1
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Głowacki P, Tręda C, Rieske P. Regulation of CAR transgene expression to design semiautonomous CAR-T. MOLECULAR THERAPY. ONCOLOGY 2024; 32:200833. [PMID: 39184876 PMCID: PMC11344471 DOI: 10.1016/j.omton.2024.200833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
Effective transgene expression is critical for genetically engineered cell therapy. Therefore, one of CAR-T cell therapy's critical areas of interest, both in registered products and next-generation approaches is the expression of transgenes. It turns out that various constitutive promoters used in clinical products may influence CAR-T cell antitumor effectiveness and impact the manufacturing process. Furthermore, next-generation CAR-T starts to install remotely controlled inducible promoters or even autonomous expression systems, opening new ways of priming, boosting, and increasing the safety of CAR-T. In this article, a wide range of constitutive and inducible promoters has been grouped and structured, making it possible to compare their pros and cons as well as clinical usage. Finally, logic gates based on Synthetic Notch have been elaborated, demonstrating the coupling of desired external signals with genetically engineered cellular responses.
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Affiliation(s)
- Paweł Głowacki
- Department of Tumor Biology, Chair of Medical Biology, Medical University of Lodz, Zeligowskiego 7/9 Street, 90-752 Lodz, Poland
| | - Cezary Tręda
- Department of Tumor Biology, Chair of Medical Biology, Medical University of Lodz, Zeligowskiego 7/9 Street, 90-752 Lodz, Poland
- Department of Research and Development Personather Ltd, Inwestycyjna 7, 95-050 Konstantynow Lodzki, Poland
| | - Piotr Rieske
- Department of Tumor Biology, Chair of Medical Biology, Medical University of Lodz, Zeligowskiego 7/9 Street, 90-752 Lodz, Poland
- Department of Research and Development Personather Ltd, Inwestycyjna 7, 95-050 Konstantynow Lodzki, Poland
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2
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Islam F, Lewis MR, Craig JD, Leyendecker PM, Deans TL. Advancing in vivo reprogramming with synthetic biology. Curr Opin Biotechnol 2024; 87:103109. [PMID: 38520824 PMCID: PMC11162311 DOI: 10.1016/j.copbio.2024.103109] [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: 12/16/2023] [Revised: 02/23/2024] [Accepted: 02/27/2024] [Indexed: 03/25/2024]
Abstract
Reprogramming cells will play a fundamental role in shaping the future of cell therapies by developing new strategies to engineer cells for improved performance and higher-order physiological functions. Approaches in synthetic biology harness cells' natural ability to sense diverse signals, integrate environmental inputs to make decisions, and execute complex behaviors based on the health of the organism or tissue. In this review, we highlight strategies in synthetic biology to reprogram cells, and discuss how recent approaches in the delivery of modified mRNA have created new opportunities to alter cell function in vivo. Finally, we discuss how combining concepts from synthetic biology and the delivery of mRNA in vivo could provide a platform for innovation to advance in vivo cellular reprogramming.
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Affiliation(s)
- Farhana Islam
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT, USA
| | - Mitchell R Lewis
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT, USA
| | - James D Craig
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT, USA
| | - Peyton M Leyendecker
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT, USA
| | - Tara L Deans
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT, USA.
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3
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Dou DR, Zhao Y, Belk JA, Zhao Y, Casey KM, Chen DC, Li R, Yu B, Srinivasan S, Abe BT, Kraft K, Hellström C, Sjöberg R, Chang S, Feng A, Goldman DW, Shah AA, Petri M, Chung LS, Fiorentino DF, Lundberg EK, Wutz A, Utz PJ, Chang HY. Xist ribonucleoproteins promote female sex-biased autoimmunity. Cell 2024; 187:733-749.e16. [PMID: 38306984 PMCID: PMC10949934 DOI: 10.1016/j.cell.2023.12.037] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 10/03/2023] [Accepted: 12/31/2023] [Indexed: 02/04/2024]
Abstract
Autoimmune diseases disproportionately affect females more than males. The XX sex chromosome complement is strongly associated with susceptibility to autoimmunity. Xist long non-coding RNA (lncRNA) is expressed only in females to randomly inactivate one of the two X chromosomes to achieve gene dosage compensation. Here, we show that the Xist ribonucleoprotein (RNP) complex comprising numerous autoantigenic components is an important driver of sex-biased autoimmunity. Inducible transgenic expression of a non-silencing form of Xist in male mice introduced Xist RNP complexes and sufficed to produce autoantibodies. Male SJL/J mice expressing transgenic Xist developed more severe multi-organ pathology in a pristane-induced lupus model than wild-type males. Xist expression in males reprogrammed T and B cell populations and chromatin states to more resemble wild-type females. Human patients with autoimmune diseases displayed significant autoantibodies to multiple components of XIST RNP. Thus, a sex-specific lncRNA scaffolds ubiquitous RNP components to drive sex-biased immunity.
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Affiliation(s)
- Diana R Dou
- Center for Personal Dynamic Regulomes, Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yanding Zhao
- Center for Personal Dynamic Regulomes, Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Julia A Belk
- Center for Personal Dynamic Regulomes, Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yang Zhao
- Center for Personal Dynamic Regulomes, Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Kerriann M Casey
- Department of Comparative Medicine, Stanford University, Stanford, CA, USA
| | - Derek C Chen
- Center for Personal Dynamic Regulomes, Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Rui Li
- Center for Personal Dynamic Regulomes, Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Bingfei Yu
- Center for Personal Dynamic Regulomes, Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Suhas Srinivasan
- Center for Personal Dynamic Regulomes, Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Brian T Abe
- Center for Personal Dynamic Regulomes, Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Katerina Kraft
- Center for Personal Dynamic Regulomes, Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ceke Hellström
- Autoimmunity and Serology Profiling, Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden
| | - Ronald Sjöberg
- Autoimmunity and Serology Profiling, Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden
| | - Sarah Chang
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Allan Feng
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Daniel W Goldman
- Department of Medicine, Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ami A Shah
- Department of Medicine, Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Michelle Petri
- Department of Medicine, Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Lorinda S Chung
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
| | - David F Fiorentino
- Department of Dermatology, Stanford University School of Medicine, Redwood City, CA, USA
| | - Emma K Lundberg
- School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden; Departments of Bioengineering and Pathology, Stanford University, Stanford, CA, USA
| | - Anton Wutz
- Department of Biology, Institute of Molecular Health Sciences, Swiss Federal Institute of Technology, ETH Hönggerberg, Zurich, Switzerland
| | - Paul J Utz
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA; Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
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4
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Otomo J, Woltjen K, Sakurai H. Uniform transgene activation in Tet-On systems depends on sustained rtTA expression. iScience 2023; 26:107685. [PMID: 37701566 PMCID: PMC10494183 DOI: 10.1016/j.isci.2023.107685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 06/13/2023] [Accepted: 08/17/2023] [Indexed: 09/14/2023] Open
Abstract
Application of the tetracycline-inducible gene expression system (Tet-On) in human induced pluripotent stem cells (hiPSCs) has become a fundamental transgenic tool owing to its regulatable gene expression. One of the major hurdles in hiPSC application is non-uniform transgene activation. Here, we report that the supplementation of reverse tetracycline transactivator (rtTA) in polyclonal hiPSCs populations can achieve the uniform transgene activation of Tet-On. Furthermore, the choice of antibiotic selection markers connected by an internal ribosomal entry site (IRES) can influence the expression of upstream transgenes. In particular, expression of the rtTA is more uniform in cell populations when linked to puromycin as compared to neomycin, obviating the need for sub-cloning or supplementation of rtTA. Finally, to expand the range of applications, we adopted our findings to tetracycline-inducible MyoD vector (Tet-MyoD). Our Tet-MyoD promises efficient, robust, and reproducible directed myogenic differentiation of hiPSCs.
