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Lai ZY, Yang CC, Chen PH, Chen WC, Lai TY, Lu GY, Yang CY, Wang KY, Liu WC, Chen YC, Liu LYM, Chuang YJ. Syndecan-4 is required for early-stage repair responses during zebrafish heart regeneration. Mol Biol Rep 2024; 51:604. [PMID: 38700644 PMCID: PMC11068835 DOI: 10.1007/s11033-024-09531-4] [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: 11/10/2023] [Accepted: 04/08/2024] [Indexed: 05/06/2024]
Abstract
BACKGROUND The healing process after a myocardial infarction (MI) in humans involves complex events that replace damaged tissue with a fibrotic scar. The affected cardiac tissue may lose its function permanently. In contrast, zebrafish display a remarkable capacity for scar-free heart regeneration. Previous studies have revealed that syndecan-4 (SDC4) regulates inflammatory response and fibroblast activity following cardiac injury in higher vertebrates. However, whether and how Sdc4 regulates heart regeneration in highly regenerative zebrafish remains unknown. METHODS AND RESULTS This study showed that sdc4 expression was differentially regulated during zebrafish heart regeneration by transcriptional analysis. Specifically, sdc4 expression increased rapidly and transiently in the early regeneration phase upon ventricular cryoinjury. Moreover, the knockdown of sdc4 led to a significant reduction in extracellular matrix protein deposition, immune cell accumulation, and cell proliferation at the lesion site. The expression of tgfb1a and col1a1a, as well as the protein expression of Fibronectin, were all down-regulated under sdc4 knockdown. In addition, we verified that sdc4 expression was required for cardiac repair in zebrafish via in vivo electrocardiogram analysis. Loss of sdc4 expression caused an apparent pathological Q wave and ST elevation, which are signs of human MI patients. CONCLUSIONS Our findings support that Sdc4 is required to mediate pleiotropic repair responses in the early stage of zebrafish heart regeneration.
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Grants
- MOST 110-2311-B-007-005-MY3 Ministry of Science and Technology, Taiwan
- MOST 110-2311-B-007-005-MY3 Ministry of Science and Technology, Taiwan
- MOST 110-2311-B-007-005-MY3 Ministry of Science and Technology, Taiwan
- MOST 110-2311-B-007-005-MY3 Ministry of Science and Technology, Taiwan
- MOST 110-2311-B-007-005-MY3 Ministry of Science and Technology, Taiwan
- MOST 110-2311-B-007-005-MY3 Ministry of Science and Technology, Taiwan
- MOST 110-2311-B-007-005-MY3 Ministry of Science and Technology, Taiwan
- MOST 110-2311-B-007-005-MY3 Ministry of Science and Technology, Taiwan
- MOST 110-2311-B-007-005-MY3 Ministry of Science and Technology, Taiwan
- MOST 110-2311-B-007-005-MY3 Ministry of Science and Technology, Taiwan
- MOST 110-2311-B-007-005-MY3 Ministry of Science and Technology, Taiwan
- MOST 110-2311-B-007-005-MY3 Ministry of Science and Technology, Taiwan
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Affiliation(s)
- Zih-Yin Lai
- School of Medicine, National Tsing Hua University, Hsinchu, 300044, Taiwan, ROC
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 300044, Taiwan, ROC
| | - Chung-Chi Yang
- School of Medicine, National Tsing Hua University, Hsinchu, 300044, Taiwan, ROC
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 300044, Taiwan, ROC
- Division of Cardiovascular Medicine, Taoyuan Armed Forces General Hospital, Taoyuan City, 325208, Taiwan, ROC
- Cardiovascular Division, Tri-Service General Hospital, National Defense Medical Center, Taipei City, 114201, Taiwan, ROC
| | - Po-Hsun Chen
- School of Medicine, National Tsing Hua University, Hsinchu, 300044, Taiwan, ROC
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 300044, Taiwan, ROC
