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Gao J, Skidmore JM, Cimerman J, Ritter KE, Qiu J, Wilson LMQ, Raphael Y, Kwan KY, Martin DM. CHD7 and SOX2 act in a common gene regulatory network during mammalian semicircular canal and cochlear development. Proc Natl Acad Sci U S A 2024; 121:e2311720121. [PMID: 38408234 DOI: 10.1073/pnas.2311720121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 01/19/2024] [Indexed: 02/28/2024] Open
Abstract
Inner ear morphogenesis requires tightly regulated epigenetic and transcriptional control of gene expression. CHD7, an ATP-dependent chromodomain helicase DNA-binding protein, and SOX2, an SRY-related HMG box pioneer transcription factor, are known to contribute to vestibular and auditory system development, but their genetic interactions in the ear have not been explored. Here, we analyzed inner ear development and the transcriptional regulatory landscapes in mice with variable dosages of Chd7 and/or Sox2. We show that combined haploinsufficiency for Chd7 and Sox2 results in reduced otic cell proliferation, severe malformations of semicircular canals, and shortened cochleae with ectopic hair cells. Examination of mice with conditional, inducible Chd7 loss by Sox2CreER reveals a critical period (~E9.5) of susceptibility in the inner ear to combined Chd7 and Sox2 loss. Data from genome-wide RNA-sequencing and CUT&Tag studies in the otocyst show that CHD7 regulates Sox2 expression and acts early in a gene regulatory network to control expression of key otic patterning genes, including Pax2 and Otx2. CHD7 and SOX2 directly bind independently and cooperatively at transcription start sites and enhancers to regulate otic progenitor cell gene expression. Together, our findings reveal essential roles for Chd7 and Sox2 in early inner ear development and may be applicable for syndromic and other forms of hearing or balance disorders.
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Affiliation(s)
- Jingxia Gao
- Department of Pediatrics, The University of Michigan, Ann Arbor, MI 48109
| | | | - Jelka Cimerman
- Department of Pediatrics, The University of Michigan, Ann Arbor, MI 48109
| | - K Elaine Ritter
- Department of Pediatrics, The University of Michigan, Ann Arbor, MI 48109
| | - Jingyun Qiu
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854
- Keck Center for Collaborative Neuroscience, Stem Cell Research Center, Rutgers University, Piscataway, NJ 08854
| | - Lindsey M Q Wilson
- Medical Scientist Training Program, The University of Michigan, Ann Arbor, MI 48109
| | - Yehoash Raphael
- Department of Otolaryngology-Head and Neck Surgery, The University of Michigan, Ann Arbor, MI 48109
| | - Kelvin Y Kwan
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854
- Keck Center for Collaborative Neuroscience, Stem Cell Research Center, Rutgers University, Piscataway, NJ 08854
| | - Donna M Martin
- Department of Pediatrics, The University of Michigan, Ann Arbor, MI 48109
- Department of Human Genetics, The University of Michigan, Ann Arbor, MI 48109
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2
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Megerson E, Kuehn M, Leifer B, Bell JM, Snyder JL, McGraw HF. Kremen1 regulates the regenerative capacity of support cells and mechanosensory hair cells in the zebrafish lateral line. iScience 2024; 27:108678. [PMID: 38205258 PMCID: PMC10776957 DOI: 10.1016/j.isci.2023.108678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/28/2023] [Accepted: 12/05/2023] [Indexed: 01/12/2024] Open
Abstract
Mechanosensory hair cells in the inner ear mediate the sensations of hearing and balance, and in the specialized lateral line sensory system of aquatic vertebrates, the sensation of water movement. In mammals, hair cells lack the ability to regenerate following damage, resulting in sensory deficits. In contrast, non-mammalian vertebrates, such as zebrafish, can renew hair cells throughout their lifespan. Wnt signaling is required for development of inner ear and lateral line hair cells and regulates regeneration. Kremen1 inhibits Wnt signaling and hair cell formation, though its role in regeneration is unknown. We used a zebrafish kremen1 mutant line to show overactive Wnt signaling results in supernumerary support cells and hair cell regeneration without increased proliferation, in contrast with the previously described role of Wnt signaling during hair cell regeneration. This work allows us to understand the biology of mechanosensory hair cells and how regeneration might be promoted following damage.
