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Patil V, Perez-Carpena P, Lopez-Escamez JA. A systematic review on the contribution of DNA methylation to hearing loss. Clin Epigenetics 2024; 16:88. [PMID: 38970134 PMCID: PMC11227199 DOI: 10.1186/s13148-024-01697-9] [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: 02/09/2024] [Accepted: 06/17/2024] [Indexed: 07/07/2024] Open
Abstract
BACKGROUND DNA methylation may have a regulatory role in monogenic sensorineural hearing loss and complex, polygenic phenotypic forms of hearing loss, including age-related hearing impairment or Meniere disease. The purpose of this systematic review is to critically assess the evidence supporting a functional role of DNA methylation in phenotypes associated with hearing loss. RESULTS The search strategy yielded a total of 661 articles. After quality assessment, 25 records were selected (12 human DNA methylation studies, 5 experimental animal studies and 8 studies reporting mutations in the DNMT1 gene). Although some methylation studies reported significant differences in CpG methylation in diverse gene promoters associated with complex hearing loss phenotypes (ARHI, otosclerosis, MD), only one study included a replication cohort that supported a regulatory role for CpG methylation in the genes TCF25 and POLE in ARHI. Conversely, several studies have independently confirmed pathogenic mutations within exon 21 of the DNMT1 gene, which encodes the DNA (cytosine-5)-methyltransferase 1 enzyme. This methylation enzyme is strongly associated with a rare disease defined by autosomal dominant cerebellar ataxia, deafness and narcolepsy (ADCA-DN). Of note, rare variants in DNMT1 and DNMT3A genes have also been reported in noise-induced hearing loss. CONCLUSIONS Evidence supporting a functional role for DNA methylation in hearing loss is limited to few genes in complex disorders such as ARHI. Mutations in the DNMT1 gene are associated with ADCA-DN, suggesting the CpG methylation in hearing loss genes deserves further attention in hearing research.
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Affiliation(s)
- Vibha Patil
- Meniere's Disease Neuroscience Research Program, Faculty of Medicine and Health, School of Medical Sciences, The Kolling Institute, University of Sydney, Rm 611024, Level 11 Kolling Institute | 10 Westbourne St, St Leonards, Sydney, NSW, 2064, Australia.
| | - Patricia Perez-Carpena
- Division of Otolaryngology, Department of Surgery, Instituto de Investigación Biosanitaria, Ibs.Granada, Universidad de Granada, Granada, Spain
- Otology & Neurotology Group CTS495, Instituto de Investigación Biosanitaria, ibs.GRANADA, Universidad de Granada, Granada, Spain
- Sensorineural Pathology Program, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, Madrid, Spain
- Department of Otolaryngology, Hospital Universitario San Cecilio, Instituto de Investigacion Biosanitaria, ibs.GRANADA, Granada, Spain
| | - Jose A Lopez-Escamez
- Meniere's Disease Neuroscience Research Program, Faculty of Medicine and Health, School of Medical Sciences, The Kolling Institute, University of Sydney, Rm 611024, Level 11 Kolling Institute | 10 Westbourne St, St Leonards, Sydney, NSW, 2064, Australia
- Division of Otolaryngology, Department of Surgery, Instituto de Investigación Biosanitaria, Ibs.Granada, Universidad de Granada, Granada, Spain
- Otology & Neurotology Group CTS495, Instituto de Investigación Biosanitaria, ibs.GRANADA, Universidad de Granada, Granada, Spain
- Sensorineural Pathology Program, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, Madrid, Spain
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Hertzano R, Gwilliam K, Rose K, Milon B, Matern MS. Cell Type-Specific Expression Analysis of the Inner Ear: A Technical Report. Laryngoscope 2021; 131 Suppl 5:S1-S16. [PMID: 32579737 PMCID: PMC8996438 DOI: 10.1002/lary.28765] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/21/2020] [Accepted: 05/01/2020] [Indexed: 01/11/2023]
Abstract
OBJECTIVE The cellular diversity of the inner ear has presented a technical challenge in obtaining molecular insight into its development and function. The application of technological advancements in cell type-specific expression enable clinicians and researchers to leap forward from classic genetics to obtaining mechanistic understanding of congenital and acquired hearing loss. This understanding is essential for development of therapeutics to prevent and reverse diseases of the inner ear, including hearing loss. The objective of this study is to describe and compare the available tools for cell type-specific analysis of the ear, as a means to support decision making in study design. STUDY DESIGN Three major approaches for cell type-specific analysis of the ear including fluorescence-activated cell sorting (FACS), ribosomal and RNA pulldown techniques, and single cell RNA-seq (scRNA-seq) are compared and contrasted using both published and original data. RESULTS We demonstrate the strength and weaknesses of these approaches leading to the inevitable conclusion that to maximize the utility of these approaches, it is important to match the experimental approach with the tissue of origin, cell type of interest, and the biological question. Often, a combined approach (eg, cell sorting and scRNA-seq or expression analysis using 2 separate approaches) is required. Finally, new tools for visualization and analysis of complex expression data, such as the gEAR platform (umgear.org), collate cell type-specific gene expression from the ear field and provide unprecedented access to both clinicians and researchers. LEVEL OF EVIDENCE N/A Laryngoscope, 131:S1-S16, 2021.
