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Zanfrini E, Bandral M, Jarc L, Ramirez-Torres MA, Pezzolla D, Kufrin V, Rodriguez-Aznar E, Avila AKM, Cohrs C, Speier S, Neumann K, Gavalas A. Generation and application of novel hES cell reporter lines for the differentiation and maturation of hPS cell-derived islet-like clusters. Sci Rep 2024; 14:19863. [PMID: 39191834 DOI: 10.1038/s41598-024-69645-4] [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: 10/27/2023] [Accepted: 08/07/2024] [Indexed: 08/29/2024] Open
Abstract
The significant advances in the differentiation of human pluripotent stem (hPS) cells into pancreatic endocrine cells, including functional β-cells, have been based on a detailed understanding of the underlying developmental mechanisms. However, the final differentiation steps, leading from endocrine progenitors to mono-hormonal and mature pancreatic endocrine cells, remain to be fully understood and this is reflected in the remaining shortcomings of the hPS cell-derived islet cells (SC-islet cells), which include a lack of β-cell maturation and variability among different cell lines. Additional signals and modifications of the final differentiation steps will have to be assessed in a combinatorial manner to address the remaining issues and appropriate reporter lines would be useful in this undertaking. Here we report the generation and functional validation of hPS cell reporter lines that can monitor the generation of INS+ and GCG+ cells and their resolution into mono-hormonal cells (INSeGFP, INSeGFP/GCGmCHERRY) as well as β-cell maturation (INSeGFP/MAFAmCHERRY) and function (INSGCaMP6). The reporter hPS cell lines maintained strong and widespread expression of pluripotency markers and differentiated efficiently into definitive endoderm and pancreatic progenitor (PP) cells. PP cells from all lines differentiated efficiently into islet cell clusters that robustly expressed the corresponding reporters and contained glucose-responsive, insulin-producing cells. To demonstrate the applicability of these hPS cell reporter lines in a high-content live imaging approach for the identification of optimal differentiation conditions, we adapted our differentiation procedure to generate SC-islet clusters in microwells. This allowed the live confocal imaging of multiple SC-islets for a single condition and, using this approach, we found that the use of the N21 supplement in the last stage of the differentiation increased the number of monohormonal β-cells without affecting the number of α-cells in the SC-islets. The hPS cell reporter lines and the high-content live imaging approach described here will enable the efficient assessment of multiple conditions for the optimal differentiation and maturation of SC-islets.
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Affiliation(s)
- Elisa Zanfrini
- Paul Langerhans Institute Dresden (PLID) of Helmholtz Center Munich at the University Clinic Carl Gustav Carus of TU Dresden, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Centre for Diabetes Research (DZD), Munich-Neuherberg, Germany
| | - Manuj Bandral
- Paul Langerhans Institute Dresden (PLID) of Helmholtz Center Munich at the University Clinic Carl Gustav Carus of TU Dresden, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Centre for Diabetes Research (DZD), Munich-Neuherberg, Germany
| | - Luka Jarc
- Paul Langerhans Institute Dresden (PLID) of Helmholtz Center Munich at the University Clinic Carl Gustav Carus of TU Dresden, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Centre for Diabetes Research (DZD), Munich-Neuherberg, Germany
| | - Maria Alejandra Ramirez-Torres
- Paul Langerhans Institute Dresden (PLID) of Helmholtz Center Munich at the University Clinic Carl Gustav Carus of TU Dresden, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Centre for Diabetes Research (DZD), Munich-Neuherberg, Germany
| | - Daniela Pezzolla
- Paul Langerhans Institute Dresden (PLID) of Helmholtz Center Munich at the University Clinic Carl Gustav Carus of TU Dresden, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Center for Regenerative Therapies Dresden (CRTD), Faculty of Medicine, TU Dresden, Dresden, Germany
| | - Vida Kufrin
- Paul Langerhans Institute Dresden (PLID) of Helmholtz Center Munich at the University Clinic Carl Gustav Carus of TU Dresden, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Centre for Diabetes Research (DZD), Munich-Neuherberg, Germany
| | - Eva Rodriguez-Aznar
- Paul Langerhans Institute Dresden (PLID) of Helmholtz Center Munich at the University Clinic Carl Gustav Carus of TU Dresden, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Centre for Diabetes Research (DZD), Munich-Neuherberg, Germany
| | - Ana Karen Mojica Avila
- Institute of Physiology, Faculty of Medicine, TU Dresden, Dresden, Germany
- Paul Langerhans Institute Dresden (PLID) of Helmholtz Center Munich at the University Clinic Carl Gustav Carus of TU Dresden, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Centre for Diabetes Research (DZD), Munich-Neuherberg, Germany
| | - Christian Cohrs
- Institute of Physiology, Faculty of Medicine, TU Dresden, Dresden, Germany
- Paul Langerhans Institute Dresden (PLID) of Helmholtz Center Munich at the University Clinic Carl Gustav Carus of TU Dresden, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Centre for Diabetes Research (DZD), Munich-Neuherberg, Germany
| | - Stephan Speier
- Institute of Physiology, Faculty of Medicine, TU Dresden, Dresden, Germany
- Paul Langerhans Institute Dresden (PLID) of Helmholtz Center Munich at the University Clinic Carl Gustav Carus of TU Dresden, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Centre for Diabetes Research (DZD), Munich-Neuherberg, Germany
| | - Katrin Neumann
- Stem Cell Engineering Facility (SCEF), CRTD, TU Dresden, Dresden, Germany
| | - Anthony Gavalas
- Paul Langerhans Institute Dresden (PLID) of Helmholtz Center Munich at the University Clinic Carl Gustav Carus of TU Dresden, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.
- German Centre for Diabetes Research (DZD), Munich-Neuherberg, Germany.
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Hiratsu K, Nunoshiba T, Togawa Y, Yamauchi Y. Development of a thermostable Cre/lox-based gene disruption system and in vivo manipulations of the megaplasmid pTT27 in Thermus thermophilus HB27. Plasmid 2024; 131-132:102730. [PMID: 39089346 DOI: 10.1016/j.plasmid.2024.102730] [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: 02/19/2024] [Revised: 06/12/2024] [Accepted: 07/25/2024] [Indexed: 08/03/2024]
Abstract
We previously reported the development of a Cre/lox-based gene disruption system for multiple markerless gene disruption in Thermus thermophilus; however, it was a time-consuming method because it functioned at 50 °C, the minimum growth temperature of T. thermophilus HB27. In the present study, we improved this system by introducing random mutations into the cre-expressing plasmid, pSH-Cre. One of the resulting mutant plasmids, pSH-CreFM allowed us to remove selection marker genes by Cre-mediated recombination at temperatures up to 70 °C. By using the thermostable Cre/lox system with pSH-CreFM, we successfully constructed two valuable pTT27 megaplasmid mutant strains, a plasmid-free strain and β-galactosidase gene deletion strain, which were produced by different methods. The thermostable Cre/lox system improved the time-consuming nature of the original Cre/lox system, but it was not suitable for multiple markerless gene disruption in T. thermophilus because of its highly efficient induction of Cre-mediated recombination even at 70 °C. However, in vivo megaplasmid manipulations performed at 65 °C were faster and easier than with the original Cre/lox system. Collectively, these results indicate that this system is a powerful tool for engineering T. thermophilus megaplasmids.
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Affiliation(s)
- Keiichiro Hiratsu
- Department of Applied Chemistry, National Defense Academy, Hashirimizu 1-10-20, Yokosuka, Kanagawa 239-8686, Japan.
| | - Tatsuo Nunoshiba
- College of Liberal Arts, International Christian University, Osawa 3-10-2, Mitaka, Tokyo 181-8585, Japan
| | - Yoichiro Togawa
- Department of Applied Chemistry, National Defense Academy, Hashirimizu 1-10-20, Yokosuka, Kanagawa 239-8686, Japan
| | - Yoshito Yamauchi
- Department of Applied Chemistry, National Defense Academy, Hashirimizu 1-10-20, Yokosuka, Kanagawa 239-8686, Japan
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3
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Wu SHS, Kim S, Lee H, Lee JH, Park SY, Bakonyi R, Teriyapirom I, Hallay N, Pilat-Carotta S, Theussl HC, Kim J, Lee JH, Simons BD, Kim JK, Colozza G, Koo BK. Red2Flpe-SCON: a versatile, multicolor strategy for generating mosaic conditional knockout mice. Nat Commun 2024; 15:4963. [PMID: 38862535 PMCID: PMC11166929 DOI: 10.1038/s41467-024-49382-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 06/04/2024] [Indexed: 06/13/2024] Open
Abstract
Image-based lineage tracing enables tissue turnover kinetics and lineage potentials of different adult cell populations to be investigated. Previously, we reported a genetic mouse model system, Red2Onco, which ectopically expressed mutated oncogenes together with red fluorescent proteins (RFP). This system enabled the expansion kinetics and neighboring effects of oncogenic clones to be dissected. We now report Red2Flpe-SCON: a mosaic knockout system that uses multicolor reporters to label both mutant and wild-type cells. We develop the Red2Flpe mouse line for red clone-specific Flpe expression, as well as the FRT-based SCON (Short Conditional IntrON) method to facilitate tunable conditional mosaic knockouts in mice. We use the Red2Flpe-SCON method to study Sox2 mutant clonal analysis in the esophageal epithelium of adult mice which reveal that the stem cell gene, Sox2, is less essential for adult stem cell maintenance itself, but rather for stem cell proliferation and differentiation.
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Affiliation(s)
- Szu-Hsien Sam Wu
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Somi Kim
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Heetak Lee
- Center for Genome Engineering, Institute for Basic Science, Expo-ro 55, Yuseong-gu, Daejeon, 34126, Republic of Korea
| | - Ji-Hyun Lee
- Center for Genome Engineering, Institute for Basic Science, Expo-ro 55, Yuseong-gu, Daejeon, 34126, Republic of Korea
| | - So-Yeon Park
- Center for Genome Engineering, Institute for Basic Science, Expo-ro 55, Yuseong-gu, Daejeon, 34126, Republic of Korea
| | - Réka Bakonyi
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Isaree Teriyapirom
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Natalia Hallay
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Sandra Pilat-Carotta
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | | | - Jihoon Kim
- Center for Genome Engineering, Institute for Basic Science, Expo-ro 55, Yuseong-gu, Daejeon, 34126, Republic of Korea
- Department of Medical and Biological Sciences, The Catholic University of Korea, Bucheon, 14662, South Korea
| | - Joo-Hyeon Lee
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Benjamin D Simons
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- The Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK
- Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, Wilberforce Road, Cambridge, CB3 0WA, UK
| | - Jong Kyoung Kim
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Gabriele Colozza
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria.
| | - Bon-Kyoung Koo
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea.
- Center for Genome Engineering, Institute for Basic Science, Expo-ro 55, Yuseong-gu, Daejeon, 34126, Republic of Korea.
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Zhu X, Yang Y, Feng D, Wang O, Chen J, Wang J, Wang B, Liu Y, Edenfield BH, Haddock AN, Wang Y, Patel T, Bi Y, Ji B. Albumin promoter-driven FlpO expression induces efficient genetic recombination in mouse liver. Am J Physiol Gastrointest Liver Physiol 2024; 326:G495-G503. [PMID: 38469630 DOI: 10.1152/ajpgi.00263.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 02/14/2024] [Accepted: 02/15/2024] [Indexed: 03/13/2024]
Abstract
Tissue-specific gene manipulations are widely used in genetically engineered mouse models. A single recombinase system, such as the one using Alb-Cre, has been commonly used for liver-specific genetic manipulations. However, most diseases are complex, involving multiple genetic changes and various cell types. A dual recombinase system is required for conditionally modifying different genes sequentially in the same cell or inducing genetic changes in different cell types within the same organism. A FlpO cDNA was inserted between the last exon and 3'-UTR of the mouse albumin gene in a bacterial artificial chromosome (BAC-Alb-FlpO). The founders were crossed with various reporter mice to examine the efficiency of recombination. Liver cancer tumorigenesis was investigated by crossing the FlpO mice with FSF-KrasG12D mice and p53frt mice (KPF mice). BAC-Alb-FlpO mice exhibited highly efficient recombination capability in both hepatocytes and intrahepatic cholangiocytes. No recombination was observed in the duodenum and pancreatic cells. BAC-Alb-FlpO-mediated liver-specific expression of mutant KrasG12D and conditional deletion of p53 gene caused the development of liver cancer. Remarkably, liver cancer in these KPF mice manifested a distinctive mixed hepatocellular carcinoma and cholangiocarcinoma phenotype. A highly efficient and liver-specific BAC-Alb-FlpO mouse model was developed. In combination with other Cre lines, different genes can be manipulated sequentially in the same cell, or distinct genetic changes can be induced in different cell types of the same organism.NEW & NOTEWORTHY A liver-specific Alb-FlpO mouse line was generated. By coupling it with other existing CreERT or Cre lines, the dual recombinase approach can enable sequential gene modifications within the same cell or across various cell types in an organism for liver research through temporal and spatial gene manipulations.
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Affiliation(s)
- Xiaohui Zhu
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States
| | - Yan Yang
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States
| | - Dongfeng Feng
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States
| | - Oliver Wang
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States
| | - Jiaxiang Chen
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States
| | - Jiale Wang
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States
| | - Bin Wang
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States
| | - Yang Liu
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States
| | - Brandy H Edenfield
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States
| | - Ashley N Haddock
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States
| | - Ying Wang
- Departments of Cardiovascular Diseases and Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, United States
| | - Tushar Patel
- Department of Transplantation, Mayo Clinic, Jacksonville, Florida, United States
| | - Yan Bi
- Department of Gastroenterology and Hepatology, Mayo Clinic, Jacksonville, Florida, United States
| | - Baoan Ji
- Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States
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Wang Z, Chen C, Ge X. Large T antigen mediated target gene replication improves site-specific recombination efficiency. Front Bioeng Biotechnol 2024; 12:1377167. [PMID: 38737535 PMCID: PMC11082406 DOI: 10.3389/fbioe.2024.1377167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 04/11/2024] [Indexed: 05/14/2024] Open
Abstract
With advantages of high-fidelity, monoclonality and large cargo capacity, site-specific recombination (SSR) holds great promises for precise genomic modifications. However, broad applications of SSR have been hurdled by low integration efficiency, and the amount of donor DNA available in nucleus for SSR presents as a limiting factor. Inspired by the DNA replication mechanisms observed in double-stranded DNA virus SV40, we hypothesized that expression of SV40 large T antigen (TAg) can increase the copy number of the donor plasmid bearing an SV40 origin, and in consequence promote recombination events. This hypothesis was tested with dual recombinase-mediated cassette exchange (RMCE) in suspension 293F cells. Results showed that TAg co-transfection significantly enhanced SSR in polyclonal cells. In the monoclonal cell line carrying a single landing pad at an identified genomic locus, 12% RMCE efficiency was achieved, and such improvement was indeed correlated with donor plasmid amplification. The developed TAg facilitated RMCE (T-RMCE) was exploited for the construction of large libraries of >107 diversity, from which GFP variants with enhanced fluorescence were isolated. We expect the underlying principle of target gene amplification can be applicable to other SSR processes and gene editing approaches in general for directed evolution and large-scale genomic screening in mammalian cells.
