1
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Lee DW, Kim KM, Park S, An SH, Lim YJ, Jang WG. Eucalyptol induces osteoblast differentiation through ERK phosphorylation in vitro and in vivo. J Mol Med (Berl) 2023; 101:1083-1095. [PMID: 37470800 DOI: 10.1007/s00109-023-02348-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/21/2023]
Abstract
Eucalyptol (EU) is monoterpene oxide that is the main component of the essential oil extracted from aromatic plants such as Eucalyptus globules. EU has therapeutic effects such as antibacterial, anti-inflammatory and antioxidant in chronic diseases including inflammation disorder, respiratory disease, and diabetic disease. However, the effects of EU on osteoblast differentiation and bone diseases such as osteoporosis have not been studied. The present study investigated the effects of EU on osteoblast differentiation and bone formation. EU induces mRNA and protein expression of osteogenic genes in osteoblast cell line MC3T3-E1 and primary calvarial osteoblasts. EU also promoted alkaline phosphatase (ALP) activity and mineralization. Here, the osteoblast differentiation effect of EU is completely reversed by ERK inhibitor. These results demonstrate that osteoblast differentiation effect of EU is mediated by ERK phosphorylation. The efficacy of EU on bone formation was investigated using surgical bone loss-induced animal models. EU dose-dependently promoted bone regeneration in zebrafish caudal fin rays. In the case of ovariectomized mice, EU increased ERK phosphorylation and ameliorated bone loss of femurs. These results indicate that EU ameliorates bone loss by promoting osteoblast differentiation through ERK phosphorylation. We suggest that EU, plant-derived monoterpenoid, may be useful for preventing bone loss. KEY MESSAGES: Eucalyptol (EU) increases osteoblast differentiation in pre-osteoblasts. EU up-regulates the osteogenic genes expression via ERK phosphorylation. EU promotes bone regeneration in partially amputated zebrafish fin rays. Oral administration of EU improves ovariectomy-induced bone loss and increases ERK phosphorylation.
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Affiliation(s)
- Do-Won Lee
- Department of Biotechnology, College of Engineering, Daegu University, Gyeongbuk, 38453, Republic of Korea
- Preclinical Research Center, Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF), Daegu, 41061, Republic of Korea
- Research Institute of Anti-Aging, Daegu University, Gyeongbuk, 38453, Republic of Korea
| | - Kyeong-Min Kim
- Department of Biotechnology, College of Engineering, Daegu University, Gyeongbuk, 38453, Republic of Korea
- Research Institute of Anti-Aging, Daegu University, Gyeongbuk, 38453, Republic of Korea
| | - Seulki Park
- Preclinical Research Center, Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF), Daegu, 41061, Republic of Korea
| | - Sang-Hyun An
- Preclinical Research Center, Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF), Daegu, 41061, Republic of Korea
| | - Young-Ju Lim
- Department of Biotechnology, College of Engineering, Daegu University, Gyeongbuk, 38453, Republic of Korea
- Research Institute of Anti-Aging, Daegu University, Gyeongbuk, 38453, Republic of Korea
| | - Won-Gu Jang
- Department of Biotechnology, College of Engineering, Daegu University, Gyeongbuk, 38453, Republic of Korea.
- Research Institute of Anti-Aging, Daegu University, Gyeongbuk, 38453, Republic of Korea.
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2
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Zhao L, Huang J, Li Y, Wu S, Kang Y. Comprehensive analysis of immune parameters, mRNA and miRNA profiles, and immune genes expression in the gill of rainbow trout infected with infectious hematopoietic necrosis virus (IHNV). FISH & SHELLFISH IMMUNOLOGY 2023; 133:108546. [PMID: 36646338 DOI: 10.1016/j.fsi.2023.108546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 01/09/2023] [Accepted: 01/12/2023] [Indexed: 06/17/2023]
Abstract
Rainbow trout (Oncorhynchus mykiss) is a species of cold-water fish with important economic values, widely cultivated worldwide. However, the outbreak of infectious hematopoietic necrosis virus (IHNV) caused the large-scale death of rainbow trout and seriously restricted the development of the trout farming industry. In this study, the changes of immune parameters in different periods (6-, 12-, 24-, 48-, 72-, 96-, 120-, and 144 h post-infection (hpi)), transcriptome profiles of 48 hpi (T48G) compared to control (C48G), and key immune-related genes expression patterns were measured in rainbow trout gill following IHNV challenge through biochemical methods, RNA sequencing (RNA-seq), and quantitative real-time polymerase chain reaction (qRT-PCR). The results showed that alkaline phosphatase (AKP), acid phosphatase (ACP), total superoxide dismutase (T-SOD), alanine aminotransferase (ALT), and aspartate aminotransferase (AST) activities, as well as lysozyme (LZM) and malonaldehyde (MDA) content decreased and then increased during infection, and remained at a high level after 48 hpi (P < 0.05), whereas catalase (CAT) activity showed a significant peak at 48 hpi (P < 0.05). The mRNA and miRNA analysis identified 4343 differentially expressed genes (DEGs) and 11 differentially expressed miRNAs (DEMs), and numerous immune-related DEGs involved in the Toll-like receptor signaling pathway, apoptosis, DNA replication, p53 signaling, RIG-I-like receptor signaling pathway, and NOD-like receptor signaling pathway and expression were significantly up-regulated in T48Gm group, including tlr3, tlr7, tlr8, traf3, ifih1, trim25, dhx58, ddh58, hsp90a.1, nlrc3, nlrc5, socs3, irf3, irf7, casp7, mx1, and vig2. The integrated analysis identified several important miRNAs (ola-miR-27d-3p_R+5, gmo-miR-124-3-5p, ssa-miR-301a-5p_L+2, and ssa-miR-146d-3p) that targeted key immune-related DEGs. Expression analysis showed that tlr3, tlr7, traf3, ifih1, dhx58, hap90a.1, irf3, irf7, and mx1 genes increased and then decreased during infection, and peaked at 72 hpi (P < 0.05). However, trim25 expression peaked at 96 hpi (P < 0.05). This study contributes to understanding immune response of rainbow trout against IHNV infection, and provides new insights into the immune regulation mechanisms and disease resistance breeding studies.
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Affiliation(s)
- Lu Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Jinqiang Huang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China.
| | - Yongjuan Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China; College of Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Shenji Wu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yujun Kang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
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3
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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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4
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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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5
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Chalmers FE, Dusold JE, Shaik JA, Walsh HA, Glick AB. Targeted deletion of TGFβ1 in basal keratinocytes causes profound defects in stratified squamous epithelia and aberrant melanocyte migration. Dev Biol 2022; 485:9-23. [PMID: 35227671 PMCID: PMC8969113 DOI: 10.1016/j.ydbio.2022.02.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 02/12/2022] [Accepted: 02/22/2022] [Indexed: 11/29/2022]
Abstract
Transforming Growth Factor Beta 1 (TGFβ1) is a multifunctional cytokine that regulates proliferation, apoptosis, and epithelial-mesenchymal transition of epithelial cells. While its role in cancer is well studied, less is known about TGFβ1 and regulation of epithelial development. To address this, we deleted TGFβ1 in basal keratinocytes of stratified squamous epithelia. Newborn mice with a homozygous TGFβ1 deletion had significant defects in proliferation and differentiation of the epidermis and oral mucosa, and died shortly after birth. Hair follicles were sparse in TGFβ1 depleted skin and had delayed development. Additionally, the Wnt pathway transcription factor LEF1 was reduced in hair follicle bulbs and nearly absent from the basal epithelial layer. Hemizygous knockout mice survived to adulthood but were runted and had sparse coats. The skin of these mice had irregular hair follicle morphology and aberrant hair cycle progression, as well as abnormally high melanin expression and delayed melanocyte migration. In contrast to newborn TGFβ1 null mice, the epidermis was hyperproliferative, acanthotic and inflamed. Expression of p63, a master regulator of stratified epithelial identity, proliferation and differentiation, was reduced in TGFβ1 null newborn epidermis but expanded in the postnatal acanthotic epidermis of TGFβ1 hemizygous mice. Thus, TGFβ1 is both essential and haploinsufficient with context dependent roles in stratified squamous epithelial development and homeostasis.
