Transcriptome and Proteome Analysis of Mouse Inner Ears

Summary

Principal Investigator: Qing Y Zheng
Abstract: The broad long-term objective of this proposed project is to uncover the pathophysiological mechanisms of human auditory diseases by analyzing mouse genetic models using genomic and proteomic approaches. Few protein-profiling studies of mouse ear tissues have been attempted because of the difficulty of accessing the small numbers of diverse cells within the hard temporal bone that encases the inner ear. To address this problem, a subtractive strategy was devised in which the digitized abundance of transcripts and proteins in mutant mice with lost inner ear structures is subtracted from those of control mice with normal inner structures. For example, a predominate histological feature of the ears of mice homozygous for the dreidel (ddl) mutation of Pou4f3 is a lack of hair cells in the organ of Corti (OC). Therefore transcripts and proteins of hair cells will be revealed by subtraction of the OC contents of ddl/ddl mutants from those of control mice. The subtractive digitized comparisons of proteome content will be performed using the newly developed two-dimensional difference in gel electrophoresis (2D DICE) method for protein separation and mass spectrometry (MS) for protein identification. Transcript comparisons between mutants and controls will be made by cDNA microarray analysis. Immunohistochemistry and real time RT- PCR approaches will be used to validate protein and mRNA expression patterns and confirm inner ear localization of genes that are identified by 2D DIGE and MS. In this way, a catalog of transcriptome and proteome contents of particular inner ear structures will be compiled for mice at different ages, and an online database will be established to execute a data-sharing plan. This proposal is in response to the NIH Program Announcement PA-03-151 "Proteomics in Auditory Developmental and Disease Processes." The relevance of the proposed research to public health: Techniques developed and data to be collected in this project will be useful for developing strategies for prevention and treatment of human ear diseases. Genes, proteins and their molecular pathways identified in this proposed research are potential targets of drug therapies for hearing loss that affects more than 28 million Americans.
Funding Period: 2005-09-19 - 2010-08-31
more information: NIH RePORT

Top Publications

  1. pmc Inner ear proteomics of mouse models for deafness, a discovery strategy
    Qing Yin Zheng
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 1500, USA
    Brain Res 1091:113-21. 2006
  2. pmc Interleukin-10 is an essential modulator of mucoid metaplasia in a mouse otitis media model
    Katsuyuki Tsuchiya
    University of Minnesota Otitis Media Research Center, Department of Otolaryngology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
    Ann Otol Rhinol Laryngol 117:630-6. 2008
  3. pmc A comparison of vestibular and auditory phenotypes in inbred mouse strains
    Sherri M Jones
    Department of Communication Sciences and Disorders, East Carolina University, Belk Annex, Greenville and Charles Boulevards, Greenville, NC 27858, USA
    Brain Res 1091:40-6. 2006
  4. pmc Characterization of neuronal cell death in the spiral ganglia of a mouse model of endolymphatic hydrops
    Maroun T Semaan
    Department of Otolaryngology Head and Neck Surgery, University Hospitals Case Medical Center, Cleveland, Ohio 44106, USA
    Otol Neurotol 34:559-69. 2013
  5. pmc Otoprotective effects of erythropoietin on Cdh23erl/erl mice
    F Han
    Transformative Otology and Neuroscience Center, Binzhou Medical University, 346 Guanhai Road, Yantai 264003, Shandong, PR China
    Neuroscience 237:1-6. 2013
  6. pmc Mutation in Phex gene predisposes BALB/c-Phex(Hyp-Duk)/Y mice to otitis media
    Fengchan Han
    The Transformative Otology and Neuroscience Center, Binzhou Medical University, Yantai, Shandong, People s Republic of China
    PLoS ONE 7:e43010. 2012
  7. pmc Pathological features in the LmnaDhe/+ mutant mouse provide a novel model of human otitis media and laminopathies
    Yan Zhang
    Department of Otolaryngology HNS, Case Western Reserve University, Cleveland, Ohio, USA
    Am J Pathol 181:761-74. 2012
  8. pmc A new mutation of the Atoh1 gene in mice with normal life span allows analysis of inner ear and cerebellar phenotype in aging
    Kianoush Sheykholeslami
    Department of Otolaryngology HNS, Case Western Reserve University, Cleveland, Ohio, United States of America
    PLoS ONE 8:e79791. 2013
  9. pmc A novel serine protease from the snake venom of Agkistrodon blomhoffii ussurensis
    Shuqing Liu
    Department of Biochemistry, Dalian Medical University, Dalian 116044, PR China
    Toxicon 52:760-8. 2008
  10. pmc A mouse model with postnatal endolymphatic hydrops and hearing loss
    Cliff A Megerian
    Department of Otolaryngology Head and Neck Surgery, Case Western Reserve University, University Hospitals Case Medical Center, 11100 Euclid Avenue, Cleveland, OH 44106, USA
    Hear Res 237:90-105. 2008