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Affiliation(s)
- Ronna Hertzano
- Department of Otorhinolaryngology Head and Neck Surgery University of Maryland School of Medicine 16 S Eutaw St. Suite 500 Baltimore Maryland 21201 U.S.A
- Institute for Genome Sciences, University of Maryland School of Medicine Baltimore Maryland U.S.A
- Department of Anatomy and Neurobiology University of Maryland School of Medicine Baltimore Maryland U.S.A
| | - Kathleen Gwilliam
- Department of Otorhinolaryngology Head and Neck Surgery University of Maryland School of Medicine 16 S Eutaw St. Suite 500 Baltimore Maryland 21201 U.S.A
| | - Kevin Rose
- Department of Otorhinolaryngology Head and Neck Surgery University of Maryland School of Medicine 16 S Eutaw St. Suite 500 Baltimore Maryland 21201 U.S.A
| | - Beatrice Milon
- Department of Otorhinolaryngology Head and Neck Surgery University of Maryland School of Medicine 16 S Eutaw St. Suite 500 Baltimore Maryland 21201 U.S.A
| | - Maggie S. Matern
- Department of Otorhinolaryngology Head and Neck Surgery University of Maryland School of Medicine 16 S Eutaw St. Suite 500 Baltimore Maryland 21201 U.S.A
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3
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Wonkam A, Lebeko K, Mowla S, Noubiap JJ, Chong M, Pare G. Whole exome sequencing reveals a biallelic frameshift mutation in GRXCR2 in hearing impairment in Cameroon. Mol Genet Genomic Med 2021; 9:e1609. [PMID: 33528103 PMCID: PMC8104159 DOI: 10.1002/mgg3.1609] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/06/2021] [Accepted: 01/11/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Hearing impairment (HI) genes are poorly studied in African populations. METHODS We used whole exome sequencing (WES) to investigate pathogenic and likely pathogenic (PLP) variants in 10 individuals with HI, from four multiplex families from Cameroon, two of which were previously unresolved with a targeted gene enrichment (TGE) panel of 116 genes. In silico protein modelling, western blotting and live imaging of transfected HEK293 cells were performed to study protein structure and functions. RESULTS All PLP variants previously identified with TGE were replicated. In one previously unresolved family, we found a homozygous frameshift PLP variant in GRXCR2 (OMIM: 615762), NM_001080516.1(GRXCR2):c.251delC p.(Ile85SerfsTer33), in two affected siblings; and additionally, in 1/80 unrelated individuals affected with non-syndromic hearing impairment (NSHI). The GRXCR2-c.251delC variant introduced a premature stop codon, leading to truncation and loss of a zinc-finger domain. Fluorescence confocal microscopy tracked the wild-type GRXCR2 protein to the cellular membrane, unlike the mutated GRXCR2 protein. CONCLUSION This study confirms GRXCR2 as a HI-associated gene. GRXCR2 should be included to the currently available TGE panels for HI diagnosis.
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Affiliation(s)
- Ambroise Wonkam
- Department of Medicine, Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Kamogelo Lebeko
- Department of Medicine, Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Shaheen Mowla
- Department of Pathology, Division of Haematology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Jean Jacques Noubiap
- Centre for Heart Rhythm Disorders, South Australian Health and Medical Research Institute (SAHMRI, University of Adelaide and Royal Adelaide Hospital, Adelaide, Australia
| | - Mike Chong
- Population Health Research Institute, Hamilton Health Sciences and McMaster University, Hamilton, ON, Canada
| | - Guillaume Pare
- Population Health Research Institute, Hamilton Health Sciences and McMaster University, Hamilton, ON, Canada
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Jongkamonwiwat N, Ramirez MA, Edassery S, Wong ACY, Yu J, Abbott T, Pak K, Ryan AF, Savas JN. Noise Exposures Causing Hearing Loss Generate Proteotoxic Stress and Activate the Proteostasis Network. Cell Rep 2020; 33:108431. [PMID: 33238128 PMCID: PMC7722268 DOI: 10.1016/j.celrep.2020.108431] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 09/24/2020] [Accepted: 11/04/2020] [Indexed: 12/20/2022] Open
Abstract
Exposure to excessive sound causes noise-induced hearing loss through complex mechanisms and represents a common and unmet neurological condition. We investigate how noise insults affect the cochlea with proteomics and functional assays. Quantitative proteomics reveals that exposure to loud noise causes proteotoxicity. We identify and confirm hundreds of proteins that accumulate, including cytoskeletal proteins, and several nodes of the proteostasis network. Transcriptomic analysis reveals that a subset of the genes encoding these proteins also increases acutely after noise exposure, including numerous proteasome subunits. Global cochlear protein ubiquitylation levels build up after exposure to excess noise, and we map numerous posttranslationally modified lysines residues. Several collagen proteins decrease in abundance, and Col9a1 specifically localizes to pillar cell heads. After two weeks of recovery, the cochlea selectively elevates the abundance of the protein synthesis machinery. We report that overstimulation of the auditory system drives a robust cochlear proteotoxic stress response.
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Affiliation(s)
- Nopporn Jongkamonwiwat
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Miguel A Ramirez
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Seby Edassery
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Ann C Y Wong
- Departments of Surgery and Neuroscience, University of California San Diego and Veterans Administration Medical Center, La Jolla, CA 92093, USA; Translational Neuroscience Facility, Department of Physiology, NSW Australia, Sydney, NSW 2052, Australia
| | - Jintao Yu
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Tirzah Abbott
- Northwestern University Atomic and Nanoscale Characterization Experimental (NUANCE) Center, Northwestern University, Evanston, IL 60208, USA
| | - Kwang Pak
- Departments of Surgery and Neuroscience, University of California San Diego and Veterans Administration Medical Center, La Jolla, CA 92093, USA
| | - Allen F Ryan
- Departments of Surgery and Neuroscience, University of California San Diego and Veterans Administration Medical Center, La Jolla, CA 92093, USA
| | - Jeffrey N Savas
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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Novel Mutations in CLPP, LARS2, CDH23, and COL4A5 Identified in Familial Cases of Prelingual Hearing Loss. Genes (Basel) 2020; 11:genes11090978. [PMID: 32842620 PMCID: PMC7564084 DOI: 10.3390/genes11090978] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/12/2020] [Accepted: 08/18/2020] [Indexed: 12/30/2022] Open
Abstract
We report the underlying genetic causes of prelingual hearing loss (HL) segregating in eight large consanguineous families, ascertained from the Punjab province of Pakistan. Exome sequencing followed by segregation analysis revealed seven potentially pathogenic variants, including four novel alleles c.257G>A, c.6083A>C, c.89A>G, and c.1249A>G of CLPP, CDH23, COL4A5, and LARS2, respectively. We also identified three previously reported HL-causing variants (c.4528C>T, c.35delG, and c.1219T>C) of MYO15A, GJB2, and TMPRSS3 segregating in four families. All identified variants were either absent or had very low frequencies in the control databases. Our in silico analyses and 3-dimensional (3D) molecular modeling support the deleterious impact of these variants on the encoded proteins. Variants identified in MYO15A, GJB2, TMPRSS3, and CDH23 were classified as “pathogenic” or “likely pathogenic”, while the variants in CLPP and LARS2 fall in the category of “uncertain significance” based on the American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) variant pathogenicity guidelines. This paper highlights the genetic diversity of hearing disorders in the Pakistani population and reports the identification of four novel mutations in four HL families.