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Affiliation(s)
- Zening Wang
- Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, United States
- Department of Chemical and Environmental Engineering, University of California Riverside, Riverside, CA, United States
| | - Chuan Chen
- Department of Chemical and Environmental Engineering, University of California Riverside, Riverside, CA, United States
| | - Xin Ge
- Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, United States
- Department of Chemical and Environmental Engineering, University of California Riverside, Riverside, CA, United States
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Elango R, Nilavar N, Li AG, Duffey EE, Jiang Y, Nguyen D, Abakir A, Willis NA, Houseley J, Scully R. Two-ended recombination at a Flp-nickase-broken replication fork. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.10.588130. [PMID: 38645103 PMCID: PMC11030319 DOI: 10.1101/2024.04.10.588130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Collision of a replication fork with a DNA nick is thought to generate a one-ended break, fostering genomic instability. Collision of the opposing converging fork with the nick could, in principle, form a second DNA end, enabling conservative repair by homologous recombination (HR). To study mechanisms of nickase-induced HR, we developed the Flp recombinase "step arrest" nickase in mammalian cells. Flp-nickase-induced HR entails two-ended, BRCA2/RAD51-dependent short tract gene conversion (STGC), BRCA2/RAD51-independent long tract gene conversion, and discoordinated two-ended invasions. HR induced by a replication-independent break and by the Flp-nickase differ in their dependence on BRCA1 . To determine the origin of the second DNA end during Flp-nickase-induced STGC, we blocked the opposing fork using a site-specific Tus/ Ter replication fork barrier. Flp-nickase-induced STGC remained robust and two-ended. Thus, collision of a single replication fork with a Flp-nick can trigger two-ended HR, possibly reflecting replicative bypass of lagging strand nicks. This response may limit genomic instability during replication of a nicked DNA template.
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Chen C, Wang Z, Kang M, Lee KB, Ge X. High-fidelity large-diversity monoclonal mammalian cell libraries by cell cycle arrested recombinase-mediated cassette exchange. Nucleic Acids Res 2023; 51:e113. [PMID: 37941133 PMCID: PMC10711435 DOI: 10.1093/nar/gkad1001] [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: 02/08/2023] [Revised: 09/26/2023] [Accepted: 10/18/2023] [Indexed: 11/10/2023] Open
Abstract
Mammalian cells carrying defined genetic variations have shown great potentials in both fundamental research and therapeutic development. However, their full use was limited by lack of a robust method to construct large monoclonal high-quality combinatorial libraries. This study developed cell cycle arrested recombinase-mediated cassette exchange (aRMCE), able to provide monoclonality, precise genomic integration and uniform transgene expression. Via optimized nocodazole-mediated mitotic arrest, 20% target gene replacement efficiency was achieved without antibiotic selection, and the improved aRMCE efficiency was applicable to a variety of tested cell clones, transgene targets and transfection methods. As a demonstration of this versatile method, we performed directed evolution of fragment crystallizable (Fc), for which error-prone libraries of over 107 variants were constructed and displayed as IgG on surface of CHO cells. Diversities of constructed libraries were validated by deep sequencing, and panels of novel Fc mutants were identified showing improved binding towards specific Fc gamma receptors and enhanced effector functions. Due to its large cargo capacity and compatibility with different mutagenesis approaches, we expect this mammalian cell platform technology has broad applications for directed evolution, multiplex genetic assays, cell line development and stem cell engineering.
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Affiliation(s)
- Chuan Chen
- Department of Chemical and Environmental Engineering, University of California Riverside, Riverside, CA 92521, USA
| | - Zening Wang
- Department of Chemical and Environmental Engineering, University of California Riverside, Riverside, CA 92521, USA
- Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Minhyo Kang
- Department of Chemical and Environmental Engineering, University of California Riverside, Riverside, CA 92521, USA
| | - Ki Baek Lee
- Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Xin Ge
- Department of Chemical and Environmental Engineering, University of California Riverside, Riverside, CA 92521, USA
- Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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8
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Zboray K, Toth AV, Miskolczi TD, Pesti K, Casanova E, Kreidl E, Mike A, Szenes Á, Sági L, Lukacs P. High-throughput ligand profile characterization in novel cell lines expressing seven heterologous insect olfactory receptors for the detection of volatile plant biomarkers. Sci Rep 2023; 13:21757. [PMID: 38066004 PMCID: PMC10709440 DOI: 10.1038/s41598-023-47455-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 11/14/2023] [Indexed: 12/18/2023] Open
Abstract
Agriculturally important crop plants emit a multitude of volatile organic compounds (VOCs), which are excellent indicators of their health status and their interactions with pathogens and pests. In this study, we have developed a novel cellular olfactory panel for detecting fungal pathogen-related VOCs we had identified in the field, as well as during controlled inoculations of several crop plants. The olfactory panel consists of seven stable HEK293 cell lines each expressing a functional Drosophila olfactory receptor as a biosensing element along with GCaMP6, a fluorescent calcium indicator protein. An automated 384-well microplate reader was used to characterize the olfactory receptor cell lines for their sensitivity to reference VOCs. Subsequently, we profiled a set of 66 VOCs on all cell lines, covering a concentration range from 1 to 100 μM. Results showed that 49 VOCs (74.2%) elicited a response in at least one olfactory receptor cell line. Some VOCs activated the cell lines even at nanomolar (ppb) concentrations. The interaction profiles obtained here will support the development of biosensors for agricultural applications. Additionally, the olfactory receptor proteins can be purified from these cell lines with sufficient yields for further processing, such as structure determination or integration with sensor devices.
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Affiliation(s)
- Katalin Zboray
- Plant Protection Institute, Centre for Agricultural Research, Martonvásár, Hungary
- TetraLab Ltd., Budapest, Hungary
| | - Adam V Toth
- Plant Protection Institute, Centre for Agricultural Research, Martonvásár, Hungary
- Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
| | - Tímea D Miskolczi
- Plant Protection Institute, Centre for Agricultural Research, Martonvásár, Hungary
- Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
| | - Krisztina Pesti
- TetraLab Ltd., Budapest, Hungary
- Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
- Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary
| | - Emilio Casanova
- Department of Pharmacology, Center of Physiology and Pharmacology, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Emanuel Kreidl
- Department of Pharmacology, Center of Physiology and Pharmacology, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
- Novartis AG, 6336, Langkampfen, Austria
| | - Arpad Mike
- Plant Protection Institute, Centre for Agricultural Research, Martonvásár, Hungary
- Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
| | - Áron Szenes
- Department of Pathology, University of Veterinary Medicine, Budapest, Hungary
| | - László Sági
- Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary
| | - Peter Lukacs
- Plant Protection Institute, Centre for Agricultural Research, Martonvásár, Hungary.
- Agricultural Institute, Centre for Agricultural Research, Martonvásár, Hungary.
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9
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Li L, Bowling S, McGeary SE, Yu Q, Lemke B, Alcedo K, Jia Y, Liu X, Ferreira M, Klein AM, Wang SW, Camargo FD. A mouse model with high clonal barcode diversity for joint lineage, transcriptomic, and epigenomic profiling in single cells. Cell 2023; 186:5183-5199.e22. [PMID: 37852258 DOI: 10.1016/j.cell.2023.09.019] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 07/11/2023] [Accepted: 09/19/2023] [Indexed: 10/20/2023]
Abstract
Cellular lineage histories and their molecular states encode fundamental principles of tissue development and homeostasis. Current lineage-recording mouse models have insufficient barcode diversity and single-cell lineage coverage for profiling tissues composed of millions of cells. Here, we developed DARLIN, an inducible Cas9 barcoding mouse line that utilizes terminal deoxynucleotidyl transferase (TdT) and 30 CRISPR target sites. DARLIN is inducible, generates massive lineage barcodes across tissues, and enables the detection of edited barcodes in ∼70% of profiled single cells. Using DARLIN, we examined fate bias within developing hematopoietic stem cells (HSCs) and revealed unique features of HSC migration. Additionally, we established a protocol for joint transcriptomic and epigenomic single-cell measurements with DARLIN and found that cellular clonal memory is associated with genome-wide DNA methylation rather than gene expression or chromatin accessibility. DARLIN will enable the high-resolution study of lineage relationships and their molecular signatures in diverse tissues and physiological contexts.
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Affiliation(s)
- Li Li
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Sarah Bowling
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Sean E McGeary
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Qi Yu
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Bianca Lemke
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Karel Alcedo
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Yuemeng Jia
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Xugeng Liu
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Mark Ferreira
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Allon M Klein
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Shou-Wen Wang
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China; School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China; School of Science, Westlake University, Hangzhou, Zhejiang 310024, China.
| | - Fernando D Camargo
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
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10
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Zhao C, Ries C, Du Y, Zhang J, Sakimura K, Itoi K, Deussing JM. Differential CRH expression level determines efficiency of Cre- and Flp-dependent recombination. Front Neurosci 2023; 17:1163462. [PMID: 37599997 PMCID: PMC10434532 DOI: 10.3389/fnins.2023.1163462] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 07/21/2023] [Indexed: 08/22/2023] Open
Abstract
Corticotropin-releasing hormone expressing (CRH+) neurons are distributed throughout the brain and play a crucial role in shaping the stress responses. Mouse models expressing site-specific recombinases (SSRs) or reporter genes are important tools providing genetic access to defined cell types and have been widely used to address CRH+ neurons and connected brain circuits. Here, we investigated a recently generated CRH-FlpO driver line expanding the CRH system-related tool box. We directly compared it to a previously established and widely used CRH-Cre line with respect to the FlpO expression pattern and recombination efficiency. In the brain, FlpO mRNA distribution fully recapitulates the expression pattern of endogenous Crh. Combining both Crh locus driven SSRs driver lines with appropriate reporters revealed an overall coherence of respective spatial patterns of reporter gene activation validating CRH-FlpO mice as a valuable tool complementing existing CRH-Cre and reporter lines. However, a substantially lower number of reporter-expressing neurons was discerned in CRH-FlpO mice. Using an additional CRH reporter mouse line (CRH-Venus) and a mouse line allowing for conversion of Cre into FlpO activity (CAG-LSL-FlpO) in combination with intersectional and subtractive mouse genetic approaches, we were able to demonstrate that the reduced number of tdTomato reporter expressing CRH+ neurons can be ascribed to the lower recombination efficiency of FlpO compared to Cre recombinase. This discrepancy particularly manifests under conditions of low CRH expression and can be overcome by utilizing homozygous CRH-FlpO mice. These findings have direct experimental implications which have to be carefully considered when targeting CRH+ neurons using CRH-FlpO mice. However, the lower FlpO-dependent recombination efficiency also entails advantages as it provides a broader dynamic range of expression allowing for the visualization of cells showing stress-induced CRH expression which is not detectable in highly sensitive CRH-Cre mice as Cre-mediated recombination has largely been completed in all cells generally possessing the capacity to express CRH. These findings underscore the importance of a comprehensive evaluation of novel SSR driver lines prior to their application.
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Affiliation(s)
- Chen Zhao
- Molecular Neurogenetics, Max Planck Institute of Psychiatry, Munich, Germany
| | - Clemens Ries
- Molecular Neurogenetics, Max Planck Institute of Psychiatry, Munich, Germany
| | - Ying Du
- Molecular Neurogenetics, Max Planck Institute of Psychiatry, Munich, Germany
| | - Jingwei Zhang
- Molecular Neurogenetics, Max Planck Institute of Psychiatry, Munich, Germany
| | - Kenji Sakimura
- Department of Animal Model Development, Brain Research Institute, Niigata University, Niigata, Japan
| | - Keiichi Itoi
- Super-Network Brain Physiology, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Jan M. Deussing
- Molecular Neurogenetics, Max Planck Institute of Psychiatry, Munich, Germany
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11
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Rapid clonal identification of biallelic CRISPR/Cas9 knock-ins using SNEAK PEEC. Sci Rep 2023; 13:1719. [PMID: 36720908 PMCID: PMC9889345 DOI: 10.1038/s41598-023-28732-8] [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] [Received: 09/17/2021] [Accepted: 01/24/2023] [Indexed: 02/02/2023] Open
Abstract
One of the challenges faced by current CRISPR/Cas9 editing strategies is the difficulty in rapidly selecting clonal populations of biallelically edited cells. Here we present Surface engiNeered fluorEscence Assisted Kit with Protein Epitope Enhanced Capture (SNEAK PEEC), a platform that combines human genome editing with cell-surface display, which enables the direct identification of biallelically edited clones with minimal screening.
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12
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Schmitt LT, Paszkowski-Rogacz M, Jug F, Buchholz F. Prediction of designer-recombinases for DNA editing with generative deep learning. Nat Commun 2022; 13:7966. [PMID: 36575171 PMCID: PMC9794738 DOI: 10.1038/s41467-022-35614-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 12/14/2022] [Indexed: 12/28/2022] Open
Abstract
Site-specific tyrosine-type recombinases are effective tools for genome engineering, with the first engineered variants having demonstrated therapeutic potential. So far, adaptation to new DNA target site selectivity of designer-recombinases has been achieved mostly through iterative cycles of directed molecular evolution. While effective, directed molecular evolution methods are laborious and time consuming. Here we present RecGen (Recombinase Generator), an algorithm for the intelligent generation of designer-recombinases. We gather the sequence information of over one million Cre-like recombinase sequences evolved for 89 different target sites with which we train Conditional Variational Autoencoders for recombinase generation. Experimental validation demonstrates that the algorithm can predict recombinase sequences with activity on novel target-sites, indicating that RecGen is useful to accelerate the development of future designer-recombinases.
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Affiliation(s)
- Lukas Theo Schmitt
- grid.4488.00000 0001 2111 7257Medical Systems Biology, Medical Faculty, TU Dresden, 01307 Dresden, Germany
| | - Maciej Paszkowski-Rogacz
- grid.4488.00000 0001 2111 7257Medical Systems Biology, Medical Faculty, TU Dresden, 01307 Dresden, Germany
| | - Florian Jug
- grid.510779.d0000 0004 9414 6915Fondazione Human Technopole, Milano, Italy ,grid.495510.c0000 0004 9335 670XCenter for Systems Biology Dresden, Dresden, Germany ,grid.419537.d0000 0001 2113 4567Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Frank Buchholz
- grid.4488.00000 0001 2111 7257Medical Systems Biology, Medical Faculty, TU Dresden, 01307 Dresden, Germany
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13
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Phillips S, Ramos PV, Veeraraghavan P, Young SM. VikAD, a Vika site-specific recombinase-based system for efficient and scalable helper-dependent adenovirus production. Mol Ther Methods Clin Dev 2022; 24:117-126. [PMID: 35024378 PMCID: PMC8718833 DOI: 10.1016/j.omtm.2021.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 12/04/2021] [Indexed: 11/09/2022]
Abstract
Recombinant viral vectors have become integral tools for basic in vivo research applications. Helper-dependent adenoviral (HdAd) vectors have a large packaging capacity of ∼36 kb of DNA that mediate long-term transgene expression in vitro and in vivo. The large carrying capacity of HdAd enables basic research or clinical applications requiring the delivery of large genes or multiple transgenes, which cannot be packaged into other widely used viral vectors. Currently, common HdAd production systems use an Ad helper virus (HV) with a packaging signal (Ψ) that is flanked by either loxP or FRT sites, which is excised in producer cells expressing Cre or Flp recombinases to prevent HV packaging. However, these production systems prevent the use of HdAd vectors for genetic strategies that rely on Cre or Flp recombination for cell-type-specific expression. To overcome these limitations, we developed the VikAD production system, which is based on producer cells expressing the Vika recombinase and an HV that contains a Ψ flanked by vox sites. The availability of this production system will greatly expand the utility and flexibility of HdAd vectors for use in research applications to monitor and manipulate cellular activity with increased specificity.
