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Grigoryan EN, Markitantova YV. Tail and Spinal Cord Regeneration in Urodelean Amphibians. Life (Basel) 2024; 14:594. [PMID: 38792615 PMCID: PMC11122520 DOI: 10.3390/life14050594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 03/21/2024] [Accepted: 04/30/2024] [Indexed: 05/26/2024] Open
Abstract
Urodelean amphibians can regenerate the tail and the spinal cord (SC) and maintain this ability throughout their life. This clearly distinguishes these animals from mammals. The phenomenon of tail and SC regeneration is based on the capability of cells involved in regeneration to dedifferentiate, enter the cell cycle, and change their (or return to the pre-existing) phenotype during de novo organ formation. The second critical aspect of the successful tail and SC regeneration is the mutual molecular regulation by tissues, of which the SC and the apical wound epidermis are the leaders. Molecular regulatory systems include signaling pathways components, inflammatory factors, ECM molecules, ROS, hormones, neurotransmitters, HSPs, transcriptional and epigenetic factors, etc. The control, carried out by regulatory networks on the feedback principle, recruits the mechanisms used in embryogenesis and accompanies all stages of organ regeneration, from the moment of damage to the completion of morphogenesis and patterning of all its structures. The late regeneration stages and the effects of external factors on them have been poorly studied. A new model for addressing this issue is herein proposed. The data summarized in the review contribute to understanding a wide range of fundamentally important issues in the regenerative biology of tissues and organs in vertebrates including humans.
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Affiliation(s)
| | - Yuliya V. Markitantova
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia;
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2
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Autumn M, Hu Y, Zeng J, McMenamin SK. Growth patterns of caudal fin rays are informed by both external signals from the regenerating organ and remembered identity autonomous to the local tissue. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.29.586899. [PMID: 38585773 PMCID: PMC10996721 DOI: 10.1101/2024.03.29.586899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Regenerating tissues must remember or interpret their spatial position, using this information to restore original size and patterning. The external skeleton of the zebrafish caudal fin is composed of 18 rays; after any portion of the fin is amputated, position-dependent regenerative growth restores each ray to its original length. We tested for transcriptional differences during regeneration of proximal versus distal tissues and identified 489 genes that differed in proximodistal expression. Thyroid hormone directs multiple aspects of ray patterning along the proximodistal axis, and we identified 364 transcripts showing a proximodistal expression pattern that was dependent on thyroid hormone context. To test what aspects of ray positional identity are directed by extrinsic cues versus remembered identity autonomous to the tissue itself, we transplanted distal portions of rays to proximal environments and evaluated regeneration within the new location. While neighboring proximal tissue showed robust expression of scpp7, a transcript with thyroid-regulated proximal enrichment, regenerating rays originating from transplanted distal tissue showed reduced (distal-like) expression during outgrowth. These distal-to-proximal transplants regenerated far beyond the length of the graft itself, indicating that cues from the proximal environment promoted additional growth. Nonetheless, these transplants initially regenerated at a much slower rate compared to controls, suggesting retained memory of distal identity. This early growth retardation caused rays that originated from transplants to become noticeably shorter than their native neighboring rays. While several aspects of fin ray morphology (bifurcation, segment length) were found to be determined by the environment, regeneration speed and ray length are remembered autonomously by tissues, persisting across multiple rounds of amputation and regeneration.
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Affiliation(s)
- Melody Autumn
- Biology Department, Boston College, Chestnut Hill, MA 02467
| | - Yinan Hu
- Biology Department, Boston College, Chestnut Hill, MA 02467
| | - Jenny Zeng
- Biology Department, Boston College, Chestnut Hill, MA 02467
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3
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Soos BL, Ballinger A, Weinstein M, Foreman H, Grampone J, Weafer S, Aylesworth C, King BL. Color-Flu Fluorescent Reporter Influenza A Viruses Allow for In Vivo Studies of Innate Immune Function in Zebrafish. Viruses 2024; 16:155. [PMID: 38275965 PMCID: PMC10818453 DOI: 10.3390/v16010155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/02/2024] [Accepted: 01/05/2024] [Indexed: 01/27/2024] Open
Abstract
Influenza virus infection can cause severe respiratory disease and is estimated to cause millions of illnesses annually. Studies on the contribution of the innate immune response to influenza A virus (IAV) to viral pathogenesis may yield new antiviral strategies. Zebrafish larvae are useful models for studying the innate immune response to pathogens, including IAV, in vivo. Here, we demonstrate how Color-flu, four fluorescent IAV strains originally developed for mice, can be used to study the host response to infection by simultaneously monitoring infected cells, neutrophils, and macrophages in vivo. Using this model, we show how the angiotensin-converting enzyme inhibitor, ramipril, and mitophagy inhibitor, MDIVI-1, improved survival, decreased viral burden, and improved the respiratory burst response to IAV infection. The Color-flu zebrafish larvae model of IAV infection is complementary to other models where the dynamics of infection and the response of innate immune cells can be visualized in a transparent host in vivo.
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Affiliation(s)
- Brandy-Lee Soos
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469, USA; (B.-L.S.); (A.B.); (M.W.); (H.F.); (J.G.); (S.W.); (C.A.)
| | - Alec Ballinger
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469, USA; (B.-L.S.); (A.B.); (M.W.); (H.F.); (J.G.); (S.W.); (C.A.)
| | - Mykayla Weinstein
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469, USA; (B.-L.S.); (A.B.); (M.W.); (H.F.); (J.G.); (S.W.); (C.A.)
| | - Haley Foreman
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469, USA; (B.-L.S.); (A.B.); (M.W.); (H.F.); (J.G.); (S.W.); (C.A.)
| | - Julianna Grampone
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469, USA; (B.-L.S.); (A.B.); (M.W.); (H.F.); (J.G.); (S.W.); (C.A.)
| | - Samuel Weafer
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469, USA; (B.-L.S.); (A.B.); (M.W.); (H.F.); (J.G.); (S.W.); (C.A.)
| | - Connor Aylesworth
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469, USA; (B.-L.S.); (A.B.); (M.W.); (H.F.); (J.G.); (S.W.); (C.A.)
| | - Benjamin L. King
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469, USA; (B.-L.S.); (A.B.); (M.W.); (H.F.); (J.G.); (S.W.); (C.A.)
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, ME 04469, USA
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4
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Zhang C, Zhang S, Liu M, Wang Y, Wang D, Xu S. Screening and identification of miRNAs regulating Tbx4/5 genes of Pampus argenteus. PeerJ 2022; 10:e14300. [PMID: 36312751 PMCID: PMC9610670 DOI: 10.7717/peerj.14300] [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: 03/08/2022] [Accepted: 10/05/2022] [Indexed: 01/24/2023] Open
Abstract
Background Silver pomfret (Pampus argenteus) is one of the most widely distributed and economically important pelagic fish species. However, an unique morphological feature of P. argenteus is the loss of pelvic fins, which can increase the energy requirement during food capture to some extent and is therefore not conducive to artificial culture. Tbx4/5 genes are highly conserved regulatory factors that regulate limb development in vertebrates and are in turn regulated by microRNAs (miRNAs). However, the miRNAs that directly regulate the Tbx4/5 genes in P. argenteus remain to be elucidated. Methods The Tbx4/5 genes of P. argenteus were first cloned, and the small RNA transcriptomes were sequenced by high-throughput sequencing during the critical period of the fin development at days 1, 7, and 13 of hatching. The miRNAs regulating the Tbx4/5 genes of P. argenteus were subsequently predicted by bioinformatics analysis, and the related miRNAs were verified in vitro using a dual fluorescence reporter system. Results A total of 662 miRNAs were identified, of which 257 were known miRNAs and 405 were novel miRNAs were identified. Compared to day 1, 182 miRNAs were differentially expressed (DE) on day 7, of which 77 and 105 miRNAs were downregulated and upregulated, respectively, while 278 miRNAs were DE on day 13, of which 136 and 142 miRNAs were downregulated and upregulated, respectively. Compared to day 13, four miRNAs were DE on day 7, of which three miRNAs were downregulated and one miRNA was upregulated. The results of hierarchical clustering of the miRNAs revealed that the DE genes were inversely expressed between days 1 and 7, and between days 1 and 13 of larval development, indicating that the larvae were in the peak stage of differentiation. However, the number of DE genes between days 7 and 13 of larval development was relatively small, suggesting the initiation of development. The potential target genes of the DE miRNAs were subsequently predicted, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of target genes were performed. The results suggested that the DE miRNAs were involved in growth, development, and signal transduction pathways, of which the Wnt and Fgfs signaling pathways are known to play important roles in the growth and development of fins. The results of dual fluorescence reporter assays demonstrated that miR-102, miR-301c, and miR-589 had a significant negative regulatory effect on the 3'-UTR of the Tbx4 gene, while miR-187, miR-201, miR-219, and miR-460 had a significant negative regulatory effect on the 3'-UTR of the Tbx5 gene. Altogether, the findings indicated that miRNAs play an important role in regulating the growth and development of pelvic fins in P. argenteus. This study provides a reference for elucidating the interactions between the miRNAs and target genes of P. argenteus in future studies.
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Affiliation(s)
| | | | | | - Yajun Wang
- Ningbo University, Zhejiang, China,Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo, China
| | | | - Shanliang Xu
- Ningbo University, Zhejiang, China,Key Laboratory of Applied Marine Biotechnology, Ningbo University, Ningbo, China
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5
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Li J, Wen W, Zhang S, Zhou C, Feng Y, Li X. The Expression and Function of lincRNA-154324 and the Adjoining Protein-Coding Gene vmp1 in the Caudal Fin Regeneration of Zebrafish. Int J Mol Sci 2022; 23:ijms23168944. [PMID: 36012210 PMCID: PMC9409064 DOI: 10.3390/ijms23168944] [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: 07/28/2022] [Revised: 08/06/2022] [Accepted: 08/09/2022] [Indexed: 11/16/2022] Open
Abstract
Caudal fin regeneration is regulated by a variety of mechanisms, but the role of long non-coding RNA (lncRNA) has rarely been studied. The present study aimed to describe the landscape of lncRNAs during caudal fin regeneration using whole transcriptome sequencing, and then to conduct a functional study on the target lncRNAs using real-time fluorescent quantitative PCR (RT-qPCR), in situ hybridization, and the CRISPR/Cas9 method for lncRNA gene knockout. The results of the transcriptome sequencing showed that a total of 381 lncRNAs were differentially expressed, among which ENSDART00000154324 (lincRNA-154324) was found to be highly related to caudal fin regeneration, and thus it was chosen as the target lncRNA for the subsequent functional study. The results regarding the temporal and spatial expression of lincRNA-154324 and the gene knockout results from CRISPR/Cas9 indicated that lincRNA-154324 is involved in the caudal fin regeneration of zebrafish. Importantly, we serendipitously discovered that the cis correlation coefficient between lincRNA-154324 and its neighboring gene vacuole membrane protein 1 (vmp1) is extremely high, and they are essential for the process of caudal fin regeneration. Moreover, studies have found that vmp1 plays an important role in protein secretion, organelle formation, multicellular development, and autophagy. Collectively, our result may provide a framework for the identification and analysis of lncRNAs involved in the regeneration of the zebrafish caudal fin.
