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Mi J, Ren L, Andersson O. Leveraging zebrafish to investigate pancreatic development, regeneration, and diabetes. Trends Mol Med 2024:S1471-4914(24)00124-2. [PMID: 38825440 DOI: 10.1016/j.molmed.2024.05.002] [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: 01/31/2024] [Revised: 04/30/2024] [Accepted: 05/01/2024] [Indexed: 06/04/2024]
Abstract
The zebrafish has become an outstanding model for studying organ development and tissue regeneration, which is prominently leveraged for studies of pancreatic development, insulin-producing β-cells, and diabetes. Although studied for more than two decades, many aspects remain elusive and it has only recently been possible to investigate these due to technical advances in transcriptomics, chemical-genetics, genome editing, drug screening, and in vivo imaging. Here, we review recent findings on zebrafish pancreas development, β-cell regeneration, and how zebrafish can be used to provide novel insights into gene functions, disease mechanisms, and therapeutic targets in diabetes, inspiring further use of zebrafish for the development of novel therapies for diabetes.
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Affiliation(s)
- Jiarui Mi
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden; Department of Gastroenterology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, China.
| | - Lipeng Ren
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden; Department of Medical Cell Biology, Uppsala University, Biomedical Centre, Uppsala, Sweden
| | - Olov Andersson
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden; Department of Medical Cell Biology, Uppsala University, Biomedical Centre, Uppsala, Sweden.
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2
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Xiu W, Dong H, Chen X, Wan L, Lu L, Yang K, Yuwen L, Li Q, Ding M, Zhang Y, Mou Y, Wang L. Metabolic Modulation-Mediated Antibiotic and Immune Activation for Treatment of Chronic Lung Infections. ACS NANO 2024. [PMID: 38803167 DOI: 10.1021/acsnano.4c03527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
The Pseudomonas aeruginosa biofilm in recalcitrant chronic lung infections not only develops high antimicrobial tolerance but also induces an aberrant host inflammatory response. The metabolic condition plays a vital role in both the antimicrobial susceptibility of bacteria and the inflammatory response of immune cells, thereby offering a potential therapeutic target. Herein, we described a metabolic modulation strategy by using ultrasound-responsive liposomal nanoparticles containing a sonosensitizer and a hypoxia-activated prodrug against biofilm-associated chronic lung infections. Under ultrasound stimulation, the sonosensitizer generates antibacterial reactive oxygen species by oxygen consumption. Subsequently, the oxygen consumption-mediated hypoxia not only induces the anaerobic metabolism of bacteria for antibiotic activation but also triggers the glycolysis pathway of immune cells for inflammatory activation. Such metabolic modulation strategy demonstrated efficient therapeutic efficacy for P. aeruginosa biofilm-induced chronic lung infections in mice models and provides a promising way for combating biofilm-associated chronic infections.
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Affiliation(s)
- Weijun Xiu
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing210023, China
| | - Heng Dong
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China
| | - Xiaolong Chen
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing210023, China
| | - Ling Wan
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing210023, China
| | - Liang Lu
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing210023, China
| | - Kaili Yang
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing210023, China
| | - Lihui Yuwen
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing210023, China
| | - Qiang Li
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China
| | - Meng Ding
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China
| | - Yu Zhang
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China
| | - Yongbin Mou
- Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China
| | - Lianhui Wang
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing210023, China
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3
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Hong J, Sohn KC, Park HW, Jeon H, Ju E, Lee JG, Lee JS, Rho J, Hur GM, Ro H. All-in-one IQ toggle switches with high versatilities for fine-tuning of transgene expression in mammalian cells and tissues. Mol Ther Methods Clin Dev 2024; 32:101202. [PMID: 38374964 PMCID: PMC10875299 DOI: 10.1016/j.omtm.2024.101202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 01/29/2024] [Indexed: 02/21/2024]
Abstract
The transgene toggling device is recognized as a powerful tool for gene- and cell-based biological research and precision medicine. However, many of these devices often operate in binary mode, exhibit unacceptable leakiness, suffer from transgene silencing, show cytotoxicity, and have low potency. Here, we present a novel transgene switch, SIQ, wherein all the elements for gene toggling are packed into a single vector. SIQ has superior potency in inducing transgene expression in response to tebufenozide compared with the Gal4/UAS system, while completely avoiding transgene leakiness. Additionally, the ease and versatility of SIQ make it possible with a single construct to perform transient transfection, establish stable cell lines by targeting a predetermined genomic locus, and simultaneously produce adenovirus for transduction into cells and mammalian tissues. Furthermore, we integrated a cumate switch into SIQ, called SIQmate, to operate a Boolean AND logic gate, enabling swift toggling-off of the transgene after the removal of chemical inducers, tebufenozide and cumate. Both SIQ and SIQmate offer precise transgene toggling, making them adjustable for various researches, including synthetic biology, genome engineering, and therapeutics.
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Affiliation(s)
- Jeongkwan Hong
- Department of Biological Sciences, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 34134, Korea (ROK)
| | - Kyung-Cheol Sohn
- Department of Pharmacology, College of Medicine, Chungnam National University, Daejeon 301 747, Korea (ROK)
| | - Hye-Won Park
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 34134, Korea (ROK)
| | - Hyoeun Jeon
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 34134, Korea (ROK)
| | - Eunjin Ju
- Department of Pharmacology, College of Medicine, Chungnam National University, Daejeon 301 747, Korea (ROK)
| | - Jae-Geun Lee
- Microbiome Convergence Research Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Jeong-Soo Lee
- Microbiome Convergence Research Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
- KRIBB School, University of Science and Technology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Jaerang Rho
- Department of Microbiology and Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 34134, Korea (ROK)
| | - Gang Min Hur
- Department of Pharmacology, College of Medicine, Chungnam National University, Daejeon 301 747, Korea (ROK)
| | - Hyunju Ro
- Department of Biological Sciences, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 34134, Korea (ROK)
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4
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Rich MH, Sharrock AV, Mulligan TS, Matthews F, Brown AS, Lee-Harwood HR, Williams EM, Copp JN, Little RF, Francis JJB, Horvat CN, Stevenson LJ, Owen JG, Saxena MT, Mumm JS, Ackerley DF. A metagenomic library cloning strategy that promotes high-level expression of captured genes to enable efficient functional screening. Cell Chem Biol 2023; 30:1680-1691.e6. [PMID: 37898120 PMCID: PMC10842177 DOI: 10.1016/j.chembiol.2023.10.001] [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: 03/24/2023] [Revised: 06/17/2023] [Accepted: 10/02/2023] [Indexed: 10/30/2023]
Abstract
Functional screening of environmental DNA (eDNA) libraries is a potentially powerful approach to discover enzymatic "unknown unknowns", but is usually heavily biased toward the tiny subset of genes preferentially transcribed and translated by the screening strain. We have overcome this by preparing an eDNA library via partial digest with restriction enzyme FatI (cuts CATG), causing a substantial proportion of ATG start codons to be precisely aligned with strong plasmid-encoded promoter and ribosome-binding sequences. Whereas we were unable to select nitroreductases from standard metagenome libraries, our FatI strategy yielded 21 nitroreductases spanning eight different enzyme families, each conferring resistance to the nitro-antibiotic niclosamide and sensitivity to the nitro-prodrug metronidazole. We showed expression could be improved by co-expressing rare tRNAs and encoded proteins purified directly using an embedded His6-tag. In a transgenic zebrafish model of metronidazole-mediated targeted cell ablation, our lead MhqN-family nitroreductase proved ∼5-fold more effective than the canonical nitroreductase NfsB.
