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Singh DJ, Tuscano KM, Ortega AL, Dimri M, Tae K, Lee W, Muslim MA, Rivera Paz IM, Liu JL, Pierce LX, McClendon A, Gibson I, Livesay J, Sakaguchi TF. Forward genetics combined with unsupervised classifications identified zebrafish mutants affecting biliary system formation. Dev Biol 2024; 512:44-56. [PMID: 38729406 DOI: 10.1016/j.ydbio.2024.05.005] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 05/02/2024] [Accepted: 05/07/2024] [Indexed: 05/12/2024]
Abstract
Impaired formation of the biliary network can lead to congenital cholestatic liver diseases; however, the genes responsible for proper biliary system formation and maintenance have not been fully identified. Combining computational network structure analysis algorithms with a zebrafish forward genetic screen, we identified 24 new zebrafish mutants that display impaired intrahepatic biliary network formation. Complementation tests suggested these 24 mutations affect 24 different genes. We applied unsupervised clustering algorithms to unbiasedly classify the recovered mutants into three classes. Further computational analysis revealed that each of the recovered mutations in these three classes has a unique phenotype on node-subtype composition and distribution within the intrahepatic biliary network. In addition, we found most of the recovered mutations are viable. In those mutant fish, which are already good animal models to study chronic cholestatic liver diseases, the biliary network phenotypes persist into adulthood. Altogether, this study provides unique genetic and computational toolsets that advance our understanding of the molecular pathways leading to biliary system malformation and cholestatic liver diseases.
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Affiliation(s)
- Divya Jyoti Singh
- Department of Inflammation and Immunity, Lerner Research Institute of Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Kathryn M Tuscano
- Department of Inflammation and Immunity, Lerner Research Institute of Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Amrhen L Ortega
- Department of Inflammation and Immunity, Lerner Research Institute of Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Manali Dimri
- Department of Inflammation and Immunity, Lerner Research Institute of Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Kevin Tae
- Department of Inflammation and Immunity, Lerner Research Institute of Cleveland Clinic, Cleveland, OH, 44195, USA
| | - William Lee
- Department of Inflammation and Immunity, Lerner Research Institute of Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Muslim A Muslim
- Department of Inflammation and Immunity, Lerner Research Institute of Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Isabela M Rivera Paz
- Department of Inflammation and Immunity, Lerner Research Institute of Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Jay L Liu
- Department of Inflammation and Immunity, Lerner Research Institute of Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Lain X Pierce
- Department of Inflammation and Immunity, Lerner Research Institute of Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Allyson McClendon
- Department of Inflammation and Immunity, Lerner Research Institute of Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Isabel Gibson
- Department of Inflammation and Immunity, Lerner Research Institute of Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Jodi Livesay
- Department of Inflammation and Immunity, Lerner Research Institute of Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Takuya F Sakaguchi
- Department of Inflammation and Immunity, Lerner Research Institute of Cleveland Clinic, Cleveland, OH, 44195, USA; Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH, 44195, USA.
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Dimri M, Bilogan C, Pierce LX, Naegele G, Vasanji A, Gibson I, McClendon A, Tae K, Sakaguchi TF. Three-dimensional structural analysis reveals a Cdk5-mediated kinase cascade regulating hepatic biliary network branching in zebrafish. Development 2017; 144:2595-2605. [PMID: 28720653 DOI: 10.1242/dev.147397] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [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: 11/21/2016] [Accepted: 05/31/2017] [Indexed: 12/17/2022]
Abstract
The intrahepatic biliary network is a highly branched three-dimensional network lined by biliary epithelial cells, but how its branching patterns are precisely established is not clear. We designed a new computer-based algorithm that quantitatively computes the structural differences of the three-dimensional networks. Utilizing the algorithm, we showed that inhibition of Cyclin-dependent kinase 5 (Cdk5) led to reduced branching in the intrahepatic biliary network in zebrafish. Further, we identified a previously unappreciated downstream kinase cascade regulated by Cdk5. Pharmacological manipulations of this downstream kinase cascade produced a crowded branching defect in the intrahepatic biliary network and influenced actin dynamics in biliary epithelial cells. We generated larvae carrying a mutation in cdk5 regulatory subunit 1a (cdk5r1a), an essential activator of Cdk5. cdk5r1a mutant larvae show similar branching defects as those observed in Cdk5 inhibitor-treated larvae. A small-molecule compound that interferes with the downstream kinase cascade rescued the mutant phenotype. These results provide new insights into branching morphogenesis of the intrahepatic biliary network.