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Affiliation(s)
- Jing Li
- The School of Medical Humanities, Xinxiang Medical University, Xinxiang 453003, China
- Henan International Joint Laboratory of Aquatic Toxicology and Health Protection, College of Life Science, Henan Normal University, Xinxiang 453007, China
| | - Wenjun Wen
- Henan International Joint Laboratory of Aquatic Toxicology and Health Protection, College of Life Science, Henan Normal University, Xinxiang 453007, China
| | - Shuqiang Zhang
- Henan International Joint Laboratory of Aquatic Toxicology and Health Protection, College of Life Science, Henan Normal University, Xinxiang 453007, China
| | - Chune Zhou
- Henan International Joint Laboratory of Aquatic Toxicology and Health Protection, College of Life Science, Henan Normal University, Xinxiang 453007, China
| | - Yiyi Feng
- Henan International Joint Laboratory of Aquatic Toxicology and Health Protection, College of Life Science, Henan Normal University, Xinxiang 453007, China
| | - Xiaoyu Li
- Henan International Joint Laboratory of Aquatic Toxicology and Health Protection, College of Life Science, Henan Normal University, Xinxiang 453007, China
- Correspondence: or
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6
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Magnuson JT, Qian L, McGruer V, Cheng V, Volz DC, Schlenk D. Relationship between miR-203a inhibition and oil-induced toxicity in early life stage zebrafish (Danio rerio). Toxicol Rep 2022; 9:373-381. [PMID: 35284238 PMCID: PMC8914477 DOI: 10.1016/j.toxrep.2022.03.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 01/28/2022] [Accepted: 03/02/2022] [Indexed: 11/18/2022] Open
Abstract
Dysregulation of microRNA (miRNA, miR) by environmental stressors influences the transcription of mRNA which may impair organism development and/or lead to adverse physiological outcomes. Early studies evaluating the effects of oil on developmental toxicity in early life stages of fish showed that reductions in expression of miR-203a were associated with enhanced expression of downstream mRNAs that predicted altered eye development, cardiovascular disease, and improper fin development. To better understand the effects of miR-203a inhibition as an outcome of oil-induced toxicity in early life stage (ELS) fish, embryonic zebrafish were injected with an miR-203a inhibitor or treated with 3.5 µM phenanthrene (Phe) as a positive control for morphological alterations of cardiovascular and eye development caused by oil. Embryos treated with Phe had diminished levels of miR-203a at 7 and 72 h after injection. Embryos treated with the miR-203a inhibitor and Phe exhibited a reduced heart rate by 48 h post fertilization (hpf), with an increased incidence of developmental deformities (including pericardial edema, altered eye development, and spinal deformities) and reduced caudal fin length by 72 hpf. There were significant reductions in lens and eye diameters in 120 hpf miR-203a-inhibitor and Phe-treated fish, as well as a significantly reduced number of eye saccades, determined by an optokinetic response (OKR) behavioral assay. The expression of vegfa, which is an important activator during neovascularization, was significantly upregulated in embryos receiving miR-203a inhibitor injections by 7 and 72 hpf with increased trends in vegfa expression in 72 hpf larvae treated with Phe. There were decreasing trends in crx, neurod1, and pde6h expression by 72 hpf in miR-203a inhibitor and Phe treatments, which are involved in photoreceptor function in developing eyes and regulated by miR-203a. These results suggest that an inhibition of miR-203a in ELS fish exhibits an oil-induced toxic response that is consistent with Phe treatment and specifically impacts retinal, cardiac, and fin development in ELS fish. miR-203a inhibitor-injected zebrafish exhibited an oil-induced toxic response. Inhibition of miR-203a impaired retinal, cardiac, and fin development in zebrafish. miR-203a inhibition validated previously predicted transcriptomic pathways.
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Affiliation(s)
- Jason T. Magnuson
- Department of Environmental Sciences, University of California, Riverside, CA, USA
- Corresponding author.
| | - Le Qian
- College of Sciences, China Agricultural University, Beijing, China
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, China
- Corresponding author at: College of Sciences, China Agricultural University, Beijing, China.
| | - Victoria McGruer
- Department of Environmental Sciences, University of California, Riverside, CA, USA
| | - Vanessa Cheng
- Department of Environmental Sciences, University of California, Riverside, CA, USA
| | - David C. Volz
- Department of Environmental Sciences, University of California, Riverside, CA, USA
| | - Daniel Schlenk
- Department of Environmental Sciences, University of California, Riverside, CA, USA
- Institute of Environmental Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
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7
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Amino Acids and IGF1 Regulation of Fish Muscle Growth Revealed by Transcriptome and microRNAome Integrative Analyses of Pacu ( Piaractus mesopotamicus) Myotubes. Int J Mol Sci 2022; 23:ijms23031180. [PMID: 35163102 PMCID: PMC8835699 DOI: 10.3390/ijms23031180] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 01/12/2022] [Accepted: 01/17/2022] [Indexed: 12/04/2022] Open
Abstract
Amino acids (AA) and IGF1 have been demonstrated to play essential roles in protein synthesis and fish muscle growth. The myoblast cell culture is useful for studying muscle regulation, and omics data have contributed enormously to understanding its molecular biology. However, to our knowledge, no study has performed the large-scale sequencing of fish-cultured muscle cells stimulated with pro-growth signals. In this work, we obtained the transcriptome and microRNAome of pacu (Piaractus mesopotamicus)-cultured myotubes treated with AA or IGF1. We identified 1228 and 534 genes differentially expressed by AA and IGF1. An enrichment analysis showed that AA treatment induced chromosomal changes, mitosis, and muscle differentiation, while IGF1 modulated IGF/PI3K signaling, metabolic alteration, and matrix structure. In addition, potential molecular markers were similarly modulated by both treatments. Muscle-miRNAs (miR-1, -133, -206 and -499) were up-regulated, especially in AA samples, and we identified molecular networks with omics integration. Two pairs of genes and miRNAs demonstrated a high-level relationship, and involvement in myogenesis and muscle growth: marcksb and miR-29b in AA, and mmp14b and miR-338-5p in IGF1. Our work helps to elucidate fish muscle physiology and metabolism, highlights potential molecular markers, and creates a perspective for improvements in aquaculture and in in vitro meat production.
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Ribeiro AO, de Oliveira AC, Costa JM, Nachtigall PG, Herkenhoff ME, Campos VF, Delella FK, Pinhal D. MicroRNA roles in regeneration: Multiple lessons from zebrafish. Dev Dyn 2021; 251:556-576. [PMID: 34547148 DOI: 10.1002/dvdy.421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 08/23/2021] [Accepted: 09/07/2021] [Indexed: 12/23/2022] Open
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs with pivotal roles in the control of gene expression. By comparing the miRNA profiles of uninjured vs. regenerating tissues and structures, several studies have found that miRNAs are potentially involved in the regenerative process. By inducing miRNA overexpression or inhibition, elegant experiments have directed regenerative responses validating relevant miRNA-to-target interactions. The zebrafish (Danio rerio) has been the epicenter of regenerative research because of its exceptional capability to self-repair damaged tissues and body structures. In this review, we discuss recent discoveries that have improved our understanding of the impact of gene regulation mediated by miRNAs in the context of the regeneration of fins, heart, retina, and nervous tissue in zebrafish. We compiled what is known about the miRNA control of regeneration in these tissues and investigated the links among up-regulated and down-regulated miRNAs, their putative or validated targets, and the regenerative process. Finally, we briefly discuss the forthcoming prospects, highlighting directions and the potential for further development of this field.
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Affiliation(s)
- Amanda Oliveira Ribeiro
- Laboratório Genômica e Evolução Molecular (LGEM), Departamento de Ciências Químicas e Biológicas, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Botucatu, SP, Brazil
| | - Arthur Casulli de Oliveira
- Laboratório Genômica e Evolução Molecular (LGEM), Departamento de Ciências Químicas e Biológicas, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Botucatu, SP, Brazil
| | - Juliana Mara Costa
- Laboratório Genômica e Evolução Molecular (LGEM), Departamento de Ciências Químicas e Biológicas, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Botucatu, SP, Brazil
| | - Pedro Gabriel Nachtigall
- Laboratório Genômica e Evolução Molecular (LGEM), Departamento de Ciências Químicas e Biológicas, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Botucatu, SP, Brazil.,Laboratório Especial de Toxicologia Aplicada (LETA), CeTICS, Instituto Butantan, São Paulo, SP, Brazil
| | - Marcos Edgar Herkenhoff
- Laboratório Genômica e Evolução Molecular (LGEM), Departamento de Ciências Químicas e Biológicas, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Botucatu, SP, Brazil.,Departamento de Tecnologia Bioquímico-Farmacêutica, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Vinicius Farias Campos
- Laboratório de Genômica Estrutural, Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Flávia Karina Delella
- Departamento de Biologia Estrutural e Funcional, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Botucatu, SP, Brazil
| | - Danillo Pinhal
- Laboratório Genômica e Evolução Molecular (LGEM), Departamento de Ciências Químicas e Biológicas, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho (UNESP), Botucatu, SP, Brazil
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9
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Khyeam S, Lee S, Huang GN. Genetic, Epigenetic, and Post-Transcriptional Basis of Divergent Tissue Regenerative Capacities Among Vertebrates. ACTA ACUST UNITED AC 2021; 2. [PMID: 34423307 DOI: 10.1002/ggn2.10042] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Regeneration is widespread across the animal kingdom but varies vastly across phylogeny and even ontogeny. Adult mammalian regeneration in most organs and appendages is limited, while vertebrates such as zebrafish and salamanders are able to regenerate various organs and body parts. Here, we focus on the regeneration of appendages, spinal cord, and heart - organs and body parts that are highly regenerative among fish and amphibian species but limited in adult mammals. We then describe potential genetic, epigenetic, and post-transcriptional similarities among these different forms of regeneration across vertebrates and discuss several theories for diminished regenerative capacity throughout evolution.
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Affiliation(s)
- Sheamin Khyeam
- Cardiovascular Research Institute and Department of Physiology, University of California, San Francisco, San Francisco, CA 94158, USA.,Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Sukjun Lee
- Cardiovascular Research Institute and Department of Physiology, University of California, San Francisco, San Francisco, CA 94158, USA.,Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Guo N Huang
- Cardiovascular Research Institute and Department of Physiology, University of California, San Francisco, San Francisco, CA 94158, USA.,Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94158, USA
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10
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Sullivan C, Soos BL, Millard PJ, Kim CH, King BL. Modeling Virus-Induced Inflammation in Zebrafish: A Balance Between Infection Control and Excessive Inflammation. Front Immunol 2021; 12:636623. [PMID: 34025644 PMCID: PMC8138431 DOI: 10.3389/fimmu.2021.636623] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 04/21/2021] [Indexed: 12/16/2022] Open
Abstract
The inflammatory response to viral infection in humans is a dynamic process with complex cell interactions that are governed by the immune system and influenced by both host and viral factors. Due to this complexity, the relative contributions of the virus and host factors are best studied in vivo using animal models. In this review, we describe how the zebrafish (Danio rerio) has been used as a powerful model to study host-virus interactions and inflammation by combining robust forward and reverse genetic tools with in vivo imaging of transparent embryos and larvae. The innate immune system has an essential role in the initial inflammatory response to viral infection. Focused studies of the innate immune response to viral infection are possible using the zebrafish model as there is a 4-6 week timeframe during development where they have a functional innate immune system dominated by neutrophils and macrophages. During this timeframe, zebrafish lack a functional adaptive immune system, so it is possible to study the innate immune response in isolation. Sequencing of the zebrafish genome has revealed significant genetic conservation with the human genome, and multiple studies have revealed both functional conservation of genes, including those critical to host cell infection and host cell inflammatory response. In addition to studying several fish viruses, zebrafish infection models have been developed for several human viruses, including influenza A, noroviruses, chikungunya, Zika, dengue, herpes simplex virus type 1, Sindbis, and hepatitis C virus. The development of these diverse viral infection models, coupled with the inherent strengths of the zebrafish model, particularly as it relates to our understanding of macrophage and neutrophil biology, offers opportunities for far more intensive studies aimed at understanding conserved host responses to viral infection. In this context, we review aspects relating to the evolution of innate immunity, including the evolution of viral pattern recognition receptors, interferons and interferon receptors, and non-coding RNAs.