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Affiliation(s)
- Jun Otomo
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Knut Woltjen
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Hidetoshi Sakurai
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
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5
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Zhang X, Zhang Y, Wang C, Wang X. TET (Ten-eleven translocation) family proteins: structure, biological functions and applications. Signal Transduct Target Ther 2023; 8:297. [PMID: 37563110 PMCID: PMC10415333 DOI: 10.1038/s41392-023-01537-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 05/24/2023] [Accepted: 06/05/2023] [Indexed: 08/12/2023] Open
Abstract
Ten-eleven translocation (TET) family proteins (TETs), specifically, TET1, TET2 and TET3, can modify DNA by oxidizing 5-methylcytosine (5mC) iteratively to yield 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxycytosine (5caC), and then two of these intermediates (5fC and 5caC) can be excised and return to unmethylated cytosines by thymine-DNA glycosylase (TDG)-mediated base excision repair. Because DNA methylation and demethylation play an important role in numerous biological processes, including zygote formation, embryogenesis, spatial learning and immune homeostasis, the regulation of TETs functions is complicated, and dysregulation of their functions is implicated in many diseases such as myeloid malignancies. In addition, recent studies have demonstrated that TET2 is able to catalyze the hydroxymethylation of RNA to perform post-transcriptional regulation. Notably, catalytic-independent functions of TETs in certain biological contexts have been identified, further highlighting their multifunctional roles. Interestingly, by reactivating the expression of selected target genes, accumulated evidences support the potential therapeutic use of TETs-based DNA methylation editing tools in disorders associated with epigenetic silencing. In this review, we summarize recent key findings in TETs functions, activity regulators at various levels, technological advances in the detection of 5hmC, the main TETs oxidative product, and TETs emerging applications in epigenetic editing. Furthermore, we discuss existing challenges and future directions in this field.
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Affiliation(s)
- Xinchao Zhang
- Department of Pathology, Ruijin Hospital and College of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yue Zhang
- Department of Pathology, Ruijin Hospital and College of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Chaofu Wang
- Department of Pathology, Ruijin Hospital and College of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Xu Wang
- Department of Pathology, Ruijin Hospital and College of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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6
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Linesch PW, Akhtar AA, Breunig JJ. Tetracycline-Inducible and Reversible Stable Gene Expression in Human iPSC-Derived Neural Progenitors and in the Postnatal Mouse Brain. Curr Protoc 2023; 3:e792. [PMID: 37283517 PMCID: PMC10264152 DOI: 10.1002/cpz1.792] [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] [Indexed: 06/08/2023]
Abstract
Our group has developed several approaches for stable, non-viral integration of inducible transgenic elements into the genome of mammalian cells. Specifically, a piggyBac tetracycline-inducible genetic element of interest (pB-tet-GOI) plasmid system allows for stable piggyBac transposition-mediated integration into cells, identification of cells that have been transfected using a fluorescent nuclear reporter, and robust transgene activation or suppression upon the addition of doxycycline (dox) to the cell culture or the diet of the animal. Furthermore, the addition of luciferase downstream of the target gene allows for quantitative assessment of gene activity in a non-invasive manner. More recently, we have developed a transgenic system as an alternative to piggyBac called mosaic analysis by dual recombinase-mediated cassette exchange (MADR), as well as additional in vitro transfection techniques and in vivo dox chow applications. The protocols herein provide instructions for the use of this system in cell lines and in the neonatal mouse brain. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Cloning of respective genetic element of interest (GOI) into response plasmid Basic Protocol 2: In vitro nucleofection of iPSC-derived human/mouse neural progenitor cells and subsequent derivation of stable inducible cell lines Alternate Protocol: In vitro electroporation of iPSC-derived human/mouse neural progenitor cells Support Protocol: Recovery stage after in vitro transfection Basic Protocol 3: Adding doxycycline to cells to induce/reverse GOI Basic Protocol 4: Assessing gene expression in vitro by non-invasive bioluminescence imaging of luciferase activity.
