1
|
Shaw DK, Saraswathy VM, McAdow AR, Zhou L, Park D, Mote R, Johnson AN, Mokalled MH. Elevated phagocytic capacity directs innate spinal cord repair. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.11.598515. [PMID: 38915507 PMCID: PMC11195157 DOI: 10.1101/2024.06.11.598515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Immune cells elicit a continuum of transcriptional and functional states after spinal cord injury (SCI). In mammals, inefficient debris clearance and chronic inflammation impede recovery and overshadow pro-regenerative immune functions. We found that, unlike mammals, zebrafish SCI elicits transient immune activation and efficient debris clearance, without causing chronic inflammation. Single-cell transcriptomics and inducible genetic ablation showed zebrafish macrophages are highly phagocytic and required for regeneration. Cross-species comparisons between zebrafish and mammalian macrophages identified transcription and immune response regulator ( tcim ) as a macrophage-enriched zebrafish gene. Genetic deletion of zebrafish tcim impairs phagocytosis and regeneration, causes aberrant and chronic immune activation, and can be rescued by transplanting wild-type immune precursors into tcim mutants. Conversely, genetic expression of human TCIM accelerates debris clearance and regeneration by reprogramming myeloid precursors into activated phagocytes. This study establishes a central requirement for elevated phagocytic capacity to achieve innate spinal cord repair.
Collapse
|
2
|
Sifuentes-Romero I, Aviles AM, Carter JL, Chan-Pong A, Clarke A, Crotty P, Engstrom D, Meka P, Perez A, Perez R, Phelan C, Sharrard T, Smirnova MI, Wade AJ, Kowalko JE. Trait Loss in Evolution: What Cavefish Have Taught Us about Mechanisms Underlying Eye Regression. Integr Comp Biol 2023; 63:393-406. [PMID: 37218721 PMCID: PMC10445413 DOI: 10.1093/icb/icad032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/18/2023] [Accepted: 04/24/2023] [Indexed: 05/24/2023] Open
Abstract
Reduction or complete loss of traits is a common occurrence throughout evolutionary history. In spite of this, numerous questions remain about why and how trait loss has occurred. Cave animals are an excellent system in which these questions can be answered, as multiple traits, including eyes and pigmentation, have been repeatedly reduced or lost across populations of cave species. This review focuses on how the blind Mexican cavefish, Astyanax mexicanus, has been used as a model system for examining the developmental, genetic, and evolutionary mechanisms that underlie eye regression in cave animals. We focus on multiple aspects of how eye regression evolved in A. mexicanus, including the developmental and genetic pathways that contribute to eye regression, the effects of the evolution of eye regression on other traits that have also evolved in A. mexicanus, and the evolutionary forces contributing to eye regression. We also discuss what is known about the repeated evolution of eye regression, both across populations of A. mexicanus cavefish and across cave animals more generally. Finally, we offer perspectives on how cavefish can be used in the future to further elucidate mechanisms underlying trait loss using tools and resources that have recently become available.
Collapse
Affiliation(s)
- Itzel Sifuentes-Romero
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Ari M Aviles
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
- Department of Cell Biology and Genetics, Texas A&M University, College Station, TX 77843, USA
| | - Joseph L Carter
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
| | - Allen Chan-Pong
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
| | - Anik Clarke
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
| | - Patrick Crotty
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
| | - David Engstrom
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
| | - Pranav Meka
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
- Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Alexandra Perez
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
| | - Riley Perez
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
| | - Christine Phelan
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
| | - Taylor Sharrard
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
| | - Maria I Smirnova
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
- Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL 33431, USA
- Stiles–Nicholson Brain Institute, Florida Atlantic University, Jupiter, FL 33458, USA
- Charles E. Schmidt College of Science, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Amanda J Wade
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
| | - Johanna E Kowalko
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter FL 33458, USA
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
| |
Collapse
|
3
|
Palmiotti A, Lichak MR, Shih PY, Kwon YM, Bendesky A. Genetic manipulation of betta fish. Front Genome Ed 2023; 5:1167093. [PMID: 37545763 PMCID: PMC10401044 DOI: 10.3389/fgeed.2023.1167093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 07/07/2023] [Indexed: 08/08/2023] Open
Abstract
Betta splendens, also known as Siamese fighting fish or "betta," is a freshwater fish species renowned for its astonishing morphological diversity and extreme aggressive behavior. Despite recent advances in our understanding of the genetics and neurobiology of betta, the lack of tools to manipulate their genome has hindered progress at functional and mechanistic levels. In this study, we outline the use of three genetic manipulation technologies, which we have optimized for use in betta: CRISPR/Cas9-mediated knockout, CRISPR/Cas9-mediated knockin, and Tol2-mediated transgenesis. We knocked out three genes: alkal2l, bco1l, and mitfa, and analyzed their effects on viability and pigmentation. Furthermore, we knocked in a fluorescent protein into the mitfa locus, a proof-of-principle experiment of this powerful technology in betta. Finally, we used Tol2-mediated transgenesis to create fish with ubiquitous expression of GFP, and then developed a bicistronic plasmid with heart-specific expression of a red fluorescent protein to serve as a visible marker of successful transgenesis. Our work highlights the potential for the genetic manipulation of betta, providing valuable resources for the effective use of genetic tools in this animal model.