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Affiliation(s)
- Con Sullivan
- College of Arts and Sciences, University of Maine at Augusta, Bangor, ME, United States
| | - Brandy-Lee Soos
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME, United States
| | - Paul J Millard
- Department of Environmental and Sustainable Engineering, University at Albany, Albany, NY, United States
| | - Carol H Kim
- Department of Biomedical Sciences, University at Albany, Albany, NY, United States.,Department of Biological Sciences, University at Albany, Albany, NY, United States
| | - Benjamin L King
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME, United States.,Graduate School of Biomedical Science and Engineering, University of Maine, Orono, ME, United States
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11
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Takemura M, Bowden N, Lu YS, Nakato E, O'Connor MB, Nakato H. Drosophila MOV10 regulates the termination of midgut regeneration. Genetics 2021; 218:6156853. [PMID: 33693718 DOI: 10.1093/genetics/iyab031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 02/23/2021] [Indexed: 12/22/2022] Open
Abstract
The molecular mechanisms by which stem cell proliferation is precisely controlled during the course of regeneration are poorly understood. Namely, how a damaged tissue senses when to terminate the regeneration process, inactivates stem cell mitotic activity, and organizes ECM integrity remain fundamental unanswered questions. The Drosophila midgut intestinal stem cell (ISC) offers an excellent model system to study the molecular basis for stem cell inactivation. Here, we show that a novel gene, CG6967 or dMOV10, is induced at the termination stage of midgut regeneration, and shows an inhibitory effect on ISC proliferation. dMOV10 encodes a putative component of the microRNA (miRNA) gene silencing complex (miRISC). Our data, along with previous studies on the mammalian MOV10, suggest that dMOV10 is not a core member of miRISC, but modulates miRISC activity as an additional component. Further analyses identified direct target mRNAs of dMOV10-containing miRISC, including Daughter against Dpp (Dad), a known inhibitor of BMP/TGF-β signaling. We show that RNAi knockdown of Dad significantly impaired ISC division during regeneration. We also identified six miRNAs that are induced at the termination stage and their potential target transcripts. One of these miRNAs, mir-1, is required for proper termination of ISC division at the end of regeneration. We propose that miRNA-mediated gene regulation contributes to the precise control of Drosophila midgut regeneration.
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Affiliation(s)
- Masahiko Takemura
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Nanako Bowden
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Yi-Si Lu
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Eriko Nakato
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Michael B O'Connor
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Hiroshi Nakato
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
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12
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Daponte V, Tylzanowski P, Forlino A. Appendage Regeneration in Vertebrates: What Makes This Possible? Cells 2021; 10:cells10020242. [PMID: 33513779 PMCID: PMC7911911 DOI: 10.3390/cells10020242] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/18/2021] [Accepted: 01/22/2021] [Indexed: 12/26/2022] Open
Abstract
The ability to regenerate amputated or injured tissues and organs is a fascinating property shared by several invertebrates and, interestingly, some vertebrates. The mechanism of evolutionary loss of regeneration in mammals is not understood, yet from the biomedical and clinical point of view, it would be very beneficial to be able, at least partially, to restore that capability. The current availability of new experimental tools, facilitating the comparative study of models with high regenerative ability, provides a powerful instrument to unveil what is needed for a successful regeneration. The present review provides an updated overview of multiple aspects of appendage regeneration in three vertebrates: lizard, salamander, and zebrafish. The deep investigation of this process points to common mechanisms, including the relevance of Wnt/β-catenin and FGF signaling for the restoration of a functional appendage. We discuss the formation and cellular origin of the blastema and the identification of epigenetic and cellular changes and molecular pathways shared by vertebrates capable of regeneration. Understanding the similarities, being aware of the differences of the processes, during lizard, salamander, and zebrafish regeneration can provide a useful guide for supporting effective regenerative strategies in mammals.
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Affiliation(s)
- Valentina Daponte
- Biochemistry Unit, Department of Molecular Medicine, University of Pavia, via Taramelli 3/B, 27100 Pavia, Italy;
| | - Przemko Tylzanowski
- Skeletal Biology and Engineering Research Center, Department of Development and Regeneration, University of Leuven, 3000 Leuven, Belgium;
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, 20-059 Lublin, Poland
| | - Antonella Forlino
- Biochemistry Unit, Department of Molecular Medicine, University of Pavia, via Taramelli 3/B, 27100 Pavia, Italy;
- Correspondence: ; Tel.: +39-0382-987235
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13
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Konar GJ, Ferguson C, Flickinger Z, Kent MR, Patton JG. miRNAs and Müller Glia Reprogramming During Retina Regeneration. Front Cell Dev Biol 2021; 8:632632. [PMID: 33537319 PMCID: PMC7848101 DOI: 10.3389/fcell.2020.632632] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 12/21/2020] [Indexed: 12/15/2022] Open
Abstract
The use of model systems that are capable of robust, spontaneous retina regeneration has allowed for the identification of genetic pathways and components that are required for retina regeneration. Complemented by mouse models in which retina regeneration can be induced after forced expression of key factors, altered chromatin accessibility, or inhibition of kinase/signaling cascades, a clearer picture of the key regulatory events that control retina regeneration is emerging. In all cases, Müller glia (MG) serve as an adult retinal stem cell that must be reprogrammed to allow for regeneration, with the end goal being to understand why regenerative pathways are blocked in mammals, but spontaneous in other vertebrates such as zebrafish. miRNAs have emerged as key gene regulatory molecules that control both development and regeneration in vertebrates. Here, we focus on a small subset of miRNAs that control MG reprogramming during retina regeneration and have the potential to serve as therapeutic targets for treatment of visual disorders and damage.
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Affiliation(s)
- Gregory J Konar
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
| | - Claire Ferguson
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
| | - Zachary Flickinger
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
| | - Matthew R Kent
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
| | - James G Patton
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
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14
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Ohgo S, Sakamoto T, Nakajima W, Matsunaga S, Wada N. Visualization of extracellular vesicles in the regenerating caudal fin blastema of zebrafish using in vivo electroporation. Biochem Biophys Res Commun 2020; 533:1371-1377. [PMID: 33077180 DOI: 10.1016/j.bbrc.2020.10.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 10/10/2020] [Indexed: 01/03/2023]
Abstract
Zebrafish have high regenerative ability in several organs including the fin. Although various mechanisms underlying fin regeneration have been revealed, some mechanisms remain to be elucidated. Recently, extracellular vesicles (EVs) have been the focus of research with regard to their role in cell-to-cell communication. It has been suggested that cells in regenerating tissues communicate using EVs. In this study, we examined the involvement of EVs in the caudal fin regeneration of zebrafish using an in vivo electroporation method. The process of regeneration appeared normal after in vivo electroporation, and the transferred plasmid showed mosaic expression in the blastema. We took advantage of this mosaic expression to observe the distribution of exosomal markers in the blastema. We transferred exosomal markers by in vivo electroporation and identified EVs in the regenerating caudal fin. The results suggest that blastemal cells communicate with other cells via EVs during caudal fin regeneration.
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Affiliation(s)
- Shiro Ohgo
- Department of Applied Biological Science, Tokyo University of Science, Noda, Japan.
| | - Takuya Sakamoto
- Department of Applied Biological Science, Tokyo University of Science, Noda, Japan
| | - Wataru Nakajima
- Department of Applied Biological Science, Tokyo University of Science, Noda, Japan
| | - Sachihiro Matsunaga
- Department of Applied Biological Science, Tokyo University of Science, Noda, Japan
| | - Naoyuki Wada
- Department of Applied Biological Science, Tokyo University of Science, Noda, Japan
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15
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Yasin JK, Mishra BK, Pillai MA, Verma N, Wani SH, Elansary HO, El-Ansary DO, Pandey PS, Chinnusamy V. Genome wide in-silico miRNA and target network prediction from stress responsive Horsegram (Macrotyloma uniflorum) accessions. Sci Rep 2020; 10:17203. [PMID: 33057204 PMCID: PMC7560861 DOI: 10.1038/s41598-020-73140-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 09/14/2020] [Indexed: 12/24/2022] Open
Abstract
Horsegram (Macrotyloma uniflorum (Lam.) Verdc.) is a drought hardy food and fodder legume of Indo-African continents with diverse germplasm sources demonstrating alternating mechanisms depicting contrasting adaptations to different climatic zones. Tissue specific expression of genes contributes substantially to location specific adaptations. Regulatory networks of such adaptive genes are elucidated for downstream translational research. MicroRNAs are small endogenous regulatory RNAs which alters the gene expression profiles at a particular time and type of tissue. Identification of such small regulatory RNAs in low moisture stress hardy crops can help in cross species transfer and validation confirming stress tolerance ability. This study outlined prediction of conserved miRNAs from transcriptome shotgun assembled sequences and EST sequences of horsegram. We could validate eight out of 15 of the identified miRNAs to demonstrate their role in deficit moisture stress tolerance mechanism of horsegram variety Paiyur1 with their target networks. The putative mumiRs were related to other food legumes indicating the presence of gene regulatory networks. Differential miRNA expression among drought specific tissues indicted the probable energy conservation mechanism. Targets were identified for functional characterization and regulatory network was constructed to find out the probable pathways of post-transcriptional regulation. The functional network revealed mechanism of biotic and abiotic stress tolerance, energy conservation and photoperiod responsiveness.
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Affiliation(s)
- Jeshima Khan Yasin
- Division of Genomic Resources, ICAR-National Bureau Plant Genetic Resources, PUSA Campus, New Delhi, 110012, India.
| | - Bharat Kumar Mishra
- Division of Genomic Resources, ICAR-National Bureau Plant Genetic Resources, PUSA Campus, New Delhi, 110012, India.,Department of Biology, University of Alabama at Birmingham, Birmingham, AL, 35294-1170, USA
| | - M Arumugam Pillai
- Department of Plant Breeding and Genetics, Agricultural College and Research Institute, Tamil Nadu Agricultural University, Killikulam, Vallanadu, Tamil Nadu, 628252, India
| | - Nidhi Verma
- Principal Scientist (Education Planning and Home Science), Agricultural Education Division Krishi Anusandhan Bhawan I, Indian Council of Agricultural Research, PUSA Campus, New Delhi, 110 012, India
| | - Shabir H Wani
- Mountain Research Centre For Field Crops, Khudwani Anantnag-192101, Sher-E-KashmiR University of Agricultural Sciences and Technology of Kashmir, Badgam, J&K, India
| | - Hosam O Elansary
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia.,Floriculture, Ornamental Horticulture, and Garden Design Department, Faculty of Agriculture (El-Shatby), Alexandria University, Alexandria, 21545, Egypt
| | - Diaa O El-Ansary
- Precision Agriculture Laboratory, Department of Pomology, Faculty of Agriculture (El-Shatby), Alexandria University, Alexandria, Egypt
| | - P S Pandey
- Indian Council of Agricultural Research (ICAR), PUSA, New Delhi, 110 012, India
| | - Viswanathan Chinnusamy
- Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi, 110012, India
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16
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Zullo L, Bozzo M, Daya A, Di Clemente A, Mancini FP, Megighian A, Nesher N, Röttinger E, Shomrat T, Tiozzo S, Zullo A, Candiani S. The Diversity of Muscles and Their Regenerative Potential across Animals. Cells 2020; 9:cells9091925. [PMID: 32825163 PMCID: PMC7563492 DOI: 10.3390/cells9091925] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/14/2020] [Accepted: 08/17/2020] [Indexed: 02/06/2023] Open
Abstract
Cells with contractile functions are present in almost all metazoans, and so are the related processes of muscle homeostasis and regeneration. Regeneration itself is a complex process unevenly spread across metazoans that ranges from full-body regeneration to partial reconstruction of damaged organs or body tissues, including muscles. The cellular and molecular mechanisms involved in regenerative processes can be homologous, co-opted, and/or evolved independently. By comparing the mechanisms of muscle homeostasis and regeneration throughout the diversity of animal body-plans and life cycles, it is possible to identify conserved and divergent cellular and molecular mechanisms underlying muscle plasticity. In this review we aim at providing an overview of muscle regeneration studies in metazoans, highlighting the major regenerative strategies and molecular pathways involved. By gathering these findings, we wish to advocate a comparative and evolutionary approach to prompt a wider use of “non-canonical” animal models for molecular and even pharmacological studies in the field of muscle regeneration.
