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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] [What about the content of this article? (0)] [Affiliation(s)] [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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2
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Emmerich K, Hageter J, Hoang T, Lyu P, Sharrock AV, Ceisel A, Thierer J, Chunawala Z, Nimmagadda S, Palazzo I, Matthews F, Zhang L, White DT, Rodriquez C, Graziano G, Marcos P, May A, Mulligan T, Reibman B, Saxena MT, Ackerley DF, Qian J, Blackshaw S, Horstick E, Mumm JS. Molecular regulation of retinal regeneration is context specific. bioRxiv 2023:2023.11.20.567904. [PMID: 38045256 PMCID: PMC10690167 DOI: 10.1101/2023.11.20.567904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Many genes are known to regulate retinal regeneration following widespread tissue damage. Conversely, genes controlling regeneration following limited retinal cell loss, akin to disease conditions, are undefined. Combining a novel retinal ganglion cell (RGC) ablation-based glaucoma model, single cell omics, and rapid CRISPR/Cas9-based knockout methods to screen 100 genes, we identified 18 effectors of RGC regeneration kinetics. Surprisingly, 32 of 33 previously known/implicated regulators of retinal tissue regeneration were not required for RGC replacement; 7 knockouts accelerated regeneration, including sox2, olig2, and ascl1a . Mechanistic analyses revealed loss of ascl1a increased "fate bias", the propensity of progenitors to produce RGCs. These data demonstrate plasticity and context-specificity in how genes function to control regeneration, insights that could help to advance disease-tailored therapeutics for replacing lost retinal cells. One sentence summary We discovered eighteen genes that regulate the regeneration of retinal ganglion cells in zebrafish.
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3
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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5
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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. bioRxiv 2023:2023.03.24.534183. [PMID: 36993673 PMCID: PMC10055417 DOI: 10.1101/2023.03.24.534183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
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
- Current address: Burnet Institute, Melbourne, Victoria 3004, Australia
| | - Janine N Copp
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
- Current addresses: Michael Smith Laboratories, University of British Columbia, Vancouver BC V6T 1Z4, Canada; Abcellera Biologics Inc, Vancouver BC V5Y 0A1, Canada
| | - Rory F Little
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
- Current address: Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Jenni JB 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
- Current address: Teva Pharmaceuticals, Sydney, New South Wales 2113, Australia
| | - 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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6
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Sharrock AV, Mulligan TS, Hall KR, Williams EM, White DT, Zhang L, Emmerich K, Matthews F, Nimmagadda S, Washington S, Le KD, Meir-Levi D, Cox OL, Saxena MT, Calof AL, Lopez-Burks ME, Lander AD, Ding D, Ji H, Ackerley DF, Mumm JS. NTR 2.0: a rationally engineered prodrug-converting enzyme with substantially enhanced efficacy for targeted cell ablation. Nat Methods 2022; 19:205-215. [PMID: 35132245 PMCID: PMC8851868 DOI: 10.1038/s41592-021-01364-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 11/29/2021] [Indexed: 11/12/2022]
Abstract
Transgenic expression of bacterial nitroreductase (NTR) enzymes sensitizes eukaryotic cells to prodrugs such as metronidazole (MTZ), enabling selective cell-ablation paradigms that have expanded studies of cell function and regeneration in vertebrates. However, first-generation NTRs required confoundingly toxic prodrug treatments to achieve effective cell ablation, and some cell types have proven resistant. Here we used rational engineering and cross-species screening to develop an NTR variant, NTR 2.0, which exhibits ~100-fold improvement in MTZ-mediated cell-specific ablation efficacy, eliminating the need for near-toxic prodrug treatment regimens. NTR 2.0 therefore enables sustained cell-loss paradigms and ablation of previously resistant cell types. These properties permit enhanced interrogations of cell function, extended challenges to the regenerative capacities of discrete stem cell niches, and novel modeling of chronic degenerative diseases. Accordingly, we have created a series of bipartite transgenic reporter/effector resources to facilitate dissemination of NTR 2.0 to the research community.
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Affiliation(s)
- Abigail V Sharrock
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Timothy S Mulligan
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Kelsi R Hall
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Elsie M Williams
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - David T White
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Liyun Zhang
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Kevin Emmerich
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Frazer Matthews
- 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
| | - Selena Washington
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Katherine D Le
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Danielle Meir-Levi
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Olivia L Cox
- 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
- Luminomics, Baltimore, MD, USA
| | - Anne L Calof
- Department of Anatomy and Neurobiology, University of California, Irvine, CA, USA
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | - Martha E Lopez-Burks
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | - Arthur D Lander
- Department of Developmental and Cell Biology, University of California, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | - Ding Ding
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Hongkai Ji
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - David F Ackerley
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand.
- Centre for Biodiscovery and Maurice Wilkins Centre for Molecular Biodiscovery, Victoria University of Wellington, Wellington, New Zealand.
| | - Jeff S Mumm
- 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.
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, MD, USA.
- Department of Genetic Medicine, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.