Collapse
Affiliation(s)
- Alec Palmiotti
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, United States
| | - Madison R. Lichak
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, United States
| | - Pei-Yin Shih
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, United States
| | - Young Mi Kwon
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, United States
| | - Andres Bendesky
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, United States
| |
Collapse
|
4
|
Jensen NO, Burris B, Zhou L, Yamada H, Reyes C, Pincus Z, Mokalled MH. Functional trajectories during innate spinal cord repair. Front Mol Neurosci 2023; 16:1155754. [PMID: 37492522 PMCID: PMC10365889 DOI: 10.3389/fnmol.2023.1155754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 05/26/2023] [Indexed: 07/27/2023] Open
Abstract
Adult zebrafish are capable of anatomical and functional recovery following severe spinal cord injury. Axon growth, glial bridging and adult neurogenesis are hallmarks of cellular regeneration during spinal cord repair. However, the correlation between these cellular regenerative processes and functional recovery remains to be elucidated. Whereas the majority of established functional regeneration metrics measure swim capacity, we hypothesize that gait quality is more directly related to neurological health. Here, we performed a longitudinal swim tracking study for 60 individual zebrafish spanning 8 weeks of spinal cord regeneration. Multiple swim parameters as well as axonal and glial bridging were integrated. We established rostral compensation as a new gait quality metric that highly correlates with functional recovery. Tensor component analysis of longitudinal data supports a correspondence between functional recovery trajectories and neurological outcomes. Moreover, our studies predicted and validated that a subset of functional regeneration parameters measured 1 to 2 weeks post-injury is sufficient to predict the regenerative outcomes of individual animals at 8 weeks post-injury. Our findings established new functional regeneration parameters and generated a comprehensive correlative database between various functional and cellular regeneration outputs.
Collapse
Affiliation(s)
- Nicholas O. Jensen
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, United States
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, United States
| | - Brooke Burris
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, United States
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, United States
| | - Lili Zhou
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, United States
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, United States
| | - Hunter Yamada
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, United States
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, United States
| | - Catrina Reyes
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, United States
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, United States
| | - Zachary Pincus
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, United States
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, United States
| | - Mayssa H. Mokalled
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, United States
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, United States
| |
Collapse
|
5
|
Parvez S, Brandt ZJ, Peterson RT. Large-scale F0 CRISPR screens in vivo using MIC-Drop. Nat Protoc 2023; 18:1841-1865. [PMID: 37069311 PMCID: PMC10419324 DOI: 10.1038/s41596-023-00821-y] [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: 08/30/2022] [Accepted: 01/26/2023] [Indexed: 04/19/2023]
Abstract
The zebrafish is a powerful model system for studying animal development, for modeling genetic diseases, and for large-scale in vivo functional genetics. Because of its ease of use and its high efficiency in targeted gene perturbation, CRISPR-Cas9 has recently gained prominence as the tool of choice for genetic manipulation in zebrafish. However, scaling up the technique for high-throughput in vivo functional genetics has been a challenge. We recently developed a method, Multiplexed Intermixed CRISPR Droplets (MIC-Drop), that makes large-scale CRISPR screening in zebrafish possible. Here, we outline the step-by-step protocol for performing functional genetic screens in zebrafish by using MIC-Drop. MIC-Drop uses multiplexed single-guide RNAs to generate biallelic mutations in injected zebrafish embryos, allowing genetic screens to be performed in F0 animals. Combining microfluidics and DNA barcoding enables simultaneous targeting of tens to hundreds of genes from a single injection needle, while also enabling retrospective and rapid identification of the genotype responsible for an observed phenotype. The primary target audiences for MIC-Drop are developmental biologists, zebrafish geneticists, and researchers interested in performing in vivo functional genetic screens in a vertebrate model system. MIC-Drop will also prove useful in the hands of chemical biologists seeking to identify targets of small molecules that cause phenotypic changes in zebrafish. By using MIC-Drop, a typical screen of 100 genes can be conducted within 2-3 weeks by a single user.