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Affiliation(s)
- Paul W. Linesch
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, California
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California
| | - Aslam Abbasi Akhtar
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, California
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California
| | - Joshua J. Breunig
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, California
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California
- Division of Applied Cell Biology and Physiology, Cedars-Sinai Medical Center, Los Angeles, California
- Department of Medicine, UCLA, Los Angeles, California
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7
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Gödecke N, Herrmann S, Weichelt V, Wirth D. A Ubiquitous Chromatin Opening Element and DNA Demethylation Facilitate Doxycycline-Controlled Expression during Differentiation and in Transgenic Mice. ACS Synth Biol 2023; 12:482-491. [PMID: 36755406 PMCID: PMC9942253 DOI: 10.1021/acssynbio.2c00450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Synthetic expression cassettes provide the ability to control transgene expression in experimental animal models through external triggers, enabling the study of gene function and the modulation of endogenous regulatory networks in vivo. The performance of synthetic expression cassettes in transgenic animals critically depends on the regulatory properties of the respective chromosomal integration sites, which are affected by the remodeling of the chromatin structure during development. The epigenetic status may affect the transcriptional activity of the synthetic cassettes and even lead to transcriptional silencing, depending on the chromosomal sites and the tissue. In this study, we investigated the influence of the ubiquitous chromosome opening element (UCOE) HNRPA2B1-CBX3 and its subfragments A2UCOE and CBX3 on doxycycline-controlled expression modules within the chromosomal Rosa26 locus. While HNRPA2B1-CBX3 and A2UCOE reduced the expression of the synthetic cassettes in mouse embryonic stem cells, CBX3 stabilized the expression and facilitated doxycycline-controlled expression after in vitro differentiation. In transgenic mice, the CBX3 element protected the cassettes from overt silencing although the expression was moderate and only partially controlled by doxycycline. We demonstrate that CBX3-flanked synthetic cassettes can be activated by decitabine-mediated blockade of DNA methylation or by specific recruitment of the catalytic demethylation domain of the ten-eleven translocation protein TET1 to the synthetic promoter. This suggests that CBX3 renders the synthetic cassettes permissive for subsequent epigenetic activation, thereby supporting doxycycline-controlled expression. Together, this study reveals a strategy for overcoming epigenetic constraints of synthetic expression cassettes, facilitating externally controlled transgene expression in mice.
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Affiliation(s)
- Natascha Gödecke
- RG
Model Systems for Infection and Immunity, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Sabrina Herrmann
- RG
Model Systems for Infection and Immunity, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Viola Weichelt
- RG
Model Systems for Infection and Immunity, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Dagmar Wirth
- RG
Model Systems for Infection and Immunity, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany,Institute
of Experimental Hematology, Medical University
Hannover (MHH), 30625 Hannover, Germany,
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8
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Vipat S, Gupta D, Jonchhe S, Anderspuk H, Rothenberg E, Moiseeva TN. The non-catalytic role of DNA polymerase epsilon in replication initiation in human cells. Nat Commun 2022; 13:7099. [PMID: 36402816 PMCID: PMC9675812 DOI: 10.1038/s41467-022-34911-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 11/10/2022] [Indexed: 11/21/2022] Open
Abstract
DNA polymerase epsilon (PolE) in an enzyme essential for DNA replication. Deficiencies and mutations in PolE cause severe developmental abnormalities and cancers. Paradoxically, the catalytic domain of yeast PolE catalytic subunit is dispensable for survival, and its non-catalytic essential function is linked with replicative helicase (CMG) assembly. Less is known about the PolE role in replication initiation in human cells. Here we use an auxin-inducible degron system to study the effect of POLE1 depletion on replication initiation in U2OS cells. POLE1-depleted cells were able to assemble CMG helicase and initiate DNA synthesis that failed shortly after. Expression of POLE1 non-catalytic domain rescued this defect resulting in slow, but continuous DNA synthesis. We propose a model where in human U2OS cells POLE1/POLE2 are dispensable for CMG assembly, but essential during later steps of replication initiation. Our study provides some insights into the role of PolE in replication initiation in human cells.
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Affiliation(s)
- Sameera Vipat
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, 12618, Estonia
| | - Dipika Gupta
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, 10016, USA
| | - Sagun Jonchhe
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, 10016, USA
| | - Hele Anderspuk
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, 12618, Estonia
| | - Eli Rothenberg
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, 10016, USA
| | - Tatiana N Moiseeva
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, 12618, Estonia.
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9
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Duran AG, Schwestka M, Nazari-Shafti TZ, Neuber S, Stamm C, Gossen M. Limiting Transactivator Amounts Contribute to Transgene Mosaicism in Tet-On All-in-One Systems. ACS Synth Biol 2022; 11:2623-2635. [PMID: 35815862 DOI: 10.1021/acssynbio.2c00036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
MicroRNAs play an essential role in cell homeostasis and have been proposed as therapeutic agents. One strategy to deliver microRNAs is to genetically engineer target cells to express microRNAs of interest. However, to control dosage and timing, as well as to limit potential side-effects, microRNAs' expression should ideally be under exogenous, inducible control. Conditional expression of miRNA-based short hairpin RNAs (shRNAmirs) via gene regulatory circuits such as the Tet-system is therefore a promising strategy to control shRNAmirs' expression in research and therapy. Single vector approaches like Tet-On all-in-one designs are more compatible with potential clinical applications by providing the Tet-On system components in a single round of genetic engineering. However, all-in-one systems often come at the expense of heterogeneous and unstable expression. In this study, we aimed to understand the causes that lead to such erratic transgene expression. By using a reporter cell, we found that the degree of heterogeneity mostly correlated with reverse tetracycline transactivator (rtTA) expression levels. Moreover, the targeted integration of a potent rtTA expression cassette into a genomic safe harbor locus functionally rescued previously silenced rtTA-responsive transcription units. Overall, our results suggest that ensuring homogenous and stable rtTA expression is essential for the robust and reliable performance of future Tet-On all-in-one designs.