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7
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Zhang L, Chen C, Fu J, Lilley B, Berlinicke C, Hansen B, Ding D, Wang G, Wang T, Shou D, Ye Y, Mulligan T, Emmerich K, Saxena MT, Hall KR, Sharrock AV, Brandon C, Park H, Kam TI, Dawson VL, Dawson TM, Shim JS, Hanes J, Ji H, Liu JO, Qian J, Ackerley DF, Rohrer B, Zack DJ, Mumm JS. Large-scale phenotypic drug screen identifies neuroprotectants in zebrafish and mouse models of retinitis pigmentosa. eLife 2021; 10:e57245. [PMID: 34184634 PMCID: PMC8425951 DOI: 10.7554/elife.57245] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 06/28/2021] [Indexed: 11/25/2022] Open
Abstract
Retinitis pigmentosa (RP) and associated inherited retinal diseases (IRDs) are caused by rod photoreceptor degeneration, necessitating therapeutics promoting rod photoreceptor survival. To address this, we tested compounds for neuroprotective effects in multiple zebrafish and mouse RP models, reasoning drugs effective across species and/or independent of disease mutation may translate better clinically. We first performed a large-scale phenotypic drug screen for compounds promoting rod cell survival in a larval zebrafish model of inducible RP. We tested 2934 compounds, mostly human-approved drugs, across six concentrations, resulting in 113 compounds being identified as hits. Secondary tests of 42 high-priority hits confirmed eleven lead candidates. Leads were then evaluated in a series of mouse RP models in an effort to identify compounds effective across species and RP models, that is, potential pan-disease therapeutics. Nine of 11 leads exhibited neuroprotective effects in mouse primary photoreceptor cultures, and three promoted photoreceptor survival in mouse rd1 retinal explants. Both shared and complementary mechanisms of action were implicated across leads. Shared target tests implicated parp1-dependent cell death in our zebrafish RP model. Complementation tests revealed enhanced and additive/synergistic neuroprotective effects of paired drug combinations in mouse photoreceptor cultures and zebrafish, respectively. These results highlight the value of cross-species/multi-model phenotypic drug discovery and suggest combinatorial drug therapies may provide enhanced therapeutic benefits for RP patients.
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Affiliation(s)
- Liyun Zhang
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
| | - Conan Chen
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
| | - Jie Fu
- The Center for Nanomedicine, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
| | - Brendan Lilley
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
| | - Cynthia Berlinicke
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
| | - Baranda Hansen
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
| | - Ding Ding
- Department of Biostatistics, Johns Hopkins UniversityBaltimoreUnited States
| | - Guohua Wang
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
| | - Tao Wang
- The Center for Nanomedicine, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
- School of Chemistry, Xuzhou College of Industrial TechnologyXuzhouChina
- College of Light Industry and Food Engineering, Nanjing Forestry UniversityNanjingChina
| | - Daniel Shou
- The Center for Nanomedicine, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
| | - Ying Ye
- The Center for Nanomedicine, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
| | - Timothy Mulligan
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
| | - Kevin Emmerich
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
- Department of Genetic Medicine, Johns Hopkins UniversityBaltimoreUnited States
| | - Meera T Saxena
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
| | - Kelsi R Hall
- School of Biological Sciences, Victoria University of WellingtonWellingtonNew Zealand
| | - Abigail V Sharrock
- Department of Biostatistics, Johns Hopkins UniversityBaltimoreUnited States
- School of Biological Sciences, Victoria University of WellingtonWellingtonNew Zealand
| | - Carlene Brandon
- Department of Ophthalmology, Medical University of South CarolinaCharlestonUnited States
| | - Hyejin Park
- Department of Neurology, Johns Hopkins UniversityBaltimoreUnited States
| | - Tae-In Kam
- Department of Neurology, Johns Hopkins UniversityBaltimoreUnited States
- Institute for Cell Engineering, Johns Hopkins UniversityBaltimoreUnited States
| | - Valina L Dawson
- Department of Neurology, Johns Hopkins UniversityBaltimoreUnited States
- Institute for Cell Engineering, Johns Hopkins UniversityBaltimoreUnited States
- Department of Pharmacology and Molecular Sciences, Johns Hopkins UniversityBaltimoreUnited States
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins UniversityBaltimoreUnited States
| | - Ted M Dawson
- Department of Neurology, Johns Hopkins UniversityBaltimoreUnited States
- Institute for Cell Engineering, Johns Hopkins UniversityBaltimoreUnited States
- Department of Pharmacology and Molecular Sciences, Johns Hopkins UniversityBaltimoreUnited States
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins UniversityBaltimoreUnited States
| | - Joong Sup Shim
- Faculty of Health Sciences, University of Macau, TaipaMacauChina
| | - Justin Hanes
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
- The Center for Nanomedicine, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
| | - Hongkai Ji
- Department of Biostatistics, Johns Hopkins UniversityBaltimoreUnited States
| | - Jun O Liu
- Department of Pharmacology and Molecular Sciences, Johns Hopkins UniversityBaltimoreUnited States
- Department of Oncology, Johns Hopkins UniversityBaltimoreUnited States
| | - Jiang Qian
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
| | - David F Ackerley
- School of Biological Sciences, Victoria University of WellingtonWellingtonNew Zealand
| | - Baerbel Rohrer
- Department of Ophthalmology, Medical University of South CarolinaCharlestonUnited States
| | - Donald J Zack
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
- The Center for Nanomedicine, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
- Department of Genetic Medicine, Johns Hopkins UniversityBaltimoreUnited States
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins UniversityBaltimoreUnited States
- Department of Molecular Biology and Genetics, Johns Hopkins UniversityBaltimoreUnited States
| | - Jeff S Mumm
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
- The Center for Nanomedicine, Wilmer Eye Institute, Johns Hopkins UniversityBaltimoreUnited States
- Department of Genetic Medicine, Johns Hopkins UniversityBaltimoreUnited States
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins UniversityBaltimoreUnited States
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8
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White DT, Saxena MT, Mumm JS. Let's get small (and smaller): Combining zebrafish and nanomedicine to advance neuroregenerative therapeutics. Adv Drug Deliv Rev 2019; 148:344-359. [PMID: 30769046 DOI: 10.1016/j.addr.2019.01.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 12/21/2018] [Accepted: 01/28/2019] [Indexed: 01/18/2023]
Abstract
Several key attributes of zebrafish make them an ideal model system for the discovery and development of regeneration promoting therapeutics; most notably their robust capacity for self-repair which extends to the central nervous system. Further, by enabling large-scale drug discovery directly in living vertebrate disease models, zebrafish circumvent critical bottlenecks which have driven drug development costs up. This review summarizes currently available zebrafish phenotypic screening platforms, HTS-ready neurodegenerative disease modeling strategies, zebrafish small molecule screens which have succeeded in identifying regeneration promoting compounds and explores how intravital imaging in zebrafish can facilitate comprehensive analysis of nanocarrier biodistribution and pharmacokinetics. Finally, we discuss the benefits and challenges attending the combination of zebrafish and nanoparticle-based drug optimization, highlighting inspiring proof-of-concept studies and looking toward implementation across the drug development community.
