1
|
Foster MP, Benedek MJ, Billings TD, Montgomery JS. Dynamics in Cre-loxP site-specific recombination. Curr Opin Struct Biol 2024; 88:102878. [PMID: 39029281 DOI: 10.1016/j.sbi.2024.102878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 06/15/2024] [Accepted: 06/17/2024] [Indexed: 07/21/2024]
Abstract
Cre recombinase is a phage-derived enzyme that has found utility for precise manipulation of DNA sequences. Cre recognizes and recombines pairs of loxP sequences characterized by an inverted repeat and asymmetric spacer. Cre cleaves and religates its DNA targets such that error-prone repair pathways are not required to generate intact DNA products. Major obstacles to broader applications are lack of knowledge of how Cre recognizes its targets, and how its activity is controlled. The picture emerging from high resolution methods is that the dynamic properties of both the enzyme and its DNA target are important determinants of its activity in both sequence recognition and DNA cleavage. Improved understanding of the role of dynamics in the key steps along the pathway of Cre-loxP recombination should significantly advance our ability to both redirect Cre to new sequences and to control its DNA cleavage activity in the test tube and in cells.
Collapse
Affiliation(s)
- Mark P Foster
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA.
| | - Matthew J Benedek
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Tyler D Billings
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| | - Jonathan S Montgomery
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, USA
| |
Collapse
|
2
|
Jahncke JN, Wright KM. Tools for Cre-Mediated Conditional Deletion of Floxed Alleles from Developing Cerebellar Purkinje Cells. eNeuro 2024; 11:ENEURO.0149-24.2024. [PMID: 38777609 PMCID: PMC11149487 DOI: 10.1523/eneuro.0149-24.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 05/13/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024] Open
Abstract
The Cre-lox system is an indispensable tool in neuroscience research for targeting gene deletions to specific cellular populations. Here we assess the utility of several transgenic Cre lines, along with a viral approach, for targeting cerebellar Purkinje cells (PCs) in mice. Using a combination of a fluorescent reporter line (Ai14) to indicate Cre-mediated recombination and a floxed Dystroglycan line (Dag1flox ), we show that reporter expression does not always align precisely with loss of protein. The commonly used Pcp2Cre line exhibits a gradual mosaic pattern of Cre recombination in PCs from Postnatal Day 7 (P7) to P14, while loss of Dag1 protein is not complete until P30. Ptf1aCre drives recombination in precursor cells that give rise to GABAergic neurons in the embryonic cerebellum, including PCs and molecular layer interneurons. However, due to its transient expression in precursors, Ptf1aCre results in stochastic loss of Dag1 protein in these neurons. NestinCre , which is often described as a "pan-neuronal" Cre line for the central nervous system, does not drive Cre-mediated recombination in PCs. We identify a Calb1Cre line that drives efficient and complete recombination in embryonic PCs, resulting in loss of Dag1 protein before the period of synaptogenesis. AAV8-mediated delivery of Cre at P0 results in gradual transduction of PCs during the second postnatal week, with loss of Dag1 protein not reaching appreciable levels until P35. These results characterize several tools for targeting conditional deletions in cerebellar PCs at different developmental stages and illustrate the importance of validating the loss of protein following recombination.
Collapse
Affiliation(s)
- Jennifer N Jahncke
- Neuroscience Graduate Program, Oregon Health & Science University, Portland, Oregon 97239
| | - Kevin M Wright
- Vollum Institute, Oregon Health & Science University, Portland, Oregon 97239
| |
Collapse
|
3
|
Stone ML, Lee HH, Levine E. Agarose disk electroporation method for ex vivo retinal tissue cultured at the air-liquid interface reveals electrical stimulus-induced cell cycle reentry in retinal cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.21.572865. [PMID: 38187784 PMCID: PMC10769434 DOI: 10.1101/2023.12.21.572865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
It is advantageous to culture the ex vivo murine retina along with many other tissue types at the air-liquid interface. However, gene delivery to these cultures can be challenging. Electroporation is a fast and robust method of gene delivery, but typically requires submergence in a liquid buffer to allow electric current flow. We have developed a submergence-free electroporation technique using an agarose disk that allows for efficient gene delivery to the ex vivo murine retina. This method advances our ability to use ex vivo retinal tissue for genetic studies and can easily be adapted for any tissue cultured at an air-liquid interface. We found an increased ability to transfected Muller glia at 14 days ex vivo and an increase in BrdU incorporation in Muller glia following electrical stimulation. Use of this method has revealed valuable insights on the state of ex vivo retinal tissues and the effects of electrical stimulation on retinal cells.
Collapse
|
4
|
de Oliveira MA, Florentino LH, Sales TT, Lima RN, Barros LRC, Limia CG, Almeida MSM, Robledo ML, Barros LMG, Melo EO, Bittencourt DM, Rehen SK, Bonamino MH, Rech E. Protocol for the establishment of a serine integrase-based platform for functional validation of genetic switch controllers in eukaryotic cells. PLoS One 2024; 19:e0303999. [PMID: 38781126 PMCID: PMC11115199 DOI: 10.1371/journal.pone.0303999] [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: 09/06/2023] [Accepted: 05/04/2024] [Indexed: 05/25/2024] Open
Abstract
Serine integrases (Ints) are a family of site-specific recombinases (SSRs) encoded by some bacteriophages to integrate their genetic material into the genome of a host. Their ability to rearrange DNA sequences in different ways including inversion, excision, or insertion with no help from endogenous molecular machinery, confers important biotechnological value as genetic editing tools with high host plasticity. Despite advances in their use in prokaryotic cells, only a few Ints are currently used as gene editors in eukaryotes, partly due to the functional loss and cytotoxicity presented by some candidates in more complex organisms. To help expand the number of Ints available for the assembly of more complex multifunctional circuits in eukaryotic cells, this protocol describes a platform for the assembly and functional screening of serine-integrase-based genetic switches designed to control gene expression by directional inversions of DNA sequence orientation. The system consists of two sets of plasmids, an effector module and a reporter module, both sets assembled with regulatory components (as promoter and terminator regions) appropriate for expression in mammals, including humans, and plants. The complete method involves plasmid design, DNA delivery, testing and both molecular and phenotypical assessment of results. This platform presents a suitable workflow for the identification and functional validation of new tools for the genetic regulation and reprogramming of organisms with importance in different fields, from medical applications to crop enhancement, as shown by the initial results obtained. This protocol can be completed in 4 weeks for mammalian cells or up to 8 weeks for plant cells, considering cell culture or plant growth time.