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Affiliation(s)
- Stacia Phillips
- Department of Anatomy and Cell Biology, University of Iowa Carver College of Medicine, PBDB 5322, 169 Newton Road, Iowa City, IA 52242, USA
| | - Paula Valino Ramos
- Department of Anatomy and Cell Biology, University of Iowa Carver College of Medicine, PBDB 5322, 169 Newton Road, Iowa City, IA 52242, USA
| | - Priyadharishini Veeraraghavan
- Department of Anatomy and Cell Biology, University of Iowa Carver College of Medicine, PBDB 5322, 169 Newton Road, Iowa City, IA 52242, USA
| | - Samuel M. Young
- Department of Anatomy and Cell Biology, University of Iowa Carver College of Medicine, PBDB 5322, 169 Newton Road, Iowa City, IA 52242, USA
- Department of Otolaryngology, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
- Iowa Neuroscience Institute, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
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14
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Artificial nondirectional site-specific recombination systems. iScience 2022; 25:103716. [PMID: 35072008 PMCID: PMC8762395 DOI: 10.1016/j.isci.2021.103716] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 10/23/2021] [Accepted: 12/29/2021] [Indexed: 11/22/2022] Open
Abstract
Site-specific recombination systems (SRSs) are widely used in studies on synthetic biology and related disciplines. Nondirectional SRSs can randomly trigger excision, integration, reversal, and translocation, which are effective tools to achieve large-scale genome recombination. In this study, we designed 6 new nondirectional SRSs named Vika/voxsym1-4 and Dre/roxsym1-2. All 6 artificial nondirectional SRSs were able to generate random deletion and inversion in Saccharomyces cerevisiae. Moreover, all six SRSs were orthogonal to Cre/loxPsym. The pairwise orthogonal nondirected SRSs can simultaneously initiate large-scale and independent gene recombination in two different regions of the genome, which could not be accomplished using previous orthogonal systems. These SRSs were found to be robust while working in the cells at different growth stages, as well as in the different spatial structure of the chromosome. These artificial pairwise orthogonal nondirected SRSs offer newfound potential for site-specific recombination in synthetic biology. Designed six new artificial nondirectional site-specific recombination systems Pairwise orthogonal nondirected recombination systems in yeast The deletion efficiency of systems is far greater than the inversion efficiency These nondirectional recombination systems were found to be robust
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15
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Lane AR, Cogdell IC, Jessell TM, Bikoff JB, Alvarez FJ. Genetic targeting of adult Renshaw cells using a Calbindin 1 destabilized Cre allele for intersection with Parvalbumin or Engrailed1. Sci Rep 2021; 11:19861. [PMID: 34615947 PMCID: PMC8494874 DOI: 10.1038/s41598-021-99333-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 09/16/2021] [Indexed: 11/09/2022] Open
Abstract
Renshaw cells (RCs) are one of the most studied spinal interneurons; however, their roles in motor control remain enigmatic in part due to the lack of experimental models to interfere with RC function, specifically in adults. To overcome this limitation, we leveraged the distinct temporal regulation of Calbindin (Calb1) expression in RCs to create genetic models for timed RC manipulation. We used a Calb1 allele expressing a destabilized Cre (dgCre) theoretically active only upon trimethoprim (TMP) administration. TMP timing and dose influenced RC targeting efficiency, which was highest within the first three postnatal weeks, but specificity was low with many other spinal neurons also targeted. In addition, dgCre showed TMP-independent activity resulting in spontaneous recombination events that accumulated with age. Combining Calb1-dgCre with Parvalbumin (Pvalb) or Engrailed1 (En1) Flpo alleles in dual conditional systems increased cellular and timing specificity. Under optimal conditions, Calb1-dgCre/Pvalb-Flpo mice targeted 90% of RCs and few dorsal horn neurons; Calb1-dgCre/En1-Flpo mice showed higher specificity, but only a maximum of 70% of RCs targeted. Both models targeted neurons throughout the brain. Restricted spinal expression was obtained by injecting intraspinally AAVs carrying dual conditional genes. These results describe the first models to genetically target RCs bypassing development.
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Affiliation(s)
- Alicia R Lane
- Department of Physiology, Emory University, Atlanta, GA, 30322, USA
| | | | - Thomas M Jessell
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Jay B Bikoff
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
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16
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Wang Y, Xue P, Cao M, Yu T, Lane ST, Zhao H. Directed Evolution: Methodologies and Applications. Chem Rev 2021; 121:12384-12444. [PMID: 34297541 DOI: 10.1021/acs.chemrev.1c00260] [Citation(s) in RCA: 196] [Impact Index Per Article: 65.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Directed evolution aims to expedite the natural evolution process of biological molecules and systems in a test tube through iterative rounds of gene diversifications and library screening/selection. It has become one of the most powerful and widespread tools for engineering improved or novel functions in proteins, metabolic pathways, and even whole genomes. This review describes the commonly used gene diversification strategies, screening/selection methods, and recently developed continuous evolution strategies for directed evolution. Moreover, we highlight some representative applications of directed evolution in engineering nucleic acids, proteins, pathways, genetic circuits, viruses, and whole cells. Finally, we discuss the challenges and future perspectives in directed evolution.
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Affiliation(s)
- Yajie Wang
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Pu Xue
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Mingfeng Cao
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Tianhao Yu
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Stephan T Lane
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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17
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Janmaat VT, Nesteruk K, Spaander MCW, Verhaar AP, Yu B, Silva RA, Phillips WA, Magierowski M, van de Winkel A, Stadler HS, Sandoval-Guzmán T, van der Laan LJW, Kuipers EJ, Smits R, Bruno MJ, Fuhler GM, Clemons NJ, Peppelenbosch MP. HOXA13 in etiology and oncogenic potential of Barrett's esophagus. Nat Commun 2021; 12:3354. [PMID: 34099670 PMCID: PMC8184780 DOI: 10.1038/s41467-021-23641-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 05/06/2021] [Indexed: 12/13/2022] Open
Abstract
Barrett's esophagus in gastrointestinal reflux patients constitutes a columnar epithelium with distal characteristics, prone to progress to esophageal adenocarcinoma. HOX genes are known mediators of position-dependent morphology. Here we show HOX collinearity in the adult gut while Barrett's esophagus shows high HOXA13 expression in stem cells and their progeny. HOXA13 overexpression appears sufficient to explain both the phenotype (through downregulation of the epidermal differentiation complex) and the oncogenic potential of Barrett's esophagus. Intriguingly, employing a mouse model that contains a reporter coupled to the HOXA13 promotor we identify single HOXA13-positive cells distally from the physiological esophagus, which is mirrored in human physiology, but increased in Barrett's esophagus. Additionally, we observe that HOXA13 expression confers a competitive advantage to cells. We thus propose that Barrett's esophagus and associated esophageal adenocarcinoma is the consequence of expansion of this gastro-esophageal HOXA13-expressing compartment following epithelial injury.
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Affiliation(s)
- Vincent T Janmaat
- Department of Gastroenterology and Hepatology, Erasmus MC - University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Kateryna Nesteruk
- Department of Gastroenterology and Hepatology, Erasmus MC - University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Manon C W Spaander
- Department of Gastroenterology and Hepatology, Erasmus MC - University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Auke P Verhaar
- Department of Gastroenterology and Hepatology, Erasmus MC - University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Bingting Yu
- Department of Gastroenterology and Hepatology, Erasmus MC - University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Rodrigo A Silva
- Department of Gastroenterology and Hepatology, Erasmus MC - University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Wayne A Phillips
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia
- Department of Surgery (St. Vincent's Hospital), The University of Melbourne, Melbourne, VIC, Australia
| | - Marcin Magierowski
- Department of Gastroenterology and Hepatology, Erasmus MC - University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Physiology, Faculty of Medicine, Jagiellonian University Medical College, Cracow, Poland
| | - Anouk van de Winkel
- Department of Gastroenterology and Hepatology, Erasmus MC - University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - H Scott Stadler
- Department of Skeletal Biology, Shriners Hospital for Children, Portland, OR, USA
| | | | - Luc J W van der Laan
- Department of Surgery, Erasmus MC - University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Ernst J Kuipers
- Department of Gastroenterology and Hepatology, Erasmus MC - University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Ron Smits
- Department of Gastroenterology and Hepatology, Erasmus MC - University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Marco J Bruno
- Department of Gastroenterology and Hepatology, Erasmus MC - University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Gwenny M Fuhler
- Department of Gastroenterology and Hepatology, Erasmus MC - University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Nicholas J Clemons
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia
| | - Maikel P Peppelenbosch
- Department of Gastroenterology and Hepatology, Erasmus MC - University Medical Center Rotterdam, Rotterdam, The Netherlands.
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18
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Nakata H, Hashimoto T, Yoshiki A. Quick validation of genetic quality for conditional alleles in mice. Genes Cells 2021; 26:240-245. [PMID: 33540482 PMCID: PMC8247991 DOI: 10.1111/gtc.12834] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 01/22/2021] [Accepted: 01/28/2021] [Indexed: 11/29/2022]
Abstract
Site-specific conditional inactivation technologies using Cre-loxP or Flp-FRT systems are becoming increasingly important for the elucidation of gene function and disease mechanism in vivo. A large number of gene knockout mouse models carrying complex conditional alleles have been generated by global community efforts and made available for biomedical researchers. The structures of conditional alleles in these mice are becoming increasingly complex and sophisticated, and so the validation of the genetic quality of these alleles is likewise becoming a laborious task for individual researchers. To ensure the reproducibility of conditional experiments, the researcher should confirm that loxP or FRT is integrated at the correct positions in the genome prior to start of the experiments. We report the successful design of universal PCR primers specific to loxP and FRT for the quick validation of conditional floxed and Flrted alleles. The primer set consists of forward and reverse primers complimentary to the loxP or FRT sequences with partial modifications at the 5' end containing 6-base restriction endonuclease recognition sites. The universal primer set was tested to detect genomic intervals between a pair of cis-integrated loxP or FRT and was useful for quickly validating various floxed or Flrted alleles in conditional mice.
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Affiliation(s)
- Hatsumi Nakata
- Experimental Animal DivisionRIKEN BioResource Research CenterTsukubaJapan
| | - Tomomi Hashimoto
- Experimental Animal DivisionRIKEN BioResource Research CenterTsukubaJapan
| | - Atsushi Yoshiki
- Experimental Animal DivisionRIKEN BioResource Research CenterTsukubaJapan
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19
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FLP-Mediated Site-Specific Gene Integration in Rice. Methods Mol Biol 2021. [PMID: 33471335 DOI: 10.1007/978-1-0716-1068-8_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Enabling precise gene integration is important for installing traits in the plants. One of the practical methods of achieving precise gene integration is by using the yeast FLP-FRT recombination system that is efficient in directing DNA integration into the "engineered" genomic sites. The critical parameters of this method include the use of the thermostable version of FLP protein and the promoter trap design to select site-specific integration clones. The resulting transgenic plants display stable expression that is transmitted to the progeny. Therefore, FLP-mediated site-specific integration method could be used for trait engineering in the crop plants or testing gene functions in the model plants.
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20
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Zhang Y, Liu G, Guo T, Liang XG, Du H, Yang L, Bhaduri A, Li X, Xu Z, Zhang Z, Li Z, He M, Tsyporin J, Kriegstein AR, Rubenstein JL, Yang Z, Chen B. Cortical Neural Stem Cell Lineage Progression Is Regulated by Extrinsic Signaling Molecule Sonic Hedgehog. Cell Rep 2021; 30:4490-4504.e4. [PMID: 32234482 PMCID: PMC7197103 DOI: 10.1016/j.celrep.2020.03.027] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 12/07/2019] [Accepted: 03/11/2020] [Indexed: 02/07/2023] Open
Abstract
Neural stem cells (NSCs) in the prenatal neocortex progressively generate different subtypes of glutamatergic projection neurons. Following that, NSCs have a major switch in their progenitor properties and produce γ-aminobutyric acid (GABAergic) interneurons for the olfactory bulb (OB), cortical oligodendrocytes, and astrocytes. Herein, we provide evidence for the molecular mechanism that underlies this switch in the state of neocortical NSCs. We show that, at around E16.5, mouse neocortical NSCs start to generate GSX2-expressing (GSX2+) intermediate progenitor cells (IPCs). In vivo lineage-tracing study revealed that GSX2+ IPC population gives rise not only to OB interneurons but also to cortical oligodendrocytes and astrocytes, suggesting that they are a tri-potential population. We demonstrated that Sonic hedgehog signaling is both necessary and sufficient for the generation of GSX2+ IPCs by reducing GLI3R protein levels. Using single-cell RNA sequencing, we identify the transcriptional profile of GSX2+ IPCs and the process of the lineage switch of cortical NSCs. Zhang et al. reveal that cortical radial glia-derived GSX2+ cells at the late embryonic stage are tri-potential intermediate progenitors, which give rise to a subset of cortical oligodendrocytes, astrocytes, and olfactory bulb interneurons. SHH signaling is crucial for the generation of GSX2+ cells by reducing GLI3R protein level.
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Affiliation(s)
- Yue Zhang
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Guoping Liu
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institute for Translational Brain Research, Institutes of Brain Science, Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Teng Guo
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institute for Translational Brain Research, Institutes of Brain Science, Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Xiaoyi G Liang
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Heng Du
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institute for Translational Brain Research, Institutes of Brain Science, Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Lin Yang
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institute for Translational Brain Research, Institutes of Brain Science, Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Aparna Bhaduri
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Xiaosu Li
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institute for Translational Brain Research, Institutes of Brain Science, Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Zhejun Xu
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institute for Translational Brain Research, Institutes of Brain Science, Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Zhuangzhi Zhang
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institute for Translational Brain Research, Institutes of Brain Science, Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Zhenmeiyu Li
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institute for Translational Brain Research, Institutes of Brain Science, Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Miao He
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institute for Translational Brain Research, Institutes of Brain Science, Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Jeremiah Tsyporin
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Arnold R Kriegstein
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - John L Rubenstein
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Zhengang Yang
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institute for Translational Brain Research, Institutes of Brain Science, Department of Neurology, Zhongshan Hospital, Fudan University, Shanghai 200032, China.
| | - Bin Chen
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.