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Affiliation(s)
- David T White
- Wilmer Eye Institute, Johns Hopkins School of Medicine, Baltimore, MD 21231, USA
| | - Meera T Saxena
- Wilmer Eye Institute, Johns Hopkins School of Medicine, Baltimore, MD 21231, USA; Luminomics Inc., Baltimore, MD 21286, USA
| | - Jeff S Mumm
- Wilmer Eye Institute, Johns Hopkins School of Medicine, Baltimore, MD 21231, USA.
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9
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Unal Eroglu A, Mulligan TS, Zhang L, White DT, Sengupta S, Nie C, Lu NY, Qian J, Xu L, Pei W, Burgess SM, Saxena MT, Mumm JS. Multiplexed CRISPR/Cas9 Targeting of Genes Implicated in Retinal Regeneration and Degeneration. Front Cell Dev Biol 2018; 6:88. [PMID: 30186835 PMCID: PMC6111214 DOI: 10.3389/fcell.2018.00088] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 07/25/2018] [Indexed: 01/28/2023] Open
Abstract
Thousands of genes have been implicated in retinal regeneration, but only a few have been shown to impact the regenerative capacity of Müller glia—an adult retinal stem cell with untapped therapeutic potential. Similarly, among nearly 300 genetic loci associated with human retinal disease, the majority remain untested in animal models. To address the large-scale nature of these problems, we are applying CRISPR/Cas9-based genome modification strategies in zebrafish to target over 300 genes implicated in retinal regeneration or degeneration. Our intent is to enable large-scale reverse genetic screens by applying a multiplexed gene disruption strategy that markedly increases the efficiency of the screening process. To facilitate large-scale phenotyping, we incorporate an automated reporter quantification-based assay to identify cellular degeneration and regeneration-deficient phenotypes in transgenic fish. Multiplexed gene targeting strategies can address mismatches in scale between “big data” bioinformatics and wet lab experimental capacities, a critical shortfall limiting comprehensive functional analyses of factors implicated in ever-expanding multiomics datasets. This report details the progress we have made to date with a multiplexed CRISPR/Cas9-based gene targeting strategy and discusses how the methodologies applied can further our understanding of the genes that predispose to retinal degenerative disease and which control the regenerative capacity of retinal Müller glia cells.
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Affiliation(s)
- Arife Unal Eroglu
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Timothy S Mulligan
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Liyun Zhang
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - David T White
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Sumitra Sengupta
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Cathy Nie
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Noela Y Lu
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Jiang Qian
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Lisha Xu
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD, United States
| | - Wuhong Pei
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD, United States
| | - Shawn M Burgess
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD, United States
| | - Meera T Saxena
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Jeff S Mumm
- Department of Ophthalmology, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, United States
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10
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Vergara MN, Flores-Bellver M, Aparicio-Domingo S, McNally M, Wahlin KJ, Saxena MT, Mumm JS, Canto-Soler MV. Three-dimensional automated reporter quantification (3D-ARQ) technology enables quantitative screening in retinal organoids. Development 2017; 144:3698-3705. [PMID: 28870990 DOI: 10.1242/dev.146290] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 08/30/2017] [Indexed: 12/20/2022]
Abstract
The advent of stem cell-derived retinal organoids has brought forth unprecedented opportunities for developmental and physiological studies, while presenting new therapeutic promise for retinal degenerative diseases. From a translational perspective, organoid systems provide exciting new prospects for drug discovery, offering the possibility to perform compound screening in a three-dimensional (3D) human tissue context that resembles the native histoarchitecture and to some extent recapitulates cellular interactions. However, inherent variability issues and a general lack of robust quantitative technologies for analyzing organoids on a large scale pose severe limitations for their use in translational applications. To address this need, we have developed a screening platform that enables accurate quantification of fluorescent reporters in complex human iPSC-derived retinal organoids. This platform incorporates a fluorescence microplate reader that allows xyz-dimensional detection and fine-tuned wavelength selection. We have established optimal parameters for fluorescent reporter signal detection, devised methods to compensate for organoid size variability, evaluated performance and sensitivity parameters, and validated this technology for functional applications.
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Affiliation(s)
- M Natalia Vergara
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Miguel Flores-Bellver
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Silvia Aparicio-Domingo
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Minda McNally
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Karl J Wahlin
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Meera T Saxena
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Jeff S Mumm
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - M Valeria Canto-Soler
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
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11
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Mathias JR, Zhang Z, Saxena MT, Mumm JS. Enhanced cell-specific ablation in zebrafish using a triple mutant of Escherichia coli nitroreductase. Zebrafish 2014; 11:85-97. [PMID: 24428354 DOI: 10.1089/zeb.2013.0937] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Transgenic expression of bacterial nitroreductase (NTR) facilitates chemically-inducible targeted cell ablation. In zebrafish, the NTR system enables studies of cell function and cellular regeneration. Metronidazole (MTZ) has become the most commonly used prodrug substrate for eliciting cell loss in NTR-expressing transgenic zebrafish due to the cell-specific nature of its cytotoxic derivatives. Unfortunately, MTZ treatments required for effective cell ablation border toxic effects, and, thus, likely incur undesirable nonspecific effects. Here, we tested whether a triple mutant variant of NTR, previously shown to display improved activity in bacterial assays, can solve this issue by promoting cell ablation in zebrafish using reduced prodrug treatment regimens. We generated several complementary transgenic zebrafish lines expressing either wild-type or mutant NTR (mutNTR) in specific neural cell types, and assayed prodrug-induced cell ablation kinetics using confocal time series imaging and plate reader-based quantification of fluorescent reporters expressed in targeted cell types. The results show that cell ablation can be achieved in mutNTR expressing transgenic lines with markedly shortened prodrug exposure times and/or at lower prodrug concentrations. The mutNTR variant characterized here can circumvent problematic nonspecific/toxic effects arising from low prodrug conversion efficiency, thus increasing the effectiveness and versatility of this selective cell ablation methodology.
