1
|
Fernandez R, Colás-Ruiz NR, Lara-Martín PA, Fernández-Cisnal R, Hampel M. Proteomic analysis in the brain and liver of sea bream (Sparus aurata) exposed to the antibiotics ciprofloxacin, sulfadiazine, and trimethoprim. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 356:124308. [PMID: 38844040 DOI: 10.1016/j.envpol.2024.124308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 05/31/2024] [Accepted: 06/01/2024] [Indexed: 06/10/2024]
Abstract
Antibiotics, frequently detected in aquatic ecosystems, can negatively impact the health of resident organisms. Although the study on the possible effects of antibiotics on these organisms has been increasing, there is still little information available on the molecular effects on exposed non-target organisms. In our study we used a label free proteomic approach and sea bream, Sparus aurata, to evaluate the effects of exposure to environmentally relevant concentrations of the antibiotic compounds ciprofloxacin (CIP), sulfadiazine (SULF) and trimethoprim (TRIM) produced at the protein level. Individuals of sea bream were exposed to single compounds at 5.2 ± 2.1 μg L-1 of CIP, 3.8 ± 2.7 μg L-1 of SULF and 25.7 ± 10.8 μg L-1 of TRIM for 21 days. After exposure, the number of differentially expressed proteins in the liver was 39, 73 and 4 for CIP, SULF and TRIM respectively. In the brain, there was no alteration of proteins after CIP and TRIM treatment, while 9 proteins were impacted after SULF treatment. The differentially expressed proteins were involved in cellular biological, metabolic, developmental, growth and biological regulatory processes. Overall, our study evidences the vulnerability of Sparus aurata, after exposure to environmentally relevant concentrations of the major antibiotics CIP, SULF and TRIM and that their chronic exposure could lead to a stress situation, altering the proteomic profile of key organs such as brain and liver.
Collapse
Affiliation(s)
- Ronield Fernandez
- Microbiology Research Laboratory, University Simon Bolivar, Carrera 59 No. 59-65, Barranquilla, Colombia; Center for Research and Innovation in Biodiversity and Climate Change (ADAPTIA), University Simón Bolívar, Barranquilla 59-65, Colombia.
| | - Nieves R Colás-Ruiz
- Department of Physical Chemistry, Faculty of Marine and Environmental Sciences, University of Cadiz, University Institute for Marine Research (INMAR), 11510, Puerto Real, Spain
| | - Pablo A Lara-Martín
- Department of Physical Chemistry, Faculty of Marine and Environmental Sciences, University of Cadiz, University Institute for Marine Research (INMAR), 11510, Puerto Real, Spain
| | - Ricardo Fernández-Cisnal
- Department of Biochemistry and Molecular Biology, University of Córdoba, Campus Universitario de Rabanales, 14071, Córdoba, Spain
| | - Miriam Hampel
- Department of Physical Chemistry, Faculty of Marine and Environmental Sciences, University of Cadiz, University Institute for Marine Research (INMAR), 11510, Puerto Real, Spain
| |
Collapse
|
2
|
Xu C, Hutchins ED, Eckalbar W, Pendarvis K, Benson DM, Lake DF, McCarthy FM, Kusumi K. Comparative proteomic analysis of tail regeneration in the green anole lizard, Anolis carolinensis. NATURAL SCIENCES (WEINHEIM, GERMANY) 2024; 4:e20210421. [PMID: 38505006 PMCID: PMC10947082 DOI: 10.1002/ntls.20210421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
As amniote vertebrates, lizards are the most closely related organisms to humans capable of appendage regeneration. Lizards can autotomize, or release their tails as a means of predator evasion, and subsequently regenerate a functional replacement. Green anoles (Anolis carolinensis) can regenerate their tails through a process that involves differential expression of hundreds of genes, which has previously been analyzed by transcriptomic and microRNA analysis. To investigate protein expression in regenerating tissue, we performed whole proteomic analysis of regenerating tail tip and base. This is the first proteomic data set available for any anole lizard. We identified a total of 2,646 proteins - 976 proteins only in the regenerating tail base, 796 only in the tail tip, and 874 in both tip and base. For over 90% of these proteins in these tissues, we were able to assign a clear orthology to gene models in either the Ensembl or NCBI databases. For 13 proteins in the tail base, 9 proteins in the tail tip, and 10 proteins in both regions, the gene model in Ensembl and NCBI matched an uncharacterized protein, confirming that these predictions are present in the proteome. Ontology and pathways analysis of proteins expressed in the regenerating tail base identified categories including actin filament-based process, ncRNA metabolism, regulation of phosphatase activity, small GTPase mediated signal transduction, and cellular component organization or biogenesis. Analysis of proteins expressed in the tail tip identified categories including regulation of organelle organization, regulation of protein localization, ubiquitin-dependent protein catabolism, small GTPase mediated signal transduction, morphogenesis of epithelium, and regulation of biological quality. These proteomic findings confirm pathways and gene families activated in tail regeneration in the green anole as well as identify uncharacterized proteins whose role in regrowth remains to be revealed. This study demonstrates the insights that are possible from the integration of proteomic and transcriptomic data in tail regrowth in the green anole, with potentially broader application to studies in other regenerative models.
Collapse
Affiliation(s)
- Cindy Xu
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Elizabeth D. Hutchins
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- Current addresses: Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Walter Eckalbar
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- Current addresses: School of Medicine, University of California, San Francisco, California, USA
| | - Ken Pendarvis
- Department of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, USA
| | - Derek M. Benson
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Douglas F. Lake
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Fiona M. McCarthy
- Department of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, USA
| | - Kenro Kusumi
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| |
Collapse
|
3
|
Bergen DJM, Maurizi A, Formosa MM, McDonald GLK, El-Gazzar A, Hassan N, Brandi ML, Riancho JA, Rivadeneira F, Ntzani E, Duncan EL, Gregson CL, Kiel DP, Zillikens MC, Sangiorgi L, Högler W, Duran I, Mäkitie O, Van Hul W, Hendrickx G. High Bone Mass Disorders: New Insights From Connecting the Clinic and the Bench. J Bone Miner Res 2023; 38:229-247. [PMID: 36161343 PMCID: PMC10092806 DOI: 10.1002/jbmr.4715] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 09/05/2022] [Accepted: 09/22/2022] [Indexed: 02/04/2023]
Abstract
Monogenic high bone mass (HBM) disorders are characterized by an increased amount of bone in general, or at specific sites in the skeleton. Here, we describe 59 HBM disorders with 50 known disease-causing genes from the literature, and we provide an overview of the signaling pathways and mechanisms involved in the pathogenesis of these disorders. Based on this, we classify the known HBM genes into HBM (sub)groups according to uniform Gene Ontology (GO) terminology. This classification system may aid in hypothesis generation, for both wet lab experimental design and clinical genetic screening strategies. We discuss how functional genomics can shape discovery of novel HBM genes and/or mechanisms in the future, through implementation of omics assessments in existing and future model systems. Finally, we address strategies to improve gene identification in unsolved HBM cases and highlight the importance for cross-laboratory collaborations encompassing multidisciplinary efforts to transfer knowledge generated at the bench to the clinic. © 2022 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research (ASBMR).