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Affiliation(s)
- Letizia Zullo
- Istituto Italiano di Tecnologia, Center for Micro-BioRobotics & Center for Synaptic Neuroscience and Technology (NSYN), 16132 Genova, Italy;
- IRCCS Ospedale Policlinico San Martino, 16132 Genova, Italy
- Correspondence: (L.Z.); (A.Z.)
| | - Matteo Bozzo
- Laboratory of Developmental Neurobiology, Department of Earth, Environment and Life Sciences, University of Genova, Viale Benedetto XV 5, 16132 Genova, Italy; (M.B.); (S.C.)
| | - Alon Daya
- Faculty of Marine Sciences, Ruppin Academic Center, Michmoret 40297, Israel; (A.D.); (N.N.); (T.S.)
| | - Alessio Di Clemente
- Istituto Italiano di Tecnologia, Center for Micro-BioRobotics & Center for Synaptic Neuroscience and Technology (NSYN), 16132 Genova, Italy;
- Department of Experimental Medicine, University of Genova, Viale Benedetto XV, 3, 16132 Genova, Italy
| | | | - Aram Megighian
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy;
- Padova Neuroscience Center, University of Padova, 35131 Padova, Italy
| | - Nir Nesher
- Faculty of Marine Sciences, Ruppin Academic Center, Michmoret 40297, Israel; (A.D.); (N.N.); (T.S.)
| | - Eric Röttinger
- Institute for Research on Cancer and Aging (IRCAN), Université Côte d’Azur, CNRS, INSERM, 06107 Nice, France;
| | - Tal Shomrat
- Faculty of Marine Sciences, Ruppin Academic Center, Michmoret 40297, Israel; (A.D.); (N.N.); (T.S.)
| | - Stefano Tiozzo
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Sorbonne Université, CNRS, 06230 Paris, France;
| | - Alberto Zullo
- Department of Science and Technology, University of Sannio, 82100 Benevento, Italy;
- Correspondence: (L.Z.); (A.Z.)
| | - Simona Candiani
- Laboratory of Developmental Neurobiology, Department of Earth, Environment and Life Sciences, University of Genova, Viale Benedetto XV 5, 16132 Genova, Italy; (M.B.); (S.C.)
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17
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Shi L, Chen C, Yin Z, Wei G, Xie G, Liu D. Systematic profiling of early regulators during tissue regeneration using zebrafish model. Wound Repair Regen 2020; 29:189-195. [PMID: 32776615 DOI: 10.1111/wrr.12852] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 06/08/2020] [Accepted: 06/11/2020] [Indexed: 11/28/2022]
Abstract
Great progresses have been made in comprehension of tissue regeneration process. However, one of the central questions in regeneration research remains to be deciphered is what factors initiate regenerative process. In present study, we focused on systematic profiling of early regulators in tissue regeneration via high-throughput screening on zebrafish caudal fin model. Firstly, 53 GO-annotated regeneration-related genes, which were specifically activated upon fin amputation, were identified according to the transcriptomic analysis. Moreover, qRT-PCR analysis of a couple of randomly selected genes from the aforementioned gene list validated our sequencing results. These studies confirmed the reliability of transcriptome sequencing analysis. Fibroblast growth factor 20a (fgf20a) is a key initial factor in the regeneration of zebrafish. Through a gene expression correlation analysis, we discovered a collection of 70 genes correlating with fgf20a, whose expression increased promptly at 2 days post amputation (dpa) and went down to the basal level until the completion of fin regeneration. In addition, two genes, socs3b and nppc, were chosen to investigate their functions during the fin regeneration. Inhibition of either of those genes significantly delayed the regenerative process. Taken together, we provided a simple and effective time-saving strategy that may serve as a tool for identifying early regulators in regeneration and identified 71 genes as early regulators of fin regeneration.
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Affiliation(s)
- Linsheng Shi
- The Second Affiliated Hospital of Nantong University, School of Life Science, Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Changsheng Chen
- The Second Affiliated Hospital of Nantong University, School of Life Science, Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Zhenhua Yin
- Institute of Reproductive Medicine, Nantong University, Nantong, China
| | - Guanyun Wei
- The Second Affiliated Hospital of Nantong University, School of Life Science, Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Gangcai Xie
- Institute of Reproductive Medicine, Nantong University, Nantong, China
| | - Dong Liu
- The Second Affiliated Hospital of Nantong University, School of Life Science, Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China
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18
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Abo-Al-Ela HG, Burgos-Aceves MA. Exploring the role of microRNAs in axolotl regeneration. J Cell Physiol 2020; 236:839-850. [PMID: 32638401 DOI: 10.1002/jcp.29920] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 05/30/2020] [Accepted: 06/21/2020] [Indexed: 12/13/2022]
Abstract
The axolotl, Ambystoma mexicanum, is used extensively for research in developmental biology, particularly for its ability to regenerate and restore lost organs, including in the nervous system, to full functionality. Regeneration in mammals typically depends on the healing process and scar formation with limited replacement of lost tissue. Other organisms, such as spiny mice (Acomys cahirinus), salamanders, and zebrafish, are able to regenerate some damaged body components. Blastema is a tissue that is formed after tissue injury in such organisms and is composed of progenitor cells or dedifferentiated cells that differentiate into various cell types during regeneration. Thus, identifying the molecules responsible for initiation of blastema formation is an important aspect for understanding regeneration. Introns, a major source of noncoding RNAs (ncRNAs), have characteristic sizes in the axolotl, particularly in genes associated with development. These ncRNAs, particularly microRNAs (miRNAs), exhibit dynamic regulation during regeneration. These miRNAs play an essential role in timing and control of gene expression to order and organize processes necessary for blastema creation. Master keys or molecules that underlie the remarkable regenerative abilities of the axolotl remain to be fully explored and exploited. Further and ongoing research on regeneration promises new knowledge that may allow improved repair and renewal of human tissues.
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Affiliation(s)
- Haitham G Abo-Al-Ela
- Department of Aquaculture, Faculty of Fish Resources, Suez University, Suez, Egypt
| | - Mario A Burgos-Aceves
- Department of Chemistry and Biology, University of Salerno, Fisciano, Salerno, Italy
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19
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Yong Huang, Xiong J, Brown PB, Sun X. Identification and Characteristics of Batrachuperus karlschmidti miRNA Using Illumina Deep Sequencing. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2020. [DOI: 10.1134/s1068162020020193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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20
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Harris MP, Daane JM, Lanni J. Through veiled mirrors: Fish fins giving insight into size regulation. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2020; 10:e381. [PMID: 32323915 DOI: 10.1002/wdev.381] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 02/13/2020] [Accepted: 03/19/2020] [Indexed: 12/25/2022]
Abstract
Faithful establishment and maintenance of proportion is seen across biological systems and provides a glimpse at fundamental rules of scaling that underlie development and evolution. Dysregulation of proportion is observed in a range of human diseases and growth disorders, indicating that proper scaling is an essential component of normal anatomy and physiology. However, when viewed through an evolutionary lens, shifts in the regulation of relative proportion are one of the most striking sources of morphological diversity among organisms. To date, the mechanisms via which relative proportion is specified and maintained remain unclear. Through the application of powerful experimental, genetic and molecular approaches, the teleost fin has provided an effective model to investigate the regulation of scaling, size, and relative growth in vertebrate organisms. This article is categorized under: Establishment of Spatial and Temporal Patterns > Regulation of Size, Proportion, and Timing Adult Stem Cells, Tissue Renewal, and Regeneration > Regeneration Comparative Development and Evolution > Regulation of Organ Diversity.
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Affiliation(s)
- Matthew P Harris
- Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jacob M Daane
- Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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21
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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
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22
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King BL, Rosenstein MC, Smith AM, Dykeman CA, Smith GA, Yin VP. RegenDbase: a comparative database of noncoding RNA regulation of tissue regeneration circuits across multiple taxa. NPJ Regen Med 2018; 3:10. [PMID: 29872545 PMCID: PMC5973935 DOI: 10.1038/s41536-018-0049-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 04/17/2018] [Accepted: 05/04/2018] [Indexed: 12/16/2022] Open
Abstract
Regeneration is an endogenous process of tissue repair that culminates in complete restoration of tissue and organ function. While regenerative capacity in mammals is limited to select tissues, lower vertebrates like zebrafish and salamanders are endowed with the capacity to regenerate entire limbs and most adult tissues, including heart muscle. Numerous profiling studies have been conducted using these research models in an effort to identify the genetic circuits that accompany tissue regeneration. Most of these studies, however, are confined to an individual injury model and/or research organism and focused primarily on protein encoding transcripts. Here we describe RegenDbase, a new database with the functionality to compare and contrast gene regulatory pathways within and across tissues and research models. RegenDbase combines pipelines that integrate analysis of noncoding RNAs in combination with protein encoding transcripts. We created RegenDbase with a newly generated comprehensive dataset for adult zebrafish heart regeneration combined with existing microarray and RNA-sequencing studies on multiple injured tissues. In this current release, we detail microRNA-mRNA regulatory circuits and the biological processes these interactions control during the early stages of heart regeneration. Moreover, we identify known and putative novel lncRNAs and identify their potential target genes based on proximity searches. We postulate that these candidate factors underscore robust regenerative capacity in lower vertebrates. RegenDbase provides a systems-level analysis of tissue regeneration genetic circuits across injury and animal models and addresses the growing need to understand how noncoding RNAs influence these changes in gene expression.
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Affiliation(s)
- Benjamin L. King
- Kathryn Davis Center for Regenerative Biology and Medicine, Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04672 USA
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469 USA
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME 04469 USA
| | - Michael C. Rosenstein
- Kathryn Davis Center for Regenerative Biology and Medicine, Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04672 USA
- Present Address: RockStep Solutions, Portland, ME 04101 USA
| | - Ashley M. Smith
- Kathryn Davis Center for Regenerative Biology and Medicine, Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04672 USA
| | - Christina A. Dykeman
- Kathryn Davis Center for Regenerative Biology and Medicine, Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04672 USA
| | - Grace A. Smith
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469 USA
- University of Maine Honors College, University of Maine, Orono, ME 04469 USA
| | - Viravuth P. Yin
- Kathryn Davis Center for Regenerative Biology and Medicine, Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04672 USA
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME 04469 USA
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23
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Differential miRNA expression in the three-spined stickleback, response to environmental changes. Sci Rep 2017; 7:18089. [PMID: 29273769 PMCID: PMC5741757 DOI: 10.1038/s41598-017-18128-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 12/01/2017] [Indexed: 12/13/2022] Open
Abstract
miRNAs play important role in the various physiological and evolutionary processes, however, there is no data allowing comparison of evolutionary differences between various ecotypes adapted to different environmental conditions and specimen demonstrating immediate physiological response to the environmental changes. We compared miRNA expression profiles between marine and freshwater stickleback populations of the three-spined stickleback to identify the evolutionary differences. To study the immediate physiological response to foreign environment, we explored the changes induced by transfer of marine sticklebacks into freshwater environment and vice versa. Comparative analysis of changes in miRNA expression suggested that they are driven by three independent factors: (1) non-specific changes in miRNA expression under different environmental conditions; (2) specific response to freshwater conditions in the marine stickleback ecotype; (3) specific response to extreme osmotic conditions for both marine and freshwater ecotypes during the contact with non-native environment. Gene Ontology enrichment analysis of differential expressed miRNA targets supports our current hypothesis.
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24
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Banerji R, Skibbens RV, Iovine MK. Cohesin mediates Esco2-dependent transcriptional regulation in a zebrafish regenerating fin model of Roberts Syndrome. Biol Open 2017; 6:1802-1813. [PMID: 29084713 PMCID: PMC5769645 DOI: 10.1242/bio.026013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Robert syndrome (RBS) and Cornelia de Lange syndrome (CdLS) are human developmental disorders characterized by craniofacial deformities, limb malformation and mental retardation. These birth defects are collectively termed cohesinopathies as both arise from mutations in cohesion genes. CdLS arises due to autosomal dominant mutations or haploinsufficiencies in cohesin subunits (SMC1A, SMC3 and RAD21) or cohesin auxiliary factors (NIPBL and HDAC8) that result in transcriptional dysregulation of developmental programs. RBS arises due to autosomal recessive mutations in cohesin auxiliary factor ESCO2, the gene that encodes an N-acetyltransferase which targets the SMC3 subunit of the cohesin complex. The mechanism that underlies RBS, however, remains unknown. A popular model states that RBS arises due to mitotic failure and loss of progenitor stem cells through apoptosis. Previous findings in the zebrafish regenerating fin, however, suggest that Esco2-knockdown results in transcription dysregulation, independent of apoptosis, similar to that observed in CdLS patients. Previously, we used the clinically relevant CX43 to demonstrate a transcriptional role for Esco2. CX43 is a gap junction gene conserved among all vertebrates that is required for direct cell-cell communication between adjacent cells such that cx43 mutations result in oculodentodigital dysplasia. Here, we show that morpholino-mediated knockdown of smc3 reduces cx43 expression and perturbs zebrafish bone and tissue regeneration similar to those previously reported for esco2 knockdown. Also similar to Esco2-dependent phenotypes, Smc3-dependent bone and tissue regeneration defects are rescued by transgenic Cx43 overexpression, suggesting that Smc3 and Esco2 cooperatively act to regulate cx43 transcription. In support of this model, chromatin immunoprecipitation assays reveal that Smc3 binds to a discrete region of the cx43 promoter, suggesting that Esco2 exerts transcriptional regulation of cx43 through modification of Smc3 bound to the cx43 promoter. These findings have the potential to unify RBS and CdLS as transcription-based mechanisms.