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Affiliation(s)
- Fiona E Chalmers
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, USA
| | - Justyn E Dusold
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, USA
| | - Javed A Shaik
- Dermatology Department, University of Minnesota, USA
| | - Hailey A Walsh
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, USA
| | - Adam B Glick
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, USA.
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6
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Genome-wide integrated analysis reveals functions of lncRNA-miRNA-mRNA interactions in Atlantic salmon challenged by Aeromonas salmonicida. Genomics 2021; 114:328-339. [PMID: 34933071 DOI: 10.1016/j.ygeno.2021.12.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 10/01/2021] [Accepted: 12/15/2021] [Indexed: 12/25/2022]
Abstract
Aeromonas salmonicida (A. salmonicida) is a pathogenic bacterium that causes serious problems in the global Atlantic salmon aquaculture industry. In this study, we comprehensively analyzed the profiles of lncRNAs, miRNAs and mRNAs in gills of Atlantic salmon at high-dose A. salmonicida infection (3.06 × 108 CFU/mL), low-dose A. salmonicida infection (3.06 × 105 CFU/mL), and a PBS (100 μL) control. We identified 65 differentially expressed lncRNAs, 41 miRNAs, and 512 mRNAs between the control group and infection groups. Functional analysis showed that these genes were significantly enriched in the p53 signaling pathway, Wnt signaling pathway, mTOR signaling pathway, JAK-STAT signaling pathway, and Toll-like receptor signaling pathway. In addition, we predicted key genes in immune-related pathways and constructed a lncRNA-miRNA-mRNA network based on whole transcriptomic analysis. We further predicted three lncRNA-miRNA-mRNA axes as potential novel biomarkers in regulating the immune response of Atlantic salmon against A. salmonicida infection.
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Chiang KY, Li YW, Li YH, Huang SJ, Wu CL, Gong HY, Wu JL. Progranulin A Promotes Compensatory Hepatocyte Proliferation via HGF/c-Met Signaling after Partial Hepatectomy in Zebrafish. Int J Mol Sci 2021; 22:ijms222011217. [PMID: 34681875 PMCID: PMC8538350 DOI: 10.3390/ijms222011217] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/14/2021] [Accepted: 10/16/2021] [Indexed: 01/11/2023] Open
Abstract
Compensatory hepatocyte proliferation and other liver regenerative processes are activated to sustain normal physiological function after liver injury. A major mitogen for liver regeneration is hepatocyte growth factor (HGF), and a previous study indicated that progranulin could modulate c-met, the receptor for HGF, to initiate hepatic outgrowth from hepatoblasts during embryonic development. However, a role for progranulin in compensatory hepatocyte proliferation has not been shown previously. Therefore, this study was undertaken to clarify whether progranulin plays a regulatory role during liver regeneration. To this end, we established a partial hepatectomy regeneration model in adult zebrafish that express a liver-specific fluorescent reporter. Using this model, we found that loss of progranulin A (GrnA) function by intraperitoneal-injection of a Vivo-Morpholino impaired and delayed liver regeneration after partial hepatectomy. Furthermore, transcriptome analysis and confirmatory quantitative real-time PCR suggested that cell cycle progression and cell proliferation was not as active in the morphants as controls, which may have been the result of comparative downregulation of the HGF/c-met axis by 36 h after partial hepatectomy. Finally, liver-specific overexpression of GrnA in transgenic zebrafish caused more abundant cell proliferation after partial hepatectomy compared to wild types. Thus, we conclude that GrnA positively regulates HGF/c-met signaling to promote hepatocyte proliferation during liver regeneration.
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Affiliation(s)
- Keng-Yu Chiang
- Department of Life Science, National Taiwan University, Taipei 10617, Taiwan;
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan; (Y.-W.L.); (Y.-H.L.); (S.-J.H.)
| | - Ya-Wen Li
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan; (Y.-W.L.); (Y.-H.L.); (S.-J.H.)
| | - Yen-Hsing Li
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan; (Y.-W.L.); (Y.-H.L.); (S.-J.H.)
| | - Shin-Jie Huang
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan; (Y.-W.L.); (Y.-H.L.); (S.-J.H.)
| | - Chih-Lu Wu
- Department of Chemistry and Biochemistry, National Chung Cheng University, Chiayi 62145, Taiwan;
| | - Hong-Yi Gong
- Department of Aquaculture, National Taiwan Ocean University, Keelung 20224, Taiwan;
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung 20224, Taiwan
| | - Jen-Leih Wu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan; (Y.-W.L.); (Y.-H.L.); (S.-J.H.)
- College of Life Sciences, National Taiwan Ocean University, Keelung 20224, Taiwan
- Correspondence: ; Tel.: +886-2-27899568
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8
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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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Liu S, Yang Q, Chen Y, Liu Q, Wang W, Song J, Zheng Y, Liu W. Integrated Analysis of mRNA- and miRNA-Seq in the Ovary of Rare Minnow Gobiocypris rarus in Response to 17α-Methyltestosterone. Front Genet 2021; 12:695699. [PMID: 34421998 PMCID: PMC8375321 DOI: 10.3389/fgene.2021.695699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 07/06/2021] [Indexed: 11/13/2022] Open
Abstract
17α-Methyltestosterone (MT) is a synthetic androgen. The objective of this study was to explore the effects of exogenous MT on the growth and gonadal development of female rare minnow Gobiocypris rarus. Female G. rarus groups were exposed to 25–100 ng/L of MT for 7 days. After exposure for 7 days, the total weight and body length were significantly decreased in the 50-ng/L MT groups. The major oocytes in the ovaries of the control group were vitellogenic oocytes (Voc) and cortical alveolus stage oocytes (Coc). In the MT exposure groups, some fish had mature ovaries with a relatively lower proportion of mature oocytes, and the diameter of the perinucleolar oocytes (Poc) was decreased compared with those of the control group. Ovarian VTG, FSH, LH, 11-KT, E2, and T were significantly increased after exposure to 50 ng/L of MT for 7 days. Unigenes (73,449), 24 known mature microRNAs (miRNAs), and 897 novel miRNAs in the gonads of G. rarus were found using high-throughput sequencing. Six mature miRNAs (miR-19, miR-183, miR-203, miR-204, miR-205, and miR-96) as well as six differentially expressed genes (fabp3, mfap4, abca1, foxo3, tgfb1, and zfp36l1) that may be associated with ovarian development and innate immune response were assayed using qPCR. Furthermore, the miR-183 cluster and miR-203 were differentially expressed in MT-exposed ovaries of the different G. rarus groups. This study provides some information about the role of miRNA–mRNA pairs in the regulation of ovarian development and innate immune system, which will facilitate future studies of the miRNA–RNA-associated regulation of teleost reproduction.
