1
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Sato K, Liu Y, Yamashita T, Ohuchi H. The medaka mutant deficient in eyes shut homolog exhibits opsin transport defects and enhanced autophagy in retinal photoreceptors. Cell Tissue Res 2023; 391:249-267. [PMID: 36418571 DOI: 10.1007/s00441-022-03702-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 11/03/2022] [Indexed: 11/27/2022]
Abstract
Eyes shut homolog (EYS) encodes a proteoglycan and the human mutation causes retinitis pigmentosa type 25 (RP25) with progressive retinal degeneration. RP25 most frequently affects autosomal recessive RP patients with many ethnic backgrounds. Although studies using RP models have facilitated the development of therapeutic medications, Eys has been lost in rodent model animals. Here we examined the roles for Eys in the maintenance of photoreceptor structure and function by generating eys-null medaka fish using the CRISPR-Cas9 system. Medaka EYS protein was present near the connecting cilium of wild-type photoreceptors, while it was absent from the eys-/- retina. The mutant larvae exhibited a reduced visual motor response compared with wild-type. In contrast to reported eys-deficient zebrafish at the similar stage, no retinal cell death was detected in the 8-month post-hatching (8-mph) medaka eys mutant. Immunohistochemistry showed a significant reduction in the length of cone outer segments (OSs), retention of OS proteins in the inner segments of photoreceptors, and abnormal filamentous actin network at the base of cone OSs in the mutant retina by 8 mph. Electron microscopy revealed aberrant structure of calyceal processes, numerous vesiculation and lamellar interruptions, and autophagosomes in the eys-mutant cone photoreceptors. In situ hybridization showed an autophagy component gene, gabarap, was ectopically expressed in the eys-null retina. These results suggest eys is required for regeneration of OS, especially of cone photoreceptors, and transport of OS proteins by regulating actin filaments. Enhanced autophagy may delay the progression of retinal degeneration when lacking EYS in the medaka retina.
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Affiliation(s)
- Keita Sato
- Department of Cytology and Histology, Faculty of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, Okayama, 700-8558, Japan.
| | - Yang Liu
- Department of Cytology and Histology, Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, Okayama, 700-8558, Japan
| | - Takahiro Yamashita
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan
| | - Hideyo Ohuchi
- Department of Cytology and Histology, Faculty of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, Okayama, 700-8558, Japan.
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2
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Crouzier L, Richard EM, Sourbron J, Lagae L, Maurice T, Delprat B. Use of Zebrafish Models to Boost Research in Rare Genetic Diseases. Int J Mol Sci 2021; 22:13356. [PMID: 34948153 PMCID: PMC8706563 DOI: 10.3390/ijms222413356] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 12/09/2021] [Accepted: 12/10/2021] [Indexed: 02/06/2023] Open
Abstract
Rare genetic diseases are a group of pathologies with often unmet clinical needs. Even if rare by a single genetic disease (from 1/2000 to 1/more than 1,000,000), the total number of patients concerned account for approximatively 400 million peoples worldwide. Finding treatments remains challenging due to the complexity of these diseases, the small number of patients and the challenge in conducting clinical trials. Therefore, innovative preclinical research strategies are required. The zebrafish has emerged as a powerful animal model for investigating rare diseases. Zebrafish combines conserved vertebrate characteristics with high rate of breeding, limited housing requirements and low costs. More than 84% of human genes responsible for diseases present an orthologue, suggesting that the majority of genetic diseases could be modelized in zebrafish. In this review, we emphasize the unique advantages of zebrafish models over other in vivo models, particularly underlining the high throughput phenotypic capacity for therapeutic screening. We briefly introduce how the generation of zebrafish transgenic lines by gene-modulating technologies can be used to model rare genetic diseases. Then, we describe how zebrafish could be phenotyped using state-of-the-art technologies. Two prototypic examples of rare diseases illustrate how zebrafish models could play a critical role in deciphering the underlying mechanisms of rare genetic diseases and their use to identify innovative therapeutic solutions.
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Affiliation(s)
- Lucie Crouzier
- MMDN, University of Montpellier, EPHE, INSERM, 34095 Montpellier, France; (L.C.); (E.M.R.); (T.M.)
| | - Elodie M. Richard
- MMDN, University of Montpellier, EPHE, INSERM, 34095 Montpellier, France; (L.C.); (E.M.R.); (T.M.)
| | - Jo Sourbron
- Department of Development and Regeneration, Section Pediatric Neurology, University Hospital KU Leuven, 3000 Leuven, Belgium; (J.S.); (L.L.)
| | - Lieven Lagae
- Department of Development and Regeneration, Section Pediatric Neurology, University Hospital KU Leuven, 3000 Leuven, Belgium; (J.S.); (L.L.)
| | - Tangui Maurice
- MMDN, University of Montpellier, EPHE, INSERM, 34095 Montpellier, France; (L.C.); (E.M.R.); (T.M.)
| | - Benjamin Delprat
- MMDN, University of Montpellier, EPHE, INSERM, 34095 Montpellier, France; (L.C.); (E.M.R.); (T.M.)
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3
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Hong Y, Luo Y. Zebrafish Model in Ophthalmology to Study Disease Mechanism and Drug Discovery. Pharmaceuticals (Basel) 2021; 14:ph14080716. [PMID: 34451814 PMCID: PMC8400593 DOI: 10.3390/ph14080716] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/16/2021] [Accepted: 07/21/2021] [Indexed: 12/14/2022] Open
Abstract
Visual impairment and blindness are common and seriously affect people’s work and quality of life in the world. Therefore, the effective therapies for eye diseases are of high priority. Zebrafish (Danio rerio) is an alternative vertebrate model as a useful tool for the mechanism elucidation and drug discovery of various eye disorders, such as cataracts, glaucoma, diabetic retinopathy, age-related macular degeneration, photoreceptor degeneration, etc. The genetic and embryonic accessibility of zebrafish in combination with a behavioral assessment of visual function has made it a very popular model in ophthalmology. Zebrafish has also been widely used in ocular drug discovery, such as the screening of new anti-angiogenic compounds or neuroprotective drugs, and the oculotoxicity test. In this review, we summarized the applications of zebrafish as the models of eye disorders to study disease mechanism and investigate novel drug treatments.
