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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.
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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
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Demircan T, Süzek BE. The Dynamic Landscapes of Circular RNAs in Axolotl, a Regenerative Medicine Model, with Implications for Early Phase of Limb Regeneration. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2023; 27:526-535. [PMID: 37943672 DOI: 10.1089/omi.2023.0158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Circular RNAs (circRNAs) are of relevance to regenerative medicine and play crucial roles in post-transcriptional and translational regulation of biological processes. circRNAs are a class of RNA molecules that are formed through a unique splicing process, resulting in a covalently closed-loop structure. Recent advancements in RNA sequencing technologies and specialized computational tools have facilitated the identification and functional characterization of circRNAs. These molecules are known to exhibit stability, developmental regulation, and specific expression patterns in different tissues and cell types across various organisms. However, our understanding of circRNA expression and putative function in model organisms for regeneration is limited. In this context, this study reports, for the first time, on the repertoire of circRNAs in axolotl, a widely used model organism for regeneration. We generated RNA-seq data from intact limb, wound, and blastema tissues of axolotl during limb regeneration. The analysis revealed the presence of 35,956 putative axolotl circRNAs, among which 5331 unique circRNAs exhibited orthology with human circRNAs. In silico data analysis underlined the potential roles of axolotl circRNAs in cell cycle, cell death, and cell senescence-related pathways during limb regeneration, suggesting the participation of circRNAs in regulation of diverse functions pertinent to regenerative medicine. These new observations help advance our understanding of the dynamic landscape of axolotl circRNAs, and by extension, inform future regenerative medicine research and innovation that harness this model organism.
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Affiliation(s)
- Turan Demircan
- Medical Biology Department, School of Medicine, Muğla Sıtkı Koçman University, Muğla, Turkey
| | - Barış Ethem Süzek
- Department of Computer Engineering, Faculty of Engineering, Muğla Sıtkı Koçman University, Muğla, Turkey
- Bioinformatics Graduate Program, Graduate School of Natural and Applied Sciences, Muğla Sıtkı Koçman University, Muğla, Turkey
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Ayan E, DeMirci H, Serdar MA, Palermo F, Baykal AT. Bridging the Gap between Gut Microbiota and Alzheimer's Disease: A Metaproteomic Approach for Biomarker Discovery in Transgenic Mice. Int J Mol Sci 2023; 24:12819. [PMID: 37629000 PMCID: PMC10454110 DOI: 10.3390/ijms241612819] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/24/2023] [Accepted: 07/28/2023] [Indexed: 08/27/2023] Open
Abstract
Alzheimer's Disease (AD) is a progressively debilitating form of dementia that affects millions of individuals worldwide. Although a vast amount of research has investigated the complex interplay between gut microbiota and neurodegeneration, the metaproteomic effects of microbiota on AD pathogenesis remain largely uncharted territory. This study aims to reveal the role of gut microbiota in AD pathogenesis, particularly regarding changes in the proteome and molecular pathways that are intricately linked to disease progression. We operated state-of-the-art Nano-Liquid Chromatography Mass Spectrometry (nLC-MS/MS) to compare the metaproteomic shifts of 3-month-old transgenic (3M-ALZ) and control (3M-ALM, Alzheimer's Littermate) mice, depicting the early onset of AD with those of 12-month-old ALZ and ALM mice displaying the late stage of AD. Combined with computational analysis, the outcomes of the gut-brain axis-focused inquiry furnish priceless knowledge regarding the intersection of gut microbiota and AD. Accordingly, our data indicate that the microbiota, proteome, and molecular changes in the intestine arise long before the manifestation of disease symptoms. Moreover, disparities exist between the normal-aged flora and the gut microbiota of late-stage AD mice, underscoring that the identified vital phyla, proteins, and pathways hold immense potential as markers for the early and late stages of AD. Our research endeavors to offer a comprehensive inquiry into the intricate interplay between gut microbiota and Alzheimer's Disease utilizing metaproteomic approaches, which have not been widely adopted in this domain. This highlights the exigency for further scientific exploration to elucidate the underlying mechanisms that govern this complex and multifaceted linkage.