Collapse
Affiliation(s)
- Saba Parvez
- Department of Pharmacology & Toxicology, College of Pharmacy, University of Utah, Salt Lake City, UT, USA
| | - Zachary J Brandt
- Department of Pharmacology & Toxicology, College of Pharmacy, University of Utah, Salt Lake City, UT, USA
| | - Randall T Peterson
- Department of Pharmacology & Toxicology, College of Pharmacy, University of Utah, Salt Lake City, UT, USA.
| |
Collapse
|
6
|
Zhou L, McAdow AR, Yamada H, Burris B, Klatt Shaw D, Oonk K, Poss KD, Mokalled MH. Progenitor-derived glia are required for spinal cord regeneration in zebrafish. Development 2023; 150:dev201162. [PMID: 37213080 PMCID: PMC10233714 DOI: 10.1242/dev.201162] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 04/26/2023] [Indexed: 05/10/2023]
Abstract
Unlike mammals, adult zebrafish undergo spontaneous recovery after major spinal cord injury. Whereas reactive gliosis presents a roadblock for mammalian spinal cord repair, glial cells in zebrafish elicit pro-regenerative bridging functions after injury. Here, we perform genetic lineage tracing, assessment of regulatory sequences and inducible cell ablation to define mechanisms that direct the molecular and cellular responses of glial cells after spinal cord injury in adult zebrafish. Using a newly generated CreERT2 transgenic line, we show that the cells directing expression of the bridging glial marker ctgfa give rise to regenerating glia after injury, with negligible contribution to either neuronal or oligodendrocyte lineages. A 1 kb sequence upstream of the ctgfa gene was sufficient to direct expression in early bridging glia after injury. Finally, ablation of ctgfa-expressing cells using a transgenic nitroreductase strategy impaired glial bridging and recovery of swim behavior after injury. This study identifies key regulatory features, cellular progeny, and requirements of glial cells during innate spinal cord regeneration.
Collapse
Affiliation(s)
- Lili Zhou
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Anthony R. McAdow
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Hunter Yamada
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Brooke Burris
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Dana Klatt Shaw
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kelsey Oonk
- Duke Regeneration Center, Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Kenneth D. Poss
- Duke Regeneration Center, Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Mayssa H. Mokalled
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| |
Collapse
|
7
|
Oprişoreanu AM, Ryan F, Richmond C, Dzekhtsiarova Y, Carragher NO, Becker T, David S, Becker CG. Drug screening in zebrafish larvae reveals inflammation-related modulators of secondary damage after spinal cord injury in mice. Theranostics 2023; 13:2531-2551. [PMID: 37215570 PMCID: PMC10196818 DOI: 10.7150/thno.81332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 04/11/2023] [Indexed: 05/24/2023] Open
Abstract
Prolonged inflammation after spinal cord injury is detrimental to recovery. To find pharmacological modulators of the inflammation response, we designed a rapid drug screening paradigm in larval zebrafish followed by testing of hit compounds in a mouse spinal cord injury model. Methods: We used reduced il-1β linked green fluorescent protein (GFP) reporter gene expression as a read-out for reduced inflammation in a screen of 1081 compounds in larval zebrafish. Hit drugs were tested in a moderate contusion model in mice for cytokine regulation, and improved tissue preservation and locomotor recovery. Results: Three compounds robustly reduced il-1β expression in zebrafish. Cimetidine, an over-the-counter H2 receptor antagonist, also reduced the number of pro-inflammatory neutrophils and rescued recovery after injury in a zebrafish mutant with prolonged inflammation. Cimetidine action on il-1β expression levels was abolished by somatic mutation of H2 receptor hrh2b, suggesting specific action. In mice, systemic treatment with Cimetidine led to significantly improved recovery of locomotor behavior as compared to controls, accompanied by decreased neuronal tissue loss and a shift towards a pro-regenerative profile of cytokine gene expression. Conclusion: Our screen revealed H2 receptor signaling as a promising target for future therapeutic interventions in spinal cord injury. This work highlights the usefulness of the zebrafish model for rapid screening of drug libraries to identify therapeutics to treat mammalian spinal cord injury.