Collapse
Affiliation(s)
- Dylan J M Bergen
- School of Physiology, Pharmacology, and Neuroscience, Faculty of Life Sciences, University of Bristol, Bristol, UK.,Musculoskeletal Research Unit, Translational Health Sciences, Bristol Medical School, Faculty of Health Sciences, University of Bristol, Bristol, UK
| | - Antonio Maurizi
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Melissa M Formosa
- Department of Applied Biomedical Science, Faculty of Health Sciences, University of Malta, Msida, Malta.,Center for Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | - Georgina L K McDonald
- School of Physiology, Pharmacology, and Neuroscience, Faculty of Life Sciences, University of Bristol, Bristol, UK
| | - Ahmed El-Gazzar
- Department of Paediatrics and Adolescent Medicine, Johannes Kepler University Linz, Linz, Austria
| | - Neelam Hassan
- Musculoskeletal Research Unit, Translational Health Sciences, Bristol Medical School, Faculty of Health Sciences, University of Bristol, Bristol, UK
| | | | - José A Riancho
- Department of Internal Medicine, Hospital U M Valdecilla, University of Cantabria, IDIVAL, Santander, Spain
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Evangelia Ntzani
- Department of Hygiene and Epidemiology, Medical School, University of Ioannina, Ioannina, Greece.,Center for Evidence Synthesis in Health, Policy and Practice, Center for Research Synthesis in Health, School of Public Health, Brown University, Providence, RI, USA.,Institute of Biosciences, University Research Center of loannina, University of Ioannina, Ioannina, Greece
| | - Emma L Duncan
- Department of Twin Research & Genetic Epidemiology, School of Life Course Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK.,Department of Endocrinology, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Celia L Gregson
- Musculoskeletal Research Unit, Translational Health Sciences, Bristol Medical School, Faculty of Health Sciences, University of Bristol, Bristol, UK
| | - Douglas P Kiel
- Marcus Institute for Aging Research, Hebrew SeniorLife and Department of Medicine Beth Israel Deaconess Medical Center and Harvard Medical School, Broad Institute of MIT & Harvard, Cambridge, MA, USA
| | - M Carola Zillikens
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Luca Sangiorgi
- Department of Rare Skeletal Diseases, IRCCS Rizzoli Orthopaedic Institute, Bologna, Italy
| | - Wolfgang Högler
- Department of Paediatrics and Adolescent Medicine, Johannes Kepler University Linz, Linz, Austria.,Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK
| | | | - Outi Mäkitie
- Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Folkhälsan Research Centre, Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Wim Van Hul
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | | |
Collapse
|
4
|
Patel S, Ranadive I, Buch P, Khaire K, Balakrishnan S. De Novo Transcriptome Sequencing and Analysis of Differential Gene Expression among Various Stages of Tail Regeneration in Hemidactylus flaviviridis. J Dev Biol 2022; 10:jdb10020024. [PMID: 35735915 PMCID: PMC9225231 DOI: 10.3390/jdb10020024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 06/08/2022] [Accepted: 06/10/2022] [Indexed: 11/16/2022] Open
Abstract
Across the animal kingdom, lizards are the only amniotes capable of regenerating their lost tail through epimorphosis. Of the many reptiles, the northern house gecko, Hemidactylus flaviviridis, is an excellent model system that is used for understanding the mechanism of epimorphic regeneration. A stage-specific transcriptome profile was generated in the current study following an autotomized tail with the HiSeq2500 platform. The reads obtained from de novo sequencing were filtered and high-quality reads were considered for gene ontology (GO) annotation and pathway analysis. Millions of reads were recorded for each stage upon de novo assembly. Up and down-regulated transcripts were categorized for early blastema (EBL), blastema (BL) and differentiation (DF) stages compared to the normal tail (NT) by differential gene expression analysis. The transcripts from developmentally significant pathways such as FGF, Wnt, Shh and TGF-β/BMP were present during tail regeneration. Additionally, differential expression of transcripts was recorded from biological processes, namely inflammation, cell proliferation, apoptosis and cell migration. Overall, the study reveals the stage-wise transcriptome analysis in conjunction with cellular processes as well as molecular signaling pathways during lizard tail regeneration. The knowledge obtained from the data can be extrapolated to configure regenerative responses in other amniotes, including humans, upon loss of a complex organ.
Collapse
|
5
|
Enayathullah MG, Parekh Y, Banu S, Ram S, Nagaraj R, Kumar BK, Idris MM. Gramicidin S and melittin: potential anti-viral therapeutic peptides to treat SARS-CoV-2 infection. Sci Rep 2022; 12:3446. [PMID: 35236909 PMCID: PMC8891299 DOI: 10.1038/s41598-022-07341-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 02/16/2022] [Indexed: 01/02/2023] Open
Abstract
The COVID19 pandemic has led to multipronged approaches for treatment of the disease. Since de novo discovery of drugs is time consuming, repurposing of molecules is now considered as one of the alternative strategies to treat COVID19. Antibacterial peptides are being recognized as attractive candidates for repurposing to treat viral infections. In this study, we describe the anti-SARS-CoV-2 activity of the well-studied antibacterial peptides gramicidin S and melittin obtained from Bacillus brevis and bee venom respectively. The EC50 values for gramicidin S and melittin were 1.571 µg and 0.656 µg respectively based on in vitro antiviral assay. Significant decrease in the viral load as compared to the untreated group with no/very less cytotoxicity was observed. Both the peptides treated to the SARS-CoV-2 infected Vero cells showed viral clearance from 12 h onwards with a maximal viral clearance after 24 h post infection. Proteomics analysis indicated that more than 250 proteins were differentially regulated in the gramicidin S and melittin treated SARS-CoV-2 infected Vero cells against control SARS-CoV-2 infected Vero cells after 24 and 48 h post infection. The identified proteins were found to be associated in the metabolic and mRNA processing of the Vero cells post-treatment and infection. Both these peptides could be attractive candidates for repurposing to treat SARS-CoV-2 infection.
Collapse
Affiliation(s)
| | - Yash Parekh
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, 500007, India
| | - Sarena Banu
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, 500007, India
| | - Sushma Ram
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, 500007, India
| | - Ramakrishnan Nagaraj
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, 500007, India
| | - Bokara Kiran Kumar
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, 500007, India.
| | - Mohammed M Idris
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, 500007, India.
| |
Collapse
|
6
|
Banu S, Gaur N, Nair S, Ravikrishnan T, Khan S, Mani S, Bharathi S, Mandal K, Kuram NA, Vuppaladadium S, Ravi R, Murthy CLN, Quoseena M, Babu NS, Idris MM. Transcriptomic and proteomic analysis of epimorphic regeneration in zebrafish caudal fin tissue. Genomics 2022; 114:110300. [DOI: 10.1016/j.ygeno.2022.110300] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 01/13/2022] [Accepted: 02/01/2022] [Indexed: 11/26/2022]
|
7
|
Ulhaq ZS, Tse WKF. A Brief Analysis of Proteomic Profile Changes during Zebrafish Regeneration. Biomolecules 2021; 12:biom12010035. [PMID: 35053182 PMCID: PMC8773715 DOI: 10.3390/biom12010035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/21/2021] [Accepted: 12/21/2021] [Indexed: 11/16/2022] Open
Abstract
Unlike mammals, zebrafish are capable to regenerate many of their organs, however, the response of tissue damage varies across tissues. Understanding the molecular mechanism behind the robust regenerative capacity in a model organism may help to identify and develop novel treatment strategies for mammals (including humans). Hence, we systematically analyzed the current literature on the proteome profile collected from different regenerated zebrafish tissues. Our analyses underlining that several proteins and protein families responsible as a component of cytoskeleton and structure, protein synthesis and degradation, cell cycle control, and energy metabolism were frequently identified. Moreover, target proteins responsible for the initiation of the regeneration process, such as inflammation and immune response were less frequently detected. This highlights the limitation of previous proteomic analysis and suggested a more sensitive modern proteomics analysis is needed to unfold the mechanism. This brief report provides a list of target proteins with predicted functions that could be useful for further biological studies.
Collapse
Affiliation(s)
- Zulvikar Syambani Ulhaq
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Maulana Malik Ibrahim State Islamic University of Malang, Batu 65144, Indonesia;
- National Research and Innovation Agency, Central Jakarta 10340, Indonesia
| | - William Ka Fai Tse
- Laboratory of Developmental Disorders and Toxicology, Center for Promotion of International Education and Research, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
- Correspondence:
| |
Collapse
|
8
|
Wandy J, Daly R. GraphOmics: an interactive platform to explore and integrate multi-omics data. BMC Bioinformatics 2021; 22:603. [PMID: 34922446 PMCID: PMC8684259 DOI: 10.1186/s12859-021-04500-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 11/30/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND An increasing number of studies now produce multiple omics measurements that require using sophisticated computational methods for analysis. While each omics data can be examined separately, jointly integrating multiple omics data allows for deeper understanding and insights to be gained from the study. In particular, data integration can be performed horizontally, where biological entities from multiple omics measurements are mapped to common reactions and pathways. However, data integration remains a challenge due to the complexity of the data and the difficulty in interpreting analysis results. RESULTS Here we present GraphOmics, a user-friendly platform to explore and integrate multiple omics datasets and support hypothesis generation. Users can upload transcriptomics, proteomics and metabolomics data to GraphOmics. Relevant entities are connected based on their biochemical relationships, and mapped to reactions and pathways from Reactome. From the Data Browser in GraphOmics, mapped entities and pathways can be ranked, sorted and filtered according to their statistical significance (p values) and fold changes. Context-sensitive panels provide information on the currently selected entities, while interactive heatmaps and clustering functionalities are also available. As a case study, we demonstrated how GraphOmics was used to interactively explore multi-omics data and support hypothesis generation using two complex datasets from existing Zebrafish regeneration and Covid-19 human studies. CONCLUSIONS GraphOmics is fully open-sourced and freely accessible from https://graphomics.glasgowcompbio.org/ . It can be used to integrate multiple omics data horizontally by mapping entities across omics to reactions and pathways. Our demonstration showed that by using interactive explorations from GraphOmics, interesting insights and biological hypotheses could be rapidly revealed.
Collapse
Affiliation(s)
- Joe Wandy
- Glasgow Polyomics, University of Glasgow, Glasgow, G61 1BD, UK
| | - Rónán Daly
- Glasgow Polyomics, University of Glasgow, Glasgow, G61 1BD, UK.
| |
Collapse
|
9
|
Sehring I, Weidinger G. Zebrafish Fin: Complex Molecular Interactions and Cellular Mechanisms Guiding Regeneration. Cold Spring Harb Perspect Biol 2021; 14:cshperspect.a040758. [PMID: 34649924 DOI: 10.1101/cshperspect.a040758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The zebrafish caudal fin has become a popular model to study cellular and molecular mechanisms of regeneration due to its high regenerative capacity, accessibility for experimental manipulations, and relatively simple anatomy. The formation of a regenerative epidermis and blastema are crucial initial events and tightly regulated. Both the regenerative epidermis and the blastema are highly organized structures containing distinct domains, and several signaling pathways regulate the formation and interaction of these domains. Bone is the major tissue regenerated from the progenitor cells of the blastema. Several cellular mechanisms can provide source cells for blastemal (pre-)osteoblasts, including dedifferentiation of differentiated osteoblasts and de novo formation from other cell types, providing intriguing examples of cellular plasticity. In recent years, omics analyses and single-cell approaches have elucidated genetic and epigenetic regulation, increasing our knowledge of the surprisingly complex coordination of various mechanisms to achieve successful restoration of a seemingly simple structure.