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Affiliation(s)
- Michelle H Rich
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Abigail V Sharrock
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Timothy S Mulligan
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Frazer Matthews
- Department of Genetic Medicine, McKusick-Nathans Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Alistair S Brown
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Hannah R Lee-Harwood
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Elsie M Williams
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Janine N Copp
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Rory F Little
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Jenni J B Francis
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Claire N Horvat
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Luke J Stevenson
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Jeremy G Owen
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Meera T Saxena
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Jeff S Mumm
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Genetic Medicine, McKusick-Nathans Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Center for Nanomedicine, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - David F Ackerley
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington 6012, New Zealand.
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5
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Lyu P, Iribarne M, Serjanov D, Zhai Y, Hoang T, Campbell LJ, Boyd P, Palazzo I, Nagashima M, Silva NJ, Hitchcock PF, Qian J, Hyde DR, Blackshaw S. Common and divergent gene regulatory networks control injury-induced and developmental neurogenesis in zebrafish retina. Nat Commun 2023; 14:8477. [PMID: 38123561 PMCID: PMC10733277 DOI: 10.1038/s41467-023-44142-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 12/01/2023] [Indexed: 12/23/2023] Open
Abstract
Following acute retinal damage, zebrafish possess the ability to regenerate all neuronal subtypes through Müller glia (MG) reprogramming and asymmetric cell division that produces a multipotent Müller glia-derived neuronal progenitor cell (MGPC). This raises three key questions. First, do MG reprogram to a developmental retinal progenitor cell (RPC) state? Second, to what extent does regeneration recapitulate retinal development? And finally, does loss of different retinal cell subtypes induce unique MG regeneration responses? We examined these questions by performing single-nuclear and single-cell RNA-Seq and ATAC-Seq in both developing and regenerating retinas. Here we show that injury induces MG to reprogram to a state similar to late-stage RPCs. However, there are major transcriptional differences between MGPCs and RPCs, as well as major transcriptional differences between activated MG and MGPCs when different retinal cell subtypes are damaged. Validation of candidate genes confirmed that loss of different subtypes induces differences in transcription factor gene expression and regeneration outcomes.
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Affiliation(s)
- Pin Lyu
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Maria Iribarne
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
- Center for Stem Cells and Regenerative Medicine, University of Notre Dame, Notre Dame, IN, 46556, USA
- Center for Zebrafish Research, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Dmitri Serjanov
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
- Center for Stem Cells and Regenerative Medicine, University of Notre Dame, Notre Dame, IN, 46556, USA
- Center for Zebrafish Research, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Yijie Zhai
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Thanh Hoang
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Leah J Campbell
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
- Center for Stem Cells and Regenerative Medicine, University of Notre Dame, Notre Dame, IN, 46556, USA
- Center for Zebrafish Research, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Patrick Boyd
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA
- Center for Stem Cells and Regenerative Medicine, University of Notre Dame, Notre Dame, IN, 46556, USA
- Center for Zebrafish Research, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Isabella Palazzo
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Mikiko Nagashima
- Department of Ophthalmology and Visual Sciences, University of Michigan School of Medicine, Ann Arbor, MI, 48105, USA
| | - Nicholas J Silva
- Department of Ophthalmology and Visual Sciences, University of Michigan School of Medicine, Ann Arbor, MI, 48105, USA
| | - Peter F Hitchcock
- Department of Ophthalmology and Visual Sciences, University of Michigan School of Medicine, Ann Arbor, MI, 48105, USA
| | - Jiang Qian
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA.
| | - David R Hyde
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46556, USA.
- Center for Stem Cells and Regenerative Medicine, University of Notre Dame, Notre Dame, IN, 46556, USA.
- Center for Zebrafish Research, University of Notre Dame, Notre Dame, IN, 46556, USA.
| | - Seth Blackshaw
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA.
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA.
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA.
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA.
- Kavli Neuroscience Discovery Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA.
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6
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Tagore M, Hergenreder E, Perlee SC, Cruz NM, Menocal L, Suresh S, Chan E, Baron M, Melendez S, Dave A, Chatila WK, Nsengimana J, Koche RP, Hollmann TJ, Ideker T, Studer L, Schietinger A, White RM. GABA Regulates Electrical Activity and Tumor Initiation in Melanoma. Cancer Discov 2023; 13:2270-2291. [PMID: 37553760 PMCID: PMC10551668 DOI: 10.1158/2159-8290.cd-23-0389] [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: 04/05/2023] [Revised: 06/27/2023] [Accepted: 08/02/2023] [Indexed: 08/10/2023]
Abstract
Oncogenes can initiate tumors only in certain cellular contexts, which is referred to as oncogenic competence. In melanoma, whether cells in the microenvironment can endow such competence remains unclear. Using a combination of zebrafish transgenesis coupled with human tissues, we demonstrate that GABAergic signaling between keratinocytes and melanocytes promotes melanoma initiation by BRAFV600E. GABA is synthesized in melanoma cells, which then acts on GABA-A receptors in keratinocytes. Electron microscopy demonstrates specialized cell-cell junctions between keratinocytes and melanoma cells, and multielectrode array analysis shows that GABA acts to inhibit electrical activity in melanoma/keratinocyte cocultures. Genetic and pharmacologic perturbation of GABA synthesis abrogates melanoma initiation in vivo. These data suggest that GABAergic signaling across the skin microenvironment regulates the ability of oncogenes to initiate melanoma. SIGNIFICANCE This study shows evidence of GABA-mediated regulation of electrical activity between melanoma cells and keratinocytes, providing a new mechanism by which the microenvironment promotes tumor initiation. This provides insights into the role of the skin microenvironment in early melanomas while identifying GABA as a potential therapeutic target in melanoma. See related commentary by Ceol, p. 2128. This article is featured in Selected Articles from This Issue, p. 2109.
