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Uribe RA. Genetic regulation of enteric nervous system development in zebrafish. Biochem Soc Trans 2024; 52:177-190. [PMID: 38174765 PMCID: PMC10903509 DOI: 10.1042/bst20230343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 12/13/2023] [Accepted: 12/15/2023] [Indexed: 01/05/2024]
Abstract
The enteric nervous system (ENS) is a complex series of interconnected neurons and glia that reside within and along the entire length of the gastrointestinal tract. ENS functions are vital to gut homeostasis and digestion, including local control of peristalsis, water balance, and intestinal cell barrier function. How the ENS develops during embryological development is a topic of great concern, as defects in ENS development can result in various diseases, the most common being Hirschsprung disease, in which variable regions of the infant gut lack ENS, with the distal colon most affected. Deciphering how the ENS forms from its progenitor cells, enteric neural crest cells, is an active area of research across various animal models. The vertebrate animal model, zebrafish, has been increasingly leveraged to understand early ENS formation, and over the past 20 years has contributed to our knowledge of the genetic regulation that underlies enteric development. In this review, I summarize our knowledge regarding the genetic regulation of zebrafish enteric neuronal development, and based on the most current literature, present a gene regulatory network inferred to underlie its construction. I also provide perspectives on areas for future zebrafish ENS research.
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Affiliation(s)
- Rosa A. Uribe
- Biosciences Department, Rice University, Houston, TX 77005, U.S.A
- Laboratory of Neural Crest and Enteric Nervous System Development, Rice University, Houston, TX 77005, U.S.A
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Cassidy RM, Flores EM, Trinh Nguyen AK, Cheruvu SS, Uribe RA, Krachler AM, Odem MA. Systematic analysis of proximal midgut- and anorectal-originating contractions in larval zebrafish using event feature detection and supervised machine learning algorithms. Neurogastroenterol Motil 2023; 35:e14675. [PMID: 37743702 PMCID: PMC10841157 DOI: 10.1111/nmo.14675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 07/16/2023] [Accepted: 08/28/2023] [Indexed: 09/26/2023]
Abstract
BACKGROUND Zebrafish larvae are translucent, allowing in vivo analysis of gut development and physiology, including gut motility. While recent progress has been made in measuring gut motility in larvae, challenges remain which can influence results, such as how data are interpreted, opportunities for technical user error, and inconsistencies in methods. METHODS To overcome these challenges, we noninvasively introduced Nile Red fluorescent dye to fill the intraluminal gut space in zebrafish larvae and collected serial confocal microscopic images of gut fluorescence. We automated the detection of fluorescent-contrasted contraction events against the median-subtracted signal and compared it to manually annotated gut contraction events across anatomically defined gut regions. Supervised machine learning (multiple logistic regression) was then used to discriminate between true contraction events and noise. To demonstrate, we analyzed motility in larvae under control and reserpine-treated conditions. We also used automated event detection analysis to compare unfed and fed larvae. KEY RESULTS Automated analysis retained event features for proximal midgut-originating retrograde and anterograde contractions and anorectal-originating retrograde contractions. While manual annotation showed reserpine disrupted gut motility, machine learning only achieved equivalent contraction discrimination in controls and failed to accurately identify contractions after reserpine due to insufficient intraluminal fluorescence. Automated analysis also showed feeding had no effect on the frequency of anorectal-originating contractions. CONCLUSIONS & INFERENCES Automated event detection analysis rapidly and accurately annotated contraction events, including the previously neglected phenomenon of anorectal contractions. However, challenges remain to discriminate contraction events based on intraluminal fluorescence under treatment conditions that disrupt functional motility.