Collapse
Affiliation(s)
- Ivonne Sehring
- Institute of Biochemistry and Molecular Biology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Gilbert Weidinger
- Institute of Biochemistry and Molecular Biology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| |
Collapse
|
10
|
Li J, Sultan Y, Sun Y, Zhang S, Liu Y, Li X. Expression analysis of Hsp90α and cytokines in zebrafish caudal fin regeneration. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 116:103922. [PMID: 33186559 DOI: 10.1016/j.dci.2020.103922] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 11/06/2020] [Accepted: 11/06/2020] [Indexed: 06/11/2023]
Abstract
Zebrafish (Danio rerio) is an ideal model organism for exploring the ability and mechanism of tissue regeneration in the vertebrate. However, the specific cellular and molecular mechanism of caudal fin regeneration in zebrafish remains largely unclear. Therefore, we first confirmed the crucial period of fin regeneration in adult zebrafish by morphological and histological analysis. Then we performed RNA-Seq analysis of the caudal fin regeneration at three key stages, which provided some clues for exploring the mechanism of caudal fin regeneration. Moreover, we also determined the expressions of inflammatory cytokines IL-1β, IL-6, IL-8, IL-10, TGF-β, and the immune-related pathway JAK2α and STAT1b in the caudal fin of zebrafish following fin amputation by quantitative real time PCR (qPCR). Particularly, Hsp90α expression at mRNA and protein level determined by qPCR and Western blotting, respectively, and whole-mount in situ hybridization of Hsp90α were also performed in this study. The results showed that inflammatory cytokines were mainly expressed in the early period of caudal fin regeneration (1-3 days post amputation, dpa), indicating that fish immune system was involved in the fin regeneration. Furthermore, the high expression of Hsp90α in the vicinity of blastema and blood vessels of the regenerating fin suggests that Hsp90α may play a role in the initiation and promotion of caudal fin regeneration. Overall, our results provide a framework for further understanding the cellular and molecular mechanism in caudal fin regeneration.
Collapse
Affiliation(s)
- Jing Li
- College of Life Science, Henan Normal University, Xinxiang, Henan, 453007, China
| | - Yousef Sultan
- College of Life Science, Henan Normal University, Xinxiang, Henan, 453007, China; Department of Food Toxicology and Contaminants, National Research Centre, Dokki, Cairo, 12622, Egypt
| | - Yaoyi Sun
- College of Life Science, Henan Normal University, Xinxiang, Henan, 453007, China
| | - Shuqiang Zhang
- College of Life Science, Henan Normal University, Xinxiang, Henan, 453007, China
| | - Yang Liu
- College of Life Science, Henan Normal University, Xinxiang, Henan, 453007, China
| | - Xiaoyu Li
- College of Life Science, Henan Normal University, Xinxiang, Henan, 453007, China.
| |
Collapse
|
11
|
Transcriptomic and proteomic analysis of Hemidactylus frenatus during initial stages of tail regeneration. Sci Rep 2021; 11:3675. [PMID: 33574494 PMCID: PMC7878758 DOI: 10.1038/s41598-021-83283-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 01/28/2021] [Indexed: 11/08/2022] Open
Abstract
Epimorphic regeneration of appendages is a complex and complete phenomenon found in selected animals. Hemidactylus frenatus, house gecko has the remarkable ability to regenerate the tail tissue upon autotomy involving epimorphic regeneration mechanism. This study has identified and evaluated the molecular changes at gene and protein level during the initial stages, i.e., during the wound healing and repair mechanism initiation stage of tail regeneration. Based on next generation transcriptomics and De novo analysis the transcriptome library of the gecko tail tissue was generated. A total of 254 genes and 128 proteins were found to be associated with the regeneration of gecko tail tissue upon amputation at 1, 2 and 5-day post amputation (dpa) against control, 0-dpa through differential transcriptomic and proteomic analysis. To authenticate the expression analysis, 50 genes were further validated involving RTPCR. 327 genes/proteins identified and mapped from the study showed association for Protein kinase A signaling, Telomerase BAG2 signaling, paxillin signaling, VEGF signaling network pathways based on network pathway analysis. This study empanelled list of transcriptome, proteome and the list of genes/proteins associated with the tail regeneration.
Collapse
|
12
|
Quoseena M, Vuppaladadium S, Hussain S, Banu S, Bharathi S, Idris MM. Functional role of annexins in zebrafish caudal fin regeneration – A gene knockdown approach in regenerating tissue. Biochimie 2020; 175:125-131. [DOI: 10.1016/j.biochi.2020.05.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 05/18/2020] [Accepted: 05/26/2020] [Indexed: 12/26/2022]
|
13
|
Marques IJ, Lupi E, Mercader N. Model systems for regeneration: zebrafish. Development 2019; 146:146/18/dev167692. [DOI: 10.1242/dev.167692] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 08/19/2019] [Indexed: 12/13/2022]
Abstract
ABSTRACT
Tissue damage can resolve completely through healing and regeneration, or can produce permanent scarring and loss of function. The response to tissue damage varies across tissues and between species. Determining the natural mechanisms behind regeneration in model organisms that regenerate well can help us develop strategies for tissue recovery in species with poor regenerative capacity (such as humans). The zebrafish (Danio rerio) is one of the most accessible vertebrate models to study regeneration. In this Primer, we highlight the tools available to study regeneration in the zebrafish, provide an overview of the mechanisms underlying regeneration in this system and discuss future perspectives for the field.
Collapse
Affiliation(s)
- Ines J. Marques
- Institute of Anatomy, University of Bern, Bern 3012, Switzerland
| | - Eleonora Lupi
- Institute of Anatomy, University of Bern, Bern 3012, Switzerland
- Acquifer, Ditabis, Digital Biomedical Imaging Systems, Pforzheim, Germany
| | - Nadia Mercader
- Institute of Anatomy, University of Bern, Bern 3012, Switzerland
- Centro Nacional de Investigaciones Cardiovasculares CNIC, Madrid 2029, Spain
| |
Collapse
|
14
|
Paredes LC, Olsen Saraiva Camara N, Braga TT. Understanding the Metabolic Profile of Macrophages During the Regenerative Process in Zebrafish. Front Physiol 2019; 10:617. [PMID: 31178754 PMCID: PMC6543010 DOI: 10.3389/fphys.2019.00617] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 05/01/2019] [Indexed: 12/14/2022] Open
Abstract
In contrast to mammals, lower vertebrates, including zebrafish (Danio rerio), have the ability to regenerate damaged or lost tissues, such as the caudal fin, which makes them an ideal model for tissue and organ regeneration studies. Since several diseases involve the process of transition between fibrosis and tissue regeneration, it is necessary to attain a better understanding of these processes. It is known that the cells of the immune system, especially macrophages, play essential roles in regeneration by participating in the removal of cellular debris, release of pro- and anti-inflammatory factors, remodeling of components of the extracellular matrix and alteration of oxidative patterns during proliferation and angiogenesis. Immune cells undergo phenotypical and functional alterations throughout the healing process due to growth factors and cytokines that are produced in the tissue microenvironment. However, some aspects of the molecular mechanisms through which macrophages orchestrate the formation and regeneration of the blastema remain unclear. In the present review, we outline how macrophages orchestrate the regenerative process in zebrafish and give special attention to the redox balance in the context of tail regeneration.