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Affiliation(s)
| | - Yan Luo
- Correspondence: ; Tel.: +86-020-87335931
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4
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Ganzen L, Ko MJ, Zhang M, Xie R, Chen Y, Zhang L, James R, Mumm J, van Rijn RM, Zhong W, Pang CP, Zhang M, Tsujikawa M, Leung YF. Drug screening with zebrafish visual behavior identifies carvedilol as a potential treatment for an autosomal dominant form of retinitis pigmentosa. Sci Rep 2021; 11:11432. [PMID: 34075074 PMCID: PMC8169685 DOI: 10.1038/s41598-021-89482-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 04/23/2021] [Indexed: 02/04/2023] Open
Abstract
Retinitis Pigmentosa (RP) is a mostly incurable inherited retinal degeneration affecting approximately 1 in 4000 individuals globally. The goal of this work was to identify drugs that can help patients suffering from the disease. To accomplish this, we screened drugs on a zebrafish autosomal dominant RP model. This model expresses a truncated human rhodopsin transgene (Q344X) causing significant rod degeneration by 7 days post-fertilization (dpf). Consequently, the larvae displayed a deficit in visual motor response (VMR) under scotopic condition. The diminished VMR was leveraged to screen an ENZO SCREEN-WELL REDOX library since oxidative stress is postulated to play a role in RP progression. Our screening identified a beta-blocker, carvedilol, that ameliorated the deficient VMR of the RP larvae and increased their rod number. Carvedilol may directly on rods as it affected the adrenergic pathway in the photoreceptor-like human Y79 cell line. Since carvedilol is an FDA-approved drug, our findings suggest that carvedilol can potentially be repurposed to treat autosomal dominant RP patients.
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Affiliation(s)
- Logan Ganzen
- grid.169077.e0000 0004 1937 2197Department of Biological Sciences, Purdue University, West Lafayette, IN 47907 USA ,grid.169077.e0000 0004 1937 2197Purdue University Life Sciences Program, Purdue University, West Lafayette, IN 47907 USA
| | - Mee Jung Ko
- grid.169077.e0000 0004 1937 2197Purdue University Life Sciences Program, Purdue University, West Lafayette, IN 47907 USA ,grid.169077.e0000 0004 1937 2197Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907 USA
| | - Mengrui Zhang
- grid.213876.90000 0004 1936 738XDepartment of Statistics, University of Georgia, Athens, GA 30602 USA
| | - Rui Xie
- grid.170430.10000 0001 2159 2859Department of Statistics and Data Science, University of Central Florida, Orlando, FL 32816 USA
| | - Yongkai Chen
- grid.213876.90000 0004 1936 738XDepartment of Statistics, University of Georgia, Athens, GA 30602 USA
| | - Liyun Zhang
- grid.21107.350000 0001 2171 9311Wilmer Eye Institute, John Hopkins School of Medicine, Baltimore, MD 21205 USA
| | - Rebecca James
- grid.169077.e0000 0004 1937 2197Department of Biological Sciences, Purdue University, West Lafayette, IN 47907 USA
| | - Jeff Mumm
- grid.21107.350000 0001 2171 9311Wilmer Eye Institute, John Hopkins School of Medicine, Baltimore, MD 21205 USA
| | - Richard M. van Rijn
- grid.169077.e0000 0004 1937 2197Purdue University Life Sciences Program, Purdue University, West Lafayette, IN 47907 USA ,grid.169077.e0000 0004 1937 2197Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907 USA ,grid.169077.e0000 0004 1937 2197Purdue Institute for Integrative Neuroscience, Purdue University, 610 Purdue Mall, West Lafayette, IN 47907 USA ,grid.169077.e0000 0004 1937 2197Purdue Institute for Drug Discovery, Purdue University, 610 Purdue Mall, West Lafayette, IN 47907 USA
| | - Wenxuan Zhong
- grid.213876.90000 0004 1936 738XDepartment of Statistics, University of Georgia, Athens, GA 30602 USA
| | - Chi Pui Pang
- grid.10784.3a0000 0004 1937 0482Department of Ophthalmology and Visual Sciences, Chinese University of Hong Kong, Hong Kong, China ,grid.263451.70000 0000 9927 110XJoint Shantou International Eye Center, Shantou University and the Chinese University of Hong Kong, Shantou, China
| | - Mingzhi Zhang
- grid.263451.70000 0000 9927 110XJoint Shantou International Eye Center, Shantou University and the Chinese University of Hong Kong, Shantou, China
| | - Motokazu Tsujikawa
- grid.136593.b0000 0004 0373 3971Department of Ophthalmology, Osaka University Graduate School of Medicine, Osaka, Japan ,grid.136593.b0000 0004 0373 3971Department of Clinical Laboratory and Biomedical Sciences, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Yuk Fai Leung
- grid.169077.e0000 0004 1937 2197Department of Biological Sciences, Purdue University, West Lafayette, IN 47907 USA ,grid.257413.60000 0001 2287 3919Department of Biochemistry and Molecular Biology, Indiana University School of Medicine Lafayette, 625 Harrison Street, West Lafayette, IN 47907 USA ,grid.169077.e0000 0004 1937 2197Purdue Institute for Integrative Neuroscience, Purdue University, 610 Purdue Mall, West Lafayette, IN 47907 USA ,grid.169077.e0000 0004 1937 2197Purdue Institute for Drug Discovery, Purdue University, 610 Purdue Mall, West Lafayette, IN 47907 USA
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Venkatraman P, Mills-Henry I, Padmanabhan KR, Pascuzzi P, Hassan M, Zhang J, Zhang X, Ma P, Pang CP, Dowling JE, Zhang M, Leung YF. Rods Contribute to Visual Behavior in Larval Zebrafish. Invest Ophthalmol Vis Sci 2021; 61:11. [PMID: 33049059 PMCID: PMC7571310 DOI: 10.1167/iovs.61.12.11] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Purpose Although zebrafish rods begin to develop as early as 2 days postfertilization (dpf), they are not deemed anatomically mature and functional until 15 to 21 dpf. A recent study detected a small electroretinogram (ERG) from rods in a cone mutant called no optokinetic response f (nof) at 5 dpf, suggesting that young rods are functional. Whether they can mediate behavioral responses in larvae is unknown. Methods We first confirmed rod function by measuring nof ERGs under photopic and scotopic illumination at 6 dpf. We evaluated the role of rods in visual behaviors using two different assays: the visual-motor response (VMR) and optokinetic response (OKR). We measured responses from wild-type (WT) larvae and nof mutants under photopic and scotopic illuminations at 6 dpf. Results Nof mutants lacked a photopic ERG. However, after prolonged dark adaptation, they displayed scotopic ERGs. Compared with WT larvae, the nof mutants displayed reduced VMRs. The VMR difference during light onset gradually diminished with decreased illumination and became nearly identical at lower light intensities. Additionally, light-adapted nof mutants did not display an OKR, whereas dark-adapted nof mutants displayed scotopic OKRs. Conclusions Because the nof mutants lacked a photopic ERG but displayed scotopic ERGs after dark adaptation, the mutants clearly had functional rods. WT larvae and the nof mutants displayed comparable scotopic light-On VMRs and scotopic OKRs after dark adaptation, suggesting that these responses were driven primarily by rods. Together, these observations indicate that rods contribute to zebrafish visual behaviors as early as 6 dpf.