Collapse
Affiliation(s)
- Marco A. de Oliveira
- Department of Cell Biology, Institute of Biological Science, University of Brasília, Brasília, Distrito Federal, Brazil
- National Institute of Science and Technology in Synthetic Biology (INCT BioSyn), Brasília, Distrito Federal, Brazil
| | - Lilian H. Florentino
- Department of Cell Biology, Institute of Biological Science, University of Brasília, Brasília, Distrito Federal, Brazil
- National Institute of Science and Technology in Synthetic Biology (INCT BioSyn), Brasília, Distrito Federal, Brazil
- Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil
| | - Thais T. Sales
- Department of Cell Biology, Institute of Biological Science, University of Brasília, Brasília, Distrito Federal, Brazil
- National Institute of Science and Technology in Synthetic Biology (INCT BioSyn), Brasília, Distrito Federal, Brazil
- Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil
| | - Rayane N. Lima
- National Institute of Science and Technology in Synthetic Biology (INCT BioSyn), Brasília, Distrito Federal, Brazil
- Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil
| | - Luciana R. C. Barros
- Center for Translational Research in Oncology, Instituto do Câncer do Estado de São Paulo, Hospital das Clínicas da Faculdade de Medicina de Universidade de São Paulo, São Paulo, Brazil
| | - Cintia G. Limia
- Molecular Carcinogenesis Program, Research Coordination, National Cancer Institute (INCA), Rio de Janeiro, Brazil
| | - Mariana S. M. Almeida
- National Institute of Science and Technology in Synthetic Biology (INCT BioSyn), Brasília, Distrito Federal, Brazil
- Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil
| | - Maria L. Robledo
- Molecular Carcinogenesis Program, Research Coordination, National Cancer Institute (INCA), Rio de Janeiro, Brazil
| | - Leila M. G. Barros
- National Institute of Science and Technology in Synthetic Biology (INCT BioSyn), Brasília, Distrito Federal, Brazil
- Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil
| | - Eduardo O. Melo
- National Institute of Science and Technology in Synthetic Biology (INCT BioSyn), Brasília, Distrito Federal, Brazil
- Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil
| | - Daniela M. Bittencourt
- National Institute of Science and Technology in Synthetic Biology (INCT BioSyn), Brasília, Distrito Federal, Brazil
- Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil
| | - Stevens K. Rehen
- D’Or Institute for Research and Education (IDOR), Rio de Janeiro, Brazil
- Institute of Biomedical Sciences, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Martín H. Bonamino
- Cell and Gene Therapy Program, Research Coordination, National Cancer Institute (INCA), Rio de Janeiro, Brazil
- Vice-Presidency of Research and Biological Collections (VPPCB), FIOCRUZ – Oswaldo Cruz Foundation Institute, Rio de Janeiro, Brazil
| | - Elibio Rech
- National Institute of Science and Technology in Synthetic Biology (INCT BioSyn), Brasília, Distrito Federal, Brazil
- Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Hernández-Morán BA, Taylor G, Lorente-Macías Á, Wood AJ. Degron tagging for rapid protein degradation in mice. Dis Model Mech 2024; 17:dmm050613. [PMID: 38666498 PMCID: PMC11073515 DOI: 10.1242/dmm.050613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024] Open
Abstract
Degron tagging allows proteins of interest to be rapidly degraded, in a reversible and tuneable manner, in response to a chemical stimulus. This provides numerous opportunities for understanding disease mechanisms, modelling therapeutic interventions and constructing synthetic gene networks. In recent years, many laboratories have applied degron tagging successfully in cultured mammalian cells, spurred by rapid advances in the fields of genome editing and targeted protein degradation. In this At a Glance article, we focus on recent efforts to apply degron tagging in mouse models, discussing the distinct set of challenges and opportunities posed by the in vivo environment.
Collapse
Affiliation(s)
- Brianda A. Hernández-Morán
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road, Edinburgh EH4, 2XR, UK
| | - Gillian Taylor
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road, Edinburgh EH4, 2XR, UK
| | - Álvaro Lorente-Macías
- Edinburgh Cancer Research, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road, Edinburgh EH4 2XR, UK
| | - Andrew J. Wood
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road, Edinburgh EH4, 2XR, UK
| |
Collapse
|
7
|
Chen X, Du J, Yun S, Xue C, Yao Y, Rao S. Recent advances in CRISPR-Cas9-based genome insertion technologies. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102138. [PMID: 38379727 PMCID: PMC10878794 DOI: 10.1016/j.omtn.2024.102138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Programmable genome insertion (or knock-in) is vital for both fundamental and translational research. The continuously expanding number of CRISPR-based genome insertion strategies demonstrates the ongoing development in this field. Common methods for site-specific genome insertion rely on cellular double-strand breaks repair pathways, such as homology-directed repair, non-homologous end-joining, and microhomology-mediated end joining. Recent advancements have further expanded the toolbox of programmable genome insertion techniques, including prime editing, integrase coupled with programmable nuclease, and CRISPR-associated transposon. These tools possess their own capabilities and limitations, promoting tremendous efforts to enhance editing efficiency, broaden targeting scope and improve editing specificity. In this review, we first summarize recent advances in programmable genome insertion techniques. We then elaborate on the cons and pros of each technique to assist researchers in making informed choices when using these tools. Finally, we identify opportunities for future improvements and applications in basic research and therapeutics.
Collapse
Affiliation(s)
- Xinwen Chen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
- Tianjin Institutes of Health Science, Tianjin 301600, China
| | - Jingjing Du
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
- Tianjin Institutes of Health Science, Tianjin 301600, China
| | - Shaowei Yun
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
- Tianjin Institutes of Health Science, Tianjin 301600, China
| | - Chaoyou Xue
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin 300308, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yao Yao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
- Tianjin Institutes of Health Science, Tianjin 301600, China
| | - Shuquan Rao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
- Tianjin Institutes of Health Science, Tianjin 301600, China
| |
Collapse
|
8
|
Devarajan A. Optically Controlled CRISPR-Cas9 and Cre Recombinase for Spatiotemporal Gene Editing: A Review. ACS Synth Biol 2024; 13:25-44. [PMID: 38134336 DOI: 10.1021/acssynbio.3c00596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
CRISPR-Cas9 and Cre recombinase, two tools extensively used for genome interrogation, have catalyzed key breakthroughs in our understanding of complex biological processes and diseases. However, the immense complexity of biological systems and off-target effects hinder clinical applications, necessitating the development of platforms to control gene editing over spatial and temporal dimensions. Among the strategies developed for inducible control, light is particularly attractive as it is noninvasive and affords high spatiotemporal resolution. The principles for optical control of Cas9 and Cre recombinase are broadly similar and involve photocaged enzymes and small molecules, engineered split- and single-chain constructs, light-induced expression, and delivery by light-responsive nanocarriers. Few systems enable spatiotemporal control with a high dynamic range without loss of wild-type editing efficiencies. Such systems posit the promise of light-activatable systems in the clinic. While the prospect of clinical applications is palpably exciting, optimization and extensive preclinical validation are warranted. Judicious integration of optically activated CRISPR and Cre, tailored for the desired application, may help to bridge the "bench-to-bedside" gap in therapeutic gene editing.
Collapse
Affiliation(s)
- Archit Devarajan
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal, Madhya Pradesh, India - 462066
| |
Collapse
|
9
|
Scharr M, Hirt B, Neckel PH. Spatial gene expression profile of Wnt-signaling components in the murine enteric nervous system. Front Immunol 2024; 15:1302488. [PMID: 38322254 PMCID: PMC10846065 DOI: 10.3389/fimmu.2024.1302488] [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: 09/26/2023] [Accepted: 01/02/2024] [Indexed: 02/08/2024] Open
Abstract
Introduction Wnt-signaling is a key regulator of stem cell homeostasis, extensively studied in the intestinal crypt and other metazoan tissues. Yet, there is hardly any data available on the presence of Wnt-signaling components in the adult enteric nervous system (ENS) in vivo. Methods Therefore, we employed RNAscope HiPlex-assay, a novel and more sensitive in situ hybridization technology. By amplifying target specific signals, this technique enables the detection of low abundance, tightly regulated RNA content as is the case for Wnt-signaling components. Additionally, we compared our data to previously published physiological single cell RNA and RiboTag-based RNA sequencing analyses of enteric gliosis using data-mining approaches. Results Our descriptive analysis shows that several components of the multidi-mensional regulatory network of the Wnt-signaling pathway are present in the murine ENS. The transport and secretion protein for Wnt-ligands Wntless as well as canonical (Wnt3a and Wnt2b) and non-canonical Wnt-ligands (Wnt5a, Wnt7a, Wnt8b and Wnt11) are detectable within submucosal and myenteric plexus. Further, corresponding Frizzled receptors (Fzd1, Fzd3, Fzd6, and Fzd7) and regulatory signaling mediators like R-Spondin/DKK ligands are present in the ENS of the small and large intestine. Further, data mining approaches revealed, that several Wnt-related molecules are expressed by enteric glial cell clusters and are dynamically regulated during the inflammatory manifestation of enteric gliosis. Discussion Our results suggest, that canonical and non-canonical Wnt-signaling has a much broader impact on the mature ENS and its cellular homeostasis in health and inflammation, than previously anticipated.