| | - Wei-Chen Chen
- School of Medicine, National Tsing Hua University, Hsinchu, 300044, Taiwan, ROC
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 300044, Taiwan, ROC
| | - Ting-Yu Lai
- School of Medicine, National Tsing Hua University, Hsinchu, 300044, Taiwan, ROC
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 300044, Taiwan, ROC
| | - Guan-Yun Lu
- School of Medicine, National Tsing Hua University, Hsinchu, 300044, Taiwan, ROC
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 300044, Taiwan, ROC
| | - Chiao-Yu Yang
- School of Medicine, National Tsing Hua University, Hsinchu, 300044, Taiwan, ROC
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 300044, Taiwan, ROC
| | - Ko-Ying Wang
- School of Medicine, National Tsing Hua University, Hsinchu, 300044, Taiwan, ROC
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 300044, Taiwan, ROC
| | - Wei-Cen Liu
- School of Medicine, National Tsing Hua University, Hsinchu, 300044, Taiwan, ROC
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 300044, Taiwan, ROC
| | - Yu-Chieh Chen
- School of Medicine, National Tsing Hua University, Hsinchu, 300044, Taiwan, ROC
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 300044, Taiwan, ROC
| | - Lawrence Yu-Min Liu
- Department of Internal Medicine, Division of Cardiology, Hsinchu MacKay Memorial Hospital, Hsinchu, 300044, Taiwan, ROC.
- Department of Medicine, MacKay Medical College, New Taipei City, 252005, Taiwan, ROC.
| | - Yung-Jen Chuang
- School of Medicine, National Tsing Hua University, Hsinchu, 300044, Taiwan, ROC.
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 300044, Taiwan, ROC.
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Shihabeddin E, Santhanam A, Aronowitz AL, O’Brien J. Cost-effective strategies to knock down genes of interest in the retinas of adult zebrafish. Front Cell Neurosci 2024; 17:1321337. [PMID: 38322239 PMCID: PMC10845135 DOI: 10.3389/fncel.2023.1321337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 12/22/2023] [Indexed: 02/08/2024] Open
Abstract
High throughput sequencing has generated an enormous amount of information about the genes expressed in various cell types and tissues throughout the body, and about how gene expression changes over time and in diseased conditions. This knowledge has made targeted gene knockdowns an important tool in screening and identifying the roles of genes that are differentially expressed among specific cells of interest. While many approaches are available and optimized in mammalian models, there are still several limitations in the zebrafish model. In this article, we describe two approaches to target specific genes in the retina for knockdown: cell-penetrating, translation-blocking Vivo-Morpholino oligonucleotides and commercially available lipid nanoparticle reagents to deliver siRNA. We targeted expression of the PCNA gene in the retina of a P23H rhodopsin transgenic zebrafish model, in which rapidly proliferating progenitor cells replace degenerated rod photoreceptors. Retinas collected 48 h after intravitreal injections in adult zebrafish reveal that both Vivo-Morpholinos and lipid encapsulated siRNAs were able to successfully knock down expression of PCNA. However, only retinas injected with Vivo-Morpholinos showed a significant decrease in the formation of P23H rhodopsin-expressing rods, a downstream effect of PCNA inhibition. Surprisingly, Vivo-Morpholinos were able to exit the injected eye and enter the contralateral non-injected eye to inhibit PCNA expression. In this article we describe the techniques, concentrations, and considerations we found necessary to successfully target and inhibit genes through Vivo-Morpholinos and lipid encapsulated siRNAs.