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21
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Feary M, Moffat MA, Casperson GF, Allen MJ, Young RJ. CHOK1SV GS-KO SSI expression system: A combination of the Fer1L4 locus and glutamine synthetase selection. Biotechnol Prog 2021; 37:e3137. [PMID: 33609084 DOI: 10.1002/btpr.3137] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/03/2021] [Accepted: 02/07/2021] [Indexed: 12/11/2022]
Abstract
There are an ever-increasing number of biopharmaceutical candidates in clinical trials fueling an urgent need to streamline the cell line development process. A critical part of the process is the methodology used to generate and screen candidate cell lines compatible with GMP manufacturing processes. The relatively large amount of clone phenotypic variation observed from conventional "random integration" (RI)-based cell line construction is thought to be the result of a combination of the position variegation effect, genome plasticity and clonal variation. Site-specific integration (SSI) has been used by several groups to temper the influence of the position variegation effect and thus reduce variability in expression of biopharmaceutical candidates. Following on from our previous reports on the application of the Fer1L4 locus for SSI in CHOK1SV (10E9), we have combined this locus and a CHOK1SV glutamine synthetase knockout (GS-KO) host to create an improved expression system. The host, CHOK1SV GS-KO SSI (HD7876), was created by homology directed integration of a targetable landing pad flanked with incompatible Frt sequences in the Fer1L4 gene. The targeting vector contains a promoterless GS expression cassette and monoclonal antibody (mAb) expression cassettes, flanked by Frt sites compatible with equivalent sites flanking the landing pad in the host cell line. SSI clones expressing four antibody candidates, selected in a streamlined cell line development process, have mAb titers which rival RI (1.0-4.5 g/L) and robust expression stability (100% of clones stable through the 50 generation "manufacturing window" which supports commercial manufacturing at 12,000 L bioreactor scale).
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Affiliation(s)
- Marc Feary
- R&D Cell Engineering, Lonza Biologics, Little Chesterford, UK
| | - Mark A Moffat
- Cell Line Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Chesterfield, MO, 63017, USA
| | - Gerald F Casperson
- Cell Line Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Chesterfield, MO, 63017, USA
| | - Martin J Allen
- Cell Line Development, Biotherapeutics Pharmaceutical Sciences, Pfizer Inc., Chesterfield, MO, 63017, USA
| | - Robert J Young
- R&D Cell Engineering, Lonza Biologics, Little Chesterford, UK
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22
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Miguel V, Tituaña J, Herrero JI, Herrero L, Serra D, Cuevas P, Barbas C, Puyol DR, Márquez-Expósito L, Ruiz-Ortega M, Castillo C, Sheng X, Susztak K, Ruiz-Canela M, Salas-Salvadó J, González MAM, Ortega S, Ramos R, Lamas S. Renal tubule Cpt1a overexpression protects from kidney fibrosis by restoring mitochondrial homeostasis. J Clin Invest 2021; 131:140695. [PMID: 33465052 DOI: 10.1172/jci140695] [Citation(s) in RCA: 154] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 01/13/2021] [Indexed: 12/14/2022] Open
Abstract
Chronic kidney disease (CKD) remains a major epidemiological, clinical, and biomedical challenge. During CKD, renal tubular epithelial cells (TECs) present a persistent inflammatory and profibrotic response. Fatty acid oxidation (FAO), the main source of energy for TECs, is reduced in kidney fibrosis and contributes to its pathogenesis. To determine whether gain of function in FAO (FAO-GOF) could protect from fibrosis, we generated a conditional transgenic mouse model with overexpression of the fatty acid shuttling enzyme carnitine palmitoyl-transferase 1A (CPT1A) in TECs. Cpt1a-knockin (CPT1A-KI) mice subjected to 3 models of renal fibrosis (unilateral ureteral obstruction, folic acid nephropathy [FAN], and adenine-induced nephrotoxicity) exhibited decreased expression of fibrotic markers, a blunted proinflammatory response, and reduced epithelial cell damage and macrophage influx. Protection from fibrosis was also observed when Cpt1a overexpression was induced after FAN. FAO-GOF restored oxidative metabolism and mitochondrial number and enhanced bioenergetics, increasing palmitate oxidation and ATP levels, changes that were also recapitulated in TECs exposed to profibrotic stimuli. Studies in patients showed decreased CPT1 levels and increased accumulation of short- and middle-chain acylcarnitines, reflecting impaired FAO in human CKD. We propose that strategies based on FAO-GOF may constitute powerful alternatives to combat fibrosis inherent to CKD.
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Affiliation(s)
- Verónica Miguel
- Program of Physiological and Pathological Processes, Centro de Biología Molecular "Severo Ochoa" (CBMSO) (CSIC-UAM), Madrid, Spain
| | - Jessica Tituaña
- Program of Physiological and Pathological Processes, Centro de Biología Molecular "Severo Ochoa" (CBMSO) (CSIC-UAM), Madrid, Spain
| | - J Ignacio Herrero
- Program of Physiological and Pathological Processes, Centro de Biología Molecular "Severo Ochoa" (CBMSO) (CSIC-UAM), Madrid, Spain
| | - Laura Herrero
- Department of Biochemistry and Physiology, School of Pharmacy and Food Sciences, Institut de Biomedicina de la Universitat de Barcelona (IBUB), Universitat de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain
| | - Dolors Serra
- Department of Biochemistry and Physiology, School of Pharmacy and Food Sciences, Institut de Biomedicina de la Universitat de Barcelona (IBUB), Universitat de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain
| | - Paula Cuevas
- Centre for Metabolomics and Bioanalysis (CEMBIO), Chemistry and Biochemistry Department, Pharmacy Faculty, Universidad San Pablo-CEU, Boadilla del Monte, Madrid, Spain
| | - Coral Barbas
- Centre for Metabolomics and Bioanalysis (CEMBIO), Chemistry and Biochemistry Department, Pharmacy Faculty, Universidad San Pablo-CEU, Boadilla del Monte, Madrid, Spain
| | - Diego Rodríguez Puyol
- Department of Medicine and Medical Specialties, Research Foundation of the University Hospital "Príncipe de Asturias," IRYCIS, Alcalá University, Alcalá de Henares, Madrid, Spain
| | - Laura Márquez-Expósito
- Cellular and Molecular Biology in Renal and Vascular Pathology Laboratory. Fundación Instituto de Investigación Sanitaria-Fundación Jiménez Díaz-Universidad Autónoma Madrid, Madrid, Spain
| | - Marta Ruiz-Ortega
- Cellular and Molecular Biology in Renal and Vascular Pathology Laboratory. Fundación Instituto de Investigación Sanitaria-Fundación Jiménez Díaz-Universidad Autónoma Madrid, Madrid, Spain
| | - Carolina Castillo
- University Hospital "Príncipe de Asturias", Alcalá de Henares, Madrid, Spain
| | - Xin Sheng
- Division of Nephrology, Department of Medicine, Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Katalin Susztak
- Division of Nephrology, Department of Medicine, Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Miguel Ruiz-Canela
- University of Navarra, Department of Preventive Medicine and Public Health, IdiSNA (Health Research Institute of Navarra), Pamplona, Spain.,CIBER de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain
| | - Jordi Salas-Salvadó
- CIBER de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain.,Human Nutrition Unit, Faculty of Medicine and Health Sciences, Pere Virgili Health Research Institute, Rovira i Virgili University, Reus, Spain
| | - Miguel A Martínez González
- University of Navarra, Department of Preventive Medicine and Public Health, IdiSNA (Health Research Institute of Navarra), Pamplona, Spain.,CIBER de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain
| | - Sagrario Ortega
- Transgenics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Ricardo Ramos
- Genomic Facility, Parque Científico de Madrid, Madrid, Spain
| | - Santiago Lamas
- Program of Physiological and Pathological Processes, Centro de Biología Molecular "Severo Ochoa" (CBMSO) (CSIC-UAM), Madrid, Spain
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23
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Biglari N, Gaziano I, Schumacher J, Radermacher J, Paeger L, Klemm P, Chen W, Corneliussen S, Wunderlich CM, Sue M, Vollmar S, Klöckener T, Sotelo-Hitschfeld T, Abbasloo A, Edenhofer F, Reimann F, Gribble FM, Fenselau H, Kloppenburg P, Wunderlich FT, Brüning JC. Functionally distinct POMC-expressing neuron subpopulations in hypothalamus revealed by intersectional targeting. Nat Neurosci 2021; 24:913-929. [PMID: 34002087 PMCID: PMC8249241 DOI: 10.1038/s41593-021-00854-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 03/31/2021] [Indexed: 02/03/2023]
Abstract
Pro-opiomelanocortin (POMC)-expressing neurons in the arcuate nucleus of the hypothalamus represent key regulators of metabolic homeostasis. Electrophysiological and single-cell sequencing experiments have revealed a remarkable degree of heterogeneity of these neurons. However, the exact molecular basis and functional consequences of this heterogeneity have not yet been addressed. Here, we have developed new mouse models in which intersectional Cre/Dre-dependent recombination allowed for successful labeling, translational profiling and functional characterization of distinct POMC neurons expressing the leptin receptor (Lepr) and glucagon like peptide 1 receptor (Glp1r). Our experiments reveal that POMCLepr+ and POMCGlp1r+ neurons represent largely nonoverlapping subpopulations with distinct basic electrophysiological properties. They exhibit a specific anatomical distribution within the arcuate nucleus and differentially express receptors for energy-state communicating hormones and neurotransmitters. Finally, we identify a differential ability of these subpopulations to suppress feeding. Collectively, we reveal a notably distinct functional microarchitecture of critical metabolism-regulatory neurons.
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Affiliation(s)
- Nasim Biglari
- grid.418034.a0000 0004 4911 0702Max Planck Institute for Metabolism Research, Department of Neuronal Control of Metabolism, Cologne, Germany ,grid.411097.a0000 0000 8852 305XPoliclinic for Endocrinology, Diabetes and Preventive Medicine (PEDP), University Hospital Cologne, Cologne, Germany ,grid.6190.e0000 0000 8580 3777Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Center of Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Isabella Gaziano
- grid.418034.a0000 0004 4911 0702Max Planck Institute for Metabolism Research, Department of Neuronal Control of Metabolism, Cologne, Germany ,grid.411097.a0000 0000 8852 305XPoliclinic for Endocrinology, Diabetes and Preventive Medicine (PEDP), University Hospital Cologne, Cologne, Germany ,grid.6190.e0000 0000 8580 3777Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Center of Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Jonas Schumacher
- grid.418034.a0000 0004 4911 0702Max Planck Institute for Metabolism Research, Department of Neuronal Control of Metabolism, Cologne, Germany ,grid.411097.a0000 0000 8852 305XPoliclinic for Endocrinology, Diabetes and Preventive Medicine (PEDP), University Hospital Cologne, Cologne, Germany ,grid.6190.e0000 0000 8580 3777Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Center of Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Jan Radermacher
- grid.6190.e0000 0000 8580 3777Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Center of Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany ,grid.6190.e0000 0000 8580 3777Institute for Zoology, Biocenter, University of Cologne, Cologne, Germany
| | - Lars Paeger
- grid.6190.e0000 0000 8580 3777Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Center of Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany ,grid.6190.e0000 0000 8580 3777Institute for Zoology, Biocenter, University of Cologne, Cologne, Germany
| | - Paul Klemm
- grid.418034.a0000 0004 4911 0702Max Planck Institute for Metabolism Research, Department of Neuronal Control of Metabolism, Cologne, Germany ,grid.411097.a0000 0000 8852 305XPoliclinic for Endocrinology, Diabetes and Preventive Medicine (PEDP), University Hospital Cologne, Cologne, Germany ,grid.6190.e0000 0000 8580 3777Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Center of Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Weiyi Chen
- grid.418034.a0000 0004 4911 0702Max Planck Institute for Metabolism Research, Department of Neuronal Control of Metabolism, Cologne, Germany ,grid.411097.a0000 0000 8852 305XPoliclinic for Endocrinology, Diabetes and Preventive Medicine (PEDP), University Hospital Cologne, Cologne, Germany ,grid.6190.e0000 0000 8580 3777Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Center of Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Svenja Corneliussen
- grid.6190.e0000 0000 8580 3777Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Center of Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany ,grid.6190.e0000 0000 8580 3777Institute for Zoology, Biocenter, University of Cologne, Cologne, Germany
| | - Claudia M. Wunderlich
- grid.418034.a0000 0004 4911 0702Max Planck Institute for Metabolism Research, Department of Neuronal Control of Metabolism, Cologne, Germany ,grid.411097.a0000 0000 8852 305XPoliclinic for Endocrinology, Diabetes and Preventive Medicine (PEDP), University Hospital Cologne, Cologne, Germany ,grid.6190.e0000 0000 8580 3777Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Center of Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Michael Sue
- grid.418034.a0000 0004 4911 0702Max Planck Institute for Metabolism Research, Department of Neuronal Control of Metabolism, Cologne, Germany
| | - Stefan Vollmar
- grid.418034.a0000 0004 4911 0702Max Planck Institute for Metabolism Research, Department of Neuronal Control of Metabolism, Cologne, Germany
| | - Tim Klöckener
- grid.418034.a0000 0004 4911 0702Max Planck Institute for Metabolism Research, Department of Neuronal Control of Metabolism, Cologne, Germany ,grid.411097.a0000 0000 8852 305XPoliclinic for Endocrinology, Diabetes and Preventive Medicine (PEDP), University Hospital Cologne, Cologne, Germany ,grid.6190.e0000 0000 8580 3777Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Center of Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Tamara Sotelo-Hitschfeld
- grid.418034.a0000 0004 4911 0702Max Planck Institute for Metabolism Research, Department of Neuronal Control of Metabolism, Cologne, Germany ,grid.411097.a0000 0000 8852 305XPoliclinic for Endocrinology, Diabetes and Preventive Medicine (PEDP), University Hospital Cologne, Cologne, Germany ,grid.6190.e0000 0000 8580 3777Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Center of Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Amin Abbasloo
- grid.418034.a0000 0004 4911 0702Max Planck Institute for Metabolism Research, Department of Neuronal Control of Metabolism, Cologne, Germany
| | - Frank Edenhofer
- grid.5771.40000 0001 2151 8122Leopold-Franzens-Universität Innsbruck, Institute for Molecular Biology, Innsbruck, Austria
| | - Frank Reimann
- grid.120073.70000 0004 0622 5016Cambridge Institute for Medical Research and Medical Research Council Metabolic Diseases Unit, Addenbrooke’s Hospital, Cambridge, UK
| | - Fiona M. Gribble
- grid.120073.70000 0004 0622 5016Cambridge Institute for Medical Research and Medical Research Council Metabolic Diseases Unit, Addenbrooke’s Hospital, Cambridge, UK
| | - Henning Fenselau
- grid.411097.a0000 0000 8852 305XPoliclinic for Endocrinology, Diabetes and Preventive Medicine (PEDP), University Hospital Cologne, Cologne, Germany ,grid.6190.e0000 0000 8580 3777Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Center of Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany ,grid.418034.a0000 0004 4911 0702Max Planck Institute for Metabolism Research, Research Group Synaptic Transmission in Energy Homeostasis, Cologne, Germany
| | - Peter Kloppenburg
- grid.6190.e0000 0000 8580 3777Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Center of Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany ,grid.6190.e0000 0000 8580 3777Institute for Zoology, Biocenter, University of Cologne, Cologne, Germany
| | - Frank T. Wunderlich
- grid.418034.a0000 0004 4911 0702Max Planck Institute for Metabolism Research, Department of Neuronal Control of Metabolism, Cologne, Germany ,grid.411097.a0000 0000 8852 305XPoliclinic for Endocrinology, Diabetes and Preventive Medicine (PEDP), University Hospital Cologne, Cologne, Germany ,grid.6190.e0000 0000 8580 3777Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Center of Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Jens C. Brüning
- grid.418034.a0000 0004 4911 0702Max Planck Institute for Metabolism Research, Department of Neuronal Control of Metabolism, Cologne, Germany ,grid.411097.a0000 0000 8852 305XPoliclinic for Endocrinology, Diabetes and Preventive Medicine (PEDP), University Hospital Cologne, Cologne, Germany ,grid.6190.e0000 0000 8580 3777Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD) and Center of Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany ,National Center for Diabetes Research (DZD), Ingolstädter Landstrasse 1, Neuherberg, Germany
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24
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Hori T, Cao J, Nishimura K, Ariyoshi M, Arimura Y, Kurumizaka H, Fukagawa T. Essentiality of CENP-A Depends on Its Binding Mode to HJURP. Cell Rep 2020; 33:108388. [PMID: 33207191 DOI: 10.1016/j.celrep.2020.108388] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 09/16/2020] [Accepted: 10/23/2020] [Indexed: 11/17/2022] Open
Abstract
CENP-A incorporation is critical for centromere specification and is mediated by the chaperone HJURP. The CENP-A-targeting domain (CATD) of CENP-A specifically binds to HJURP, and this binding is conserved. However, the binding interface of CENP-A-HJURP is yet to be understood. Here, we identify the critical residues for chicken CENP-A or HJURP. The A59Q mutation in the α1-helix of chicken CENP-A causes CENP-A mis-incorporation and subsequent cell death, whereas the corresponding mutation in human CENP-A does not. We also find that W53 of HJURP, which is a contact site of A59 in CENP-A, is also essential in chicken cells. Our comprehensive analyses reveal that the affinities of HJURP to CATD differ between chickens and humans. However, the introduction of two arginine residues to the chicken HJURP αA-helix suppresses CENP-A mis-incorporation in chicken cells expressing CENP-AA59Q. Our data explain the mechanisms and evolution of CENP-A essentiality by the CENP-A-HJURP interaction.