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Affiliation(s)
- Rajeswari Banerji
- Department of Biological Science, Lehigh University, Bethlehem, Pennsylvania 18015, USA
| | - Robert V Skibbens
- Department of Biological Science, Lehigh University, Bethlehem, Pennsylvania 18015, USA
| | - M Kathryn Iovine
- Department of Biological Science, Lehigh University, Bethlehem, Pennsylvania 18015, USA
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25
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Maddaluno L, Urwyler C, Werner S. Fibroblast growth factors: key players in regeneration and tissue repair. Development 2017; 144:4047-4060. [PMID: 29138288 DOI: 10.1242/dev.152587] [Citation(s) in RCA: 154] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Tissue injury initiates a complex repair process, which in some organisms can lead to the complete regeneration of a tissue. In mammals, however, the repair of most organs is imperfect and results in scar formation. Both regeneration and repair are orchestrated by a highly coordinated interplay of different growth factors and cytokines. Among the key players are the fibroblast growth factors (FGFs), which control the migration, proliferation, differentiation and survival of different cell types. In addition, FGFs influence the expression of other factors involved in the regenerative response. Here, we summarize current knowledge on the roles of endogenous FGFs in regeneration and repair in different organisms and in different tissues and organs. Gaining a better understanding of these FGF activities is important for appropriate modulation of FGF signaling after injury to prevent impaired healing and to promote organ regeneration in humans.
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Affiliation(s)
- Luigi Maddaluno
- Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology (ETH) Zurich, Otto-Stern-Weg 7, 8093 Zürich, Switzerland
| | - Corinne Urwyler
- Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology (ETH) Zurich, Otto-Stern-Weg 7, 8093 Zürich, Switzerland
| | - Sabine Werner
- Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology (ETH) Zurich, Otto-Stern-Weg 7, 8093 Zürich, Switzerland
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26
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Huang R, Chen M, Yang L, Wagle M, Guo S, Hu B. MicroRNA-133b Negatively Regulates Zebrafish Single Mauthner-Cell Axon Regeneration through Targeting tppp3 in Vivo. Front Mol Neurosci 2017; 10:375. [PMID: 29209165 PMCID: PMC5702462 DOI: 10.3389/fnmol.2017.00375] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 10/27/2017] [Indexed: 12/30/2022] Open
Abstract
Axon regeneration, fundamental to nerve repair, and functional recovery, relies on rapid changes in gene expression attributable to microRNA (miRNA) regulation. MiR-133b has been proved to play an important role in different organ regeneration in zebrafish, but its role in regulating axon regeneration in vivo is still controversial. Here, combining single-cell electroporation with a vector-based miRNA-expression system, we have modulated the expression of miR-133b in Mauthner-cells (M-cells) at the single-cell level in zebrafish. Through in vivo imaging, we show that overexpression of miR-133b inhibits axon regeneration, whereas down-regulation of miR-133b, promotes axon outgrowth. We further show that miR-133b regulates axon regeneration by directly targeting a novel regeneration-associated gene, tppp3, which belongs to Tubulin polymerization-promoting protein family. Gain or loss-of-function of tppp3 experiments indicated that tppp3 was a novel gene that could promote axon regeneration. In addition, we observed a reduction of mitochondrial motility, which have been identified to have a positive correlation with axon regeneration, in miR-133b overexpressed M-cells. Taken together, our work provides a novel way to study the role of miRNAs in individual cell and establishes a critical cell autonomous role of miR-133b in zebrafish M-cell axon regeneration. We propose that up-regulation of the newly founded regeneration-associated gene tppp3 may enhance axonal regeneration.
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Affiliation(s)
- Rongchen Huang
- Chinese Academy of Sciences Key Laboratory of Brain Function and Disease, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Min Chen
- Chinese Academy of Sciences Key Laboratory of Brain Function and Disease, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Leiqing Yang
- Chinese Academy of Sciences Key Laboratory of Brain Function and Disease, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Mahendra Wagle
- Programs in Human Genetics and Biological Sciences, Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, United States
| | - Su Guo
- Programs in Human Genetics and Biological Sciences, Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, United States
| | - Bing Hu
- Chinese Academy of Sciences Key Laboratory of Brain Function and Disease, School of Life Sciences, University of Science and Technology of China, Hefei, China
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27
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Yamada T, Wondergem R, Morrison R, Yin VP, Strange K. Leucine-rich repeat containing protein LRRC8A is essential for swelling-activated Cl- currents and embryonic development in zebrafish. Physiol Rep 2017; 4:4/19/e12940. [PMID: 27688432 PMCID: PMC5064130 DOI: 10.14814/phy2.12940] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 08/05/2016] [Indexed: 11/24/2022] Open
Abstract
A volume‐regulated anion channel (VRAC) has been electrophysiologically characterized in innumerable mammalian cell types. VRAC is activated by cell swelling and mediates the volume regulatory efflux of Cl− and small organic solutes from cells. Two groups recently identified the mammalian leucine‐rich repeat containing protein LRRC8A as an essential VRAC component. LRRC8A must be coexpressed with at least one of the other four members of this gene family, LRRC8B‐E, to reconstitute VRAC activity in LRRC8−/− cells. LRRC8 genes likely arose with the origin of chordates. We identified LRRC8A and LRRC8C‐E orthologs in the zebrafish genome and demonstrate that zebrafish embryo cells and differentiated adult cell types express a swelling‐activated Cl− current indistinguishable from mammalian VRAC currents. Embryo cell VRAC currents are virtually eliminated by morpholino knockdown of the zebrafish LRRC8A ortholog lrrc8aa. VRAC activity is fully reconstituted in LRRC8−/− human cells by coexpression of zebrafish lrrc8aa and human LRRC8C cDNAs. lrrc8aa expression varies during zebrafish embryogenesis and lrrc8aa knockdown causes pericardial edema and defects in trunk elongation and somatogenesis. Our studies provide confirmation of the importance of LRRC8A in VRAC activity and establish the zebrafish as a model system for characterizing the molecular regulation and physiological roles of VRAC and LRRC8 proteins.
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Affiliation(s)
- Toshiki Yamada
- MDI Biological Laboratory, Davis Center for Regenerative Biology and Medicine, Salisbury Cove, Maine
| | - Robert Wondergem
- Department of Biomedical Sciences, James H. Quillen College of Medicine East Tennessee State University, Johnson City, Tennessee
| | - Rebecca Morrison
- MDI Biological Laboratory, Davis Center for Regenerative Biology and Medicine, Salisbury Cove, Maine
| | - Viravuth P Yin
- MDI Biological Laboratory, Davis Center for Regenerative Biology and Medicine, Salisbury Cove, Maine
| | - Kevin Strange
- MDI Biological Laboratory, Davis Center for Regenerative Biology and Medicine, Salisbury Cove, Maine
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28
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Dardis G, Tryon R, Ton Q, Johnson SL, Iovine MK. Cx43 suppresses evx1 expression to regulate joint initiation in the regenerating fin. Dev Dyn 2017; 246:691-699. [PMID: 28577298 DOI: 10.1002/dvdy.24531] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 05/08/2017] [Accepted: 05/30/2017] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND How joints are correctly positioned in the vertebrate skeleton remains poorly understood. From our studies on the regenerating fin, we have evidence that the gap junction protein Cx43 suppresses joint formation by suppressing the expression of the evx1 transcription factor. Joint morphogenesis proceeds through at least two discrete stages. First, cells that will produce the joint condense in a single row on the bone matrix ("initiation"). Second, these cells separate coincident with articulation of the bone matrix. We propose that Cx43 activity is transiently reduced prior to joint initiation. RESULTS We first define the timing of joint initiation with respect to regeneration. We next correlate reduced cx43 expression and increased evx1 expression with initiation. Through manipulation of cx43 expression, we demonstrate that Cx43 negatively influences evx1 expression and joint formation. We further demonstrate that Cx43 activity in the dermal fibroblasts is required to rescue joint formation in the cx43 mutant, short finb123 . CONCLUSIONS We conclude that Cx43 activity in the dermal fibroblasts influences the expression of evx1, and therefore the differentiation of the precursor cells that give rise to the joint-forming osteoblasts. Developmental Dynamics 246:691-699, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Gabrielle Dardis
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania
| | - Robert Tryon
- Genetics Department, Washington University School of Medicine, St. Louis, Missouri
| | - Quynh Ton
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania
| | - Stephen L Johnson
- Genetics Department, Washington University School of Medicine, St. Louis, Missouri
| | - M Kathryn Iovine
- Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania
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29
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Spina EJ, Guzman E, Zhou H, Kosik KS, Smith WC. A microRNA-mRNA expression network during oral siphon regeneration in Ciona. Development 2017; 144:1787-1797. [PMID: 28432214 DOI: 10.1242/dev.144097] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 04/10/2017] [Indexed: 12/14/2022]
Abstract
Here we present a parallel study of mRNA and microRNA expression during oral siphon (OS) regeneration in Ciona robusta, and the derived network of their interactions. In the process of identifying 248 mRNAs and 15 microRNAs as differentially expressed, we also identified 57 novel microRNAs, several of which are among the most highly differentially expressed. Analysis of functional categories identified enriched transcripts related to stress responses and apoptosis at the wound healing stage, signaling pathways including Wnt and TGFβ during early regrowth, and negative regulation of extracellular proteases in late stage regeneration. Consistent with the expression results, we found that inhibition of TGFβ signaling blocked OS regeneration. A correlation network was subsequently inferred for all predicted microRNA-mRNA target pairs expressed during regeneration. Network-based clustering associated transcripts into 22 non-overlapping groups, the functional analysis of which showed enrichment of stress response, signaling pathway and extracellular protease categories that could be related to specific microRNAs. Predicted targets of the miR-9 cluster suggest a role in regulating differentiation and the proliferative state of neural progenitors through regulation of the cytoskeleton and cell cycle.
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Affiliation(s)
- Elijah J Spina
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Elmer Guzman
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Hongjun Zhou
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Kenneth S Kosik
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA.,Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - William C Smith
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA .,Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
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30
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Liu Y, Liang Y, Zhang JF, Fu WM. MicroRNA-133 mediates cardiac diseases: Mechanisms and clinical implications. Exp Cell Res 2017; 354:65-70. [PMID: 28322824 DOI: 10.1016/j.yexcr.2017.03.037] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 03/15/2017] [Accepted: 03/17/2017] [Indexed: 12/28/2022]
Abstract
MicroRNAs (miRNAs) belong to the family of small non-coding RNAs that mediate gene expression by post-transcriptional regulation. Increasing evidence have demonstrated that miR-133 is enriched in muscle tissues and myogenic cells, and its aberrant expression could induce the occurrence and development of cardiac disorders, such as cardiac hypertrophy, heart failure, etc. In this review, we summarized the regulatory roles of miR-133 in cardiac disorders and the underlying mechanisms, which suggest that miR-133 may be a potential diagnostic and therapeutic tool for cardiac disorders.
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Affiliation(s)
- Yi Liu
- Guangdong Key Laboratory for Research and Development of Natural Drugs, Guangdong Medical University, Zhanjiang 524023, Guangdong, China
| | - Yan Liang
- Guangdong Key Laboratory for Research and Development of Natural Drugs, Guangdong Medical University, Zhanjiang 524023, Guangdong, China
| | - Jin-Fang Zhang
- Department of Orthopaedics and Traumatology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, China
| | - Wei-Ming Fu
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China.