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Affiliation(s)
- Ellen Megerson
- Division of Biological and Biomedical Systems, School of Science and Engineering, University of Missouri-Kansas City, Kansas City, MO 64110, USA
- Integrated DNA Technologies, Inc, Coralville, IA 52241, USA
| | - Michael Kuehn
- Division of Biological and Biomedical Systems, School of Science and Engineering, University of Missouri-Kansas City, Kansas City, MO 64110, USA
- Department of Cell Biology and Physiology, University of Kansas Medical Center, Kansas City, KS 66103, USA
| | - Ben Leifer
- Division of Biological and Biomedical Systems, School of Science and Engineering, University of Missouri-Kansas City, Kansas City, MO 64110, USA
- Department of Population Health, University of Kansas Medical Center, Kansas City, KS 66103, USA
| | - Jon M. Bell
- Division of Biological and Biomedical Systems, School of Science and Engineering, University of Missouri-Kansas City, Kansas City, MO 64110, USA
| | - Julia L. Snyder
- Division of Biological and Biomedical Systems, School of Science and Engineering, University of Missouri-Kansas City, Kansas City, MO 64110, USA
| | - Hillary F. McGraw
- Division of Biological and Biomedical Systems, School of Science and Engineering, University of Missouri-Kansas City, Kansas City, MO 64110, USA
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3
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Megerson E, Kuehn M, Leifer B, Bell J, McGraw HF. Kremen1 regulates the regenerative capacity of support cells and mechanosensory hair cells in the zebrafish lateral line. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.27.550825. [PMID: 37546780 PMCID: PMC10402150 DOI: 10.1101/2023.07.27.550825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Mechanosensory hair cells in the inner ear mediate the sensations of hearing and balance, and in a specialize lateral line sensory system of aquatic vertebrates, the sensation of water movement. In mammals, hair cells lack the ability of regenerate following damage, resulting in sensory deficits. In contrast, non-mammalian vertebrates, such zebrafish, can renew hair cells throughout the life of the animal. Wnt signaling is required for development of inner ear and lateral line hair cells and regulates regeneration. Kremen1 inhibits Wnt signaling and hair cell formation, though its role in regeneration has not been established. We use a zebrafish kremen1 mutant line, to show that when Wnt signaling is overactivated in the lateral line, excessive regeneration occurs in the absence of increased proliferation, due to an increase in support cells. This contrasts with the previously described role of Wnt signaling during hair cell regeneration. This work will allow us to understand the biology of mechanosensory hair cells, and how regeneration might be promoted following damage.
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4
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Shan H, Ren K, Liu J, Rehman SU, Yan X, Ma X, Zheng Y, Feng T, Wang X, Li Z, Zhou W, Chuang C, Liang M, Zheng J, Liu Q. Comprehensive Transcriptome Sequencing Analysis of Hirudinaria manillensis in Different Growth Periods. Front Physiol 2022; 13:897458. [PMID: 35694407 PMCID: PMC9174698 DOI: 10.3389/fphys.2022.897458] [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: 03/16/2022] [Accepted: 04/22/2022] [Indexed: 02/04/2023] Open
Abstract
Medical leeches are widely been used in biochemical and clinical medical studies, helping to restore blood circulation to grafted or severely injured tissue. Mostly, adult leeches are being used in the traditional pharmacopeia, but the gene expression profiling of leeches in different growth periods is not well-reported. So, in this study, we used transcriptome analysis to analyze the comparative gene expression patterns of Hirudinaria manillensis (H. manillensis) in different growth periods, including larval, young, and adult stages. We constructed 24 cDNA libraries from H. manillensis larval, young, and adult stages, and about 54,639,118 sequences were generated, 18,106 mRNA transcripts of which 958 novel mRNAs and 491 lncRNAs were also assembled as well. Furthermore, the results of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that the differentially upregulated genes from the larval to adult stages were enriched in pathways such as cilium, myofibril, contractile fiber, cytoskeleton proteins, dilated cardiomyopathy, adrenergic signaling in cardiomyocytes, etc. Moreover, in the adult stages, a significant increase in the expression of the Hirudin-HM (HIRM2) genes was detected. In addition, our comparative transcriptome profiling data from different growth stages of H. manillensis also identified a large number of DEGs and DElncRNAs which were tentatively found to be associated with the growth of H. manillensis; as it grew, the muscle-related gene expression increased, while the lipid metabolism and need for stimulation and nutrition-related genes decreased. Similarly, the higher expression of HIRM2 might attribute to the high expression of protein disulfide isomerase gene family (PDI) family genes in adulthood, which provides an important clue that why adult leeches rather than young leeches are widely used in clinical therapeutics and traditional Chinese medicine.