Collapse
Affiliation(s)
| | - Niels Olsen Saraiva Camara
- Department of Immunology, Institute of Biomedical Sciences IV, University of São Paulo, São Paulo, Brazil.,Nephrology Division, Federal University of São Paulo, São Paulo, Brazil.,Renal Pathophysiology Laboratory, Faculty of Medicine, University of São Paulo, São Paulo, Brazil
| | | |
Collapse
|
15
|
Yu Y, Tang J, Su J, Cui J, Xie X, Chen F. Integrative Analysis of MicroRNAome, Transcriptome, and Proteome during the Limb Regeneration of Cynops orientalis. J Proteome Res 2019; 18:1088-1098. [DOI: 10.1021/acs.jproteome.8b00778] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Yuan Yu
- Lab of Tissue Engineering, College of Life Sciences, Northwest University, Xi’an 710069, PR China
- Provincial Key Laboratory of Biotechnology of Shaanxi, Xi’an 710069, PR China
- Key Laboratory of Resource Biology and Biotechnology in Western China Ministry of Education, Xi’an 710069, PR China
| | - Jie Tang
- Lab of Tissue Engineering, College of Life Sciences, Northwest University, Xi’an 710069, PR China
- Shaanxi Institute of Zoology, 88 Xingqing Road, Xi’an 710032, PR China
| | - Jiaojiao Su
- Lab of Tissue Engineering, College of Life Sciences, Northwest University, Xi’an 710069, PR China
| | - Jihong Cui
- Lab of Tissue Engineering, College of Life Sciences, Northwest University, Xi’an 710069, PR China
- Provincial Key Laboratory of Biotechnology of Shaanxi, Xi’an 710069, PR China
- Key Laboratory of Resource Biology and Biotechnology in Western China Ministry of Education, Xi’an 710069, PR China
| | - Xin Xie
- Lab of Tissue Engineering, College of Life Sciences, Northwest University, Xi’an 710069, PR China
- Provincial Key Laboratory of Biotechnology of Shaanxi, Xi’an 710069, PR China
- Key Laboratory of Resource Biology and Biotechnology in Western China Ministry of Education, Xi’an 710069, PR China
| | - Fulin Chen
- Lab of Tissue Engineering, College of Life Sciences, Northwest University, Xi’an 710069, PR China
- Provincial Key Laboratory of Biotechnology of Shaanxi, Xi’an 710069, PR China
- Key Laboratory of Resource Biology and Biotechnology in Western China Ministry of Education, Xi’an 710069, PR China
| |
Collapse
|
16
|
Schmidt JR, Geurtzen K, von Bergen M, Schubert K, Knopf F. Glucocorticoid Treatment Leads to Aberrant Ion and Macromolecular Transport in Regenerating Zebrafish Fins. Front Endocrinol (Lausanne) 2019; 10:674. [PMID: 31636606 PMCID: PMC6787175 DOI: 10.3389/fendo.2019.00674] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 09/17/2019] [Indexed: 12/13/2022] Open
Abstract
Long-term glucocorticoid administration in patients undergoing immunosuppressive and anti-inflammatory treatment is accompanied by impaired bone formation and increased fracture risk. Furthermore, glucocorticoid treatment can lead to impaired wound healing and altered cell metabolism. Recently, we showed that exposure of zebrafish to the glucocorticoid prednisolone during fin regeneration impacts negatively on the length, bone formation, and osteoblast function of the regenerate. The underlying cellular and molecular mechanisms of impairment, however, remain incompletely understood. In order to further elucidate the anti-regenerative effects of continued glucocorticoid exposure on fin tissues, we performed proteome profiling of fin regenerates undergoing prednisolone treatment, in addition to profiling of homeostatic fin tissue and fins undergoing undisturbed regeneration. By using LC-MS (liquid chromatography-mass spectrometry) we identified more than 6,000 proteins across all tissue samples. In agreement with previous reports, fin amputation induces changes in chromatin structure and extracellular matrix (ECM) composition within the tissue. Notably, prednisolone treatment leads to impaired expression of selected ECM components in the fin regenerate. Moreover, the function of ion transporting ATPases and other proteins involved in macromolecule and vesicular transport mechanisms of the cell appears to be altered by prednisolone treatment. In particular, acidification of membrane-enclosed organelles such as lysosomes is inhibited. Taken together, our data indicate that continued synthetic glucocorticoid exposure in zebrafish deteriorates cellular trafficking processes in the regenerating fin, which interferes with appropriate tissue restoration upon injury.
Collapse
Affiliation(s)
- Johannes R. Schmidt
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research GmbH—UFZ, Leipzig, Germany
| | - Karina Geurtzen
- CRTD—Center for Regenerative Therapies Dresden, Technische Universität (TU) Dresden, Dresden, Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research GmbH—UFZ, Leipzig, Germany
- Institute of Biochemistry, Faculty of Life Sciences, University of Leipzig, Leipzig, Germany
| | - Kristin Schubert
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research GmbH—UFZ, Leipzig, Germany
- *Correspondence: Kristin Schubert
| | - Franziska Knopf
- CRTD—Center for Regenerative Therapies Dresden, Technische Universität (TU) Dresden, Dresden, Germany
- Center for Healthy Aging, Technische Universität (TU) Dresden, Dresden, Germany
- Franziska Knopf
| |
Collapse
|
17
|
Hasson SS, H Al-Shubi AS, Al-Busaidi JZ, Al-Balushi MS, Hakkim FL, Rashan L, Aleemallah GM, Al-Jabri AA. Potential of Aucklandia Lappa Decne Ethanolic Extract to Trigger Apoptosis of Human T47D and Hela Cells. Asian Pac J Cancer Prev 2018; 19:1917-1925. [PMID: 30051673 PMCID: PMC6165671 DOI: 10.22034/apjcp.2018.19.7.1917] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Breast and cervical cancers are global health concerns and major cause of deaths among women. Current treatments such as chemotherapy are associated with several drawbacks that limit their effectiveness. Several anticancer remedies have been found with natural products in the past and the search continues for more examples. Cytotoxic natural compounds may have considerable benefits for cancer therapy either in potentiating the impact of chemotherapy or curtailment of harmful effects. Therefore, discovery and identification of new drugs for breast and cervical cancer treatment are of high priority. The present study addressed the potential role of the ALD (Aucklandia lappa Decne) in suppressing proliferation of T-47D, HeLa and HEp-2 cells in comparison with the non-cancer HCC1937 BL cell line. Treatment with an ALD extract of T-47D, HeLa, and HEp-2 cells resulted in reduction in cell viability in MMT assays. Furthermore, lyophilized ALD principally suppressed cancer cell line growth and proliferation through induction of either intrinsic or extrinsic apoptotic pathways as demonstrated by significantly suppressed release of LDH, and NO production in a dose-dependent manner, and activation of death receptors in T-47D and HeLa cells but not the HEp-2 cell line. Interestingly, lyophilized ALD significantly (p<0.005) repressed the growth of HEp-2 and T-47D cells after treatment for 48hrs while 24hrs treatment significantly suppressed T-47D and HeLa cells. We report for the first time that lyophilized ALD selectively influences apoptosis through alternative apoptotic pathways in both breast and cervical human cancer cells.
Collapse
Affiliation(s)
- S S Hasson
- Department of Microbiology and Immunology, College of Medicine and Health Sciences, Sultan Qaboos University, Oman
| | | | | | | | | | | | | | | |
Collapse
|
18
|
iTRAQ-based proteomic analysis identifies proteins involved in limb regeneration of swimming crab Portunus trituberculatus. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2018; 26:10-19. [PMID: 29482113 DOI: 10.1016/j.cbd.2018.02.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 02/06/2018] [Accepted: 02/11/2018] [Indexed: 11/22/2022]
Abstract
The swimming crab (Portunus trituberculatus) has a striking capacity for limb regeneration, which has drawn the interest of many researchers. In this study, isobaric tag for relative and absolute quantitation (iTRAQ) approach was utilised to investigate protein abundance changes during limb regeneration in this species. A total of 1830 proteins were identified, of which 181 were significantly differentially expressed, with 94 upregulated and 87 downregulated. Our results highlight the complexity of limb regeneration and its regulation through cooperation of various biological processes including cytoskeletal changes, extracellular matrix (ECM) remodelling and ECM-receptor interactions, protein synthesis, signal recognition and transduction, energy production and conversion, and substance transport and metabolism. Additionally, real-time PCR confirmed that mRNA levels of differentially expressed genes were correlated with protein levels. Our results provide a basis for studying the regulatory mechanisms associated with crab limb regeneration.
Collapse
|
19
|
Ma D, Tu C, Sheng Q, Yang Y, Kan Z, Guo Y, Shyr Y, Scott IC, Lou X. Dynamics of Zebrafish Heart Regeneration Using an HPLC-ESI-MS/MS Approach. J Proteome Res 2018; 17:1300-1308. [PMID: 29369637 DOI: 10.1021/acs.jproteome.7b00915] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Failure to properly repair damaged due to myocardial infarction is a major cause of heart failure. In contrast with adult mammals, zebrafish hearts show remarkable regenerative capabilities after substantial damage. To characterize protein dynamics during heart regeneration, we employed an HPLC-ESI-MS/MS (mass spectrometry) approach. Myocardium tissues were taken from sham-operated fish and ventricle-resected sample at three different time points (2, 7, and 14 days); dynamics of protein expression were analyzed by an ion-current-based quantitative platform. More than 2000 protein groups were quantified in all 16 experiments. Two hundred and nine heart-regeneration-related protein groups were quantified and clustered into six time-course patterns. Functional analysis indicated that multiple molecular function and metabolic pathways were involved in heart regeneration. Interestingly, Ingenuity Pathway Analysis revealed that P53 signaling was inhibited during the heart regeneration, which was further verified by real-time quantitative polymerase chain reaction (Q-PCR). In summary, we applied systematic proteomics analysis on regenerating zebrafish heart, uncovered the dynamics of regenerative genes expression and regulatory pathways, and provided invaluable insight into design regenerative-based strategies in human hearts.