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Affiliation(s)
- Tetsuya Hori
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan.
| | - JingHui Cao
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Kohei Nishimura
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Mariko Ariyoshi
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yasuhiro Arimura
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Tatsuo Fukagawa
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan.
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25
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Ge MH, Wang W, Wu TH, Wen X, Al-Sheikh U, Chen LL, Yin SW, Wu JJ, Huang JH, He QQ, Liu H, Li R, Wang PZ, Wu ZX. Dual Recombining-out System for Spatiotemporal Gene Expression in C. elegans. iScience 2020; 23:101567. [PMID: 33083734 PMCID: PMC7549056 DOI: 10.1016/j.isci.2020.101567] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/12/2020] [Accepted: 09/11/2020] [Indexed: 01/01/2023] Open
Abstract
Specific recording, labeling, and spatiotemporal manipulating neurons are essential for neuroscience research. In this study, we developed a tripartite spatiotemporal gene induction system in C. elegans, which is based on the knockout of two transcriptional terminators (stops in short) by two different recombinases FLP and CRE. The recombinase sites (loxP and FRT) flanked stops after a ubiquitous promoter terminate transcription of target genes. FLP and CRE, induced by two promoters of overlapping expression, remove the stops (subsequent FLP/CRE-out). The system provides an "AND" gate strategy for specific gene expression in single types of cell(s). Combined with an inducible promoter or element, the system can control the spatiotemporal expression of genes in defined cell types, especially in cells or tissues lacking a specific promoter. This tripartite FLP/CRE-out gene expression system is a simple, labor- and cost-saving toolbox for cell type-specific and inducible gene expression in C. elegans.
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Affiliation(s)
- Ming-Hai Ge
- Key Laboratory of Molecular Biophysics of Ministry of Education, Institute of Biophysics and Biochemistry, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Wei Wang
- Key Laboratory of Molecular Biophysics of Ministry of Education, Institute of Biophysics and Biochemistry, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Tai-Hong Wu
- Key Laboratory of Molecular Biophysics of Ministry of Education, Institute of Biophysics and Biochemistry, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Xin Wen
- Key Laboratory of Molecular Biophysics of Ministry of Education, Institute of Biophysics and Biochemistry, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Umar Al-Sheikh
- Key Laboratory of Molecular Biophysics of Ministry of Education, Institute of Biophysics and Biochemistry, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Li-Li Chen
- Key Laboratory of Molecular Biophysics of Ministry of Education, Institute of Biophysics and Biochemistry, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Sheng-Wu Yin
- Key Laboratory of Molecular Biophysics of Ministry of Education, Institute of Biophysics and Biochemistry, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Jing-Jing Wu
- Key Laboratory of Molecular Biophysics of Ministry of Education, Institute of Biophysics and Biochemistry, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Jia-Hao Huang
- Key Laboratory of Molecular Biophysics of Ministry of Education, Institute of Biophysics and Biochemistry, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Qing-Qin He
- Key Laboratory of Molecular Biophysics of Ministry of Education, Institute of Biophysics and Biochemistry, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Hui Liu
- Key Laboratory of Molecular Biophysics of Ministry of Education, Institute of Biophysics and Biochemistry, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Rong Li
- Key Laboratory of Molecular Biophysics of Ministry of Education, Institute of Biophysics and Biochemistry, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Ping-Zhou Wang
- Key Laboratory of Molecular Biophysics of Ministry of Education, Institute of Biophysics and Biochemistry, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Zheng-Xing Wu
- Key Laboratory of Molecular Biophysics of Ministry of Education, Institute of Biophysics and Biochemistry, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
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26
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Voziyanova E, Li F, Shah R, Voziyanov Y. Genome targeting by hybrid Flp-TAL recombinases. Sci Rep 2020; 10:17479. [PMID: 33060660 PMCID: PMC7562724 DOI: 10.1038/s41598-020-74474-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 09/08/2020] [Indexed: 11/09/2022] Open
Abstract
Genome engineering is a rapidly evolving field that benefits from the availability of different tools that can be used to perform genome manipulation tasks. We describe here the development of the Flp-TAL recombinases that can target genomic FRT-like sequences in their native chromosomal locations. Flp-TAL recombinases are hybrid enzymes that are composed of two functional modules: a variant of site-specific tyrosine recombinase Flp, which can have either narrow or broad target specificity, and the DNA-binding domain of the transcription activator-like effector, TAL. In Flp-TAL, the TAL module is responsible for delivering and stabilizing the Flp module onto the desired genomic FRT-like sequence where the Flp module mediates recombination. We demonstrate the functionality of the Flp-TAL recombinases by performing integration and deletion experiments in human HEK-293 cells. In the integration experiments we targeted a vector to three genomic FRT-like sequences located in the β-globin locus. In the deletion experiments we excised ~ 15 kilobases of DNA that contained a fragment of the integrated vector sequence and the neighboring genome sequence. On average, the efficiency of the integration and deletion reactions was about 0.1% and 20%, respectively.
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Affiliation(s)
- Eugenia Voziyanova
- School of Biological Sciences, Louisiana Tech University, 1 Adams Blvd., Ruston, LA, 71272, USA
| | - Feng Li
- School of Biological Sciences, Louisiana Tech University, 1 Adams Blvd., Ruston, LA, 71272, USA
| | - Riddhi Shah
- Department of Medicine, Columbia University Medical Center, New York, NY, 10032, USA
| | - Yuri Voziyanov
- School of Biological Sciences, Louisiana Tech University, 1 Adams Blvd., Ruston, LA, 71272, USA.
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27
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Abstract
The mouse is one of the most widely used model organisms for genetic study. The tools available to alter the mouse genome have developed over the preceding decades from forward screens to gene targeting in stem cells to the recent influx of CRISPR approaches. In this review, we first consider the history of mice in genetic study, the development of classic approaches to genome modification, and how such approaches have been used and improved in recent years. We then turn to the recent surge of nuclease-mediated techniques and how they are changing the field of mouse genetics. Finally, we survey common classes of alleles used in mice and discuss how they might be engineered using different methods.
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Affiliation(s)
- James F Clark
- Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mt. Sinai, New York, New York 10029, USA
| | - Colin J Dinsmore
- Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mt. Sinai, New York, New York 10029, USA
| | - Philippe Soriano
- Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mt. Sinai, New York, New York 10029, USA
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28
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Fenno LE, Ramakrishnan C, Kim YS, Evans KE, Lo M, Vesuna S, Inoue M, Cheung KYM, Yuen E, Pichamoorthy N, Hong ASO, Deisseroth K. Comprehensive Dual- and Triple-Feature Intersectional Single-Vector Delivery of Diverse Functional Payloads to Cells of Behaving Mammals. Neuron 2020; 107:836-853.e11. [PMID: 32574559 PMCID: PMC7687746 DOI: 10.1016/j.neuron.2020.06.003] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 05/08/2020] [Accepted: 05/29/2020] [Indexed: 01/12/2023]
Abstract
The resolution and dimensionality with which biologists can characterize cell types have expanded dramatically in recent years, and intersectional consideration of such features (e.g., multiple gene expression and anatomical parameters) is increasingly understood to be essential. At the same time, genetically targeted technology for writing in and reading out activity patterns for cells in living organisms has enabled causal investigation in physiology and behavior; however, cell-type-specific delivery of these tools (including microbial opsins for optogenetics and genetically encoded Ca2+ indicators) has thus far fallen short of versatile targeting to cells jointly defined by many individually selected features. Here, we develop a comprehensive intersectional targeting toolbox including 39 novel vectors for joint-feature-targeted delivery of 13 molecular payloads (including opsins, indicators, and fluorophores), systematic approaches for development and optimization of new intersectional tools, hardware for in vivo monitoring of expression dynamics, and the first versatile single-virus tools (Triplesect) that enable targeting of triply defined cell types.
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Affiliation(s)
- Lief E Fenno
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Charu Ramakrishnan
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Yoon Seok Kim
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Kathryn E Evans
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Maisie Lo
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Sam Vesuna
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Masatoshi Inoue
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Kathy Y M Cheung
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Elle Yuen
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | | | - Alice S O Hong
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Karl Deisseroth
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
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29
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Bowling S, Sritharan D, Osorio FG, Nguyen M, Cheung P, Rodriguez-Fraticelli A, Patel S, Yuan WC, Fujiwara Y, Li BE, Orkin SH, Hormoz S, Camargo FD. An Engineered CRISPR-Cas9 Mouse Line for Simultaneous Readout of Lineage Histories and Gene Expression Profiles in Single Cells. Cell 2020; 181:1410-1422.e27. [PMID: 32413320 PMCID: PMC7529102 DOI: 10.1016/j.cell.2020.04.048] [Citation(s) in RCA: 139] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 02/20/2020] [Accepted: 04/24/2020] [Indexed: 12/29/2022]
Abstract
Tracing the lineage history of cells is key to answering diverse and fundamental questions in biology. Coupling of cell ancestry information with other molecular readouts represents an important goal in the field. Here, we describe the CRISPR array repair lineage tracing (CARLIN) mouse line and corresponding analysis tools that can be used to simultaneously interrogate the lineage and transcriptomic information of single cells in vivo. This model exploits CRISPR technology to generate up to 44,000 transcribed barcodes in an inducible fashion at any point during development or adulthood, is compatible with sequential barcoding, and is fully genetically defined. We have used CARLIN to identify intrinsic biases in the activity of fetal liver hematopoietic stem cell (HSC) clones and to uncover a previously unappreciated clonal bottleneck in the response of HSCs to injury. CARLIN also allows the unbiased identification of transcriptional signatures associated with HSC activity without cell sorting.
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Affiliation(s)
- Sarah Bowling
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Duluxan Sritharan
- Harvard Graduate Program in Biophysics, Harvard University, Cambridge, MA, USA; Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Fernando G Osorio
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Maximilian Nguyen
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Priscilla Cheung
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Alejo Rodriguez-Fraticelli
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Sachin Patel
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Wei-Chien Yuan
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Yuko Fujiwara
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Bin E Li
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Stuart H Orkin
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Boston, MA, USA
| | - Sahand Hormoz
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Systems Biology, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Fernando D Camargo
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
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30
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Wen W, Song S, Han Y, Chen H, Liu X, Qian Q. An efficient Screening System in Yeast to Select a Hyperactive piggyBac Transposase for Mammalian Applications. Int J Mol Sci 2020; 21:ijms21093064. [PMID: 32357554 PMCID: PMC7247424 DOI: 10.3390/ijms21093064] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/15/2020] [Accepted: 04/24/2020] [Indexed: 12/31/2022] Open
Abstract
As non-viral transgenic vectors, the piggyBac transposon system represents an attractive tool for gene delivery to achieve a long-term gene expression in immunotherapy applications due to its large cargo capacity, its lack of a trace of transposon and of genotoxic potential, and its highly engineered structure. However, further improvements in transpose activity are required for industrialization and clinical applications. Herein, we established a one-plasmid effective screening system and a two-step high-throughput screening process in yeast to isolate hyperactive mutants for mammalian cell applications. By applying this screening system, 15 hyperactive piggyBac transposases that exhibited higher transpose activity compared with optimized hyPBase in yeast and four mutants that showed higher transpose activity in mammalian cells were selected among 3000 hyPBase mutants. The most hyperactive transposase, bz-hyPBase, with four mutation sites showed an ability to yield high-efficiency editing in Chinese hamster ovarian carcinoma (CHO) cells and T cells, indicating that they could be expanded for gene therapy approaches. Finally, we tested the potential of this screening system in other versions of piggyBac transposase.
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Affiliation(s)
- Wen Wen
- Shanghai Cell Therapy Research Institute, Shanghai 201805, China; (W.W.); (S.S.); (Y.H.); (H.C.)
- Shanghai Cell Therapy Group, Shanghai 201805, China
| | - Shanshan Song
- Shanghai Cell Therapy Research Institute, Shanghai 201805, China; (W.W.); (S.S.); (Y.H.); (H.C.)
- Shanghai Cell Therapy Group, Shanghai 201805, China
| | - Yuchun Han
- Shanghai Cell Therapy Research Institute, Shanghai 201805, China; (W.W.); (S.S.); (Y.H.); (H.C.)
- Shanghai Cell Therapy Group, Shanghai 201805, China
| | - Haibin Chen
- Shanghai Cell Therapy Research Institute, Shanghai 201805, China; (W.W.); (S.S.); (Y.H.); (H.C.)
- Shanghai Cell Therapy Group, Shanghai 201805, China
| | - Xiangzhen Liu
- Shanghai Cell Therapy Research Institute, Shanghai 201805, China; (W.W.); (S.S.); (Y.H.); (H.C.)
- Shanghai Cell Therapy Group, Shanghai 201805, China
- Correspondence: (X.L.); (Q.Q.); Tel.: +86-021-5959-3168
| | - Qijun Qian
- Shanghai Cell Therapy Research Institute, Shanghai 201805, China; (W.W.); (S.S.); (Y.H.); (H.C.)