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Affiliation(s)
- Shaozhen Liu
- College of Animal Science, Shanxi Agriculture University, Jinzhong, China
| | - Qiong Yang
- College of Animal Science, Shanxi Agriculture University, Jinzhong, China
| | - Yue Chen
- College of Animal Science, Shanxi Agriculture University, Jinzhong, China
| | - Qing Liu
- College of Animal Science, Shanxi Agriculture University, Jinzhong, China
| | - Weiwei Wang
- College of Animal Science, Shanxi Agriculture University, Jinzhong, China
| | - Jing Song
- College of Animal Science, Shanxi Agriculture University, Jinzhong, China
| | - Yao Zheng
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Wenzhong Liu
- College of Animal Science, Shanxi Agriculture University, Jinzhong, China
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10
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Dalle Carbonare L, Bertacco J, Marchetto G, Cheri S, Deiana M, Minoia A, Tiso N, Mottes M, Valenti MT. Methylsulfonylmethane enhances MSC chondrogenic commitment and promotes pre-osteoblasts formation. Stem Cell Res Ther 2021; 12:326. [PMID: 34090529 PMCID: PMC8180127 DOI: 10.1186/s13287-021-02396-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 05/18/2021] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Methylsulfonylmethane (MSM) is a nutraceutical compound which has been indicated to counteract osteoarthritis, a cartilage degenerative disorder. In addition, MSM has also been shown to increase osteoblast differentiation. So far, few studies have investigated MSM role in the differentiation of mesenchymal stem cells (MSCs), and no study has been performed to evaluate its overall effects on both osteogenic and chondrogenic differentiation. These two mutually regulated processes share the same progenitor cells. METHODS Therefore, with the aim to evaluate the effects of MSM on chondrogenesis and osteogenesis, we analyzed the expression of SOX9, RUNX2, and SP7 transcription factors in vitro (mesenchymal stem cells and chondrocytes cell lines) and in vivo (zebrafish model). Real-time PCR as well Western blotting, immunofluorescence, and specific in vitro and in vivo staining have been performed. Student's paired t test was used to compare the variation between the groups. RESULTS Our data demonstrated that MSM modulates the expression of differentiation-related genes both in vitro and in vivo. The increased SOX9 expression suggests that MSM promotes chondrogenesis in treated samples. In addition, RUNX2 expression was not particularly affected by MSM while SP7 expression increased in all MSM samples/model analyzed. As SP7 is required for the final commitment of progenitors to preosteoblasts, our data suggest a role of MSM in promoting preosteoblast formation. In addition, we observed a reduced expression of the osteoclast-surface receptor RANK in larvae and in scales as well as a reduced pERK/ERK ratio in fin and scale of MSM treated zebrafish. CONCLUSIONS In conclusion, our study provides new insights into MSM mode of action and suggests that MSM is a useful tool to counteract skeletal degenerative diseases by targeting MSC commitment and differentiation.
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Affiliation(s)
- Luca Dalle Carbonare
- Department of Medicine, University of Verona and Azienda Ospedaliera Universitaria Integrata Verona, Verona, Italy
| | - Jessica Bertacco
- Department of Medicine, University of Verona and Azienda Ospedaliera Universitaria Integrata Verona, Verona, Italy
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Strada Le Grazie, 10, 37100, Verona, Italy
| | - Giulia Marchetto
- Department of Medicine, University of Verona and Azienda Ospedaliera Universitaria Integrata Verona, Verona, Italy
| | - Samuele Cheri
- Department of Medicine, University of Verona and Azienda Ospedaliera Universitaria Integrata Verona, Verona, Italy
| | - Michela Deiana
- Department of Medicine, University of Verona and Azienda Ospedaliera Universitaria Integrata Verona, Verona, Italy
| | - Arianna Minoia
- Department of Medicine, University of Verona and Azienda Ospedaliera Universitaria Integrata Verona, Verona, Italy
| | - Natascia Tiso
- Department of Biology, University of Padova, I-35131, Padova, Italy
| | - Monica Mottes
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Strada Le Grazie, 10, 37100, Verona, Italy
| | - Maria Teresa Valenti
- Department of Medicine, University of Verona and Azienda Ospedaliera Universitaria Integrata Verona, Verona, Italy.
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11
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Khyeam S, Lee S, Huang GN. Genetic, Epigenetic, and Post-Transcriptional Basis of Divergent Tissue Regenerative Capacities Among Vertebrates. ADVANCED GENETICS (HOBOKEN, N.J.) 2021; 2:e10042. [PMID: 34423307 PMCID: PMC8372189 DOI: 10.1002/ggn2.10042] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 05/02/2021] [Accepted: 05/03/2021] [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 PhysiologyUniversity of CaliforniaSan FranciscoCaliforniaUSA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell ResearchUniversity of CaliforniaSan FranciscoCaliforniaUSA
| | - Sukjun Lee
- Cardiovascular Research Institute and Department of PhysiologyUniversity of CaliforniaSan FranciscoCaliforniaUSA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell ResearchUniversity of CaliforniaSan FranciscoCaliforniaUSA
| | - Guo N. Huang
- Cardiovascular Research Institute and Department of PhysiologyUniversity of CaliforniaSan FranciscoCaliforniaUSA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell ResearchUniversity of CaliforniaSan FranciscoCaliforniaUSA
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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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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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16
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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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17
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Jacques C, Tesfaye R, Lavaud M, Georges S, Baud’huin M, Lamoureux F, Ory B. Implication of the p53-Related miR-34c, -125b, and -203 in the Osteoblastic Differentiation and the Malignant Transformation of Bone Sarcomas. Cells 2020; 9:cells9040810. [PMID: 32230926 PMCID: PMC7226610 DOI: 10.3390/cells9040810] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/24/2020] [Accepted: 03/25/2020] [Indexed: 02/07/2023] Open
Abstract
The formation of the skeleton occurs throughout the lives of vertebrates and is achieved through the balanced activities of two kinds of specialized bone cells: the bone-forming osteoblasts and the bone-resorbing osteoclasts. Impairment in the remodeling processes dramatically hampers the proper healing of fractures and can also result in malignant bone diseases such as osteosarcoma. MicroRNAs (miRNAs) are a class of small non-coding single-strand RNAs implicated in the control of various cellular activities such as proliferation, differentiation, and apoptosis. Their post-transcriptional regulatory role confers on them inhibitory functions toward specific target mRNAs. As miRNAs are involved in the differentiation program of precursor cells, it is now well established that this class of molecules also influences bone formation by affecting osteoblastic differentiation and the fate of osteoblasts. In response to various cell signals, the tumor-suppressor protein p53 activates a huge range of genes, whose miRNAs promote genomic-integrity maintenance, cell-cycle arrest, cell senescence, and apoptosis. Here, we review the role of three p53-related miRNAs, miR-34c, -125b, and -203, in the bone-remodeling context and, in particular, in osteoblastic differentiation. The second aim of this study is to deal with the potential implication of these miRNAs in osteosarcoma development and progression.