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Affiliation(s)
- Esra Ayan
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul 34450, Turkey; (E.A.); (M.A.S.)
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul 34450, Turkey;
| | - Hasan DeMirci
- Department of Molecular Biology and Genetics, Faculty of Science, Koç University, Istanbul 34450, Turkey;
- Koç University Isbank Center for Infectious Diseases (KUISCID), Koç University, Istanbul 34450, Turkey
- Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, CA 94305, USA
| | - Muhittin Abdulkadir Serdar
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul 34450, Turkey; (E.A.); (M.A.S.)
| | | | - Ahmet Tarık Baykal
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul 34450, Turkey; (E.A.); (M.A.S.)
- Acıbadem Labmed Clinical Laboratories, R&D Center, İstanbul 34450, Turkey
- Department of Medical Biochemistry, Faculty of Medicine, Acibadem Mehmet Ali Aydınlar University, Istanbul 34450, Turkey
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Bay S, Öztürk G, Emekli N, Demircan T. Downregulation of Yap1 during limb regeneration results in defective bone formation in axolotl. Dev Biol 2023:S0012-1606(23)00094-5. [PMID: 37271360 DOI: 10.1016/j.ydbio.2023.06.001] [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: 02/05/2022] [Revised: 05/25/2023] [Accepted: 06/01/2023] [Indexed: 06/06/2023]
Abstract
The Hippo pathway plays an imperative role in cellular processes such as differentiation, regeneration, cell migration, organ growth, apoptosis, and cell cycle. Transcription coregulator component of Hippo pathway, YAP1, promotes transcription of genes involved in cell proliferation, migration, differentiation, and suppressing apoptosis. However, its role in epimorphic regeneration has not been fully explored. The axolotl is a well-established model organism for developmental biology and regeneration studies. By exploiting its remarkable regenerative capacity, we investigated the role of Yap1 in the early blastema stage of limb regeneration. Depleting Yap1 using gene-specific morpholinos attenuated the competence of axolotl limb regeneration evident in bone formation defects. To explore the affected downstream pathways from Yap1 down-regulation, the gene expression profile was examined by employing LC-MS/MS technology. Based on the generated data, we provided a new layer of evidence on the putative roles of increased protease inhibition and immune system activities and altered ECM composition in diminished bone formation capacity during axolotl limb regeneration upon Yap1 deficiency. We believe that new insights into the roles of the Hippo pathway in complex structure regeneration were granted in this study.
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Affiliation(s)
- Sadık Bay
- Regenerative and Restorative Medicine Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, 34810, Turkey; Graduate School of Health Sciences, İstanbul Medipol University, İstanbul, Turkey.
| | - Gürkan Öztürk
- Regenerative and Restorative Medicine Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, 34810, Turkey; Department of Physiology, International School of Medicine, Istanbul Medipol University, Istanbul, Turkey
| | - Nesrin Emekli
- Department of Medical Biochemistry, Faculty of Medicine, Istanbul Medipol University, Istanbul, Turkey
| | - Turan Demircan
- Department of Medical Biology, School of Medicine, Muğla Sıtkı Koçman University, Muğla, Turkey; Department of Bioinformatics, Muğla Sıtkı Koçman University, Muğla, Turkey.
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Bölük A, Yavuz M, Demircan T. Axolotl: A resourceful vertebrate model for regeneration and beyond. Dev Dyn 2022; 251:1914-1933. [PMID: 35906989 DOI: 10.1002/dvdy.520] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/04/2022] [Accepted: 07/21/2022] [Indexed: 01/30/2023] Open
Abstract
The regenerative capacity varies significantly among the animal kingdom. Successful regeneration program in some animals results in the functional restoration of tissues and lost structures. Among the highly regenerative animals, axolotl provides multiple experimental advantages with its many extraordinary characteristics. It has been positioned as a regeneration model organism due to its exceptional renewal capacity, including the internal organs, central nervous system, and appendages, in a scar-free manner. In addition to this unique regeneration ability, the observed low cancer incidence, its resistance to carcinogens, and the reversing effect of its cell extract on neoplasms strongly suggest its usability in cancer research. Axolotl's longevity and efficient utilization of several anti-aging mechanisms underline its potential to be employed in aging studies.