Collapse
Affiliation(s)
| | | | - Peter H. Neckel
- Institute of Clinical Anatomy and Cell Analysis, University of Tübingen, Tübingen, Germany
| |
Collapse
|
10
|
Jeong M, Choi JH, Jang H, Sohn DH, Wang Q, Lee J, Yao L, Lee EJ, Fan J, Pratelli M, Wang EH, Snyder CN, Wang XY, Shin S, Gittis AH, Sung TC, Spitzer NC, Lim BK. Viral vector-mediated transgene delivery with novel recombinase systems for targeting neuronal populations defined by multiple features. Neuron 2024; 112:56-72.e4. [PMID: 37909037 PMCID: PMC10916502 DOI: 10.1016/j.neuron.2023.09.038] [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: 07/18/2022] [Revised: 05/21/2023] [Accepted: 09/26/2023] [Indexed: 11/02/2023]
Abstract
A comprehensive understanding of neuronal diversity and connectivity is essential for understanding the anatomical and cellular mechanisms that underlie functional contributions. With the advent of single-cell analysis, growing information regarding molecular profiles leads to the identification of more heterogeneous cell types. Therefore, the need for additional orthogonal recombinase systems is increasingly apparent, as heterogeneous tissues can be further partitioned into increasing numbers of specific cell types defined by multiple features. Critically, new recombinase systems should work together with pre-existing systems without cross-reactivity in vivo. Here, we introduce novel site-specific recombinase systems based on ΦC31 bacteriophage recombinase for labeling multiple cell types simultaneously and a novel viral strategy for versatile and robust intersectional expression of any transgene. Together, our system will help researchers specifically target different cell types with multiple features in the same animal.
Collapse
Affiliation(s)
- Minju Jeong
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jun-Hyeok Choi
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Hyeonseok Jang
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Dong Hyun Sohn
- Department of Microbiology and Immunology, Pusan National University School of Medicine, Yangsan 50612, Republic of Korea
| | - Qingdi Wang
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Joann Lee
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Li Yao
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Eun Ji Lee
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jiachen Fan
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Marta Pratelli
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Eric H Wang
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Christen N Snyder
- Department of Biological Sciences and Center for the Neural Basis of Cognition, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Xiao-Yun Wang
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sora Shin
- Center for Neurobiology Research, Fralin Biomedical Research Institute at Virginia Tech Carilion, Virginia Tech, Roanoke, VA, USA; Department of Human Nutrition, Foods, and Exercise, Virginia Tech, Blacksburg, VA, USA
| | - Aryn H Gittis
- Department of Biological Sciences and Center for the Neural Basis of Cognition, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Tsung-Chang Sung
- Transgenic Core, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Nicholas C Spitzer
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Byung Kook Lim
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
| |
Collapse
|
11
|
Guo L, Yang G. Pioneering DNA assembling techniques and their applications in eukaryotic microalgae. Biotechnol Adv 2024; 70:108301. [PMID: 38101551 DOI: 10.1016/j.biotechadv.2023.108301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/12/2023] [Accepted: 12/08/2023] [Indexed: 12/17/2023]
Abstract
Assembling DNA fragments is a fundamental manipulation of cloning microalgal genes and carrying out microalgal synthetic biological studies. From the earliest DNA recombination to current trait and metabolic pathway engineering, we are always accompanied by homology-based DNA assembling. The improvement and modification of pioneering DNA assembling techniques and the combinational applications of the available assembling techniques have diversified and complicated the literature environment and aggravated our identification of the core and pioneering methodologies. Identifying the core assembling methodologies and using them appropriately and flourishing them even are important for researchers. A group of microalgae have been evolving as the models for both industrial applications and biological studies. DNA assembling requires researchers to know the methods available and their improvements and evolvements. In this review, we summarized the pioneering (core; leading) DNA assembling techniques developed previously, extended these techniques to their modifications, improvements and their combinations, and highlighted their applications in eukaryotic microalgae. We predicted that the gene(s) will be assembled into a functional cluster (e.g., those involving in a metabolic pathway, and stacked on normal microalgal chromosomes, their artificial episomes and looming artificial chromosomes. It should be particularly pointed out that the techniques mentioned in this review are classified according to the strategy used to assemble the final construct.
Collapse
Affiliation(s)
- Li Guo
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Guanpin Yang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China; Institutes of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China; MoE Laboratory of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China; Key Laboratory of Marine Genetics and Breeding of Ministry of Education, Ocean University of China, Qingdao 266003, China.
| |
Collapse
|
12
|
Tabatabai A, Arora A, Höfmann S, Jauch M, von Tresckow B, Hansen J, Flümann R, Jachimowicz RD, Klein S, Reinhardt HC, Knittel G. Mouse models of diffuse large B cell lymphoma. Front Immunol 2023; 14:1313371. [PMID: 38124747 PMCID: PMC10731046 DOI: 10.3389/fimmu.2023.1313371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 11/10/2023] [Indexed: 12/23/2023] Open
Abstract
Diffuse large B cell lymphoma (DLBCL) is a genetically highly heterogeneous disease. Yet, to date, the vast majority of patients receive standardized frontline chemo-immune-therapy consisting of an anthracycline backbone. Using these regimens, approximately 65% of patients can be cured, whereas the remaining 35% of patients will face relapsed or refractory disease, which, even in the era of CAR-T cells, is difficult to treat. To systematically tackle this high medical need, it is important to design, generate and deploy suitable in vivo model systems that capture disease biology, heterogeneity and drug response. Recently published, large comprehensive genomic characterization studies, which defined molecular sub-groups of DLBCL, provide an ideal framework for the generation of autochthonous mouse models, as well as an ideal benchmark for cell line-derived or patient-derived mouse models of DLBCL. Here we discuss the current state of the art in the field of mouse modelling of human DLBCL, with a particular focus on disease biology and genetically defined molecular vulnerabilities, as well as potential targeting strategies.
Collapse
Affiliation(s)
- Areya Tabatabai
- Department of Hematology and Stem Cell Transplantation, University Hospital Essen, West German Cancer Center, German Cancer Consortium Partner Site Essen, Center for Molecular Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Aastha Arora
- Department of Hematology and Stem Cell Transplantation, University Hospital Essen, West German Cancer Center, German Cancer Consortium Partner Site Essen, Center for Molecular Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Svenja Höfmann
- Department of Hematology and Stem Cell Transplantation, University Hospital Essen, West German Cancer Center, German Cancer Consortium Partner Site Essen, Center for Molecular Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Maximilian Jauch
- Department of Hematology and Stem Cell Transplantation, University Hospital Essen, West German Cancer Center, German Cancer Consortium Partner Site Essen, Center for Molecular Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Bastian von Tresckow
- Department of Hematology and Stem Cell Transplantation, University Hospital Essen, West German Cancer Center, German Cancer Consortium Partner Site Essen, Center for Molecular Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Julia Hansen
- Department I of Internal Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Center for Integrated Oncology Aachen Bonn, Cologne, Germany
- Center for Molecular Medicine, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Mildred Scheel School of Oncology Aachen Bonn Cologne Düsseldorf (MSSO ABCD), Faculty of Medicine and University Hospital of Cologne, Cologne, Germany
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Ruth Flümann
- Department I of Internal Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Center for Integrated Oncology Aachen Bonn, Cologne, Germany
- Center for Molecular Medicine, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Mildred Scheel School of Oncology Aachen Bonn Cologne Düsseldorf (MSSO ABCD), Faculty of Medicine and University Hospital of Cologne, Cologne, Germany