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GJB2 and GJB6 Mutations in Hereditary Recessive Non-Syndromic Hearing Impairment in Cameroon. Genes (Basel) 2019; 10:genes10110844. [PMID: 31731535 PMCID: PMC6895965 DOI: 10.3390/genes10110844] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/07/2019] [Accepted: 10/23/2019] [Indexed: 02/06/2023] Open
Abstract
This study aimed to investigate GJB2 (connexin 26) and GJB6 (connexin 30) mutations associated with familial non-syndromic childhood hearing impairment (HI) in Cameroon. We selected only families segregating HI, with at least two affected individuals and with strong evidence of non-environmental causes. DNA was extracted from peripheral blood, and the entire coding region of GJB2 was interrogated using Sanger sequencing. Multiplex PCR and Sanger sequencing were used to analyze the prevalence of the GJB6-D3S1830 deletion. A total of 93 patients, belonging to 41 families, were included in the analysis. Hearing impairment was sensorineural in 51 out of 54 (94.4%) patients. Pedigree analysis suggested autosomal recessive inheritance in 85.4% (35/41) of families. Hearing impairment was inherited in an autosomal dominant and mitochondrial mode in 12.2% (5/41) and 2.4% (1/41) of families, respectively. Most HI participants were non-syndromic (92.5%; 86/93). Four patients from two families presented with type 2 Waardenburg syndrome, and three cases of type 2 Usher syndrome were identified in one family. No GJB2 mutations were found in any of the 29 families with non-syndromic HI. Additionally, the GJB6-D3S1830 deletion was not identified in any of the HI patients. This study confirms that mutations in the GJB2 gene and the del(GJB6-D13S1830) mutation do not contribute to familial HI in Cameroon.
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Adadey SM, Manyisa N, Mnika K, de Kock C, Nembaware V, Quaye O, Amedofu GK, Awandare GA, Wonkam A. GJB2 and GJB6 Mutations in Non-Syndromic Childhood Hearing Impairment in Ghana. Front Genet 2019; 10:841. [PMID: 31620164 PMCID: PMC6759689 DOI: 10.3389/fgene.2019.00841] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 08/13/2019] [Indexed: 01/16/2023] Open
Abstract
Our study aimed to investigate GJB2 (connexin 26) and GJB6 (connexin 30) mutations associated with non-syndromic childhood hearing impairment (HI) as well as the environmental causes of HI in Ghana. Medical reports of 1,104 students attending schools for the deaf were analyzed. Families segregating HI, as well as isolated cases of HI of putative genetic origin were recruited. DNA was extracted from peripheral blood followed by Sanger sequencing of the entire coding region of GJB2. Multiplex PCR and Sanger sequencing were used to analyze the prevalence of GJB6-D3S1830 deletion. Ninety-seven families segregating HI were identified, with 235 affected individuals; and a total of 166 isolated cases of putative genetic causes, were sampled from 11 schools for the deaf in Ghana. The environmental factors, particularly meningitis, remain a major cause of HI impairment in Ghana. The male/female ratio was 1.49. Only 59.6% of the patients had their first comprehensive HI test between 6 to 11 years of age. Nearly all the participants had sensorineural HI (99.5%; n = 639). The majority had pre-lingual HI (68.3%, n = 754), of which 92.8% were congenital. Pedigree analysis suggested autosomal recessive inheritance in 96.9% of the familial cases. GJB2-R143W mutation, previously reported as founder a mutation in Ghana accounted for 25.9% (21/81) in the homozygous state in familial cases, and in 7.9% (11/140) of non-familial non-syndromic congenital HI cases, of putative genetic origin. In a control population without HI, we found a prevalent of GJB2-R143W carriers of 1.4% (2/145), in the heterozygous state. No GJB6-D3S1830 deletion was identified in any of the HI patients. GJB2-R143W mutation accounted for over a quarter of familial non-syndromic HI in Ghana and should be investigated in clinical practice. The large connexin 30 gene deletion (GJB6-D3S1830 deletion) does not account for of congenital non-syndromic HI in Ghana. There is a need to employ next generation sequencing approaches and functional genomics studies to identify the other genes involved in most families and isolated cases of HI in Ghana.
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Affiliation(s)
- Samuel M. Adadey
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Noluthando Manyisa
- Division of Human Genetics, Faculty of Health Sciences—University of Cape Town, Cape Town , South Africa
| | - Khuthala Mnika
- Division of Human Genetics, Faculty of Health Sciences—University of Cape Town, Cape Town , South Africa
| | - Carmen de Kock
- Division of Human Genetics, Faculty of Health Sciences—University of Cape Town, Cape Town , South Africa
| | - Victoria Nembaware
- Division of Human Genetics, Faculty of Health Sciences—University of Cape Town, Cape Town , South Africa
| | - Osbourne Quaye
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Geoffrey K. Amedofu
- Department of Eye, Ear, Nose and Throat, School of Medical Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Gordon A. Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Ambroise Wonkam
- Division of Human Genetics, Faculty of Health Sciences—University of Cape Town, Cape Town , South Africa
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Adadey SM, Awandare G, Amedofu GK, Wonkam A. Public Health Burden of Hearing Impairment and the Promise of Genomics and Environmental Research: A Case Study in Ghana, Africa. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2018; 21:638-646. [PMID: 29140768 DOI: 10.1089/omi.2017.0145] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Hearing impairment (HI) is one of the most disabling conditions of major global health burden that contributes adversely to the social and economic development of a country, if not managed properly. A proper assessment of the nationwide burden and etiology of HI is instrumental in the prevention, treatment, and management of the condition. This article sought to perform an expert review of HI in Ghana to determine the present knowledge of its burden and possible causes of the condition. A literature search was conducted in PubMed using the following keywords: "hearing loss" OR "hearing impairment" OR "deafness" AND "Ghana." The literature was scanned until July 20, 2017, with specific inclusion of targeted landmark and background articles on HI. From the search, 18 of out 5869 articles were selected and considered for the review. The results of the search indicated that there were no extensive studies to determine the national burden of HI in Ghana. However, the few studies assessed suggested that the disease is either acquired or inherited. The burden of acquired HI was higher in adults than children, women than men, and people working in a noisy environment. Regarding the genetic cause, specific founder mutations in GJB2 gene (R143W, L79P, V178A, R184Q, A197S, I203K, and L214P) was the only identified genetic cause of HI in Ghana, but the other HI genes were not investigated. There has been some modest effort to study HI in Ghana, but comprehensive studies on the genetic and environmental etiologies (using the "multi-OMICS" approaches), classification, and burden of HI on Ghana are needed.