Collapse
Affiliation(s)
- Danjun Ma
- College of Mechanical Engineering, Dongguan University of Technology , 1 Daxue Road, Dongguan, Guangdong 523808, China
| | - Chengjian Tu
- Department of Pharmaceutical Sciences, State University of New York at Buffalo , 285 Kapoor Hall, Buffalo, New York 14260, United States
| | - Quanhu Sheng
- Center for Quantitative Sciences, Department of Biostatistics, Vanderbilt University School of Medicine , 2220 Pierce Avenue, Nashville, Tennessee 37232, United States
| | - Yuxi Yang
- Model Animal Research Center, Nanjing University , Nanjing 210093, China
| | - Zhisheng Kan
- Department of Neurosurgery, Beijing Anzhen Hospital, Capital Medical University , Beijing 100029, China
| | - Yan Guo
- Department of Internal Medicine, University of New Mexico, Comprehensive Cancer Center , Albuquerque, New Mexico 87131, United States
| | - Yu Shyr
- Center for Quantitative Sciences, Department of Biostatistics, Vanderbilt University School of Medicine , 2220 Pierce Avenue, Nashville, Tennessee 37232, United States
| | - Ian C Scott
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children , Toronto, Ontario M5G 1X8, Canada.,Department of Molecular Genetics, University of Toronto , Toronto, Ontario M5S 1A8, Canada
| | - Xin Lou
- Model Animal Research Center, Nanjing University , Nanjing 210093, China
| |
Collapse
|
20
|
Sarasamma S, Varikkodan MM, Liang ST, Lin YC, Wang WP, Hsiao CD. Zebrafish: A Premier Vertebrate Model for Biomedical Research in Indian Scenario. Zebrafish 2017; 14:589-605. [PMID: 29023224 DOI: 10.1089/zeb.2017.1447] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The zebrafish (Danio rerio) is a versatile model organism that has been used in biomedical research for several decades to study a wide range of biological phenomena. There are many technical advantages of using zebrafish over other vertebrate models. They are readily available, hardy, easy, and inexpensive to maintain in the laboratory, have a short life cycle, and have excellent fecundity. Due to its optical clarity and reproducible capabilities, it has become one of the predominant models of human genetic diseases. Zebrafish research has made rapid strides in the United States and Europe, but in India the field is at an early stage and many researchers still remain unaware of the full research potential of this tiny fish. The zebrafish model system was introduced into India in the early 2000s. Up to now, more than 200 scientific referred articles have been published by Indian researchers. This review gives an overview of the current state of knowledge for zebrafish research in India, with the aim of promoting wider utilization of zebrafish for high level biological studies.
Collapse
Affiliation(s)
- Sreeja Sarasamma
- 1 Department of Chemistry, Chung Yuan Christian University , Chung-Li, Taiwan .,2 Department of Bioscience Technology, Chung Yuan Christian University , Chung-Li, Taiwan .,3 Department of Chemical Biology, Rajiv Gandhi Centre for Biotechnology , Thiruvananthapuram, Kerala, India
| | - Muhammed Muhsin Varikkodan
- 1 Department of Chemistry, Chung Yuan Christian University , Chung-Li, Taiwan .,2 Department of Bioscience Technology, Chung Yuan Christian University , Chung-Li, Taiwan .,4 Department of Biotechnology and Genetic Engineering, Bharathidasan University , Tiruchirapalli, India
| | - Sung-Tzu Liang
- 1 Department of Chemistry, Chung Yuan Christian University , Chung-Li, Taiwan
| | - Yen-Chang Lin
- 5 Graduate Institute of Biotechnology, Chinese Culture University , Taipei, Taiwan
| | - Wen-Pin Wang
- 6 Institute of Medical Sciences, Tzu-Chi University , Hualien, Taiwan .,7 Department of Molecular Biology and Human Genetics, Tzu-Chi University , Hualien, Taiwan
| | - Chung-Der Hsiao
- 1 Department of Chemistry, Chung Yuan Christian University , Chung-Li, Taiwan .,8 Center for Biomedical Technology, Chung Yuan Christian University , Chung-Li, Taiwan .,9 Center for Nanotechnology, Chung Yuan Christian University , Chung-Li, Taiwan
| |
Collapse
|
21
|
Sun L, Xu D, Xu Q, Sun J, Xing L, Zhang L, Yang H. iTRAQ reveals proteomic changes during intestine regeneration in the sea cucumber Apostichopus japonicus. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2017; 22:39-49. [PMID: 28189057 DOI: 10.1016/j.cbd.2017.02.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 01/25/2017] [Accepted: 02/02/2017] [Indexed: 12/14/2022]
Abstract
Sea cucumbers have a striking capacity to regenerate most of their viscera after evisceration, which has drawn the interest of many researchers. In this study, the isobaric tag for relative and absolute quantitation (iTRAQ) was utilized to investigate protein abundance changes during intestine regeneration in sea cucumbers. A total of 4073 proteins were identified, and 2321 proteins exhibited significantly differential expressions, with 1100 upregulated and 1221 downregulated proteins. Our results suggest that intestine regeneration constitutes a complex life activity regulated by the cooperation of various biological processes, including cytoskeletal changes, extracellular matrix (ECM) remodeling and ECM-receptor interactions, protein synthesis, signal recognition and transduction, energy production and conversion, and substance transport and metabolism. Additionally, real-time PCR showed mRNA expression of differentially expressed genes correlated positively with their protein levels. Our results provided a basis for studying the regulatory mechanisms associated with sea cucumber regeneration.
Collapse
Affiliation(s)
- Lina Sun
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Dongxue Xu
- Marine Science and Engineering College, Qingdao Agricultural University, Qingdao, China
| | - Qinzeng Xu
- Key Laboratory of Marine Ecology and Environmental Science and Engineering, First Institute of Oceanography, State Oceanic Administration, Qingdao, China
| | - Jingchun Sun
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Lili Xing
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China
| | - Libin Zhang
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
| | - Hongsheng Yang
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| |
Collapse
|
22
|
Sarath Babu N, Krishnan S, Brahmendra Swamy CV, Venkata Subbaiah GP, Gurava Reddy AV, Idris MM. Quantitative proteomic analysis of normal and degenerated human intervertebral disc. Spine J 2016; 16:989-1000. [PMID: 27125197 DOI: 10.1016/j.spinee.2016.03.051] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 03/04/2016] [Accepted: 03/31/2016] [Indexed: 02/03/2023]
Abstract
BACKGROUND CONTEXT Degenerative disc disease (DDD) is the most common disease of aging in humans. DDD is characterized by the gradual damage of the intervertebral discs. The disease is characterized by progressive dehydration of nucleus pulposus and disruption of annulus fibrosus of intervertebral disc. PURPOSE Even though it is highly prevalent, there is no effective therapy to regenerate the degenerated disc, or decrease or halt the disease progression. Therefore, novel monitoring and diagnostic tests are essential to develop an alternative therapeutic strategies which can prevent further progression of disc degeneration. STUDY DESIGN The study was designed to understand the proteome map of annulus fibrosus and nucleus pulposus tissues of intervertebral disc and its differential expression in patients with DDD. METHODS The proteome map of the annulus fibrosus and nucleus pulposus tissues of intervertebral disc was cataloged involving one-dimensional gel electrophoresis-Fourier transform mass spectrometry/ion trap tandem mass spectrometry (FTMS/ITMSMS) analysis. The altered proteome patterns of annulus fibrosus and nucleus pulposus tissues for DDD were identified using Isobaric tag for relative and absolute quantification (iTRAQ)-based quantitative proteomics coupled with FTMS/ITMSMS and network pathway analysis. RESULTS The study identified a total of 759 and 692 proteins from the annulus fibrosus and the nucleus pulposus tissues of the disc based on FTMS/ITMSMS analysis, which includes 118 proteins commonly identified between the two tissues. Vibrant changes were observed between the normal and the degenerating annulus fibrosus and nucleus pulposus tissues. A total of 73 and 54 proteins were identified as differentially regulated in the annulus and the nucleus tissues, respectively, between the normal and the degenerated tissues independently. Network pathway analysis mapped the differentially expressed proteins to cell adhesion, cell migration, and interleukin13 signaling pathways. CONCLUSIONS Altogether, the current study provides a novel vision in the biomechanism of human disc degeneration and a certain number of proteins with the potential biomarker value for the preliminary diagnosis and scenario of DDD.