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Affiliation(s)
- Ana G Duran
- Institute of Active Polymers, Helmholtz-Zentrum Hereon, 14513 Teltow, Germany.,Berlin-Brandenburg School for Regenerative Therapies (BSRT), 13353 Berlin, Germany.,Berlin-Brandenburg Center for Regenerative Therapies (BCRT), 13353 Berlin, Germany.,Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin-Brandenburg Center for Regenerative Therapies, Berlin 13353, Germany
| | - Marko Schwestka
- Institute of Active Polymers, Helmholtz-Zentrum Hereon, 14513 Teltow, Germany.,Berlin-Brandenburg Center for Regenerative Therapies (BCRT), 13353 Berlin, Germany
| | - Timo Z Nazari-Shafti
- Department of Cardiothoracic and Vascular Surgery, German Heart Center Berlin, 13353 Berlin, Germany.,Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Center for Regenerative Therapies, 13353 Berlin, Germany.,German Centre for Cardiovascular Research, Partner Site Berlin, 13353 Berlin, Germany
| | - Sebastian Neuber
- Department of Cardiothoracic and Vascular Surgery, German Heart Center Berlin, 13353 Berlin, Germany.,Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Center for Regenerative Therapies, 13353 Berlin, Germany.,German Centre for Cardiovascular Research, Partner Site Berlin, 13353 Berlin, Germany
| | - Christof Stamm
- Institute of Active Polymers, Helmholtz-Zentrum Hereon, 14513 Teltow, Germany.,Department of Cardiothoracic and Vascular Surgery, German Heart Center Berlin, 13353 Berlin, Germany.,German Centre for Cardiovascular Research, Partner Site Berlin, 13353 Berlin, Germany
| | - Manfred Gossen
- Institute of Active Polymers, Helmholtz-Zentrum Hereon, 14513 Teltow, Germany.,Berlin-Brandenburg Center for Regenerative Therapies (BCRT), 13353 Berlin, Germany
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10
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Sakamoto M, Inoue M, Takeuchi A, Kobari S, Yokoyama T, Horigane SI, Takemoto-Kimura S, Abe M, Sakimura K, Kano M, Kitamura K, Fujii H, Bito H. A Flp-dependent G-CaMP9a transgenic mouse for neuronal imaging in vivo. CELL REPORTS METHODS 2022; 2:100168. [PMID: 35474964 PMCID: PMC9017135 DOI: 10.1016/j.crmeth.2022.100168] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 12/09/2021] [Accepted: 01/21/2022] [Indexed: 12/16/2022]
Abstract
Genetically encoded calcium indicators (GECIs) are widely used to measure calcium transients in neuronal somata and processes, and their use enables the determination of action potential temporal series in a large population of neurons. Here, we generate a transgenic mouse line expressing a highly sensitive green GECI, G-CaMP9a, in a Flp-dependent manner in excitatory and inhibitory neuronal subpopulations downstream of a strong CAG promoter. Combining this reporter mouse with viral or mouse genetic Flp delivery methods produces a robust and stable G-CaMP9a expression in defined neuronal populations without detectable detrimental effects. In vivo two-photon imaging reveals spontaneous and sensory-evoked calcium transients in excitatory and inhibitory ensembles with cellular resolution. Our results show that this reporter line allows long-term, cell-type-specific investigation of neuronal activity with enhanced resolution in defined populations and facilitates dissecting complex dynamics of neural networks in vivo.
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Affiliation(s)
- Masayuki Sakamoto
- Department of Neurochemistry, Graduate School of Medicine, The University of Tokyo, Hongo7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
- Department of Optical Neural and Molecular Physiology, Graduate School of Biostudies, Kyoto University, Kyoto 606-8507, Japan
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, Kyoto 606-8507, Japan
| | - Masatoshi Inoue
- Department of Neurochemistry, Graduate School of Medicine, The University of Tokyo, Hongo7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Atsuya Takeuchi
- Department of Neurophysiology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Department of Neurophysiology, School of Dentistry, Tokyo Medical and Dental University, Tokyo, Japan
| | - Shigetaka Kobari
- Department of Neurochemistry, Graduate School of Medicine, The University of Tokyo, Hongo7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Tatsushi Yokoyama
- Department of Neurochemistry, Graduate School of Medicine, The University of Tokyo, Hongo7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
- Department of Optical Neural and Molecular Physiology, Graduate School of Biostudies, Kyoto University, Kyoto 606-8507, Japan
| | - Shin-ichiro Horigane
- Department of Neurochemistry, Graduate School of Medicine, The University of Tokyo, Hongo7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
- Department of Neuroscience I, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Aichi 464-8602, Japan
- Department of Molecular/Cellular Neuroscience, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Sayaka Takemoto-Kimura
- Department of Neurochemistry, Graduate School of Medicine, The University of Tokyo, Hongo7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, Kyoto 606-8507, Japan
- Department of Neuroscience I, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Aichi 464-8602, Japan
- Department of Molecular/Cellular Neuroscience, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Manabu Abe
- Department of Animal Model Development, Brain Research Institute, Niigata University, Niigata 951-8585, Japan
| | - Kenji Sakimura
- Department of Animal Model Development, Brain Research Institute, Niigata University, Niigata 951-8585, Japan
| | - Masanobu Kano
- Department of Neurophysiology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kazuo Kitamura
- Department of Neurophysiology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
- Department of Neurophysiology, Faculty of Medicine, University of Yamanashi, Chuo, Yamanashi 409-3898, Japan
| | - Hajime Fujii
- Department of Neurochemistry, Graduate School of Medicine, The University of Tokyo, Hongo7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Haruhiko Bito
- Department of Neurochemistry, Graduate School of Medicine, The University of Tokyo, Hongo7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
- International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
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11
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Smirnov A, Battulin N. Concatenation of Transgenic DNA: Random or Orchestrated? Genes (Basel) 2021; 12:genes12121969. [PMID: 34946918 PMCID: PMC8701086 DOI: 10.3390/genes12121969] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 12/18/2022] Open
Abstract
Generation of transgenic organisms by pronuclear microinjection has become a routine procedure. However, while the process of DNA integration in the genome is well understood, we still do not know much about the recombination between transgene molecules that happens in the first moments after DNA injection. Most of the time, injected molecules are joined together in head-to-tail tandem repeats-the so-called concatemers. In this review, we focused on the possible concatenation mechanisms and how they could be studied with genetic reporters tracking individual copies in concatemers. We also discuss various features of concatemers, including palindromic junctions and repeat-induced gene silencing (RIGS). Finally, we speculate how cooperation of DNA repair pathways creates a multicopy concatenated insert.
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Affiliation(s)
- Alexander Smirnov
- Laboratory of Developmental Genetics, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia;
| | - Nariman Battulin
- Laboratory of Developmental Genetics, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia;
- Institute of Genetic Technologies, Novosibirsk State University, 630090 Novosibirsk, Russia
- Correspondence:
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12
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Furukawa A, Tanaka A, Yamaguchi S, Kosuda M, Yamana M, Nagasawa A, Kohno G, Ishihara H. Using recombinase-mediated cassette exchange to engineer MIN6 insulin-secreting cells based on a newly identified safe harbor locus. J Diabetes Investig 2021; 12:2129-2140. [PMID: 34382357 PMCID: PMC8668067 DOI: 10.1111/jdi.13646] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 08/03/2021] [Accepted: 08/09/2021] [Indexed: 12/04/2022] Open
Abstract
AIMS/INTRODUCTION Recent studies have identified genomic and transcript level changes along with alterations in insulin secretion in patients with diabetes and in rodent models of diabetes. It is important to establish an efficient system for testing functional consequences of these changes. We aimed to generate such a system using insulin-secreting MIN6 cells. MATERIALS AND METHODS MIN6 cells were first engineered to have a tetracycline-regulated expression system. Then, we used the recombination-mediated cassette exchange strategy to explore the silencing-resistant site in the genome and generated a master cell line based on this site. RESULTS We identified a site 10.5 kbps upstream from the Zxdb gene as a locus that allows homogenous transgene expression from a tetracycline responsible promoter. Placing the Flip/Frt-based platform on this locus using CRISPR/Cas9 technology generated modified MIN6 cells applicable to achieving cassette exchange on the genome. Using this cell line, we generated MIN6 subclones with over- or underexpression of glucokinase. By analyzing a mixed population of these cells, we obtained an initial estimate of effects on insulin secretion within 6 weeks. Furthermore, we generated six MIN6 cell sublines simultaneously harboring genes of inducible overexpression with unknown functions in insulin secretion, and found that Cited4 and Arhgef3 overexpressions increased and decreased insulin secretion, respectively. CONCLUSIONS We engineered MIN6 cells, which can serve as a powerful tool for testing genetic alterations associated with diabetes, and studied the molecular mechanisms of insulin secretion.