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18
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Rana MA, Ijaz B, Daud M, Tariq S, Nadeem T, Husnain T. Interplay of Wnt β-catenin pathway and miRNAs in HBV pathogenesis leading to HCC. Clin Res Hepatol Gastroenterol 2019; 43:373-386. [PMID: 30377095 DOI: 10.1016/j.clinre.2018.09.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 09/05/2018] [Accepted: 09/24/2018] [Indexed: 02/04/2023]
Abstract
The prevalence of Hepatocellular carcinoma (HCC) has been identified world-wide. Plethora of factors including chronic infection of HBV/HCV has been characterized for the development of HCC. Although the onset and progression of HCC has been linked with awry of various signaling pathways but precise mechanism, still lies under the multitude layers of curiosity. HBV is spreading with insane speed throughout the world and has been found a main culprit in HCC development after regulating the several cellular pathways including Wnt/β-catenin, Raf/MAPK, Akt and affecting cell multiplication to genomic instability. The role of Wnt/FZD/β-catenin signaling pathway is centralized in liver functions and its anomalous activation leads to HCC development. β-catenin mainly plays a pivotal role in canonical pathway of the system. Altered mainly overexpression of β-catenin along its nuclear localization tunes the aberrations in liver functions and set disease progression. In the development of HCC, modulation of Wnt/FZD/β-catenin signaling pathway by HBV has been established. As HBV infects the cell it affects the miRNAs, the master regulators of cell. Previous studies showed the connection between HBV and cellular miRNAs. In the present review, we unveiled how HBV is deciphering the cellular miRNAs like miR-26a, miR-15a, miR-16-1, miR-148a, miR-132, miR-122, miR-34a, miR-21, miR-29a, miR-222 and miR-199a/b-3p to modulate the Wnt/FZD/β-catenin signaling pathway and develop HCC. These HBV mediated miRNAs may prove future therapeutic options to treat HBV-Wnt/FZD/β-catenin associated HCC.
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Affiliation(s)
- Muhammad Adeel Rana
- Department of microbiology, Quaid-i-Azam University, Islamabad, Pakistan; Centre of Excellence in Molecular Biology, University of the Punjab, Lahore Pakistan
| | - Bushra Ijaz
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore Pakistan.
| | - Muhammad Daud
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore Pakistan
| | - Sommyya Tariq
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore Pakistan
| | - Tariq Nadeem
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore Pakistan
| | - Tayyab Husnain
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore Pakistan
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19
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Sabin KZ, Jiang P, Gearhart MD, Stewart R, Echeverri K. AP-1 cFos/JunB/miR-200a regulate the pro-regenerative glial cell response during axolotl spinal cord regeneration. Commun Biol 2019; 2:91. [PMID: 30854483 PMCID: PMC6403268 DOI: 10.1038/s42003-019-0335-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 02/04/2019] [Indexed: 12/30/2022] Open
Abstract
Salamanders have the remarkable ability to functionally regenerate after spinal cord transection. In response to injury, GFAP+ glial cells in the axolotl spinal cord proliferate and migrate to replace the missing neural tube and create a permissive environment for axon regeneration. Molecular pathways that regulate the pro-regenerative axolotl glial cell response are poorly understood. Here we show axolotl glial cells up-regulate AP-1cFos/JunB after injury, which promotes a pro-regenerative glial cell response. Injury induced upregulation of miR-200a in glial cells supresses c-Jun expression in these cells. Inhibition of miR-200a during regeneration causes defects in axonal regrowth and transcriptomic analysis revealed that miR-200a inhibition leads to differential regulation of genes involved with reactive gliosis, the glial scar, extracellular matrix remodeling and axon guidance. This work identifies a unique role for miR-200a in inhibiting reactive gliosis in axolotl glial cells during spinal cord regeneration. Keith Sabin et al. showed that upregulation of the AP-1 complex, composed of c-Fos and JunB, in the axolotl spinal cord promotes a pro-regenerative glial cell response. This response is impaired by inhibition of miR-200a; suggesting an important role for this microRNA in axolotl spinal cord regeneration.
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Affiliation(s)
- Keith Z Sabin
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, 55455, USA.,Marine Biological Laboratory, Eugene Bell Center for Regenerative Biology and Tissue Engineering, Woods Hole, 02543, MA, USA
| | - Peng Jiang
- Morgridge Institute for Research, Madison, 53715, WI, USA
| | - Micah D Gearhart
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Ron Stewart
- Morgridge Institute for Research, Madison, 53715, WI, USA
| | - Karen Echeverri
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, 55455, USA. .,Marine Biological Laboratory, Eugene Bell Center for Regenerative Biology and Tissue Engineering, Woods Hole, 02543, MA, USA.
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20
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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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21
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Epigenetic Regulation of Organ Regeneration in Zebrafish. J Cardiovasc Dev Dis 2018; 5:jcdd5040057. [PMID: 30558240 PMCID: PMC6306890 DOI: 10.3390/jcdd5040057] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 12/11/2018] [Accepted: 12/12/2018] [Indexed: 02/06/2023] Open
Abstract
The zebrafish is broadly used for investigating de novo organ regeneration, because of its strong regenerative potential. Over the past two decades of intense study, significant advances have been made in identifying both the regenerative cell sources and molecular signaling pathways in a variety of organs in adult zebrafish. Epigenetic regulation has gradually moved into the center-stage of this research area, aided by comprehensive work demonstrating that DNA methylation, histone modifications, chromatin remodeling complexes, and microRNAs are essential for organ regeneration. Here, we present a brief review of how these epigenetic components are induced upon injury, and how they are involved in sophisticated organ regeneration. In addition, we highlight several prospective research directions and their potential implications for regenerative medicine.
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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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Abstract
Antisense morpholino oligonucleotides have been commonly used in zebrafish to inhibit mRNA function, either by inhibiting pre-mRNA splicing or by blocking translation initiation. Even with the advent of genome editing by CRISP/Cas9 technology, morpholinos provide a useful and rapid tool to knockdown gene expression. This is especially true when dealing with multiple alleles and large gene families where genetic redundancy can complicate knockout of all family members. miRNAs are small noncoding RNAs that are often encoded in gene families and can display extensive genetic redundancy. This redundancy, plus their small size which can limit targeting by CRISPR/Cas9, makes morpholino-based strategies particularly attractive for inhibition of miRNA function. We provide the rationale, background, and methods to inhibit miRNA function with antisense morpholinos during early development and in the adult retina in zebrafish.
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Affiliation(s)
- Alex Sutton Flynt
- Department of Biological Sciences, University of Southern Mississippi, Hattiesburg, MS, USA
| | - Mahesh Rao
- Department of Biological Sciences, Vanderbilt University, 2325 Stevenson Center, Box 1820 Station B, Nashville, TN, 37235, USA
| | - James G Patton
- Department of Biological Sciences, Vanderbilt University, 2325 Stevenson Center, Box 1820 Station B, Nashville, TN, 37235, USA.