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Affiliation(s)
- Mohita Tagore
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Emiliano Hergenreder
- The Center for Stem Cell Biology, Sloan Kettering Institute for Cancer Research, New York, New York
- Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, New York
- Weill Graduate School of Medical Sciences of Cornell University, New York, New York
| | - Sarah C. Perlee
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nelly M. Cruz
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Laura Menocal
- Weill Graduate School of Medical Sciences of Cornell University, New York, New York
| | - Shruthy Suresh
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Eric Chan
- Molecular Cytology Core Facility, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Maayan Baron
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, California
| | - Stephanie Melendez
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Asim Dave
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Walid K. Chatila
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jeremie Nsengimana
- Biostatistics Research Group, Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Richard P. Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Travis J. Hollmann
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Trey Ideker
- Division of Genetics, Department of Medicine, University of California San Diego, La Jolla, California
| | - Lorenz Studer
- The Center for Stem Cell Biology, Sloan Kettering Institute for Cancer Research, New York, New York
- Developmental Biology Program, Sloan Kettering Institute for Cancer Research, New York, New York
| | - Andrea Schietinger
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Richard M. White
- Department of Cancer Biology and Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
- Weill Cornell Medical College, New York, New York
- Nuffield Department of Medicine, Ludwig Institute for Cancer Research, University of Oxford, Oxford, United Kingdom
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Emmerich K, Walker SL, Wang G, White DT, Ceisel A, Wang F, Teng Y, Chunawala Z, Graziano G, Nimmagadda S, Saxena MT, Qian J, Mumm JS. Transcriptomic comparison of two selective retinal cell ablation paradigms in zebrafish reveals shared and cell-specific regenerative responses. PLoS Genet 2023; 19:e1010905. [PMID: 37819938 PMCID: PMC10593236 DOI: 10.1371/journal.pgen.1010905] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 10/23/2023] [Accepted: 08/07/2023] [Indexed: 10/13/2023] Open
Abstract
Retinal Müller glia (MG) can act as stem-like cells to generate new neurons in both zebrafish and mice. In zebrafish, retinal regeneration is innate and robust, resulting in the replacement of lost neurons and restoration of visual function. In mice, exogenous stimulation of MG is required to reveal a dormant and, to date, limited regenerative capacity. Zebrafish studies have been key in revealing factors that promote regenerative responses in the mammalian eye. Increased understanding of how the regenerative potential of MG is regulated in zebrafish may therefore aid efforts to promote retinal repair therapeutically. Developmental signaling pathways are known to coordinate regeneration following widespread retinal cell loss. In contrast, less is known about how regeneration is regulated in the context of retinal degenerative disease, i.e., following the loss of specific retinal cell types. To address this knowledge gap, we compared transcriptomic responses underlying regeneration following targeted loss of rod photoreceptors or bipolar cells. In total, 2,531 differentially expressed genes (DEGs) were identified, with the majority being paradigm specific, including during early MG activation phases, suggesting the nature of the injury/cell loss informs the regenerative process from initiation onward. For example, early modulation of Notch signaling was implicated in the rod but not bipolar cell ablation paradigm and components of JAK/STAT signaling were implicated in both paradigms. To examine candidate gene roles in rod cell regeneration, including several immune-related factors, CRISPR/Cas9 was used to create G0 mutant larvae (i.e., "crispants"). Rod cell regeneration was inhibited in stat3 crispants, while mutating stat5a/b, c7b and txn accelerated rod regeneration kinetics. These data support emerging evidence that discrete responses follow from selective retinal cell loss and that the immune system plays a key role in regulating "fate-biased" regenerative processes.
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Affiliation(s)
- Kevin Emmerich
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, Maryland, United States of America
- McKusick-Nathans Institute of the Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Steven L. Walker
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, Georgia, United States of America
| | - Guohua Wang
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - David T. White
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Anneliese Ceisel
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Fang Wang
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Yong Teng
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, Georgia, United States of America
| | - Zeeshaan Chunawala
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Gianna Graziano
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Saumya Nimmagadda
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Meera T. Saxena
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Jiang Qian
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Jeff S. Mumm
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, Maryland, United States of America
- McKusick-Nathans Institute of the Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, Georgia, United States of America
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, Maryland, United States of America
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8
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Blackshaw S, Lyu P, Zhai Y, Qian J, Iribarne M, Serjanov D, Campbell L, Boyd P, Hyde D, Palazzo I, Hoang T, Nagashima M, Silva N, Hitchcock P. Common and divergent gene regulatory networks control injury-induced and developmental neurogenesis in zebrafish retina. RESEARCH SQUARE 2023:rs.3.rs-3294233. [PMID: 37790324 PMCID: PMC10543505 DOI: 10.21203/rs.3.rs-3294233/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Following acute retinal damage, zebrafish possess the ability to regenerate all neuronal subtypes. This regeneration requires Müller glia (MG) to reprogram and divide asymmetrically to produce a multipotent Müller glia-derived neuronal progenitor cell (MGPC). This raises three key questions. First, does loss of different retinal cell subtypes induce unique MG regeneration responses? Second, do MG reprogram to a developmental retinal progenitor cell state? And finally, to what extent does regeneration recapitulate retinal development? We examined these questions by performing single-nuclear and single-cell RNA-Seq and ATAC-Seq in both developing and regenerating retinas. While MG reprogram to a state similar to late-stage retinal progenitors in developing retinas, there are transcriptional differences between reprogrammed MG/MGPCs and late progenitors, as well as reprogrammed MG in outer and inner retinal damage models. Validation of candidate genes confirmed that loss of different subtypes induces differences in transcription factor gene expression and regeneration outcomes. This work identifies major differences between gene regulatory networks activated following the selective loss of different subtypes of retina neurons, as well as between retinal regeneration and development.
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Affiliation(s)
| | | | - Yijie Zhai
- Johns Hopkins University School of Medicine
| | - Jiang Qian
- Johns Hopkins University School of Medicine
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9
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Darroch H, Keerthisinghe P, Sung YJ, Rolland L, Prankerd-Gough A, Crosier PS, Astin JW, Hall CJ. Infection-experienced HSPCs protect against infections by generating neutrophils with enhanced mitochondrial bactericidal activity. SCIENCE ADVANCES 2023; 9:eadf9904. [PMID: 37672586 PMCID: PMC10482338 DOI: 10.1126/sciadv.adf9904] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 08/03/2023] [Indexed: 09/08/2023]
Abstract
Hematopoietic stem and progenitor cells (HSPCs) respond to infection by proliferating and generating in-demand neutrophils through a process called emergency granulopoiesis (EG). Recently, infection-induced changes in HSPCs have also been shown to underpin the longevity of trained immunity, where they generate innate immune cells with enhanced responses to subsequent microbial threats. Using larval zebrafish to live image neutrophils and HSPCs, we show that infection-experienced HSPCs generate neutrophils with enhanced bactericidal functions. Transcriptomic analysis of EG neutrophils uncovered a previously unknown function for mitochondrial reactive oxygen species in elevating neutrophil bactericidal activity. We also reveal that driving expression of zebrafish C/EBPβ within infection-naïve HSPCs is sufficient to generate neutrophils with similarly enhanced bactericidal capacity. Our work suggests that this demand-adapted source of neutrophils contributes to trained immunity by providing enhanced protection toward subsequent infections. Manipulating demand-driven granulopoiesis may provide a therapeutic strategy to boost neutrophil function and treat infectious disease.
