of Systems Biology,CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Yu Chen
- Human Oncology and Pathogenesis Program, Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA.,Genitourinary Oncology Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA.,Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, New York, New York 10065, USA
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11
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Abstract
Metastasis is often modeled by xenotransplantation of cell lines in immunodeficient mice. A wealth of information about tumor cell behavior in the new environment is obtained from these efforts. Yet by design, this approach is "tumor-centric," as it focuses on cell-autonomous determinants of human tumor dissemination in mouse tissues, in effect using the animal body as a sophisticated "Petri dish" providing nutrients and support for tumor growth. Transgenic or gene knockout mouse models of cancer allow the study of tumor spread as a systemic disease and offer a complimentary approach for studying the natural history of cancer. This introduction is aimed at describing the overall methodological approach to studying metastasis in genetically modified mice, with a particular focus on using animals with regulated expression of potent human oncogenes in the breast.
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12
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Lee SH, Shen MM. Cell types of origin for prostate cancer. Curr Opin Cell Biol 2015; 37:35-41. [PMID: 26506127 DOI: 10.1016/j.ceb.2015.10.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 10/06/2015] [Indexed: 12/22/2022]
Abstract
Analyses of cell types of origin for prostate cancer should result in new insights into mechanisms of tumor initiation, and may lead to improved prognosis and selection of appropriate therapies. Here, we review studies using a range of methodologies to investigate the cell of origin for mouse and human prostate cancer. Notably, analyses using tissue recombination assays support basal epithelial cells as a cell of origin, whereas in vivo lineage-tracing studies in genetically-engineered mice implicate luminal cells. We describe how these results can be potentially reconciled by a conceptual distinction between cells of origin and cells of mutation, and outline how new experimental approaches can address the potential relationship between cell types of origin and disease outcome.
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Affiliation(s)
- Suk Hyung Lee
- Department of Medicine, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA; Department of Genetics & Development, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA; Department of Urology, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA; Department of Systems Biology, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Michael M Shen
- Department of Medicine, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA; Department of Genetics & Development, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA; Department of Urology, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA; Department of Systems Biology, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA.
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13
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Miao Y, Cui L, Chen Z, Zhang L. Gene expression profiling of DMU-212-induced apoptosis and anti-angiogenesis in vascular endothelial cells. PHARMACEUTICAL BIOLOGY 2015; 54:660-666. [PMID: 26428916 DOI: 10.3109/13880209.2015.1071414] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
CONTEXT trans-3,4,5,4'-Tetramethoxystilbene (DMU-212), an derivative of resveratrol, shows strong antiproliferative activities against many cancer cells. In our previous study, we demonstrated that DMU-212 possesses potent proapoptosis and antiangiogenesis effects on vascular endothelial cells (VECs), which made it a promising agent for the treatment of angiogenesis-related diseases. OBJECTIVE We studied the gene expression profile of DMU-212-treated VECs to gain further insight into the mechanisms by which DMU-212 exerts its potent pro-apoptosis and antiangiogenesis effects. MATERIALS AND METHODS The potential changes in the gene expression of VECs incubated with DMU-212 were identified and analyzed using the Affymetrix HG-U133 Plus 1.0 array. In addition, the gene expression profile was validated by quantitative real-time PCR (qRT-PCR) analysis for seven of those altered genes. RESULTS AND CONCLUSION DMU-212 was found to regulate a diverse range of genes, including cytokines (IL8, selectin E, MPZL2, EGR1, CCL20, ITGB8, CXCL1, VCAM1, KITLG, and AREG), transport proteins (TRPC4, SLC41A2, SLC17A5, and CREB5), metabolism (CYP1B1, CYP1A1, PDK4, CSNK1G1, MVK, TCEB3C, and CDKN3), enzymes (RAB23, SPHK1, CHSY3, PLAU, PLA2G4C, and MMP10), and genes involved in signal transduction (TMEM217, DUSP8, and SPRY4), chromosome organization (HIST1H2BH and GEM), cell migration and angiogenesis (ERRFI1, HBEGF, and NEDD9), and apoptosis (TNFSF15, TNFRSF9, CD274, BCL2L11, BIRC3, TNFAIP3, and TIFA), as well as other genes with unknown function (PGM5P2, SNORD1142, LOC151760, KRTAP5-2, C1orf110, SNORA14A, MIR31, C2CD4B, SCARNA4, C2orf66, SC4MOL, LOC644714, and LOC283392). This is the first application of microarray technique to investigate and analyze the profile of genes regulated by DMU-212 in VECs. Our results lead to an increased understanding of the signaling pathways involved in DMU-212-induced apoptosis and antiangiogenesis.