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Affiliation(s)
- Prahatha Venkatraman
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States
| | - Ishara Mills-Henry
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States
| | | | - Pete Pascuzzi
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, United States.,Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana, United States.,Purdue University Libraries, Purdue University, West Lafayette, Indiana, United States
| | - Menna Hassan
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States
| | - Jingyi Zhang
- Center for Statistical Science, Tsinghua University, Beijing, China
| | - Xinlian Zhang
- Department of Statistics, University of Georgia, Athens, Georgia, United States
| | - Ping Ma
- Department of Statistics, University of Georgia, Athens, Georgia, United States
| | - Chi Pui Pang
- Department of Ophthalmology and Visual Sciences, Chinese University of Hong Kong, Hong Kong.,Joint Shantou International Eye Center, Shantou University and the Chinese University of Hong Kong, Shantou, China
| | - John E Dowling
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, United States
| | - Mingzhi Zhang
- Joint Shantou International Eye Center, Shantou University and the Chinese University of Hong Kong, Shantou, China
| | - Yuk Fai Leung
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States.,Department of Biochemistry and Molecular Biology, Indiana University School of Medicine Lafayette, West Lafayette, Indiana, United States.,Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, Indiana, United States.,Purdue Institute for Drug Discovery, Purdue University, West Lafayette, Indiana, United States
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6
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Neurodegeneration, Neuroprotection and Regeneration in the Zebrafish Retina. Cells 2021; 10:cells10030633. [PMID: 33809186 PMCID: PMC8000332 DOI: 10.3390/cells10030633] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/10/2021] [Accepted: 03/01/2021] [Indexed: 12/15/2022] Open
Abstract
Neurodegenerative retinal diseases, such as glaucoma and diabetic retinopathy, involve a gradual loss of neurons in the retina as the disease progresses. Central nervous system neurons are not able to regenerate in mammals, therefore, an often sought after course of treatment for neuronal loss follows a neuroprotective or regenerative strategy. Neuroprotection is the process of preserving the structure and function of the neurons that have survived a harmful insult; while regenerative approaches aim to replace or rewire the neurons and synaptic connections that were lost, or induce regrowth of damaged axons or dendrites. In order to test the neuroprotective effectiveness or the regenerative capacity of a particular agent, a robust experimental model of retinal neuronal damage is essential. Zebrafish are being used more often in this type of study because their eye structure and development is well-conserved between zebrafish and mammals. Zebrafish are robust genetic tools and are relatively inexpensive to maintain. The large array of functional and behavioral tests available in zebrafish makes them an attractive model for neuroprotection studies. Some common insults used to model retinal disease and study neuroprotection in zebrafish include intense light, chemical toxicity and mechanical damage. This review covers the existing retinal neuroprotection and regeneration literature in the zebrafish and highlights their potential for future studies.
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7
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Noel NCL, MacDonald IM, Allison WT. Zebrafish Models of Photoreceptor Dysfunction and Degeneration. Biomolecules 2021; 11:78. [PMID: 33435268 PMCID: PMC7828047 DOI: 10.3390/biom11010078] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 01/02/2021] [Accepted: 01/04/2021] [Indexed: 12/15/2022] Open
Abstract
Zebrafish are an instrumental system for the generation of photoreceptor degeneration models, which can be utilized to determine underlying causes of photoreceptor dysfunction and death, and for the analysis of potential therapeutic compounds, as well as the characterization of regenerative responses. We review the wealth of information from existing zebrafish models of photoreceptor disease, specifically as they relate to currently accepted taxonomic classes of human rod and cone disease. We also highlight that rich, detailed information can be derived from studying photoreceptor development, structure, and function, including behavioural assessments and in vivo imaging of zebrafish. Zebrafish models are available for a diversity of photoreceptor diseases, including cone dystrophies, which are challenging to recapitulate in nocturnal mammalian systems. Newly discovered models of photoreceptor disease and drusenoid deposit formation may not only provide important insights into pathogenesis of disease, but also potential therapeutic approaches. Zebrafish have already shown their use in providing pre-clinical data prior to testing genetic therapies in clinical trials, such as antisense oligonucleotide therapy for Usher syndrome.
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Affiliation(s)
- Nicole C. L. Noel
- Department of Medical Genetics, University of Alberta, Edmonton, AB T6G 2H7, Canada; (I.M.M.); (W.T.A.)
| | - Ian M. MacDonald
- Department of Medical Genetics, University of Alberta, Edmonton, AB T6G 2H7, Canada; (I.M.M.); (W.T.A.)
- Department of Ophthalmology and Visual Sciences, University of Alberta, Edmonton, AB T6G 2R7, Canada
| | - W. Ted Allison
- Department of Medical Genetics, University of Alberta, Edmonton, AB T6G 2H7, Canada; (I.M.M.); (W.T.A.)