Scientific Experts

  • Qing Y Zheng
  • Ge Jin
  • Kianoush Sheykholeslami
  • Kenneth Johnson
  • Fengchan Han
  • Heping Yu
  • Cong Tian
  • F Han
  • Bin Yang
  • Shengli Li
  • Maroun T Semaan
  • Denise Yan
  • Cliff A Megerian
  • H Yu
  • Siwei Liu
  • Yan Zhang
  • James E Arnold
  • Ye Zheng
  • Cindy Benedict-Alderfer
  • Jiangping Zhang
  • Dennis R Trune
  • Mao Mao
  • Katsuyuki Tsuchiya
  • Shuqing Liu
  • Xiaoming Zhou
  • Sherri M Jones
  • X Ma
  • L Le
  • P Li
  • X Zhao
  • T Zheng
  • Yuxi Zheng
  • Y Su
  • John C Heaphy
  • Elisha Fredman
  • Hongbo Li
  • Min Xu
  • Shaoli Cheng
  • X Han
  • Deborah Schelling
  • Jin Zhang
  • H E Chen
  • Cynthia F Bartels
  • Y Zheng
  • C Tian
  • C Benedict-Alderfer
  • Hongliang Zhu
  • Q Wang
  • Suejin Kim
  • Ping Li
  • Peter C Scacheri
  • Feng chan Han
  • Kazusaku Kamiya
  • Rami Azem
  • Zhi Guang Zhang
  • Xiao Mei Ouyang
  • Xue Zhong Liu
  • Chantal Longo-Guess
  • Changjun Lu
  • Xue Z Liu
  • Michael R Jacobs
  • Muriel T Davisson
  • Michael G Anderson
  • Leah Rae Donahue
  • Casey Nava
  • Cecilia Schmidt
  • Belinda S Harris
  • Bo Chang
  • Daniel R Thedens
  • Hong Liang Zhu
  • Kumar N Alagramam
  • Saba Aftab
  • Patricia Ferrieri
  • Karen S Pawlowski
  • Jizhen Lin
  • Si Wei Liu
  • Bai Ya Li
  • Ming Zhong Sun
  • Lauren B Kisley
  • Shao Qiang Zhang
  • Changkai Sun
  • Charles G Wright
  • Baochang Zhao
  • Masahiro Komori
  • Frederick T Greenaway
  • Wayne N Frankel
  • Timothy A Jones
  • Lawrence C Erway
  • Philip H S Jen
  • Kevin L Seburn