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Affiliation(s)
- Ryan M. Cassidy
- Brown Foundation Institute of Molecular Medicine, McGovern
Medical School at UTHealth, Houston, TX 77030, USA
| | - Erika M. Flores
- Department of Microbiology and Molecular Genetics, McGovern
Medical School at UTHealth, Houston, TX 77030, USA
| | - Anh K. Trinh Nguyen
- Department of Microbiology and Molecular Genetics, McGovern
Medical School at UTHealth, Houston, TX 77030, USA
| | - Sai S. Cheruvu
- Department of Integrative Biology and Pharmacology,
McGovern Medical School at UTHealth, Houston, TX 77030, USA
| | - Rosa A. Uribe
- Department of Biosciences, Rice University, Houston, TX
77005, USA
| | - Anne Marie Krachler
- Department of Microbiology and Molecular Genetics, McGovern
Medical School at UTHealth, Houston, TX 77030, USA
| | - Max A. Odem
- Department of Microbiology and Molecular Genetics, McGovern
Medical School at UTHealth, Houston, TX 77030, USA
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Locascio A, Annona G, Caccavale F, D'Aniello S, Agnisola C, Palumbo A. Nitric Oxide Function and Nitric Oxide Synthase Evolution in Aquatic Chordates. Int J Mol Sci 2023; 24:11182. [PMID: 37446358 DOI: 10.3390/ijms241311182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/03/2023] [Accepted: 07/04/2023] [Indexed: 07/15/2023] Open
Abstract
Nitric oxide (NO) is a key signaling molecule in almost all organisms and is active in a variety of physiological and pathological processes. Our understanding of the peculiarities and functions of this simple gas has increased considerably by extending studies to non-mammal vertebrates and invertebrates. In this review, we report the nitric oxide synthase (Nos) genes so far characterized in chordates and provide an extensive, detailed, and comparative analysis of the function of NO in the aquatic chordates tunicates, cephalochordates, teleost fishes, and amphibians. This comprehensive set of data adds new elements to our understanding of Nos evolution, from the single gene commonly found in invertebrates to the three genes present in vertebrates.
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Affiliation(s)
- Annamaria Locascio
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Giovanni Annona
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
- Department of Research Infrastructure for Marine Biological Resources (RIMAR), Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Filomena Caccavale
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Salvatore D'Aniello
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Claudio Agnisola
- Department of Biology, University of Naples Federico II, Via Cinthia 4, 80126 Naples, Italy
| | - Anna Palumbo
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
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Fujii K, Nakajo K, Egashira Y, Yamamoto Y, Kitada K, Taniguchi K, Kawai M, Tomiyama H, Kawakami K, Uchiyama K, Ono F. Gastrointestinal Neurons Expressing HCN4 Regulate Retrograde Peristalsis. Cell Rep 2021; 30:2879-2888.e3. [PMID: 32130893 DOI: 10.1016/j.celrep.2020.02.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 09/30/2019] [Accepted: 02/06/2020] [Indexed: 12/31/2022] Open
Abstract
Peristalsis is indispensable for physiological function of the gut. The enteric nervous system (ENS) plays an important role in regulating peristalsis. While the neural network regulating anterograde peristalsis, which migrates from the oral end to the anal end, is characterized to some extent, retrograde peristalsis remains unresolved with regards to its neural regulation. Using forward genetics in zebrafish, we reveal that a population of neurons expressing a hyperpolarization-activated nucleotide-gated channel HCN4 specifically regulates retrograde peristalsis. When HCN4 channels are blocked by an HCN channel inhibitor or morpholinos blocking the protein expression, retrograde peristalsis is specifically attenuated. Conversely, when HCN4(+) neurons expressing channelrhodopsin are activated by illumination, retrograde peristalsis is enhanced while anterograde peristalsis remains unchanged. We propose that HCN4(+) neurons in the ENS forward activating signals toward the oral end and simultaneously stimulate local circuits regulating the circular muscle.