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12
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Xie X, Mathias JR, Smith MA, Walker SL, Teng Y, Distel M, Köster RW, Sirotkin HI, Saxena MT, Mumm JS. Silencer-delimited transgenesis: NRSE/RE1 sequences promote neural-specific transgene expression in a NRSF/REST-dependent manner. BMC Biol 2012. [PMID: 23198762 PMCID: PMC3529185 DOI: 10.1186/1741-7007-10-93] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND We have investigated a simple strategy for enhancing transgene expression specificity by leveraging genetic silencer elements. The approach serves to restrict transgene expression to a tissue of interest - the nervous system in the example provided here - thereby promoting specific/exclusive targeting of discrete cellular subtypes. Recent innovations are bringing us closer to understanding how the brain is organized, how neural circuits function, and how neurons can be regenerated. Fluorescent proteins enable mapping of the 'connectome', optogenetic tools allow excitable cells to be short-circuited or hyperactivated, and targeted ablation of neuronal subtypes facilitates investigations of circuit function and neuronal regeneration. Optimally, such toolsets need to be expressed solely within the cell types of interest as off-site expression makes establishing causal relationships difficult. To address this, we have exploited a gene 'silencing' system that promotes neuronal specificity by repressing expression in non-neural tissues. This methodology solves non-specific background issues that plague large-scale enhancer trap efforts and may provide a means of leveraging promoters/enhancers that otherwise express too broadly to be of value for in vivo manipulations. RESULTS We show that a conserved neuron-restrictive silencer element (NRSE) can function to restrict transgene expression to the nervous system. The neuron-restrictive silencing factor/repressor element 1 silencing transcription factor (NRSF/REST) transcriptional repressor binds NRSE/repressor element 1 (RE1) sites and silences gene expression in non-neuronal cells. Inserting NRSE sites into transgenes strongly biased expression to neural tissues. NRSE sequences were effective in restricting expression of bipartite Gal4-based 'driver' transgenes within the context of an enhancer trap and when associated with a defined promoter and enhancer. However, NRSE sequences did not serve to restrict expression of an upstream activating sequence (UAS)-based reporter/effector transgene when associated solely with the UAS element. Morpholino knockdown assays showed that NRSF/REST expression is required for NRSE-based transgene silencing. CONCLUSIONS Our findings demonstrate that the addition of NRSE sequences to transgenes can provide useful new tools for functional studies of the nervous system. However, the general approach may be more broadly applicable; tissue-specific silencer elements are operable in tissues other than the nervous system, suggesting this approach can be similarly applied to other paradigms. Thus, creating synthetic associations between endogenous regulatory elements and tissue-specific silencers may facilitate targeting of cellular subtypes for which defined promoters/enhancers are lacking.
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Affiliation(s)
- Xiayang Xie
- Department of Cellular Biology and Anatomy, Georgia Health Sciences University, Augusta, GA 30912, USA
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13
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Walker SL, Ariga J, Mathias JR, Coothankandaswamy V, Xie X, Distel M, Köster RW, Parsons MJ, Bhalla KN, Saxena MT, Mumm JS. Automated reporter quantification in vivo: high-throughput screening method for reporter-based assays in zebrafish. PLoS One 2012; 7:e29916. [PMID: 22238673 PMCID: PMC3251595 DOI: 10.1371/journal.pone.0029916] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Accepted: 12/06/2011] [Indexed: 11/18/2022] Open
Abstract
Reporter-based assays underlie many high-throughput screening (HTS) platforms, but most are limited to in vitro applications. Here, we report a simple whole-organism HTS method for quantifying changes in reporter intensity in individual zebrafish over time termed, Automated Reporter Quantification in vivo (ARQiv). ARQiv differs from current “high-content” (e.g., confocal imaging-based) whole-organism screening technologies by providing a purely quantitative data acquisition approach that affords marked improvements in throughput. ARQiv uses a fluorescence microplate reader with specific detection functionalities necessary for robust quantification of reporter signals in vivo. This approach is: 1) Rapid; achieving true HTS capacities (i.e., >50,000 units per day), 2) Reproducible; attaining HTS-compatible assay quality (i.e., Z'-factors of ≥0.5), and 3) Flexible; amenable to nearly any reporter-based assay in zebrafish embryos, larvae, or juveniles. ARQiv is used here to quantify changes in: 1) Cell number; loss and regeneration of two different fluorescently tagged cell types (pancreatic beta cells and rod photoreceptors), 2) Cell signaling; relative activity of a transgenic Notch-signaling reporter, and 3) Cell metabolism; accumulation of reactive oxygen species. In summary, ARQiv is a versatile and readily accessible approach facilitating evaluation of genetic and/or chemical manipulations in living zebrafish that complements current “high-content” whole-organism screening methods by providing a first-tier in vivo HTS drug discovery platform.