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Affiliation(s)
- Hannah Darroch
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Pramuk Keerthisinghe
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Yih Jian Sung
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Leah Rolland
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Anneke Prankerd-Gough
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | | | - Jonathan W. Astin
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
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10
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Lyu P, Iribarne M, Serjanov D, Zhai Y, Hoang T, Campbell LJ, Boyd P, Palazzo I, Nagashima M, Silva NJ, HItchcock PF, Qian J, Hyde DR, Blackshaw S. Common and divergent gene regulatory networks control injury-induced and developmental neurogenesis in zebrafish retina. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.08.552451. [PMID: 37609307 PMCID: PMC10441373 DOI: 10.1101/2023.08.08.552451] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Following acute retinal damage, zebrafish possess the ability to regenerate all neuronal subtypes. This regeneration requires Müller glia (MG) to reprogram and divide asymmetrically to produce a multipotent Müller glia-derived neuronal progenitor cell (MGPC). This raises three key questions. First, does loss of different retinal cell subtypes induce unique MG regeneration responses? Second, do MG reprogram to a developmental retinal progenitor cell state? And finally, to what extent does regeneration recapitulate retinal development? We examined these questions by performing single-nuclear and single-cell RNA-Seq and ATAC-Seq in both developing and regenerating retinas. While MG reprogram to a state similar to late-stage retinal progenitors in developing retinas, there are transcriptional differences between reprogrammed MG/MGPCs and late progenitors, as well as reprogrammed MG in outer and inner retinal damage models. Validation of candidate genes confirmed that loss of different subtypes induces differences in transcription factor gene expression and regeneration outcomes. This work identifies major differences between gene regulatory networks activated following the selective loss of different subtypes of retina neurons, as well as between retinal regeneration and development.
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11
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Tucker TR, Knitter CA, Khoury DM, Eshghi S, Tran S, Sharrock AV, Wiles TJ, Ackerley DF, Mumm JS, Parsons MJ. An inducible model of chronic hyperglycemia. Dis Model Mech 2023; 16:dmm050215. [PMID: 37401381 PMCID: PMC10417516 DOI: 10.1242/dmm.050215] [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: 04/04/2023] [Accepted: 06/28/2023] [Indexed: 07/05/2023] Open
Abstract
Transgene driven expression of Escherichia coli nitroreductase (NTR1.0) renders animal cells susceptible to the antibiotic metronidazole (MTZ). Many NTR1.0/MTZ ablation tools have been reported in zebrafish, which have significantly impacted regeneration studies. However, NTR1.0-based tools are not appropriate for modeling chronic cell loss as prolonged application of the required MTZ dose (10 mM) is deleterious to zebrafish health. We established that this dose corresponds to the median lethal dose (LD50) of MTZ in larval and adult zebrafish and that it induced intestinal pathology. NTR2.0 is a more active nitroreductase engineered from Vibrio vulnificus NfsB that requires substantially less MTZ to induce cell ablation. Here, we report on the generation of two new NTR2.0-based zebrafish lines in which acute β-cell ablation can be achieved without MTZ-associated intestinal pathology. For the first time, we were able to sustain β-cell loss and maintain elevated glucose levels (chronic hyperglycemia) in larvae and adults. Adult fish showed significant weight loss, consistent with the induction of a diabetic state, indicating that this paradigm will allow the modeling of diabetes and associated pathologies.
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Affiliation(s)
- Tori R. Tucker
- Department of Developmental and Cell Biology, University of California, Irvine, Natural Sciences II, Irvine, CA 92697, USA
| | - Courtney A. Knitter
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Natural Sciences II, Irvine, CA 92697, USA
| | - Deena M. Khoury
- Department of Developmental and Cell Biology, University of California, Irvine, Natural Sciences II, Irvine, CA 92697, USA
| | - Sheida Eshghi
- Department of Developmental and Cell Biology, University of California, Irvine, Natural Sciences II, Irvine, CA 92697, USA
| | - Sophia Tran
- Department of Developmental and Cell Biology, University of California, Irvine, Natural Sciences II, Irvine, CA 92697, USA
| | - Abigail V. Sharrock
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Travis J. Wiles
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Natural Sciences II, Irvine, CA 92697, USA
| | - David F. Ackerley
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Jeff S. Mumm
- Department of Ophthalmology, The Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Michael J. Parsons
- Department of Developmental and Cell Biology, University of California, Irvine, Natural Sciences II, Irvine, CA 92697, USA
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12
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Chen Y, Li P, Chen T, Liu H, Wang P, Dai X, Zou Q. Ronidazole Is a Superior Prodrug to Metronidazole for Nitroreductase-Mediated Hepatocytes Ablation in Zebrafish Larvae. Zebrafish 2023. [PMID: 37229597 DOI: 10.1089/zeb.2022.0066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023] Open
Abstract
The liver plays a very important role in physiological processes of the human body. Liver regeneration has developed into an important area of study in liver disease. The Mtz (metronidazole)/NTR (nitroreductase)-mediated cell ablation system has been widely used to study the processes and mechanisms of liver injury and regeneration. However, high concentrations and toxic side effects of Mtz severely limit the application of the Mtz/NTR system. Therefore, screening new analogs to replace Mtz has become an important means to optimize the NTR ablation system. In this study, we screened five Mtz analogs including furazolidone, ronidazole, ornidazole, nitromide, and tinidazole. We compared their toxicity on the transgenic fish line Tg(fabp10a: mCherry-NTR) and their specific ablation ability on liver cells. The results showed that Ronidazole at a lower concentration (2 mM) had the same ability to ablate liver cells comparable with that of Mtz (10 mM), almost without toxic side effects on juvenile fish. Further study found that zebrafish hepatocyte injury caused by the Ronidazole/NTR system achieved the same liver regenerative effect as the Mtz/NTR system. The above results show that Ronidazole can replace Mtz with NTR to achieve superior damage and ablation effects in zebrafish liver.