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Affiliation(s)
- Asami Furukawa
- Division of Diabetes and Metabolic DiseasesNihon University School of MedicineItabashiJapan
| | - Aya Tanaka
- Division of Diabetes and Metabolic DiseasesNihon University School of MedicineItabashiJapan
| | - Suguru Yamaguchi
- Division of Diabetes and Metabolic DiseasesNihon University School of MedicineItabashiJapan
| | - Minami Kosuda
- Division of Diabetes and Metabolic DiseasesNihon University School of MedicineItabashiJapan
| | - Midori Yamana
- Division of Diabetes and Metabolic DiseasesNihon University School of MedicineItabashiJapan
| | - Akiko Nagasawa
- Division of Diabetes and Metabolic DiseasesNihon University School of MedicineItabashiJapan
| | - Genta Kohno
- Division of Diabetes and Metabolic DiseasesNihon University School of MedicineItabashiJapan
| | - Hisamitsu Ishihara
- Division of Diabetes and Metabolic DiseasesNihon University School of MedicineItabashiJapan
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13
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Desaulniers D, Vasseur P, Jacobs A, Aguila MC, Ertych N, Jacobs MN. Integration of Epigenetic Mechanisms into Non-Genotoxic Carcinogenicity Hazard Assessment: Focus on DNA Methylation and Histone Modifications. Int J Mol Sci 2021; 22:10969. [PMID: 34681626 PMCID: PMC8535778 DOI: 10.3390/ijms222010969] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/30/2021] [Accepted: 10/04/2021] [Indexed: 12/15/2022] Open
Abstract
Epigenetics involves a series of mechanisms that entail histone and DNA covalent modifications and non-coding RNAs, and that collectively contribute to programing cell functions and differentiation. Epigenetic anomalies and DNA mutations are co-drivers of cellular dysfunctions, including carcinogenesis. Alterations of the epigenetic system occur in cancers whether the initial carcinogenic events are from genotoxic (GTxC) or non-genotoxic (NGTxC) carcinogens. NGTxC are not inherently DNA reactive, they do not have a unifying mode of action and as yet there are no regulatory test guidelines addressing mechanisms of NGTxC. To fil this gap, the Test Guideline Programme of the Organisation for Economic Cooperation and Development is developing a framework for an integrated approach for the testing and assessment (IATA) of NGTxC and is considering assays that address key events of cancer hallmarks. Here, with the intent of better understanding the applicability of epigenetic assays in chemical carcinogenicity assessment, we focus on DNA methylation and histone modifications and review: (1) epigenetic mechanisms contributing to carcinogenesis, (2) epigenetic mechanisms altered following exposure to arsenic, nickel, or phenobarbital in order to identify common carcinogen-specific mechanisms, (3) characteristics of a series of epigenetic assay types, and (4) epigenetic assay validation needs in the context of chemical hazard assessment. As a key component of numerous NGTxC mechanisms of action, epigenetic assays included in IATA assay combinations can contribute to improved chemical carcinogen identification for the better protection of public health.
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Affiliation(s)
- Daniel Desaulniers
- Environmental Health Sciences and Research Bureau, Hazard Identification Division, Health Canada, AL:2203B, Ottawa, ON K1A 0K9, Canada
| | - Paule Vasseur
- CNRS, LIEC, Université de Lorraine, 57070 Metz, France;
| | - Abigail Jacobs
- Independent at the Time of Publication, Previously US Food and Drug Administration, Rockville, MD 20852, USA;
| | - M. Cecilia Aguila
- Toxicology Team, Division of Human Food Safety, Center for Veterinary Medicine, US Food and Drug Administration, Department of Health and Human Services, Rockville, MD 20852, USA;
| | - Norman Ertych
- German Centre for the Protection of Laboratory Animals (Bf3R), German Federal Institute for Risk Assessment, Diedersdorfer Weg 1, 12277 Berlin, Germany;
| | - Miriam N. Jacobs
- Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton OX11 0RQ, UK;
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14
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Rauschendorfer T, Gurri S, Heggli I, Maddaluno L, Meyer M, Inglés-Prieto Á, Janovjak H, Werner S. Acute and chronic effects of a light-activated FGF receptor in keratinocytes in vitro and in mice. Life Sci Alliance 2021; 4:4/11/e202101100. [PMID: 34548382 PMCID: PMC8473723 DOI: 10.26508/lsa.202101100] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 09/06/2021] [Accepted: 09/07/2021] [Indexed: 11/24/2022] Open
Abstract
Optogenetic activation of FGFR2 allowed temporally precise induction of signaling and behavioural changes, but counter-regulation at multiple levels prevented a sustained response in keratinocytes. FGFs and their high-affinity receptors (FGFRs) play key roles in development, tissue repair, and disease. Because FGFRs bind overlapping sets of ligands, their individual functions cannot be determined using ligand stimulation. Here, we generated a light-activated FGFR2 variant (OptoR2) to selectively activate signaling by the major FGFR in keratinocytes. Illumination of OptoR2-expressing HEK 293T cells activated FGFR signaling with remarkable temporal precision and promoted cell migration and proliferation. In murine and human keratinocytes, OptoR2 activation rapidly induced the classical FGFR signaling pathways and expression of FGF target genes. Surprisingly, multi-level counter-regulation occurred in keratinocytes in vitro and in transgenic mice in vivo, including OptoR2 down-regulation and loss of responsiveness to light activation. These results demonstrate unexpected cell type–specific limitations of optogenetic FGFRs in long-term in vitro and in vivo settings and highlight the complex consequences of transferring optogenetic cell signaling tools into their relevant cellular contexts.