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Ron D. Jachimowicz
- Department I of Internal Medicine, University of Cologne, Faculty of Medicine and University Hospital Cologne, Center for Integrated Oncology Aachen Bonn, Cologne, Germany
- Center for Molecular Medicine, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Mildred Scheel School of Oncology Aachen Bonn Cologne Düsseldorf (MSSO ABCD), Faculty of Medicine and University Hospital of Cologne, Cologne, Germany
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Sebastian Klein
- Department of Hematology and Stem Cell Transplantation, University Hospital Essen, West German Cancer Center, German Cancer Consortium Partner Site Essen, Center for Molecular Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Hans Christian Reinhardt
- Department of Hematology and Stem Cell Transplantation, University Hospital Essen, West German Cancer Center, German Cancer Consortium Partner Site Essen, Center for Molecular Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Gero Knittel
- Department of Hematology and Stem Cell Transplantation, University Hospital Essen, West German Cancer Center, German Cancer Consortium Partner Site Essen, Center for Molecular Biotechnology, University of Duisburg-Essen, Essen, Germany
| |
Collapse
|
13
|
Ueki K, Nishida Y, Aoyama S, Uzawa H, Kanai A, Ito M, Ikeda K, Iida H, Miyatsuka T, Watada H. Establishment of Pancreatic β-Cell-Specific Gene Knockout System Based on CRISPR-Cas9 Technology With AAV8-Mediated gRNA Delivery. Diabetes 2023; 72:1609-1620. [PMID: 37625131 DOI: 10.2337/db23-0445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 08/21/2023] [Indexed: 08/27/2023]
Abstract
The Cre-loxP system provides valuable resources to analyze the importance of tissue-specific gene knockout (KO), including pancreatic β-cells associated with the pathogenesis of diabetes. However, it is expensive and time consuming to generate transgenic mice harboring floxed genes of interest and cross them with cell-specific Cre expression mice. We establish a βCas9 system with mice expressing Cas9 in pancreatic β-cells and adeno-associated virus 8 (AAV8)-mediated guide RNA (gRNA) delivery based on CRISPR-Cas9 technology to overcome those shortcomings. Interbreeding CAG-loxP-STOP-loxP (LSL)-Cas9 with Ins1-Cre mice generates normal glucose-tolerant βCas9 mice expressing Cas9 with fluorescent reporter EGFP specifically in β-cells. We also show significant β-cell-specific gene KO efficiency with AAV8-mediated delivery of gRNA for EGFP reporter by intraperitoneal injection in the mice. As a proof of concept, we administered AAV8 to βCas9 mice for expressing gRNA for Pdx1, a culprit gene of maturity-onset diabetes of the young 4. As reported previously, we demonstrate that those mice show glucose intolerance with transdifferentiation of Pdx1 KO β-cells into glucagon-expressing cells. We successfully generated a convenient β-cell-specific gene KO system with βCas9 mice and AAV8-mediated gRNA delivery. ARTICLE HIGHLIGHTS
Collapse
Affiliation(s)
- Kyosei Ueki
- Department of Metabolism and Endocrinology, Juntendo University Graduate School of Medicine, Japan
| | - Yuya Nishida
- Department of Metabolism and Endocrinology, Juntendo University Graduate School of Medicine, Japan
| | - Shuhei Aoyama
- Department of Metabolism and Endocrinology, Juntendo University Graduate School of Medicine, Japan
| | - Hirotsugu Uzawa
- Department of Metabolism and Endocrinology, Juntendo University Graduate School of Medicine, Japan
| | - Akiko Kanai
- Department of Metabolism and Endocrinology, Juntendo University Graduate School of Medicine, Japan
| | - Minami Ito
- Department of Metabolism and Endocrinology, Juntendo University Graduate School of Medicine, Japan
| | - Koki Ikeda
- Department of Metabolism and Endocrinology, Juntendo University Graduate School of Medicine, Japan
| | - Hitoshi Iida
- Department of Metabolism and Endocrinology, Juntendo University Graduate School of Medicine, Japan
| | - Takeshi Miyatsuka
- Department of Endocrinology, Diabetes and Metabolism, Kitasato University School of Medicine, Sagamihara, Japan
| | - Hirotaka Watada
- Department of Metabolism and Endocrinology, Juntendo University Graduate School of Medicine, Japan
| |
Collapse
|
14
|
Zhong Y, Tan X, Wang X, Jiang J, Song K, Chen H, Zhang H, Wang Z, Zhang L, Guo C, Liang H, Yu W. Generation of Vgll4-DreER transgenic mouse for visualizing and manipulating VGLL4-expressing cells in vivo. J Biochem Mol Toxicol 2023; 37:e23435. [PMID: 37352117 DOI: 10.1002/jbt.23435] [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: 11/15/2022] [Revised: 03/29/2023] [Accepted: 06/12/2023] [Indexed: 06/25/2023]
Abstract
Vestigial like family member 4 (VGLL4), a member of the Hippo pathway, is a transcriptional cofactor involved in many biological processes, such as tumor progression, postnatal heart growth, and muscle regeneration. However, the VGLL4 expression pattern in vivo remains unclear. To detect and trace Vgll4-expressing cells and their progeny, we generated and characterized a new tamoxifen-inducible Dre knock-in mouse line, Vgll4-DreER. This mouse line expressed DreER (Dre recombinase fused to the estrogen receptor) under the control of the endogenous Vgll4 promoter. After crossing the Vgll4-DreER mouse line with the Dre-responsive reporter H11-rRFP, Dre-mediated recombination in the tissue was monitored on the basis of red fluorescent protein (RFP) signals, which indicated the distribution of VGLL4-positive cells in vivo. Our data revealed that VGLL4 is widely expressed in various cell types at embryonic and neonatal stages. After comparison with our previously reported Vgll4-GFP mouse, we found that the RFP signal profile was wider than the green fluorescent protein (GFP) pattern, indicating that Vgll4-DreER is more sensitive for labeling VGLL4-expressing cells. We next used a dual-recombination system to simultaneously label VGLL4- and keratin 5 (KRT5)-positive cell populations, and no crosstalk was observed in the Krt5-CreER;Vgll4-DreER;R26-rGlR mice. Taken together, the Vgll4-DreER mouse line is a valuable new tool for examining the precise VGLL4 expression profile and conditional manipulating of VGLL4-expressing cells and their progeny.
Collapse
Affiliation(s)
- Yazhu Zhong
- Key Laboratory of Respiratory Disease, People's Hospital of Yangjiang, Yangjiang, Guangdong, China
| | - Xixi Tan
- Key Laboratory of Respiratory Disease, People's Hospital of Yangjiang, Yangjiang, Guangdong, China
| | - Xiaodong Wang
- School of Life Science and Technology, Shanghai Tech University, Shanghai, China
| | - Jun Jiang
- School of Life Science, Yunnan University, Kunming, Yunnan, China
| | - Kai Song
- School of Life Science, Yunnan University, Kunming, Yunnan, China
| | - Haiyuan Chen
- Key Laboratory of Respiratory Disease, People's Hospital of Yangjiang, Yangjiang, Guangdong, China
| | - Hao Zhang
- Key Laboratory of Respiratory Disease, People's Hospital of Yangjiang, Yangjiang, Guangdong, China
| | - Zuoyun Wang
- Department of Human Anatomy and Histoembryology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lei Zhang
- School of Life Science and Technology, Shanghai Tech University, Shanghai, China
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Chunming Guo
- School of Life Science, Yunnan University, Kunming, Yunnan, China
| | - Hongfeng Liang
- Key Laboratory of Respiratory Disease, People's Hospital of Yangjiang, Yangjiang, Guangdong, China
| | - Wei Yu
- Key Laboratory of Respiratory Disease, People's Hospital of Yangjiang, Yangjiang, Guangdong, China
| |
Collapse
|
15
|
Müller-Nedebock AC, Dekker MCJ, Farrer MJ, Hattori N, Lim SY, Mellick GD, Rektorová I, Salama M, Schuh AFS, Stoessl AJ, Sue CM, Tan AH, Vidal RL, Klein C, Bardien S. Different pieces of the same puzzle: a multifaceted perspective on the complex biological basis of Parkinson's disease. NPJ Parkinsons Dis 2023; 9:110. [PMID: 37443150 DOI: 10.1038/s41531-023-00535-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 05/22/2023] [Indexed: 07/15/2023] Open
Abstract
The biological basis of the neurodegenerative movement disorder, Parkinson's disease (PD), is still unclear despite it being 'discovered' over 200 years ago in Western Medicine. Based on current PD knowledge, there are widely varying theories as to its pathobiology. The aim of this article was to explore some of these different theories by summarizing the viewpoints of laboratory and clinician scientists in the PD field, on the biological basis of the disease. To achieve this aim, we posed this question to thirteen "PD experts" from six continents (for global representation) and collated their personal opinions into this article. The views were varied, ranging from toxin exposure as a PD trigger, to LRRK2 as a potential root cause, to toxic alpha-synuclein being the most important etiological contributor. Notably, there was also growing recognition that the definition of PD as a single disease should be reconsidered, perhaps each with its own unique pathobiology and treatment regimen.