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Affiliation(s)
- Yuhang Chen
- Schools of Laboratory Medicine, Chengdu Medical College, Chengdu, China
| | - Peipei Li
- Schools of Laboratory Medicine, Chengdu Medical College, Chengdu, China
| | - Ting Chen
- Schools of Biosciences and Technology, Chengdu Medical College, Chengdu, China
| | - Hanjie Liu
- Schools of Laboratory Medicine, Chengdu Medical College, Chengdu, China
| | - Peijian Wang
- Department of Cardiology, The First Affiliated Hospital of Chengdu Medical College, Chengdu, China
- Key Laboratory of Aging and Vascular Homeostasis of Sichuan Higher Education Institutes, Chengdu, China
| | - Xiaozhen Dai
- Schools of Biosciences and Technology, Chengdu Medical College, Chengdu, China
| | - Qingliang Zou
- Department of Cardiology, The First Affiliated Hospital of Chengdu Medical College, Chengdu, China
- Key Laboratory of Aging and Vascular Homeostasis of Sichuan Higher Education Institutes, Chengdu, China
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13
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Emmerich K, White DT, Kambhampati SP, Casado GL, Fu TM, Chunawala Z, Sahoo A, Nimmagadda S, Krishnan N, Saxena MT, Walker SL, Betzig E, Kannan RM, Mumm JS. Nanoparticle-based targeting of microglia improves the neural regeneration enhancing effects of immunosuppression in the zebrafish retina. Commun Biol 2023; 6:534. [PMID: 37202450 PMCID: PMC10193316 DOI: 10.1038/s42003-023-04898-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 05/02/2023] [Indexed: 05/20/2023] Open
Abstract
Retinal Müller glia function as injury-induced stem-like cells in zebrafish but not mammals. However, insights gleaned from zebrafish have been applied to stimulate nascent regenerative responses in the mammalian retina. For instance, microglia/macrophages regulate Müller glia stem cell activity in the chick, zebrafish, and mouse. We previously showed that post-injury immunosuppression by the glucocorticoid dexamethasone accelerated retinal regeneration kinetics in zebrafish. Similarly, microglia ablation enhances regenerative outcomes in the mouse retina. Targeted immunomodulation of microglia reactivity may therefore enhance the regenerative potential of Müller glia for therapeutic purposes. Here, we investigated potential mechanisms by which post-injury dexamethasone accelerates retinal regeneration kinetics, and the effects of dendrimer-based targeting of dexamethasone to reactive microglia. Intravital time-lapse imaging revealed that post-injury dexamethasone inhibited microglia reactivity. The dendrimer-conjugated formulation: (1) decreased dexamethasone-associated systemic toxicity, (2) targeted dexamethasone to reactive microglia, and (3) improved the regeneration enhancing effects of immunosuppression by increasing stem/progenitor proliferation rates. Lastly, we show that the gene rnf2 is required for the enhanced regeneration effect of D-Dex. These data support the use of dendrimer-based targeting of reactive immune cells to reduce toxicity and enhance the regeneration promoting effects of immunosuppressants in the retina.
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Affiliation(s)
- Kevin Emmerich
- McKusick-Nathans Institute of the Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA
| | - David T White
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Siva P Kambhampati
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA
- The Center for Nanomedicine, Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Grace L Casado
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Tian-Ming Fu
- Janelia Farms Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Department of Electrical and Computer Engineering and Princeton Bioengineering Initiative, Princeton University, Princeton, NJ, USA
| | - Zeeshaan Chunawala
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Arpan Sahoo
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Saumya Nimmagadda
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Nimisha Krishnan
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Meera T Saxena
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Steven L Walker
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Eric Betzig
- Janelia Farms Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
| | - Rangaramanujam M Kannan
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA.
- The Center for Nanomedicine, Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA.
| | - Jeff S Mumm
- McKusick-Nathans Institute of the Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA.
- The Center for Nanomedicine, Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA.
- Solomon H Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, MD, USA.
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14
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Pan YK, Perry SF. The control of breathing in fishes - historical perspectives and the path ahead. J Exp Biol 2023; 226:307288. [PMID: 37097020 DOI: 10.1242/jeb.245529] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
The study of breathing in fishes has featured prominently in Journal of Experimental Biology (JEB), particularly during the latter half of the past century. Indeed, many of the seminal discoveries in this important sub-field of comparative respiratory physiology were reported first in JEB. The period spanning 1960-1990 (the 'golden age of comparative respiratory physiology') witnessed intense innovation in the development of methods to study the control of breathing. Many of the guiding principles of piscine ventilatory control originated during this period, including our understanding of the dominance of O2 as the driver of ventilation in fish. However, a critical issue - the identity of the peripheral O2 chemoreceptors - remained unanswered until methods for cell isolation, culture and patch-clamp recording established that gill neuroepithelial cells (NECs) respond to hypoxia in vitro. Yet, the role of the NECs and other putative peripheral or central chemoreceptors in the control of ventilation in vivo remains poorly understood. Further progress will be driven by the implementation of genetic tools, most of which can be used in zebrafish (Danio rerio). These tools include CRISPR/Cas9 for selective gene knockout, and Tol2 systems for transgenesis, the latter of which enables optogenetic stimulation of cellular pathways, cellular ablation and in vivo cell-specific biosensing. Using these methods, the next period of discovery will see the identification of the peripheral sensory pathways that initiate ventilatory responses, and will elucidate the nature of their integration within the central nervous system and their link to the efferent motor neurons that control breathing.
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Affiliation(s)
- Yihang Kevin Pan
- Department of Biology, University of Ottawa, Ottawa, ON, Canada, K1N 6N5
| | - Steve F Perry
- Department of Biology, University of Ottawa, Ottawa, ON, Canada, K1N 6N5
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15
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Coomer C, Naumova D, Talay M, Zolyomi B, Snell N, Sorkac A, Chanchu JM, Cheng J, Roman I, Li J, Robson D, Barnea G, Halpern ME. Transsynaptic labeling and transcriptional control of zebrafish neural circuits. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.03.535421. [PMID: 37066422 PMCID: PMC10103993 DOI: 10.1101/2023.04.03.535421] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Deciphering the connectome, the ensemble of synaptic connections that underlie brain function is a central goal of neuroscience research. The trans-Tango genetic approach, initially developed for anterograde transsynaptic tracing in Drosophila, can be used to map connections between presynaptic and postsynaptic partners and to drive gene expression in target neurons. Here, we describe the successful adaptation of trans-Tango to visualize neural connections in a living vertebrate nervous system, that of the zebrafish. Connections were validated between synaptic partners in the larval retina and brain. Results were corroborated by functional experiments in which optogenetic activation of retinal ganglion cells elicited responses in neurons of the optic tectum, as measured by trans-Tango-dependent expression of a genetically encoded calcium indicator. Transsynaptic signaling through trans-Tango reveals predicted as well as previously undescribed synaptic connections, providing a valuable in vivo tool to monitor and interrogate neural circuits over time.