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Chen Q, Ma JX. Canonical Wnt signaling in diabetic retinopathy. Vision Res 2017; 139:47-58. [PMID: 28545982 DOI: 10.1016/j.visres.2017.02.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 02/21/2017] [Accepted: 02/22/2017] [Indexed: 11/16/2022]
Abstract
Diabetic retinopathy (DR) is a common eye complication of diabetes, and the pathogenic mechanism of DR is still under investigation. The canonical Wnt signaling pathway is an evolutionarily conserved pathway that plays fundamental roles in embryogenesis and adult tissue homeostasis. Wnt signaling regulates expression of multiple genes that control retinal development and eye organogenesis, and dysregulated Wnt signaling plays pathophysiological roles in many ocular diseases, including DR. This review highlights recent progress in studies of Wnt signaling in DR. We discuss Wnt signaling regulation in the retina and dysregulation of Wnt signaling associated with ocular diseases with an emphasis on DR. We also discuss the therapeutic potential of modulating Wnt signaling in DR. Continued studies in this field will advance our current understanding on DR and contribute to the development of new treatments.
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Affiliation(s)
- Qian Chen
- Department of Physiology, Harold Hamm Diabetes Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, United States
| | - Jian-Xing Ma
- Department of Physiology, Harold Hamm Diabetes Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, United States.
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25
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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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26
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Sun L, Sun J, Li X, Zhang L, Yang H, Wang Q. Understanding regulation of microRNAs on intestine regeneration in the sea cucumber Apostichopus japonicus using high-throughput sequencing. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2017; 22:1-9. [PMID: 28160609 DOI: 10.1016/j.cbd.2017.01.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 12/20/2016] [Accepted: 01/21/2017] [Indexed: 12/13/2022]
Abstract
The sea cucumber, as a member of the Echinodermata, has the capacity to restore damaged organs and body parts, which has always been a key scientific issue. MicroRNAs (miRNAs), a class of short noncoding RNAs, play important roles in regulating gene expression. In the present study, we applied high-throughput sequencing to investigate alterations of miRNA expression in regenerative intestine compared to normal intestine. A total of 73 differentially expressed miRNAs were obtained, including 59 up-regulated miRNAs and 14 down-regulated miRNAs. Among these molecules, Aja-miR-1715-5p, Aja-miR-153, Aja-miR-252a, Aja-miR-153-5p, Aja-miR-252b, Aja-miR-2001, Aja-miR-64d-3p, and Aja-miR-252-5p were differentially expressed over 10-fold at 3days post-evisceration (dpe). Notably, real-time PCR revealed that Aja-miR-1715-5p was up-regulated 1390-fold at 3dpe. Moreover, putative target gene co-expression analyses, gene ontology, and pathway analyses suggest that these miRNAs play important roles in specific cellular events (cell proliferation, migration, and apoptosis), metabolic regulation, and energy redistribution. These results will provide a basis for future studies of miRNA regulation in sea cucumber regeneration.
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Affiliation(s)
- Lina Sun
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Jingchun Sun
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Xiaoni Li
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Libin Zhang
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
| | - Hongsheng Yang
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qing Wang
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, China
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27
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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: 31] [Impact Index Per Article: 4.4] [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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28
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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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MicroRNA-142-3p Negatively Regulates Canonical Wnt Signaling Pathway. PLoS One 2016; 11:e0158432. [PMID: 27348426 PMCID: PMC4922628 DOI: 10.1371/journal.pone.0158432] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 06/15/2016] [Indexed: 12/21/2022] Open
Abstract
Wnt/β-catenin signaling pathway plays essential roles in mammalian development and tissue homeostasis. MicroRNAs (miRNAs) are a class of regulators involved in modulating this pathway. In this study, we screened miRNAs regulating Wnt/β-catenin signaling by using a TopFlash based luciferase reporter. Surprisingly, we found that miR-142 inhibited Wnt/β-catenin signaling, which was inconsistent with a recent study showing that miR-142-3p targeted Adenomatous Polyposis Coli (APC) to upregulate Wnt/β-catenin signaling. Due to the discordance, we elaborated experiments by using extensive mutagenesis, which demonstrated that the stem-loop structure was important for miR-142 to efficiently suppress Wnt/β-catenin signaling. Moreover, the inhibitory effect of miR-142 relies on miR-142-3p rather than miR-142-5p. Further, we found that miR-142-3p directly modulated translation of Ctnnb1 mRNA (encoding β-catenin) through binding to its 3’ untranslated region (3’ UTR). Finally, miR-142 was able to repress cell cycle progression by inhibiting active Wnt/β-catenin signaling. Thus, our findings highlight the inhibitory role of miR-142-3p in Wnt/β-catenin signaling, which help to understand the complex regulation of Wnt/β-catenin signaling.
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30
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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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31
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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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32
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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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Regeneration: Lessons from the Lizard. INNOVATIONS IN MOLECULAR MECHANISMS AND TISSUE ENGINEERING 2016. [DOI: 10.1007/978-3-319-44996-8_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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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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35
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Lepp AC, Carlone RL. MicroRNA dysregulation in response to RARβ2 inhibition reveals a negative feedback loop between MicroRNAs 1, 133a, and RARβ2 during tail and spinal cord regeneration in the adult newt. Dev Dyn 2015; 244:1519-37. [PMID: 26332998 DOI: 10.1002/dvdy.24342] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 08/07/2015] [Accepted: 08/23/2015] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The molecular events underlying epimorphic regeneration of the adult urodele amphibian tail and caudal spinal cord are undetermined. Given the dynamic nature of gene expression control by retinoic acid (RA) signaling and the pleiotropic effects of microRNAs (miRNAs) on multiple mRNA targets in this complex system, we examined whether RA signaling through a specific receptor, RARβ2, alters expression of select miRNAs during spinal cord regeneration. RESULTS An initial screen identified 18 highly conserved miRNAs dysregulated in regenerating tail and spinal cord tissues after inhibition of RARβ2 signaling with a selective antagonist, LE135. miRNAs let-7c, miR-1, and miR-223 were expressed within the ependymoglial cells, coincident spatially with the expression of RARβ2. Altering the expression pattern of these three miRNAs led to a significant inhibition of caudal ependymal tube outgrowth by 21 days post tail amputation. We demonstrated that miR-1 targets the 3'-untranslated region of RARβ2 mRNA in vitro; and in vivo, up-regulation of miR-1 led to a significant decrease in RARβ2 protein. CONCLUSIONS These and previous data suggest that miR-1 and miR-133a, both members of the same miRNA gene cluster, may participate with RARβ2 in a negative feedback loop contributing to the regulation of the ependymal response after tail amputation.
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Affiliation(s)
- Amanda C Lepp
- Department of Biological Sciences, Brock University, St. Catharines, Ontario, Canada
| | - Robert L Carlone
- Department of Biological Sciences, Brock University, St. Catharines, Ontario, Canada
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Integrated analyses of zebrafish miRNA and mRNA expression profiles identify miR-29b and miR-223 as potential regulators of optic nerve regeneration. BMC Genomics 2015; 16:591. [PMID: 26265132 PMCID: PMC4534052 DOI: 10.1186/s12864-015-1772-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 07/14/2015] [Indexed: 12/27/2022] Open
Abstract
Background Unlike mammals, zebrafish have the ability to regenerate damaged parts of their central nervous system (CNS) and regain functionality of the affected area. A better understanding of the molecular mechanisms involved in zebrafish regeneration may therefore provide insight into how CNS repair might be induced in mammals. Although many studies have described differences in gene expression in zebrafish during CNS regeneration, the regulatory mechanisms underpinning the differential expression of these genes have not been examined. Results We used microarrays to analyse and integrate the mRNA and microRNA (miRNA) expression profiles of zebrafish retina after optic nerve crush to identify potential regulatory mechanisms that underpin central nerve regeneration. Bioinformatic analysis identified 3 miRNAs and 657 mRNAs that were differentially expressed after injury. We then combined inverse correlations between our miRNA expression and mRNA expression, and integrated these findings with target predictions from TargetScan Fish to identify putative miRNA-gene target pairs. We focused on two over-expressed miRNAs (miR-29b and miR-223), and functionally validated seven of their predicted gene targets using RT-qPCR and luciferase assays to confirm miRNA-mRNA binding. Gene ontology analysis placed the miRNA-regulated genes (eva1a, layna, nefmb, ina, si:ch211-51a6.2, smoc1, sb:cb252) in key biological processes that included cell survival/apoptosis, ECM-cytoskeleton signaling, and heparan sulfate proteoglycan binding, Conclusion Our results suggest a key role for miR-29b and miR-223 in zebrafish regeneration. The identification of miRNA regulation in a zebrafish injury model provides a framework for future studies in which to investigate not only the cellular processes required for CNS regeneration, but also how these mechanisms might be regulated to promote successful repair and return of function in the injured mammalian brain. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1772-1) contains supplementary material, which is available to authorized users.
