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Xia Y, Duca S, Perder B, Dündar F, Zumbo P, Qiu M, Yao J, Cao Y, Harrison MRM, Zangi L, Betel D, Cao J. Activation of a transient progenitor state in the epicardium is required for zebrafish heart regeneration. Nat Commun 2022; 13:7704. [PMID: 36513650 PMCID: PMC9747719 DOI: 10.1038/s41467-022-35433-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 12/02/2022] [Indexed: 12/15/2022] Open
Abstract
The epicardium, a mesothelial cell tissue that encompasses vertebrate hearts, supports heart regeneration after injury through paracrine effects and as a source of multipotent progenitors. However, the progenitor state in the adult epicardium has yet to be defined. Through single-cell RNA-sequencing of isolated epicardial cells from uninjured and regenerating adult zebrafish hearts, we define the epithelial and mesenchymal subsets of the epicardium. We further identify a transiently activated epicardial progenitor cell (aEPC) subpopulation marked by ptx3a and col12a1b expression. Upon cardiac injury, aEPCs emerge from the epithelial epicardium, migrate to enclose the wound, undergo epithelial-mesenchymal transition (EMT), and differentiate into mural cells and pdgfra+hapln1a+ mesenchymal epicardial cells. These EMT and differentiation processes are regulated by the Tgfβ pathway. Conditional ablation of aEPCs blocks heart regeneration through reduced nrg1 expression and mesenchymal cell number. Our findings identify a transient progenitor population of the adult epicardium that is indispensable for heart regeneration and highlight it as a potential target for enhancing cardiac repair.
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Affiliation(s)
- Yu Xia
- Cardiovascular Research Institute, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
| | - Sierra Duca
- Cardiovascular Research Institute, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
| | - Björn Perder
- Cardiovascular Research Institute, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
| | - Friederike Dündar
- Department of Physiology and Biophysics, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
- Applied Bioinformatics Core, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
| | - Paul Zumbo
- Department of Physiology and Biophysics, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
- Applied Bioinformatics Core, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
| | - Miaoyan Qiu
- Cardiovascular Research Institute, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
| | - Jun Yao
- Cardiovascular Research Institute, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
| | - Yingxi Cao
- Cardiovascular Research Institute, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
| | - Michael R M Harrison
- Cardiovascular Research Institute, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
| | - Lior Zangi
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Doron Betel
- Applied Bioinformatics Core, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
- Division of Hematology and Oncology, Department of Medicine, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
- Institute for Computational Biomedicine, Department of Medicine, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA
| | - Jingli Cao
- Cardiovascular Research Institute, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA.
- Department of Cell and Developmental Biology, Weill Cornell Medical College, 1300 York Avenue, New York, NY, 10065, USA.
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Chen W, Tsissios G, Sallese A, Smucker B, Nguyen AT, Chen J, Wang H, Del Rio-Tsonis K. In Vivo Imaging of Newt Lens Regeneration: Novel Insights Into the Regeneration Process. Transl Vis Sci Technol 2021; 10:4. [PMID: 34383878 PMCID: PMC8362625 DOI: 10.1167/tvst.10.10.4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Purpose To establish optical coherence tomography (OCT) as an in vivo imaging modality for investigating the process of newt lens regeneration. Methods Spectral-domain OCT was employed for in vivo imaging of the newt lens regeneration process. A total of 37 newts were lentectomized and followed by OCT imaging over the course of 60 to 80 days. Histological images were obtained at several time points to compare with the corresponding OCT images. Volume measurements were also acquired. Results OCT can identify the key features observed in corresponding histological images based on the scattering differences from various eye tissues, such as the cornea, intact and regenerated lens, and the iris. Lens volume measurements from three-dimensional OCT images showed that the regenerating lens size increased linearly until 60 days post-lentectomy. Conclusions Using OCT imaging, we were able to track the entire process of newt lens regeneration in vivo for the first time. Three-dimensional OCT images allowed us to volumetrically quantify and visualize the dynamic spatial relationships between tissues during the regeneration process. Our results establish OCT as anin vivo imaging modality to track/analyze the entire lens regeneration process from the same animal. Translational Relevance Lens regeneration in newts represents a unique example of vertebrate tissue plasticity. Investigating the cellular and morphological events that govern this extraordinary process in vivo will advance our understanding and shed light on developing new therapies to treat blinding disorders in higher vertebrates.