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Affiliation(s)
- Aydın Bölük
- School of Medicine, Muğla Sıtkı Koçman University, Muğla, Turkey
| | - Mervenur Yavuz
- Institute of Health Sciences, Muğla Sıtkı Koçman University, Muğla, Turkey
| | - Turan Demircan
- Department of Medical Biology, School of Medicine, Muğla Sıtkı Koçman University, Muğla, Turkey
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Demircan T, Hacıbektaşoğlu H, Sibai M, Fesçioğlu EC, Altuntaş E, Öztürk G, Süzek BE. Preclinical Molecular Signatures of Spinal Cord Functional Restoration: Optimizing the Metamorphic Axolotl ( Ambystoma mexicanum) Model in Regenerative Medicine. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2021; 24:370-378. [PMID: 32496969 DOI: 10.1089/omi.2020.0024] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Regenerative medicine offers hope for patients with diseases of the central and peripheral nervous system. Urodele amphibians such as axolotl display an exceptional regenerative capacity and are considered as essential preclinical model organisms in neurology and regenerative medicine research. Earlier studies have suggested that the limb regeneration ability of this salamander notably decreases with induction of metamorphosis by thyroid hormones. Metamorphic axolotl requires further validation as a negative control in preclinical regenerative medicine research, not to mention the study of molecular substrates of its regenerative abilities. In this study, we report new observations on the effect of experimentally induced metamorphosis on spinal cord regeneration in axolotl. Surprisingly, we found that metamorphic animals were successful to functionally restore the spinal cord after an experimentally induced injury. To discern the molecular signatures of spinal cord regeneration, we performed transcriptomics analyses at 1- and 7-days postinjury (dpi) for both spinal cord injury (SCI)-induced (experimental) and laminectomy (sham) groups. We observed 119 and 989 differentially expressed genes at 1- and 7-dpi, respectively, while the corresponding mouse orthologous genes were enriched in junction-, immune system-, and extracellular matrix-related pathways. Taken together, our findings challenge the prior notions of limited regenerative ability of metamorphic axolotl which exhibited successful spinal cord regeneration in our experience. Moreover, we report on molecular signatures that can potentially explain the mechanistic substrates of the regenerative capacity of the metamorphic axolotl. To the best of our knowledge, this is the first report on molecular responses to SCI and functional restoration in metamorphic axolotls. These new findings advance our understanding of spinal cord regeneration, and may thus help optimize the future use of axolotl as a preclinical model in regenerative medicine and integrative biology fields.
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Affiliation(s)
- Turan Demircan
- Department of Medical Biology, School of Medicine, Mugla Sitki Kocman University, Mugla, Turkey.,Regenerative and Restorative Medicine Research Center (REMER), Istanbul Medipol University, Istanbul, Turkey
| | - Harbiye Hacıbektaşoğlu
- Regenerative and Restorative Medicine Research Center (REMER), Istanbul Medipol University, Istanbul, Turkey
| | - Mustafa Sibai
- Graduate School of Natural and Applied Sciences, Mugla Sitki Kocman University, Mugla, Turkey
| | - Ece Cana Fesçioğlu
- Regenerative and Restorative Medicine Research Center (REMER), Istanbul Medipol University, Istanbul, Turkey
| | - Ebru Altuntaş
- Graduate School of Natural and Applied Sciences, Mugla Sitki Kocman University, Mugla, Turkey
| | - Gürkan Öztürk
- Department of Physiology, International School of Medicine, Istanbul Medipol University, Istanbul, Turkey
| | - Barış Ethem Süzek
- Department of Computer Engineering, Faculty of Engineering, Mugla Sitki Kocman University, Mugla, Turkey
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7
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Demircan T, Sibai M, Altuntaş E. Proteome data to explore the axolotl limb regeneration capacity at neotenic and metamorphic stages. Data Brief 2020; 29:105179. [PMID: 32055664 PMCID: PMC7005509 DOI: 10.1016/j.dib.2020.105179] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/02/2020] [Accepted: 01/16/2020] [Indexed: 12/04/2022] Open