Collapse
Affiliation(s)
| | | | | | - Goli P Venkata Subbaiah
- Sunshine Hospitals, SMART (Sunshine Medical Academy For Research and Training), Penderghast Rd, Secunderabad, 500003, India
| | | | | |
Collapse
|
23
|
Saxena S, Purushothaman S, Meghah V, Bhatti B, Poruri A, Meena Lakshmi MG, Sarath Babu N, Narasimha Murthy CL, Mandal KK, Kumar A, Idris MM. Role of annexin gene and its regulation during zebrafish caudal fin regeneration. Wound Repair Regen 2016; 24:551-9. [DOI: 10.1111/wrr.12429] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 03/10/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Sandeep Saxena
- CSIR-Centre for Cellular and Molecular Biology (CCMB); Hyderabad India
| | | | | | - Bhawna Bhatti
- CSIR-Centre for Cellular and Molecular Biology (CCMB); Hyderabad India
| | - Akhila Poruri
- CSIR-Centre for Cellular and Molecular Biology (CCMB); Hyderabad India
| | | | | | | | - Komal K. Mandal
- CSIR-Centre for Cellular and Molecular Biology (CCMB); Hyderabad India
| | - Arvind Kumar
- CSIR-Centre for Cellular and Molecular Biology (CCMB); Hyderabad India
| | - Mohammed M. Idris
- CSIR-Centre for Cellular and Molecular Biology (CCMB); Hyderabad India
| |
Collapse
|
24
|
Langdon YG, Fuentes R, Zhang H, Abrams EW, Marlow FL, Mullins MC. Split top: a maternal cathepsin B that regulates dorsoventral patterning and morphogenesis. Development 2016; 143:1016-28. [PMID: 26893345 PMCID: PMC4813285 DOI: 10.1242/dev.128900] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 01/29/2016] [Indexed: 12/28/2022]
Abstract
The vertebrate embryonic dorsoventral axis is established and patterned by Wnt and bone morphogenetic protein (BMP) signaling pathways, respectively. Whereas Wnt signaling establishes the dorsal side of the embryo and induces the dorsal organizer, a BMP signaling gradient patterns tissues along the dorsoventral axis. Early Wnt signaling is provided maternally, whereas BMP ligand expression in the zebrafish is zygotic, but regulated by maternal factors. Concomitant with BMP activity patterning dorsoventral axial tissues, the embryo also undergoes dramatic morphogenetic processes, including the cell movements of gastrulation, epiboly and dorsal convergence. Although the zygotic regulation of these cell migration processes is increasingly understood, far less is known of the maternal regulators of these processes. Similarly, the maternal regulation of dorsoventral patterning, and in particular the maternal control of ventral tissue specification, is poorly understood. We identified split top, a recessive maternal-effect zebrafish mutant that disrupts embryonic patterning upstream of endogenous BMP signaling. Embryos from split top mutant females exhibit a dorsalized embryonic axis, which can be rescued by BMP misexpression or by derepressing endogenous BMP signaling. In addition to dorsoventral patterning defects, split top mutants display morphogenesis defects that are both BMP dependent and independent. These morphogenesis defects include incomplete dorsal convergence, delayed epiboly progression and an early lysis phenotype during gastrula stages. The latter two morphogenesis defects are associated with disruption of the actin and microtubule cytoskeleton within the yolk cell and defects in the outer enveloping cell layer, which are both known mediators of epiboly movements. Through chromosomal mapping and RNA sequencing analysis, we identified the lysosomal endopeptidase cathepsin Ba (ctsba) as the gene deficient in split top embryos. Our results identify a novel role for Ctsba in morphogenesis and expand our understanding of the maternal regulation of dorsoventral patterning.
Collapse
Affiliation(s)
- Yvette G Langdon
- University of Pennsylvania Perelman School of Medicine, Department of Cell and Developmental Biology, 421 Curie Blvd., Philadelphia, PA 19104, USA Millsaps College, Department of Biology, Jackson, MS 39210, USA
| | - Ricardo Fuentes
- University of Pennsylvania Perelman School of Medicine, Department of Cell and Developmental Biology, 421 Curie Blvd., Philadelphia, PA 19104, USA
| | - Hong Zhang
- University of Pennsylvania Perelman School of Medicine, Department of Cell and Developmental Biology, 421 Curie Blvd., Philadelphia, PA 19104, USA
| | - Elliott W Abrams
- University of Pennsylvania Perelman School of Medicine, Department of Cell and Developmental Biology, 421 Curie Blvd., Philadelphia, PA 19104, USA
| | - Florence L Marlow
- University of Pennsylvania Perelman School of Medicine, Department of Cell and Developmental Biology, 421 Curie Blvd., Philadelphia, PA 19104, USA
| | - Mary C Mullins
- University of Pennsylvania Perelman School of Medicine, Department of Cell and Developmental Biology, 421 Curie Blvd., Philadelphia, PA 19104, USA
| |
Collapse
|
25
|
Nolte H, Hölper S, Housley MP, Islam S, Piller T, Konzer A, Stainier DYR, Braun T, Krüger M. Dynamics of zebrafish fin regeneration using a pulsed SILAC approach. Proteomics 2015; 15:739-51. [PMID: 25504979 DOI: 10.1002/pmic.201400316] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 12/08/2014] [Accepted: 12/10/2014] [Indexed: 01/03/2023]
Abstract
The zebrafish owns remarkable regenerative capacities allowing regeneration of several tissues, including the heart, liver, and brain. To identify protein dynamics during fin regeneration we used a pulsed SILAC approach that enabled us to detect the incorporation of (13) C6 -lysine (Lys6) into newly synthesized proteins. Samples were taken at four different time points from noninjured and regrowing fins and incorporation rates were monitored using a combination of single-shot 4-h gradients and high-resolution tandem MS. We identified more than 5000 labeled proteins during the first 3 weeks of fin regeneration and were able to monitor proteins that are responsible for initializing and restoring the shape of these appendages. The comparison of Lys6 incorporation rates between noninjured and regrowing fins enabled us to identify proteins that are directly involved in regeneration. For example, we observed increased incorporation rates of two actinodin family members at the actinotrichia, which is a hairlike fiber structure at the tip of regrowing fins. Moreover, we used quantitative real-time RNA measurements of several candidate genes, including osteoglycin, si:ch211-288h17.3, and prostaglandin reductase 1 to correlate the mRNA expression to Lys6 incorporation data. This novel pulsed SILAC methodology in fish can be used as a versatile tool to monitor newly synthesized proteins and will help to characterize protein dynamics during regenerative processes in zebrafish beyond fin regeneration.
Collapse
Affiliation(s)
- Hendrik Nolte
- Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Xia L, Zheng L, Zhou JL. Transcriptional and morphological effects of tamoxifen on the early development of zebrafish (Danio rerio). J Appl Toxicol 2015; 36:853-62. [PMID: 26584595 DOI: 10.1002/jat.3257] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Revised: 09/26/2015] [Accepted: 09/29/2015] [Indexed: 11/10/2022]
Abstract
Tamoxifen is a widely used anticancer drug with both an estrogen agonist and antagonist effect. This study focused on its endocrine disrupting effect, and overall environmental significance. Zebrafish embryos were exposed to different concentrations (0.5, 5, 50 and 500 µg l(-1) ) of tamoxifen for 96 h. The results showed a complex effect of tamoxifen on zebrafish embryo development. For the 500 µg l(-1) exposure group, the heart rate was decreased by 20% and mild defects in caudal fin and skin were observed. Expressions of a series of genes related to endocrine and morphological changes were subsequently tested through quantitative real-time polymerase chain reaction. Bisphenol A as a known estrogen was also tested as an endocrine-related comparison. Among the expression of endocrine-related genes, esr1, ar, cyp19a1b, hsd3b1 and ugt1a1 were all increased by tamoxifen exposure, similar to bisphenol A. The cyp19a1b is a key gene that controls estrogen synthesis. Exposure to 0.5, 5, 50 and 500 µg l(-1) of tamoxifen caused upregulation of cyp19a1b expression to 152%, 568%, 953% and 2024% compared to controls, higher than the effects from the same concentrations of bisphenol A treatment, yet vtg1 was suppressed by 24% from exposure to 500 µg l(-1) tamoxifen. The expression of metabolic-related genes such as cyp1a, cyp1c2, cyp3a65, gpx1a, gstp1, gsr and genes related to observed morphological changes such as krt17 were also found to be upregulated by high concentrations of tamoxifen. These findings indicated the potential environmental effect of tamoxifen on teleost early development. Copyright © 2015 John Wiley & Sons, Ltd.