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Affiliation(s)
- Weihao Chen
- Department of Chemical, Paper and Biomedical Engineering, Miami University, Oxford, OH, USA
| | - Georgios Tsissios
- Department of Biology Miami University, Oxford, OH, USA.,Center for Visual Sciences at Miami University, Oxford, OH, USA.,Cellular Molecular and Structural Biology Program, Miami University, Oxford, OH, USA
| | - Anthony Sallese
- Department of Biology Miami University, Oxford, OH, USA.,Center for Visual Sciences at Miami University, Oxford, OH, USA
| | - Byran Smucker
- Center for Visual Sciences at Miami University, Oxford, OH, USA.,Department of Statistics, Miami University, Oxford, OH, USA
| | - Anh-Thu Nguyen
- Department of Chemical, Paper and Biomedical Engineering, Miami University, Oxford, OH, USA
| | - Junfan Chen
- Department of Chemistry and Biochemistry, Miami University, Oxford OH, USA
| | - Hui Wang
- Department of Chemical, Paper and Biomedical Engineering, Miami University, Oxford, OH, USA.,Center for Visual Sciences at Miami University, Oxford, OH, USA
| | - Katia Del Rio-Tsonis
- Department of Biology Miami University, Oxford, OH, USA.,Center for Visual Sciences at Miami University, Oxford, OH, USA.,Cellular Molecular and Structural Biology Program, Miami University, Oxford, OH, USA
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3
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Byrne AQ, Richards-Zawacki CL, Voyles J, Bi K, Ibáñez R, Rosenblum EB. Whole exome sequencing identifies the potential for genetic rescue in iconic and critically endangered Panamanian harlequin frogs. GLOBAL CHANGE BIOLOGY 2021; 27:50-70. [PMID: 33150627 DOI: 10.1111/gcb.15405] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 09/24/2020] [Accepted: 10/02/2020] [Indexed: 06/11/2023]
Abstract
Avoiding extinction in a rapidly changing environment often relies on a species' ability to quickly adapt in the face of extreme selective pressures. In Panamá, two closely related harlequin frog species (Atelopus varius and Atelopus zeteki) are threatened with extinction due to the fungal pathogen Batrachochytrium dendrobatidis (Bd). Once thought to be nearly extirpated from Panamá, A. varius have recently been rediscovered in multiple localities across their historical range; however, A. zeteki are possibly extinct in the wild. By leveraging a unique collection of 186 Atelopus tissue samples collected before and after the Bd outbreak in Panama, we describe the genetics of persistence for these species on the brink of extinction. We sequenced the transcriptome and developed an exome-capture assay to sequence the coding regions of the Atelopus genome. Using these genetic data, we evaluate the population genetic structure of historical A. varius and A. zeteki populations, describe changes in genetic diversity over time, assess the relationship between contemporary and historical individuals, and test the hypothesis that some A. varius populations have rapidly evolved to resist or tolerate Bd infection. We found a significant decrease in genetic diversity in contemporary (compared to historical) A. varius populations. We did not find strong evidence of directional allele frequency change or selection for Bd resistance genes, but we uncovered a set of candidate genes that warrant further study. Additionally, we found preliminary evidence of recent migration and gene flow in one of the largest persisting A. varius populations in Panamá, suggesting the potential for genetic rescue in this system. Finally, we propose that previous conservation units should be modified, as clear genetic breaks do not exist beyond the local population level. Our data lay the groundwork for genetically informed conservation and advance our understanding of how imperiled species might be rescued from extinction.