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Affiliation(s)
- Kensuke Fujii
- Department of General and Gastroenterological Surgery, Osaka Medical College, Takatsuki, Japan
| | - Koichi Nakajo
- Department of Physiology, Osaka Medical College, Takatsuki, Japan; Division of Integrative Physiology, Department of Physiology, Jichi Medical University, Shimotsuke, Japan
| | | | | | - Kazuya Kitada
- Department of General and Gastroenterological Surgery, Osaka Medical College, Takatsuki, Japan
| | - Kohei Taniguchi
- Department of General and Gastroenterological Surgery, Osaka Medical College, Takatsuki, Japan
| | - Masaru Kawai
- Department of General and Gastroenterological Surgery, Osaka Medical College, Takatsuki, Japan
| | - Hideki Tomiyama
- Department of General and Gastroenterological Surgery, Osaka Medical College, Takatsuki, Japan
| | - Koichi Kawakami
- Laboratory of Molecular and Developmental Biology, National Institute of Genetics and Department of Genetics, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Japan
| | - Kazuhisa Uchiyama
- Department of General and Gastroenterological Surgery, Osaka Medical College, Takatsuki, Japan
| | - Fumihito Ono
- Department of Physiology, Osaka Medical College, Takatsuki, Japan.
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Kuil LE, Chauhan RK, Cheng WW, Hofstra RMW, Alves MM. Zebrafish: A Model Organism for Studying Enteric Nervous System Development and Disease. Front Cell Dev Biol 2021; 8:629073. [PMID: 33553169 PMCID: PMC7859111 DOI: 10.3389/fcell.2020.629073] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 12/23/2020] [Indexed: 12/11/2022] Open
Abstract
The Enteric Nervous System (ENS) is a large network of enteric neurons and glia that regulates various processes in the gastrointestinal tract including motility, local blood flow, mucosal transport and secretion. The ENS is derived from stem cells coming from the neural crest that migrate into and along the primitive gut. Defects in ENS establishment cause enteric neuropathies, including Hirschsprung disease (HSCR), which is characterized by an absence of enteric neural crest cells in the distal part of the colon. In this review, we discuss the use of zebrafish as a model organism to study the development of the ENS. The accessibility of the rapidly developing gut in zebrafish embryos and larvae, enables in vivo visualization of ENS development, peristalsis and gut transit. These properties make the zebrafish a highly suitable model to bring new insights into ENS development, as well as in HSCR pathogenesis. Zebrafish have already proven fruitful in studying ENS functionality and in the validation of novel HSCR risk genes. With the rapid advancements in gene editing techniques and their unique properties, research using zebrafish as a disease model, will further increase our understanding on the genetics underlying HSCR, as well as possible treatment options for this disease.
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Affiliation(s)
- Laura E. Kuil
- Department of Clinical Genetics, Erasmus University Medical Centre, Rotterdam, Netherlands
| | - Rajendra K. Chauhan
- Department of Clinical Genetics, Erasmus University Medical Centre, Rotterdam, Netherlands
| | - William W. Cheng
- Department of Clinical Genetics, Erasmus University Medical Centre, Rotterdam, Netherlands
| | - Robert M. W. Hofstra
- Department of Clinical Genetics, Erasmus University Medical Centre, Rotterdam, Netherlands
- Stem Cells and Regenerative Medicine, University College London (UCL) Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Maria M. Alves
- Department of Clinical Genetics, Erasmus University Medical Centre, Rotterdam, Netherlands
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James DM, Kozol RA, Kajiwara Y, Wahl AL, Storrs EC, Buxbaum JD, Klein M, Moshiree B, Dallman JE. Intestinal dysmotility in a zebrafish ( Danio rerio) shank3a;shank3b mutant model of autism. Mol Autism 2019; 10:3. [PMID: 30733854 PMCID: PMC6357389 DOI: 10.1186/s13229-018-0250-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 11/26/2018] [Indexed: 02/06/2023] Open
Abstract