Abstract
The presented data article reports protein expression profiles during a time course of limb regeneration in the highly regenerative neotenic and regeneration-deficient metamorphic axolotl (Ambystoma mexicanum). A protein database was first generated from transcriptome data, which was used concomitantly with nanoLC-MS/MS to identify and assess significant changes of protein levels among 0, 1, 4, and 7 days post-amputation (dpa) in both animal stages, yielding a total of 714 significant differentially expressed proteins. Gene ontology categories of these identified proteins were examined in terms of biological processes, molecular function and cellular components. Innate clustering patterns of the samples were investigated using hierarchical clustering and were visualized on a heatmap. The data reported here constitutes an extension of “Comparison of protein expression profile of limb regeneration between neotenic and metamorphic axolotl” article Sibai et al., 2019 [1]. The associated mass spectrometry raw data have been deposited in the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) with the dataset identifier PXD014806.
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Affiliation(s)
- Turan Demircan
- Muğla Sıtkı Koçman University, School of Medicine, Department of Medical Biology, Turkey.,Regenerative and Restorative Medicine Research Center, REMER, Istanbul Medipol University, Istanbul, Turkey
| | - Mustafa Sibai
- Muğla Sıtkı Koçman University, Graduate School of Natural and Applied Sciences, Turkey
| | - Ebru Altuntaş
- Muğla Sıtkı Koçman University, Graduate School of Natural and Applied Sciences, Turkey
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Sibai M, Parlayan C, Tuğlu P, Öztürk G, Demircan T. Integrative Analysis of Axolotl Gene Expression Data from Regenerative and Wound Healing Limb Tissues. Sci Rep 2019; 9:20280. [PMID: 31889169 PMCID: PMC6937273 DOI: 10.1038/s41598-019-56829-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 12/09/2019] [Indexed: 01/08/2023] Open
Abstract
Axolotl (Ambystoma mexicanum) is a urodele amphibian endowed with remarkable regenerative capacities manifested in scarless wound healing and restoration of amputated limbs, which makes it a powerful experimental model for regenerative biology and medicine. Previous studies have utilized microarrays and RNA-Seq technologies for detecting differentially expressed (DE) genes in different phases of the axolotl limb regeneration. However, sufficient consistency may be lacking due to statistical limitations arising from intra-laboratory analyses. This study aims to bridge such gaps by performing an integrative analysis of publicly available microarray and RNA-Seq data from axolotl limb samples having comparable study designs using the "merging" method. A total of 351 genes were found DE in regenerative samples compared to the control in data of both technologies, showing an adjusted p-value < 0.01 and log fold change magnitudes >1. Downstream analyses illustrated consistent correlations of the directionality of DE genes within and between data of both technologies, as well as concordance with the literature on regeneration related biological processes. qRT-PCR analysis validated the observed expression level differences of five of the top DE genes. Future studies may benefit from the utilized concept and approach for enhanced statistical power and robust discovery of biomarkers of regeneration.
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Affiliation(s)
- Mustafa Sibai
- Graduate School of Engineering and Natural Sciences, Istanbul Medipol University, Istanbul, Turkey
| | - Cüneyd Parlayan
- Regenerative and Restorative Medicine Research Center, REMER, Istanbul Medipol University, Istanbul, Turkey.
- Department of Biomedical Engineering, Faculty of Engineering, İstanbul Medipol University, Istanbul, Turkey.
| | - Pelin Tuğlu
- Regenerative and Restorative Medicine Research Center, REMER, Istanbul Medipol University, Istanbul, Turkey
| | - Gürkan Öztürk
- Regenerative and Restorative Medicine Research Center, REMER, Istanbul Medipol University, Istanbul, Turkey
- Department of Physiology, International School of Medicine, İstanbul Medipol University, Istanbul, Turkey
| | - Turan Demircan
- Regenerative and Restorative Medicine Research Center, REMER, Istanbul Medipol University, Istanbul, Turkey.