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Li W, Han W, Ma Y, Cui L, Tian Y, Zhou Z, Wang H. P53-dependent miRNAs mediate nitric oxide-induced apoptosis in colonic carcinogenesis. Free Radic Biol Med 2015; 85:105-13. [PMID: 25912478 DOI: 10.1016/j.freeradbiomed.2015.04.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 03/18/2015] [Accepted: 04/13/2015] [Indexed: 01/30/2023]
Abstract
Both miRNAs and nitric oxide (NO) play important roles in colonic inflammation and tumorigenesis. Resistance of colonic epithelial cells to apoptosis may contribute to tumor development. We hypothesized that some miRNAs could increase the resistance of colonic cancer cells to nitric oxide-induced apoptotic cell death. Here we show that NO induced apoptosis and stimulated expression of some miRNAs. Loss of p53 not only blocked NO-induced apoptosis but also dramatically inhibited the expression of NO-related miRNAs, such as miR-34, miR-203, and miR-1301. In addition, blockage of p53-dependent miRNAs significantly reduced NO-induced apoptosis. Furthermore, forced expression of these miRNAs rendered HT-29 cells, which are resistant to apoptosis with mutant p53, more sensitive to NO-induced apoptotic cell death. Most interestingly, in a colitis-associated colon cancer mouse model, the level of miRNAs dropped significantly, accompanied by downregulation of p21, which is a key target gene of p53. In human colorectal cancer samples, the expression of miR-34 significantly correlated with the level of inducible nitric oxide synthase (iNOS). We contend that increased NO production may select cells with low levels of p53-dependent miRNAs which contributes to human colonic carcinogenesis and tumor progression.
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Affiliation(s)
- Weiwei Li
- State Key Laboratory of Molecular Oncology, Peking Union Medical College, Beijing, China
| | - Wenxiao Han
- State Key Laboratory of Molecular Oncology, Peking Union Medical College, Beijing, China
| | - Yiming Ma
- State Key Laboratory of Molecular Oncology, Peking Union Medical College, Beijing, China
| | - Liang Cui
- Department of Gastrointestinal Cancer Surgery, Cancer Institute/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Yantao Tian
- Department of Gastrointestinal Cancer Surgery, Cancer Institute/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Zhixiang Zhou
- Department of Gastrointestinal Cancer Surgery, Cancer Institute/Cancer Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Hongying Wang
- State Key Laboratory of Molecular Oncology, Peking Union Medical College, Beijing, China.
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38
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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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Ohana R, Weiman-Kelman B, Raviv S, Tamm ER, Pasmanik-Chor M, Rinon A, Netanely D, Shamir R, Solomon AS, Ashery-Padan R. MicroRNAs are essential for differentiation of the retinal pigmented epithelium and maturation of adjacent photoreceptors. Development 2015; 142:2487-98. [PMID: 26062936 DOI: 10.1242/dev.121533] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 06/03/2015] [Indexed: 12/21/2022]
Abstract
Dysfunction of the retinal pigmented epithelium (RPE) results in degeneration of photoreceptors and vision loss and is correlated with common blinding disorders in humans. Although many protein-coding genes are known to be expressed in RPE and are important for its development and maintenance, virtually nothing is known about the in vivo roles of non-coding transcripts. The expression patterns of microRNAs (miRNAs) have been analyzed in a variety of ocular tissues, and a few were implicated to play role in RPE based on studies in cell lines. Here, through RPE-specific conditional mutagenesis of Dicer1 or Dgcr8 in mice, the importance of miRNAs for RPE differentiation was uncovered. miRNAs were found to be dispensable for maintaining RPE fate and survival, and yet they are essential for the acquisition of important RPE properties such as the expression of genes involved in the visual cycle pathway, pigmentation and cell adhesion. Importantly, miRNAs of the RPE are required for maturation of adjacent photoreceptors, specifically for the morphogenesis of the outer segments. The alterations in the miRNA and mRNA profiles in the Dicer1-deficient RPE point to a key role of miR-204 in regulation of the RPE differentiation program in vivo and uncover the importance of additional novel RPE miRNAs. This study reveals the combined regulatory activity of miRNAs that is required for RPE differentiation and for the development of the adjacent neuroretina.
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Affiliation(s)
- Reut Ohana
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
| | - Benjamin Weiman-Kelman
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
| | - Shaul Raviv
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ernst R Tamm
- Institute of Human Anatomy and Embryology, University of Regensburg, D-93053 Regensburg, Germany
| | - Metsada Pasmanik-Chor
- Bioinformatics Unit, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ariel Rinon
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
| | - Dvir Netanely
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ron Shamir
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
| | - Arie S Solomon
- The Goldschleger Eye Research Institute, Sackler Faculty of Medicine, Tel Aviv University Sheba Medical Center, Tel Hashomer 52621, Israel
| | - Ruth Ashery-Padan
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
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40
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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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41
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Stepicheva N, Nigam PA, Siddam AD, Peng CF, Song JL. microRNAs regulate β-catenin of the Wnt signaling pathway in early sea urchin development. Dev Biol 2015; 402:127-41. [PMID: 25614238 DOI: 10.1016/j.ydbio.2015.01.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Revised: 12/18/2014] [Accepted: 01/09/2015] [Indexed: 12/19/2022]
Abstract
Development of complex multicellular organisms requires careful regulation at both transcriptional and post-transcriptional levels. Post-transcriptional gene regulation is in part mediated by a class of non-coding RNAs of 21-25 nucleotides in length known as microRNAs (miRNAs). β-catenin, regulated by the canonical Wnt signaling pathway, has a highly evolutionarily conserved function in patterning early metazoan embryos, in forming the Anterior-Posterior axis, and in establishing the endomesoderm. Using reporter constructs and site-directed mutagenesis, we identified at least three miRNA binding sites within the 3' untranslated region (3'UTR) of the sea urchin β-catenin. Further, blocking these three miRNA binding sites within the β-catenin 3'UTR to prevent regulation of endogenous β-catenin by miRNAs resulted in a minor increase in β-catenin protein accumulation that is sufficient to induce aberrant gut morphology and circumesophageal musculature. These phenotypes are likely the result of increased transcript levels of Wnt responsive endomesodermal regulatory genes. This study demonstrates the importance of miRNA regulation of β-catenin in early development.