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Affiliation(s)
- Theresa Rauschendorfer
- Department of Biology, Institute of Molecular Health Sciences, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Selina Gurri
- Department of Biology, Institute of Molecular Health Sciences, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Irina Heggli
- Department of Biology, Institute of Molecular Health Sciences, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Luigi Maddaluno
- Department of Biology, Institute of Molecular Health Sciences, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | - Michael Meyer
- Department of Biology, Institute of Molecular Health Sciences, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
| | | | - Harald Janovjak
- Institute of Science and Technology (IST) Austria, Klosterneuburg, Austria .,Australian Regenerative Medicine Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Australia.,European Molecular Biology Laboratory Australia, Monash University, Clayton, Australia
| | - Sabine Werner
- Department of Biology, Institute of Molecular Health Sciences, Eidgenössische Technische Hochschule (ETH) Zurich, Zurich, Switzerland
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15
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Gurumurthy CB, Saunders TL, Ohtsuka M. Designing and generating a mouse model: frequently asked questions. J Biomed Res 2021; 35:76-90. [PMID: 33797414 PMCID: PMC8038528 DOI: 10.7555/jbr.35.20200197] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Genetically engineered mouse (GEM) models are commonly used in biomedical research. Generating GEMs involve complex set of experimental procedures requiring sophisticated equipment and highly skilled technical staff. Because of these reasons, most research institutes set up centralized core facilities where custom GEMs are created for research groups. Researchers, on the other hand, when they begin thinking about generating GEMs for their research, several questions arise in their minds. For example, what type of model(s) would be best useful for my research, how do I design them, what are the latest technologies and tools available for developing my model(s), and finally how to breed GEMs in my research. As there are several considerations and options in mouse designs, and as it is an expensive and time-consuming endeavor, careful planning upfront can ensure the highest chance of success. In this article, we provide brief answers to several frequently asked questions that arise when researchers begin thinking about generating mouse model(s) for their work.
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Affiliation(s)
- Channabasavaiah B Gurumurthy
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68106-5915, USA.,Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68106-5915, USA
| | - Thomas L Saunders
- Department of Internal Medicine, Division of Genetic Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Transgenic Animal Model Core, University of Michigan, Ann Arbor, MI 48109, USA
| | - Masato Ohtsuka
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Isehara, Kanagawa 259-1193, Japan.,The Institute of Medical Sciences, Tokai University, Isehara, Kanagawa 259-1193, Japan
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16
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Gödecke N, Herrmann S, Hauser H, Mayer-Bartschmid A, Trautwein M, Wirth D. Rational Design of Single Copy Expression Cassettes in Defined Chromosomal Sites Overcomes Intraclonal Cell-to-Cell Expression Heterogeneity and Ensures Robust Antibody Production. ACS Synth Biol 2021; 10:145-157. [PMID: 33382574 DOI: 10.1021/acssynbio.0c00519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The expression of endogenous genes as well as transgenes depends on regulatory elements within and surrounding genes as well as their epigenetic modifications. Members of a cloned cell population often show pronounced cell-to-cell heterogeneity with respect to the expression of a certain gene. To investigate the heterogeneity of recombinant protein expression we targeted cassettes into two preselected chromosomal hot-spots in Chinese hamster ovary (CHO) cells. Depending on the gene of interest and the design of the expression cassette, we found strong expression variability that could be reduced by epigenetic modifiers, but not by site-specific recruitment of the modulator dCas9-VPR. In particular, the implementation of ubiquitous chromatin opening elements (UCOEs) reduced cell-to-cell heterogeneity and concomitantly increased expression. The application of this method to recombinant antibody expression confirmed that rational design of cell lines for production of transgenes with predictable and high titers is a promising approach.
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Affiliation(s)
- Natascha Gödecke
- RG Model Systems for Infection and Immunity, Helmholtz Centre for Infection Research, Braunschweig 38124, Germany
| | - Sabrina Herrmann
- RG Model Systems for Infection and Immunity, Helmholtz Centre for Infection Research, Braunschweig 38124, Germany
| | - Hansjörg Hauser
- Staff Unit Scientific Strategy, Helmholtz Centre for Infection Research, Braunschweig 38124, Germany
| | | | | | - Dagmar Wirth
- RG Model Systems for Infection and Immunity, Helmholtz Centre for Infection Research, Braunschweig 38124, Germany
- Institute of Experimental Hematology, Medical University Hannover, Hannover 30625, Germany
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17
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Moreno E, Toussaint MJ, van Essen SC, Bongiovanni L, van Liere EA, Koster MH, Yuan R, van Deursen JM, Westendorp B, de Bruin A. E2F7 Is a Potent Inhibitor of Liver Tumor Growth in Adult Mice. Hepatology 2021; 73:303-317. [PMID: 32259305 PMCID: PMC7898887 DOI: 10.1002/hep.31259] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 03/12/2020] [Accepted: 03/19/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND AND AIMS Up-regulation of the E2F-dependent transcriptional network has been identified in nearly every human malignancy and is an important driver of tumorigenesis. Two members of the E2F family, E2F7 and E2F8, are potent repressors of E2F-dependent transcription. They are atypical in that they do not bind to dimerization partner proteins and are not controlled by retinoblastoma protein. The physiological relevance of E2F7 and E2F8 remains incompletely understood, largely because tools to manipulate their activity in vivo have been lacking. APPROACH AND RESULTS Here, we generated transgenic mice with doxycycline-controlled transcriptional activation of E2f7 and E2f8 and induced their expression during postnatal development, in adulthood, and in the context of cancer. Systemic induction of E2f7 and, to lesser extent, E2f8 transgenes in juvenile mice impaired cell proliferation, caused replication stress, DNA damage, and apoptosis, and inhibited animal growth. In adult mice, however, E2F7 and E2F8 induction was well tolerated, yet profoundly interfered with DNA replication, DNA integrity, and cell proliferation in diethylnitrosamine-induced liver tumors. CONCLUSION Collectively, our findings demonstrate that atypical E2Fs can override cell-cycle entry and progression governed by other E2F family members and suggest that this property can be exploited to inhibit proliferation of neoplastic hepatocytes when growth and development have subsided during adulthood.