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Affiliation(s)
- Eyad Shihabeddin
- Department of Ophthalmology and Visual Science, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States
- MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States
| | - Abirami Santhanam
- University of Houston College of Optometry, Houston, TX, United States
| | - Alexandra L. Aronowitz
- Department of Ophthalmology and Visual Science, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - John O’Brien
- Department of Ophthalmology and Visual Science, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States
- MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States
- University of Houston College of Optometry, Houston, TX, United States
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Griffiths G, Gruenberg J, Marsh M, Wohlmann J, Jones AT, Parton RG. Nanoparticle entry into cells; the cell biology weak link. Adv Drug Deliv Rev 2022; 188:114403. [PMID: 35777667 DOI: 10.1016/j.addr.2022.114403] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 06/22/2022] [Accepted: 06/23/2022] [Indexed: 12/22/2022]
Abstract
Nanoparticles (NP) are attractive options for the therapeutic delivery of active pharmaceutical drugs, proteins and nucleic acids into cells, tissues and organs. Research into the development and application of NP most often starts with a diverse group of scientists, including chemists, bioengineers and material and pharmaceutical scientists, who design, fabricate and characterize NP in vitro (Stage 1). The next step (Stage 2) generally investigates cell toxicity as well as the processes by which NP bind, are internalized and deliver their cargo to appropriate model tissue culture cells. Subsequently, in Stage 3, selected NP are tested in animal systems, mostly mouse. Whereas the chemistry-based development and analysis in Stage 1 is increasingly sophisticated, the investigations in Stage 2 are not what could be regarded as 'state-of-the-art' for the cell biology field and the quality of research into NP interactions with cells is often sub-standard. In this review we describe our current understanding of the mechanisms by which particles gain entry into mammalian cells via endocytosis. We summarize the most important areas for concern, highlight some of the most common mis-conceptions, and identify areas where NP scientists could engage with trained cell biologists. Our survey of the different mechanisms of uptake into cells makes us suspect that claims for roles for caveolae, as well as macropinocytosis, in NP uptake into cells have been exaggerated, whereas phagocytosis has been under-appreciated.
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Affiliation(s)
- Gareth Griffiths
- Department Biosciences, University of Oslo, Blindernveien 31, PO Box 1041, 0316 Oslo, Norway.
| | - Jean Gruenberg
- Department of Biochemistry, University of Geneva, 30 quai E. Ansermet, 1211-Geneva-4, Switzerland
| | - Mark Marsh
- Laboratory for Molecular Cell Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Jens Wohlmann
- Department Biosciences, University of Oslo, Blindernveien 31, PO Box 1041, 0316 Oslo, Norway
| | - Arwyn T Jones
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Redwood Building, Cardiff, Wales CF103NB, UK
| | - Robert G Parton
- Institute for Molecular Bioscience and Centre for Microscopy and Microanalysis, The University of Queensland, Qld 4072, Australia
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Chowdhury K, Lin S, Lai SL. Comparative Study in Zebrafish and Medaka Unravels the Mechanisms of Tissue Regeneration. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.783818] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Tissue regeneration has been in the spotlight of research for its fascinating nature and potential applications in human diseases. The trait of regenerative capacity occurs diversely across species and tissue contexts, while it seems to decline over evolution. Organisms with variable regenerative capacity are usually distinct in phylogeny, anatomy, and physiology. This phenomenon hinders the feasibility of studying tissue regeneration by directly comparing regenerative with non-regenerative animals, such as zebrafish (Danio rerio) and mice (Mus musculus). Medaka (Oryzias latipes) is a fish model with a complete reference genome and shares a common ancestor with zebrafish approximately 110–200 million years ago (compared to 650 million years with mice). Medaka shares similar features with zebrafish, including size, diet, organ system, gross anatomy, and living environment. However, while zebrafish regenerate almost every organ upon experimental injury, medaka shows uneven regenerative capacity. Their common and distinct biological features make them a unique platform for reciprocal analyses to understand the mechanisms of tissue regeneration. Here we summarize current knowledge about tissue regeneration in these fish models in terms of injured tissues, repairing mechanisms, available materials, and established technologies. We further highlight the concept of inter-species and inter-organ comparisons, which may reveal mechanistic insights and hint at therapeutic strategies for human diseases.