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Affiliation(s)
- Steven L. Walker
- Department of Cellular Biology and Anatomy, Georgia Health Sciences University, Augusta, Georgia, United States of America
| | - Junko Ariga
- Department of Cellular Biology and Anatomy, Georgia Health Sciences University, Augusta, Georgia, United States of America
| | | | - Veena Coothankandaswamy
- Cancer Center, Georgia Health Sciences University, Augusta, Georgia, United States of America
| | - Xiayang Xie
- Department of Cellular Biology and Anatomy, Georgia Health Sciences University, Augusta, Georgia, United States of America
| | - Martin Distel
- Institute of Developmental Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Reinhard W. Köster
- Institute of Developmental Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Michael J. Parsons
- Department of Surgery, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Kapil N. Bhalla
- Cancer Center, Georgia Health Sciences University, Augusta, Georgia, United States of America
| | - Meera T. Saxena
- Luminomics, Inc., Augusta, Georgia, United States of America
| | - Jeff S. Mumm
- Department of Cellular Biology and Anatomy, Georgia Health Sciences University, Augusta, Georgia, United States of America
- * E-mail:
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14
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Saxena MT, Aton SJ, Hildebolt C, Prior JL, Abraham U, Piwnica-Worms D, Herzog ED. Bioluminescence imaging of period1 gene expression in utero. Mol Imaging 2007; 6:68-72. [PMID: 17311766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023] Open
Abstract
The use of real-time reporters has accelerated our understanding of gene expression in vivo. This study examined the feasibility of a luciferase-based reporter to image spatiotemporal changes in fetal gene expression in utero. We chose to monitor Period1 (Per1) because it is expressed broadly in the body and plays a role in circadian rhythmicity. Using rats carrying a Per1::luc transgene, we repetitively imaged fetuses in utero throughout gestation. We found that bioluminescence was specific to transgenic pups, increased dramatically on embryonic day 10 (10 days after successful mating), and continued to increase logarithmically until birth. Diurnal fluctuations in Per1 expression were apparent several days prior to birth. These results demonstrate the feasibility of in utero imaging of mammalian gene expression, tracking of fetal gene expression from the same litter, and early detection of mammalian clock gene expression. We conclude that luciferase-based reporters can provide a sensitive, noninvasive measure of in utero gene expression.
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Affiliation(s)
- Meera T Saxena
- Department of Biology, Washington University, St. Louis, MO 63110, USA
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15
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Saxena MT, Aton SJ, Hildebolt C, Prior JL, Abraham U, Piwnica-Worms D, Herzog ED. Bioluminescence Imaging ofPeriod1Gene Expression in Utero. Mol Imaging 2007. [DOI: 10.2310/7290.2007.00003] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Meera T. Saxena
- From the Department of Biology, Washington University, St. Louis, MO, and Molecular Imaging Center, Mallinckrodt Institute of Radiology and Department of Molecular Biology and Pharmacology, Washington University Medical School, St. Louis, MO
| | - Sara J. Aton
- From the Department of Biology, Washington University, St. Louis, MO, and Molecular Imaging Center, Mallinckrodt Institute of Radiology and Department of Molecular Biology and Pharmacology, Washington University Medical School, St. Louis, MO
| | - Charles Hildebolt
- From the Department of Biology, Washington University, St. Louis, MO, and Molecular Imaging Center, Mallinckrodt Institute of Radiology and Department of Molecular Biology and Pharmacology, Washington University Medical School, St. Louis, MO
| | - Julie L. Prior
- From the Department of Biology, Washington University, St. Louis, MO, and Molecular Imaging Center, Mallinckrodt Institute of Radiology and Department of Molecular Biology and Pharmacology, Washington University Medical School, St. Louis, MO
| | - Ute Abraham
- From the Department of Biology, Washington University, St. Louis, MO, and Molecular Imaging Center, Mallinckrodt Institute of Radiology and Department of Molecular Biology and Pharmacology, Washington University Medical School, St. Louis, MO
| | - David Piwnica-Worms
- From the Department of Biology, Washington University, St. Louis, MO, and Molecular Imaging Center, Mallinckrodt Institute of Radiology and Department of Molecular Biology and Pharmacology, Washington University Medical School, St. Louis, MO
| | - Erik D. Herzog
- From the Department of Biology, Washington University, St. Louis, MO, and Molecular Imaging Center, Mallinckrodt Institute of Radiology and Department of Molecular Biology and Pharmacology, Washington University Medical School, St. Louis, MO
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Abstract
Circadian pacemakers drive many daily molecular, physiological and behavioural rhythms. We investigated whether the main olfactory bulb is a functional circadian pacemaker in rats. Long-term, multielectrode recordings revealed that individual, cultured bulb neurons expressed near 24-h oscillations in firing rate. Real-time recordings of Period1 gene activity showed that a population of cells within the bulb expressed synchronized rhythmicity starting on embryonic day 19. This rhythmicity was intrinsic to the mitral, and not the granule, cell layer, entrainable to physiological temperature cycles and temperature compensated in its period. However, removal of the olfactory bulbs had no effect on running wheel behaviour. These results indicate that individual mitral/tufted cells are competent circadian pacemakers which normally synchronize to each other. The daily rhythms in gene expression and firing rate intrinsic to the olfactory bulb are not required for circadian patterns of locomotion, indicating that they are involved in rhythms outside the canonical circadian system.
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Schroeter EH, Ilagan MXG, Brunkan AL, Hecimovic S, Li YM, Xu M, Lewis HD, Saxena MT, De Strooper B, Coonrod A, Tomita T, Iwatsubo T, Moore CL, Goate A, Wolfe MS, Shearman M, Kopan R. A presenilin dimer at the core of the gamma-secretase enzyme: insights from parallel analysis of Notch 1 and APP proteolysis. Proc Natl Acad Sci U S A 2003; 100:13075-80. [PMID: 14566063 PMCID: PMC240747 DOI: 10.1073/pnas.1735338100] [Citation(s) in RCA: 167] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Notch receptors and the amyloid precursor protein are type I membrane proteins that are proteolytically cleaved within their transmembrane domains by a presenilin (PS)-dependent gamma-secretase activity. In both proteins, two peptide bonds are hydrolyzed: one near the inner leaflet and the other in the middle of the transmembrane domain. Under saturating conditions the substrates compete with each other for proteolysis, but not for binding to PS. At least some Alzheimer's disease-causing PS mutations reside in proteins possessing low catalytic activity. We demonstrate (i) that differentially tagged PS molecules coimmunoprecipitate, and (ii) that PS N-terminal fragment dimers exist by using a photoaffinity probe based on a transition state analog gamma-secretase inhibitor. We propose that gamma-secretase contains a PS dimer in its catalytic core, that binding of substrate is at a site separate from the active site, and that substrate is cleaved at the interface of two PS molecules.