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Affiliation(s)
- Allison Q Byrne
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, CA, USA
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA, USA
| | | | - Jamie Voyles
- Department of Biology, University of Nevada Reno, Reno, NV, USA
| | - Ke Bi
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA, USA
| | - Roberto Ibáñez
- Smithsonian Tropical Research Institute, Panamá, República de Panamá
- Sistema Nacional de Investigación, SENACYT, Clayton, Panamá, República de Panamá
| | - Erica Bree Rosenblum
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, CA, USA
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA, USA
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4
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Liu Z, Wang R, Lin H, Liu Y. Lens regeneration in humans: using regenerative potential for tissue repairing. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:1544. [PMID: 33313289 PMCID: PMC7729322 DOI: 10.21037/atm-2019-rcs-03] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The crystalline lens is an important optic element in human eyes. It is transparent and biconvex, refracting light and accommodating to form a clear retinal image. The lens originates from the embryonic ectoderm. The epithelial cells at the lens equator proliferate, elongate and differentiate into highly aligned lens fiber cells, which are the structural basis for maintaining the transparency of the lens. Cataract refers to the opacity of the lens. Currently, the treatment of cataract is to remove the opaque lens and implant an intraocular lens (IOL). This strategy is inappropriate for children younger than 2 years, because a developing eyeball is prone to have severe complications such as inflammatory proliferation and secondary glaucoma. On the other hand, the absence of the crystalline lens greatly affects visual function rehabilitation. The researchers found that mammalian lenses possess regenerative potential. We identified lens stem cells through linear tracking experiments and designed a minimally invasive lens-content removal surgery (MILS) to remove the opaque lens material while preserving the lens capsule, stem cells and microenvironment. In infants with congenital cataract, functional lens regeneration in situ can be observed after MILS, and the prognosis of visual function is better than that of traditional surgery. Because of insufficient regenerative ability in humans, the morphology and volume of the regenerated lens cannot reach the level of a normal lens. The activation, proliferation and differentiation of lens stem cells and the alignment of lens fibers are regulated by epigenetic factors, growth factors, transcription factors, immune system and other signals and their interactions. The construction of appropriate microenvironment can accelerate lens regeneration and improve its morphology. The therapeutic concept of MILS combined with microenvironment manipulation to activate endogenous stem cells for functional regeneration of organs in situ can be extended to other tissues and organs with strong self-renewal and repair ability.
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Affiliation(s)
- Zhenzhen Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Ruixin Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Haotian Lin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Yizhi Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
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5
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Markitantova YV, Simirskii VN. Role of the Redox System in Initiation of a Regenerative Response of Neural Eye Tissues in Vertebrates. Russ J Dev Biol 2020. [DOI: 10.1134/s106236042001004x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Sousounis K, Bryant DM, Martinez Fernandez J, Eddy SS, Tsai SL, Gundberg GC, Han J, Courtemanche K, Levin M, Whited JL. Eya2 promotes cell cycle progression by regulating DNA damage response during vertebrate limb regeneration. eLife 2020; 9:51217. [PMID: 32142407 PMCID: PMC7093111 DOI: 10.7554/elife.51217] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 03/05/2020] [Indexed: 02/06/2023] Open
Abstract
How salamanders accomplish progenitor cell proliferation while faithfully maintaining genomic integrity and regenerative potential remains elusive. Here we found an innate DNA damage response mechanism that is evident during blastema proliferation (early- to late-bud) and studied its role during tissue regeneration by ablating the function of one of its components, Eyes absent 2. In eya2 mutant axolotls, we found that DNA damage signaling through the H2AX histone variant was deregulated, especially within the proliferating progenitors during limb regeneration. Ultimately, cell cycle progression was impaired at the G1/S and G2/M transitions and regeneration rate was reduced. Similar data were acquired using acute pharmacological inhibition of the Eya2 phosphatase activity and the DNA damage checkpoint kinases Chk1 and Chk2 in wild-type axolotls. Together, our data indicate that highly-regenerative animals employ a robust DNA damage response pathway which involves regulation of H2AX phosphorylation via Eya2 to facilitate proper cell cycle progression upon injury.