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Affiliation(s)
- Huiquan Shan
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro- Bioresources, Guangxi University, Nanning, China
| | - Ke Ren
- Department of Cardiology, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning, China
| | - Jiasheng Liu
- Department of Cardiology, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning, China
| | - Saif ur Rehman
- State Key Laboratory for Conservation and Utilization of Subtropical Agro- Bioresources, Guangxi University, Nanning, China
| | - Xiuying Yan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro- Bioresources, Guangxi University, Nanning, China
| | - Xiaocong Ma
- Department of Cardiology, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning, China
| | - Yalin Zheng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro- Bioresources, Guangxi University, Nanning, China
| | - Tong Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro- Bioresources, Guangxi University, Nanning, China
| | - Xiaobo Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro- Bioresources, Guangxi University, Nanning, China
| | - Zhipeng Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro- Bioresources, Guangxi University, Nanning, China
| | - Weiguan Zhou
- THAI Natural Hirudin Co., Ltd., Bangkok, Thailand
| | - Chen Chuang
- Guangxi Medical University Cancer Hospital, Nanning, China
| | - Mingkun Liang
- Department of Cardiology, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning, China
| | - Jinghui Zheng
- Department of Cardiology, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning, China
- *Correspondence: Jinghui Zheng, ; Qingyou Liu,
| | - Qingyou Liu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, China
- *Correspondence: Jinghui Zheng, ; Qingyou Liu,
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5
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Fan C, Ouyang Y, Yuan X, Wang J. An enhancer trap zebrafish line for lateral line development and regulation of six2b expression. Gene Expr Patterns 2022; 43:119231. [PMID: 34995793 DOI: 10.1016/j.gep.2022.119231] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/30/2021] [Accepted: 01/01/2022] [Indexed: 11/30/2022]
Abstract
Zebrafish lateral line system which is derived from neurogenic placodes has become a popular model for developmental biology since its formation involves cell migration, pattern formation, organogenesis, and hair cell regeneration. Transgenic lines play a crucial role in lateral line system study. Here, we identified an enhancer trap transgenic zebrafish line Et(gata2a:EGFP)189b (ET189b for short), which expressed enhanced green fluorescent protein (EGFP) in the pituitary, otic, and lateral line placodes and their derivatives. Especially, in neuromast, the accessory cells rather than hair cells were labeled by EGFP. Furthermore, we found the Tol2 transposon construct is integrated at the proximal upstream region of six2b gene locus. And EGFP expression of ET189b closely reflects the expression of endogenous six2b during development and after dkk1b over-expression. Taken together, our results indicated that ET189b is an ideal line for research on lateral line development and regulation of six2b expression.
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Affiliation(s)
- Chunxin Fan
- Institute for Marine Biosystem and Neuroscience, International Center for Marine Studies, Shanghai Ocean University, Shanghai, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, China; International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, China.
| | - Yajing Ouyang
- Institute for Marine Biosystem and Neuroscience, International Center for Marine Studies, Shanghai Ocean University, Shanghai, China
| | - Xiaoyi Yuan
- Institute for Marine Biosystem and Neuroscience, International Center for Marine Studies, Shanghai Ocean University, Shanghai, China
| | - Jian Wang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, China; International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, China.
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6
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Sabaie H, Amirinejad N, Asadi MR, Jalaiei A, Daneshmandpour Y, Rezaei O, Taheri M, Rezazadeh M. Molecular Insight Into the Therapeutic Potential of Long Non-coding RNA-Associated Competing Endogenous RNA Axes in Alzheimer's Disease: A Systematic Scoping Review. Front Aging Neurosci 2021; 13:742242. [PMID: 34899268 PMCID: PMC8656158 DOI: 10.3389/fnagi.2021.742242] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/25/2021] [Indexed: 01/16/2023] Open
Abstract
Alzheimer’s disease (AD) is a heterogeneous degenerative brain disorder with a rising prevalence worldwide. The two hallmarks that characterize the AD pathophysiology are amyloid plaques, generated via aggregated amyloid β, and neurofibrillary tangle, generated via accumulated phosphorylated tau. At the post-transcriptional and transcriptional levels, the regulatory functions of non-coding RNAs, in particular long non-coding RNAs (lncRNAs), have been ascertained in gene expressions. It is noteworthy that a number of lncRNAs feature a prevalent role in their potential of regulating gene expression through modulation of microRNAs via a process called the mechanism of competing endogenous RNA (ceRNA). Given the multifactorial nature of ceRNA interaction networks, they might be advantageous in complex disorders (e.g., AD) investigations at the therapeutic targets level. We carried out scoping review in this research to analyze validated loops of ceRNA in AD and focus on ceRNA axes associated with lncRNA. This scoping review was performed according to a six-stage methodology structure and PRISMA guideline. A systematic search of seven databases was conducted to find eligible articles prior to July 2021. Two reviewers independently performed publications screening and data extraction, and quantitative and qualitative analyses were conducted. Fourteen articles were identified that fulfill the inclusion criteria. Studies with different designs reported nine lncRNAs that were experimentally validated to act as ceRNA in AD in human-related studies, including BACE1-AS, SNHG1, RPPH1, NEAT1, LINC00094, SOX21-AS1, LINC00507, MAGI2-AS3, and LINC01311. The BACE1-AS/BACE1 was the most frequent ceRNA pair. Among miRNAs, miR-107 played a key role by regulating three different loops. Understanding the various aspects of this regulatory mechanism can help elucidate the unknown etiology of AD and provide new molecular targets for use in therapeutic and clinical applications.