Collapse
Affiliation(s)
- Ana-Maria Oprişoreanu
- Centre for Discovery Brain Sciences, University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB, UK
- Center for Regenerative Therapies Dresden, TU Dresden, Fetscherstraße 105, 01307 Dresden, Germany
| | - Fari Ryan
- Centre for Research in Neuroscience, Research Institute of the McGill University Health Centre, 1650 Cedar Ave., Montreal, Quebec, H3G 1A4
| | - Claire Richmond
- Centre for Discovery Brain Sciences, University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB, UK
| | - Yuliya Dzekhtsiarova
- Center for Regenerative Therapies Dresden, TU Dresden, Fetscherstraße 105, 01307 Dresden, Germany
| | - Neil O. Carragher
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XR, UK
| | - Thomas Becker
- Centre for Discovery Brain Sciences, University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB, UK
- Center for Regenerative Therapies Dresden, TU Dresden, Fetscherstraße 105, 01307 Dresden, Germany
| | - Samuel David
- Centre for Research in Neuroscience, Research Institute of the McGill University Health Centre, 1650 Cedar Ave., Montreal, Quebec, H3G 1A4
| | - Catherina G. Becker
- Centre for Discovery Brain Sciences, University of Edinburgh, The Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB, UK
- Center for Regenerative Therapies Dresden, TU Dresden, Fetscherstraße 105, 01307 Dresden, Germany
| |
Collapse
|
8
|
Palmiotti A, Lichak MR, Shih PY, Bendesky A. Genetic manipulation of betta fish. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.16.528733. [PMID: 36824853 PMCID: PMC9948955 DOI: 10.1101/2023.02.16.528733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Betta splendens , also known as Siamese fighting fish or 'betta', are renowned for their astonishing morphological diversity and extreme aggressive behavior. Despite recent advances in our understanding of the genetics and neurobiology of betta, the lack of tools to manipulate their genome has hindered progress at functional and mechanistic levels. In this study, we outline the use of three genetic manipulation technologies, which we have optimized for use in betta: CRISPR/Cas9-mediated knockout, CRISPR/Cas9-mediated knockin, and Tol2-mediated transgenesis. We knocked out three genes: alkal2l, bco1l , and mitfa , and analyzed their effects on viability and pigmentation. Furthermore, we successfully knocked in a fluorescent protein into the mitfa locus, a proof-of-principle experiment of this powerful technology in betta. Finally, we used Tol2-mediated transgenesis to create fish with ubiquitous expression of GFP, and then developed a bicistronic plasmid with heart-specific expression of a red fluorescent protein to serve as a visible marker of successful transgenesis. Our work highlights the potential for the genetic manipulation of betta, providing valuable resources for the effective use of genetic tools in this animal model.