Collapse
Affiliation(s)
- Liang Xia
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 3663 Zhongshan North Road, Shanghai, 200062, China
| | - Liang Zheng
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 3663 Zhongshan North Road, Shanghai, 200062, China
| | - Jun Liang Zhou
- State Key Laboratory of Estuarine and Coastal Research, East China Normal University, 3663 Zhongshan North Road, Shanghai, 200062, China
| |
Collapse
|
27
|
Sapan CV, Lundblad RL. Review of methods for determination of total protein and peptide concentration in biological samples. Proteomics Clin Appl 2015; 9:268-76. [DOI: 10.1002/prca.201400088] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 01/08/2015] [Accepted: 01/27/2015] [Indexed: 11/06/2022]
|
28
|
Purushothaman S, Saxena S, Meghah V, Meena Lakshmi MG, Singh SK, Brahmendra Swamy CV, Idris MM. Proteomic and gene expression analysis of zebrafish brain undergoing continuous light/dark stress. J Sleep Res 2015; 24:458-65. [DOI: 10.1111/jsr.12287] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 01/27/2015] [Indexed: 11/28/2022]
Affiliation(s)
| | - Sandeep Saxena
- CSIR - Centre for Cellular and Molecular Biology (CCMB); Hyderabad India
| | - Vupalapathy Meghah
- CSIR - Centre for Cellular and Molecular Biology (CCMB); Hyderabad India
| | | | - Sachin K. Singh
- CSIR - Centre for Cellular and Molecular Biology (CCMB); Hyderabad India
| | | | - Mohammed M. Idris
- CSIR - Centre for Cellular and Molecular Biology (CCMB); Hyderabad India
| |
Collapse
|
29
|
Groh KJ, Suter MJF. Stressor-induced proteome alterations in zebrafish: a meta-analysis of response patterns. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2015; 159:1-12. [PMID: 25498419 DOI: 10.1016/j.aquatox.2014.11.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Revised: 11/05/2014] [Accepted: 11/18/2014] [Indexed: 06/04/2023]
Abstract
Proteomics approaches are being increasingly applied in ecotoxicology on the premise that the identification of specific protein expression changes in response to a particular chemical would allow elucidation of the underlying molecular pathways leading to an adverse effect. This in turn is expected to promote the development of focused testing strategies for specific groups of toxicants. Although both gel-based and gel-free global characterization techniques provide limited proteome coverage, the conclusions regarding the cellular processes affected are still being drawn based on the few changes detected. To investigate how specific the detected responses are, we analyzed a set of studies that characterized proteome alterations induced by various physiological, chemical and biological stressors in zebrafish, a popular model organism. Our analysis highlights several proteins and protein groups, including heat shock and oxidative stress defense proteins, energy metabolism enzymes and cytoskeletal proteins, to be most frequently identified as responding to diverse stressors. In contrast, other potentially more specifically responding protein groups are detected much less frequently. Thus, zebrafish proteome responses to stress reported by different studies appear to depend mostly on the level of stress rather than on the specific stressor itself. This suggests that the most broadly used current proteomics technologies do not provide sufficient proteome coverage to allow in-depth investigation of specific mechanisms of toxicant action. We suggest that the results of any differential proteomics experiment performed with zebrafish should be interpreted keeping in mind the list of the most frequent responders that we have identified. Similar reservations should apply to any other species where proteome responses are analyzed by global proteomics methods. Careful consideration of the reliability and significance of observed changes is necessary in order not to over-interpret the experimental results and to prevent the proliferation of false positive linkages between the chemical and the cellular functions it perturbs. We further discuss the implications of the identified "top lists" of frequently responding proteins and protein families, and suggest further directions for proteomics research in ecotoxicology. Apart from improving the proteome coverage, further research should focus on defining the significance of the observed stress response patterns for organism phenotypes and on searching for common upstream regulators that can be targeted by specific assays.
Collapse
Affiliation(s)
- Ksenia J Groh
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland; ETH Zürich, Swiss Federal Institute of Technology, Department of Chemistry and Applied Biosciences, 8093 Zürich, Switzerland.
| | - Marc J-F Suter
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland; ETH Zürich, Swiss Federal Institute of Technology, Department of Environmental Systems Science, 8092 Zürich, Switzerland
| |
Collapse
|
30
|
Singh SK, Aravamudhan S, Armant O, Krüger M, Grabher C. Proteome dynamics in neutrophils of adult zebrafish upon chemically-induced inflammation. FISH & SHELLFISH IMMUNOLOGY 2014; 40:217-224. [PMID: 25014315 DOI: 10.1016/j.fsi.2014.06.035] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 06/23/2014] [Accepted: 06/27/2014] [Indexed: 06/03/2023]
Abstract
Neutrophils are the most abundant polymorphonuclear leukocytes, presenting the first line of defence against infection or tissue damage. To characterize the molecular changes on the protein level in neutrophils during sterile inflammation we established the chemically-induced inflammation (ChIn) assay in adult zebrafish and investigated the proteome dynamics within neutrophils of adult zebrafish upon inflammation. Through label-free proteomics we identified 48 proteins that were differentially regulated during inflammation. Gene ontology analysis revealed that these proteins were associated with cell cycle, nitric oxide signalling, regulation of cytoskeleton rearrangement and intermediate filaments as well as immune-related processes such as antigen presentation, leucocyte chemotaxis and IL-6 signalling. Comparison of protein expression dynamics with transcript expression dynamics suggests the existence of regulatory mechanisms confined to the protein level for some genes. This is the first proteome analysis of adult zebrafish neutrophils upon chemically-induced inflammation providing a valuable reference for future studies using zebrafish inflammation models.
Collapse
Affiliation(s)
- Sachin Kumar Singh
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Sriram Aravamudhan
- Max Planck Institute for Heart and Lung Research, Ludwigstr. 43, 61231 Bad Nauheim, Germany
| | - Olivier Armant
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany
| | - Marcus Krüger
- Max Planck Institute for Heart and Lung Research, Ludwigstr. 43, 61231 Bad Nauheim, Germany
| | - Clemens Grabher
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), 76344 Eggenstein-Leopoldshafen, Germany.
| |
Collapse
|
31
|
Transcriptomic and proteomic analyses of Amphiura filiformis arm tissue-undergoing regeneration. J Proteomics 2014; 112:113-24. [PMID: 25178173 DOI: 10.1016/j.jprot.2014.08.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 08/17/2014] [Accepted: 08/23/2014] [Indexed: 12/27/2022]
Abstract
UNLABELLED The extensive arm regeneration of brittle stars following amputation is becoming increasingly recognized as a model system for understanding cellular differentiation and regeneration in a whole animal context. In this study we have used the emerging brittle star model Amphiura filiformis to investigate the initial step of the regeneration process- the early repair phase, at the transcriptome and proteome level. Arm tissues were collected at 1 and 3days post amputation and were analyzed for the differential expression at the transcript and proteome level. A total of 694 genes and 194 proteins were found undergoing differential expression during the initiation of regeneration process. Comparison of transcriptomic and proteomic analysis showed 23 genes/proteins commonly between them with 40% having similar expression patterns. Validation of 33 differentially regulated genes based on RTPCR showed 22 and 19 genes expression as similar to the transcriptome expression during the first and third day post amputation respectively. Based on cellular network and molecular pathway analysis it was found that the differentially regulated transcripts and proteins were involved in structural and developmental network pathways such as cytoskeleton remodeling, cell adhesion integrin and translation initiation pathways for the instigation of regeneration process in brittle star. BIOLOGICAL SIGNIFICANCE This study identified various genes and proteins involved in brittle star arm regeneration based on high throughput transcriptomics and proteomics studies. In this study the genes and proteins associated with regeneration were validated and mapped for biological and molecular pathways involved in regeneration mechanism. This study will lead to discovery of marker associated with tissue or organ regeneration.
Collapse
|
32
|
Forn-Cuní G, Reis ES, Dios S, Posada D, Lambris JD, Figueras A, Novoa B. The evolution and appearance of C3 duplications in fish originate an exclusive teleost c3 gene form with anti-inflammatory activity. PLoS One 2014; 9:e99673. [PMID: 24926798 PMCID: PMC4057122 DOI: 10.1371/journal.pone.0099673] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 05/18/2014] [Indexed: 11/19/2022] Open
Abstract
The complement system acts as a first line of defense and promotes organism homeostasis by modulating the fates of diverse physiological processes. Multiple copies of component genes have been previously identified in fish, suggesting a key role for this system in aquatic organisms. Herein, we confirm the presence of three different previously reported complement c3 genes (c3.1, c3.2, c3.3) and identify five additional c3 genes (c3.4, c3.5, c3.6, c3.7, c3.8) in the zebrafish genome. Additionally, we evaluate the mRNA expression levels of the different c3 genes during ontogeny and in different tissues under steady-state and inflammatory conditions. Furthermore, while reconciling the phylogenetic tree with the fish species tree, we uncovered an event of c3 duplication common to all teleost fishes that gave rise to an exclusive c3 paralog (c3.7 and c3.8). These paralogs showed a distinct ability to regulate neutrophil migration in response to injury compared with the other c3 genes and may play a role in maintaining the balance between inflammatory and homeostatic processes in zebrafish.
Collapse
Affiliation(s)
- Gabriel Forn-Cuní
- Institute of Marine Research, Consejo Superior de Investigaciones Científicas (CSIC), Vigo, Spain
| | - Edimara S. Reis
- Department of Pathology and Laboratory Medicine, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Sonia Dios
- Institute of Marine Research, Consejo Superior de Investigaciones Científicas (CSIC), Vigo, Spain
| | - David Posada
- Department of Biochemistry, Genetics and Immunology, Universidad de Vigo, Vigo, Spain
| | - John D. Lambris
- Department of Pathology and Laboratory Medicine, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Antonio Figueras
- Institute of Marine Research, Consejo Superior de Investigaciones Científicas (CSIC), Vigo, Spain
| | - Beatriz Novoa
- Institute of Marine Research, Consejo Superior de Investigaciones Científicas (CSIC), Vigo, Spain
| |
Collapse
|
33
|
Varga M, Sass M, Papp D, Takács-Vellai K, Kobolak J, Dinnyés A, Klionsky DJ, Vellai T. Autophagy is required for zebrafish caudal fin regeneration. Cell Death Differ 2013; 21:547-56. [PMID: 24317199 DOI: 10.1038/cdd.2013.175] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 10/29/2013] [Accepted: 10/31/2013] [Indexed: 11/09/2022] Open
Abstract
Regeneration is the ability of multicellular organisms to replace damaged tissues and regrow lost body parts. This process relies on cell fate transformation that involves changes in gene expression as well as in the composition of the cytoplasmic compartment, and exhibits a characteristic age-related decline. Here, we present evidence that genetic and pharmacological inhibition of autophagy - a lysosome-mediated self-degradation process of eukaryotic cells, which has been implicated in extensive cellular remodelling and aging - impairs the regeneration of amputated caudal fins in the zebrafish (Danio rerio). Thus, autophagy is required for injury-induced tissue renewal. We further show that upregulation of autophagy in the regeneration zone occurs downstream of mitogen-activated protein kinase/extracellular signal-regulated kinase signalling to protect cells from undergoing apoptosis and enable cytosolic restructuring underlying terminal cell fate determination. This novel cellular function of the autophagic process in regeneration implies that the role of cellular self-digestion in differentiation and tissue patterning is more fundamental than previously thought.