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Affiliation(s)
- Samuel Mawuli Adadey
- 1 West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana , Accra, Ghana
| | - Gordon Awandare
- 1 West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana , Accra, Ghana
| | | | - Ambroise Wonkam
- 3 Division of Human Genetics, Department of Medicine, Faculty of Health Sciences, University of Cape Town , Cape Town, South Africa
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Booth KT, Azaiez H, Jahan I, Smith RJH, Fritzsch B. Intracellular Regulome Variability Along the Organ of Corti: Evidence, Approaches, Challenges, and Perspective. Front Genet 2018; 9:156. [PMID: 29868110 PMCID: PMC5951964 DOI: 10.3389/fgene.2018.00156] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 04/13/2018] [Indexed: 12/13/2022] Open
Abstract
The mammalian hearing organ is a regular array of two types of hair cells (HCs) surrounded by six types of supporting cells. Along the tonotopic axis, this conserved radial array of cell types shows longitudinal variations to enhance the tuning properties of basilar membrane. We present the current evidence supporting the hypothesis that quantitative local variations in gene expression profiles are responsible for local cell responses to global gene manipulations. With the advent of next generation sequencing and the unprecedented array of technologies offering high throughput analyses at the single cell level, transcriptomics will become a common tool to enhance our understanding of the inner ear. We provide an overview of the approaches and landmark studies undertaken to date to analyze single cell variations in the organ of Corti and discuss the current limitations. We next provide an overview of the complexity of known regulatory mechanisms in the inner ear. These mechanisms are tightly regulated temporally and spatially at the transcription, RNA-splicing, mRNA-regulation, and translation levels. Understanding the intricacies of regulatory mechanisms at play in the inner ear will require the use of complementary approaches, and most probably, a combinatorial strategy coupling transcriptomics, proteomics, and epigenomics technologies. We highlight how these data, in conjunction with recent insights into molecular cell transformation, can advance attempts to restore lost hair cells.
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Affiliation(s)
- Kevin T Booth
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, University of Iowa, Iowa City, IA, United States.,Interdisciplinary Graduate Program in Molecular Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Hela Azaiez
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, University of Iowa, Iowa City, IA, United States
| | - Israt Jahan
- Department of Biology, University of Iowa, Iowa City, IA, United States
| | - Richard J H Smith
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, University of Iowa, Iowa City, IA, United States
| | - Bernd Fritzsch
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology, University of Iowa, Iowa City, IA, United States.,Department of Biology, University of Iowa, Iowa City, IA, United States
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10
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Matern MS, Beirl A, Ogawa Y, Song Y, Paladugu N, Kindt KS, Hertzano R. Transcriptomic Profiling of Zebrafish Hair Cells Using RiboTag. Front Cell Dev Biol 2018; 6:47. [PMID: 29765956 PMCID: PMC5939014 DOI: 10.3389/fcell.2018.00047] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 04/13/2018] [Indexed: 01/27/2023] Open
Abstract
The zebrafish inner ear organs and lateral line neuromasts are comprised of a variety of cell types, including mechanosensitive hair cells. Zebrafish hair cells are evolutionarily homologous to mammalian hair cells, and have been particularly useful for studying normal hair cell development and function. However, the relative scarcity of hair cells within these complex organs, as well as the difficulty of fine dissection at early developmental time points, makes hair cell-specific gene expression profiling technically challenging. Cell sorting methods, as well as single-cell RNA-Seq, have proved to be very informative in studying hair cell-specific gene expression. However, these methods require that tissues are dissociated, the processing for which can lead to changes in gene expression prior to RNA extraction. To bypass this problem, we have developed a transgenic zebrafish model to evaluate the translatome of the inner ear and lateral line hair cells in their native tissue environment; the Tg(myo6b:RiboTag) zebrafish. This model expresses both GFP and a hemagglutinin (HA) tagged rpl10a gene under control of the myo6b promoter (myo6b:GFP-2A-rpl10a-3xHA), resulting in HA-tagged ribosomes expressed specifically in hair cells. Consequently, intact zebrafish larvae can be used to enrich for actively translated hair cell mRNA via an immunoprecipitation protocol using an antibody for the HA-tag (similar to the RiboTag mice). We demonstrate that this model can be used to reliably enrich for actively translated zebrafish hair cell mRNA. Additionally, we perform a global hair cell translatome analysis using RNA-Seq and show enrichment of known hair cell expressed transcripts and depletion of non-hair cell expressed transcripts in the immunoprecipitated material compared with mRNA extracted from whole fish (input). Our results show that our model can identify novel hair cell expressed genes in intact zebrafish, without inducing changes to gene expression that result from tissue dissociation and delays during cell sorting. Overall, we believe that this model will be highly useful for studying changes in zebrafish hair cell-specific gene expression in response to developmental progression, mutations, as well as hair cell damage by noise or ototoxic drug exposure.
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Affiliation(s)
- Maggie S. Matern
- Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Alisha Beirl
- Section on Sensory Cell Development and Function, National Institute on Deafness and Other Communication Disorders, Bethesda, MD, United States
| | - Yoko Ogawa
- Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Yang Song
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Nikhil Paladugu
- Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Katie S. Kindt
- Section on Sensory Cell Development and Function, National Institute on Deafness and Other Communication Disorders, Bethesda, MD, United States
| | - Ronna Hertzano
- Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD, United States,Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States,Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, United States,*Correspondence: Ronna Hertzano
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Lebeko K, Manyisa N, Chimusa ER, Mulder N, Dandara C, Wonkam A. A Genomic and Protein-Protein Interaction Analyses of Nonsyndromic Hearing Impairment in Cameroon Using Targeted Genomic Enrichment and Massively Parallel Sequencing. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2017; 21:90-99. [PMID: 28075205 DOI: 10.1089/omi.2016.0171] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Hearing impairment (HI) is one of the leading causes of disability in the world, impacting the social, economic, and psychological well-being of the affected individual. This is particularly true in sub-Saharan Africa, which carries one of the highest burdens of this condition. Despite this, there are limited data on the most prevalent genes or mutations that cause HI among sub-Saharan Africans. Next-generation technologies, such as targeted genomic enrichment and massively parallel sequencing, offer new promise in this context. This study reports, for the first time to the best of our knowledge, on the prevalence of novel mutations identified through a platform of 116 HI genes (OtoSCOPE®), among 82 African probands with HI. Only variants OTOF NM_194248.2:c.766-2A>G and MYO7A NM_000260.3:c.1996C>T, p.Arg666Stop were found in 3 (3.7%) and 5 (6.1%) patients, respectively. In addition and uniquely, the analysis of protein-protein interactions (PPI), through interrogation of gene subnetworks, using a custom script and two databases (Enrichr and PANTHER), and an algorithm in the igraph package of R, identified the enrichment of sensory perception and mechanical stimulus biological processes, and the most significant molecular functions of these variants pertained to binding or structural activity. Furthermore, 10 genes (MYO7A, MYO6, KCTD3, NUMA1, MYH9, KCNQ1, UBC, DIAPH1, PSMC2, and RDX) were identified as significant hubs within the subnetworks. Results reveal that the novel variants identified among familial cases of HI in Cameroon are not common, and PPI analysis has highlighted the role of 10 genes, potentially important in understanding HI genomics among Africans.