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Affiliation(s)
- Hani Sabaie
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Nazanin Amirinejad
- Department of Biology, Faculty of Sciences, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Mohammad Reza Asadi
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Abbas Jalaiei
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Yousef Daneshmandpour
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Omidvar Rezaei
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Maryam Rezazadeh
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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Hu SQ, Xu HM, Qian F, Chen CS, Wang X, Liu D, Cheng L. Interferon regulatory factor-7 is required for hair cell development during zebrafish embryogenesis. Dev Neurobiol 2021; 82:88-97. [PMID: 34779143 PMCID: PMC9305156 DOI: 10.1002/dneu.22860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 09/24/2021] [Accepted: 11/04/2021] [Indexed: 11/08/2022]
Abstract
Interferon regulatory factor‐7 (IRF7) is an essential regulator of both innate and adaptive immunity. It is also expressed in the otic vesicle of zebrafish embryos. However, any role for irf7 in hair cell development was uncharacterized. Does it work as a potential deaf gene to regulate hair cell development? We used whole‐mount in situ hybridization (WISH) assay and morpholino‐mediated gene knockdown method to investigate the role of irf7 in the development of otic vesicle hair cells during zebrafish embryogenesis. We performed RNA sequencing to gain a detailed insight into the molecules/genes which are altered upon downregulation of irf7. Compared to the wild‐type siblings, knockdown of irf7 resulted in severe developmental retardation in zebrafish embryos as well as loss of neuromasts and damage to hair cells at an early stage (within 3 days post fertilization). Coinjection of zebrafish irf7 mRNA could partially rescued the defects of the morphants. atp1b2b mRNA injection can also partially rescue the phenotype induced by irf7 gene deficiency. Loss of hair cells in irf7‐morphants does not result from cell apoptosis. Gene expression profiles show that, compared to wild‐type, knockdown of irf7 can lead to 2053 and 2678 genes being upregulated and downregulated, respectively. Among them, 18 genes were annotated to hair cell (HC) development or posterior lateral line (PLL) development. All results suggest that irf7 plays an essential role in hair cell development in zebrafish, indicating that irf7 may be a member of deafness gene family.
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Affiliation(s)
- Song-Qun Hu
- Department of Otorhinolaryngology, The First Affiliated Hospital, Nanjing Medical University, Nanjing, China.,Department of Otorhinolaryngology, Affiliated Hospital of Nantong University, Nantong, China
| | - Hui-Min Xu
- Department of Otorhinolaryngology, The Second Affiliated Hospital of Nantong University, Nantong, China
| | - Fuping Qian
- School of Life Sciences, Co-innovation Center of Neuroregeneration, Key Laboratory of Neuroregeneration of Ministry of Education, Nantong University, Nantong, China
| | - Chang-Sheng Chen
- School of Life Sciences, Co-innovation Center of Neuroregeneration, Key Laboratory of Neuroregeneration of Ministry of Education, Nantong University, Nantong, China
| | - Xin Wang
- School of Life Sciences, Co-innovation Center of Neuroregeneration, Key Laboratory of Neuroregeneration of Ministry of Education, Nantong University, Nantong, China
| | - Dong Liu
- School of Life Sciences, Co-innovation Center of Neuroregeneration, Key Laboratory of Neuroregeneration of Ministry of Education, Nantong University, Nantong, China
| | - Lei Cheng
- Department of Otorhinolaryngology, The First Affiliated Hospital, Nanjing Medical University, Nanjing, China.,WHO Collaborating Centre for the Prevention of Deafness and Hearing Impairment, Nanjing Medical University, Nanjing, China
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8
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Oliver BL, Young CA, Munnamalai V. Spatial and temporal expression of PORCN is highly dynamic in the developing mouse cochlea. Gene Expr Patterns 2021; 42:119214. [PMID: 34547456 DOI: 10.1016/j.gep.2021.119214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/08/2021] [Accepted: 09/17/2021] [Indexed: 10/20/2022]
Abstract
The mammalian organ of Corti is a highly specialized sensory organ of the cochlea with a fine-grained pattern that is essential for auditory function. The sensory epithelium, the organ of Corti consists of a single row of inner hair cells and three rows of outer hair cells that are intercalated by support cells in a mosaic pattern. Previous studies show that the Wnt pathway regulates proliferation, promotes medial compartment formation in the cochlea, differentiation of the mechanosensory hair cells and axon guidance of Type II afferent neurons. WNT ligand expressions are highly dynamic throughout development but are insufficient to explain the roles of the Wnt pathway. We address a potential way for how WNTs specify the medial compartment by characterizing the expression of Porcupine (PORCN), an O-acyltransferase that is required for WNT secretion. We show PORCN expression across embryonic ages (E)12.5 - E14.5, E16.5, and postnatal day (P)1. Our results showed enriched PORCN in the medial domains during early stages of development, indicating that WNTs have a stronger influence on patterning of the medial compartment. PORCN was rapidly downregulated after E14.5, following the onset of sensory cell differentiation; residual expression remained in some hair cells and supporting cells. On E14.5 and E16.5, we also examined the spatial expression of Gsk3β, an inhibitor of canonical Wnt signaling to determine its potential role in radial patterning of the cochlea. Gsk3β was broadly expressed across the radial axis of the epithelium; therefore, unlikely to control WNT-mediated medial specification. In conclusion, the spatial expression of PORCN enriches WNT secretion from the medial domains of the cochlea to influence the specification of cell fates in the medial sensory domain.