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Affiliation(s)
- Eric H. Schroeter
- Departments of Molecular Biology and Pharmacology and Psychiatry, Washington University School of Medicine, St. Louis, MO 63110; Department of Biological Chemistry, Merck Research Laboratories, West Point, PA 19486-0004; Department of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo Bunkyoku, Tokyo 113-0033, Japan; Department of Biochemistry and Molecular Biology, Merck Sharp and Dohme Research Laboratories, Neuroscience Research Centre, Terlings Park, Harlow, Essex CM20 2QR, United Kingdom; Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115; Department of Pharmaceutical Sciences, University of Tennessee, Memphis, TN 38163; and Neuronal Cell Biology and Gene Transfer Laboratory, Center for Human Genetics, Katholieke Universiteit and Flanders Interuniversity Institute for Biotechnology, VIB4 Leuven, Belgium
| | - Ma. Xenia G. Ilagan
- Departments of Molecular Biology and Pharmacology and Psychiatry, Washington University School of Medicine, St. Louis, MO 63110; Department of Biological Chemistry, Merck Research Laboratories, West Point, PA 19486-0004; Department of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo Bunkyoku, Tokyo 113-0033, Japan; Department of Biochemistry and Molecular Biology, Merck Sharp and Dohme Research Laboratories, Neuroscience Research Centre, Terlings Park, Harlow, Essex CM20 2QR, United Kingdom; Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115; Department of Pharmaceutical Sciences, University of Tennessee, Memphis, TN 38163; and Neuronal Cell Biology and Gene Transfer Laboratory, Center for Human Genetics, Katholieke Universiteit and Flanders Interuniversity Institute for Biotechnology, VIB4 Leuven, Belgium
| | - Anne L. Brunkan
- Departments of Molecular Biology and Pharmacology and Psychiatry, Washington University School of Medicine, St. Louis, MO 63110; Department of Biological Chemistry, Merck Research Laboratories, West Point, PA 19486-0004; Department of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo Bunkyoku, Tokyo 113-0033, Japan; Department of Biochemistry and Molecular Biology, Merck Sharp and Dohme Research Laboratories, Neuroscience Research Centre, Terlings Park, Harlow, Essex CM20 2QR, United Kingdom; Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115; Department of Pharmaceutical Sciences, University of Tennessee, Memphis, TN 38163; and Neuronal Cell Biology and Gene Transfer Laboratory, Center for Human Genetics, Katholieke Universiteit and Flanders Interuniversity Institute for Biotechnology, VIB4 Leuven, Belgium
| | - Silva Hecimovic
- Departments of Molecular Biology and Pharmacology and Psychiatry, Washington University School of Medicine, St. Louis, MO 63110; Department of Biological Chemistry, Merck Research Laboratories, West Point, PA 19486-0004; Department of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo Bunkyoku, Tokyo 113-0033, Japan; Department of Biochemistry and Molecular Biology, Merck Sharp and Dohme Research Laboratories, Neuroscience Research Centre, Terlings Park, Harlow, Essex CM20 2QR, United Kingdom; Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115; Department of Pharmaceutical Sciences, University of Tennessee, Memphis, TN 38163; and Neuronal Cell Biology and Gene Transfer Laboratory, Center for Human Genetics, Katholieke Universiteit and Flanders Interuniversity Institute for Biotechnology, VIB4 Leuven, Belgium
| | - Yue-ming Li
- Departments of Molecular Biology and Pharmacology and Psychiatry, Washington University School of Medicine, St. Louis, MO 63110; Department of Biological Chemistry, Merck Research Laboratories, West Point, PA 19486-0004; Department of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo Bunkyoku, Tokyo 113-0033, Japan; Department of Biochemistry and Molecular Biology, Merck Sharp and Dohme Research Laboratories, Neuroscience Research Centre, Terlings Park, Harlow, Essex CM20 2QR, United Kingdom; Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115; Department of Pharmaceutical Sciences, University of Tennessee, Memphis, TN 38163; and Neuronal Cell Biology and Gene Transfer Laboratory, Center for Human Genetics, Katholieke Universiteit and Flanders Interuniversity Institute for Biotechnology, VIB4 Leuven, Belgium
| | - Min Xu
- Departments of Molecular Biology and Pharmacology and Psychiatry, Washington University School of Medicine, St. Louis, MO 63110; Department of Biological Chemistry, Merck Research Laboratories, West Point, PA 19486-0004; Department of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo Bunkyoku, Tokyo 113-0033, Japan; Department of Biochemistry and Molecular Biology, Merck Sharp and Dohme Research Laboratories, Neuroscience Research Centre, Terlings Park, Harlow, Essex CM20 2QR, United Kingdom; Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115; Department of Pharmaceutical Sciences, University of Tennessee, Memphis, TN 38163; and Neuronal Cell Biology and Gene Transfer Laboratory, Center for Human Genetics, Katholieke Universiteit and Flanders Interuniversity Institute for Biotechnology, VIB4 Leuven, Belgium
| | - Huw D. Lewis
- Departments of Molecular Biology and Pharmacology and Psychiatry, Washington University School of Medicine, St. Louis, MO 63110; Department of Biological Chemistry, Merck Research Laboratories, West Point, PA 19486-0004; Department of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo Bunkyoku, Tokyo 113-0033, Japan; Department of Biochemistry and Molecular Biology, Merck Sharp and Dohme Research Laboratories, Neuroscience Research Centre, Terlings Park, Harlow, Essex CM20 2QR, United Kingdom; Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115; Department of Pharmaceutical Sciences, University of Tennessee, Memphis, TN 38163; and Neuronal Cell Biology and Gene Transfer Laboratory, Center for Human Genetics, Katholieke Universiteit and Flanders Interuniversity Institute for Biotechnology, VIB4 Leuven, Belgium
| | - Meera T. Saxena
- Departments of Molecular Biology and Pharmacology and Psychiatry, Washington University School of Medicine, St. Louis, MO 63110; Department of Biological Chemistry, Merck Research Laboratories, West Point, PA 19486-0004; Department of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo Bunkyoku, Tokyo 113-0033, Japan; Department of Biochemistry and Molecular Biology, Merck Sharp and Dohme Research Laboratories, Neuroscience Research Centre, Terlings Park, Harlow, Essex CM20 2QR, United Kingdom; Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115; Department of Pharmaceutical Sciences, University of Tennessee, Memphis, TN 38163; and Neuronal Cell Biology and Gene Transfer Laboratory, Center for Human Genetics, Katholieke Universiteit and Flanders Interuniversity Institute for Biotechnology, VIB4 Leuven, Belgium