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Affiliation(s)
- Nadezda Stepicheva
- Department of Biological Sciences, University of Delaware, 323 Wolf Hall, Newark, DE 19716, USA
| | - Priya A Nigam
- Department of Biological Sciences, University of Delaware, 323 Wolf Hall, Newark, DE 19716, USA
| | - Archana D Siddam
- Department of Biological Sciences, University of Delaware, 323 Wolf Hall, Newark, DE 19716, USA
| | - Chieh Fu Peng
- Department of Biology, University of Miami, Coral Gables, FL 33124, USA
| | - Jia L Song
- Department of Biological Sciences, University of Delaware, 323 Wolf Hall, Newark, DE 19716, USA.
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42
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Wang Q, Lam JCW, Man YC, Lai NLS, Kwok KY, Guo YY, Lam PKS, Zhou B. Bioconcentration, metabolism and neurotoxicity of the organophorous flame retardant 1,3-dichloro 2-propyl phosphate (TDCPP) to zebrafish. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2015; 158:108-15. [PMID: 25461749 DOI: 10.1016/j.aquatox.2014.11.001] [Citation(s) in RCA: 168] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 10/23/2014] [Accepted: 11/01/2014] [Indexed: 05/04/2023]
Abstract
Organophosphate flame retardants are ubiquitous environmental contaminants; however, knowledge is limited regarding their environmental health risks and toxicity. Here, we investigated the effects of acute and long-term exposure to tris(1,3-dichloro-2-propyl) phosphate (TDCPP) to the nervous system of zebrafish. Zebrafish embryos (2 h post-fertilization) were exposed to TDCPP (0-100 μg/L) for 6 months up until sexual maturation. Concentrations of TDCPP and its metabolic product (bis(1,3-dichloro-2-propyl) phosphate, BDCPP) were measured in the tissues of 5 day post-fertilization (dpf) larvae. There was no effect on locomotion, acetylcholinesterase activity, levels of the neurotransmitters dopamine and serotonin, and expression of mRNAs and proteins related to central nervous system development (e.g., myelin basic protein, α1-tubulin) in any exposure group. However, in adult fish, reductions of dopamine and serotonin levels were detected in the brains of females but not males. Downregulation of nervous system development genes was observed in both the male and female brain tissues. TDCPP concentrations were measured in adult fish tissues including the brain, and greater levels were detected in females. Our results showed that females are more sensitive to TDCPP stress than males in terms of TDCPP-induced neurotoxicity. We demonstrate that long-term exposure to lower concentrations of TDCPP in fish can lead to neurotoxicity.
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Affiliation(s)
- Qiangwei Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - James Chung-Wah Lam
- State Key Laboratory in Marine Pollution; Department of Biology and Chemistry, City University of Hong Kong, Kowloon, Hong Kong SAR, China; Research Centre for the Oceans and Human Health, City University of Hong Kong, Shenzhen Research Institute Building, Shenzhen 518057, China; Department of Biology and Chemistry, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Yin-Chung Man
- State Key Laboratory in Marine Pollution; Department of Biology and Chemistry, City University of Hong Kong, Kowloon, Hong Kong SAR, China; Research Centre for the Oceans and Human Health, City University of Hong Kong, Shenzhen Research Institute Building, Shenzhen 518057, China; Department of Biology and Chemistry, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Nelson Lok-Shun Lai
- State Key Laboratory in Marine Pollution; Department of Biology and Chemistry, City University of Hong Kong, Kowloon, Hong Kong SAR, China; Research Centre for the Oceans and Human Health, City University of Hong Kong, Shenzhen Research Institute Building, Shenzhen 518057, China; Department of Biology and Chemistry, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Karen Ying Kwok
- State Key Laboratory in Marine Pollution; Department of Biology and Chemistry, City University of Hong Kong, Kowloon, Hong Kong SAR, China; Research Centre for the Oceans and Human Health, City University of Hong Kong, Shenzhen Research Institute Building, Shenzhen 518057, China; Department of Biology and Chemistry, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Yong yong Guo
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Paul Kwan-Sing Lam
- State Key Laboratory in Marine Pollution; Department of Biology and Chemistry, City University of Hong Kong, Kowloon, Hong Kong SAR, China; Research Centre for the Oceans and Human Health, City University of Hong Kong, Shenzhen Research Institute Building, Shenzhen 518057, China; Department of Biology and Chemistry, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Bingsheng Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
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43
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Lepp AC, Carlone RL. RARβ2 expression is induced by the down-regulation of microRNA 133a during caudal spinal cord regeneration in the adult newt. Dev Dyn 2014; 243:1581-90. [DOI: 10.1002/dvdy.24210] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2014] [Revised: 09/15/2014] [Accepted: 09/20/2014] [Indexed: 11/09/2022] Open
Affiliation(s)
- A. C. Lepp
- Department of Biological Sciences; Brock University; St. Catharines Ontario Canada
| | - R. L. Carlone
- Department of Biological Sciences; Brock University; St. Catharines Ontario Canada
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44
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Rajaram K, Harding RL, Bailey T, Patton JG, Hyde DR. Dynamic miRNA expression patterns during retinal regeneration in zebrafish: reduced dicer or miRNA expression suppresses proliferation of Müller glia-derived neuronal progenitor cells. Dev Dyn 2014; 243:1591-605. [PMID: 25220904 DOI: 10.1002/dvdy.24188] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 08/06/2014] [Accepted: 08/26/2014] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Adult zebrafish spontaneously regenerate their retinas after damage. Although a number of genes and signaling pathways involved in regeneration have been identified, the exact mechanisms regulating various aspects of regeneration are unclear. microRNAs (miRNAs) were examined for their potential roles in regulating zebrafish retinal regeneration. RESULTS To investigate the requirement of miRNAs during zebrafish retinal regeneration, we knocked down the expression of Dicer in retinas prior to light-induced damage. Reduced Dicer expression significantly decreased the number of proliferating Müller glia-derived neuronal progenitor cells during regeneration. To identify individual miRNAs with roles in neuronal progenitor cell proliferation, we collected retinas at different stages of light damage and performed small RNA high-throughput sequencing. We identified subsets of miRNAs that were differentially expressed during active regeneration but returned to basal levels once regeneration was completed. We then knocked down five different miRNAs that increased in expression and assessed the effects on retinal regeneration. Reduction of miR-142b and miR-146a expression significantly reduced INL proliferation at 51 h of light treatment, while knockdown of miR-7a, miR-27c, and miR-31 expression significantly reduced INL proliferation at 72 h of constant light. CONCLUSIONS miRNAs exhibit dynamic expression profiles during retinal regeneration and are necessary for neuronal progenitor cell proliferation.
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Affiliation(s)
- Kamya Rajaram
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee
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45
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The link between injury-induced stress and regenerative phenomena: A cellular and genetic synopsis. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1849:454-61. [PMID: 25088176 DOI: 10.1016/j.bbagrm.2014.07.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 07/25/2014] [Accepted: 07/28/2014] [Indexed: 12/24/2022]
Abstract
Injury is an inescapable phenomenon of life that affects animals at every physiological level. Yet, some animals respond to injury by rebuilding the damaged tissues whereas others are limited to scarring. Elucidating how a tissue insult from wounding leads to a regenerative response at the genetic level is essential to make regenerative advantages translational. It has become clear that animals with regenerative abilities recycle developmental programs after injury, reactivating genes that have lied dormant throughout adulthood. The question that is critical to our understanding of regeneration is how a specific set of developmentally important genes can be reactivated only after an acute tissue insult. Here, we review how injury-induced cellular stresses such as hypoxic, oxidative, and mechanical stress may contribute to the genomic and epigenetic changes that promote regeneration in animals. This article is part of a Special Issue entitled: Stress as a fundamental theme in cell plasticity.