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16
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Sharrock AV, Mumm JS, Bagdžiūnas G, Čėnas N, Arcus VL, Ackerley DF. The Crystal Structure of Engineered Nitroreductase NTR 2.0 and Impact of F70A and F108Y Substitutions on Substrate Specificity. Int J Mol Sci 2023; 24:ijms24076633. [PMID: 37047605 PMCID: PMC10095097 DOI: 10.3390/ijms24076633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/25/2023] [Accepted: 03/30/2023] [Indexed: 04/05/2023] Open
Abstract
Bacterial nitroreductase enzymes that convert prodrugs to cytotoxins are valuable tools for creating transgenic targeted ablation models to study cellular function and cell-specific regeneration paradigms. We recently engineered a nitroreductase (“NTR 2.0”) for substantially enhanced reduction of the prodrug metronidazole, which permits faster cell ablation kinetics, cleaner interrogations of cell function, ablation of previously recalcitrant cell types, and extended ablation paradigms useful for modelling chronic diseases. To provide insight into the enhanced enzymatic mechanism of NTR 2.0, we have solved the X-ray crystal structure at 1.85 Angstroms resolution and compared it to the parental enzyme, NfsB from Vibrio vulnificus. We additionally present a survey of reductive activity with eight alternative nitroaromatic substrates, to provide access to alternative ablation prodrugs, and explore applications such as remediation of dinitrotoluene pollutants. The predicted binding modes of four key substrates were investigated using molecular modelling.
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Affiliation(s)
- Abigail V. Sharrock
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Jeff S. Mumm
- Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Gintautas Bagdžiūnas
- Institute of Biochemistry, University of Vilnius, Saulėtekio 7, LT-10257 Vilnius, Lithuania
| | - Narimantas Čėnas
- Institute of Biochemistry, University of Vilnius, Saulėtekio 7, LT-10257 Vilnius, Lithuania
| | - Vickery L. Arcus
- Te Aka Mātuatua-School of Science, University of Waikato, Hamilton 3240, New Zealand
| | - David F. Ackerley
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
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17
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Day MA, Christofferson AJ, Anderson JLR, Vass SO, Evans A, Searle PF, White SA, Hyde EI. Structure and Dynamics of Three Escherichia coli NfsB Nitro-Reductase Mutants Selected for Enhanced Activity with the Cancer Prodrug CB1954. Int J Mol Sci 2023; 24:ijms24065987. [PMID: 36983061 PMCID: PMC10051150 DOI: 10.3390/ijms24065987] [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: 01/23/2023] [Revised: 02/16/2023] [Accepted: 02/27/2023] [Indexed: 03/30/2023] Open
Abstract
Escherichia coli NfsB has been studied extensively for its potential for cancer gene therapy by reducing the prodrug CB1954 to a cytotoxic derivative. We have previously made several mutants with enhanced activity for the prodrug and characterised their activity in vitro and in vivo. Here, we determine the X-ray structure of our most active triple and double mutants to date, T41Q/N71S/F124T and T41L/N71S. The two mutant proteins have lower redox potentials than wild-type NfsB, and the mutations have lowered activity with NADH so that, in contrast to the wild-type enzyme, the reduction of the enzyme by NADH, rather than the reaction with CB1954, has a slower maximum rate. The structure of the triple mutant shows the interaction between Q41 and T124, explaining the synergy between these two mutations. Based on these structures, we selected mutants with even higher activity. The most active one contains T41Q/N71S/F124T/M127V, in which the additional M127V mutation enlarges a small channel to the active site. Molecular dynamics simulations show that the mutations or reduction of the FMN cofactors of the protein has little effect on its dynamics and that the largest backbone fluctuations occur at residues that flank the active site, contributing towards its broad substrate range.
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Affiliation(s)
- Martin A Day
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
- Institute for Cancer Studies, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | | | | | - Simon O Vass
- Institute for Cancer Studies, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Adam Evans
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Peter F Searle
- Institute for Cancer Studies, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Scott A White
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Eva I Hyde
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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18
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Weng C, Yang H, Loh BS, Wong MW, Ang WH. Targeting Pathogenic Formate-Dependent Bacteria with a Bioinspired Metallo-Nitroreductase Complex. J Am Chem Soc 2023; 145:6453-6461. [PMID: 36881731 DOI: 10.1021/jacs.3c00237] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
Nitroreductases (NTRs) constitute an important class of oxidoreductase enzymes that have evolved to metabolize nitro-containing compounds. Their unique characteristics have spurred an array of potential uses in medicinal chemistry, chemical biology, and bioengineering toward harnessing nitro caging groups and constructing NTR variants for niche applications. Inspired by how they carry out enzymatic reduction via a cascade of hydride transfer reactions, we sought to develop a synthetic small-molecule NTR system based on transfer hydrogenation mediated by transition metal complexes harnessing native cofactors. We report the first water-stable Ru-arene complex capable of selectively and fully reducing nitroaromatics into anilines in a biocompatible buffered aqueous environment using formate as the hydride source. We further demonstrated its application to activate nitro-caged sulfanilamide prodrug in formate-abundant bacteria, specifically pathogenic methicillin-resistant Staphylococcus aureus. This proof of concept paves the way for a new targeted antibacterial chemotherapeutic approach leveraging on redox-active metal complexes for prodrug activation via bioinspired nitroreduction.
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Affiliation(s)
- Cheng Weng
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, Singapore 117543, Singapore
| | - Hui Yang
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, Singapore 117543, Singapore
| | - Boon Shing Loh
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, Singapore 117543, Singapore
| | - Ming Wah Wong
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, Singapore 117543, Singapore
- NUS Graduate School─Integrative Sciences and Engineering Programme, National University of Singapore, 21 Lower Kent Ridge Road, Singapore 119077, Singapore
| | - Wee Han Ang
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, Singapore 117543, Singapore
- NUS Graduate School─Integrative Sciences and Engineering Programme, National University of Singapore, 21 Lower Kent Ridge Road, Singapore 119077, Singapore
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19
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Starkey J, Hageter J, Kozol R, Emmerich K, Mumm JS, Dubou ER, Horstick EJ. Thalamic neurons drive distinct forms of motor asymmetry that are conserved in teleost and dependent on visual evolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.20.533538. [PMID: 36993391 PMCID: PMC10055245 DOI: 10.1101/2023.03.20.533538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Brain laterality is a prominent feature in Bilateria, where neural functions are favored in a single brain hemisphere. These hemispheric specializations are thought to improve behavioral performance and are commonly observed as sensory or motor asymmetries, such as handedness in humans. Despite its prevalence, our understanding of the neural and molecular substrates instructing functional lateralization is limited. Moreover, how functional lateralization is selected for or modulated throughout evolution is poorly understood. While comparative approaches offer a powerful tool for addressing this question, a major obstacle has been the lack of a conserved asymmetric behavior in genetically tractable organisms. Previously, we described a robust motor asymmetry in larval zebrafish. Following the loss of illumination, individuals show a persistent turning bias that is associated with search pattern behavior with underlying functional lateralization in the thalamus. This behavior permits a simple yet robust assay that can be used to address fundamental principles underlying lateralization in the brain across taxa. Here, we take a comparative approach and show that motor asymmetry is conserved across diverse larval teleost species, which have diverged over the past 200 million years. Using a combination of transgenic tools, ablation, and enucleation, we show that teleosts exhibit two distinct forms of motor asymmetry, vision-dependent and - independent. These asymmetries are directionally uncorrelated, yet dependent on the same subset of thalamic neurons. Lastly, we leverage Astyanax sighted and blind morphs, which show that fish with evolutionarily derived blindness lack both retinal-dependent and -independent motor asymmetries, while their sighted surface conspecifics retained both forms. Our data implicate that overlapping sensory systems and neuronal substrates drive functional lateralization in a vertebrate brain that are likely targets for selective modulation during evolution.