| | - Bart De Strooper
- Departments of Molecular Biology and Pharmacology and Psychiatry, Washington University School of Medicine, St. Louis, MO 63110; Department of Biological Chemistry, Merck Research Laboratories, West Point, PA 19486-0004; Department of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo Bunkyoku, Tokyo 113-0033, Japan; Department of Biochemistry and Molecular Biology, Merck Sharp and Dohme Research Laboratories, Neuroscience Research Centre, Terlings Park, Harlow, Essex CM20 2QR, United Kingdom; Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115; Department of Pharmaceutical Sciences, University of Tennessee, Memphis, TN 38163; and Neuronal Cell Biology and Gene Transfer Laboratory, Center for Human Genetics, Katholieke Universiteit and Flanders Interuniversity Institute for Biotechnology, VIB4 Leuven, Belgium
| | - Archie Coonrod
- Departments of Molecular Biology and Pharmacology and Psychiatry, Washington University School of Medicine, St. Louis, MO 63110; Department of Biological Chemistry, Merck Research Laboratories, West Point, PA 19486-0004; Department of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo Bunkyoku, Tokyo 113-0033, Japan; Department of Biochemistry and Molecular Biology, Merck Sharp and Dohme Research Laboratories, Neuroscience Research Centre, Terlings Park, Harlow, Essex CM20 2QR, United Kingdom; Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115; Department of Pharmaceutical Sciences, University of Tennessee, Memphis, TN 38163; and Neuronal Cell Biology and Gene Transfer Laboratory, Center for Human Genetics, Katholieke Universiteit and Flanders Interuniversity Institute for Biotechnology, VIB4 Leuven, Belgium
| | - Taisuke Tomita
- Departments of Molecular Biology and Pharmacology and Psychiatry, Washington University School of Medicine, St. Louis, MO 63110; Department of Biological Chemistry, Merck Research Laboratories, West Point, PA 19486-0004; Department of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo Bunkyoku, Tokyo 113-0033, Japan; Department of Biochemistry and Molecular Biology, Merck Sharp and Dohme Research Laboratories, Neuroscience Research Centre, Terlings Park, Harlow, Essex CM20 2QR, United Kingdom; Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115; Department of Pharmaceutical Sciences, University of Tennessee, Memphis, TN 38163; and Neuronal Cell Biology and Gene Transfer Laboratory, Center for Human Genetics, Katholieke Universiteit and Flanders Interuniversity Institute for Biotechnology, VIB4 Leuven, Belgium
| | - Takeshi Iwatsubo
- Departments of Molecular Biology and Pharmacology and Psychiatry, Washington University School of Medicine, St. Louis, MO 63110; Department of Biological Chemistry, Merck Research Laboratories, West Point, PA 19486-0004; Department of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo Bunkyoku, Tokyo 113-0033, Japan; Department of Biochemistry and Molecular Biology, Merck Sharp and Dohme Research Laboratories, Neuroscience Research Centre, Terlings Park, Harlow, Essex CM20 2QR, United Kingdom; Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115; Department of Pharmaceutical Sciences, University of Tennessee, Memphis, TN 38163; and Neuronal Cell Biology and Gene Transfer Laboratory, Center for Human Genetics, Katholieke Universiteit and Flanders Interuniversity Institute for Biotechnology, VIB4 Leuven, Belgium
| | - Chad L. Moore
- Departments of Molecular Biology and Pharmacology and Psychiatry, Washington University School of Medicine, St. Louis, MO 63110; Department of Biological Chemistry, Merck Research Laboratories, West Point, PA 19486-0004; Department of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo Bunkyoku, Tokyo 113-0033, Japan; Department of Biochemistry and Molecular Biology, Merck Sharp and Dohme Research Laboratories, Neuroscience Research Centre, Terlings Park, Harlow, Essex CM20 2QR, United Kingdom; Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115; Department of Pharmaceutical Sciences, University of Tennessee, Memphis, TN 38163; and Neuronal Cell Biology and Gene Transfer Laboratory, Center for Human Genetics, Katholieke Universiteit and Flanders Interuniversity Institute for Biotechnology, VIB4 Leuven, Belgium
| | - Alison Goate
- Departments of Molecular Biology and Pharmacology and Psychiatry, Washington University School of Medicine, St. Louis, MO 63110; Department of Biological Chemistry, Merck Research Laboratories, West Point, PA 19486-0004; Department of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo Bunkyoku, Tokyo 113-0033, Japan; Department of Biochemistry and Molecular Biology, Merck Sharp and Dohme Research Laboratories, Neuroscience Research Centre, Terlings Park, Harlow, Essex CM20 2QR, United Kingdom; Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115; Department of Pharmaceutical Sciences, University of Tennessee, Memphis, TN 38163; and Neuronal Cell Biology and Gene Transfer Laboratory, Center for Human Genetics, Katholieke Universiteit and Flanders Interuniversity Institute for Biotechnology, VIB4 Leuven, Belgium
| | - Michael S. Wolfe
- Departments of Molecular Biology and Pharmacology and Psychiatry, Washington University School of Medicine, St. Louis, MO 63110; Department of Biological Chemistry, Merck Research Laboratories, West Point, PA 19486-0004; Department of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo Bunkyoku, Tokyo 113-0033, Japan; Department of Biochemistry and Molecular Biology, Merck Sharp and Dohme Research Laboratories, Neuroscience Research Centre, Terlings Park, Harlow, Essex CM20 2QR, United Kingdom; Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115; Department of Pharmaceutical Sciences, University of Tennessee, Memphis, TN 38163; and Neuronal Cell Biology and Gene Transfer Laboratory, Center for Human Genetics, Katholieke Universiteit and Flanders Interuniversity Institute for Biotechnology, VIB4 Leuven, Belgium
| | - Mark Shearman