Collapse
Affiliation(s)
- M Varga
- Department of Genetics, Eötvös Loránd University, Budapest, Hungary
| | - M Sass
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest, Hungary
| | - D Papp
- Department of Genetics, Eötvös Loránd University, Budapest, Hungary
| | - K Takács-Vellai
- Department of Genetics, Eötvös Loránd University, Budapest, Hungary
| | - J Kobolak
- BioTalentum Ltd., H-2100, Gödöllő, Hungary
| | - A Dinnyés
- BioTalentum Ltd., H-2100, Gödöllő, Hungary
| | - D J Klionsky
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - T Vellai
- Department of Genetics, Eötvös Loránd University, Budapest, Hungary
| |
Collapse
|
34
|
Singh SK, Sethi S, Aravamudhan S, Krüger M, Grabher C. Proteome mapping of adult zebrafish marrow neutrophils reveals partial cross species conservation to human peripheral neutrophils. PLoS One 2013; 8:e73998. [PMID: 24019943 PMCID: PMC3760823 DOI: 10.1371/journal.pone.0073998] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 07/30/2013] [Indexed: 11/18/2022] Open
Abstract
Neutrophil granulocytes are pivotal cells within the first line of host defense of the innate immune system. In this study, we have used a gel-based LC-MS/MS approach to explore the proteome of primary marrow neutrophils from adult zebrafish. The identified proteins originated from all major cellular compartments. Gene ontology analysis revealed significant association of proteins with different immune-related network and pathway maps. 75% of proteins identified in neutrophils were identified in neutrophils only when compared to neutrophil-free brain tissue. Moreover, cross-species comparison with human peripheral blood neutrophils showed partial conservation of immune-related proteins between human and zebrafish. This study provides the first zebrafish neutrophil proteome and may serve as a valuable resource for an understanding of neutrophil biology and innate immunity.
Collapse
Affiliation(s)
- Sachin Kumar Singh
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Sachin Sethi
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | | | - Marcus Krüger
- Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Clemens Grabher
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Karlsruhe, Germany
- * E-mail:
| |
Collapse
|
35
|
Chakravarty S, Reddy BR, Sudhakar SR, Saxena S, Das T, Meghah V, Brahmendra Swamy CV, Kumar A, Idris MM. Chronic unpredictable stress (CUS)-induced anxiety and related mood disorders in a zebrafish model: altered brain proteome profile implicates mitochondrial dysfunction. PLoS One 2013; 8:e63302. [PMID: 23691016 PMCID: PMC3653931 DOI: 10.1371/journal.pone.0063302] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 04/02/2013] [Indexed: 11/18/2022] Open
Abstract
Anxiety and depression are major chronic mood disorders, and the etiopathology for each appears to be repeated exposure to diverse unpredictable stress factors. Most of the studies on anxiety and related mood disorders are performed in rodents, and a good model is chronic unpredictable stress (CUS). In this study, we have attempted to understand the molecular basis of the neuroglial and behavioral changes underlying CUS-induced mood disorders in the simplest vertebrate model, the zebrafish, Danio rerio. Zebrafish were subjected to a CUS paradigm in which two different stressors were used daily for 15 days, and thorough behavioral analyses were performed to assess anxiety and related mood disorder phenotypes using the novel tank test, shoal cohesion and scototaxis. Fifteen days of exposure to chronic stressors appears to induce an anxiety and related mood disorder phenotype. Decreased neurogenesis, another hallmark of anxiety and related disorders in rodents, was also observed in this zebrafish model. The common molecular markers of rodent anxiety and related disorders, corticotropin-releasing factor (CRF), calcineurin (ppp3r1a) and phospho cyclic AMP response element binding protein (pCREB), were also replicated in the fish model. Finally, using 2DE FTMS/ITMSMS proteomics analyses, 18 proteins were found to be deregulated in zebrafish anxiety and related disorders. The most affected process was mitochondrial function, 4 of the 18 differentially regulated proteins were mitochondrial proteins: PHB2, SLC25A5, VDAC3 and IDH2, as reported in rodent and clinical samples. Thus, the zebrafish CUS model and proteomics can facilitate not only uncovering new molecular targets of anxiety and related mood disorders but also the routine screening of compounds for drug development.
Collapse
Affiliation(s)
- Sumana Chakravarty
- Chemical Biology Division, CSIR-Indian Institute of Chemical Technology (IICT), Hyderabad, India
- * E-mail: (SC); (MMI)
| | - Bommana R. Reddy
- Chemical Biology Division, CSIR-Indian Institute of Chemical Technology (IICT), Hyderabad, India
| | - Sreesha R. Sudhakar
- CSIR-Centre for Cellular and Molecular Biology (CCMB), Habsiguda, Hyderabad, India
| | - Sandeep Saxena
- CSIR-Centre for Cellular and Molecular Biology (CCMB), Habsiguda, Hyderabad, India
| | - Tapatee Das
- Chemical Biology Division, CSIR-Indian Institute of Chemical Technology (IICT), Hyderabad, India
| | - Vuppalapaty Meghah
- CSIR-Centre for Cellular and Molecular Biology (CCMB), Habsiguda, Hyderabad, India
| | | | - Arvind Kumar
- CSIR-Centre for Cellular and Molecular Biology (CCMB), Habsiguda, Hyderabad, India
| | - Mohammed M. Idris
- CSIR-Centre for Cellular and Molecular Biology (CCMB), Habsiguda, Hyderabad, India
- * E-mail: (SC); (MMI)
| |
Collapse
|
36
|
Wulff T, Silva T, Nielsen ME. Tissue damage in organic rainbow trout muscle investigated by proteomics and bioinformatics. Proteomics 2013; 13:2180-90. [PMID: 23596053 DOI: 10.1002/pmic.201200488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Revised: 02/13/2013] [Accepted: 03/26/2013] [Indexed: 11/08/2022]
Abstract
The response to tissue damage is a complex process, which involves the coordinated regulation of multiple proteins to ensure tissue repair. In order to investigate the effect of tissue damage in a lower vertebrate, samples were taken from rainbow trout (Oncorhynchus mykiss) at day 7 after damage and proteins were separated using 2DE. The experimental design included two groups of rainbow trout, which were fed organic feed either with or without astaxanthin. In total, 96 proteins were found to be affected by tissue damage, clearly demonstrating in this lower vertebrate the complexity and magnitude of the cellular response, in the context of a regenerative process. Using a bioinformatics approach, the main biological function of these proteins were assigned, showing the regulation of proteins involved in processes such as apoptosis, iron homeostasis, and regulation of muscular structure. Interestingly, it was established that exclusively within the astaxanthin feed group, three members of the annexin protein family (annexin IV, V, and VI) were regulated in response to tissue damage.
Collapse
Affiliation(s)
- Tune Wulff
- DTU Food, National Food Institute, Technical University of Denmark, Søltofts Plads, Lyngby, Denmark.
| | | | | |
Collapse
|
37
|
Franco C, Soares R, Pires E, Koci K, Almeida AM, Santos R, Coelho AV. Understanding regeneration through proteomics. Proteomics 2013; 13:686-709. [DOI: 10.1002/pmic.201200397] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Revised: 10/31/2012] [Accepted: 11/06/2012] [Indexed: 12/29/2022]
Affiliation(s)
- Catarina Franco
- Instituto de Tecnologia Química e Biológica; Universidade Nova de Lisboa; Oeiras Portugal
| | - Renata Soares
- Instituto de Tecnologia Química e Biológica; Universidade Nova de Lisboa; Oeiras Portugal
| | - Elisabete Pires
- Instituto de Tecnologia Química e Biológica; Universidade Nova de Lisboa; Oeiras Portugal
| | - Kamila Koci
- Instituto de Tecnologia Química e Biológica; Universidade Nova de Lisboa; Oeiras Portugal
| | - André M. Almeida
- Instituto de Tecnologia Química e Biológica; Universidade Nova de Lisboa; Oeiras Portugal
- Instituto de Investigação Científica Tropical; Lisboa Portugal
| | - Romana Santos
- Unidade de Investigação em Ciências Orais e Biomédicas, Faculdade de Medicina Dentária; Universidade de Lisboa; Portugal
| | - Ana Varela Coelho
- Instituto de Tecnologia Química e Biológica; Universidade Nova de Lisboa; Oeiras Portugal
| |
Collapse
|