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20
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Nakajima H, Ishikawa H, Yamamoto T, Chiba A, Fukui H, Sako K, Fukumoto M, Mattonet K, Kwon HB, Hui SP, Dobreva GD, Kikuchi K, Helker CSM, Stainier DYR, Mochizuki N. Endoderm-derived islet1-expressing cells differentiate into endothelial cells to function as the vascular HSPC niche in zebrafish. Dev Cell 2023; 58:224-238.e7. [PMID: 36693371 DOI: 10.1016/j.devcel.2022.12.013] [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: 11/20/2021] [Revised: 10/26/2022] [Accepted: 12/29/2022] [Indexed: 01/25/2023]
Abstract
Endothelial cells (ECs) line blood vessels and serve as a niche for hematopoietic stem and progenitor cells (HSPCs). Recent data point to tissue-specific EC specialization as well as heterogeneity; however, it remains unclear how ECs acquire these properties. Here, by combining live-imaging-based lineage-tracing and single-cell transcriptomics in zebrafish embryos, we identify an unexpected origin for part of the vascular HSPC niche. We find that islet1 (isl1)-expressing cells are the progenitors of the venous ECs that constitute the majority of the HSPC niche. These isl1-expressing cells surprisingly originate from the endoderm and differentiate into ECs in a process dependent on Bmp-Smad signaling and subsequently requiring npas4l (cloche) function. Single-cell RNA sequencing analyses show that isl1-derived ECs express a set of genes that reflect their distinct origin. This study demonstrates that endothelial specialization in the HSPC niche is determined at least in part by the origin of the ECs.
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Affiliation(s)
- Hiroyuki Nakajima
- Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute, Suita, Osaka 564-8565, Japan.
| | - Hiroyuki Ishikawa
- Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute, Suita, Osaka 564-8565, Japan
| | - Takuya Yamamoto
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan; Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan; AMED-CREST, AMED, Tokyo 100-0004, Japan; Medical-risk Avoidance based on iPS Cells Team, RIKEN Center for Advanced Intelligence Project (AIP), Kyoto 606-8507, Japan
| | - Ayano Chiba
- Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute, Suita, Osaka 564-8565, Japan
| | - Hajime Fukui
- Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute, Suita, Osaka 564-8565, Japan
| | - Keisuke Sako
- Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute, Suita, Osaka 564-8565, Japan
| | - Moe Fukumoto
- Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute, Suita, Osaka 564-8565, Japan
| | - Kenny Mattonet
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim 61231, Germany
| | - Hyouk-Bum Kwon
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim 61231, Germany; Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Subhra P Hui
- S. N. Pradhan Centre for Neurosciences, University of Calcutta, Kolkata 700019, India
| | - Gergana D Dobreva
- Department of Cardiovascular Genomics and Epigenomics, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim 68167, Germany
| | - Kazu Kikuchi
- Department of Cardiac Regeneration Biology, National Cerebral and Cardiovascular Center Research Institute, Suita, Osaka 564-8565, Japan
| | - Christian S M Helker
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim 61231, Germany; Philipps-University Marburg, Faculty of Biology, Cell Signaling and Dynamics, Marburg 35043, Germany
| | - Didier Y R Stainier
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim 61231, Germany.
| | - Naoki Mochizuki
- Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute, Suita, Osaka 564-8565, Japan.
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21
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Perry SF, Pan YK, Gilmour KM. Insights into the control and consequences of breathing adjustments in fishes-from larvae to adults. Front Physiol 2023; 14:1065573. [PMID: 36793421 PMCID: PMC9923008 DOI: 10.3389/fphys.2023.1065573] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 01/11/2023] [Indexed: 01/31/2023] Open
Abstract
Adjustments of ventilation in fishes to regulate the volume of water flowing over the gills are critically important responses to match branchial gas transfer with metabolic needs and to defend homeostasis during environmental fluctuations in O2 and/or CO2 levels. In this focused review, we discuss the control and consequences of ventilatory adjustments in fish, briefly summarizing ventilatory responses to hypoxia and hypercapnia before describing the current state of knowledge of the chemoreceptor cells and molecular mechanisms involved in sensing O2 and CO2. We emphasize, where possible, insights gained from studies on early developmental stages. In particular, zebrafish (Danio rerio) larvae have emerged as an important model for investigating the molecular mechanisms of O2 and CO2 chemosensing as well as the central integration of chemosensory information. Their value stems, in part, from their amenability to genetic manipulation, which enables the creation of loss-of-function mutants, optogenetic manipulation, and the production of transgenic fish with specific genes linked to fluorescent reporters or biosensors.
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22
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Khor JM, Ettensohn CA. An optimized Tet-On system for conditional control of gene expression in sea urchins. Development 2023; 150:dev201373. [PMID: 36607745 PMCID: PMC10108607 DOI: 10.1242/dev.201373] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 11/28/2022] [Indexed: 01/07/2023]
Abstract
Sea urchins and other echinoderms are important experimental models for studying developmental processes. The lack of approaches for conditional gene perturbation, however, has made it challenging to investigate the late developmental functions of genes that have essential roles during early embryogenesis and genes that have diverse functions in multiple tissues. The doxycycline-controlled Tet-On system is a widely used molecular tool for temporally and spatially regulated transgene expression. Here, we optimized the Tet-On system to conditionally induce gene expression in sea urchin embryos. Using this approach, we explored the roles the MAPK signaling plays in skeletogenesis by expressing genes that perturb the pathway specifically in primary mesenchyme cells during later stages of development. We demonstrated the wide utility of the Tet-On system by applying it to a second sea urchin species and in cell types other than the primary mesenchyme cells. Our work provides a robust and flexible platform for the spatiotemporal regulation of gene expression in sea urchins, which will considerably enhance the utility of this prominent model system.
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Affiliation(s)
- Jian Ming Khor
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Charles A. Ettensohn
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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23
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Labbaf Z, Petratou K, Ermlich L, Backer W, Tarbashevich K, Reichman-Fried M, Luschnig S, Schulte-Merker S, Raz E. A robust and tunable system for targeted cell ablation in developing embryos. Dev Cell 2022; 57:2026-2040.e5. [PMID: 35914525 DOI: 10.1016/j.devcel.2022.07.008] [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: 02/01/2022] [Revised: 05/10/2022] [Accepted: 07/07/2022] [Indexed: 11/03/2022]
Abstract
Cell ablation is a key method in the research fields of developmental biology, tissue regeneration, and tissue homeostasis. Eliminating specific cell populations allows for characterizing interactions that control cell differentiation, death, behavior, and spatial organization of cells. Current methodologies for inducing cell death suffer from relatively slow kinetics, making them unsuitable for analyzing rapid events and following primary and immediate consequences of the ablation. To address this, we developed a cell-ablation system that is based on bacterial toxin/anti-toxin proteins and enables rapid and cell-autonomous elimination of specific cell types and organs in zebrafish embryos. A unique feature of this system is that it uses an anti-toxin, which allows for controlling the degree and timing of ablation and the resulting phenotypes. The transgenic zebrafish generated in this work represent a highly efficient tool for cell ablation, and this approach is applicable to other model organisms as demonstrated here for Drosophila.