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Affiliation(s)
- Eva Moreno
- Department of Biomolecular Health SciencesFaculty of Veterinary MedicineUtrecht UniversityUtrechtthe Netherlands
| | - Mathilda J.M. Toussaint
- Department of Biomolecular Health SciencesFaculty of Veterinary MedicineUtrecht UniversityUtrechtthe Netherlands
| | - Saskia C. van Essen
- Department of Biomolecular Health SciencesFaculty of Veterinary MedicineUtrecht UniversityUtrechtthe Netherlands
| | - Laura Bongiovanni
- Department of Biomolecular Health SciencesFaculty of Veterinary MedicineUtrecht UniversityUtrechtthe Netherlands
| | - Elsbeth A. van Liere
- Department of Biomolecular Health SciencesFaculty of Veterinary MedicineUtrecht UniversityUtrechtthe Netherlands
| | - Mirjam H. Koster
- Division Molecular GeneticsDepartment of PediatricsUniversity Medical Center GroningenUniversity of GroningenGroningenthe Netherlands
| | - Ruixue Yuan
- Department of Biomolecular Health SciencesFaculty of Veterinary MedicineUtrecht UniversityUtrechtthe Netherlands,Department of PathologyAcademic Medical CenterAmsterdamthe Netherlands
| | - Jan M. van Deursen
- Department of Biochemistry and Molecular BiologyMayo ClinicRochesterMN,Department of Pediatric and Adolescent MedicineMayo ClinicRochesterMN
| | - Bart Westendorp
- Department of Biomolecular Health SciencesFaculty of Veterinary MedicineUtrecht UniversityUtrechtthe Netherlands
| | - Alain de Bruin
- Department of Biomolecular Health SciencesFaculty of Veterinary MedicineUtrecht UniversityUtrechtthe Netherlands,Division Molecular GeneticsDepartment of PediatricsUniversity Medical Center GroningenUniversity of GroningenGroningenthe Netherlands
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18
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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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19
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Fitzgerald M, Livingston M, Gibbs C, Deans TL. Rosa26 docking sites for investigating genetic circuit silencing in stem cells. Synth Biol (Oxf) 2020; 5:ysaa014. [PMID: 33195816 PMCID: PMC7644442 DOI: 10.1093/synbio/ysaa014] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 08/01/2020] [Accepted: 08/04/2020] [Indexed: 12/31/2022] Open
Abstract
Approaches in mammalian synthetic biology have transformed how cells can be programmed to have reliable and predictable behavior, however, the majority of mammalian synthetic biology has been accomplished using immortalized cell lines that are easy to grow and easy to transfect. Genetic circuits that integrate into the genome of these immortalized cell lines remain functional for many generations, often for the lifetime of the cells, yet when genetic circuits are integrated into the genome of stem cells gene silencing is observed within a few generations. To investigate the reactivation of silenced genetic circuits in stem cells, the Rosa26 locus of mouse pluripotent stem cells was modified to contain docking sites for site-specific integration of genetic circuits. We show that the silencing of genetic circuits can be reversed with the addition of sodium butyrate, a histone deacetylase inhibitor. These findings demonstrate an approach to reactivate the function of genetic circuits in pluripotent stem cells to ensure robust function over many generations. Altogether, this work introduces an approach to overcome the silencing of genetic circuits in pluripotent stem cells that may enable the use of genetic circuits in pluripotent stem cells for long-term function.
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Affiliation(s)
- Michael Fitzgerald
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112, USA
| | - Mark Livingston
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112, USA
| | - Chelsea Gibbs
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112, USA
| | - Tara L Deans
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112, USA
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20
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Wahlicht T, Vièyres G, Bruns SA, Meumann N, Büning H, Hauser H, Schmitz I, Pietschmann T, Wirth D. Controlled Functional Zonation of Hepatocytes In Vitro by Engineering of Wnt Signaling. ACS Synth Biol 2020; 9:1638-1649. [PMID: 32551516 DOI: 10.1021/acssynbio.9b00435] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Key liver functions, including protein synthesis, carbohydrate metabolism, and detoxification, are performed by specific populations of hepatocytes that are defined by their relative positions within the liver lobules. On a molecular level, the functional heterogeneity with periportal and pericentral phenotypes, so-called metabolic liver zonation, is mainly established by a gradient of canonical Wnt signaling activity. Since the relevant physiological cues are missing in in vitro liver models, they fail to reflect the functional heterogeneity and thus lack many liver functions. We synthetically re-engineered Wnt signaling in murine and human hepatocytes using a doxycycline-dependent cassette for externally controlled digital expression of stabilized β-catenin. Thereby, we achieved adjustable mosaic-like activation of Wnt signaling in in vitro-cultured hepatocytes that was resistant to negative-feedback loops. This allowed the establishment of long-term-stable periportal-like and pericentral-like phenotypes that mimic the heterogeneity observed in vivo. The in vitro-zonated hepatocytes show differential expression of drug-metabolizing enzymes and associated differential toxicity and higher levels of autophagy. Furthermore, recombinant adeno-associated virus and hepatitis C virus preferentially transduce the pericentral-like zonation phenotype, suggesting a bias of these viruses that has been unappreciated to date. These tightly controlled in vivo-like systems will be important for studies evaluating aspects of liver zonation and for the assessment of drug toxicity for mouse and man.