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, AB T6G 2M8, Canada
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8
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Elovl2 Is Required for Robust Visual Function in Zebrafish. Cells 2020; 9:cells9122583. [PMID: 33276584 PMCID: PMC7761535 DOI: 10.3390/cells9122583] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/12/2020] [Accepted: 11/29/2020] [Indexed: 12/11/2022] Open
Abstract
Omega-3 and omega-6 polyunsaturated fatty acids (PUFAs) play critical roles in membrane stability and cell signaling within the retina. ELOVL2 (Elongation of Very Long Chain Fatty Acids-Like 2), an elongase involved in the synthesis of long chain polyunsaturated fatty acids (LC-PUFAs), has recently been implicated in regulating aging in the mammalian retina. In this work, we characterize the expression and function of elovl2 in the retina development in embryonic zebrafish. Whole mount in situ hybridization shows elovl2 is expressed in the Muller glia in embryonic and adult zebrafish. Lipidomics analysis of elovl2 crispants whole embryos at day 2 and eyes at day 7 demonstrated significant changes in lipids composition, especially on the level of lipids containing docosahexaenoic acid (DHA). Histological analysis of zebrafish lacking elovl2 revealed increased retinal thickness compared to controls at day 7 without gross disruptions of the retinal architecture. Finally, elovl2 crispants showed differences in the visual motor reflex light off (VMR-OFF) at day 7 compared to controls. In sum, inactivation of elovl2 in zebrafish embryos caused changes in lipid composition and in visual behavior, further confirming the important role of LC-PUFAs in healthy vision.
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9
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Saddala MS, Lennikov A, Bouras A, Huang H. RNA-Seq reveals differential expression profiles and functional annotation of genes involved in retinal degeneration in Pde6c mutant Danio rerio. BMC Genomics 2020; 21:132. [PMID: 32033529 PMCID: PMC7006399 DOI: 10.1186/s12864-020-6550-z] [Citation(s) in RCA: 6] [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: 05/29/2019] [Accepted: 01/31/2020] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Retinal degenerative diseases affect millions of people and represent the leading cause of vision loss around the world. Retinal degeneration has been attributed to a wide variety of causes, such as disruption of genes involved in phototransduction, biosynthesis, folding of the rhodopsin molecule, and the structural support of the retina. The molecular pathogenesis of the biological events in retinal degeneration is unclear; however, the molecular basis of the retinal pathological defect can be potentially determined by gene-expression profiling of the whole retina. In the present study, we analyzed the differential gene expression profile of the retina from a wild-type zebrafish and phosphodiesterase 6c (pde6c) mutant. RESULTS The datasets were downloaded from the Sequence Read Archive (SRA), and adaptors and unbiased bases were removed, and sequences were checked to ensure the quality. The reads were further aligned to the reference genome of zebrafish, and the gene expression was calculated. The differentially expressed genes (DEGs) were filtered based on the log fold change (logFC) (±4) and p-values (p < 0.001). We performed gene annotation (molecular function [MF], biological process [BP], cellular component [CC]), and determined the functional pathways Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway for the DEGs. Our result showed 216 upregulated and 3527 downregulated genes between normal and pde6c mutant zebrafish. These DEGs are involved in various KEGG pathways, such as the phototransduction (12 genes), mRNA surveillance (17 genes), phagosome (25 genes), glycolysis/gluconeogenesis (15 genes), adrenergic signaling in cardiomyocytes (29 genes), ribosome (20 genes), the citrate cycle (TCA cycle; 8 genes), insulin signaling (24 genes), oxidative phosphorylation (20 genes), and RNA transport (22 genes) pathways. Many more of all the pathway genes were down-regulated, while fewer were up-regulated in the retina of pde6c mutant zebrafish. CONCLUSIONS Our data strongly indicate that, among these genes, the above-mentioned pathways' genes as well as calcium-binding, neural damage, peptidase, immunological, and apoptosis proteins are mostly involved in the retinal and neural degeneration that cause abnormalities in photoreceptors or retinal pigment epithelium (RPE) cells.
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Affiliation(s)
- Madhu Sudhana Saddala
- School of Medicine, Department Ophthalmology, Mason Eye Institute, University of Missouri-Columbia, One Hospital Drive, MA102C, Columbia, MO, 65212, USA
- Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Anton Lennikov
- School of Medicine, Department Ophthalmology, Mason Eye Institute, University of Missouri-Columbia, One Hospital Drive, MA102C, Columbia, MO, 65212, USA
- Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Adam Bouras
- School of Medicine, Department Ophthalmology, Mason Eye Institute, University of Missouri-Columbia, One Hospital Drive, MA102C, Columbia, MO, 65212, USA
| | - Hu Huang
- School of Medicine, Department Ophthalmology, Mason Eye Institute, University of Missouri-Columbia, One Hospital Drive, MA102C, Columbia, MO, 65212, USA.
- Wilmer Eye Institute, Johns Hopkins University, Baltimore, MD, USA.
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10
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Zhuang YY, Xiang L, Wen XR, Shen RJ, Zhao N, Zheng SS, Han RY, Qu J, Lu F, Jin ZB. Slc7a14 Is Indispensable in Zebrafish Retinas. Front Cell Dev Biol 2019; 7:333. [PMID: 31921845 PMCID: PMC6920099 DOI: 10.3389/fcell.2019.00333] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 11/27/2019] [Indexed: 12/13/2022] Open
Abstract
Previous study has identified SLC7A14 as a new causative gene of retinitis pigmentosa (RP). However, the role of SLC7A14 has not been fully characterized. The goal of this study was to investigate the biological features of slc7a14 in zebrafish. To determine the expression of slc7a14 in developing zebrafish, we performed in situ hybridization (ISH) and quantitative real-time PCR. Morpholino knockdown and overexpression experiments were performed to study the role of slc7a14 in zebrafish retinas. Immunostaining was carried out to observe structural changes. Visual motor responses (VMR) and optokinetic responses (OKR) were analyzed to assess visual behaviors. Terminal deoxynucleotidyl transferase (dUTP) nick-end labeling (TUNEL) staining was performed to survey apoptotic retinal cells. We found that slc7a14 was highly expressed in neuronal tissues, including the brain, spinal cord and retina, and that the expression levels increased during early embryogenesis. Consistently, ISH showed a similar expression pattern. Knockdown of slc7a14 led to dose-dependent microphthalmia that was reversed by overexpression. The immunostaining results revealed that the rod-specific protein zpr-3 and the retinal pigment epithelium-specific protein zpr-2 (decreased to 44.48%) were significantly suppressed in the slc7a14-silenced morphants. Notably, visual behaviors (the VMR and the OKR) were severely impaired in the slc7a14-deficient morphant, especially the VMR OFF response. In addition, apoptotic cells were observed in the retina at 3 days post fertilization (dpf) and 5 dpf by TUNEL assay. Our results demonstrated that slc7a14 is essential for visually mediated behaviors in zebrafish. Temporary silencing of slc7a14 in larvae led to severe visual impairments, consistent with the manifestations observed in RP patients. Our findings provide further insights into the genetic mechanisms of RP predisposition caused by SLC7A14 mutations.