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Affiliation(s)
- Kamogelo Lebeko
- 1 Division of Human Genetics, Department of Pathology, Faculty of Health Sciences - University of Cape Town , Cap Town, South Africa
| | - Noluthando Manyisa
- 1 Division of Human Genetics, Department of Pathology, Faculty of Health Sciences - University of Cape Town , Cap Town, South Africa
| | - Emile R Chimusa
- 1 Division of Human Genetics, Department of Pathology, Faculty of Health Sciences - University of Cape Town , Cap Town, South Africa
| | - Nicola Mulder
- 2 Division of Computational Biology, Faculty of Health Sciences - University of Cape Town , Cap Town, South Africa
| | - Collet Dandara
- 1 Division of Human Genetics, Department of Pathology, Faculty of Health Sciences - University of Cape Town , Cap Town, South Africa
| | - Ambroise Wonkam
- 1 Division of Human Genetics, Department of Pathology, Faculty of Health Sciences - University of Cape Town , Cap Town, South Africa .,3 Department of Medicine, Faculty of Health Sciences - University of Cape Town , Cap Town, South Africa
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13
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Smith ME, Rajadinakaran G. The Transcriptomics to Proteomics of Hair Cell Regeneration: Looking for a Hair Cell in a Haystack. MICROARRAYS 2016; 2. [PMID: 24416530 PMCID: PMC3886832 DOI: 10.3390/microarrays2030186] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Mature mammals exhibit very limited capacity for regeneration of auditory hair cells, while all non-mammalian vertebrates examined can regenerate them. In an effort to find therapeutic targets for deafness and balance disorders, scientists have examined gene expression patterns in auditory tissues under different developmental and experimental conditions. Microarray technology has allowed the large-scale study of gene expression profiles (transcriptomics) at whole-genome levels, but since mRNA expression does not necessarily correlate with protein expression, other methods, such as microRNA analysis and proteomics, are needed to better understand the process of hair cell regeneration. These technologies and some of the results of them are discussed in this review. Although there is a considerable amount of variability found between studies owing to different species, tissues and treatments, there is some concordance between cellular pathways important for hair cell regeneration. Since gene expression and proteomics data is now commonly submitted to centralized online databases, meta-analyses of these data may provide a better picture of pathways that are common to the process of hair cell regeneration and lead to potential therapeutics. Indeed, some of the proteins found to be regulated in the inner ear of animal models (e.g., IGF-1) have now gone through human clinical trials.
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Affiliation(s)
- Michael E. Smith
- Bioinformatics and Information Science Center, Department of Biology, Western Kentucky University, Bowling Green, KY 42101, USA
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-270-745-2405; Fax: +1-270-745-6856
| | - Gopinath Rajadinakaran
- Department of Genetics and Developmental Biology, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT 06030, USA; E-Mail:
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Abstract
The identification of transcriptional differences has served as an important starting point in understanding the molecular mechanisms behind biological processes and systems. The developmental biology of the inner ear, the biology of hearing and of course the pathology of deafness are all processes that warrant a molecular description if we are to improve human health. To this end, technological innovation has meant that larger scale analysis of gene transcription has been possible for a number of years now, extending our molecular analysis of genes to beyond those that are currently in vogue for a given system. In this review, some of the contributions gene profiling has made to understanding developmental, pathological and physiological processes in the inner ear are highlighted.
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Affiliation(s)
- Thomas Schimmang
- Instituto de Biología y Genética MolecularUniversidad de Valladolid y Consejo Superior de Investigaciones CientíficasValladolidSpain
| | - Mark Maconochie
- School of Biological and Chemical SciencesQueen Mary University of LondonLondonUK
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Faber-Hammond J, Samanta MP, Whitchurch EA, Manning D, Sisneros JA, Coffin AB. Saccular Transcriptome Profiles of the Seasonal Breeding Plainfin Midshipman Fish (Porichthys notatus), a Teleost with Divergent Sexual Phenotypes. PLoS One 2015; 10:e0142814. [PMID: 26560106 PMCID: PMC4641692 DOI: 10.1371/journal.pone.0142814] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 10/27/2015] [Indexed: 11/18/2022] Open
Abstract
Acoustic communication is essential for the reproductive success of the plainfin midshipman fish (Porichthys notatus). During the breeding season, type I males use acoustic cues to advertise nest location to potential mates, creating an audible signal that attracts reproductive females. Type II (sneaker) males also likely use this social acoustic signal to find breeding pairs from which to steal fertilizations. Estrogen-induced changes in the auditory system of breeding females are thought to enhance neural encoding of the advertisement call, and recent anatomical data suggest the saccule (the main auditory end organ) as one possible target for this seasonal modulation. Here we describe saccular transcriptomes from all three sexual phenotypes (females, type I and II males) collected during the breeding season as a first step in understanding the mechanisms underlying sexual phenotype-specific and seasonal differences in auditory function. We used RNA-Seq on the Ion Torrent platform to create a combined transcriptome dataset containing over 79,000 assembled transcripts representing almost 9,000 unique annotated genes. These identified genes include several with known inner ear function and multiple steroid hormone receptors. Transcripts most closely matched to published genomes of nile tilapia and large yellow croaker, inconsistent with the phylogenetic relationship between these species but consistent with the importance of acoustic communication in their life-history strategies. We then compared the RNA-Seq results from the saccules of reproductive females with a separate transcriptome from the non-reproductive female phenotype and found over 700 differentially expressed transcripts, including members of the Wnt and Notch signaling pathways that mediate cell proliferation and hair cell addition in the inner ear. These data constitute a valuable resource for furthering our understanding of the molecular basis for peripheral auditory function as well as a range of future midshipman and cross-species comparative studies of the auditory periphery.