- Department of Medical Biology, School of Medicine, Mugla Sitki Kocman University, Mugla, Turkey.
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Sibai M, Altuntaş E, Süzek BE, Şahin B, Parlayan C, Öztürk G, Baykal AT, Demircan T. Comparison of protein expression profile of limb regeneration between neotenic and metamorphic axolotl. Biochem Biophys Res Commun 2019; 522:428-434. [PMID: 31767146 DOI: 10.1016/j.bbrc.2019.11.118] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 11/18/2019] [Indexed: 11/29/2022]
Abstract
The axolotl (Ambystoma mexicanum) salamander, a urodele amphibian, has an exceptional regenerative capacity to fully restore an amputated limb throughout the life-long lasting neoteny. By contrast, when axolotls are experimentally induced to metamorphosis, attenuation of the limb's regenerative competence is noticeable. Here, we sought to discern the proteomic profiles of the early stages of blastema formation of neotenic and metamorphic axolotls after limb amputation by employing LC-MS/MS technology. We quantified a total of 714 proteins and qRT-PCR for selected genes was performed to validate the proteomics results and provide evidence for the putative link between immune system activity and regenerative potential. This study provides new insights for examination of common and distinct molecular mechanisms in regeneration-permissive neotenic and regeneration-deficient metamorphic stages at the proteome level.
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Affiliation(s)
- Mustafa Sibai
- Regenerative and Restorative Medicine Research Center, REMER, Istanbul Medipol University, Istanbul, Turkey
| | - Ebru Altuntaş
- Regenerative and Restorative Medicine Research Center, REMER, Istanbul Medipol University, Istanbul, Turkey
| | - Barış Ethem Süzek
- Department of Computer Engineering, Faculty of Engineering, Mugla Sitki Kocman University, Mugla, Turkey; Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, DC, 20007, USA
| | - Betül Şahin
- Acibadem Labmed Research and Development Center, Istanbul, Turkey
| | - Cüneyd Parlayan
- Regenerative and Restorative Medicine Research Center, REMER, Istanbul Medipol University, Istanbul, Turkey; Department of Biomedical Engineering, Faculty of Engineering, Istanbul Medipol University, Istanbul, Turkey
| | - Gürkan Öztürk
- Regenerative and Restorative Medicine Research Center, REMER, Istanbul Medipol University, Istanbul, Turkey; Department of Physiology, International School of Medicine, Istanbul Medipol University, Istanbul, Turkey
| | - Ahmet Tarık Baykal
- Acibadem Labmed Research and Development Center, Istanbul, Turkey; Department of Biochemistry, School of Medicine, Istanbul Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Turan Demircan
- Regenerative and Restorative Medicine Research Center, REMER, Istanbul Medipol University, Istanbul, Turkey; Department of Medical Biology, School of Medicine, Mugla Sitki Kocman University, Mugla, Turkey.
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Geng X, Guo J, Zang X, Chang C, Shang H, Wei H, Xu C. Proteomic analysis of eleven tissues in the Chinese giant salamander (Andrias davidianus). Sci Rep 2019; 9:16415. [PMID: 31712686 PMCID: PMC6848178 DOI: 10.1038/s41598-019-50909-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 12/11/2018] [Indexed: 02/08/2023] Open
Abstract
The Chinese giant salamander (Andrias davidianus, CGS) is the largest extant amphibian species in the world. Global quantitative proteome analysis of multiple tissues would indicate tissue-specific physiological processes and clarify the function of each protein from a whole-organism perspective. This study performed proteome analysis of eleven tissues collected from adult CGSs using iTRAQ coupled with LC-MS/MS technology. Based on the predicted protein database from previously obtained CGS transcriptome data, 2153 proteins were identified for subsequent analysis. A weighted gene co-expression network analysis (WGCNA) clustered 2153 proteins into 17 co-expressed modules, which will be useful for predicting the functions of unannotated proteins. The protein levels of molecular complexes with housekeeping functions, such as ribosomes, spliceosomes and mitochondrial respiratory chain complexes, were tightly regulated in different tissues of the CGS, as they are in mammalian tissues. Transcription regulator, pathway and bio-functional analysis of tissue-specific proteins showed that highly expressed proteins largely reflected the physiological functions of specific tissues. Our data, as an initial atlas of protein expression of an amphibian species, will be useful for further molecular biology research on CGS.