Collapse
Affiliation(s)
- Alec Palmiotti
- Zuckerman Mind Brain Behavior Institute, Columbia University, NY, USA
- Department of Ecology, Evolution and Environmental Biology, Columbia University, NY, USA
| | - Madison R Lichak
- Zuckerman Mind Brain Behavior Institute, Columbia University, NY, USA
- Department of Ecology, Evolution and Environmental Biology, Columbia University, NY, USA
- Present address: Department of Ecology and Evolutionary Biology, Princeton University, NJ, USA
| | - Pei-Yin Shih
- Zuckerman Mind Brain Behavior Institute, Columbia University, NY, USA
- Department of Ecology, Evolution and Environmental Biology, Columbia University, NY, USA
| | - Andres Bendesky
- Zuckerman Mind Brain Behavior Institute, Columbia University, NY, USA
- Department of Ecology, Evolution and Environmental Biology, Columbia University, NY, USA
| |
Collapse
|
9
|
Jensen NO, Burris B, Zhou L, Yamada H, Reyes C, Mokalled MH. Functional Trajectories during innate spinal cord repair. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.31.526502. [PMID: 36778427 PMCID: PMC9915574 DOI: 10.1101/2023.01.31.526502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Adult zebrafish are capable of anatomical and functional recovery following severe spinal cord injury. Axon growth, glial bridging and adult neurogenesis are hallmarks of cellular regeneration during spinal cord repair. However, the correlation between these cellular regenerative processes and functional recovery remains to be elucidated. Whereas the majority of established functional regeneration metrics measure swim capacity, we hypothesize that gait quality is more directly related to neurological health. Here, we performed a longitudinal swim tracking study for sixty individual zebrafish spanning eight weeks of spinal cord regeneration. Multiple swim parameters as well as axonal and glial bridging were integrated. We established rostral compensation as a new gait quality metric that highly correlates with functional recovery. Tensor component analysis of longitudinal data supports a correspondence between functional recovery trajectories and neurological outcomes. Moreover, our studies predicted and validated that a subset of functional regeneration parameters measured 1 to 2 weeks post-injury is sufficient to predict the regenerative outcomes of individual animals at 8 weeks post-injury. Our findings established new functional regeneration parameters and generated a comprehensive correlative database between various functional and cellular regeneration outputs.
Collapse
|
10
|
Drake LK, Keatinge M, Tsarouchas TM, Becker CG, Lyons DA, Becker T. Rapid Testing of Gene Function in Axonal Regeneration After Spinal Cord Injury Using Larval Zebrafish. Methods Mol Biol 2023; 2636:263-277. [PMID: 36881306 DOI: 10.1007/978-1-0716-3012-9_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
Larval zebrafish show axonal regrowth over a complex spinal injury site and recovery of function within days after injury. Here we describe a simple protocol to disrupt gene function in this model using acute injections of highly active synthetic gRNAs to rapidly detect loss-of-function phenotypes without the need for breeding.
Collapse
Affiliation(s)
- Louisa K Drake
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Marcus Keatinge
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Catherina G Becker
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK.,Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany
| | - David A Lyons
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Thomas Becker
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK. .,Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Germany.
| |
Collapse
|
11
|
Carrington B, Ramanagoudr-Bhojappa R, Bresciani E, Han TU, Sood R. A robust pipeline for efficient knock-in of point mutations and epitope tags in zebrafish using fluorescent PCR based screening. BMC Genomics 2022; 23:810. [PMID: 36476416 PMCID: PMC9730659 DOI: 10.1186/s12864-022-08971-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 10/26/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Genome editing using CRISPR/Cas9 has become a powerful tool in zebrafish to generate targeted gene knockouts models. However, its use for targeted knock-in remains challenging due to inefficient homology directed repair (HDR) pathway in zebrafish, highlighting the need for efficient and cost-effective screening methods. RESULTS: Here, we present our fluorescent PCR and capillary electrophoresis based screening approach for knock-in using a single-stranded oligodeoxynucleotide donor (ssODN) as a repair template for the targeted insertion of epitope tags, or single nucleotide changes to recapitulate pathogenic human alleles. For the insertion of epitope tags, we took advantage of the expected change in size of the PCR product. For point mutations, we combined fluorescent PCR with restriction fragment length polymorphism (RFLP) analysis to distinguish the fish with the knock-in allele. As a proof-of-principle, we present our data on the generation of fish lines with insertion of a FLAG tag at the tcnba locus, an HA tag at the gata2b locus, and a point mutation observed in Gaucher disease patients in the gba gene. Despite the low number of germline transmitting founders (1-5%), combining our screening methods with prioritization of founder fish by fin biopsies allowed us to establish stable knock-in lines by screening 12 or less fish per gene. CONCLUSIONS We have established a robust pipeline for the generation of zebrafish models with precise integration of small DNA sequences and point mutations at the desired sites in the genome. Our screening method is very efficient and easy to implement as it is PCR-based and only requires access to a capillary sequencer.