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Affiliation(s)
- Joshua Faber-Hammond
- College of Arts and Sciences, Washington State University, Vancouver, WA, United States of America
| | | | - Elizabeth A. Whitchurch
- Department of Biological Sciences, Humboldt State University, Arcata, CA, United States of America
| | - Dustin Manning
- College of Arts and Sciences, Washington State University, Vancouver, WA, United States of America
| | - Joseph A. Sisneros
- Department of Psychology, University of Washington, Seattle, WA, United States of America
| | - Allison B. Coffin
- College of Arts and Sciences, Washington State University, Vancouver, WA, United States of America
- Department of Integrative Physiology and Neuroscience, Washington State University, Vancouver, WA, United States of America
- * E-mail:
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16
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Elkon R, Milon B, Morrison L, Shah M, Vijayakumar S, Racherla M, Leitch CC, Silipino L, Hadi S, Weiss-Gayet M, Barras E, Schmid CD, Ait-Lounis A, Barnes A, Song Y, Eisenman DJ, Eliyahu E, Frolenkov GI, Strome SE, Durand B, Zaghloul NA, Jones SM, Reith W, Hertzano R. RFX transcription factors are essential for hearing in mice. Nat Commun 2015; 6:8549. [PMID: 26469318 PMCID: PMC4634137 DOI: 10.1038/ncomms9549] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 09/04/2015] [Indexed: 01/23/2023] Open
Abstract
Sensorineural hearing loss is a common and currently irreversible disorder, because mammalian hair cells (HCs) do not regenerate and current stem cell and gene delivery protocols result only in immature HC-like cells. Importantly, although the transcriptional regulators of embryonic HC development have been described, little is known about the postnatal regulators of maturating HCs. Here we apply a cell type-specific functional genomic analysis to the transcriptomes of auditory and vestibular sensory epithelia from early postnatal mice. We identify RFX transcription factors as essential and evolutionarily conserved regulators of the HC-specific transcriptomes, and detect Rfx1,2,3,5 and 7 in the developing HCs. To understand the role of RFX in hearing, we generate Rfx1/3 conditional knockout mice. We show that these mice are deaf secondary to rapid loss of initially well-formed outer HCs. These data identify an essential role for RFX in hearing and survival of the terminally differentiating outer HCs.
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Affiliation(s)
- Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Beatrice Milon
- Department of Otorhinolaryngology, School of Medicine, University of Maryland Baltimore, 16 South Eutaw Street Suite 500, Baltimore, Maryland 21201, USA
| | - Laura Morrison
- Department of Otorhinolaryngology, School of Medicine, University of Maryland Baltimore, 16 South Eutaw Street Suite 500, Baltimore, Maryland 21201, USA
| | - Manan Shah
- Department of Otorhinolaryngology, School of Medicine, University of Maryland Baltimore, 16 South Eutaw Street Suite 500, Baltimore, Maryland 21201, USA
| | - Sarath Vijayakumar
- Department of Special Education and Communication Disorders, University of Nebraska Lincoln, Lincoln, Nebraska 68583-0738, USA
| | - Manoj Racherla
- Department of Otorhinolaryngology, School of Medicine, University of Maryland Baltimore, 16 South Eutaw Street Suite 500, Baltimore, Maryland 21201, USA
| | - Carmen C. Leitch
- Department of Medicine, Division of Endocrinology, Diabetes and Nutrition, School of Medicine, University of Maryland Baltimore, Baltimore, Maryland 21201, USA
| | - Lorna Silipino
- Department of Otorhinolaryngology, School of Medicine, University of Maryland Baltimore, 16 South Eutaw Street Suite 500, Baltimore, Maryland 21201, USA
| | - Shadan Hadi
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, Kentucky 40536-0298, USA
| | - Michèle Weiss-Gayet
- Centre de Génétique et de Physiologie Moléculaire et Cellulaire, CNRS UMR 5534, Université Claude Bernard Lyon-1, 69622 Villeurbanne, France
| | - Emmanuèle Barras
- Department of Pathology and Immunology, University of Geneva Medical School, CH-1211 Geneva, Switzerland
| | - Christoph D. Schmid
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, and University of Basel, 4051 Basel, Switzerland
| | - Aouatef Ait-Lounis
- Department of Pathology and Immunology, University of Geneva Medical School, CH-1211 Geneva, Switzerland
| | - Ashley Barnes
- Department of Otorhinolaryngology, School of Medicine, University of Maryland Baltimore, 16 South Eutaw Street Suite 500, Baltimore, Maryland 21201, USA
| | - Yang Song
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - David J. Eisenman
- Department of Otorhinolaryngology, School of Medicine, University of Maryland Baltimore, 16 South Eutaw Street Suite 500, Baltimore, Maryland 21201, USA
| | - Efrat Eliyahu
- Department of Genetics and Genomic Sciences, Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Gregory I. Frolenkov
- Department of Physiology, College of Medicine, University of Kentucky, Lexington, Kentucky 40536-0298, USA
| | - Scott E. Strome
- Department of Otorhinolaryngology, School of Medicine, University of Maryland Baltimore, 16 South Eutaw Street Suite 500, Baltimore, Maryland 21201, USA
| | - Bénédicte Durand
- Centre de Génétique et de Physiologie Moléculaire et Cellulaire, CNRS UMR 5534, Université Claude Bernard Lyon-1, 69622 Villeurbanne, France
| | - Norann A. Zaghloul
- Department of Medicine, Division of Endocrinology, Diabetes and Nutrition, School of Medicine, University of Maryland Baltimore, Baltimore, Maryland 21201, USA
| | - Sherri M. Jones
- Department of Special Education and Communication Disorders, University of Nebraska Lincoln, Lincoln, Nebraska 68583-0738, USA
| | - Walter Reith
- Department of Pathology and Immunology, University of Geneva Medical School, CH-1211 Geneva, Switzerland
| | - Ronna Hertzano
- Department of Otorhinolaryngology, School of Medicine, University of Maryland Baltimore, 16 South Eutaw Street Suite 500, Baltimore, Maryland 21201, USA,Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA,Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA,
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17
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Schrauwen I, Hasin-Brumshtein Y, Corneveaux JJ, Ohmen J, White C, Allen AN, Lusis AJ, Van Camp G, Huentelman MJ, Friedman RA. A comprehensive catalogue of the coding and non-coding transcripts of the human inner ear. Hear Res 2015; 333:266-274. [PMID: 26341477 DOI: 10.1016/j.heares.2015.08.013] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 08/12/2015] [Accepted: 08/27/2015] [Indexed: 10/23/2022]
Abstract