Collapse
Affiliation(s)
- Amica C Müller-Nedebock
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders Research Unit, Stellenbosch University, Cape Town, South Africa
| | - Marieke C J Dekker
- Department of Internal Medicine, Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - Matthew J Farrer
- Norman Fixel Institute for Neurological Diseases, McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - Nobutaka Hattori
- Research Institute of Disease of Old Age, Graduate School of Medicine, Juntendo University, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
- Department of Neurology, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
- Neurodegenerative Disorders Collaborative Laboratory, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama, 351-0106, Japan
| | - Shen-Yang Lim
- Division of Neurology, Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
- The Mah Pooi Soo & Tan Chin Nam Centre for Parkinson's & Related Disorders, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - George D Mellick
- Griffith Institute of Drug Discovery (GRIDD), Griffith University, Brisbane, QLD, Australia
| | - Irena Rektorová
- First Department of Neurology and International Clinical Research Center, St. Anne's University Hospital and Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Applied Neuroscience Research Group, CEITEC, Masaryk University, Brno, Czech Republic
| | - Mohamed Salama
- Institute of Global Health and Human Ecology (I-GHHE), The American University in Cairo (AUC), New Cairo, 11835, Egypt
- Faculty of Medicine, Mansoura University, Dakahleya, Egypt
- Atlantic Senior Fellow for Equity in Brain Health at the Global Brain Health Institute (GBHI), Trinity College Dublin (TCD), Dublin, Ireland
| | - Artur F S Schuh
- Departamento de Farmacologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Serviço de Neurologia, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - A Jon Stoessl
- Pacific Parkinson's Research Centre, Department of Medicine (Division of Neurology), Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada
| | - Carolyn M Sue
- Neuroscience Research Australia; Faculty of Medicine, University of New South Wales; Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst; Department of Neurology, Prince of Wales Hospital, South Eastern Sydney Local Health District, Randwick, NSW, Australia
| | - Ai Huey Tan
- Division of Neurology, Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
- The Mah Pooi Soo & Tan Chin Nam Centre for Parkinson's & Related Disorders, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Rene L Vidal
- Instituto de Neurociencia Biomédica (BNI), Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Centro FONDAP de Gerociencia, Salud Mental y Metabolismo (GERO), Santiago, Chile
- Centro de Biología Integrativa, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Christine Klein
- Institute of Neurogenetics, University of Lübeck and University Hospital Schleswig-Holstein, Lübeck, Germany.
| | - Soraya Bardien
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.
- South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders Research Unit, Stellenbosch University, Cape Town, South Africa.
| |
Collapse
|
16
|
Robbins L, Balaram A, Dejneka S, McMahon M, Najibi Z, Pawlowicz P, Conrad WH. Heterologous production of the D-cycloserine intermediate O-acetyl-L-serine in a human type II pulmonary cell model. Sci Rep 2023; 13:8551. [PMID: 37237156 DOI: 10.1038/s41598-023-35632-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 05/21/2023] [Indexed: 05/28/2023] Open
Abstract
Tuberculosis (TB) is the second leading cause of death by a single infectious disease behind COVID-19. Despite a century of effort, the current TB vaccine does not effectively prevent pulmonary TB, promote herd immunity, or prevent transmission. Therefore, alternative approaches are needed. We seek to develop a cell therapy that produces an effective antibiotic in response to TB infection. D-cycloserine (D-CS) is a second-line antibiotic for TB that inhibits bacterial cell wall synthesis. We have determined D-CS to be the optimal candidate for anti-TB cell therapy due to its effectiveness against TB, relatively short biosynthetic pathway, and its low-resistance incidence. The first committed step towards D-CS synthesis is catalyzed by the L-serine-O-acetyltransferase (DcsE) which converts L-serine and acetyl-CoA to O-acetyl-L-serine (L-OAS). To test if the D-CS pathway could be an effective prophylaxis for TB, we endeavored to express functional DcsE in A549 cells as a human pulmonary model. We observed DcsE-FLAG-GFP expression using fluorescence microscopy. DcsE purified from A549 cells catalyzed the synthesis of L-OAS as observed by HPLC-MS. Therefore, human cells synthesize functional DcsE capable of converting L-serine and acetyl-CoA to L-OAS demonstrating the first step towards D-CS production in human cells.
Collapse
Affiliation(s)
- Laurel Robbins
- Department of Chemistry and Biochemistry and Molecular Biology Program, Lake Forest College, Lake Forest, USA
| | - Ariane Balaram
- Department of Chemistry and Biochemistry and Molecular Biology Program, Lake Forest College, Lake Forest, USA
| | - Stefanie Dejneka
- Department of Chemistry and Biochemistry and Molecular Biology Program, Lake Forest College, Lake Forest, USA
| | - Matthew McMahon
- Department of Chemistry and Biochemistry and Molecular Biology Program, Lake Forest College, Lake Forest, USA
| | - Zarina Najibi
- Department of Chemistry and Biochemistry and Molecular Biology Program, Lake Forest College, Lake Forest, USA
| | - Peter Pawlowicz
- Department of Chemistry and Biochemistry and Molecular Biology Program, Lake Forest College, Lake Forest, USA
| | - William H Conrad
- Department of Chemistry and Biochemistry and Molecular Biology Program, Lake Forest College, Lake Forest, USA.
| |
Collapse
|
17
|
Otsuka T, Matsui H. Fish Models for Exploring Mitochondrial Dysfunction Affecting Neurodegenerative Disorders. Int J Mol Sci 2023; 24:ijms24087079. [PMID: 37108237 PMCID: PMC10138900 DOI: 10.3390/ijms24087079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/05/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
Neurodegenerative disorders are characterized by the progressive loss of neuronal structure or function, resulting in memory loss and movement disorders. Although the detailed pathogenic mechanism has not been elucidated, it is thought to be related to the loss of mitochondrial function in the process of aging. Animal models that mimic the pathology of a disease are essential for understanding human diseases. In recent years, small fish have become ideal vertebrate models for human disease due to their high genetic and histological homology to humans, ease of in vivo imaging, and ease of genetic manipulation. In this review, we first outline the impact of mitochondrial dysfunction on the progression of neurodegenerative diseases. Then, we highlight the advantages of small fish as model organisms, and present examples of previous studies regarding mitochondria-related neuronal disorders. Lastly, we discuss the applicability of the turquoise killifish, a unique model for aging research, as a model for neurodegenerative diseases. Small fish models are expected to advance our understanding of the mitochondrial function in vivo, the pathogenesis of neurodegenerative diseases, and be important tools for developing therapies to treat diseases.
Collapse
Affiliation(s)
- Takayoshi Otsuka
- Department of Neuroscience of Disease, Brain Research Institute, Niigata University, Niigata 951-8585, Japan
| | - Hideaki Matsui
- Department of Neuroscience of Disease, Brain Research Institute, Niigata University, Niigata 951-8585, Japan
| |
Collapse
|
18
|
Sheets MB, Tague N, Dunlop MJ. An optogenetic toolkit for light-inducible antibiotic resistance. Nat Commun 2023; 14:1034. [PMID: 36823420 PMCID: PMC9950086 DOI: 10.1038/s41467-023-36670-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 02/13/2023] [Indexed: 02/25/2023] Open
Abstract
Antibiotics are a key control mechanism for synthetic biology and microbiology. Resistance genes are used to select desired cells and regulate bacterial populations, however their use to-date has been largely static. Precise spatiotemporal control of antibiotic resistance could enable a wide variety of applications that require dynamic control of susceptibility and survival. Here, we use light-inducible Cre recombinase to activate expression of drug resistance genes in Escherichia coli. We demonstrate light-activated resistance to four antibiotics: carbenicillin, kanamycin, chloramphenicol, and tetracycline. Cells exposed to blue light survive in the presence of lethal antibiotic concentrations, while those kept in the dark do not. To optimize resistance induction, we vary promoter, ribosome binding site, and enzyme variant strength using chromosome and plasmid-based constructs. We then link inducible resistance to expression of a heterologous fatty acid enzyme to increase production of octanoic acid. These optogenetic resistance tools pave the way for spatiotemporal control of cell survival.