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Affiliation(s)
- Xiaofang Geng
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, College of Life Science, Henan Normal University, Xinxiang, China.,Henan Key Laboratory of immunology and targeted therapy, Henan Collaborative Innovation Center of Molecular Diagnosis and Laboratory Medicine, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
| | - Jianlin Guo
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, College of Life Science, Henan Normal University, Xinxiang, China
| | - Xiayan Zang
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, College of Life Science, Henan Normal University, Xinxiang, China
| | - Cuifang Chang
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, College of Life Science, Henan Normal University, Xinxiang, China
| | - Haitao Shang
- Department of Laboratory Animal Science, College of Basic Medical Sciences, Third Military Medical University, Chongqing, China
| | - Hong Wei
- The Engineering Technology Research Center for Germ-free and Genome-editing animal, Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China.
| | - Cunshuan Xu
- State Key Laboratory Cultivation Base for Cell Differentiation Regulation, College of Life Science, Henan Normal University, Xinxiang, China.
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11
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Longitudinal 16S rRNA data derived from limb regenerative tissue samples of axolotl Ambystoma mexicanum. Sci Data 2019; 6:70. [PMID: 31123261 PMCID: PMC6533342 DOI: 10.1038/s41597-019-0077-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 04/16/2019] [Indexed: 12/05/2022] Open
Abstract
The Mexican axolotl (Ambystoma mexicanum) is a critically endangered species and a fruitful amphibian model for regenerative biology. Despite growing body of research on the cellular and molecular biology of axolotl limb regeneration, microbiological aspects of this process remain poorly understood. Here, we describe bacterial 16S rRNA amplicon dataset derived from axolotl limb tissue samples in the course of limb regeneration. The raw data was obtained by sequencing V3–V4 region of 16S rRNA gene and comprised 14,569,756 paired-end raw reads generated from 21 samples. Initial data analysis using DADA2 pipeline resulted in amplicon sequence variant (ASV) table containing a total of ca. 5.9 million chimera-removed, high-quality reads and a median of 296,971 reads per sample. The data constitute a useful resource for the research on the microbiological aspects of axolotl limb regeneration and will also broadly facilitate comparative studies in the developmental and conservation biology of this critically endangered species. Design Type(s) | time series design • organism development design | Measurement Type(s) | rRNA 16S | Technology Type(s) | DNA sequencing | Factor Type(s) | biological replicate • temporal_interval | Sample Characteristic(s) | Ambystoma mexicanum • limb • laboratory environment |
Machine-accessible metadata file describing the reported data (ISA-Tab format)
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12
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Timirci-Kahraman O, Karaaslan Z, Tuzun E, Kurtuncu M, Baykal AT, Gunduz T, Tuzuner MB, Akgun E, Gurel B, Eraksoy M, Kucukali CI. Identification of candidate biomarkers in converting and non-converting clinically isolated syndrome by proteomics analysis of cerebrospinal fluid. Acta Neurol Belg 2019; 119:101-111. [PMID: 29873030 DOI: 10.1007/s13760-018-0954-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 05/24/2018] [Indexed: 01/28/2023]
Abstract