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Shan C, Li M, Liu Z, Xu R, Qiao F, Du ZY, Zhang ML. Pediococcus pentosaceus Enhances Host Resistance Against Pathogen by Increasing IL-1β Production: Understanding Probiotic Effectiveness and Administration Duration. Front Immunol 2021; 12:766401. [PMID: 34899717 PMCID: PMC8662542 DOI: 10.3389/fimmu.2021.766401] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 11/04/2021] [Indexed: 12/13/2022] Open
Abstract
Probiotic administration is a potential strategy against enteric pathogen infection in either clinical treatment or animal nutrition industry, but the administration duration of probiotics varied and the underlying mechanisms remain unclear. A strain (YC) affiliated to Pediococcus pentosaceus, a commonly used probiotic, was isolated from fish gut and the potential role of YC against Aeromonas hydrophila was detected in zebrafish. We found that 3- or 4-week YC administration (YC3W or YC4W) increased the resistance against A. hydrophila while 1- or 2-week treatment (YC1W or YC2W) did not. To determine the possible reason, intestinal microbiota analysis and RNAseq were conducted. The results showed that compared with CON and YC1W, YC4W significantly increased the abundance of short-chain fatty acids (SCFAs) producing bacteria and elevated the gene expression of nlrp3. Higher butyrate content and enhanced expression of IL1β were subsequently found in YC4W. To identify the causal relationship between butyrate and the higher pathogen resistance, different concentrations of sodium butyrate (SB) were supplemented. The results suggested that 10 mmol/kg SB addition mirrored the protective effect of YC4W by increasing the production of IL-1β. Furthermore, the increased IL-1β raised the percentage of intestinal neutrophils, which endued the zebrafish with A. hydrophila resistance. In vivo knockdown of intestinal il1b eliminated the anti-infection effect. Collectively, our data suggested that the molecular mechanism of probiotics determined the administration duration, which is vital for the efficiency of probiotics. Promoting host inflammation by probiotic pretreatment is one potential way for probiotics to provide their protective effects against pathogens.
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Affiliation(s)
- Chengjie Shan
- Laboratory of Aquaculture Nutrition and Environmental Health, School of Life Sciences, East China Normal University, Shanghai, China
| | - Miao Li
- Laboratory of Aquaculture Nutrition and Environmental Health, School of Life Sciences, East China Normal University, Shanghai, China
| | - Zhu Liu
- Laboratory of Aquaculture Nutrition and Environmental Health, School of Life Sciences, East China Normal University, Shanghai, China.,School of Basic Medical Sciences, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Rong Xu
- Laboratory of Aquaculture Nutrition and Environmental Health, School of Life Sciences, East China Normal University, Shanghai, China
| | - Fang Qiao
- Laboratory of Aquaculture Nutrition and Environmental Health, School of Life Sciences, East China Normal University, Shanghai, China
| | - Zhen-Yu Du
- Laboratory of Aquaculture Nutrition and Environmental Health, School of Life Sciences, East China Normal University, Shanghai, China
| | - Mei-Ling Zhang
- Laboratory of Aquaculture Nutrition and Environmental Health, School of Life Sciences, East China Normal University, Shanghai, China
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The Zebrafish Model to Understand Epigenetics in Renal Diseases. Int J Mol Sci 2021; 22:ijms22179152. [PMID: 34502062 PMCID: PMC8431166 DOI: 10.3390/ijms22179152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/22/2021] [Accepted: 08/23/2021] [Indexed: 11/24/2022] Open
Abstract
Epigenetic modifications are able to alter gene expression and include DNA methylation, different histone variants, and post-transcriptional modifications (PTMs), such as acetylation or phosphorylation, and through short/long RNAs, respectively. In this review, we focus on current knowledge concerning epigenetic modifications in gene regulation. We describe different forms of epigenetic modifications and explain how epigenetic changes can be detected. The relevance of epigenetics in renal diseases is highlighted with multiple examples and the use of the zebrafish model to study glomerular diseases in general and epigenetics in renal diseases in particular is discussed. We end with an outlook on how to use epigenetic modifications as a therapeutic target for different diseases. Here, the zebrafish model can be employed as a high-throughput screening tool not only to discover epigenetic alterations contributing to disease, but also to test novel substances that change epigenetic signatures in vivo. Therefore, the zebrafish model harbors the opportunity to find novel pathogenic pathways allowing a pre-selection of potential targets and compounds to be tested for renal diseases.
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