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46
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Frith JE, Porrello ER, Cooper-White JJ. Concise review: new frontiers in microRNA-based tissue regeneration. Stem Cells Transl Med 2014; 3:969-76. [PMID: 24873861 PMCID: PMC4116250 DOI: 10.5966/sctm.2014-0032] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 04/23/2014] [Indexed: 01/13/2023] Open
Abstract
In recent years, the role of miRNAs in post-transcriptional gene regulation has come to the fore with strong evidence to indicate an important role for microRNAs (miRNAs) in the regulation of a wide range of fundamental biological processes. Notably, this includes the regulation of both endogenous tissue repair mechanisms and the growth and differentiation of stem cells (both adult and pluripotent). As a result, manipulation of miRNA signaling holds great promise for regenerative medicine, which aims to harness either endogenous or implanted cells to promote tissue repair. However, to fully realize this potential, it will be necessary to combine advances in our biological understanding with new technologies that allow precise spatiotemporal modulation of specific miRNA candidates. In this review, we highlight the role of miRNAs in tissue regeneration, discuss key challenges in translating this knowledge to the clinic, and outline recent technological advances that aim to address these issues. By combining a comprehensive knowledge of miRNA biology with cutting-edge delivery technologies, it is clear that miRNAs hold significant promise for tissue regenerative therapies in the future.
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Affiliation(s)
- Jessica E Frith
- Tissue Engineering and Microfluidics Laboratory, Australian Institute for Bioengineering and Nanotechnology, School of Biomedical Sciences, and School of Chemical Engineering, University of Queensland, St. Lucia, Queensland, Australia; Materials Science and Engineering Division, Commonwealth Scientific and Industrial Research Organisation, Clayton, Victoria, Australia
| | - Enzo R Porrello
- Tissue Engineering and Microfluidics Laboratory, Australian Institute for Bioengineering and Nanotechnology, School of Biomedical Sciences, and School of Chemical Engineering, University of Queensland, St. Lucia, Queensland, Australia; Materials Science and Engineering Division, Commonwealth Scientific and Industrial Research Organisation, Clayton, Victoria, Australia
| | - Justin J Cooper-White
- Tissue Engineering and Microfluidics Laboratory, Australian Institute for Bioengineering and Nanotechnology, School of Biomedical Sciences, and School of Chemical Engineering, University of Queensland, St. Lucia, Queensland, Australia; Materials Science and Engineering Division, Commonwealth Scientific and Industrial Research Organisation, Clayton, Victoria, Australia
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47
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Abstract
MicroRNAs (miRNAs) are transcriptional and posttranscriptional regulators involved in nearly all known biological processes in distant eukaryotic clades. Their discovery and functional characterization have broadened our understanding of biological regulatory mechanisms in animals and plants. They show both evolutionary conserved and unique features across Metazoa. Here, we present the current status of the knowledge about the role of miRNA in development, growth, and physiology of teleost fishes, in comparison to other vertebrates. Infraclass Teleostei is the most abundant group among vertebrate lineage. Fish are an important component of aquatic ecosystems and human life, being the prolific source of animal proteins worldwide and a vertebrate model for biomedical research. We review miRNA biogenesis, regulation, modifications, and mechanisms of action. Specific sections are devoted to the role of miRNA in teleost development, organogenesis, tissue differentiation, growth, regeneration, reproduction, endocrine system, and responses to environmental stimuli. Each section discusses gaps in the current knowledge and pinpoints the future directions of research on miRNA in teleosts.
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Affiliation(s)
| | - Igor Babiak
- Faculty of Aquaculture and Biosciences, University of Nordland, Bodø, Norway
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48
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RNAi-mediated gene silencing in zebrafish triggered by convergent transcription. Sci Rep 2014; 4:5222. [PMID: 24909225 PMCID: PMC4048883 DOI: 10.1038/srep05222] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 05/20/2014] [Indexed: 12/02/2022] Open
Abstract
RNAi based strategies to induce gene silencing are commonly employed in numerous model organisms but have not been extensively used in zebrafish. We found that introduction of transgenes containing convergent transcription units in zebrafish embryos induced stable transcriptional gene silencing (TGS) in cis and trans for reporter (mCherry) and endogenous (One-Eyed Pinhead (OEP) and miR-27a/b) genes. Convergent transcription enabled detection of both sense and antisense transcripts and silencing was suppressed upon Dicer knockdown, indicating processing of double stranded RNA. By ChIP analyses, increased silencing was accompanied by enrichment of the heterochromatin mark H3K9me3 in the two convergently arranged promoters and in the intervening reading frame. Our work demonstrates that convergent transcription can induce gene silencing in zebrafish providing another tool to create specific temporal and spatial control of gene expression.
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49
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Rajaram K, Harding RL, Hyde DR, Patton JG. miR-203 regulates progenitor cell proliferation during adult zebrafish retina regeneration. Dev Biol 2014; 392:393-403. [PMID: 24858486 DOI: 10.1016/j.ydbio.2014.05.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 05/06/2014] [Accepted: 05/07/2014] [Indexed: 02/04/2023]
Abstract
Damage of the zebrafish retina triggers a spontaneous regeneration response that is initiated by Müller Glia (MG) dedifferentiation and asymmetric cell division to produce multipotent progenitor cells. Subsequent expansion of the progenitor pool by proliferation is critical for retina regeneration. Pax6b expression in the progenitor cells is necessary for their proliferation, but exact regulation of its expression is unclear. Here, we show that miR-203 is downregulated during regeneration in proliferating progenitor cells. Elevated miR-203 levels inhibit progenitor cell expansion without affecting MG dedifferentiation or progenitor cell generation. Using GFP-reporter assays and gain and loss of function experiments in the retina, we show that miR-203 expression must be suppressed to allow pax6b expression and subsequent progenitor cell proliferation.
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Affiliation(s)
- Kamya Rajaram
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Rachel L Harding
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - David R Hyde
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - James G Patton
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.
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50
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Abstract
Epigenetic interventions are required to induce reprogramming from one cell type to another. At present, various cellular reprogramming methods such as somatic cell nuclear transfer, cell fusion, and direct reprogramming using transcription factors have been reported. In particular, direct reprogramming from somatic cells to induced pluripotent stem cells (iPSCs) has been achieved using defined factors that play important epigenetic roles. Although the mechanisms underlying cellular reprogramming and vertebrate regeneration, including appendage regeneration, remain unknown, dedifferentiation occurs at an early phase in both the events, and both events are contrasting with regard to cell death. We compared the current status of changes in cell fate of iPSCs with that of vertebrate regeneration and suggested that substantial insights into vertebrate regeneration should be helpful for safe applications of iPSCs to medicine.
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Affiliation(s)
- Daisuke Kami
- Department of Regenerative Medicine; Kyoto Prefectural University of Medicine; Kyoto, Japan
| | - Satoshi Gojo
- Department of Regenerative Medicine; Kyoto Prefectural University of Medicine; Kyoto, Japan
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