Detail Information

Publications32

  1. pmc Inner ear proteomics of mouse models for deafness, a discovery strategy
    Qing Yin Zheng
    The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609 1500, USA
    Brain Res 1091:113-21. 2006
    ..In this short technical report, we also discuss protein-profiling approaches suitable for SSUMM and briefly discuss other approaches used in the field of proteomics...
  2. pmc Interleukin-10 is an essential modulator of mucoid metaplasia in a mouse otitis media model
    Katsuyuki Tsuchiya
    University of Minnesota Otitis Media Research Center, Department of Otolaryngology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
    Ann Otol Rhinol Laryngol 117:630-6. 2008
    ..Inflammatory cytokines are involved in the development of mucous cell metaplasia and hyperplasia (MCM) in otitis media (OM). However, which cytokines play an essential role in the MCM of OM is not clear at the moment...
  3. pmc A comparison of vestibular and auditory phenotypes in inbred mouse strains
    Sherri M Jones
    Department of Communication Sciences and Disorders, East Carolina University, Belk Annex, Greenville and Charles Boulevards, Greenville, NC 27858, USA
    Brain Res 1091:40-6. 2006
    ..In addition, some genetic mutations may produce primarily gravity receptor deficits. Potential genes responsible for selective gravity receptor impairment demonstrated herein remain to be identified...
  4. pmc Characterization of neuronal cell death in the spiral ganglia of a mouse model of endolymphatic hydrops
    Maroun T Semaan
    Department of Otolaryngology Head and Neck Surgery, University Hospitals Case Medical Center, Cleveland, Ohio 44106, USA
    Otol Neurotol 34:559-69. 2013
    ....
  5. pmc Otoprotective effects of erythropoietin on Cdh23erl/erl mice
    F Han
    Transformative Otology and Neuroscience Center, Binzhou Medical University, 346 Guanhai Road, Yantai 264003, Shandong, PR China
    Neuroscience 237:1-6. 2013
    ..05). This is the first report that EPO acts as an otoprotectant in a DFNB12 mouse model with progressive hearing loss...
  6. pmc Mutation in Phex gene predisposes BALB/c-Phex(Hyp-Duk)/Y mice to otitis media
    Fengchan Han
    The Transformative Otology and Neuroscience Center, Binzhou Medical University, Yantai, Shandong, People s Republic of China
    PLoS ONE 7:e43010. 2012
    ..The Hyp-Duk/Y mouse is a new genetic mouse model of OM...
  7. pmc Pathological features in the LmnaDhe/+ mutant mouse provide a novel model of human otitis media and laminopathies
    Yan Zhang
    Department of Otolaryngology HNS, Case Western Reserve University, Cleveland, Ohio, USA
    Am J Pathol 181:761-74. 2012
    ..The Lmna(Dhe/+) mutant mouse provides a novel model of human OM and laminopathy...
  8. pmc A new mutation of the Atoh1 gene in mice with normal life span allows analysis of inner ear and cerebellar phenotype in aging
    Kianoush Sheykholeslami
    Department of Otolaryngology HNS, Case Western Reserve University, Cleveland, Ohio, United States of America
    PLoS ONE 8:e79791. 2013
    ..Normal lifespan and fecundity of Atoh1(trhl) mice provide a complementary model to facilitate elucidation of ATOH1 function in hearing,central nervous system and cancer biology. ..
  9. pmc A novel serine protease from the snake venom of Agkistrodon blomhoffii ussurensis
    Shuqing Liu
    Department of Biochemistry, Dalian Medical University, Dalian 116044, PR China
    Toxicon 52:760-8. 2008
    ....
  10. pmc A mouse model with postnatal endolymphatic hydrops and hearing loss
    Cliff A Megerian
    Department of Otolaryngology Head and Neck Surgery, Case Western Reserve University, University Hospitals Case Medical Center, 11100 Euclid Avenue, Cleveland, OH 44106, USA
    Hear Res 237:90-105. 2008
    ....
  11. pmc Auditory brainstem responses in 10 inbred strains of mice
    Xiaoming Zhou
    College of Life Sciences, East China Normal University, Shanghai 200062, PR China
    Brain Res 1091:16-26. 2006
    ..I-IV inter-peak latencies for MRL/MpJ, C3HeB/FeJ, NZB/BlNJ, and C3H/HeJ strains are longer than FVB/NJ, SJL/J, or CAST/EiJ. This work is the first step to study the genetic basis underlying strain-related differences in auditory pathway...
  12. pmc Strain background effects and genetic modifiers of hearing in mice
    Kenneth R Johnson
    The Jackson Laboratory, Bar Harbor, ME 04609, USA
    Brain Res 1091:79-88. 2006
    ..Because modifier genes and digenic inheritance are not always distinguishable, we also include in this review several examples of digenic inheritance of hearing loss that have been reported in both mice and humans...
  13. pmc Mouse models as a tool to unravel the genetic basis for human otitis media
    Qing Yin Zheng
    Department of Otolaryngology, Case Western Reserve Universuty, Cleveland, OH 44106, USA
    Brain Res 1091:9-15. 2006
    ..We review the literature and discuss recent progresses in developing mouse models and using mouse models to uncover the genetic basis for human OM...
  14. pmc An antimicrobial peptide regulates tumor-associated macrophage trafficking via the chemokine receptor CCR2, a model for tumorigenesis
    Ge Jin
    Department of Biological Sciences, Case Western Reserve University School of Dental Medicine, Cleveland, Ohio, USA
    PLoS ONE 5:e10993. 2010
    ..Tumor cell-produced human beta-defensin-3 (hBD-3) has been associated with TAM trafficking in oral cancer; however, its involvement in tumor-related inflammatory processes remains largely unknown...
  15. pmc Analysis of subcellular localization of Myo7a, Pcdh15 and Sans in Ush1c knockout mice
    Denise Yan