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Affiliation(s)
- You-Yuan Zhuang
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China.,State Key Laboratory of Ophthalmology, Optometry and Visual Science, National Clinical Research Center for Ophthalmology, National Center for International Research in Regenerative Medicine and Neurogenetics, Wenzhou, China
| | - Lue Xiang
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China.,State Key Laboratory of Ophthalmology, Optometry and Visual Science, National Clinical Research Center for Ophthalmology, National Center for International Research in Regenerative Medicine and Neurogenetics, Wenzhou, China
| | - Xin-Ran Wen
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China.,State Key Laboratory of Ophthalmology, Optometry and Visual Science, National Clinical Research Center for Ophthalmology, National Center for International Research in Regenerative Medicine and Neurogenetics, Wenzhou, China
| | - Ren-Juan Shen
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China.,State Key Laboratory of Ophthalmology, Optometry and Visual Science, National Clinical Research Center for Ophthalmology, National Center for International Research in Regenerative Medicine and Neurogenetics, Wenzhou, China
| | - Ning Zhao
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China.,State Key Laboratory of Ophthalmology, Optometry and Visual Science, National Clinical Research Center for Ophthalmology, National Center for International Research in Regenerative Medicine and Neurogenetics, Wenzhou, China
| | - Si-Si Zheng
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China.,State Key Laboratory of Ophthalmology, Optometry and Visual Science, National Clinical Research Center for Ophthalmology, National Center for International Research in Regenerative Medicine and Neurogenetics, Wenzhou, China
| | - Ru-Yi Han
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China.,State Key Laboratory of Ophthalmology, Optometry and Visual Science, National Clinical Research Center for Ophthalmology, National Center for International Research in Regenerative Medicine and Neurogenetics, Wenzhou, China
| | - Jia Qu
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China.,State Key Laboratory of Ophthalmology, Optometry and Visual Science, National Clinical Research Center for Ophthalmology, National Center for International Research in Regenerative Medicine and Neurogenetics, Wenzhou, China
| | - Fan Lu
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China.,State Key Laboratory of Ophthalmology, Optometry and Visual Science, National Clinical Research Center for Ophthalmology, National Center for International Research in Regenerative Medicine and Neurogenetics, Wenzhou, China
| | - Zi-Bing Jin
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China.,State Key Laboratory of Ophthalmology, Optometry and Visual Science, National Clinical Research Center for Ophthalmology, National Center for International Research in Regenerative Medicine and Neurogenetics, Wenzhou, China
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11
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Xie R, Zhang M, Venkatraman P, Zhang X, Zhang G, Carmer R, Kantola SA, Pang CP, Ma P, Zhang M, Zhong W, Leung YF. Normalization of large-scale behavioural data collected from zebrafish. PLoS One 2019; 14:e0212234. [PMID: 30768618 PMCID: PMC6377122 DOI: 10.1371/journal.pone.0212234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 01/29/2019] [Indexed: 11/19/2022] Open
Abstract
Many contemporary neuroscience experiments utilize high-throughput approaches to simultaneously collect behavioural data from many animals. The resulting data are often complex in structure and are subjected to systematic biases, which require new approaches for analysis and normalization. This study addressed the normalization need by establishing an approach based on linear-regression modeling. The model was established using a dataset of visual motor response (VMR) obtained from several strains of wild-type (WT) zebrafish collected at multiple stages of development. The VMR is a locomotor response triggered by drastic light change, and is commonly measured repeatedly from multiple larvae arrayed in 96-well plates. This assay is subjected to several systematic variations. For example, the light emitted by the machine varies slightly from well to well. In addition to the light-intensity variation, biological replication also created batch-batch variation. These systematic variations may result in differences in the VMR and must be normalized. Our normalization approach explicitly modeled the effect of these systematic variations on VMR. It also normalized the activity profiles of different conditions to a common baseline. Our approach is versatile, as it can incorporate different normalization needs as separate factors. The versatility was demonstrated by an integrated normalization of three factors: light-intensity variation, batch-batch variation and baseline. After normalization, new biological insights were revealed from the data. For example, we found larvae of TL strain at 6 days post-fertilization (dpf) responded to light onset much stronger than the 9-dpf larvae, whereas previous analysis without normalization shows that their responses were relatively comparable. By removing systematic variations, our model-based normalization can facilitate downstream statistical comparisons and aid detecting true biological differences in high-throughput studies of neurobehaviour.