- Departments of Molecular Biology and Pharmacology and Psychiatry, Washington University School of Medicine, St. Louis, MO 63110; Department of Biological Chemistry, Merck Research Laboratories, West Point, PA 19486-0004; Department of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo Bunkyoku, Tokyo 113-0033, Japan; Department of Biochemistry and Molecular Biology, Merck Sharp and Dohme Research Laboratories, Neuroscience Research Centre, Terlings Park, Harlow, Essex CM20 2QR, United Kingdom; Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115; Department of Pharmaceutical Sciences, University of Tennessee, Memphis, TN 38163; and Neuronal Cell Biology and Gene Transfer Laboratory, Center for Human Genetics, Katholieke Universiteit and Flanders Interuniversity Institute for Biotechnology, VIB4 Leuven, Belgium
| | - Raphael Kopan
- Departments of Molecular Biology and Pharmacology and Psychiatry, Washington University School of Medicine, St. Louis, MO 63110; Department of Biological Chemistry, Merck Research Laboratories, West Point, PA 19486-0004; Department of Neuropathology and Neuroscience, Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo Bunkyoku, Tokyo 113-0033, Japan; Department of Biochemistry and Molecular Biology, Merck Sharp and Dohme Research Laboratories, Neuroscience Research Centre, Terlings Park, Harlow, Essex CM20 2QR, United Kingdom; Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115; Department of Pharmaceutical Sciences, University of Tennessee, Memphis, TN 38163; and Neuronal Cell Biology and Gene Transfer Laboratory, Center for Human Genetics, Katholieke Universiteit and Flanders Interuniversity Institute for Biotechnology, VIB4 Leuven, Belgium
- To whom correspondence should be addressed. E-mail:
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Abstract
Oncogenic forms of Notch1, Notch2, and Notch4 appear to mimic signaling intermediates of Notch1 and suggest that the role of proteolysis in Notch signaling has been conserved. Here we demonstrate that extracellularly truncated Notch homologs are substrates for a presenilin-dependent gamma-secretase activity. Despite minimal conservation within the transmembrane domain, the requirement for a specific amino acid (P1' valine) and its position at the cleavage site relative to the cytosolic border of the transmembrane domain are preserved. Cleaved, untethered Notch intracellular domains from each receptor translocate to the nucleus and interact with the transcriptional regulatory protein CSL. All four Notch proteins display presenilin-dependent transactivating potential on a minimal promoter reporter. Thus, this study increases the number of biochemically characterized gamma-secretase substrates from two to five. Despite a high degree of structural homology and the presenilin-dependent activity of truncated Notch proteins, the extent that this reflects functional redundancy is unknown.
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Affiliation(s)
- M T Saxena
- Department of Molecular Biology and Pharmacology, Washington University School of Medicine, 660 South Euclid Ave., St. Louis, MO 63110, USA
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Huppert SS, Le A, Schroeter EH, Mumm JS, Saxena MT, Milner LA, Kopan R. Embryonic lethality in mice homozygous for a processing-deficient allele of Notch1. Nature 2000; 405:966-70. [PMID: 10879540 DOI: 10.1038/35016111] [Citation(s) in RCA: 258] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The Notch genes encode single-pass transmembrane receptors that transduce the extracellular signals responsible for cell fate determination during several steps of metazoan development. The mechanism by which extracellular signals affect gene transcription and ultimately cell fate decisions is beginning to emerge for the Notch signalling pathway. One paradigm is that ligand binding to Notch triggers a Presenilin1-dependent proteolytic release of the Notch intracellular domain from the membrane, resulting in low amounts of Notch intracellular domain which form a nuclear complex with CBF1/Su(H)/Lag1 to activate transcription of downstream targets. Not all observations clearly support this processing model, and the most rigorous test of it is to block processing in vivo and then determine the ability of unprocessed Notch to signal. Here we report that the phenotypes associated with a single point mutation at the intramembranous processing site of Notch1, Val1,744-->Gly, resemble the null Notch1 phenotype. Our results show that efficient intramembranous processing of Notch1 is indispensable for embryonic viability and proper early embryonic development in vivo.
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Affiliation(s)
- S S Huppert
- Department of Molecular Biology and Pharmacology, Washington University School of Medicine, St Louis, Missouri 63110, USA
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Kopan R, Mumm JS, Schroeter EH, Saxena MT, Ray WJ, Goate AM. The next step in notch processing and its relevance to APP biology. Neurobiol Aging 2000. [DOI: 10.1016/s0197-4580(00)82693-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Mumm JS, Schroeter EH, Saxena MT, Griesemer A, Tian X, Pan DJ, Ray WJ, Kopan R. A ligand-induced extracellular cleavage regulates gamma-secretase-like proteolytic activation of Notch1. Mol Cell 2000; 5:197-206. [PMID: 10882062 DOI: 10.1016/s1097-2765(00)80416-5] [Citation(s) in RCA: 636] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Gamma-secretase-like proteolysis at site 3 (S3), within the transmembrane domain, releases the Notch intracellular domain (NICD) and activates CSL-mediated Notch signaling. S3 processing occurs only in response to ligand binding; however, the molecular basis of this regulation is unknown. Here we demonstrate that ligand binding facilitates cleavage at a novel site (S2), within the extracellular juxtamembrane region, which serves to release ectodomain repression of NICD production. Cleavage at S2 generates a transient intermediate peptide termed NEXT (Notch extracellular truncation). NEXT accumulates when NICD production is blocked by point mutations or gamma-secretase inhibitors or by loss of presenilin 1, and inhibition of NEXT eliminates NICD production. Our data demonstrate that S2 cleavage is a ligand-regulated step in the proteolytic cascade leading to Notch activation.
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Affiliation(s)
- J S Mumm
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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