Collapse
Affiliation(s)
- Blake Carrington
- Translational and Functional Genomics Branch, Zebrafish Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ramanagouda Ramanagoudr-Bhojappa
- Cancer Genetics Unit, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Erica Bresciani
- Oncogenesis and Development Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Tae-Un Han
- Molecular Neurogenetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Raman Sood
- Translational and Functional Genomics Branch, Zebrafish Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
- Oncogenesis and Development Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
| |
Collapse
|
12
|
Saraswathy VM, Zhou L, McAdow AR, Burris B, Dogra D, Reischauer S, Mokalled MH. Myostatin is a negative regulator of adult neurogenesis after spinal cord injury in zebrafish. Cell Rep 2022; 41:111705. [PMID: 36417881 PMCID: PMC9742758 DOI: 10.1016/j.celrep.2022.111705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 05/16/2022] [Accepted: 11/01/2022] [Indexed: 11/23/2022] Open
Abstract
Intrinsic and extrinsic inhibition of neuronal regeneration obstruct spinal cord (SC) repair in mammals. In contrast, adult zebrafish achieve functional recovery after complete SC transection. While studies of innate SC regeneration have focused on axon regrowth as a primary repair mechanism, how local adult neurogenesis affects functional recovery is unknown. Here, we uncover dynamic expression of zebrafish myostatin b (mstnb) in a niche of dorsal SC progenitors after injury. mstnb mutants show impaired functional recovery, normal glial and axonal bridging across the lesion, and an increase in the profiles of newborn neurons. Molecularly, neuron differentiation genes are upregulated, while the neural stem cell maintenance gene fgf1b is downregulated in mstnb mutants. Finally, we show that human fibroblast growth factor 1 (FGF1) treatment rescues the molecular and cellular phenotypes of mstnb mutants. These studies uncover unanticipated neurogenic functions for mstnb and establish the importance of local adult neurogenesis for innate SC repair.
Collapse
Affiliation(s)
- Vishnu Muraleedharan Saraswathy
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Lili Zhou
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Anthony R McAdow
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Brooke Burris
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Deepika Dogra
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany; Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Sven Reischauer
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany; Medical Clinic I, (Cardiology/Angiology) and Campus Kerckhoff, Justus Liebig University, Giessen, 35392 Giessen, Germany; The Cardio-Pulmonary Institute, Frankfurt, Germany
| | - Mayssa H Mokalled
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.
| |
Collapse
|
13
|
Carrington B, Bishop K, Sood R. A Comprehensive Review of Indel Detection Methods for Identification of Zebrafish Knockout Mutants Generated by Genome-Editing Nucleases. Genes (Basel) 2022; 13:857. [PMID: 35627242 PMCID: PMC9141975 DOI: 10.3390/genes13050857] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/06/2022] [Accepted: 05/10/2022] [Indexed: 11/16/2022] Open
Abstract
The use of zebrafish in functional genomics and disease modeling has become popular due to the ease of targeted mutagenesis with genome editing nucleases, i.e., zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats/Cas9 (CRISPR/Cas9). These nucleases, specifically CRISPR/Cas9, are routinely used to generate gene knockout mutants by causing a double stranded break at the desired site in the target gene and selecting for frameshift insertions or deletions (indels) caused by the errors during the repair process. Thus, a variety of methods have been developed to identify fish with indels during the process of mutant generation and phenotypic analysis. These methods range from PCR and gel-based low-throughput methods to high-throughput methods requiring specific reagents and/or equipment. Here, we provide a comprehensive review of currently used indel detection methods in zebrafish. By discussing the molecular basis for each method as well as their pros and cons, we hope that this review will serve as a comprehensive resource for zebrafish researchers, allowing them to choose the most appropriate method depending upon their budget, access to required equipment and the throughput needs of the projects.