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Affiliation(s)
- Konstantinos Sousounis
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, United States.,The Allen Discovery Center at Tufts University, Medford, United States
| | - Donald M Bryant
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, United States
| | - Jose Martinez Fernandez
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, United States
| | - Samuel S Eddy
- Department of Orthopedic Surgery, Boston, United States
| | - Stephanie L Tsai
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, United States.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Gregory C Gundberg
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, United States.,The Allen Discovery Center at Tufts University, Medford, United States
| | - Jihee Han
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, United States
| | - Katharine Courtemanche
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, United States
| | - Michael Levin
- The Allen Discovery Center at Tufts University, Medford, United States.,Department of Biology, Tufts University, Medford, United States
| | - Jessica L Whited
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, United States.,The Allen Discovery Center at Tufts University, Medford, United States.,The Harvard Stem Cell Institute, Cambridge, United States.,The Broad Institute of MIT and Harvard, Cambridge, United States
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7
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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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Kumar B, Reilly MA. The Development, Growth, and Regeneration of the Crystalline Lens: A Review. Curr Eye Res 2019; 45:313-326. [DOI: 10.1080/02713683.2019.1681003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Bharat Kumar
- Department of Biomedical Engineering, The Ohio State University, Columbus, Ohio, USA
| | - M. A. Reilly
- Department of Biomedical Engineering, The Ohio State University, Columbus, Ohio, USA
- Department of Ophthalmology and Visual Science, The Ohio State University, Columbus, Ohio, USA
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9
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Vergara MN, Tsissios G, Del Rio-Tsonis K. Lens regeneration: a historical perspective. THE INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY 2019; 62:351-361. [PMID: 29877565 PMCID: PMC6378223 DOI: 10.1387/ijdb.180084nv] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The idea of regenerating injured body parts has captivated human imagination for centuries, and the topic still remains an area of extensive scientific research. This review focuses on the process of lens regeneration: its history, our current knowledge, and the questions that remain unanswered. By highlighting some of the milestones that have shaped our understanding of this phenomenon and the contributions of scientists who have dedicated their lives to investigating these questions, we explore how regeneration enquiry evolved into the science it is today, and how technological advances accelerated our understanding of these remarkable processes.
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Affiliation(s)
- M Natalia Vergara
- Department of Ophthalmology, University of Colorado Denver School of Medicine, Aurora, CO, USA
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10
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Bichirs employ similar genetic pathways for limb regeneration as are used in lungfish and salamanders. Gene 2019; 690:68-74. [DOI: 10.1016/j.gene.2018.12.031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 10/29/2018] [Accepted: 12/12/2018] [Indexed: 11/22/2022]
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11
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Ertl NG, O'Connor WA, Elizur A. Molecular effects of a variable environment on Sydney rock oysters, Saccostrea glomerata: Thermal and low salinity stress, and their synergistic effect. Mar Genomics 2019; 43:19-32. [DOI: 10.1016/j.margen.2018.10.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 10/07/2018] [Accepted: 10/18/2018] [Indexed: 12/26/2022]
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12
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Arenas Gómez CM, Woodcock RM, Smith JJ, Voss RS, Delgado JP. Using transcriptomics to enable a plethodontid salamander (Bolitoglossa ramosi) for limb regeneration research. BMC Genomics 2018; 19:704. [PMID: 30253734 PMCID: PMC6157048 DOI: 10.1186/s12864-018-5076-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 09/13/2018] [Indexed: 12/05/2022] Open
Abstract