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31
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Smith AM, Maguire-Nguyen KK, Rando TA, Zasloff MA, Strange KB, Yin VP. The protein tyrosine phosphatase 1B inhibitor MSI-1436 stimulates regeneration of heart and multiple other tissues. NPJ Regen Med 2017; 2:4. [PMID: 29302341 PMCID: PMC5677970 DOI: 10.1038/s41536-017-0008-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 01/13/2017] [Accepted: 01/20/2017] [Indexed: 12/13/2022] Open
Abstract
Regenerative medicine holds substantial promise for repairing or replacing tissues and organs damaged by disease, injury, and degeneration. Much of the field has focused on development of cell-based therapeutics, gene-based therapeutics, and tissue engineering-based therapeutics. In contrast, development of small molecule regenerative medicine therapies is an emerging area. Using the adult zebrafish as a novel screening platform, we identified MSI-1436 as a first-in-class regenerative medicine drug candidate. MSI-1436 is a naturally occurring aminosterol that inhibits protein tyrosine phosphatase 1B. Treatment of adult zebrafish by intraperitoneal injection of MSI-1436 increased the rate of regeneration of the amputated caudal fin, which is comprised of bone, connective, skin, vascular and nervous tissues and also increased the rate of adult zebrafish heart regeneration. Intraperitoneal administration of MSI-1436 to adult mice for 4 weeks after induction of myocardial infarction increased survival, improved heart function, reduced infarct size, reduced ventricular wall thinning and increased cardiomyocyte proliferation. Satellite cell activation in injured mouse skeletal muscle was stimulated by MSI-1436. MSI-1436 was well tolerated by patients in Phase 1 and 1b obesity and type 2 diabetes clinical trials. Doses effective at stimulating regeneration are 5–50-times lower than the maximum well tolerated human dose. The demonstrated safety and well established pharmacological properties of MSI-1436 underscore the potential of this molecule as a novel treatment for heart attack and multiple other degenerative diseases. A naturally occurring small molecule shows promise as a drug for tissue and organ repair and regeneration. Viravuth Yin of the Kathryn W. Davis Center for Regenerative Biology and Medicine with colleagues in the US found that treating zebrafish with an intraperitoneal injection of MSI-1436, which inhibits the enzyme ‘protein tyrosine phosphatase 1B’, increased the rate of regeneration of an amputated caudal fin and of partially removed heart muscle without apparent tissue malformation. Intraperitoneal injection of MSI-1436 in adult mice also reduced the size of an induced heart infarction, improved survivability, triggered new heart muscle formation and stimulated regeneration after skeletal muscle injury. Effective doses for tissue regeneration in both animals were much lower than the maximum tolerated doses found for humans in clinical trials for potential treatment of obesity and diabetes.
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Affiliation(s)
- Ashley M Smith
- Kathryn W. Davis Center for Regenerative Biology and Medicine, MDI Biological Laboratory, Salisbury Cove, ME 04672 USA
| | - Katie K Maguire-Nguyen
- Department of Neurology, Stanford University Medical Center, Stanford, CA 94305-5235 USA
| | - Thomas A Rando
- Department of Neurology, Stanford University Medical Center, Stanford, CA 94305-5235 USA
| | - Michael A Zasloff
- Novo Biosciences, Bar Harbor, ME 04609 USA.,MedStar Georgetown Transplant Institute, Georgetown University Hospital, Washington DC, 20007 USA
| | - Kevin B Strange
- Kathryn W. Davis Center for Regenerative Biology and Medicine, MDI Biological Laboratory, Salisbury Cove, ME 04672 USA.,Novo Biosciences, Bar Harbor, ME 04609 USA
| | - Viravuth P Yin
- Kathryn W. Davis Center for Regenerative Biology and Medicine, MDI Biological Laboratory, Salisbury Cove, ME 04672 USA.,Novo Biosciences, Bar Harbor, ME 04609 USA
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32
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Bhattacharya M, Sharma AR, Sharma G, Patra BC, Nam JS, Chakraborty C, Lee SS. The crucial role and regulations of miRNAs in zebrafish development. PROTOPLASMA 2017; 254:17-31. [PMID: 26820151 DOI: 10.1007/s00709-015-0931-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 12/10/2015] [Indexed: 06/05/2023]
Abstract
To comprehend the events during developmental biology, fundamental knowledge about the basic machinery of regulation is a prerequisite. MicroRNA (miRNAs) act as regulators in most of the biological processes and recently, it has been concluded that miRNAs can act as modulatory factors even during developmental process from lower to higher animal. Zebrafish, because of its favorable attributes like tiny size, transparent embryo, and rapid external embryonic development, has gained a preferable status among all other available experimental animal models. Currently, zebrafish is being utilized for experimental studies related to stem cells, regenerative molecular medicine as well drug discovery. Therefore, it is important to understand precisely about the various miRNAs that controls developmental biology of this vertebrate model. In here, we have discussed about the miRNA-controlled zebrafish developmental stages with a special emphasis on different miRNA families such as miR-430, miR-200, and miR-133. Moreover, we have also reviewed the role of various miRNAs during embryonic and vascular development stages of zebrafish. In addition, efforts have been made to summarize the involvement of miRNAs in the development of different body parts such as the brain, eye, heart, muscle, and fin, etc. In each section, we have tried to fulfill the gaps of zebrafish developmental biology with the help of available knowledge of miRNA research. We hope that precise knowledge about the miRNA-regulated developmental stages of zebrafish may further help the researchers to efficiently utilize this vertebrate model for experimental purpose.
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Affiliation(s)
- Manojit Bhattacharya
- Aquaculture Research Unit, Department of Zoology, Vidyasagar University, Midnapore, 721102, West Bengal, India
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon, 200704, South Korea
| | - Ashish Ranjan Sharma
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon, 200704, South Korea
| | - Garima Sharma
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon, 200704, South Korea
- Amity Institute of Nanotechnology, Amity University Uttar Pradesh, Noida, 201313, India
| | - Bidhan Chandra Patra
- Aquaculture Research Unit, Department of Zoology, Vidyasagar University, Midnapore, 721102, West Bengal, India
| | - Ju-Suk Nam
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon, 200704, South Korea
| | - Chiranjib Chakraborty
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon, 200704, South Korea.
- Department of Bio-informatics, School of Computer and Information Sciences, Galgotias University, Greater Noida, 201306, India.
| | - Sang-Soo Lee
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon, 200704, South Korea.
- Department of Orthopedic Surgery, Hallym University Hospital-College of Medicine, Chuncheon-si, Gangwon-do, 200-704, Republic of Korea.
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33
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King BL, Yin VP. Prioritizing studies on regeneration in nontraditional model organisms. Regen Med 2016; 12:1-3. [PMID: 27925505 DOI: 10.2217/rme-2016-0159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Affiliation(s)
- Benjamin L King
- MDI Biological Laboratory, Kathryn W Davis Center for Regenerative Biology & Medicine, Salisbury Cove, ME 04672, USA
| | - Viravuth P Yin
- MDI Biological Laboratory, Kathryn W Davis Center for Regenerative Biology & Medicine, Salisbury Cove, ME 04672, USA
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34
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Burgos-Aceves MA, Cohen A, Smith Y, Faggio C. Estrogen regulation of gene expression in the teleost fish immune system. FISH & SHELLFISH IMMUNOLOGY 2016; 58:42-49. [PMID: 27633675 DOI: 10.1016/j.fsi.2016.09.006] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Revised: 09/01/2016] [Accepted: 09/10/2016] [Indexed: 05/02/2023]
Abstract
Elucidating the mechanisms of estrogens-induced immunomodulation in teleost fish is of great importance due to the observed worldwide continuing decrease in pristine environments. However, little is know about the immunotoxicological consequences of exposure to these chemicals in fish, or of the mechanisms through which these effects are mediated. In this review, we summarize the results showing estrogens (natural or synthetic) acting through estrogen receptors and regulating specific target genes, also through microRNAs (miRNAs), leading to modulation of the immune functioning. The identification and characterization of miRNAs will provide new opportunities for functional genome research on teleost immune system and can also be useful when screening for novel molecule biomarkers for environmental pollution.
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Affiliation(s)
- Mario Alberto Burgos-Aceves
- Centro de Investigaciones Biológicas de Noroeste, S.C., Mar Bermejo 195, Col. Playa Palo de Sta. Rita, La Paz BCS, 23090, México
| | - Amit Cohen
- Genomic Data Analysis Unit, The Hebrew University of Jerusalem-Hadassah Medical School, P.O. Box 12272, Jerusalem 91120, Israel
| | - Yoav Smith
- Genomic Data Analysis Unit, The Hebrew University of Jerusalem-Hadassah Medical School, P.O. Box 12272, Jerusalem 91120, Israel
| | - Caterina Faggio
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, Viale F. Stagno d'Alcontres, 31, 98166 Messina, Italy.
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35
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Xiang MSW, Kikuchi K. Endogenous Mechanisms of Cardiac Regeneration. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 326:67-131. [PMID: 27572127 DOI: 10.1016/bs.ircmb.2016.04.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Zebrafish possess a remarkable capacity for cardiac regeneration throughout their lifetime, providing a model for investigating endogenous cellular and molecular mechanisms regulating myocardial regeneration. By contrast, adult mammals have an extremely limited capacity for cardiac regeneration, contributing to mortality and morbidity from cardiac diseases such as myocardial infarction and heart failure. However, the viewpoint of the mammalian heart as a postmitotic organ was recently revised based on findings that the mammalian heart contains multiple undifferentiated cell types with cardiogenic potential as well as a robust regenerative capacity during a short period early in life. Although it occurs at an extremely low level, continuous cardiomyocyte turnover has been detected in adult mouse and human hearts, which could potentially be enhanced to restore lost myocardium in damaged human hearts. This review summarizes and discusses recent advances in the understanding of endogenous mechanisms of cardiac regeneration.
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Affiliation(s)
- M S W Xiang
- Developmental and Stem Cell Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst NSW, Australia
| | - K Kikuchi
- Developmental and Stem Cell Biology Division, Victor Chang Cardiac Research Institute, Darlinghurst NSW, Australia; St. Vincent's Clinical School, University of New South Wales, Kensington NSW, Australia.
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36
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Rastorguev SM, Nedoluzhko AV, Sharko FS, Boulygina ES, Sokolov AS, Gruzdeva NM, Skryabin KG, Prokhortchouk EB. Identification of novel microRNA genes in freshwater and marine ecotypes of the three-spined stickleback (Gasterosteus aculeatus). Mol Ecol Resour 2016; 16:1491-1498. [PMID: 27238497 DOI: 10.1111/1755-0998.12545] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 04/26/2016] [Accepted: 05/13/2016] [Indexed: 11/30/2022]
Abstract
The three-spined stickleback (Gasterosteus aculeatus L.) is an important model organism for studying the molecular mechanisms of speciation and adaptation to salinity. Despite increased interest to microRNA discovery and recent publication on microRNA prediction in the three-spined stickleback using bioinformatics approaches, there is still a lack of experimental support for these data. In this paper, high-throughput sequencing technology was applied to identify microRNA genes in gills of the three-spined stickleback. In total, 595 miRNA genes were discovered; half of them were predicted in previous computational studies and were confirmed here as microRNAs expressed in gill tissue. Moreover, 298 novel microRNA genes were identified. The presence of miRNA genes in selected 'divergence islands' was analysed and 10 miRNA genes were identified as not randomly located in 'divergence islands'. Regulatory regions of miRNA genes were found enriched with selective SNPs that may play a role in freshwater adaptation.