Multiple sclerosis (MS) often starts in the form of clinically isolated syndrome (CIS) and only some of the CIS patients progress to relapsing-remitting MS (RRMS). Biomarkers to predict conversion from CIS to MS are thus greatly needed for making correct treatment decisions. To identify a predictive cerebrospinal fluid (CSF) protein, we analyzed the first-attack CSF samples of CIS patients who converted (CIS-MS) (n = 23) and did not convert (CIS-CIS) (n = 19) to RRMS in a follow-up period of 5 years using proteomics analysis by liquid chromatography tandem-mass spectrometry (LC-MS/MS) and verified by ELISA. Label-free differential proteomics analysis of CSF ensured that 637 proteins were identified and 132 of these proteins were found to be statistically significant. Further investigation with the ingenuity pathway analysis (IPA) software led to identification of three pathway networks mostly comprised proteins involved in inflammatory response, cellular growth and tissue proliferation. CSF levels of four of the most differentially expressed proteins belonging to the cellular proliferation network function, chitinase-3-like protein 1 (CHI3L1), tumor necrosis factor receptor superfamily member 21 (TNFRSF21), homeobox protein Hox-B3 (HOXB3) and iduronate 2-sulfatase (IDS), were measured by ELISA. CSF levels of HOXB3 were significantly increased in CIS-MS patients. Our results indicate that cell and tissue proliferation functions are dysregulated in MS as early as the first clinical episode. HOXB3 has emerged as a potential novel biomarker which might be used for prediction of CIS-MS conversion.
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Demircan T, Ovezmyradov G, Yıldırım B, Keskin İ, İlhan AE, Fesçioğlu EC, Öztürk G, Yıldırım S. Experimentally induced metamorphosis in highly regenerative axolotl (ambystoma mexicanum) under constant diet restructures microbiota. Sci Rep 2018; 8:10974. [PMID: 30030457 PMCID: PMC6054665 DOI: 10.1038/s41598-018-29373-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 07/02/2018] [Indexed: 02/07/2023] Open
Abstract
Axolotl (Ambystoma mexicanum) is a critically endangered salamander species and a model organism for regenerative and developmental biology. Despite life-long neoteny in nature and in captive-bred colonies, metamorphosis of these animals can be experimentally induced by administering Thyroid hormones (THs). However, microbiological consequences of this experimental procedure, such as host microbiota response, remain largely unknown. Here, we systematically compared host bacterial microbiota associated with skin, stomach, gut tissues and fecal samples, between neotenic and metamorphic axolotls based on 16S rRNA gene sequences. Our results show that distinct bacterial communities inhabit individual organs of axolotl and undergo substantial restructuring through metamorphosis. Skin microbiota among others, shifted sharply, as highlighted by a major transition from Firmicutes-enriched to Proteobacteria-enriched relative abundance and precipitously decreased diversity. Fecal microbiota of neotenic and metamorphic axolotl shared relatively higher similarity, suggesting that diet continues to shape microbiota despite fundamental transformations in the host digestive organs. We also reproduced the previous finding on reduction in regenerative capacity in limbs of axolotl following metamorphosis, highlighting the need to investigate whether shifts in microbiota is causally linked to regenerative capacity of axolotl. The initial results on axolotl microbiota provide novel insights into microbiological aspects of axolotl metamorphosis and will establish a baseline for future in-depth studies.
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Affiliation(s)
- Turan Demircan
- Department of Medical Biology, International School of Medicine, İstanbul Medipol University, Istanbul, Turkey. .,Regenerative and Restorative Medicine Research Center, REMER, İstanbul Medipol University, Istanbul, Turkey.