Background and aims Autism spectrum disorder (ASD) is currently estimated to affect more than 1% of the world population. For people with ASD, gastrointestinal (GI) distress is a commonly reported but a poorly understood co-occurring symptom. Here, we investigate the physiological basis for GI distress in ASD by studying gut function in a zebrafish model of Phelan-McDermid syndrome (PMS), a condition caused by mutations in the SHANK3 gene. Methods To generate a zebrafish model of PMS, we used CRISPR/Cas9 to introduce clinically related C-terminal frameshift mutations in shank3a and shank3b zebrafish paralogues (shank3abΔC). Because PMS is caused by SHANK3 haploinsufficiency, we assessed the digestive tract (DT) structure and function in zebrafish shank3abΔC+/− heterozygotes. Human SHANK3 mRNA was then used to rescue DT phenotypes in larval zebrafish. Results Significantly slower rates of DT peristaltic contractions (p < 0.001) with correspondingly prolonged passage time (p < 0.004) occurred in shank3abΔC+/− mutants. Rescue injections of mRNA encoding the longest human SHANK3 isoform into shank3abΔC+/− mutants produced larvae with intestinal bulb emptying similar to wild type (WT), but still deficits in posterior intestinal motility. Serotonin-positive enteroendocrine cells (EECs) were significantly reduced in both shank3abΔC+/− and shank3abΔC−/− mutants (p < 0.05) while enteric neuron counts and overall structure of the DT epithelium, including goblet cell number, were unaffected in shank3abΔC+/− larvae. Conclusions Our data and rescue experiments support mutations in SHANK3 as causal for GI transit and motility abnormalities. Reductions in serotonin-positive EECs and serotonin-filled ENS boutons suggest an endocrine/neural component to this dysmotility. This is the first study to date demonstrating DT dysmotility in a zebrafish single gene mutant model of ASD. Electronic supplementary material The online version of this article (10.1186/s13229-018-0250-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- David M James
- 1Department of Biology, University of Miami, Coral Gables, FL USA
| | - Robert A Kozol
- 1Department of Biology, University of Miami, Coral Gables, FL USA
| | - Yuji Kajiwara
- 2Seaver Autism Center for Research and Treatment, Department of Psychiatry, Friedman Brain Institute and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA.,5Denali Therapeutics, South San Francisco, CA USA
| | - Adam L Wahl
- 1Department of Biology, University of Miami, Coral Gables, FL USA
| | - Emily C Storrs
- 1Department of Biology, University of Miami, Coral Gables, FL USA
| | - Joseph D Buxbaum
- 2Seaver Autism Center for Research and Treatment, Department of Psychiatry, Friedman Brain Institute and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Mason Klein
- 3Department of Physics, University of Miami, Coral Gables, FL USA
| | - Baharak Moshiree
- Division of Gastroenterology, Atrium Health, University of North Carolina, Charlotte, NC USA
| | - Julia E Dallman
- 1Department of Biology, University of Miami, Coral Gables, FL USA
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Ganz J, Baker RP, Hamilton MK, Melancon E, Diba P, Eisen JS, Parthasarathy R. Image velocimetry and spectral analysis enable quantitative characterization of larval zebrafish gut motility. Neurogastroenterol Motil 2018; 30:e13351. [PMID: 29722095 PMCID: PMC6150784 DOI: 10.1111/nmo.13351] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 03/11/2018] [Indexed: 12/21/2022]
Abstract
BACKGROUND Normal gut function requires rhythmic and coordinated movements that are affected by developmental processes, physical and chemical stimuli, and many debilitating diseases. The imaging and characterization of gut motility, especially regarding periodic, propagative contractions driving material transport, are therefore critical goals. Previous image analysis approaches have successfully extracted properties related to the temporal frequency of motility modes, but robust measures of contraction magnitude, especially from in vivo image data, remain challenging to obtain. METHODS We developed a new image analysis method based on image velocimetry and spectral analysis that reveals temporal characteristics such as frequency and wave propagation speed, while also providing quantitative measures of the amplitude of gut motion. KEY RESULTS We validate this approach using several challenges to larval zebrafish, imaged with differential interference contrast microscopy. Both acetylcholine exposure and feeding increase frequency and amplitude of motility. Larvae lacking enteric nervous system gut innervation show the same average motility frequency, but reduced and less variable amplitude compared to wild types. CONCLUSIONS & INFERENCES Our image analysis approach enables insights into gut dynamics in a wide variety of developmental and physiological contexts and can also be extended to analyze other types of cell movements.