- Shanghai Cell Therapy Group, Shanghai 201805, China
- Correspondence: (X.L.); (Q.Q.); Tel.: +86-021-5959-3168
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31
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Cardot-Ruffino V, Chauvet V, Caligaris C, Bertrand-Chapel A, Chuvin N, Pommier RM, Valcourt U, Vincent D, Martel S, Aires S, Kaniewski B, Dubus P, Cassier P, Sentis S, Bartholin L. Generation of an Fsp1 (fibroblast-specific protein 1)-Flpo transgenic mouse strain. Genesis 2020; 58:e23359. [PMID: 32191380 PMCID: PMC7317532 DOI: 10.1002/dvg.23359] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 03/06/2020] [Accepted: 03/06/2020] [Indexed: 12/12/2022]
Abstract
Recombination systems represent a major breakthrough in the field of genetic model engineering. The Flp recombinases (Flp, Flpe, and Flpo) bind and cleave DNA Frt sites. We created a transgenic mouse strain ([Fsp1‐Flpo]) expressing the Flpo recombinase in fibroblasts. This strain was obtained by random insertion inside mouse zygotes after pronuclear injection. Flpo expression was placed under the control of the promoter of Fsp1 (fibroblast‐specific protein 1) gene, whose expression starts after gastrulation at Day 8.5 in cells of mesenchymal origin. We verified the correct expression and function of the Flpo enzyme by several ex vivo and in vivo approaches. The [Fsp1‐Flpo] strain represents a genuine tool to further target the recombination of transgenes with Frt sites specifically in cells of mesenchymal origin or with a fibroblastic phenotype.
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Affiliation(s)
- Victoire Cardot-Ruffino
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,Université de Lyon, Lyon, France.,Université Lyon 1, Lyon, France.,Centre Léon Bérard, Lyon, France
| | - Véronique Chauvet
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,Université de Lyon, Lyon, France.,Université Lyon 1, Lyon, France.,Centre Léon Bérard, Lyon, France
| | - Cassandre Caligaris
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,Université de Lyon, Lyon, France.,Université Lyon 1, Lyon, France.,Centre Léon Bérard, Lyon, France
| | - Adrien Bertrand-Chapel
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,Université de Lyon, Lyon, France.,Université Lyon 1, Lyon, France.,Centre Léon Bérard, Lyon, France
| | - Nicolas Chuvin
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,Université de Lyon, Lyon, France.,Université Lyon 1, Lyon, France.,Centre Léon Bérard, Lyon, France
| | - Roxane M Pommier
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,Université de Lyon, Lyon, France.,Université Lyon 1, Lyon, France.,Centre Léon Bérard, Lyon, France
| | - Ulrich Valcourt
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,Université de Lyon, Lyon, France.,Université Lyon 1, Lyon, France.,Centre Léon Bérard, Lyon, France
| | - David Vincent
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,Université de Lyon, Lyon, France.,Université Lyon 1, Lyon, France.,Centre Léon Bérard, Lyon, France.,Beatson Institute for Cancer Research, Glasgow, UK
| | - Sylvie Martel
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,Université de Lyon, Lyon, France.,Université Lyon 1, Lyon, France.,Centre Léon Bérard, Lyon, France
| | - Sophie Aires
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,Université de Lyon, Lyon, France.,Université Lyon 1, Lyon, France.,Centre Léon Bérard, Lyon, France
| | - Bastien Kaniewski
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,Université de Lyon, Lyon, France.,Université Lyon 1, Lyon, France.,Centre Léon Bérard, Lyon, France
| | - Pierre Dubus
- INSERM, Univ Bordeaux UMR1053 Bordeaux Research in Translational Oncology, Bordeaux, France.,CHU de Bordeaux, Bordeaux, France
| | - Philippe Cassier
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,Université de Lyon, Lyon, France.,Université Lyon 1, Lyon, France.,Centre Léon Bérard, Lyon, France.,Departement d'Oncologie Médicale, Centre Léon Bérard, Lyon, France
| | - Stéphanie Sentis
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,Université de Lyon, Lyon, France.,Université Lyon 1, Lyon, France.,Centre Léon Bérard, Lyon, France
| | - Laurent Bartholin
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,Université de Lyon, Lyon, France.,Université Lyon 1, Lyon, France.,Centre Léon Bérard, Lyon, France
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32
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Abstract
Cre-mediated recombination has become a powerful tool to confine gene deletions (conditional knockouts) or overexpression of genes (conditional knockin/overexpression). By spatiotemporal restriction of genetic manipulations, major problems of classical knockouts such as embryonic lethality or pleiotropy can be circumvented. Furthermore, Cre-mediated recombination has broad applications in the analysis of the cellular behavior of subpopulations and cell types as well as for genetic fate mapping. This chapter gives an overview about applications for the Cre/LoxP system and their execution.
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Affiliation(s)
- Claudius F Kratochwil
- Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Filippo M Rijli
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
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33
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Navabpour S, Kwapis JL, Jarome TJ. A neuroscientist's guide to transgenic mice and other genetic tools. Neurosci Biobehav Rev 2020; 108:732-748. [PMID: 31843544 PMCID: PMC8049509 DOI: 10.1016/j.neubiorev.2019.12.013] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 11/05/2019] [Accepted: 12/09/2019] [Indexed: 12/14/2022]
Abstract
The past decade has produced an explosion in the number and variety of genetic tools available to neuroscientists, resulting in an unprecedented ability to precisely manipulate the genome and epigenome in behaving animals. However, no single resource exists that describes all of the tools available to neuroscientists. Here, we review the genetic, transgenic, and viral techniques that are currently available to probe the complex relationship between genes and cognition. Topics covered include types of traditional transgenic mouse models (knockout, knock-in, reporter lines), inducible systems (Cre-loxP, Tet-On, Tet-Off) and cell- and circuit-specific systems (TetTag, TRAP, DIO-DREADD). Additionally, we provide details on virus-mediated and siRNA/shRNA approaches, as well as a comprehensive discussion of the myriad manipulations that can be made using the CRISPR-Cas9 system, including single base pair editing and spatially- and temporally-regulated gene-specific transcriptional control. Collectively, this review will serve as a guide to assist neuroscientists in identifying and choosing the appropriate genetic tools available to study the complex relationship between the brain and behavior.
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Affiliation(s)
- Shaghayegh Navabpour
- Fralin Biomedical Research Institute, Translational Biology, Medicine and Health, Roanoke, VA, USA
| | - Janine L Kwapis
- Department of Biology, Pennsylvania State University, College Park, PA, USA; Center for the Molecular Investigation of Neurological Disorders (CMIND), Pennsylvania State University, College Park, PA, USA.
| | - Timothy J Jarome
- Fralin Biomedical Research Institute, Translational Biology, Medicine and Health, Roanoke, VA, USA; Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA; School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.
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34
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Cela E, Sjöström PJ. Novel Optogenetic Approaches in Epilepsy Research. Front Neurosci 2019; 13:947. [PMID: 31551699 PMCID: PMC6743373 DOI: 10.3389/fnins.2019.00947] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/22/2019] [Indexed: 11/13/2022] Open
Abstract
Epilepsy is a major neurological disorder characterized by repeated seizures afflicting 1% of the global population. The emergence of seizures is associated with several comorbidities and severely decreases the quality of life of patients. Unfortunately, around 30% of patients do not respond to first-line treatment using anti-seizure drugs (ASDs). Furthermore, it is still unclear how seizures arise in the healthy brain. Therefore, it is critical to have well developed models where a causal understanding of epilepsy can be investigated. While the development of seizures has been studied in several animal models, using chemical or electrical induction, deciphering the results of such studies has been difficult due to the uncertainty of the cell population being targeted as well as potential confounds such as brain damage from the procedure itself. Here we describe novel approaches using combinations of optical and genetic methods for studying epileptogenesis. These approaches can circumvent some shortcomings associated with the classical animal models and may thus increase the likelihood of developing new treatment options.
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Affiliation(s)
- Elvis Cela
- Brain Repair and Integrative Neuroscience Program, Centre for Research in Neuroscience, Department of Medicine, Department of Neurology and Neurosurgery, The Research Institute of the McGill University Health Centre, Montreal General Hospital, Montreal, QC, Canada.,Integrated Program in Neuroscience, McGill University, Montreal, QC, Canada
| | - Per Jesper Sjöström
- Brain Repair and Integrative Neuroscience Program, Centre for Research in Neuroscience, Department of Medicine, Department of Neurology and Neurosurgery, The Research Institute of the McGill University Health Centre, Montreal General Hospital, Montreal, QC, Canada
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35
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Mutations in topoisomerase IIβ result in a B cell immunodeficiency. Nat Commun 2019; 10:3644. [PMID: 31409799 PMCID: PMC6692411 DOI: 10.1038/s41467-019-11570-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 07/23/2019] [Indexed: 02/01/2023] Open
Abstract
B cell development is a highly regulated process involving multiple differentiation steps, yet many details regarding this pathway remain unknown. Sequencing of patients with B cell-restricted immunodeficiency reveals autosomal dominant mutations in TOP2B. TOP2B encodes a type II topoisomerase, an essential gene required to alleviate topological stress during DNA replication and gene transcription, with no previously known role in B cell development. We use Saccharomyces cerevisiae, and knockin and knockout murine models, to demonstrate that patient mutations in TOP2B have a dominant negative effect on enzyme function, resulting in defective proliferation, survival of B-2 cells, causing a block in B cell development, and impair humoral function in response to immunization. Topoisomerases are required to release topological stress on DNA during replication and transcription. Here, Broderick et al. report genetic variants in TOP2B that cause a syndromic B cell immunodeficiency associated with reduced TOP2B function, defects in B cell development and B cell activation.
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36
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English JG, Olsen RHJ, Lansu K, Patel M, White K, Cockrell AS, Singh D, Strachan RT, Wacker D, Roth BL. VEGAS as a Platform for Facile Directed Evolution in Mammalian Cells. Cell 2019; 178:748-761.e17. [PMID: 31280962 DOI: 10.1016/j.cell.2019.05.051] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 02/06/2019] [Accepted: 05/23/2019] [Indexed: 02/08/2023]
Abstract
Directed evolution, artificial selection toward designed objectives, is routinely used to develop new molecular tools and therapeutics. Successful directed molecular evolution campaigns repeatedly test diverse sequences with a designed selective pressure. Unicellular organisms and their viral pathogens are exceptional for this purpose and have been used for decades. However, many desirable targets of directed evolution perform poorly or unnaturally in unicellular backgrounds. Here, we present a system for facile directed evolution in mammalian cells. Using the RNA alphavirus Sindbis as a vector for heredity and diversity, we achieved 24-h selection cycles surpassing 10-3 mutations per base. Selection is achieved through genetically actuated sequences internal to the host cell, thus the system's name: viral evolution of genetically actuating sequences, or "VEGAS." Using VEGAS, we evolve transcription factors, GPCRs, and allosteric nanobodies toward functional signaling endpoints each in less than 1 weeks' time.
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Affiliation(s)
- Justin G English
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27514, USA.
| | - Reid H J Olsen
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Katherine Lansu
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Michael Patel
- Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Karoline White
- Department of Biology, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Adam S Cockrell
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Darshan Singh
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Ryan T Strachan
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Daniel Wacker
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Bryan L Roth
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27514, USA.
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37
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Zhao Y, Kim JY, Karan R, Jung JH, Pathak B, Williamson B, Kannan B, Wang D, Fan C, Yu W, Dong S, Srivastava V, Altpeter F. Generation of a selectable marker free, highly expressed single copy locus as landing pad for transgene stacking in sugarcane. PLANT MOLECULAR BIOLOGY 2019; 100:247-263. [PMID: 30919152 DOI: 10.1007/s11103-019-00856-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 03/15/2019] [Indexed: 05/23/2023]
Abstract
A selectable marker free, highly expressed single copy locus flanked by insulators was created as landing pad for transgene stacking in sugarcane. These events displayed superior transgene expression compared to single-copy transgenic lines lacking insulators. Excision of the selectable marker gene from transgenic sugarcane lines was supported by FLPe/FRT site-specific recombination. Sugarcane, a tropical C4 grass in the genus Saccharum (Poaceae), accounts for nearly 80% of sugar produced worldwide and is also an important feedstock for biofuel production. Generating transgenic sugarcane with predictable and stable transgene expression is critical for crop improvement. In this study, we generated a highly expressed single copy locus as landing pad for transgene stacking. Transgenic sugarcane lines with stable integration of a single copy nptII expression cassette flanked by insulators supported higher transgene expression along with reduced line to line variation when compared to single copy events without insulators by NPTII ELISA analysis. Subsequently, the nptII selectable marker gene was efficiently excised from the sugarcane genome by the FLPe/FRT site-specific recombination system to create selectable marker free plants. This study provides valuable resources for future gene stacking using site-specific recombination or genome editing tools.
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Affiliation(s)
- Yang Zhao
- Agronomy Department, Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida - IFAS, Gainesville, FL, 32611, USA
| | - Jae Y Kim
- Agronomy Department, Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida - IFAS, Gainesville, FL, 32611, USA
- Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan, 32439, Republic of Korea
| | - Ratna Karan
- Agronomy Department, Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida - IFAS, Gainesville, FL, 32611, USA
| | - Je H Jung
- Agronomy Department, Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida - IFAS, Gainesville, FL, 32611, USA
- Smart Farm Research Center, Institute of Natural Products, Korea Institute of Science and Technology (KIST), Gangwon-do, 25451, Republic of Korea
| | - Bhuvan Pathak
- Agronomy Department, Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida - IFAS, Gainesville, FL, 32611, USA
| | - Bruce Williamson
- Agronomy Department, Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida - IFAS, Gainesville, FL, 32611, USA
| | - Baskaran Kannan
- Agronomy Department, Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida - IFAS, Gainesville, FL, 32611, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Florida - IFAS, Gainesville, FL, 32611, USA
| | - Duoduo Wang
- Agronomy Department, Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida - IFAS, Gainesville, FL, 32611, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Florida - IFAS, Gainesville, FL, 32611, USA
| | - Chunyang Fan
- Syngenta Crop Protection, LLC, Research Triangle Park, NC, 27709, USA
| | - Wenjin Yu
- Syngenta Crop Protection, LLC, Research Triangle Park, NC, 27709, USA
| | - Shujie Dong
- Syngenta Crop Protection, LLC, Research Triangle Park, NC, 27709, USA
| | - Vibha Srivastava
- Crop, Soil and Environmental Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Fredy Altpeter
- Agronomy Department, Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida - IFAS, Gainesville, FL, 32611, USA.
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Florida - IFAS, Gainesville, FL, 32611, USA.