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Affiliation(s)
- S M Rastorguev
- National Research Center 'Kurchatov Institute', Kurchatov sq. 1, Moscow, 123182, Russia. .,Russian Federal Research Institute of Fisheries and Oceanography, (VNIRO) V. Krasnoselskaya str. 17, Moscow, 107140, Russia.
| | - A V Nedoluzhko
- National Research Center 'Kurchatov Institute', Kurchatov sq. 1, Moscow, 123182, Russia
| | - F S Sharko
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave., Moscow, 119071, Russia
| | - E S Boulygina
- National Research Center 'Kurchatov Institute', Kurchatov sq. 1, Moscow, 123182, Russia
| | - A S Sokolov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave., Moscow, 119071, Russia
| | - N M Gruzdeva
- National Research Center 'Kurchatov Institute', Kurchatov sq. 1, Moscow, 123182, Russia
| | - K G Skryabin
- National Research Center 'Kurchatov Institute', Kurchatov sq. 1, Moscow, 123182, Russia.,Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave., Moscow, 119071, Russia.,Faculty of Biology, Lomonosov Moscow State University, Leninskie Gory 1-12, Moscow, 119991, Russia
| | - E B Prokhortchouk
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave., Moscow, 119071, Russia.,Faculty of Biology, Lomonosov Moscow State University, Leninskie Gory 1-12, Moscow, 119991, Russia
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37
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King BL, Yin VP. A Conserved MicroRNA Regulatory Circuit Is Differentially Controlled during Limb/Appendage Regeneration. PLoS One 2016; 11:e0157106. [PMID: 27355827 PMCID: PMC4927183 DOI: 10.1371/journal.pone.0157106] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 05/24/2016] [Indexed: 01/25/2023] Open
Abstract
Background Although regenerative capacity is evident throughout the animal kingdom, it is not equally distributed throughout evolution. For instance, complex limb/appendage regeneration is muted in mammals but enhanced in amphibians and teleosts. The defining characteristic of limb/appendage regenerative systems is the formation of a dedifferentiated tissue, termed blastema, which serves as the progenitor reservoir for regenerating tissues. In order to identify a genetic signature that accompanies blastema formation, we employ next-generation sequencing to identify shared, differentially regulated mRNAs and noncoding RNAs in three different, highly regenerative animal systems: zebrafish caudal fins, bichir pectoral fins and axolotl forelimbs. Results These studies identified a core group of 5 microRNAs (miRNAs) that were commonly upregulated and 5 miRNAs that were commonly downregulated, as well as 4 novel tRNAs fragments with sequences conserved with humans. To understand the potential function of these miRNAs, we built a network of 1,550 commonly differentially expressed mRNAs that had functional relationships to 11 orthologous blastema-associated genes. As miR-21 was the most highly upregulated and most highly expressed miRNA in all three models, we validated the expression of known target genes, including the tumor suppressor, pdcd4, and TGFβ receptor subunit, tgfbr2 and novel putative target genes such as the anti-apoptotic factor, bcl2l13, Choline kinase alpha, chka and the regulator of G-protein signaling, rgs5. Conclusions Our extensive analysis of RNA-seq transcriptome profiling studies in three regenerative animal models, that diverged in evolution ~420 million years ago, reveals a common miRNA-regulated genetic network of blastema genes. These comparative studies extend our current understanding of limb/appendage regeneration by identifying previously unassociated blastema genes and the extensive regulation by miRNAs, which could serve as a foundation for future functional studies to examine the process of natural cellular reprogramming in an injury context.
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Affiliation(s)
- Benjamin L. King
- Kathryn W. Davis Center for Regenerative Biology and Medicine, Mount Desert Island, Biological Laboratory, Salisbury Cove, Maine, United States of America
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, Maine, United States of America
| | - Viravuth P. Yin
- Kathryn W. Davis Center for Regenerative Biology and Medicine, Mount Desert Island, Biological Laboratory, Salisbury Cove, Maine, United States of America
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, Maine, United States of America
- * E-mail:
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38
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Cruz-Santos MC, Aragón-Raygoza A, Espinal-Centeno A, Arteaga-Vázquez M, Cruz-Hernández A, Bako L, Cruz-Ramírez A. The Role of microRNAs in Animal Cell Reprogramming. Stem Cells Dev 2016; 25:1035-49. [PMID: 27224014 DOI: 10.1089/scd.2015.0359] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Our concept of cell reprogramming and cell plasticity has evolved since John Gurdon transferred the nucleus of a completely differentiated cell into an enucleated Xenopus laevis egg, thereby generating embryos that developed into tadpoles. More recently, induced expression of transcription factors, oct4, sox2, klf4, and c-myc has evidenced the plasticity of the genome to change the expression program and cell phenotype by driving differentiated cells to the pluripotent state. Beyond these milestone achievements, research in artificial cell reprogramming has been focused on other molecules that are different than transcription factors. Among the candidate molecules, microRNAs (miRNAs) stand out due to their potential to control the levels of proteins that are involved in cellular processes such as self-renewal, proliferation, and differentiation. Here, we review the role of miRNAs in the maintenance and differentiation of mesenchymal stem cells, epimorphic regeneration, and somatic cell reprogramming to induced pluripotent stem cells.
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Affiliation(s)
- María Concepción Cruz-Santos
- 1 Molecular and Developmental Complexity Group, Unidad de Genómica Avanzada (U.G.A.-LANGEBIO) CINVESTAV , Irapuato, México
| | - Alejandro Aragón-Raygoza
- 1 Molecular and Developmental Complexity Group, Unidad de Genómica Avanzada (U.G.A.-LANGEBIO) CINVESTAV , Irapuato, México
| | - Annie Espinal-Centeno
- 1 Molecular and Developmental Complexity Group, Unidad de Genómica Avanzada (U.G.A.-LANGEBIO) CINVESTAV , Irapuato, México
| | - Mario Arteaga-Vázquez
- 2 Laboratory of Epigenetics and Developmental Biology, Institute for Biotechnology and Applied Ecology (INBIOTECA) , Universidad Veracruzana, Xalapa, México
| | - Andrés Cruz-Hernández
- 3 Facultad of Chemistry, Autonomous University of Querétaro, Santiago de Querétaro, México
| | - Laszlo Bako
- 4 Department of Plant Physiology, Umeå University , Umeå, Sweden
| | - Alfredo Cruz-Ramírez
- 1 Molecular and Developmental Complexity Group, Unidad de Genómica Avanzada (U.G.A.-LANGEBIO) CINVESTAV , Irapuato, México
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39
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Sehring IM, Jahn C, Weidinger G. Zebrafish fin and heart: what's special about regeneration? Curr Opin Genet Dev 2016; 40:48-56. [PMID: 27351724 DOI: 10.1016/j.gde.2016.05.011] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 05/22/2016] [Indexed: 01/01/2023]
Abstract
Many organs regenerate well in adult zebrafish, but most research has been directed toward fin and heart regeneration. Cells have been found to remain generally lineage-restricted during regeneration, and proliferative regenerative progenitors can be formed by dedifferentiation from differentiated cells. Recent studies begin to shed light on the molecular underpinnings of differences between development and regeneration. Retinoic acid, BMP and NF-κB signaling are emerging as regulators of cellular dedifferentiation. Reactive oxygen species promote regeneration, and the dynamics of ROS signaling might help explain differences between wound healing and regeneration. Finally, the heart has been added to those organs that require a nerve supply to regenerate, and a trade-off between regeneration and tumor suppression has been proposed to help explain why mammals regenerate poorly.
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Affiliation(s)
- Ivonne M Sehring
- Institute of Biochemistry and Molecular Biology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Christopher Jahn
- 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.
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40
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Beauchemin M, Smith A, Yin VP. Dynamic microRNA-101a and Fosab expression controls zebrafish heart regeneration. Development 2016; 142:4026-37. [PMID: 26628091 DOI: 10.1242/dev.126649] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Cardiovascular disease is the leading cause of morbidity and mortality in the Western world owing to the limited regenerative capacity of the mammalian cardiovascular system. In lieu of new muscle synthesis, the human heart replaces necrotic tissue with deposition of a noncontractile scar. By contrast, the adult zebrafish is endowed with a remarkable regenerative capacity, capable of de novo cardiomyocyte (CM) creation and scar tissue removal when challenged with an acute injury. In these studies, we examined the contributions of the dynamically regulated microRNA miR-101a during adult zebrafish heart regeneration. We demonstrate that miR-101a expression is rapidly depleted within 3 days post-amputation (dpa) but is highly upregulated by 7-14 dpa, before returning to uninjured levels at the completion of the regenerative process. Employing heat-inducible transgenic strains and antisense oligonucleotides, we demonstrate that decreases in miR-101a levels at the onset of cardiac injury enhanced CM proliferation. Interestingly, prolonged suppression of miR-101a activity stimulates new muscle synthesis but with defects in scar tissue clearance. Upregulation of miR-101a expression between 7 and 14 dpa is essential to stimulate removal of the scar. Through a series of studies, we identified the proto-oncogene fosab (cfos) as a potent miR-101a target gene, stimulator of CM proliferation, and inhibitor of scar tissue removal. Importantly, combinatorial depletion of fosab and miR-101a activity rescued defects in scar tissue clearance mediated by miR-101a inhibition alone. In summation, our studies indicate that the precise temporal modulation of the miR-101a/fosab genetic axis is crucial for coordinating CM proliferation and scar tissue removal during zebrafish heart regeneration.
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Affiliation(s)
- Megan Beauchemin
- Kathryn W. Davis Center for Regenerative Biology and Medicine, Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04672, USA Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME 04469, USA
| | - Ashley Smith
- Kathryn W. Davis Center for Regenerative Biology and Medicine, Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04672, USA
| | - Viravuth P Yin
- Kathryn W. Davis Center for Regenerative Biology and Medicine, Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04672, USA Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME 04469, USA
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41
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Hutchins ED, Eckalbar WL, Wolter JM, Mangone M, Kusumi K. Differential expression of conserved and novel microRNAs during tail regeneration in the lizard Anolis carolinensis. BMC Genomics 2016; 17:339. [PMID: 27150582 PMCID: PMC4858913 DOI: 10.1186/s12864-016-2640-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 04/22/2016] [Indexed: 12/25/2022] Open
Abstract
Background Lizards are evolutionarily the most closely related vertebrates to humans that can lose and regrow an entire appendage. Regeneration in lizards involves differential expression of hundreds of genes that regulate wound healing, musculoskeletal development, hormonal response, and embryonic morphogenesis. While microRNAs are able to regulate large groups of genes, their role in lizard regeneration has not been investigated. Results MicroRNA sequencing of green anole lizard (Anolis carolinensis) regenerating tail and associated tissues revealed 350 putative novel and 196 known microRNA precursors. Eleven microRNAs were differentially expressed between the regenerating tail tip and base during maximum outgrowth (25 days post autotomy), including miR-133a, miR-133b, and miR-206, which have been reported to regulate regeneration and stem cell proliferation in other model systems. Three putative novel differentially expressed microRNAs were identified in the regenerating tail tip. Conclusions Differentially expressed microRNAs were identified in the regenerating lizard tail, including known regulators of stem cell proliferation. The identification of 3 putative novel microRNAs suggests that regulatory networks, either conserved in vertebrates and previously uncharacterized or specific to lizards, are involved in regeneration. These findings suggest that differential regulation of microRNAs may play a role in coordinating the timing and expression of hundreds of genes involved in regeneration. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2640-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elizabeth D Hutchins
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA.,Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA
| | - Walter L Eckalbar
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA.,Department of Bioengineering and Therapeutic Sciences, Institute for Human Genetics, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Justin M Wolter
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA.,Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute at Arizona State University, Tempe, AZ, 85287, USA
| | - Marco Mangone
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA.,Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute at Arizona State University, Tempe, AZ, 85287, USA
| | - Kenro Kusumi
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA. .,Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, 85004, USA.
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42
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Ning MS, Andl T. Concise review: custodians of the transcriptome: how microRNAs guard stemness in squamous epithelia. Stem Cells 2016; 33:1047-54. [PMID: 25524325 DOI: 10.1002/stem.1922] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2014] [Accepted: 11/14/2014] [Indexed: 12/19/2022]
Abstract
At the core of every dynamic epithelium resides a population of carefully regulated stem cells ensuring its maintenance and balance. The complex mammalian epidermis is no exception to this rule. The last decade has delivered a wealth of knowledge regarding the biology of adult stem cells, but questions still remain regarding the intricate details of their function and maintenance. To help address these gaps, we turn to the small, single-stranded RNA molecules known as microRNAs. Since their discovery, microRNAs have provided us with novel insights and ground-breaking impulses to enhance our understanding of the biological sciences. Due to their unique role in post-transcriptional regulation, microRNAs are essential to cutaneous biology as well as the epidermal stem cell. By serving as buffers to balance between epithelial stemness, proliferation, and differentiation, microRNAs play essential roles in the maintenance of cutaneous stem cells and their transition out of the stem cell compartment. Following an updated overview of microRNA biology, we summarize the current knowledge of the role of microRNAs in cutaneous stem cells, focusing on three major players that have dominated the recent literature: miR-205, miR-203, and miR-125b. We then review clinical applications, discussing the potential of microRNAs as therapeutic targets in regenerative and oncological stem cell-based medicine.