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Affiliation(s)
- Rui Xie
- Department of Statistics, University of Georgia, Athens, Georgia, United States of America
| | - Mengrui Zhang
- Department of Statistics, University of Georgia, Athens, Georgia, United States of America
| | - Prahatha Venkatraman
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America
| | - Xinlian Zhang
- Department of Statistics, University of Georgia, Athens, Georgia, United States of America
| | - Gaonan Zhang
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America
| | - Robert Carmer
- Department of Statistics, Purdue University, West Lafayette, Indiana, United States of America
| | - Skylar A. Kantola
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America
| | - Chi Pui Pang
- Department of Ophthalmology and Visual Sciences, Chinese University of Hong Kong, Hong Kong SAR, China
- Joint Shantou International Eye Center of Shantou University and The Chinese University of Hong Kong, Shantou, China
| | - Ping Ma
- Department of Statistics, University of Georgia, Athens, Georgia, United States of America
| | - Mingzhi Zhang
- Joint Shantou International Eye Center of Shantou University and The Chinese University of Hong Kong, Shantou, China
- * E-mail: (MZ); (WZ); (YFL)
| | - Wenxuan Zhong
- Department of Statistics, University of Georgia, Athens, Georgia, United States of America
- * E-mail: (MZ); (WZ); (YFL)
| | - Yuk Fai Leung
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, United States of America
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine Lafayette, West Lafayette, Indiana, United States of America
- Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, Indiana, United States of America
- Purdue Institute for Drug Discovery, Purdue University, West Lafayette, Indiana, United States of America
- * E-mail: (MZ); (WZ); (YFL)
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12
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Zheng SS, Han RY, Xiang L, Zhuang YY, Jin ZB. Versatile Genome Engineering Techniques Advance Human Ocular Disease Researches in Zebrafish. Front Cell Dev Biol 2018; 6:75. [PMID: 30050903 PMCID: PMC6052052 DOI: 10.3389/fcell.2018.00075] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 06/25/2018] [Indexed: 12/18/2022] Open
Abstract
Over recent decades, zebrafish has been established as a sophisticated vertebrate model for studying human ocular diseases due to its high fecundity, short generation time and genetic tractability. With the invention of morpholino (MO) technology, it became possible to study the genetic basis and relevant genes of ocular diseases in vivo. Many genes have been shown to be related to ocular diseases. However, the issue of specificity is the major concern in defining gene functions with MO technology. The emergence of the first- and second-generation genetic modification tools zinc-finger nucleases (ZFNs) and TAL effector nucleases (TALENs), respectively, eliminated the potential phenotypic risk induced by MOs. Nevertheless, the efficiency of these nucleases remained relatively low until the third technique, the clustered regularly interspersed short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system, was discovered. This review highlights the application of multiple genome engineering techniques, especially the CRISPR/Cas9 system, in the study of human ocular diseases in zebrafish.
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Affiliation(s)
- Si-Si Zheng
- Division of Ophthalmic Genetics, Laboratory for Stem Cell and Retinal Regeneration, Institute of Stem Cell Research, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National International Joint Research Center for Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China
| | - Ru-Yi Han
- Division of Ophthalmic Genetics, Laboratory for Stem Cell and Retinal Regeneration, Institute of Stem Cell Research, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National International Joint Research Center for Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China
| | - Lue Xiang
- Division of Ophthalmic Genetics, Laboratory for Stem Cell and Retinal Regeneration, Institute of Stem Cell Research, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National International Joint Research Center for Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Wenzhou, China
| | - You-Yuan Zhuang
- Division of Ophthalmic Genetics, Laboratory for Stem Cell and Retinal Regeneration, Institute of Stem Cell Research, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National International Joint Research Center for Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China
| | - Zi-Bing Jin
- Division of Ophthalmic Genetics, Laboratory for Stem Cell and Retinal Regeneration, Institute of Stem Cell Research, The Eye Hospital, Wenzhou Medical University, Wenzhou, China
- National International Joint Research Center for Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Wenzhou, China
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13
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Jaafaru MS, Nordin N, Shaari K, Rosli R, Abdull Razis AF. Isothiocyanate from Moringa oleifera seeds mitigates hydrogen peroxide-induced cytotoxicity and preserved morphological features of human neuronal cells. PLoS One 2018; 13:e0196403. [PMID: 29723199 PMCID: PMC5933767 DOI: 10.1371/journal.pone.0196403] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 04/12/2018] [Indexed: 01/12/2023] Open
Abstract
Reactive oxygen species are well known for induction of oxidative stress conditions through oxidation of vital biomarkers leading to cellular death via apoptosis and other process, thereby causing devastative effects on the host organs. This effect is believed to be linked with pathological alterations seen in several neurodegenerative disease conditions. Many phytochemical compounds proved to have robust antioxidant activities that deterred cells against cytotoxic stress environment, thus protect apoptotic cell death. In view of that we studied the potential of glucomoringin-isothiocyanate (GMG-ITC) or moringin to mitigate the process that lead to neurodegeneration in various ways. Neuroprotective effect of GMG-ITC was performed on retinoic acid (RA) induced differentiated neuroblastoma cells (SHSY5Y) via cell viability assay, flow cytometry analysis and fluorescence microscopy by means of acridine orange and propidium iodide double staining, to evaluate the anti-apoptotic activity and morphology conservation ability of the compound. Additionally, neurite surface integrity and ultrastructural analysis were carried out by means of scanning and transmission electron microscopy to assess the orientation of surface and internal features of the treated neuronal cells. GMG-ITC pre-treated neuron cells showed significant resistance to H2O2-induced apoptotic cell death, revealing high level of protection by the compound. Increase of intracellular oxidative stress induced by H2O2 was mitigated by GMG-ITC. Thus, pre-treatment with the compound conferred significant protection to cytoskeleton and cytoplasmic inclusion coupled with conservation of surface morphological features and general integrity of neuronal cells. Therefore, the collective findings in the presence study indicated the potentials of GMG-ITC to protect the integrity of neuron cells against induced oxidative-stress related cytotoxic processes, the hallmark of neurodegenerative diseases.