Collapse
Affiliation(s)
- Michael B Sheets
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA.,Biological Design Center, Boston University, Boston, MA, 02215, USA
| | - Nathan Tague
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA.,Biological Design Center, Boston University, Boston, MA, 02215, USA
| | - Mary J Dunlop
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA. .,Biological Design Center, Boston University, Boston, MA, 02215, USA.
| |
Collapse
|
19
|
Li H, Wu Y, Qiu Y, Li X, Guan Y, Cao X, Liu M, Zhang D, Huang S, Lin L, Hui L, Ma X, Liu M, Zhang X, Wang L, Li D. Stable Transgenic Mouse Strain with Enhanced Photoactivatable Cre Recombinase for Spatiotemporal Genome Manipulation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2201352. [PMID: 36266974 PMCID: PMC9731692 DOI: 10.1002/advs.202201352] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 09/27/2022] [Indexed: 06/16/2023]
Abstract
Optogenetic genome engineering is a powerful technology for high-resolution spatiotemporal genetic manipulation, especially for in vivo studies. It is difficult to generate stable transgenic animals carrying a tightly regulated optogenetic system, as its long-term expression induces high background activity. Here, the generation of an enhanced photoactivatable Cre recombinase (ePA-Cre) transgenic mouse strain with stringent light responsiveness and high recombination efficiency is reported. Through serial optimization, ePA-Cre is developed to generate a transgenic mouse line that exhibits 175-fold induction upon illumination. Efficient light-dependent recombination is detected in embryos and various adult tissues of ePA-Cre mice crossed with the Ai14 tdTomato reporter. Importantly, no significant background Cre activity is detected in the tested tissues except the skin. Moreover, efficient light-inducible cell ablation is achieved in ePA-Cre mice crossed with Rosa26-LSL-DTA mice. In conclusion, ePA-Cre mice offer a tightly inducible, highly efficient, and spatiotemporal-specific genome engineering tool for multiple applications.
Collapse
Affiliation(s)
- Huiying Li
- Shanghai Frontiers Science Center of Genome Editing and Cell TherapyShanghai Key Laboratory of Regulatory Biology and School of Life SciencesEast China Normal UniversityShanghai200241China
- Southern Medical University Affiliated Fengxian HospitalShanghai201499China
| | - Yingyin Wu
- Shanghai Frontiers Science Center of Genome Editing and Cell TherapyShanghai Key Laboratory of Regulatory Biology and School of Life SciencesEast China Normal UniversityShanghai200241China
| | - Yuhao Qiu
- Shanghai Frontiers Science Center of Genome Editing and Cell TherapyShanghai Key Laboratory of Regulatory Biology and School of Life SciencesEast China Normal UniversityShanghai200241China
| | - Xinru Li
- Shanghai Frontiers Science Center of Genome Editing and Cell TherapyShanghai Key Laboratory of Regulatory Biology and School of Life SciencesEast China Normal UniversityShanghai200241China
| | - Yuting Guan
- Shanghai Frontiers Science Center of Genome Editing and Cell TherapyShanghai Key Laboratory of Regulatory Biology and School of Life SciencesEast China Normal UniversityShanghai200241China
| | - Xiya Cao
- Shanghai Frontiers Science Center of Genome Editing and Cell TherapyShanghai Key Laboratory of Regulatory Biology and School of Life SciencesEast China Normal UniversityShanghai200241China
| | - Meizhen Liu
- Shanghai Frontiers Science Center of Genome Editing and Cell TherapyShanghai Key Laboratory of Regulatory Biology and School of Life SciencesEast China Normal UniversityShanghai200241China
| | - Dan Zhang
- Shanghai Frontiers Science Center of Genome Editing and Cell TherapyShanghai Key Laboratory of Regulatory Biology and School of Life SciencesEast China Normal UniversityShanghai200241China
| | - Sijie Huang
- Key Laboratory of Brain Functional Genomics (Ministry of Education)Institute of Brain Functional GenomicsEast China Normal UniversityShanghai200062China
| | - Longnian Lin
- Key Laboratory of Brain Functional Genomics (Ministry of Education)Institute of Brain Functional GenomicsEast China Normal UniversityShanghai200062China
| | - Lijian Hui
- State Key Laboratory of Cell BiologyCAS Center for Excellence in Molecular Cell ScienceShanghai Institute of Biochemistry and Cell BiologyUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghai200031China
| | - Xueyun Ma
- Shanghai Frontiers Science Center of Genome Editing and Cell TherapyShanghai Key Laboratory of Regulatory Biology and School of Life SciencesEast China Normal UniversityShanghai200241China
| | - Mingyao Liu
- Shanghai Frontiers Science Center of Genome Editing and Cell TherapyShanghai Key Laboratory of Regulatory Biology and School of Life SciencesEast China Normal UniversityShanghai200241China
| | - Xueli Zhang
- Southern Medical University Affiliated Fengxian HospitalShanghai201499China
| | - Liren Wang
- Shanghai Frontiers Science Center of Genome Editing and Cell TherapyShanghai Key Laboratory of Regulatory Biology and School of Life SciencesEast China Normal UniversityShanghai200241China
| | - Dali Li
- Shanghai Frontiers Science Center of Genome Editing and Cell TherapyShanghai Key Laboratory of Regulatory Biology and School of Life SciencesEast China Normal UniversityShanghai200241China
| |
Collapse
|
20
|
Siddiqui M, Tous C, Wong WW. Small molecule-inducible gene regulatory systems in mammalian cells: progress and design principles. Curr Opin Biotechnol 2022; 78:102823. [PMID: 36332343 PMCID: PMC9951109 DOI: 10.1016/j.copbio.2022.102823] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/06/2022] [Accepted: 09/15/2022] [Indexed: 12/14/2022]
Abstract
Small molecule-inducible gene circuits are some of the most important tools in biology because they provide a convenient way to exert precise regulation of biological systems. These systems typically are designed to govern gene activation, repression, or disruption at multiple levels, such as through genome modification, transcription, translation, or post-translational regulation of protein activity. Due to their importance, many new systems have been created in the past few years to address different needs or afford orthogonality. They can be broadly characterized based on the inducer used, the mode of regulation, and the effector protein enabling the regulation. Furthermore, each synthetic circuit has varying performance metrics and design considerations. Here, we provide a concise comparison of recently developed tools and recommend standardized metrics for evaluating their performance and potential as biological interrogators or therapeutics.
Collapse
Affiliation(s)
- Menna Siddiqui
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA 02215, USA
| | - Cristina Tous
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA 02215, USA
| | - Wilson W Wong
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA 02215, USA.
| |
Collapse
|
21
|
Recent Advances in Antibiotic-Free Markers; Novel Technologies to Enhance Safe Human Food Production in the World. Mol Biotechnol 2022:10.1007/s12033-022-00609-7. [DOI: 10.1007/s12033-022-00609-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/07/2022] [Indexed: 11/30/2022]
|
22
|
Williams JD, Voziyanova E, Voziyanov Y. The bacteriophage lambda integrase catalytic domain can be modified to act with the regulatory domain as a recombination-competent binary recombinase. J Biol Chem 2022; 299:102721. [PMID: 36410432 PMCID: PMC9791396 DOI: 10.1016/j.jbc.2022.102721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 11/21/2022] Open
Abstract
Site-specific recombinase Int mediates integration of the bacteriophage λ genome into the Escherichia coli chromosome. Integration occurs once the Int tetramer, assisted by the integration host factor IHF, forms the intasome, a higher order structure, within which Int, a heterobivalent protein, interacts with two nonhomologous DNA sequences: the core recombination sites and the accessory arm sites. The binding to these sites is mediated by the catalytic C-terminal domain (CTD) and the regulatory N-terminal domain (NTD) of Int, respectively. Within Int, the NTD can activate or inhibit the recombination activity of the CTD depending on whether the NTD is bound to the arm sites. The CTD alone cannot mediate recombination, and even when the NTD and the CTD are mixed together as individual polypeptides, the NTD cannot trigger recombination in the CTD. In this work, we set to determine what modifications can unlock the recombination activity in the CTD alone and how the CTD can be modified to respond to recombination-triggering signals from the NTD. For this, we performed a series of genetic analyses, which showed that a single mutation that stabilizes the CTD on DNA, E174K, allows the CTD to recombine the core DNA sequences. When the NTD is paired with the CTD (E174K) that also bears a short polypeptide from the C terminus of the NTD, the resulting binary Int can recombine arm-bearing substrates. Our results provide insights into the molecular basis of the regulation of the Int activity and suggest how binary recombinases of the integrase type can be engineered.