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Affiliation(s)
- Matthew S Ning
- Division of Dermatology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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43
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Ba H, Wang D, Li C. MicroRNA profiling of antler stem cells in potentiated and dormant states and their potential roles in antler regeneration. Mol Genet Genomics 2016; 291:943-55. [PMID: 26738876 DOI: 10.1007/s00438-015-1158-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 12/09/2015] [Indexed: 01/10/2023]
Abstract
MicroRNAs (miRNAs) can effectively regulate gene expression at the post-transcriptional level and play a critical role in tissue growth, development and regeneration. Our previous studies showed that antler regeneration is a stem cell-based process and antler stem cells reside in the periosteum of a pedicle, the permanent bony protuberance, from which antler regeneration takes place. Antlers are the only mammalian organ that can fully regenerate and hence provide a unique opportunity to identify miRNAs that are involved in organ regeneration. In the present study, we used next generation sequencing technology sequenced miRNAs of the stem cells derived from either the potentiated or the dormant pedicle periosteum. A population of both conserved and 20 deer-specific miRNAs was identified. These conserved miRNAs were derived from 453 homologous hairpin precursors across 88 animal species, and were further grouped into 167 miRNA families. Among them, the miR-296 is embryonic stem cell-specific. The potentiation process resulted in the significant regulation (>±2 Fold, q value <0.05) of conserved miRNAs; 8 miRNA transcripts were down- and 6 up-regulated. Several GO biology processes and the Wnt, MAPK and TGF-beta signaling pathways were found to be up-regulated as part of antlerogenic stem cell potentiation process. This research has identified miRNAs that are associated either with the dormant or the potentiated antler stem cells and identified some target miRNAs for further research into their role played in mammalian organ regeneration.
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Affiliation(s)
- Hengxing Ba
- Institute of Special Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences, Jilin, 130112, People's Republic of China.,State Key Laboratory for Molecular Biology of Special Economic Animals, Jilin, 130112, People's Republic of China
| | - Datao Wang
- Institute of Special Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences, Jilin, 130112, People's Republic of China.,State Key Laboratory for Molecular Biology of Special Economic Animals, Jilin, 130112, People's Republic of China
| | - Chunyi Li
- Institute of Special Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences, Jilin, 130112, People's Republic of China. .,State Key Laboratory for Molecular Biology of Special Economic Animals, Jilin, 130112, People's Republic of China.
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44
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Yun MH. Changes in Regenerative Capacity through Lifespan. Int J Mol Sci 2015; 16:25392-432. [PMID: 26512653 PMCID: PMC4632807 DOI: 10.3390/ijms161025392] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 09/30/2015] [Accepted: 09/30/2015] [Indexed: 12/14/2022] Open
Abstract
Most organisms experience changes in regenerative abilities through their lifespan. During aging, numerous tissues exhibit a progressive decline in homeostasis and regeneration that results in tissue degeneration, malfunction and pathology. The mechanisms responsible for this decay are both cell intrinsic, such as cellular senescence, as well as cell-extrinsic, such as changes in the regenerative environment. Understanding how these mechanisms impact on regenerative processes is essential to devise therapeutic approaches to improve tissue regeneration and extend healthspan. This review offers an overview of how regenerative abilities change through lifespan in various organisms, the factors that underlie such changes and the avenues for therapeutic intervention. It focuses on established models of mammalian regeneration as well as on models in which regenerative abilities do not decline with age, as these can deliver valuable insights for our understanding of the interplay between regeneration and aging.
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Affiliation(s)
- Maximina H Yun
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, UK.
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45
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Gearhart MD, Erickson JR, Walsh A, Echeverri K. Identification of Conserved and Novel MicroRNAs during Tail Regeneration in the Mexican Axolotl. Int J Mol Sci 2015; 16:22046-61. [PMID: 26378530 PMCID: PMC4613296 DOI: 10.3390/ijms160922046] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 08/28/2015] [Accepted: 09/02/2015] [Indexed: 01/11/2023] Open
Abstract
The Mexican axolotl salamander (Ambystoma mexicanum) is one member of a select group of vertebrate animals that have retained the amazing ability to regenerate multiple body parts. In addition to being an important model system for regeneration, the axolotl has also contributed extensively to studies of basic development. While many genes known to play key roles during development have now been implicated in various forms of regeneration, much of the regulatory apparatus controlling the underlying molecular circuitry remains unknown. In recent years, microRNAs have been identified as key regulators of gene expression during development, in many diseases and also, increasingly, in regeneration. Here, we have used deep sequencing combined with qRT-PCR to undertake a comprehensive identification of microRNAs involved in regulating regeneration in the axolotl. Specifically, among the microRNAs that we have found to be expressed in axolotl tissues, we have identified 4564 microRNA families known to be widely conserved among vertebrates, as well as 59,811 reads of putative novel microRNAs. These findings support the hypothesis that microRNAs play key roles in managing the precise spatial and temporal patterns of gene expression that ensures the correct regeneration of missing tissues.
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Affiliation(s)
- Micah D Gearhart
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Jami R Erickson
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Andrew Walsh
- Cenix BioScience GmbH, Dresden 01307, Germany.
- Sitools Biotech GmbH, Planegg-Martinsried 82152, Germany.
| | - Karen Echeverri
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA.
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46
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Mitchelson KR, Qin WY. Roles of the canonical myomiRs miR-1, -133 and -206 in cell development and disease. World J Biol Chem 2015; 6:162-208. [PMID: 26322174 PMCID: PMC4549760 DOI: 10.4331/wjbc.v6.i3.162] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 03/13/2015] [Accepted: 05/28/2015] [Indexed: 02/05/2023] Open
Abstract
MicroRNAs are small non-coding RNAs that participate in different biological processes, providing subtle combinational regulation of cellular pathways, often by regulating components of signalling pathways. Aberrant expression of miRNAs is an important factor in the development and progression of disease. The canonical myomiRs (miR-1, -133 and -206) are central to the development and health of mammalian skeletal and cardiac muscles, but new findings show they have regulatory roles in the development of other mammalian non-muscle tissues, including nerve, brain structures, adipose and some specialised immunological cells. Moreover, the deregulation of myomiR expression is associated with a variety of different cancers, where typically they have tumor suppressor functions, although examples of an oncogenic role illustrate their diverse function in different cell environments. This review examines the involvement of the related myomiRs at the crossroads between cell development/tissue regeneration/tissue inflammation responses, and cancer development.
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47
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Beavers KR, Nelson CE, Duvall CL. MiRNA inhibition in tissue engineering and regenerative medicine. Adv Drug Deliv Rev 2015; 88:123-37. [PMID: 25553957 PMCID: PMC4485980 DOI: 10.1016/j.addr.2014.12.006] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 11/25/2014] [Accepted: 12/20/2014] [Indexed: 12/17/2022]
Abstract
MicroRNAs (miRNAs) are noncoding RNAs that provide an endogenous negative feedback mechanism for translation of messenger RNA (mRNA) into protein. Single miRNAs can regulate hundreds of mRNAs, enabling miRNAs to orchestrate robust biological responses by simultaneously impacting multiple gene networks. MiRNAs can act as master regulators of normal and pathological tissue development, homeostasis, and repair, which has motivated expanding efforts toward the development of technologies for therapeutically modulating miRNA activity for regenerative medicine and tissue engineering applications. This review highlights the tools currently available for miRNA inhibition and their recent therapeutic applications for improving tissue repair.
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Affiliation(s)
- Kelsey R Beavers
- Interdisciplinary Graduate Program in Materials Science, Vanderbilt University, Nashville, TN 37235, USA
| | | | - Craig L Duvall
- Interdisciplinary Graduate Program in Materials Science, Vanderbilt University, Nashville, TN 37235, USA; Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37235, USA.
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48
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Update on the Pathogenic Implications and Clinical Potential of microRNAs in Cardiac Disease. BIOMED RESEARCH INTERNATIONAL 2015. [PMID: 26221581 PMCID: PMC4499420 DOI: 10.1155/2015/105620] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
miRNAs, a unique class of endogenous noncoding RNAs, are highly conserved across species, repress gene translation upon binding to mRNA, and thereby influence many biological processes. As such, they have been recently recognized as regulators of virtually all aspects of cardiac biology, from the development and cell lineage specification of different cell populations within the heart to the survival of cardiomyocytes under stress conditions. Various miRNAs have been recently established as powerful mediators of distinctive aspects in many cardiac disorders. For instance, acute myocardial infarction induces cardiac tissue necrosis and apoptosis but also initiates a pathological remodelling response of the left ventricle that includes hypertrophic growth of cardiomyocytes and fibrotic deposition of extracellular matrix components. In this regard, recent findings place various miRNAs as unquestionable contributing factors in the pathogenesis of cardiac disorders, thus begging the question of whether miRNA modulation could become a novel strategy for clinical intervention. In the present review, we aim to expose the latest mechanistic concepts regarding miRNA function within the context of CVD and analyse the reported roles of specific miRNAs in the different stages of left ventricular remodelling as well as their potential use as a new class of disease-modifying clinical options.
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49
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Shi W, Fang Z, Li L, Luo L. Using zebrafish as the model organism to understand organ regeneration. SCIENCE CHINA-LIFE SCIENCES 2015; 58:343-51. [PMID: 25862658 DOI: 10.1007/s11427-015-4838-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 01/27/2015] [Indexed: 01/11/2023]
Abstract
The limited regenerative capacity of several organs, such as central nervous system (CNS), heart and limb in mammals makes related major diseases quite difficult to recover. Therefore, dissection of the cellular and molecular mechanisms underlying organ regeneration is of great scientific and clinical interests. Tremendous progression has already been made after extensive investigations using several model organisms for decades. Unfortunately, distance to the final achievement of the goal still remains. Recently, zebrafish became a popular model organism for the deep understanding of regeneration based on its powerful regenerative capacity, in particular the organs that are limitedly regenerated in mammals. Additionally, zebrafish are endowed with other advantages good for the study of organ regeneration. This review summarizes the recent progress in the study of zebrafish organ regeneration, in particular regeneration of fin, heart, CNS, and liver as the representatives. We also discuss reasons of the reduced regenerative capacity in higher vertebrate, the roles of inflammation during regeneration, and the difference between organogenesis and regeneration.
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Affiliation(s)
- WenChao Shi
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Laboratory of Molecular Developmental Biology, School of Life Sciences, Southwest University, Chongqing, 400715, China
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50
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Erickson JR, Echeverri K. In vivo modulation and quantification of microRNAs during axolotl tail regeneration. Methods Mol Biol 2015; 1290:159-67. [PMID: 25740485 PMCID: PMC5896293 DOI: 10.1007/978-1-4939-2495-0_13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The ability to regenerate diseased, injured, or missing complex tissue is widespread throughout lower vertebrates and invertebrates; however, our knowledge of the molecular mechanisms that regulate this amazing ability is still in its infancy. Many recent papers have shown important roles for microRNAs in regulating regeneration in a number of species. The ability to detect and quantify miRNA expression fluctuations at a single cell level in vivo in different cell types during processes like regeneration is very informative. In this chapter, we describe how to use a dual-fluorescent green fluorescent protein (GFP)-reporter/monomeric red fluorescent protein (mRFP)-sensor (DFRS) plasmid to quantitate the dynamics of specific miRNAs over time following miRNA mimic injection as well as during regeneration. In this bicistronic vector, the mRFP allows for verification of miRNA expression, while the GFP functions as an internal control to normalize miRNA expression and thus obtain quantitative results. In addition, we demonstrate how this technique revealed dynamic miR-23a expression and function during tail regeneration.
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Affiliation(s)
- Jami R. Erickson
- Dept. of Genetics, Cell Biology and Development, Stem Cell Institute, University of Minnesota, Minneapolis, USA
| | - Karen Echeverri
- Dept. of Genetics, Cell Biology and Development, Stem Cell Institute, University of Minnesota, Minneapolis, USA
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