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Affiliation(s)
- Manali Dimri
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Cassandra Bilogan
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Lain X Pierce
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Gregory Naegele
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | | | - Isabel Gibson
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Allyson McClendon
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Kevin Tae
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Takuya F Sakaguchi
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA .,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH 44195, USA
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Dimri M, Bilogan C, Pierce LX, Naegele G, Vasanji A, Gibson I, McClendon A, Tae K, Sakaguchi TF. Three-dimensional structural analysis reveals a Cdk5-mediated kinase cascade regulating hepatic biliary network branching in zebrafish. J Cell Sci 2017. [DOI: 10.1242/jcs.208702] [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: 11/20/2022] Open
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Nussbaum JM, Liu LJ, Hasan SA, Schaub M, McClendon A, Stainier DY, Sakaguchi TF. Homeostatic generation of reactive oxygen species protects the zebrafish liver from steatosis. Hepatology 2013; 58:1326-38. [PMID: 23744565 PMCID: PMC3791216 DOI: 10.1002/hep.26551] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Accepted: 05/21/2013] [Indexed: 12/11/2022]
Abstract
UNLABELLED Nonalcoholic fatty liver disease is the most common liver disease in both adults and children. The earliest stage of this disease is hepatic steatosis, in which triglycerides are deposited as cytoplasmic lipid droplets in hepatocytes. Through a forward genetic approach in zebrafish, we found that guanosine monophosphate (GMP) synthetase mutant larvae develop hepatic steatosis. We further demonstrate that activity of the small GTPase Rac1 and Rac1-mediated production of reactive oxygen species (ROS) are down-regulated in GMP synthetase mutant larvae. Inhibition of Rac1 activity or ROS production in wild-type larvae by small molecule inhibitors was sufficient to induce hepatic steatosis. More conclusively, treating larvae with hydrogen peroxide, a diffusible ROS that has been implicated as a signaling molecule, alleviated hepatic steatosis in both GMP synthetase mutant and Rac1 inhibitor-treated larvae, indicating that homeostatic production of ROS is required to prevent hepatic steatosis. We further found that ROS positively regulate the expression of the triglyceride hydrolase gene, which is responsible for the mobilization of stored triglycerides in hepatocytes. Consistently, inhibition of triglyceride hydrolase activity in wild-type larvae by a small molecule inhibitor was sufficient to induce hepatic steatosis. CONCLUSION De novo GMP synthesis influences the activation of the small GTPase Rac1, which controls hepatic lipid dynamics through ROS-mediated regulation of triglyceride hydrolase expression in hepatocytes.
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Affiliation(s)
- Justin M. Nussbaum
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - Liuhong J. Liu
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - Syeda A. Hasan
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - Madeline Schaub
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - Allyson McClendon
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA
| | - Didier Y.R. Stainier
- Department of Biochemistry and Biophysics, Programs in Developmental and Stem Cell Biology, Genetics, and Human Genetics, and Liver Center, University of California, San Francisco, San Francisco, CA 94158
| | - Takuya F. Sakaguchi
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA,Department of Biochemistry and Biophysics, Programs in Developmental and Stem Cell Biology, Genetics, and Human Genetics, and Liver Center, University of California, San Francisco, San Francisco, CA 94158,Author for correspondence: ()
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