Collapse
Affiliation(s)
- Joe D Williams
- School of Biosciences, Louisiana Tech University, Ruston, Louisiana, USA
| | - Eugenia Voziyanova
- School of Biosciences, Louisiana Tech University, Ruston, Louisiana, USA
| | - Yuri Voziyanov
- School of Biosciences, Louisiana Tech University, Ruston, Louisiana, USA.
| |
Collapse
|
23
|
Mark JKK, Lim CSY, Nordin F, Tye GJ. Expression of mammalian proteins for diagnostics and therapeutics: a review. Mol Biol Rep 2022; 49:10593-10608. [PMID: 35674877 PMCID: PMC9175168 DOI: 10.1007/s11033-022-07651-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 05/25/2022] [Indexed: 11/07/2022]
Abstract
BACKGROUND Antibodies have proven to be remarkably successful for biomedical applications. They play important roles in epidemiology and medicine from diagnostics of diseases to therapeutics, treating diseases from incessant chronic diseases such as rheumatology to pandemic outbreaks. With no end in sight for the demand for antibody products, optimizations and new techniques must be expanded to accommodate this. METHODS AND RESULTS This review discusses optimizations and techniques for antibody production through choice of discovery platforms, expression systems, cell culture mediums, and other strategies to increase expression yield. Each system has its own merits and demerits, and the strategy chosen is critical in addressing various biological aspects. CONCLUSIONS There is still insufficient evidence to validate the efficacy of some of these techniques, and further research is needed to consolidate these industrial production systems. There is no doubt that more strategies, systems, and pipelines will contribute to enhance biopharmaceutical production.
Collapse
Affiliation(s)
- Jacqueline Kar Kei Mark
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 11800, Penang, Minden, Malaysia
| | - Crystale Siew Ying Lim
- Department of Biotechnology, Faculty of Applied Sciences, UCSI University, No 1 Jalan Menara Gading, UCSI Heights, Taman Connaught, 56000, Kuala Lumpur, Cheras, Malaysia
| | - Fazlina Nordin
- Tissue Engineering Centre (TEC), Universiti Kebangsaan Malaysia Medical Centre (UKMMC), 56000, Kuala Lumpur, Cheras, Malaysia
| | - Gee Jun Tye
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 11800, Penang, Minden, Malaysia.
| |
Collapse
|
24
|
Arias A, Manubens-Gil L, Dierssen M. Fluorescent transgenic mouse models for whole-brain imaging in health and disease. Front Mol Neurosci 2022; 15:958222. [PMID: 36211979 PMCID: PMC9538927 DOI: 10.3389/fnmol.2022.958222] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 08/08/2022] [Indexed: 11/25/2022] Open
Abstract
A paradigm shift is occurring in neuroscience and in general in life sciences converting biomedical research from a descriptive discipline into a quantitative, predictive, actionable science. Living systems are becoming amenable to quantitative description, with profound consequences for our ability to predict biological phenomena. New experimental tools such as tissue clearing, whole-brain imaging, and genetic engineering technologies have opened the opportunity to embrace this new paradigm, allowing to extract anatomical features such as cell number, their full morphology, and even their structural connectivity. These tools will also allow the exploration of new features such as their geometrical arrangement, within and across brain regions. This would be especially important to better characterize brain function and pathological alterations in neurological, neurodevelopmental, and neurodegenerative disorders. New animal models for mapping fluorescent protein-expressing neurons and axon pathways in adult mice are key to this aim. As a result of both developments, relevant cell populations with endogenous fluorescence signals can be comprehensively and quantitatively mapped to whole-brain images acquired at submicron resolution. However, they present intrinsic limitations: weak fluorescent signals, unequal signal strength across the same cell type, lack of specificity of fluorescent labels, overlapping signals in cell types with dense labeling, or undetectable signal at distal parts of the neurons, among others. In this review, we discuss the recent advances in the development of fluorescent transgenic mouse models that overcome to some extent the technical and conceptual limitations and tradeoffs between different strategies. We also discuss the potential use of these strains for understanding disease.
Collapse
Affiliation(s)
- Adrian Arias
- Department of System Biology, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Linus Manubens-Gil
- Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Mara Dierssen
- Department of System Biology, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Experimental and Health Sciences, University Pompeu Fabra, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain
- *Correspondence: Mara Dierssen,
| |
Collapse
|
25
|
Lacroix M, Beauchemin H, Fraszczak J, Ross J, Shooshtarizadeh P, Chen R, Moroy T. The X-linked helicase DDX3X is required for lymphoid differentiation and MYC-driven lymphomagenesis. Cancer Res 2022; 82:3172-3186. [PMID: 35815807 DOI: 10.1158/0008-5472.can-21-2454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 03/29/2022] [Accepted: 06/29/2022] [Indexed: 11/16/2022]
Abstract
The X-linked gene DDX3X encodes an RNA helicase that is mutated at high frequencies in several types of human B-cell lymphoma. Females have two active DDX3X alleles and males carry a DDX3Y homolog on the Y chromosome. We show here that pan-hematopoietic, homozygous deletion of Ddx3x in female mice perturbs erythropoiesis, causing early developmental arrest. However, both hemizygous male and heterozygous female embryos develop normally, suggesting that one Ddx3x allele is sufficient for fetal hematopoietic development in females and that the Ddx3y allele can compensate for the loss of Ddx3x in males. In adult mice, DDX3X deficiency altered hematopoietic progenitors, early lymphoid development, marginal zone and germinal center B-cells, and lymphomagenesis in a sex-dependent manner. Loss of both Ddx3x alleles abrogated MYC-driven lymphomagenesis in females, while Ddx3x-deletion in males did not affect the formation of B-cell lymphoma in both mouse models. Moreover, tumors that appeared in male mice lacking DDX3X showed upregulated expression of DDX3Y, indicating a critical requirement for DDX3 activity for lymphomagenesis. These data reveal sex-specific roles of DDX3X in erythro- and lymphopoiesis as well as in MYC-driven lymphomagenesis.
Collapse
Affiliation(s)
- Marion Lacroix
- IRCM (Institut de Recherches Cliniques de Montr�al), Montreal, Quebec, Canada
| | | | | | - Julie Ross
- Montreal Clinical Research Institute, Montreal, Quebec, Canada
| | | | | | - Tarik Moroy
- Institut de recherches cliniques de Montr�al, Montreal, Canada
| |
Collapse
|
26
|
A Novel Cre/lox71-Based System for Inducible Expression of Recombinant Proteins and Genome Editing. Cells 2022; 11:cells11142141. [PMID: 35883584 PMCID: PMC9324666 DOI: 10.3390/cells11142141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 06/28/2022] [Accepted: 07/06/2022] [Indexed: 01/15/2023] Open
Abstract
In this study, we developed a novel Cre/lox71-based system for the controlled transient expression of target genes. We used the bacteriophage P1 Cre recombinase, which harbors a short, highly specific DNA-binding site and does not have endogenous binding sites within mouse or human genomes. Fusing the catalytically inactive form of Cre recombinase and the VP64 transactivation domain (VP16 tetramer), we constructed the artificial transcription factor Cre-VP64. This transcription factor binds to the lox71 sites within the promoter region of the target gene and, therefore, upregulates its expression. We tested the Cre-VP64/lox71 system for the controlled expression of several genes, including growth factors and the genome editor CRISPR/Cas9, and obtained superior efficiency in the regulation of transgene expression, achieving a high expression level upon induction together with low basal activity. This system or its modified forms can be suggested as a novel effective tool for the transitory controlled expression of target genes for functional genomic studies, as well as for gene therapy approaches.