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Affiliation(s)
| | - Caryl A Young
- The Jackson Laboratory, Bar Harbor, ME, 04609, United States; The University of Maine, Graduate School of Biomedical Sciences and Engineering, Orono, ME, 04469, United States
| | - Vidhya Munnamalai
- The Jackson Laboratory, Bar Harbor, ME, 04609, United States; The University of Maine, Graduate School of Biomedical Sciences and Engineering, Orono, ME, 04469, United States.
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Competing Endogenous RNA Networks as Biomarkers in Neurodegenerative Diseases. Int J Mol Sci 2020; 21:ijms21249582. [PMID: 33339180 PMCID: PMC7765627 DOI: 10.3390/ijms21249582] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/11/2020] [Accepted: 12/12/2020] [Indexed: 12/14/2022] Open
Abstract
Protein aggregation is classically considered the main cause of neuronal death in neurodegenerative diseases (NDDs). However, increasing evidence suggests that alteration of RNA metabolism is a key factor in the etiopathogenesis of these complex disorders. Non-coding RNAs are the major contributor to the human transcriptome and are particularly abundant in the central nervous system, where they have been proposed to be involved in the onset and development of NDDs. Interestingly, some ncRNAs (such as lncRNAs, circRNAs and pseudogenes) share a common functionality in their ability to regulate gene expression by modulating miRNAs in a phenomenon known as the competing endogenous RNA mechanism. Moreover, ncRNAs are found in body fluids where their presence and concentration could serve as potential non-invasive biomarkers of NDDs. In this review, we summarize the ceRNA networks described in Alzheimer's disease, Parkinson's disease, multiple sclerosis, amyotrophic lateral sclerosis and spinocerebellar ataxia type 7, and discuss their potential as biomarkers of these NDDs. Although numerous studies have been carried out, further research is needed to validate these complex interactions between RNAs and the alterations in RNA editing that could provide specific ceRNET profiles for neurodegenerative disorders, paving the way to a better understanding of these diseases.
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Xu Y, Nowrangi D, Liang H, Wang T, Yu L, Lu T, Lu Z, Zhang JH, Luo B, Tang J. DKK3 attenuates JNK and AP-1 induced inflammation via Kremen-1 and DVL-1 in mice following intracerebral hemorrhage. J Neuroinflammation 2020; 17:130. [PMID: 32331523 PMCID: PMC7181567 DOI: 10.1186/s12974-020-01794-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 03/27/2020] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Intracerebral hemorrhage (ICH) is the most devastating stroke subtype, with a poor prognosis and few proven treatments. Neuroinflammation is associated with ICH-induced brain injury and unfavorable outcomes. There is growing evidence that Dickkopf (DKK) 3 plays a key role in the adaptive anti-inflammatory and neuroprotective responses following intracerebral hemorrhage. This study aimed to evaluate the protective effects of DKK3 against brain edema and neuroinflammation in a mice model of ICH. METHODS Male, adult CD1 mice were subjected to sham or ICH surgery using a collagenase injection model. ICH animals received either recombinant DKK3, Kremen-1 siRNA, or DVL-1 siRNA. The neurobehavioral deficits were evaluated at 24 h, 72 h, and 28 days after ICH induction. Western blot and immunofluorescence were employed to examine the expression and localization of DKK3, Kremen-1, Dishevelled-1 (DVL-1), c-JUN N-terminal kinase (JNK), Activator protein-1 (AP-1), cleaved caspase-1, NF-κB, and IL-1β in the brain. RESULTS The expression of endogenous DKK3 and DVL-1 was transiently decreased after ICH compared to that in the sham group. Compared to the mice of ICH, exogenous rDKK3 administration reduced the brain water content and affected the neurological functions in ICH mice. Moreover, DKK3 was colocalized with Kremen-1 in microglia. Using a Kremen-1 or DVL-1 siRNA-induced in vivo knockdown approach, we demonstrated that the effects of DKK3 against ICH were mediated, at least partly, by the Kremen-1 and DVL-1 pathways. CONCLUSIONS DKK3 improves the neurological outcomes, potentially by decreasing JNK/AP-1-mediated inflammation, thereby ameliorating the short- and long-term sequelae after ICH.