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Affiliation(s)
- YiMing Miao
- a College of Bioengineering, Henan University of Technology , Zhengzhou , China
| | - LiuQing Cui
- a College of Bioengineering, Henan University of Technology , Zhengzhou , China
| | - ZhiQiang Chen
- a College of Bioengineering, Henan University of Technology , Zhengzhou , China
| | - Lu Zhang
- a College of Bioengineering, Henan University of Technology , Zhengzhou , China
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14
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Beta-catenin is vital for the integrity of mouse embryonic stem cells. PLoS One 2014; 9:e86691. [PMID: 24466203 PMCID: PMC3897734 DOI: 10.1371/journal.pone.0086691] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 12/09/2013] [Indexed: 01/08/2023] Open
Abstract
β-Catenin mediated Wnt-signaling is assumed to play a major function in embryonic stem cells in maintaining their stem cell character and the exit from this unique trait. The complexity of β-catenin action and conflicting results on the role of β-catenin in maintaining the pluripotent state have made it difficult to understand its precise cellular and molecular functions. To attempt this issue we have generated new genetically modified mouse embryonic stem cell lines allowing for the deletion of β-catenin in a controlled manner by taking advantage of the Cre-ER-T2 system and analyzed the effects in a narrow time window shortly after ablation. By using this approach, rather then taking long term cultured β-catenin null cell lines we demonstrate that β-catenin is dispensable for the maintenance of pluripotency associated genes. In addition we observed that the removal of β-catenin leads to a strong increase of cell death, the appearance of multiple clustered functional centrosomes most likely due to a mis-regulation of the polo-like-kinase 2 and furthermore, alterations in chromosome segregation. Our study demonstrates the importance of β-catenin in maintaining correct cellular functions and helps to understand its role in embryonic stem cells.
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15
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Bersell K, Choudhury S, Mollova M, Polizzotti BD, Ganapathy B, Walsh S, Wadugu B, Arab S, Kühn B. Moderate and high amounts of tamoxifen in αMHC-MerCreMer mice induce a DNA damage response, leading to heart failure and death. Dis Model Mech 2013; 6:1459-69. [PMID: 23929941 PMCID: PMC3820268 DOI: 10.1242/dmm.010447] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Numerous mouse models have utilized Cre-loxP technology to modify gene expression. Adverse effects of Cre recombinase activity have been reported, including in the heart. However, the mechanisms associated with cardiac Cre toxicity are largely unknown. Here, we show that expression of Cre in cardiomyocytes induces a DNA damage response, resulting in cardiomyocyte apoptosis, cardiac fibrosis and cardiac dysfunction. In an effort to increase the recombination efficiency of a widely used tamoxifen-sensitive Cre transgene under control of the α-myosin-heavy-chain promoter (αMHC-MerCreMer), we observed myocardial dysfunction and decreased survival, which were dependent on the dose of tamoxifen injected. After excluding a Cre-independent contribution by tamoxifen, we found that Cre induced myocardial fibrosis, activation of pro-fibrotic genes and cardiomyocyte apoptosis. Examination of the molecular mechanisms showed activation of DNA damage response signaling and p53 stabilization in the absence of loxP sites, suggesting that Cre induced illegitimate DNA breaks. Cardiomyocyte apoptosis was also induced by expressing Cre using adenoviral transduction, indicating that the effect was not dependent on genomic integration of the transgene. Cre-mediated homologous recombination at loxP sites was dose-dependent and had a ceiling effect at ∼80% of cardiomyocytes showing recombination. By titrating the amount of tamoxifen to maximize recombination while minimizing animal lethality, we determined that 30 μg tamoxifen/g body weight/day injected on three consecutive days is the optimal condition for the αMHC-MerCreMer system to induce recombination in the Rosa26-lacZ strain. Our results further highlight the importance of experimental design, including the use of appropriate genetic controls for Cre expression.