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38
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A single reporter mouse line for Vika, Flp, Dre, and Cre-recombination. Sci Rep 2018; 8:14453. [PMID: 30262904 PMCID: PMC6160450 DOI: 10.1038/s41598-018-32802-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 09/13/2018] [Indexed: 11/28/2022] Open
Abstract
Site-specific recombinases (SSR) are utilized as important genome engineering tools to precisely modify the genome of mice and other model organisms. Reporter mice that mark cells that at any given time had expressed the enzyme are frequently used for lineage tracing and to characterize newly generated mice expressing a recombinase from a chosen promoter. With increasing sophistication of genome alteration strategies, the demand for novel SSR systems that efficiently and specifically recombine their targets is rising and several SSR-systems are now used in combination to address complex biological questions in vivo. Generation of reporter mice for each one of these recombinases is cumbersome and increases the number of mouse lines that need to be maintained in animal facilities. Here we present a multi-reporter mouse line for loci-of-recombination (X) (MuX) that streamlines the characterization of mice expressing prominent recombinases. MuX mice constitutively express nuclear green fluorescent protein after recombination by either Cre, Flp, Dre or Vika recombinase, rationalizing the number of animal lines that need to be maintained. We also pioneer the use of the Vika/vox system in mice, illustrating its high efficacy and specificity, thereby facilitating future designs of sophisticated recombinase-based in vivo genome engineering strategies.
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39
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Godfrey TC, Wildman BJ, Beloti MM, Kemper AG, Ferraz EP, Roy B, Rehan M, Afreen LH, Kim E, Lengner CJ, Hassan Q. The microRNA-23a cluster regulates the developmental HoxA cluster function during osteoblast differentiation. J Biol Chem 2018; 293:17646-17660. [PMID: 30242124 DOI: 10.1074/jbc.ra118.003052] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 08/22/2018] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRs) and Hox transcription factors have decisive roles in postnatal bone formation and homeostasis. In silico analysis identified extensive interaction between HOXA cluster mRNA and microRNAs from the miR-23a cluster. However, Hox regulation by the miR-23a cluster during osteoblast differentiation remains undefined. We examined this regulation in preosteoblasts and in a novel miR-23a cluster knockdown mouse model. Overexpression and knockdown of the miR-23a cluster in preosteoblasts decreased and increased, respectively, the expression of the proteins HOXA5, HOXA10, and HOXA11; these proteins' mRNAs exhibited significant binding with the miR-23a cluster miRNAs, and miRNA 3'-UTR reporter assays confirmed repression. Importantly, during periods correlating with development and differentiation of bone cells, we found an inverse pattern of expression between HoxA factors and members of the miR-23a cluster. HOXA5 and HOXA11 bound to bone-specific promoters, physically interacted with transcription factor RUNX2, and regulated bone-specific genes. Depletion of HOXA5 or HOXA11 in preosteoblasts also decreased cellular differentiation. Additionally, stable overexpression of the miR-23a cluster in osteoblasts decreased the recruitment of HOXA5 and HOXA11 to osteoblast gene promoters, significantly inhibiting histone H3 acetylation. Heterozygous miR-23a cluster knockdown female mice (miR-23a ClWT/ZIP) had significantly increased trabecular bone mass when compared with WT mice. Furthermore, miR-23a cluster knockdown in calvarial osteoblasts of these mice increased the recruitment of HOXA5 and HOXA11, with a substantial enrichment of promoter histone H3 acetylation. Taken together, these findings demonstrate that the miR-23a cluster is required for maintaining stage-specific HoxA factor expression during osteogenesis.
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Affiliation(s)
- Tanner C Godfrey
- From the RNA Biology and Epigenetics Laboratory, Department of Oral and Maxillofacial Surgery, School of Dentistry, University of Alabama Birmingham, Birmingham, Alabama 35294
| | - Benjamin J Wildman
- From the RNA Biology and Epigenetics Laboratory, Department of Oral and Maxillofacial Surgery, School of Dentistry, University of Alabama Birmingham, Birmingham, Alabama 35294
| | - Marcio M Beloti
- the School of Dentistry of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, SP 14040-904, Brazil, and
| | - Austin G Kemper
- From the RNA Biology and Epigenetics Laboratory, Department of Oral and Maxillofacial Surgery, School of Dentistry, University of Alabama Birmingham, Birmingham, Alabama 35294
| | - Emanuela P Ferraz
- the School of Dentistry of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, SP 14040-904, Brazil, and
| | - Bhaskar Roy
- From the RNA Biology and Epigenetics Laboratory, Department of Oral and Maxillofacial Surgery, School of Dentistry, University of Alabama Birmingham, Birmingham, Alabama 35294
| | - Mohammad Rehan
- From the RNA Biology and Epigenetics Laboratory, Department of Oral and Maxillofacial Surgery, School of Dentistry, University of Alabama Birmingham, Birmingham, Alabama 35294
| | - Lubana H Afreen
- From the RNA Biology and Epigenetics Laboratory, Department of Oral and Maxillofacial Surgery, School of Dentistry, University of Alabama Birmingham, Birmingham, Alabama 35294
| | - Eddy Kim
- From the RNA Biology and Epigenetics Laboratory, Department of Oral and Maxillofacial Surgery, School of Dentistry, University of Alabama Birmingham, Birmingham, Alabama 35294
| | - Christopher J Lengner
- the Department of Biomedical Sciences, School of Veterinary Medicine, and Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Quamarul Hassan
- From the RNA Biology and Epigenetics Laboratory, Department of Oral and Maxillofacial Surgery, School of Dentistry, University of Alabama Birmingham, Birmingham, Alabama 35294,
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40
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Lamas-Toranzo I, Ramos-Ibeas P, Pericuesta E, Bermejo-Álvarez P. Directions and applications of CRISPR technology in livestock research. Anim Reprod 2018; 15:292-300. [PMID: 34178152 PMCID: PMC8202460 DOI: 10.21451/1984-3143-ar2018-0075] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The ablation (KO) or targeted insertion (KI) of specific genes or sequences has been essential
to test their roles on a particular biological process. Unfortunately, such genome modifications
have been largely limited to the mouse model, as the only way to achieve targeted mutagenesis
in other mammals required from somatic cell nuclear transfer, a time- and resource-consuming
technique. This difficulty has left research in livestock species largely devoided of KO
and targeted KI models, crucial tools to uncover the molecular roots of any physiological
or pathological process. Luckily, the eruption of site-specific endonucleases, and particularly
CRISPR technology, has empowered farm animal scientists to consider projects that could
not develop before. In this sense, the availability of genome modification in livestock species
is meant to change the way research is performed on many fields, switching from descriptive
and correlational approaches to experimental research. In this review we will provide some
guidance about how the genome can be edited by CRISPR and the possible strategies to achieve
KO or KI, paying special attention to an initially overlooked phenomenon: mosaicism. Mosaicism
is produced when the zygote´s genome edition occurs after its DNA has replicated,
and is characterized by the presence of more than two alleles in the same individual, an undesirable
outcome when attempting direct KO generation. Finally, the possible applications on different
fields of livestock research, such as reproduction or infectious diseases are discussed.
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Affiliation(s)
| | | | - Eva Pericuesta
- Department Reproducción Animal, INIA, 28040 Madrid, Spain
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41
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Hobeika E, Dautzenberg M, Levit-Zerdoun E, Pelanda R, Reth M. Conditional Selection of B Cells in Mice With an Inducible B Cell Development. Front Immunol 2018; 9:1806. [PMID: 30127788 PMCID: PMC6087743 DOI: 10.3389/fimmu.2018.01806] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 07/23/2018] [Indexed: 11/13/2022] Open
Abstract
Developing B cells undergo defined maturation steps in the bone marrow and in the spleen. The timing and the factors that control these differentiation steps are not fully understood. By targeting the B cell-restricted mb-1 locus to generate an mb-1 allele that expresses a tamoxifen inducible Cre and another allele in which mb-1 expression can be controlled by Cre, we have established a mouse model with an inducible B cell compartment. With these mice, we studied in detail the kinetics of B cell development and the consequence of BCR activation at a defined B cell maturation stage. Contrary to expectations, transitional 1-B cells exposed to anti-IgM reagents in vivo did not die but instead developed into transitional 2 (T2)-B cells with upregulated Bcl-2 expression. We show, however, that these T2-B cells had an increased dependency on the B cell survival factor B cell activating factor when compared to non-stimulated B cells. Overall, our findings indicate that the inducible mb-1 mouse strain represents a useful model, which allows studying the signals that control the selection of B cells in greater detail.
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Affiliation(s)
- Elias Hobeika
- Centre for Biological Signaling Studies (BIOSS), Biology III, Faculty of Biology, Albert-Ludwigs-University of Freiburg, Freiburg, Germany.,Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Marcel Dautzenberg
- Centre for Biological Signaling Studies (BIOSS), Biology III, Faculty of Biology, Albert-Ludwigs-University of Freiburg, Freiburg, Germany.,Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Ella Levit-Zerdoun
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.,Department of Molecular Immunology, Biology III, Faculty of Biology, Albert-Ludwigs-University of Freiburg, Freiburg, Germany.,International Max Planck Research School for Molecular and Cellular Biology, Freiburg, Germany
| | - Roberta Pelanda
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States
| | - Michael Reth
- Centre for Biological Signaling Studies (BIOSS), Biology III, Faculty of Biology, Albert-Ludwigs-University of Freiburg, Freiburg, Germany.,Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
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42
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Yu J, Zanotti S, Schilling L, Canalis E. Nuclear factor of activated T cells 2 is required for osteoclast differentiation and function in vitro but not in vivo. J Cell Biochem 2018; 119:9334-9345. [PMID: 30010214 DOI: 10.1002/jcb.27212] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 05/30/2018] [Indexed: 01/09/2023]
Abstract
Nuclear factor of activated T cells (NFAT) c2 is important for the immune response and it compensates for NFATc1 for its effects on osteoclastogenesis, but its role in this process is not established. To study the function of NFATc2 in the skeleton, Nfatc2loxP/loxP mice, where the Nfact2 exon 2 is flanked by loxP sequences, were created and mated with mice expressing the Cre recombinase under the control of the Lyz2 promoter. Bone marrow-derived macrophage (BMM) from Lyz2Cre/WT ;Nfatc2Δ/Δ mice cultured in the presence of macrophage-colony stimulating factor and receptor activator of NF-κB ligand exhibited a decrease in the number and size of osteoclasts and a smaller sealing zone when compared to BMMs from Nfatc2loxP/loxP littermate controls. Bone resorption was decreased in osteoclasts from Lyz2Cre/WT ;Nfatc2Δ/Δ mice. This demonstrates that NFATc2 is necessary for optimal osteoclast maturation and function in vitro. Male and female Lyz2Cre/WT ;Nfatc2Δ/Δ mice did not exhibit an obvious skeletal phenotype by microcomputed tomography (μCT) at either 1 or 4 months of age when compared to Nfatc2loxP/loxP sex-matched littermates. Bone histomorphometry confirmed the μCT results, and conditional 4-month-old Lyz2Cre/WT ;Nfatc2Δ/Δ mice did not exhibit changes in parameters of bone histomorphometry. In conclusion, NFATc2 is necessary for optimal osteoclastogenesis in vitro, but its downregulation in the myeloid lineage has no consequences in skeletal remodeling in vivo.
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Affiliation(s)
- Jungeun Yu
- Department of Orthopaedic Surgery, UConn Musculoskeletal Institute, UConn Health, Farmington, Connecticut
| | - Stefano Zanotti
- Department of Orthopaedic Surgery, UConn Musculoskeletal Institute, UConn Health, Farmington, Connecticut
- Department of Medicine, UConn Musculoskeletal Institute, UConn Health, Farmington, Connecticut
| | - Lauren Schilling
- Department of Orthopaedic Surgery, UConn Musculoskeletal Institute, UConn Health, Farmington, Connecticut
| | - Ernesto Canalis
- Department of Orthopaedic Surgery, UConn Musculoskeletal Institute, UConn Health, Farmington, Connecticut
- Department of Medicine, UConn Musculoskeletal Institute, UConn Health, Farmington, Connecticut
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43
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Bogdanove AJ, Bohm A, Miller JC, Morgan RD, Stoddard BL. Engineering altered protein-DNA recognition specificity. Nucleic Acids Res 2018; 46:4845-4871. [PMID: 29718463 PMCID: PMC6007267 DOI: 10.1093/nar/gky289] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 04/03/2018] [Accepted: 04/06/2018] [Indexed: 02/07/2023] Open
Abstract
Protein engineering is used to generate novel protein folds and assemblages, to impart new properties and functions onto existing proteins, and to enhance our understanding of principles that govern protein structure. While such approaches can be employed to reprogram protein-protein interactions, modifying protein-DNA interactions is more difficult. This may be related to the structural features of protein-DNA interfaces, which display more charged groups, directional hydrogen bonds, ordered solvent molecules and counterions than comparable protein interfaces. Nevertheless, progress has been made in the redesign of protein-DNA specificity, much of it driven by the development of engineered enzymes for genome modification. Here, we summarize the creation of novel DNA specificities for zinc finger proteins, meganucleases, TAL effectors, recombinases and restriction endonucleases. The ease of re-engineering each system is related both to the modularity of the protein and the extent to which the proteins have evolved to be capable of readily modifying their recognition specificities in response to natural selection. The development of engineered DNA binding proteins that display an ideal combination of activity, specificity, deliverability, and outcomes is not a fully solved problem, however each of the current platforms offers unique advantages, offset by behaviors and properties requiring further study and development.
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Affiliation(s)
- Adam J Bogdanove
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Andrew Bohm
- Sackler School of Graduate Biomedical Sciences, Tufts University, 136 Harrison Avenue, Boston, MA 02111, USA
| | - Jeffrey C Miller
- Sangamo Therapeutics Inc. 501 Canal Blvd., Richmond, CA 94804, USA
| | - Richard D Morgan
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Barry L Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98019, USA
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44
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Szczesny RJ, Kowalska K, Klosowska-Kosicka K, Chlebowski A, Owczarek EP, Warkocki Z, Kulinski TM, Adamska D, Affek K, Jedroszkowiak A, Kotrys AV, Tomecki R, Krawczyk PS, Borowski LS, Dziembowski A. Versatile approach for functional analysis of human proteins and efficient stable cell line generation using FLP-mediated recombination system. PLoS One 2018; 13:e0194887. [PMID: 29590189 PMCID: PMC5874048 DOI: 10.1371/journal.pone.0194887] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 03/12/2018] [Indexed: 12/21/2022] Open
Abstract
Deciphering a function of a given protein requires investigating various biological aspects. Usually, the protein of interest is expressed with a fusion tag that aids or allows subsequent analyses. Additionally, downregulation or inactivation of the studied gene enables functional studies. Development of the CRISPR/Cas9 methodology opened many possibilities but in many cases it is restricted to non-essential genes. Recombinase-dependent gene integration methods, like the Flp-In system, are very good alternatives. The system is widely used in different research areas, which calls for the existence of compatible vectors and efficient protocols that ensure straightforward DNA cloning and generation of stable cell lines. We have created and validated a robust series of 52 vectors for streamlined generation of stable mammalian cell lines using the FLP recombinase-based methodology. Using the sequence-independent DNA cloning method all constructs for a given coding-sequence can be made with just three universal PCR primers. Our collection allows tetracycline-inducible expression of proteins with various tags suitable for protein localization, FRET, bimolecular fluorescence complementation (BiFC), protein dynamics studies (FRAP), co-immunoprecipitation, the RNA tethering assay and cell sorting. Some of the vectors contain a bidirectional promoter for concomitant expression of miRNA and mRNA, so that a gene can be silenced and its product replaced by a mutated miRNA-insensitive version. Our toolkit and protocols have allowed us to create more than 500 constructs with ease. We demonstrate the efficacy of our vectors by creating stable cell lines with various tagged proteins (numatrin, fibrillarin, coilin, centrin, THOC5, PCNA). We have analysed transgene expression over time to provide a guideline for future experiments and compared the effectiveness of commonly used inducers for tetracycline-responsive promoters. As proof of concept we examined the role of the exoribonuclease XRN2 in transcription termination by RNAseq.