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Affiliation(s)
- Yang Xu
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institutes, Wannan Medical College, Wuhu, 241000, Anhui, China
- Department of Basic Sciences, Division of Physiology, Loma Linda University School of Medicine, 11041 Campus St, Risley Hall, Room 219, Loma Linda, CA, 92350, USA
- Department of Neurology, Wannan Medical College First Affiliated Hospital, Wuhu, 241000, Anhui, China
| | - Derek Nowrangi
- Department of Basic Sciences, Division of Physiology, Loma Linda University School of Medicine, 11041 Campus St, Risley Hall, Room 219, Loma Linda, CA, 92350, USA
| | - Hui Liang
- Department of Neurology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Qingchun Road 79, Zhejiang, 310003, Hangzhou, China
| | - Tian Wang
- Department of Basic Sciences, Division of Physiology, Loma Linda University School of Medicine, 11041 Campus St, Risley Hall, Room 219, Loma Linda, CA, 92350, USA
| | - Lingyan Yu
- Department of Basic Sciences, Division of Physiology, Loma Linda University School of Medicine, 11041 Campus St, Risley Hall, Room 219, Loma Linda, CA, 92350, USA
| | - Tai Lu
- Department of Basic Sciences, Division of Physiology, Loma Linda University School of Medicine, 11041 Campus St, Risley Hall, Room 219, Loma Linda, CA, 92350, USA
| | - Zhengyang Lu
- Department of Basic Sciences, Division of Physiology, Loma Linda University School of Medicine, 11041 Campus St, Risley Hall, Room 219, Loma Linda, CA, 92350, USA
| | - John H Zhang
- Department of Basic Sciences, Division of Physiology, Loma Linda University School of Medicine, 11041 Campus St, Risley Hall, Room 219, Loma Linda, CA, 92350, USA
- Department of Anesthesiology, Loma Linda University School of Medicine, Loma Linda, CA, 92350, USA
| | - Benyan Luo
- Department of Neurology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Qingchun Road 79, Zhejiang, 310003, Hangzhou, China.
| | - Jiping Tang
- Department of Basic Sciences, Division of Physiology, Loma Linda University School of Medicine, 11041 Campus St, Risley Hall, Room 219, Loma Linda, CA, 92350, USA.
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Cassar S, Adatto I, Freeman JL, Gamse JT, Iturria I, Lawrence C, Muriana A, Peterson RT, Van Cruchten S, Zon LI. Use of Zebrafish in Drug Discovery Toxicology. Chem Res Toxicol 2019; 33:95-118. [PMID: 31625720 DOI: 10.1021/acs.chemrestox.9b00335] [Citation(s) in RCA: 275] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Unpredicted human safety events in clinical trials for new drugs are costly in terms of human health and money. The drug discovery industry attempts to minimize those events with diligent preclinical safety testing. Current standard practices are good at preventing toxic compounds from being tested in the clinic; however, false negative preclinical toxicity results are still a reality. Continual improvement must be pursued in the preclinical realm. Higher-quality therapies can be brought forward with more information about potential toxicities and associated mechanisms. The zebrafish model is a bridge between in vitro assays and mammalian in vivo studies. This model is powerful in its breadth of application and tractability for research. In the past two decades, our understanding of disease biology and drug toxicity has grown significantly owing to thousands of studies on this tiny vertebrate. This Review summarizes challenges and strengths of the model, discusses the 3Rs value that it can deliver, highlights translatable and untranslatable biology, and brings together reports from recent studies with zebrafish focusing on new drug discovery toxicology.