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Affiliation(s)
- Tom Wahlicht
- Model Systems for Infection and Immunity, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Gabrielle Vièyres
- Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, 30625 Hannover, Germany
| | - Svenja A. Bruns
- Systems-Oriented Immunology and Inflammation Research, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
- Institute for Molecular and Clinical Immunology, Otto von Guericke University Magdeburg, 39106 Magdeburg, Germany
| | - Nadja Meumann
- German Center for Infection Research (DZIF), Hannover−Braunschweig Partner Site, 38124 Braunschweig, Germany
| | - Hildegard Büning
- German Center for Infection Research (DZIF), Hannover−Braunschweig Partner Site, 38124 Braunschweig, Germany
- REBIRTH Cluster of Excellence, Hannover Medical School, 30625 Hannover, Germany
| | - Hansjörg Hauser
- Department of Scientific Strategy, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Ingo Schmitz
- Systems-Oriented Immunology and Inflammation Research, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
- Institute for Molecular and Clinical Immunology, Otto von Guericke University Magdeburg, 39106 Magdeburg, Germany
| | - Thomas Pietschmann
- Institute of Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, 30625 Hannover, Germany
| | - Dagmar Wirth
- Model Systems for Infection and Immunity, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
- Institute of Experimental Hematology, Medical University Hannover, 30625 Hannover, Germany
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21
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Ahmadzadeh E, Bayin NS, Qu X, Singh A, Madisen L, Stephen D, Zeng H, Joyner AL, Rosello-Diez A. A collection of genetic mouse lines and related tools for inducible and reversible intersectional mis-expression. Development 2020; 147:dev.186650. [PMID: 32366677 DOI: 10.1242/dev.186650] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 04/16/2020] [Indexed: 12/30/2022]
Abstract
Thanks to many advances in genetic manipulation, mouse models have become very powerful in their ability to interrogate biological processes. In order to precisely target expression of a gene of interest to particular cell types, intersectional genetic approaches using two promoter/enhancers unique to a cell type are ideal. Within these methodologies, variants that add temporal control of gene expression are the most powerful. We describe the development, validation and application of an intersectional approach that involves three transgenes, requiring the intersection of two promoter/enhancers to target gene expression to precise cell types. Furthermore, the approach uses available lines expressing tTA/rTA to control the timing of gene expression based on whether doxycycline is absent or present, respectively. We also show that the approach can be extended to other animal models, using chicken embryos. We generated three mouse lines targeted at the Tigre (Igs7) locus with TRE-loxP-tdTomato-loxP upstream of three genes (p21, DTA and Ctgf), and combined them with Cre and tTA/rtTA lines that target expression to the cerebellum and limbs. Our tools will facilitate unraveling biological questions in multiple fields and organisms.
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Affiliation(s)
- Elham Ahmadzadeh
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800. Australia
| | - N Sumru Bayin
- Developmental Biology Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Xinli Qu
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800. Australia
| | - Aditi Singh
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800. Australia
| | - Linda Madisen
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Daniel Stephen
- Developmental Biology Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Alexandra L Joyner
- Developmental Biology Program, Sloan Kettering Institute, New York, NY 10065, USA
| | - Alberto Rosello-Diez
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800. Australia
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Silencing Trisomy 21 with XIST in Neural Stem Cells Promotes Neuronal Differentiation. Dev Cell 2020; 52:294-308.e3. [PMID: 31978324 DOI: 10.1016/j.devcel.2019.12.015] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 09/23/2019] [Accepted: 12/19/2019] [Indexed: 12/18/2022]
Abstract
The ability of XIST to dosage compensate a trisomic autosome presents unique experimental opportunities and potentially transformative therapeutic prospects. However, it is currently thought that XIST requires the natural context surrounding pluripotency to initiate chromosome silencing. Here, we demonstrate that XIST RNA induced in differentiated neural cells can trigger chromosome-wide silencing of chromosome 21 in Down syndrome patient-derived cells. Use of this tightly controlled system revealed a deficiency in differentiation of trisomic neural stem cells to neurons, correctible by inducing XIST at different stages of neurogenesis. Single-cell transcriptomics and other analyses strongly implicate elevated Notch signaling due to trisomy 21, thereby promoting neural stem cell cycling that delays terminal differentiation. These findings have significance for illuminating the epigenetic plasticity of cells during development, the understanding of how human trisomy 21 effects Down syndrome neurobiology, and the translational potential of XIST, a unique non-coding RNA.
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Cullmann K, Blokland KEC, Sebe A, Schenk F, Ivics Z, Heinz N, Modlich U. Sustained and regulated gene expression by Tet-inducible "all-in-one" retroviral vectors containing the HNRPA2B1-CBX3 UCOE ®. Biomaterials 2018; 192:486-499. [PMID: 30508767 DOI: 10.1016/j.biomaterials.2018.11.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 11/01/2018] [Accepted: 11/06/2018] [Indexed: 12/13/2022]
Abstract
Genetic modification of induced pluripotent stem (iPS) cells may be necessary for the generation of effector cells for cellular therapies. Hereby, it can be important to induce transgene expression at restricted and defined time windows, especially if it interferes with pluripotency or differentiation. To achieve this, inducible expression systems can be used such as the tetracycline-inducible retroviral vector system, however, retroviral expression can be subjected to epigenetic silencing or to position-effect variegation. One strategy to overcome this is the incorporation of ubiquitous chromatin opening elements (UCOE®'s) into retroviral vectors to maintain a transcriptionally permissive chromatin state at the integration site. In this study, we developed Tet-inducible all-in-one gammaretroviral vectors carrying different sized UCOE®'s derived from the A2UCOE. The ability to prevent vector silencing by preserving the Tet-regulatory potential was investigated in different cell lines, and in murine and human iPS cells. A 670-bp fragment spanning the CBX3 promoter region of A2UCOE (U670) was the most potent element in preventing silencing, and conferred the strongest expression from the vector in the induced state. While longer fragments of A2UCOEs also sustained expression, vector titers and induction efficiencies were impaired. Finally, we demonstrate that U670 can be used for constitutive expression of the transactivator in the all-in-one vector for faithful regulation of transgenes by doxycycline, including the thrombopoietin receptor Mpl conferring cytokine-dependent cell growth.
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Affiliation(s)
- Katharina Cullmann
- Research Group for Gene Modification in Stem Cells, Div. of Veterinary Medicine, Paul-Ehrlich-Institute, Langen, Germany
| | - Kaj E C Blokland
- Research Group for Gene Modification in Stem Cells, Div. of Veterinary Medicine, Paul-Ehrlich-Institute, Langen, Germany
| | - Attila Sebe
- Div. of Medical Biotechnology, Paul-Ehrlich-Institute, Langen, Germany
| | - Franziska Schenk
- Research Group for Gene Modification in Stem Cells, Div. of Veterinary Medicine, Paul-Ehrlich-Institute, Langen, Germany
| | - Zoltán Ivics
- Div. of Medical Biotechnology, Paul-Ehrlich-Institute, Langen, Germany
| | - Niels Heinz
- Research Group for Gene Modification in Stem Cells, Div. of Veterinary Medicine, Paul-Ehrlich-Institute, Langen, Germany; BioNTech Innovative Manufacturing Services GmbH, Idar-Oberstein, Germany
| | - Ute Modlich
- Research Group for Gene Modification in Stem Cells, Div. of Veterinary Medicine, Paul-Ehrlich-Institute, Langen, Germany.
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