| | - Guvanch Ovezmyradov
- Department of Biostatistics and Medical Informatics, International School of Medicine, Istanbul Medipol University, Istanbul, Turkey.,Regenerative and Restorative Medicine Research Center, REMER, İstanbul Medipol University, Istanbul, Turkey
| | - Berna Yıldırım
- Regenerative and Restorative Medicine Research Center, REMER, İstanbul Medipol University, Istanbul, Turkey
| | - İlknur Keskin
- Department of Histology and Embryology, School of Medicine, Istanbul Medipol University, Istanbul, Turkey.,Regenerative and Restorative Medicine Research Center, REMER, İstanbul Medipol University, Istanbul, Turkey
| | - Ayşe Elif İlhan
- Regenerative and Restorative Medicine Research Center, REMER, İstanbul Medipol University, Istanbul, Turkey
| | - Ece Cana Fesçioğlu
- Regenerative and Restorative Medicine Research Center, REMER, İstanbul Medipol University, Istanbul, Turkey
| | - Gürkan Öztürk
- Department of Physiology, International School of Medicine, İstanbul Medipol University, Istanbul, Turkey.,Regenerative and Restorative Medicine Research Center, REMER, İstanbul Medipol University, Istanbul, Turkey
| | - Süleyman Yıldırım
- Department of Microbiology, International School of Medicine, İstanbul Medipol University, Istanbul, Turkey. .,Regenerative and Restorative Medicine Research Center, REMER, İstanbul Medipol University, Istanbul, Turkey.
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Mazi AR, Arzuman AS, Gurel B, Sahin B, Tuzuner MB, Ozansoy M, Baykal AT. Neonatal Neurodegeneration in Alzheimer's Disease Transgenic Mouse Model. J Alzheimers Dis Rep 2018; 2:79-91. [PMID: 30480251 PMCID: PMC6159732 DOI: 10.3233/adr-170049] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Alzheimer’s disease (AD) is a progressive disorder characterized by a variety of molecular pathologies causing cortical dementia with a prominent memory deficit. Formation of the pathology, which begins decades before the diagnosis of the disease, is highly correlated with the clinical symptoms. Several proteomics studies were performed using animal models to monitor the alterations of the brain tissue proteome at different stages of AD. However, proteome changes in the brain regions of newborn transgenic mouse model have not been investigated yet. To this end, we analyzed protein expression alterations in cortex, hippocampus and cerebellum of transgenic mice carrying five familial AD mutations (5XFAD) at neonatal day-1. Our results indicate a remarkable difference in protein expression profile of newborn 5XFAD brain with region specific variations. Additionally, the proteins, which show similar expression alteration pattern in postmortem human AD brains, were determined. Bioinformatics analysis showed that the molecular alterations were mostly related to the cell morphology, cellular assembly and organization, and neuroinflammation. Moreover, morphological analysis revealed that there is an increase in neurite number of 5XFAD mouse neurons in vitro. We suggest that, molecular alterations in the AD brain exist even at birth, and perhaps the disease is silenced until older ages when the brain becomes vulnerable.
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Affiliation(s)
- Aise Rumeysa Mazi
- Regenerative and Restorative Medicine Research Center, REMER, Istanbul, Turkey.,Institute of Health Science, Istanbul Medipol University, Istanbul, Turkey.,Department of Medical Biochemistry, Acibadem Mehmet Ali Aydinlar University, School of Medicine, Istanbul, Turkey
| | - Aysegul Sumeyye Arzuman
- Regenerative and Restorative Medicine Research Center, REMER, Istanbul, Turkey.,Institute of Health Science, Istanbul Medipol University, Istanbul, Turkey.,Department of Medical Biochemistry, Acibadem Mehmet Ali Aydinlar University, School of Medicine, Istanbul, Turkey
| | - Busra Gurel
- Regenerative and Restorative Medicine Research Center, REMER, Istanbul, Turkey.,Institute of Health Science, Istanbul Medipol University, Istanbul, Turkey.,Department of Medical Biochemistry, Acibadem Mehmet Ali Aydinlar University, School of Medicine, Istanbul, Turkey
| | - Betul Sahin
- Acibadem Labmed R&D Laboratory, Istanbul, Turkey
| | | | - Mehmet Ozansoy
- Regenerative and Restorative Medicine Research Center, REMER, Istanbul, Turkey.,Department of Physiology, International School of Medicine, Istanbul Medipol University, Istanbul, Turkey
| | - Ahmet Tarik Baykal
- Acibadem Labmed R&D Laboratory, Istanbul, Turkey.,Department of Medical Biochemistry, Acibadem Mehmet Ali Aydinlar University, School of Medicine, Istanbul, Turkey
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