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Affiliation(s)
- Steven Cassar
- Preclinical Safety , AbbVie , North Chicago , Illinois 60064 , United States
| | - Isaac Adatto
- Stem Cell and Regenerative Biology , Harvard University , Cambridge , Massachusetts 02138 , United States
| | - Jennifer L Freeman
- School of Health Sciences , Purdue University , West Lafayette , Indiana 47907 , United States
| | - Joshua T Gamse
- Drug Safety Evaluation , Bristol-Myers Squibb , New Brunswick , New Jersey 08901 , United States
| | | | - Christian Lawrence
- Aquatic Resources Program , Boston Children's Hospital , Boston , Massachusetts 02115 , United States
| | | | - Randall T Peterson
- Pharmacology and Toxicology, College of Pharmacy , University of Utah , Salt Lake City , Utah 84112 , United States
| | | | - Leonard I Zon
- Stem Cell Program and Division of Hematology/Oncology, Children's Hospital and Dana Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Medical School, Harvard Stem Cell Institute, Stem Cell and Regenerative Biology Department , Harvard University , Boston , Massachusetts 02138 , United States
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12
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Munnamalai V, Fekete DM. The acquisition of positional information across the radial axis of the cochlea. Dev Dyn 2019; 249:281-297. [PMID: 31566832 DOI: 10.1002/dvdy.118] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 09/10/2019] [Accepted: 09/10/2019] [Indexed: 12/11/2022] Open
Affiliation(s)
- Vidhya Munnamalai
- The Jackson Laboratory Bar Harbor Maine
- Graduate Program of Biomedical Sciences and EngineeringUniversity of Maine Orono Maine
- The Neuroscience ProgramSackler School of Biomedical Sciences, Tufts University Boston Massachusetts
| | - Donna M. Fekete
- Department of Biological SciencesPurdue University West Lafayette Indiana
- Purdue Institute for Integrative Neuroscience West Lafayette Indiana
- Purdue Center for Cancer Research West Lafayette Indiana
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Knockdown of lncRNA SNHG1 attenuated Aβ25-35-inudced neuronal injury via regulating KREMEN1 by acting as a ceRNA of miR-137 in neuronal cells. Biochem Biophys Res Commun 2019; 518:438-444. [DOI: 10.1016/j.bbrc.2019.08.033] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 08/07/2019] [Indexed: 02/05/2023]
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14
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Samarajeewa A, Jacques BE, Dabdoub A. Therapeutic Potential of Wnt and Notch Signaling and Epigenetic Regulation in Mammalian Sensory Hair Cell Regeneration. Mol Ther 2019; 27:904-911. [PMID: 30982678 PMCID: PMC6520458 DOI: 10.1016/j.ymthe.2019.03.017] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 03/25/2019] [Accepted: 03/26/2019] [Indexed: 02/07/2023] Open
Abstract
Hearing loss is one of the most prevalent sensory deficits worldwide and can result from the death of mechanosensory hair cells that transduce auditory signals in the cochlea. The mammalian cochlea lacks the capacity to regenerate these hair cells once damaged, and currently there are no biological therapies for hearing loss. Understanding the signaling pathways responsible for hair cell development can inform regenerative strategies and identify targets for treating hearing loss. The canonical Wnt and Notch pathways are critical for cochlear development; they converge on several key molecules, such as Atoh1, to regulate prosensory specification, proliferation, hair cell differentiation, and cellular organization. Much work has focused on Wnt and Notch modulation in the neonatal mouse cochlea, where they can promote hair cell regeneration. However, this regenerative response is limited in the adult cochlea and this might be attributed to age-dependent epigenetic modifications. Indeed, the epigenetic status at key gene loci undergoes dynamic changes during cochlear development, maturation, and aging. Therefore, strategies to improve regenerative success in the adult cochlea might require the modulation of Wnt, Notch, or other pathways, as well as targeted epigenetic modifications to alter the activity of key genes critical for supporting cell proliferation or transdifferentiation.
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Affiliation(s)
- Anshula Samarajeewa
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | | | - Alain Dabdoub
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada; Biological Sciences, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, ON M4N 3M5, Canada; Department of Otolaryngology - Head & Neck Surgery, University of Toronto, Toronto, ON M5G 2C4, Canada.
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Samarajeewa A, Lenz DR, Xie L, Chiang H, Kirchner R, Mulvaney JF, Edge ASB, Dabdoub A. Transcriptional response to Wnt activation regulates the regenerative capacity of the mammalian cochlea. Development 2018; 145:dev.166579. [PMID: 30389848 PMCID: PMC6288390 DOI: 10.1242/dev.166579] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 10/25/2018] [Indexed: 01/04/2023]
Abstract
Lack of sensory hair cell (HC) regeneration in mammalian adults is a major contributor to hearing loss. In contrast, the neonatal mouse cochlea retains a transient capacity for regeneration, and forced Wnt activation in neonatal stages promotes supporting cell (SC) proliferation and induction of ectopic HCs. We currently know little about the temporal pattern and underlying mechanism of this age-dependent regenerative response. Using an in vitro model, we show that Wnt activation promotes SC proliferation following birth, but prior to postnatal day (P) 5. This age-dependent decline in proliferation occurs despite evidence that the Wnt pathway is postnatally active and can be further enhanced by Wnt stimulators. Using an in vivo mouse model and RNA sequencing, we show that proliferation in the early neonatal cochlea is correlated with a unique transcriptional response that diminishes with age. Furthermore, we find that augmenting Wnt signaling through the neonatal stages extends the window for HC induction in response to Notch signaling inhibition. Our results suggest that the downstream transcriptional response to Wnt activation, in part, underlies the regenerative capacity of the mammalian cochlea. Summary: Canonical Wnt activation in the mammalian cochlea elicits a unique, age-dependent transcriptional response, which in part regulates the regenerative capacity of supporting cells during cochlear maturation.