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Affiliation(s)
- Mohammed Sani Jaafaru
- UPM-MAKNA Cancer Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
- Department of Biochemistry, Kaduna State University, Main Campus, Kaduna, Nigeria
| | - Norshariza Nordin
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
| | - Khozirah Shaari
- Laboratory of Natural Product, Institute of Bioscience, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
| | - Rozita Rosli
- UPM-MAKNA Cancer Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
| | - Ahmad Faizal Abdull Razis
- Laboratory of Molecular Biomedicine, Institute of Bioscience, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
- Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia
- * E-mail:
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14
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Huang DF, Wang MY, Yin W, Ma YQ, Wang H, Xue T, Ren DL, Hu B. Zebrafish Lacking Circadian Gene per2 Exhibit Visual Function Deficiency. Front Behav Neurosci 2018; 12:53. [PMID: 29593513 PMCID: PMC5859089 DOI: 10.3389/fnbeh.2018.00053] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 03/01/2018] [Indexed: 01/09/2023] Open
Abstract
The retina has an intrinsic circadian clock, but the importance of this clock for vision is unknown. Zebrafish offer many advantages for studying vertebrate vision and circadian rhythm. Here, we explored the role of zebrafish per2, a light-regulated gene, in visual behavior and the underlying mechanisms. We observed that per2 mutant zebrafish larvae showed decreased contrast sensitivity and visual acuity using optokinetic response (OKR) assays. Using a visual motor response (VMR) assay, we observed normal OFF responses but abnormal ON responses in mutant zebrafish larvae. Immunofluorescence showed that mutants had a normal morphology of cone photoreceptor cells and retinal organization. However, electron microscopy showed that per2 mutants displayed abnormal and decreased photoreceptor ribbon synapses with arciform density, which resulted in retinal ON pathway defect. We also examined the expression of three cone opsins by quantitative real-time PCR (qRT-PCR), and the expression of long-wave-sensitive opsin (opn1lw) and short-wave-sensitive opsin (opn1sw) was reduced in mutant zebrafish larvae. qRT-PCR analyses also showed a down-regulation of the clock genes cry1ba and bmal1b in the adult eye of per2 mutant zebrafish. This study identified a mechanism by which a clock gene affects visual function and defined important roles of per2 in retinal information processing.
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Affiliation(s)
- Deng-Feng Huang
- Hefei National Laboratory for Physical Sciences at the Microscale and CAS Key Laboratory of Brain Function & Disease, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Ming-Yong Wang
- School of Biology & Basic Medical Sciences, Medical College, Soochow University, Suzhou, China
| | - Wu Yin
- Hefei National Laboratory for Physical Sciences at the Microscale and CAS Key Laboratory of Brain Function & Disease, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Yu-Qian Ma
- Neurodegenerative Disorder Research Center, University of Science and Technology of China, Hefei, China
| | - Han Wang
- School of Biology & Basic Medical Sciences, Medical College, Soochow University, Suzhou, China
| | - Tian Xue
- Neurodegenerative Disorder Research Center, University of Science and Technology of China, Hefei, China
| | - Da-Long Ren
- Hefei National Laboratory for Physical Sciences at the Microscale and CAS Key Laboratory of Brain Function & Disease, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Bing Hu
- Hefei National Laboratory for Physical Sciences at the Microscale and CAS Key Laboratory of Brain Function & Disease, School of Life Sciences, University of Science and Technology of China, Hefei, China
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15
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Zhang L, Zhang X, Zhang G, Pang CP, Leung YF, Zhang M, Zhong W. Expression profiling of the retina of pde6c, a zebrafish model of retinal degeneration. Sci Data 2017; 4:170182. [PMID: 29231925 PMCID: PMC5726315 DOI: 10.1038/sdata.2017.182] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 10/24/2017] [Indexed: 11/25/2022] Open
Abstract
Retinal degeneration often affects the whole retina even though the disease-causing gene is specifically expressed in the light-sensitive photoreceptors. The molecular basis of the retinal defect can potentially be determined by gene-expression profiling of the whole retina. In this study, we measured the gene-expression profile of retinas microdissected from a zebrafish pde6cw59 (pde6c) mutant. This retinal-degeneration model not only displays cone degeneration caused by a cone-specific mutation, but also other secondary cellular changes starting from 4 days postfertilization (dpf). To capture the underlying molecular changes, we subjected pde6c and wild-type (WT) retinas at 5 dpf/ 120 h postfertilization (hpf) to RNA sequencing (RNA-Seq) on the Illumina HiSeq 2,000 platform. We also validated the RNA-Seq results by Reverse Transcription Quantitative Polymerase Chain Reaction (RT-qPCR) of seven phototransduction genes. Our analyses indicate that the RNA-Seq dataset was of high quality, and effectively captured the molecular changes in the whole pde6c retina. This dataset will facilitate the characterization of the molecular defects in the pde6c retina at the initial stage of retinal degeneration.
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Affiliation(s)
- Liyun Zhang
- Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN 47907, USA
| | - Xinlian Zhang
- Department of Statistics, University of Georgia, 101 Cedar St, Athens, GA 30602, USA
| | - Gaonan Zhang
- Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN 47907, USA
| | - Chi Pui Pang
- Department of Ophthalmology and Visual Sciences, Chinese University of Hong Kong, Hong Kong
| | - Yuk Fai Leung
- Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN 47907, USA.,Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.,Purdue Institute for Drug Discovery, 610 Purdue Mall, Purdue University, West Lafayette, IN 47907, USA.,Purdue Institute for Integrative Neuroscience, Purdue University, 610 Purdue Mall, West Lafayette, IN 47907, USA
| | - Mingzhi Zhang
- Joint Shantou International Eye Center, Shantou University & the Chinese University of Hong Kong, Shantou 515041, China
| | - Wenxuan Zhong
- Department of Statistics, University of Georgia, 101 Cedar St, Athens, GA 30602, USA
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16
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Hong M, Zhang Y, Li S, Tan HY, Wang N, Mu S, Hao X, Feng Y. A Network Pharmacology-Based Study on the Hepatoprotective Effect of Fructus Schisandrae. Molecules 2017; 22:E1617. [PMID: 28956809 PMCID: PMC6151775 DOI: 10.3390/molecules22101617] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 09/17/2017] [Indexed: 12/19/2022] Open
Abstract
Fructus schisandrae (Wuweizi in Chinese), a common traditional Chinese herbal medicine, has been used for centuries to treat chronic liver disease. The therapeutic efficacy of Wuweizi has also been validated in clinical practice. In this study, molecular docking and network analysis were carried out to explore the hepatoprotective mechanism of Wuweizi as an effective therapeutic approach to treat liver disease. Multiple active compounds of Wuweizi were docked with 44 protein targets related with viral hepatitis, fatty liver, liver fibrosis, cirrhosis, and liver cancer. A compound-target network was constructed through network pharmacology analysis, predicting the relationships of active ingredients to the targets. Our results demonstrated that schisantherin, schisandrin B, schisandrol B, kadsurin, Wuweizisu C, Gomisin A, Gomisin G, and angeloylgomisin may target with 21 intracellular proteins associated with liver diseases, especially with fatty liver disease. The CYP2E1, PPARα, and AMPK genes and their related pathway may play a pivotal role in the hepatoprotective effects of Wuweizi. The network pharmacology strategy used provides a forceful tool for searching the action mechanism of traditional herbal medicines and novel bioactive ingredients.