Background Tissue regeneration is widely distributed across the tree of life. Among vertebrates, salamanders possess an exceptional ability to regenerate amputated limbs and other complex structures. Thus far, molecular insights about limb regeneration have come from a relatively limited number of species from two closely related salamander families. To gain a broader perspective on the molecular basis of limb regeneration and enhance the molecular toolkit of an emerging plethodontid salamander (Bolitoglossa ramosi), we used RNA-Seq to generate a de novo reference transcriptome and identify differentially expressed genes during limb regeneration. Results Using paired-end Illumina sequencing technology and Trinity assembly, a total of 433,809 transcripts were recovered and we obtained functional annotation for 142,926 non-redundant transcripts of the B. ramosi de novo reference transcriptome. Among the annotated transcripts, 602 genes were identified as differentially expressed during limb regeneration. This list was further processed to identify a core set of genes that exhibit conserved expression changes between B. ramosi and the Mexican axolotl (Ambystoma mexicanum), and presumably their common ancestor from approximately 180 million years ago. Conclusions We identified genes from B. ramosi that are differentially expressed during limb regeneration, including multiple conserved protein-coding genes and possible putative species-specific genes. Comparative analyses reveal a subset of genes that show similar patterns of expression with ambystomatid species, which highlights the importance of developing comparative gene expression data for studies of limb regeneration among salamanders. Electronic supplementary material The online version of this article (10.1186/s12864-018-5076-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Claudia M Arenas Gómez
- Grupo de Genética, Regeneración y Cáncer, Universidad de Antioquia, Sede de Investigación Universitaria, Torre 2, laboratorio 432. Calle 62 No. 52 - 59, Medellín, Colombia
| | - Ryan M Woodcock
- Department of Biology, University of Kentucky, Lexington, KY, 40506, USA.,Keene State College, Keene, NH, USA
| | - Jeramiah J Smith
- Department of Biology, University of Kentucky, Lexington, KY, 40506, USA
| | - Randal S Voss
- Department of Neuroscience, Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, KY, 40536, USA
| | - Jean Paul Delgado
- Grupo de Genética, Regeneración y Cáncer, Universidad de Antioquia, Sede de Investigación Universitaria, Torre 2, laboratorio 432. Calle 62 No. 52 - 59, Medellín, Colombia.
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El Amri M, Fitzgerald U, Schlosser G. MARCKS and MARCKS-like proteins in development and regeneration. J Biomed Sci 2018; 25:43. [PMID: 29788979 PMCID: PMC5964646 DOI: 10.1186/s12929-018-0445-1] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 05/07/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Myristoylated Alanine-Rich C-kinase Substrate (MARCKS) and MARCKS-like protein 1 (MARCKSL1) have a wide range of functions, ranging from roles in embryonic development to adult brain plasticity and the inflammatory response. Recently, both proteins have also been identified as important players in regeneration. Upon phosphorylation by protein kinase C (PKC) or calcium-dependent calmodulin-binding, MARCKS and MARCKSL1 translocate from the membrane into the cytosol, modulating cytoskeletal actin dynamics and vesicular trafficking and activating various signal transduction pathways. As a consequence, the two proteins are involved in the regulation of cell migration, secretion, proliferation and differentiation in many different tissues. MAIN BODY Throughout vertebrate development, MARCKS and MARCKSL1 are widely expressed in tissues derived from all germ layers, with particularly strong expression in the nervous system. They have been implicated in the regulation of gastrulation, myogenesis, brain development, and other developmental processes. Mice carrying loss of function mutations in either Marcks or Marcksl1 genes die shortly after birth due to multiple deficiencies including detrimental neural tube closure defects. In adult vertebrates, MARCKS and MARCKL1 continue to be important for multiple regenerative processes including peripheral nerve, appendage, and tail regeneration, making them promising targets for regenerative medicine. CONCLUSION This review briefly summarizes the molecular interactions and cellular functions of MARCKS and MARCKSL1 proteins and outlines their vital roles in development and regeneration.
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Affiliation(s)
- Mohamed El Amri
- Centre for Research in Medical Devices (CÚRAM), National University of Ireland, Galway, Biomedical Sciences Building, Newcastle Road, Galway, Ireland
| | - Una Fitzgerald
- Galway Neuroscience Centre, School of Natural Sciences, Biomedical Sciences Building, National University of Ireland, Newcastle Road, Galway, Ireland
| | - Gerhard Schlosser
- Centre for Research in Medical Devices (CÚRAM), National University of Ireland, Galway, Biomedical Sciences Building, Newcastle Road, Galway, Ireland. .,School of Natural Sciences and Regenerative Medicine Institute (REMEDI), National University of Ireland, Galway, Biomedical Sciences Building, Newcastle Road, Galway, Ireland.
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