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Affiliation(s)
- Julia Ganz
- Institute of Neuroscience, 1254 University of Oregon, Eugene, OR 97403
| | - Ryan P. Baker
- Department of Physics, 1274 University of Oregon, Eugene, OR 97403
| | | | - Ellie Melancon
- Institute of Neuroscience, 1254 University of Oregon, Eugene, OR 97403
| | - Parham Diba
- Institute of Neuroscience, 1254 University of Oregon, Eugene, OR 97403
| | - Judith S. Eisen
- Institute of Neuroscience, 1254 University of Oregon, Eugene, OR 97403,Corresponding authors (JSE, ; RP, )
| | - Raghuveer Parthasarathy
- Department of Physics, 1274 University of Oregon, Eugene, OR 97403,Corresponding authors (JSE, ; RP, )
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Ganz J. Gut feelings: Studying enteric nervous system development, function, and disease in the zebrafish model system. Dev Dyn 2018; 247:268-278. [PMID: 28975691 DOI: 10.1002/dvdy.24597] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 07/14/2017] [Accepted: 09/15/2017] [Indexed: 12/15/2022] Open
Abstract
The enteric nervous system (ENS) is the largest part of the peripheral nervous system and is entirely neural crest-derived. It provides the intrinsic innervation of the gut, controlling different aspects of gut function, such as motility. In this review, we will discuss key points of Zebrafish ENS development, genes, and signaling pathways regulating ENS development, as well as contributions of the Zebrafish model system to better understand ENS disorders. During their migration, enteric progenitor cells (EPCs) display a gradient of developmental states based on their proliferative and migratory characteristics, and show spatiotemporal heterogeneity based on gene expression patterns. Many genes and signaling pathways that regulate the migration and proliferation of EPCs have been identified, but later stages of ENS development, especially steps of neuronal and glial differentiation, remain poorly understood. In recent years, Zebrafish have become increasingly important to test candidate genes for ENS disorders (e.g., from genome-wide association studies), to identify environmental influences on ENS development (e.g., through large-scale drug screens), and to investigate the role the gut microbiota play in ENS development and disease. With its unique advantages as a model organism, Zebrafish will continue to contribute to a better understanding of ENS development, function, and disease. Developmental Dynamics 247:268-278, 2018. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Julia Ganz
- Department of Integrative Biology, Michigan State University, East Lansing, Michigan
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Abstract
Although the zebrafish was initially developed as a model system to study embryonic development, it has gained increasing attention as an advantageous system to investigate human diseases, including intestinal disorders. Zebrafish embryos develop rapidly, and their digestive system is fully functional and visible by 5days post fertilization. There is a large degree of homology between the intestine of zebrafish and higher vertebrate organisms in terms of its cellular composition and function as both a digestive and immune organ. Furthermore, molecular pathways regulating injury and immune responses are highly conserved. In this chapter, we provide an overview of studies addressing developmental and physiological processes relevant to human intestinal disease. These studies include those related to congenital disorders, host-microbiota interactions, inflammatory diseases, motility disorders, and intestinal cancer. We also highlight the utility of zebrafish to functionally validate candidate genes identified through mutational analyses and genome-wide association studies, and discuss methodologies to investigate the intestinal biology that are unique to zebrafish.
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Affiliation(s)
- X Zhao
- University of Pennsylvania, Philadelphia, PA, United States
| | - M Pack
- University of Pennsylvania, Philadelphia, PA, United States
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