Collapse
|
27
|
Spiller C, Bowles J. Instructing Mouse Germ Cells to Adopt a Female Fate. Sex Dev 2022:1-13. [PMID: 35320803 DOI: 10.1159/000523763] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 02/20/2022] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Germ cells are critical for the survival of our species. They are the only cells that undergo meiosis - the reductive form of cell division that is necessary for genetic reassortment of chromosomes and production of the haploid gametes, the sperm and eggs. Remarkably, the initial female/male fate decision in fetal germ cells does not depend on whether they are chromosomally XX or XY; rather, initial sexual fate is imposed by influences from the surrounding tissue. In mammals, the female germline is particularly precious: despite recent suggestions that germline stem cells exist in the ovary, it is still generally accepted that the ovarian reserve is finite, and its size is dependant on germ cells of the fetal ovary initiating meiosis in a timely manner. SUMMARY Prior to 2006, evidence suggested that gonadal germ cells initiate meiotic prophase I by default, but more recent data support a key role for the signalling molecule retinoic acid (RA) in instructing female germ cell fate. Newer findings also support a key meiosis-inducing role for another signalling molecule, bone morphogenic protein (BMP). Nonetheless, many questions remain. KEY MESSAGES Here, we review knowledge thus far regarding extrinsic and intrinsic determinants of a female germ cell fate, focusing on the mouse model.
Collapse
Affiliation(s)
- Cassy Spiller
- School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Josephine Bowles
- School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, Australia
| |
Collapse
|
28
|
Burgstaller S, Bischof H, Matt L, Lukowski R. Assessing K + ions and K + channel functions in cancer cell metabolism using fluorescent biosensors. Free Radic Biol Med 2022; 181:43-51. [PMID: 35091062 DOI: 10.1016/j.freeradbiomed.2022.01.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 01/15/2022] [Accepted: 01/24/2022] [Indexed: 12/17/2022]
Abstract
Cancer represents a leading cause of death worldwide. Hence, a better understanding of the molecular mechanisms causing and propelling the disease is of utmost importance. Several cancer entities are associated with altered K+ channel expression which is frequently decisive for malignancy and disease outcome. The impact of such oncogenic K+ channels on cell patho-/physiology and homeostasis and their roles in different subcellular compartments is, however, far from being understood. A refined method to simultaneously investigate metabolic and ionic signaling events on the level of individual cells and their organelles represent genetically encoded fluorescent biosensors, that allow a high-resolution investigation of compartmentalized metabolite or ion dynamics in a non-invasive manner. This feature of these probes makes them versatile tools to visualize and understand subcellular consequences of aberrant K+ channel expression and activity in K+ channel related cancer research.
Collapse
Affiliation(s)
- Sandra Burgstaller
- Department of Pharmacology, Toxicology and Clinical Pharmacy, Institute of Pharmacy, University of Tübingen, Germany; NMI Natural and Medical Sciences Institute at the University of Tübingen, Reutlingen, 72770, Germany.
| | - Helmut Bischof
- Department of Pharmacology, Toxicology and Clinical Pharmacy, Institute of Pharmacy, University of Tübingen, Germany
| | - Lucas Matt
- Department of Pharmacology, Toxicology and Clinical Pharmacy, Institute of Pharmacy, University of Tübingen, Germany
| | - Robert Lukowski
- Department of Pharmacology, Toxicology and Clinical Pharmacy, Institute of Pharmacy, University of Tübingen, Germany.
| |
Collapse
|
29
|
Son S, Park SR. Challenges Facing CRISPR/Cas9-Based Genome Editing in Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:902413. [PMID: 35677236 PMCID: PMC9169250 DOI: 10.3389/fpls.2022.902413] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 04/29/2022] [Indexed: 05/18/2023]
Abstract
The development of plant varieties with desired traits is imperative to ensure future food security. The revolution of genome editing technologies based on the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated nuclease 9 (Cas9) system has ushered in a new era in plant breeding. Cas9 and the single-guide RNA (sgRNA) form an effective targeting complex on a locus or loci of interest, enabling genome editing in all plants with high accuracy and efficiency. Therefore, CRISPR/Cas9 can save both time and labor relative to what is typically associated with traditional breeding methods. However, despite improvements in gene editing, several challenges remain that limit the application of CRISPR/Cas9-based genome editing in plants. Here, we focus on four issues relevant to plant genome editing: (1) plant organelle genome editing; (2) transgene-free genome editing; (3) virus-induced genome editing; and (4) editing of recalcitrant elite crop inbred lines. This review provides an up-to-date summary on the state of CRISPR/Cas9-mediated genome editing in plants that will push this technique forward.
Collapse
|
30
|
Zingg B, Dong HW, Tao HW, Zhang LI. Application of AAV1 for Anterograde Transsynaptic Circuit Mapping and Input-Dependent Neuronal Cataloging. Curr Protoc 2022; 2:e339. [PMID: 35044725 PMCID: PMC8852298 DOI: 10.1002/cpz1.339] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Viruses that spread transsynaptically provide a powerful means to study interconnected circuits in the brain. Here we describe the use of adeno-associated virus, serotype 1 (AAV1), as a tool to achieve robust, anterograde transsynaptic spread in a variety of unidirectional pathways. A protocol for performing intracranial AAV1 injections in mice is presented, along with additional guidance for planning experiments, sourcing materials, and optimizing the approach to achieve the most successful outcomes. By following the methods presented here, researchers will be able to reveal postsynaptically connected neurons downstream of a given AAV1 injection site and access these input-defined cells for subsequent mapping, recording, and manipulation to characterize their anatomical and functional properties. © 2022 Wiley Periodicals LLC. Basic Protocol: Stereotaxic injection of AAV1 for anterograde transsynaptic spread.
Collapse
Affiliation(s)
- Brian Zingg
- Department of Neurobiology, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
| | - Hong-Wei Dong
- Department of Neurobiology, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
| | - Huizhong Whit Tao
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Li I. Zhang
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| |
Collapse
|
31
|
Recent Advances in Implantation-Based Genetic Modeling of Biliary Carcinogenesis in Mice. Cancers (Basel) 2021; 13:cancers13102292. [PMID: 34064809 PMCID: PMC8151177 DOI: 10.3390/cancers13102292] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 05/07/2021] [Accepted: 05/10/2021] [Indexed: 12/22/2022] Open
Abstract
Simple Summary Biliary tract cancer (BTC) is often refractory to conventional therapeutics and is difficult to diagnose in the early stages. In addition, the pathogenesis of BTC is not fully understood, despite recent advances in cancer genome analysis. To address these issues, the development of fine disease models is critical for BTC. Although still limited in number, there are various platforms for genetic models of BTC owing to newly emerging technology. Among these, implantation-based models have recently drawn attention for their convenience, flexibility, and scalability. To highlight the relevance of this approach, we comprehensively summarize the advantages and disadvantages of BTC models developed using diverse approaches. Currently available research data on intra- and extrahepatic cholangiocarcinoma and gallbladder carcinoma are presented in this review. This information will likely help in selecting the optimal models for various applications and develop novel innovative models based on these technologies. Abstract Epithelial cells in the biliary system can develop refractory types of cancers, which are often associated with inflammation caused by viruses, parasites, stones, and chemicals. Genomic studies have revealed recurrent genetic changes and deregulated signaling pathways in biliary tract cancer (BTC). The causal roles have been at least partly clarified using various genetically engineered mice. Technical advances in Cre-LoxP technology, together with hydrodynamic tail injection, CRISPR/Cas9 technology, in vivo electroporation, and organoid culture have enabled more precise modeling of BTC. Organoid-based genetic modeling, combined with implantation in mice, has recently drawn attention as a means to accelerate the development of BTC models. Although each model may not perfectly mimic the disease, they can complement one another, or two different approaches can be integrated to establish a novel model. In addition, a comparison of the outcomes among these models with the same genotype provides mechanistic insights into the interplay between genetic alterations and the microenvironment in the pathogenesis of BTCs. Here, we review the current status of genetic models of BTCs in mice to provide information that facilitates the wise selection of models and to inform the future development of ideal disease models.
Collapse
|