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Affiliation(s)
- Anshula Samarajeewa
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto ON, M5S 1A8, Canada
| | - Danielle R Lenz
- Department of Otolaryngology, Harvard Medical School, Boston, MA 02114, USA.,Eaton-Peabody Laboratory, Massachusetts Eye and Ear, Boston, MA 02114, USA
| | - Lihong Xie
- Biological Sciences, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto ON, M4N 3M5, Canada.,Department of Otolaryngology-Head and Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning Guangxi, 530021, China
| | - Hao Chiang
- Department of Otolaryngology, Harvard Medical School, Boston, MA 02114, USA.,Eaton-Peabody Laboratory, Massachusetts Eye and Ear, Boston, MA 02114, USA
| | - Rory Kirchner
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Joanna F Mulvaney
- Biological Sciences, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto ON, M4N 3M5, Canada
| | - Albert S B Edge
- Department of Otolaryngology, Harvard Medical School, Boston, MA 02114, USA.,Eaton-Peabody Laboratory, Massachusetts Eye and Ear, Boston, MA 02114, USA
| | - Alain Dabdoub
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto ON, M5S 1A8, Canada .,Biological Sciences, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto ON, M4N 3M5, Canada.,Department of Otolaryngology - Head & Neck Surgery, University of Toronto, Toronto ON, M5G 2C4, Canada
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Mittal R, Nguyen D, Patel AP, Debs LH, Mittal J, Yan D, Eshraghi AA, Van De Water TR, Liu XZ. Recent Advancements in the Regeneration of Auditory Hair Cells and Hearing Restoration. Front Mol Neurosci 2017; 10:236. [PMID: 28824370 PMCID: PMC5534485 DOI: 10.3389/fnmol.2017.00236] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 07/11/2017] [Indexed: 12/18/2022] Open
Abstract
Neurosensory responses of hearing and balance are mediated by receptors in specialized neuroepithelial sensory cells. Any disruption of the biochemical and molecular pathways that facilitate these responses can result in severe deficits, including hearing loss and vestibular dysfunction. Hearing is affected by both environmental and genetic factors, with impairment of auditory function being the most common neurosensory disorder affecting 1 in 500 newborns, as well as having an impact on the majority of elderly population. Damage to auditory sensory cells is not reversible, and if sufficient damage and cell death have taken place, the resultant deficit may lead to permanent deafness. Cochlear implants are considered to be one of the most successful and consistent treatments for deaf patients, but only offer limited recovery at the expense of loss of residual hearing. Recently there has been an increased interest in the auditory research community to explore the regeneration of mammalian auditory hair cells and restoration of their function. In this review article, we examine a variety of recent therapies, including genetic, stem cell and molecular therapies as well as discussing progress being made in genome editing strategies as applied to the restoration of hearing function.
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Affiliation(s)
- Rahul Mittal
- Department of Otolaryngology, University of Miami Miller School of MedicineMiami, FL, United States
| | - Desiree Nguyen
- Department of Otolaryngology, University of Miami Miller School of MedicineMiami, FL, United States
| | - Amit P. Patel
- Department of Otolaryngology, University of Miami Miller School of MedicineMiami, FL, United States
| | - Luca H. Debs
- Department of Otolaryngology, University of Miami Miller School of MedicineMiami, FL, United States
| | - Jeenu Mittal
- Department of Otolaryngology, University of Miami Miller School of MedicineMiami, FL, United States
| | - Denise Yan
- Department of Otolaryngology, University of Miami Miller School of MedicineMiami, FL, United States
| | - Adrien A. Eshraghi
- Department of Otolaryngology, University of Miami Miller School of MedicineMiami, FL, United States
| | - Thomas R. Van De Water
- Department of Otolaryngology, University of Miami Miller School of MedicineMiami, FL, United States
| | - Xue Z. Liu
- Department of Otolaryngology, University of Miami Miller School of MedicineMiami, FL, United States
- Department of Otolaryngology, Xiangya Hospital, Central South UniversityChangsha, China
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