The mammalian inner ear consists of the cochlea and the vestibular labyrinth (utricle, saccule, and semicircular canals), which participate in both hearing and balance. Proper development and life-long function of these structures involves a highly complex coordinated system of spatial and temporal gene expression. The characterization of the inner ear transcriptome is likely important for the functional study of auditory and vestibular components, yet, primarily due to tissue unavailability, detailed expression catalogues of the human inner ear remain largely incomplete. We report here, for the first time, comprehensive transcriptome characterization of the adult human cochlea, ampulla, saccule and utricle of the vestibule obtained from patients without hearing abnormalities. Using RNA-Seq, we measured the expression of >50,000 predicted genes corresponding to approximately 200,000 transcripts, in the adult inner ear and compared it to 32 other human tissues. First, we identified genes preferentially expressed in the inner ear, and unique either to the vestibule or cochlea. Next, we examined expression levels of specific groups of potentially interesting RNAs, such as genes implicated in hearing loss, long non-coding RNAs, pseudogenes and transcripts subject to nonsense mediated decay (NMD). We uncover the spatial specificity of expression of these RNAs in the hearing/balance system, and reveal evidence of tissue specific NMD. Lastly, we investigated the non-syndromic deafness loci to which no gene has been mapped, and narrow the list of potential candidates for each locus. These data represent the first high-resolution transcriptome catalogue of the adult human inner ear. A comprehensive identification of coding and non-coding RNAs in the inner ear will enable pathways of auditory and vestibular function to be further defined in the study of hearing and balance. Expression data are freely accessible at https://www.tgen.org/home/research/research-divisions/neurogenomics/supplementary-data/inner-ear-transcriptome.aspx.
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Affiliation(s)
- Isabelle Schrauwen
- Department of Medical Genetics, University of Antwerp, 2610 Antwerp, Belgium.,Neurogenomics Division and The Dorrance Center for Rare Childhood Disorders, Translational Genomics Research Institute, 85004 Phoenix, AZ
| | - Yehudit Hasin-Brumshtein
- Department of Medicine/Division of Cardiology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Jason J Corneveaux
- Neurogenomics Division and The Dorrance Center for Rare Childhood Disorders, Translational Genomics Research Institute, 85004 Phoenix, AZ
| | - Jeffrey Ohmen
- House Ear Institute, Los Angeles 90057, CA, United States
| | - Cory White
- House Ear Institute, Los Angeles 90057, CA, United States.,Keck School of Medicine, USC, Los Angeles, CA, United States
| | - April N Allen
- Neurogenomics Division and The Dorrance Center for Rare Childhood Disorders, Translational Genomics Research Institute, 85004 Phoenix, AZ
| | - Aldons J Lusis
- Department of Medicine/Division of Cardiology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Guy Van Camp
- Department of Medical Genetics, University of Antwerp, 2610 Antwerp, Belgium
| | - Matthew J Huentelman
- Neurogenomics Division and The Dorrance Center for Rare Childhood Disorders, Translational Genomics Research Institute, 85004 Phoenix, AZ
| | - Rick A Friedman
- Keck School of Medicine, USC, Los Angeles, CA, United States
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High quality RNA extraction of the mammalian cochlea for qRT-PCR and transcriptome analyses. Hear Res 2015; 325:42-8. [PMID: 25818515 DOI: 10.1016/j.heares.2015.03.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 02/08/2015] [Accepted: 03/13/2015] [Indexed: 11/23/2022]
Abstract
Molecular investigations of the hearing organ, the cochlea, have been hampered due to the difficulty of isolating pure RNA and in quantities sufficient enough for quantitative real-time RT-PCR or microarray analysis. The complex architecture of the cochlea, the presence of liquids, bone and cartilage tissue, are a major hurdle in obtaining contamination-free RNA to a level that does not affect downstream applications. Here, we present a protocol to extract RNA from the mouse cochlea, with yields and quality suitable for real-time RT-PCR or Affymetrix labeling. In contrast to current methods, such as TRIZOL or column-based extraction, this protocol combines the two and, within 4 h, yields a 2 μg of total RNA from a single pair of adult mouse cochleae. This protocol allows the isolation of RNA molecules from the mammalian cochlea providing access to whole-transcript expression analyses.
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19
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Hartman BH, Durruthy-Durruthy R, Laske RD, Losorelli S, Heller S. Identification and characterization of mouse otic sensory lineage genes. Front Cell Neurosci 2015; 9:79. [PMID: 25852475 PMCID: PMC4365716 DOI: 10.3389/fncel.2015.00079] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 02/22/2015] [Indexed: 11/23/2022] Open
Abstract
Vertebrate embryogenesis gives rise to all cell types of an organism through the development of many unique lineages derived from the three primordial germ layers. The otic sensory lineage arises from the otic vesicle, a structure formed through invagination of placodal non-neural ectoderm. This developmental lineage possesses unique differentiation potential, giving rise to otic sensory cell populations including hair cells, supporting cells, and ganglion neurons of the auditory and vestibular organs. Here we present a systematic approach to identify transcriptional features that distinguish the otic sensory lineage (from early otic progenitors to otic sensory populations) from other major lineages of vertebrate development. We used a microarray approach to analyze otic sensory lineage populations including microdissected otic vesicles (embryonic day 10.5) as well as isolated neonatal cochlear hair cells and supporting cells at postnatal day 3. Non-otic tissue samples including periotic tissues and whole embryos with otic regions removed were used as reference populations to evaluate otic specificity. Otic populations shared transcriptome-wide correlations in expression profiles that distinguish members of this lineage from non-otic populations. We further analyzed the microarray data using comparative and dimension reduction methods to identify individual genes that are specifically expressed in the otic sensory lineage. This analysis identified and ranked top otic sensory lineage-specific transcripts including Fbxo2, Col9a2, and Oc90, and additional novel otic lineage markers. To validate these results we performed expression analysis on select genes using immunohistochemistry and in situ hybridization. Fbxo2 showed the most striking pattern of specificity to the otic sensory lineage, including robust expression in the early otic vesicle and sustained expression in prosensory progenitors and auditory and vestibular hair cells and supporting cells.