Collapse
Affiliation(s)
| | | | - Raman Sood
- Zebrafish Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA; (B.C.); (K.B.)
| |
Collapse
|
14
|
Nathan FM, Kibat C, Goel T, Stewart J, Claridge‐Chang A, Mathuru AS. Contingent stimulus delivery assay for zebrafish reveals a role for CCSER1 in alcohol preference. Addict Biol 2022; 27:e13126. [PMID: 35229935 DOI: 10.1111/adb.13126] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 10/02/2021] [Accepted: 12/03/2021] [Indexed: 12/21/2022]
Abstract
Alcohol use disorders are complex, multifactorial phenomena with a large footprint within the global burden of diseases. Here, we report the development of an accessible, two-choice self-administration zebrafish assay (SAZA) to study the neurobiology of addiction. Using this assay, we first demonstrated that, although zebrafish avoid higher concentrations of alcohol, they are attracted to low concentrations. Pre-exposure to alcohol did not change this relative preference, but acute exposure to an alcohol deterrent approved for human use decreased alcohol self-administration. A pigment mutant used in whole-brain imaging studies displayed a similar relative alcohol preference profile; however, mutants in CCSER1, a gene associated with alcohol dependence in human genetic studies, showed a reversal in relative preference. The presence of a biphasic response (hormesis) in zebrafish validated a key aspect of vertebrate responses to alcohol. SAZA adds a new dimension for discovering novel alcohol deterrents and studying the neurogenetics of addiction using the zebrafish.
Collapse
Affiliation(s)
| | - Caroline Kibat
- Department of Physiology, YLL School of Medicine National University of Singapore Singapore Singapore
| | - Tanisha Goel
- Department of Physiology, YLL School of Medicine National University of Singapore Singapore Singapore
| | - James Stewart
- Institute of Molecular and Cell Biology Singapore Singapore
- Duke‐NUS Medical School Singapore Singapore
| | - Adam Claridge‐Chang
- Institute of Molecular and Cell Biology Singapore Singapore
- Duke‐NUS Medical School Singapore Singapore
| | - Ajay S. Mathuru
- Yale‐NUS College Singapore Singapore
- Department of Physiology, YLL School of Medicine National University of Singapore Singapore Singapore
- Institute of Molecular and Cell Biology Singapore Singapore
| |
Collapse
|
15
|
Neely SA, Lyons DA. Insights Into Central Nervous System Glial Cell Formation and Function From Zebrafish. Front Cell Dev Biol 2021; 9:754606. [PMID: 34912801 PMCID: PMC8666443 DOI: 10.3389/fcell.2021.754606] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 10/05/2021] [Indexed: 12/23/2022] Open
Abstract
The term glia describes a heterogenous collection of distinct cell types that make up a large proportion of our nervous system. Although once considered the glue of the nervous system, the study of glial cells has evolved significantly in recent years, with a large body of literature now highlighting their complex and diverse roles in development and throughout life. This progress is due, in part, to advances in animal models in which the molecular and cellular mechanisms of glial cell development and function as well as neuron-glial cell interactions can be directly studied in vivo in real time, in intact neural circuits. In this review we highlight the instrumental role that zebrafish have played as a vertebrate model system for the study of glial cells, and discuss how the experimental advantages of the zebrafish lend themselves to investigate glial cell interactions and diversity. We focus in particular on recent studies that have provided insight into the formation and function of the major glial cell types in the central nervous system in zebrafish.