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Affiliation(s)
- Ming Hong
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 10 Sassoon Road, Pokfulam, Hong Kong, China.
- Institute of Clinical Pharmacology, Guangzhou University of Chinese Medicine, 12 Jichang Road, Guangzhou 510405, China.
| | - Yongsheng Zhang
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 10 Sassoon Road, Pokfulam, Hong Kong, China.
- Zhejiang Chinese Medical University, 548 Binwen Road, Hangzhou 310053, China.
| | - Sha Li
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 10 Sassoon Road, Pokfulam, Hong Kong, China.
| | - Hor Yue Tan
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 10 Sassoon Road, Pokfulam, Hong Kong, China.
| | - Ning Wang
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 10 Sassoon Road, Pokfulam, Hong Kong, China.
| | - Shuzhen Mu
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academy of Sciences, Guiyang 55500, China.
| | - Xiaojiang Hao
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academy of Sciences, Guiyang 55500, China.
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650000, China.
| | - Yibin Feng
- School of Chinese Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 10 Sassoon Road, Pokfulam, Hong Kong, China.
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17
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Liu Y, Ma P, Cassidy PA, Carmer R, Zhang G, Venkatraman P, Brown SA, Pang CP, Zhong W, Zhang M, Leung YF. Statistical Analysis of Zebrafish Locomotor Behaviour by Generalized Linear Mixed Models. Sci Rep 2017; 7:2937. [PMID: 28592855 PMCID: PMC5462837 DOI: 10.1038/s41598-017-02822-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 04/19/2017] [Indexed: 12/13/2022] Open
Abstract
Upon a drastic change in environmental illumination, zebrafish larvae display a rapid locomotor response. This response can be simultaneously tracked from larvae arranged in multi-well plates. The resulting data have provided new insights into neuro-behaviour. The features of these data, however, present a challenge to traditional statistical tests. For example, many larvae display little or no movement. Thus, the larval responses have many zero values and are imbalanced. These responses are also measured repeatedly from the same well, which results in correlated observations. These analytical issues were addressed in this study by the generalized linear mixed model (GLMM). This approach deals with binary responses and characterizes the correlation of observations in the same group. It was used to analyze a previously reported dataset. Before applying the GLMM, the activity values were transformed to binary responses (movement vs. no movement) to reduce data imbalance. Moreover, the GLMM estimated the variations among the effects of different well locations, which would eliminate the location effects when two biological groups or conditions were compared. By addressing the data-imbalance and location-correlation issues, the GLMM effectively quantified true biological effects on zebrafish locomotor response.
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Affiliation(s)
- Yiwen Liu
- Department of Statistics, University of Georgia, 101 Cedar St, Athens, GA, 30602, USA
| | - Ping Ma
- Department of Statistics, University of Georgia, 101 Cedar St, Athens, GA, 30602, USA
| | - Paige A Cassidy
- Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN, 47907, USA
| | - Robert Carmer
- Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN, 47907, USA.,Department of Statistics, 250 N University Street, Purdue University, West Lafayette, IN, 47907, USA
| | - Gaonan Zhang
- Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN, 47907, USA
| | - Prahatha Venkatraman
- Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN, 47907, USA
| | - Skye A Brown
- Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN, 47907, USA
| | - Chi Pui Pang
- Department of Ophthalmology and Visual Sciences, Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Wenxuan Zhong
- Department of Statistics, University of Georgia, 101 Cedar St, Athens, GA, 30602, USA.
| | - Mingzhi Zhang
- Joint Shantou International Eye Center, Shantou University & the Chinese University of Hong Kong, Shantou, China.
| | - Yuk Fai Leung
- Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN, 47907, USA. .,Department of Biochemistry and Molecular Biology, Indiana University School of Medicine Lafayette, 625 Harrison Street, West Lafayette, IN, 47907, USA. .,Purdue Institute for Integrative neuroscience, 610 Purdue Mall, Purdue University, West Lafayette, IN, 47907, USA. .,Purdue Institute for Drug Discovery, 610 Purdue Mall, Purdue University, West Lafayette, IN, 47907, USA.
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18
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Utilizing Zebrafish Visual Behaviors in Drug Screening for Retinal Degeneration. Int J Mol Sci 2017; 18:ijms18061185. [PMID: 28574477 PMCID: PMC5486008 DOI: 10.3390/ijms18061185] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Revised: 05/14/2017] [Accepted: 05/16/2017] [Indexed: 12/15/2022] Open
Abstract
Zebrafish are a popular vertebrate model in drug discovery. They produce a large number of small and rapidly-developing embryos. These embryos display rich visual-behaviors that can be used to screen drugs for treating retinal degeneration (RD). RD comprises blinding diseases such as Retinitis Pigmentosa, which affects 1 in 4000 people. This disease has no definitive cure, emphasizing an urgency to identify new drugs. In this review, we will discuss advantages, challenges, and research developments in using zebrafish behaviors to screen drugs in vivo. We will specifically discuss a visual-motor response that can potentially expedite discovery of new RD drugs.
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19
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Zhang L, Xiang L, Liu Y, Venkatraman P, Chong L, Cho J, Bonilla S, Jin ZB, Pang CP, Ko KM, Ma P, Zhang M, Leung YF. Correction: A Naturally-Derived Compound Schisandrin B Enhanced Light Sensation in the pde6c Zebrafish Model of Retinal Degeneration. PLoS One 2016; 11:e0154552. [PMID: 27111849 PMCID: PMC4844144 DOI: 10.1371/journal.pone.0154552] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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