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Affiliation(s)
- Kevin Bersell
- Department of Cardiology, Boston Children's Hospital, MA 02115, USA
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16
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Abstract
For tumours to develop, mutations must disrupt tissue homeostasis in favour of deregulated proliferation. Genetic lineage tracing has uncovered the behaviour of proliferating cells that underpins the maintenance of epithelial tissues and the barriers that are broken in neoplastic transformation. In this Review, we focus on new insights revealed by quantifying the behaviour of normal, preneoplastic and tumour cells in epithelia in transgenic mice and consider their potential importance in humans.
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17
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Zhu Y, Huang YF, Kek C, Bulavin DV. Apoptosis differently affects lineage tracing of Lgr5 and Bmi1 intestinal stem cell populations. Cell Stem Cell 2013; 12:298-303. [PMID: 23415913 DOI: 10.1016/j.stem.2013.01.003] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Revised: 08/22/2012] [Accepted: 01/03/2013] [Indexed: 12/12/2022]
Abstract
Emerging lineage-tracing data support the existence of several pools of intestinal stem cells (ISCs) in the adult mouse. The +4 location is known to harbor proliferative cells undergoing robust apoptosis in response to irradiation, but their relationship with recently reported ISC models is unclear. Here, we found that tamoxifen, at doses commonly used to induce lineage tracing, mimics the irradiation-induced apoptotic response of the +4 cells. We found that about 40% of apoptotic cells were Lgr5-positive whereas Bmi1-positive ISCs became sensitive to tamoxifen upon entering a proliferative state. In turn, when we suppressed apoptosis by either Bcl2 overexpression or Chk2 deletion, we found that lineage tracing of Lgr5-positive cells was efficiently reduced. In contrast, lineage tracing from Bmi1-positive ISCs was substantially increased in apoptosis-deficient backgrounds. We propose that apoptosis plays an important role in controlling lineage tracing from different ISC populations in the mouse intestine.
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Affiliation(s)
- Yunhua Zhu
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
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18
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Recombinase-mediated cassette exchange (RMCE) — A rapidly-expanding toolbox for targeted genomic modifications. Gene 2013. [DOI: 10.1016/j.gene.2012.11.016] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Murray SA, Eppig JT, Smedley D, Simpson EM, Rosenthal N. Beyond knockouts: cre resources for conditional mutagenesis. Mamm Genome 2012; 23:587-99. [PMID: 22926223 PMCID: PMC3655717 DOI: 10.1007/s00335-012-9430-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Accepted: 08/07/2012] [Indexed: 12/12/2022]
Abstract
With the effort of the International Phenotyping Consortium to produce thousands of strains with conditional potential gathering steam, there is growing recognition that it must be supported by a rich toolbox of cre driver strains. The approaches to build cre strains have evolved in both sophistication and reliability, replacing first-generation strains with tools that can target individual cell populations with incredible precision and specificity. The modest set of cre drivers generated by individual labs over the past 15+ years is now growing rapidly, thanks to a number of large-scale projects to produce new cre strains for the community. The power of this growing resource, however, depends upon the proper deep characterization of strain function, as even the best designed strain can display a variety of undesirable features that must be considered in experimental design. This must be coupled with the parallel development of informatics tools to provide functional data to the user and facilitated access to the strains through public repositories. We discuss the current progress on all of these fronts and the challenges that remain to ensure the scientific community can capitalize on the tremendous number of mouse resources at their disposal.
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Affiliation(s)
- Stephen A Murray
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA.
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