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Affiliation(s)
- Zahra Labbaf
- Institute of Cell Biology, Center for Molecular Biology of Inflammation, University of Münster, Münster 48149, Germany
| | - Kleio Petratou
- Institute for Cardiovascular Organogenesis and Regeneration, Faculty of Medicine, Münster 48149, Germany
| | - Laura Ermlich
- Institute of Cell Biology, Center for Molecular Biology of Inflammation, University of Münster, Münster 48149, Germany
| | - Wilko Backer
- Institute for Integrative Cell Biology and Physiology, University of Münster, Münster 48149, Germany
| | - Katsiaryna Tarbashevich
- Institute of Cell Biology, Center for Molecular Biology of Inflammation, University of Münster, Münster 48149, Germany
| | - Michal Reichman-Fried
- Institute of Cell Biology, Center for Molecular Biology of Inflammation, University of Münster, Münster 48149, Germany
| | - Stefan Luschnig
- Institute for Integrative Cell Biology and Physiology, University of Münster, Münster 48149, Germany
| | - Stefan Schulte-Merker
- Institute for Cardiovascular Organogenesis and Regeneration, Faculty of Medicine, Münster 48149, Germany
| | - Erez Raz
- Institute of Cell Biology, Center for Molecular Biology of Inflammation, University of Münster, Münster 48149, Germany.
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24
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Chiang VSC, DeRosa H, Park JH, Hunter RG. The Role of Transposable Elements in Sexual Development. Front Behav Neurosci 2022; 16:923732. [PMID: 35874645 PMCID: PMC9301316 DOI: 10.3389/fnbeh.2022.923732] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 06/20/2022] [Indexed: 11/19/2022] Open
Abstract
Up to 50% of most mammalian genomes are made up of transposable elements (TEs) that have the potential to mobilize around the genome. Despite this prevalence, research on TEs is only beginning to gain traction within the field of neuroscience. While TEs have long been regarded as “junk” or parasitic DNA, it has become evident that they are adaptive DNA and RNA regulatory elements. In addition to their vital role in normal development, TEs can also interact with steroid receptors, which are key elements to sexual development. In this review, we provide an overview of the involvement of TEs in processes related to sexual development- from TE activity in the germline to TE accumulation in sex chromosomes. Moreover, we highlight sex differences in TE activity and their regulation of genes related to sexual development. Finally, we speculate on the epigenetic mechanisms that may govern TEs’ role in sexual development. In this context, we emphasize the need to further the understanding of sexual development through the lens of TEs including in a variety of organs at different developmental stages, their molecular networks, and evolution.
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25
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Hall CJ, Astin JW, Mumm JS, Ackerley DF. A New Transgenic Line for Rapid and Complete Neutrophil Ablation. Zebrafish 2022; 19:109-113. [PMID: 35617702 DOI: 10.1089/zeb.2022.0020] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Zebrafish lines expressing nitroreductase (NTR) in specific cell compartments, which sensitizes those cells to metronidazole (MTZ)-mediated ablation, have proven extremely useful for studying tissue regeneration and investigating cell function. In contrast to many cells, neutrophils are comparatively resistant to the NTR/MTZ targeted ablation strategy. Recently, a rationally engineered variant of NTR (NTR 2.0) has been described that exhibits greatly improved MTZ-mediated ablation efficacy in zebrafish. We show that a transgenic line with neutrophil-restricted expression of NTR 2.0 demonstrates complete neutrophil ablation, with an MTZ dose 100-fold less than current treatment regimens, and with treatment durations as short as 5 h.
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Affiliation(s)
- Christopher J Hall
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Jonathan W Astin
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Jeff S Mumm
- Department of Ophthalmology, Johns Hopkins University, Baltimore, Maryland, USA.,Department of Neuroscience, Johns Hopkins University, Baltimore, Maryland, USA.,Department of Human Genetics, Johns Hopkins University, Baltimore, Maryland, USA
| | - David F Ackerley
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
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26
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Higashi SL, Isogami A, Takahashi J, Shibata A, Hirosawa KM, Suzuki KGN, Sawada S, Tsukiji S, Matsuura K, Ikeda M. Construction of a Reduction-responsive DNA Microsphere using a Reduction-cleavable Spacer based on a Nitrobenzene Scaffold. Chem Asian J 2022; 17:e202200142. [PMID: 35338588 DOI: 10.1002/asia.202200142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/24/2022] [Indexed: 11/07/2022]
Abstract
Here, we describe the design and synthesis of a new reduction-cleavable spacer (RCS) based on a nitrobenzene scaffold for constructing reduction-responsive oligonucleotides according to standard phosphoramidite chemistry. In addition, we demonstrate that the introduction of the RCS in the middle of an oligonucleotide (30 nt) enables the construction of a self-assembled microsphere capable of exhibiting a reduction-responsive disassembly.
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Affiliation(s)
- Sayuri L Higashi
- Gifu University: Gifu Daigaku, United Graduate School of Drug Discovery and Medical Information Sciences, 1-1 Yanagido, Gifu, 501-1193, Gifu, JAPAN
| | - Ayaka Isogami
- Gifu University: Gifu Daigaku, Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, JAPAN
| | - Junko Takahashi
- Gifu University: Gifu Daigaku, Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, JAPAN
| | - Aya Shibata
- Gifu University: Gifu Daigaku, Department of Life Science and Chemistry, Graduate School of Natural Science and Technology, JAPAN
| | - Koichiro M Hirosawa
- Gifu University: Gifu Daigaku, Institute for Glyco-core Research (iGCORE), JAPAN
| | - Kenichi G N Suzuki
- Gifu University: Gifu Daigaku, Institute for Glyco-core Research (iGCORE), JAPAN
| | - Shunsuke Sawada
- Nagoya Institute of Technology: Nagoya Kogyo Daigaku, Department of Nanopharmaceutical Sciences, JAPAN
| | - Shinya Tsukiji
- Nagoya Institute of Technology: Nagoya Kogyo Daigaku, Department of Nanopharmaceutical Sciences, JAPAN
| | - Kazunori Matsuura
- Tottori University: Tottori Daigaku, Department of Chemistry and Biotechnology, JAPAN
| | - Masato Ikeda
- GIFU University, Chemistry and Biomolecular Science, 1-1, Yanagido, 501-1193, Gifu, JAPAN
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