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Affiliation(s)
- Roman J. Szczesny
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
- * E-mail: (RJS); (AD)
| | - Katarzyna Kowalska
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Kamila Klosowska-Kosicka
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Aleksander Chlebowski
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Ewelina P. Owczarek
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Zbigniew Warkocki
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Tomasz M. Kulinski
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Dorota Adamska
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Kamila Affek
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Agata Jedroszkowiak
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Anna V. Kotrys
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Rafal Tomecki
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Pawel S. Krawczyk
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Lukasz S. Borowski
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Andrzej Dziembowski
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
- * E-mail: (RJS); (AD)
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45
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Sanclemente M, Francoz S, Esteban-Burgos L, Bousquet-Mur E, Djurec M, Lopez-Casas PP, Hidalgo M, Guerra C, Drosten M, Musteanu M, Barbacid M. c-RAF Ablation Induces Regression of Advanced Kras/Trp53 Mutant Lung Adenocarcinomas by a Mechanism Independent of MAPK Signaling. Cancer Cell 2018; 33:217-228.e4. [PMID: 29395869 DOI: 10.1016/j.ccell.2017.12.014] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 10/24/2017] [Accepted: 12/21/2017] [Indexed: 02/07/2023]
Abstract
A quarter of all solid tumors harbor KRAS oncogenes. Yet, no selective drugs have been approved to treat these malignancies. Genetic interrogation of the MAPK pathway revealed that systemic ablation of MEK or ERK kinases in adult mice prevent tumor development but are unacceptably toxic. Here, we demonstrate that ablation of c-RAF expression in advanced tumors driven by KrasG12V/Trp53 mutations leads to significant tumor regression with no detectable appearance of resistance mechanisms. Tumor regression results from massive apoptosis. Importantly, systemic abrogation of c-RAF expression does not inhibit canonical MAPK signaling, hence, resulting in limited toxicities. These results are of significant relevance for the design of therapeutic strategies to treat K-RAS mutant cancers.
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Affiliation(s)
- Manuel Sanclemente
- Molecular Oncology Program, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid 28029, Spain
| | - Sarah Francoz
- Molecular Oncology Program, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid 28029, Spain
| | - Laura Esteban-Burgos
- Molecular Oncology Program, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid 28029, Spain
| | - Emilie Bousquet-Mur
- Molecular Oncology Program, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid 28029, Spain
| | - Magdolna Djurec
- Molecular Oncology Program, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid 28029, Spain
| | - Pedro P Lopez-Casas
- Clinical Research Program, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid 28029, Spain
| | - Manuel Hidalgo
- Clinical Research Program, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid 28029, Spain
| | - Carmen Guerra
- Molecular Oncology Program, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid 28029, Spain
| | - Matthias Drosten
- Molecular Oncology Program, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid 28029, Spain
| | - Monica Musteanu
- Molecular Oncology Program, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid 28029, Spain.
| | - Mariano Barbacid
- Molecular Oncology Program, Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid 28029, Spain.
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46
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Beel S, Moisse M, Damme M, De Muynck L, Robberecht W, Van Den Bosch L, Saftig P, Van Damme P. Progranulin functions as a cathepsin D chaperone to stimulate axonal outgrowth in vivo. Hum Mol Genet 2018; 26:2850-2863. [PMID: 28453791 PMCID: PMC5886064 DOI: 10.1093/hmg/ddx162] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 04/21/2017] [Indexed: 12/12/2022] Open
Abstract
Loss of function mutations in progranulin (GRN) cause frontotemporal dementia, but how GRN haploinsufficiency causes neuronal dysfunction remains unclear. We previously showed that GRN is neurotrophic in vitro. Here, we used an in vivo axonal outgrowth system and observed a delayed recovery in GRN-/- mice after facial nerve injury. This deficit was rescued by reintroduction of human GRN and relied on its C-terminus and on neuronal GRN production. Transcriptome analysis of the facial motor nucleus post injury identified cathepsin D (CTSD) as the most upregulated gene. In aged GRN-/- cortices, CTSD was also upregulated, but the relative CTSD activity was reduced and improved upon exogenous GRN addition. Moreover, GRN and its C-terminal granulin domain granulinE (GrnE) both stimulated the proteolytic activity of CTSD in vitro. Pull-down experiments confirmed a direct interaction between GRN and CTSD. This interaction was also observed with GrnE and stabilized the CTSD enzyme at different temperatures. Investigating the importance of this interaction for axonal regeneration in vivo we found that, although individually tolerated, a combined reduction of GRN and CTSD synergistically reduced axonal outgrowth. Our data links the neurotrophic effect of GRN and GrnE with a lysosomal chaperone function on CTSD to maintain its proteolytic capacity.
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Affiliation(s)
- Sander Beel
- Department of Neurosciences, Experimental Neurology and Leuven Institute for Neuroscience and Disease (LIND), KU Leuven - University of Leuven, B-3000 Leuven, Belgium.,VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, B-3000 Leuven, Belgium
| | - Matthieu Moisse
- Department of Neurosciences, Experimental Neurology and Leuven Institute for Neuroscience and Disease (LIND), KU Leuven - University of Leuven, B-3000 Leuven, Belgium.,VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, B-3000 Leuven, Belgium
| | - Markus Damme
- Biochemical Institute of the Christian-Albrechts University Kiel, D-24098 Kiel, Germany
| | - Louis De Muynck
- Department of Neurosciences, Experimental Neurology and Leuven Institute for Neuroscience and Disease (LIND), KU Leuven - University of Leuven, B-3000 Leuven, Belgium.,VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, B-3000 Leuven, Belgium
| | - Wim Robberecht
- Department of Neurosciences, Experimental Neurology and Leuven Institute for Neuroscience and Disease (LIND), KU Leuven - University of Leuven, B-3000 Leuven, Belgium.,Department of Neurology, University Hospitals Leuven, B-3000 Leuven, Belgium
| | - Ludo Van Den Bosch
- Department of Neurosciences, Experimental Neurology and Leuven Institute for Neuroscience and Disease (LIND), KU Leuven - University of Leuven, B-3000 Leuven, Belgium.,VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, B-3000 Leuven, Belgium
| | - Paul Saftig
- Biochemical Institute of the Christian-Albrechts University Kiel, D-24098 Kiel, Germany
| | - Philip Van Damme
- Department of Neurosciences, Experimental Neurology and Leuven Institute for Neuroscience and Disease (LIND), KU Leuven - University of Leuven, B-3000 Leuven, Belgium.,VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, B-3000 Leuven, Belgium.,Department of Neurology, University Hospitals Leuven, B-3000 Leuven, Belgium
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47
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Inducible knockdown of procollagen I protects mice from liver fibrosis and leads to dysregulated matrix genes and attenuated inflammation. Matrix Biol 2017; 66:34-49. [PMID: 29122677 DOI: 10.1016/j.matbio.2017.11.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 11/01/2017] [Accepted: 11/02/2017] [Indexed: 02/06/2023]
Abstract
Organ fibrosis is characterized by a chronic wound-healing response, with excess deposition of extracellular matrix components. Here, collagen type I represents the most abundant scar component and a primary target for antifibrotic therapies. Liver fibrosis can progress to cirrhosis and primary liver cancer, which are the major causes of liver related morbidity and mortality. However, a (pro-)collagen type I specific therapy remains difficult and its therapeutic abrogation may incur unwanted side effects. We therefore designed tetracycline-regulated procollagen alpha1(I) short hairpin (sh)RNA expressing mice that permit a highly efficient inducible knockdown of the procollagen alpha1(I) gene in activated (myo-)fibroblasts, to study the effect of induced procollagen type I deficiency. Transgenic mice were generated using recombinase-mediated integration in embryonic stem cells or zinc-finger nuclease-aided genomic targeting combined with miR30-shRNA technology. Liver fibrosis was induced in transgenic mice by carbon tetrachloride, either without or with doxycycline supplementation. Doxycycline treated mice showed an 80-90% suppression of procollagen alpha1(I) transcription and a 40-50% reduction in hepatic collagen accumulation. Procollagen alpha1(I) knockdown also downregulated procollagens type III, IV and VI and other fibrosis related parameters. Moreover, this was associated with an attenuation of chronic inflammation, suggesting that collagen type I serves not only as major scar component, but also as modulator of other collagens and promoter of chronic inflammation.
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Baker O, Tsurkan S, Fu J, Klink B, Rump A, Obst M, Kranz A, Schröck E, Anastassiadis K, Stewart AF. The contribution of homology arms to nuclease-assisted genome engineering. Nucleic Acids Res 2017; 45:8105-8115. [PMID: 28582546 PMCID: PMC5570031 DOI: 10.1093/nar/gkx497] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 05/30/2017] [Indexed: 01/29/2023] Open
Abstract
Designer nucleases like CRISPR/Cas9 enable fluent site-directed damage or small mutations in many genomes. Strategies for their use to achieve more complex tasks like regional exchanges for gene humanization or the establishment of conditional alleles are still emerging. To optimize Cas9-assisted targeting, we measured the relationship between targeting frequency and homology length in targeting constructs using a hypoxanthine-guanine phosphoribosyl-transferase assay in mouse embryonic stem cells. Targeting frequency with supercoiled plasmids improved steeply up to 2 kb total homology and continued to increase with even longer homology arms, thereby implying that Cas9-assisted targeting efficiencies can be improved using homology arms of 1 kb or greater. To humanize the Kmt2d gene, we built a hybrid mouse/human targeting construct in a bacterial artificial chromosome by recombineering. To simplify the possible outcomes, we employed a single Cas9 cleavage strategy and best achieved the intended 42 kb regional exchange with a targeting construct including a very long homology arm to recombine ∼42 kb away from the cleavage site. We recommend the use of long homology arm targeting constructs for accurate and efficient complex genome engineering, particularly when combined with the simplifying advantages of using just one Cas9 cleavage at the genome target site.
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Affiliation(s)
- Oliver Baker
- Stem Cell Engineering, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany.,Genomics, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | - Sarah Tsurkan
- Genomics, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | - Jun Fu
- Genomics, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany.,Shandong University-Helmholtz Joint Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Shanda Nanlu 27, 250100 Jinan, People's Republic of China
| | - Barbara Klink
- Institute for Clinical Genetics, Faculty of Medicine, Carl Gustav Carus, Technische Universität Dresden, Fetscherstrasse 74, Dresden 01307, Germany
| | - Andreas Rump
- Institute for Clinical Genetics, Faculty of Medicine, Carl Gustav Carus, Technische Universität Dresden, Fetscherstrasse 74, Dresden 01307, Germany
| | - Mandy Obst
- Stem Cell Engineering, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany.,Genomics, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | - Andrea Kranz
- Genomics, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | - Evelin Schröck
- Institute for Clinical Genetics, Faculty of Medicine, Carl Gustav Carus, Technische Universität Dresden, Fetscherstrasse 74, Dresden 01307, Germany
| | - Konstantinos Anastassiadis
- Stem Cell Engineering, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | - A Francis Stewart
- Genomics, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
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49
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Togawa Y, Nunoshiba T, Hiratsu K. Cre/lox-based multiple markerless gene disruption in the genome of the extreme thermophile Thermus thermophilus. Mol Genet Genomics 2017; 293:277-291. [PMID: 28840320 DOI: 10.1007/s00438-017-1361-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 08/20/2017] [Indexed: 12/01/2022]
Abstract
Markerless gene-disruption technology is particularly useful for effective genetic analyses of Thermus thermophilus (T. thermophilus), which have a limited number of selectable markers. In an attempt to develop a novel system for the markerless disruption of genes in T. thermophilus, we applied a Cre/lox system to construct a triple gene disruptant. To achieve this, we constructed two genetic tools, a loxP-htk-loxP cassette and cre-expressing plasmid, pSH-Cre, for gene disruption and removal of the selectable marker by Cre-mediated recombination. We found that the Cre/lox system was compatible with the proliferation of the T. thermophilus HB27 strain at the lowest growth temperature (50 °C), and thus succeeded in establishing a triple gene disruptant, the (∆TTC1454::loxP, ∆TTC1535KpnI::loxP, ∆TTC1576::loxP) strain, without leaving behind a selectable marker. During the process of the sequential disruption of multiple genes, we observed the undesired deletion and inversion of the chromosomal region between multiple loxP sites that were induced by Cre-mediated recombination. Therefore, we examined the effects of a lox66-htk-lox71 cassette by exploiting the mutant lox sites, lox66 and lox71, instead of native loxP sites. We successfully constructed a (∆TTC1535::lox72, ∆TTC1537::lox72) double gene disruptant without inducing the undesired deletion of the 0.7-kbp region between the two directly oriented lox72 sites created by the Cre-mediated recombination of the lox66-htk-lox71 cassette. This is the first demonstration of a Cre/lox system being applicable to extreme thermophiles in a genetic manipulation. Our results indicate that this system is a powerful tool for multiple markerless gene disruption in T. thermophilus.
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Affiliation(s)
- Yoichiro Togawa
- Department of Applied Chemistry, National Defense Academy, Hashirimizu 1-10-20, Yokosuka, Kanagawa, 239-8686, Japan
| | - Tatsuo Nunoshiba
- College of Liberal Arts, International Christian University, Osawa 3-10-2, Mitaka, Tokyo, 181-8585, Japan
| | - Keiichiro Hiratsu
- Department of Applied Chemistry, National Defense Academy, Hashirimizu 1-10-20, Yokosuka, Kanagawa, 239-8686, Japan.
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Kolb AF, Knowles C, Pultinevicius P, Harbottle JA, Petrie L, Robinson C, Sorrell DA. Recombinase-Mediated Cassette Exchange Using Adenoviral Vectors. Methods Mol Biol 2017; 1642:127-150. [PMID: 28815498 DOI: 10.1007/978-1-4939-7169-5_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
Site-specific recombinases are important tools for the modification of mammalian genomes. In conjunction with viral vectors, they can be utilized to mediate site-specific gene insertions in animals and in cell lines which are difficult to transfect. Here we describe a method for the generation and analysis of an adenovirus vector supporting a recombinase-mediated cassette exchange reaction and discuss the advantages and limitations of this approach.
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Affiliation(s)
- Andreas F Kolb
- Metabolic Health Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK. .,Hannah Research Institute, Ayr, UK.
| | - Christopher Knowles
- Metabolic Health Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
| | - Patrikas Pultinevicius
- Metabolic Health Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
| | - Jennifer A Harbottle
- Metabolic Health Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
| | - Linda Petrie
- Metabolic Health Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, UK
| | | | - David A Sorrell
- Hannah Research Institute, Ayr, UK.,Horizon Biodiscovery, Cambridge, UK
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