Collapse
Affiliation(s)
- Sarah A. Neely
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - David A. Lyons
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| |
Collapse
|
16
|
Quick RE, Buck LD, Parab S, Tolbert ZR, Matsuoka RL. Highly Efficient Synthetic CRISPR RNA/Cas9-Based Mutagenesis for Rapid Cardiovascular Phenotypic Screening in F0 Zebrafish. Front Cell Dev Biol 2021; 9:735598. [PMID: 34746131 PMCID: PMC8570140 DOI: 10.3389/fcell.2021.735598] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 10/01/2021] [Indexed: 12/13/2022] Open
Abstract
The zebrafish is a valuable vertebrate model to study cardiovascular formation and function due to the facile visualization and rapid development of the circulatory system in its externally growing embryos. Despite having distinct advantages, zebrafish have paralogs of many important genes, making reverse genetics approaches inefficient since generating animals bearing multiple gene mutations requires substantial efforts. Here, we present a simple and robust synthetic CRISPR RNA/Cas9-based mutagenesis approach for generating biallelic F0 zebrafish knockouts. Using a dual-guide synthetic CRISPR RNA/Cas9 ribonucleoprotein (dgRNP) system, we compared the efficiency of biallelic gene disruptions following the injections of one, two, and three dgRNPs per gene into the cytoplasm or yolk. We show that simultaneous cytoplasmic injections of three distinct dgRNPs per gene into one-cell stage embryos resulted in the most efficient and consistent biallelic gene disruptions. Importantly, this triple dgRNP approach enables efficient inactivation of cell autonomous and cell non-autonomous gene function, likely due to the low mosaicism of biallelic disruptions. In support of this finding, we provide evidence that the F0 animals generated by this method fully phenocopied the endothelial and peri-vascular defects observed in corresponding stable mutant homozygotes. Moreover, this approach faithfully recapitulated the trunk vessel phenotypes resulting from the genetic interaction between two vegfr2 zebrafish paralogs. Mechanistically, investigation of genome editing and mRNA decay indicates that the combined mutagenic actions of three dgRNPs per gene lead to an increased probability of frameshift mutations, enabling efficient biallelic gene disruptions. Therefore, our approach offers a highly robust genetic platform to quickly assess novel and redundant gene function in F0 zebrafish.
Collapse
Affiliation(s)
- Rachael E Quick
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, United States.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, United States
| | - Luke D Buck
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, United States.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, United States
| | - Sweta Parab
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, United States.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, United States
| | - Zane R Tolbert
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, United States.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, United States
| | - Ryota L Matsuoka
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Lerner Research Institute, Cleveland, OH, United States.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, United States
| |
Collapse
|
17
|
Keatinge M, Tsarouchas TM, Munir T, Porter NJ, Larraz J, Gianni D, Tsai HH, Becker CG, Lyons DA, Becker T. CRISPR gRNA phenotypic screening in zebrafish reveals pro-regenerative genes in spinal cord injury. PLoS Genet 2021; 17:e1009515. [PMID: 33914736 PMCID: PMC8084196 DOI: 10.1371/journal.pgen.1009515] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 03/28/2021] [Indexed: 12/30/2022] Open
Abstract
Zebrafish exhibit robust regeneration following spinal cord injury, promoted by macrophages that control post-injury inflammation. However, the mechanistic basis of how macrophages regulate regeneration is poorly understood. To address this gap in understanding, we conducted a rapid in vivo phenotypic screen for macrophage-related genes that promote regeneration after spinal injury. We used acute injection of synthetic RNA Oligo CRISPR guide RNAs (sCrRNAs) that were pre-screened for high activity in vivo. Pre-screening of over 350 sCrRNAs allowed us to rapidly identify highly active sCrRNAs (up to half, abbreviated as haCRs) and to effectively target 30 potentially macrophage-related genes. Disruption of 10 of these genes impaired axonal regeneration following spinal cord injury. We selected 5 genes for further analysis and generated stable mutants using haCRs. Four of these mutants (tgfb1a, tgfb3, tnfa, sparc) retained the acute haCR phenotype, validating the approach. Mechanistically, tgfb1a haCR-injected and stable mutant zebrafish fail to resolve post-injury inflammation, indicated by prolonged presence of neutrophils and increased levels of il1b expression. Inhibition of Il-1β rescues the impaired axon regeneration in the tgfb1a mutant. Hence, our rapid and scalable screening approach has identified functional regulators of spinal cord regeneration, but can be applied to any biological function of interest.
Collapse
Affiliation(s)
- Marcus Keatinge
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Tahimina Munir
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Nicola J. Porter
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Juan Larraz
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Davide Gianni
- Biogen, Cambridge, Massachusetts, United States of America
| | - Hui-Hsin Tsai
- Biogen, Cambridge, Massachusetts, United States of America
| | - Catherina G. Becker
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - David A. Lyons
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Thomas Becker
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| |
Collapse
|