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Affiliation(s)
- Byron H Hartman
- Department of Otolaryngology, Head and Neck Surgery, Stanford University School of Medicine Stanford, CA, USA
| | - Robert Durruthy-Durruthy
- Department of Otolaryngology, Head and Neck Surgery, Stanford University School of Medicine Stanford, CA, USA
| | - Roman D Laske
- Department of Otolaryngology, Head and Neck Surgery, Stanford University School of Medicine Stanford, CA, USA
| | - Steven Losorelli
- Department of Otolaryngology, Head and Neck Surgery, Stanford University School of Medicine Stanford, CA, USA
| | - Stefan Heller
- Department of Otolaryngology, Head and Neck Surgery, Stanford University School of Medicine Stanford, CA, USA
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21
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Dong D, Lei M, Liu Y, Zhang S. Comparative inner ear transcriptome analysis between the Rickett's big-footed bats (Myotis ricketti) and the greater short-nosed fruit bats (Cynopterus sphinx). BMC Genomics 2013; 14:916. [PMID: 24365273 PMCID: PMC3879654 DOI: 10.1186/1471-2164-14-916] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2013] [Accepted: 12/18/2013] [Indexed: 11/22/2022] Open
Abstract
Background Bats have aroused great interests of researchers for the sake of their advanced echolocation system. However, this highly specialized trait is not characteristic of Old World fruit bats. Results To comprehensively explore the underlying molecular basis between echolocating and non-echolocating bats, we employed a sequence-based approach to compare the inner ear expression difference between the Rickett’s big-footed bat (Myotis ricketti, echolocating bat) and the Greater short-nosed fruit bat (Cynopterus sphinx, non-echolocating bat). De novo sequence assemblies were developed for both species. The results showed that the biological implications of up-regulated genes in M. ricketti were significantly over-represented in biological process categories such as ‘cochlea morphogenesis’, ‘inner ear morphogenesis’ and ‘sensory perception of sound’, which are consistent with the inner ear morphological and physiological differentiation between the two bat species. Moreover, the expression of TMC1 gene confirmed its important function in echolocating bats. Conclusion Our work presents the first transcriptome comparison between echolocating and non-echolocating bats, and provides information about the genetic basis of their distinct hearing traits.
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Affiliation(s)
- Dong Dong
- Institute for Advanced Interdisciplinary Research in Science and Technology, East China Normal University, Shanghai, China.
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22
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Conte I, Banfi S, Bovolenta P. Non-coding RNAs in the development of sensory organs and related diseases. Cell Mol Life Sci 2013; 70:4141-55. [PMID: 23588489 PMCID: PMC11113508 DOI: 10.1007/s00018-013-1335-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 03/25/2013] [Accepted: 03/27/2013] [Indexed: 12/21/2022]
Abstract
Genomes are transcribed well beyond the conventionally annotated protein-encoding genes and produce many thousands of regulatory non-coding RNAs (ncRNAs). In the last few years, ncRNAs, especially microRNAs and long non-coding RNA, have received increasing attention because of their implication in the function of chromatin-modifying complexes and in the regulation of transcriptional and post-transcriptional events. The morphological events and the genetic networks responsible for the development of sensory organs have been well delineated and therefore sensory organs have provided a useful scenario to address the role of ncRNAs. In this review, we summarize the current information on the importance of microRNAs and long non-coding RNAs during the development of the eye, inner ear, and olfactory system in vertebrates. We will also discuss those cases in which alteration of ncRNA expression has been linked to pathological conditions affecting these organs.
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Affiliation(s)
- Ivan Conte
- Telethon Institute of Genetics and Medicine, Via Pietro Castellino, 111, 80131 Naples, Italy
| | - Sandro Banfi
- Telethon Institute of Genetics and Medicine, Via Pietro Castellino, 111, 80131 Naples, Italy
- Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, Naples, Italy
| | - Paola Bovolenta
- Centro de Biología Molecular ‘Severo Ochoa’, CSIC–UAM, c/Nicolas Cabrera 1, Cantoblanco, 28049 Madrid, Spain
- CIBER de Enfermedades Raras, ISCIII, Madrid, Spain
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Cai Q, Wang B, Patel M, Yang SM, Hu BH. RNAlater facilitates microdissection of sensory cell-enriched samples from the mouse cochlea for transcriptional analyses. J Neurosci Methods 2013; 219:240-51. [PMID: 23958750 DOI: 10.1016/j.jneumeth.2013.08.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 08/03/2013] [Accepted: 08/05/2013] [Indexed: 10/26/2022]
Abstract
Molecular analyses of cochlear pathology rely on the acquisition of high-quality cochlear samples. For small rodents, isolating sensory cell-enriched samples with well-preserved RNA integrity for transcriptional analyses poses a significant challenge. Here, we report a microdissection technique for isolating sensory cell-enriched samples from the cochlea. We found that treating the tissue with RNAlater, a RNA preservation medium, alters the physical properties of the tissue and facilitates the dissection. Unlike previous samples that have been isolated from the sensory epithelium, our samples contain defined cell populations that have a consistent ratio of sensory cells to supporting cells. Importantly, the RNA components were well preserved. With this microdissection method, we collected three types of samples: sensory cell-enriched, outer hair cell-enriched, and inner hair cell-enriched. To demonstrate the feasibility of the method, we screened multiple reference genes in the sensory cell-enriched samples and identified stable genes in noise-traumatized cochleae. The method described here balances the need for both quality and purity of sensory cells and also circumvents many limitations of the currently available techniques for collecting cochlear tissues. With our approach, the collected samples can be used in diverse downstream analyses, including qRT-PCR, microarray, and RNA sequencing.
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Affiliation(s)
- Qunfeng Cai
- Center for Hearing and Deafness, State University of New York at Buffalo, 137 Cary Hall, 3435 Main Street, Buffalo, NY 14214, USA
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Canlon B. Introduction to Annual Reviews 2012. Hear Res 2012. [DOI: 10.1016/j.heares.2012.05.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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