    Department of Otolaryngology, University of Miami, Miami, FL, USA
    Int J Exp Pathol 92:66-71. 2011
    ..Our data indicate that the disassembly of the USH1 network caused by absence of harmonin may have led to the mis-localization of the Protocadherin 15 and Sans proteins in the cochlear hair cells of Ush1c(-/-) knockout mice...
  16. pmc Ush1c gene expression levels in the ear and eye suggest different roles for Ush1c in neurosensory organs in a new Ush1c knockout mouse
    Cong Tian
    Department of Otolaryngology, Case Western Reserve University, Cleveland, OH 44106, USA
    Brain Res 1328:57-70. 2010
    ..The fact that Ush1c expression is much higher in the ear than in the eye suggests a different role for Ush1c in ear function than in the eye and may explain why Ush1c mutant mice do not recapitulate vision defects...
  17. pmc Sh3pxd2b mice are a model for craniofacial dysmorphology and otitis media
    Bin Yang
    Department of Oral and Maxillofacial Surgery, Guanghua School of Stomatology, Sun Yat Sen University, Guangzhou, China
    PLoS ONE 6:e22622. 2011
    ..The mouse model with a mutation in the Sh3pxd2b gene (Sh3pxd2b(nee)) mirrors craniofacial dysmorphology and otitis media in humans...
  18. pmc The podosomal-adaptor protein SH3PXD2B is essential for normal postnatal development
    Mao Mao
    Department of Molecular Physiology and Biophysics, The University of Iowa, Iowa City, IA 52242, USA
    Mamm Genome 20:462-75. 2009
    ..These results identify SH3PXD2B as a podosomal-adaptor protein required for postnatal growth and development, particularly within physiologic contexts involving extracellular matrix regulation...
  19. pmc A mutation in the cdh23 gene causes age-related hearing loss in Cdh23(nmf308/nmf308) mice
    Siwei Liu
    Department of Otolaryngology HNS, Case Western Reserve University, Cleveland, OH 44106, USA
    Gene 499:309-17. 2012
    ..Due to the same cdh23 mutations in human subjects with presbycusis (Petit et al., 2001; Zheng et al., 2005), the Cdh23(nmf308/nmf308) mouse is an excellent animal model for investigating the mechanisms involved in human AHL...
  20. pmc Digenic inheritance of deafness caused by 8J allele of myosin-VIIA and mutations in other Usher I genes
    Qing Yin Zheng
    Otolaryngology Head and Neck Surgery, Case Western Reserve University, 11100 Euclid Avenue, Cleveland, OH 44106, USA
    Hum Mol Genet 21:2588-98. 2012
    ..MYO7A, USH1G and PCDH15 may form another complex in stereocilia. USH1G may be a limiting factor in both complexes...
  21. pmc Otitis media in a new mouse model for CHARGE syndrome with a deletion in the Chd7 gene
    Cong Tian
    Department of Otolaryngology Head and Neck Surgery, University Hospitals of Cleveland, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
    PLoS ONE 7:e34944. 2012
    ..This is the first mouse model of CHARGE syndrome reported to show otitis media with effusion and it will be valuable for studying the etiology of otitis media and other symptoms in CHARGE syndrome...
  22. pmc A new mouse mutant of the Cdh23 gene with early-onset hearing loss facilitates evaluation of otoprotection drugs
    F Han
    Department of Otolaryngology HNS, Case Western Reserve University, Cleveland, OH 44106, USA
    Pharmacogenomics J 12:30-44. 2012
    ..The short interval from initial hearing loss to deafness (P27-P90) makes this model ideal for screening and validating otoprotective drugs...
  23. pmc A new spontaneous mutation in the mouse protocadherin 15 gene
    Q Y Zheng
    Otolaryngology Head and Neck Surgery, Case Western Reserve University, 11100 Euclid Avenue, Cleveland, OH 44106, USA
    Hear Res 219:110-20. 2006
    ..Since these animals show severe functional deficits but have relatively mild stereocilia defects at a young age they may provide an appropriate model to test for a direct role of Pcdh15 in mechanotransduction...
  24. pmc A locus on distal chromosome 10 (ahl4) affecting age-related hearing loss in A/J mice
    Qing Yin Zheng
    Department of Otolaryngology HNS, Case Western Reserve University, 11100 Euclid Avenue, LKS 5045, Cleveland, OH 44106, USA
    Neurobiol Aging 30:1693-705. 2009
    ..Spiral ganglion neurons, cells of the stria vascularis, and vestibular hair cell densities, however, appeared normal in 20-week-old A/J mice...
  25. pmc Assessment criteria for rotated stereociliary bundles in the guinea pig cochlea
    Shengli Li
    Department of Hearing Research, Center of Neuroscience and Otolaryngology of Second Hospital, Xi an Jiaotong University of Medicine, Xi an, China
    Otol Neurotol 29:86-92. 2008
    ..Our study examined the relationship between variant stereociliary bundles of cochlear outer hair cells (OHCs) and auditory function to analyze assessment criteria for rotated stereociliary bundles in the guinea pig cochlea...
  26. pmc A locus on distal chromosome 11 (ahl8) and its interaction with Cdh23 ahl underlie the early onset, age-related hearing loss of DBA/2J mice
    Kenneth R Johnson
    The Jackson Laboratory, Bar Harbor, ME 04609, USA
    Genomics 92:219-25. 2008
    ..We conclude that ahl8 is a major contributor to the hearing loss of DBA/2J mice and that its effects are dependent on the predisposing Cdh23 ahl genotype of this strain...
  27. pmc Tympanometry assessment of 61 inbred strains of mice
    Qing Yin Zheng
    Department of Otolaryngology Head and Neck Surgery, Case Western Reserve University, 11100 Euclid Avenue, LKS 5045, Cleveland, OH 44106, USA
    Hear Res 231:23-31. 2007
    ..This is the first report to successfully use tympanometry to measure mouse middle ear function, which has been a challenge for the hearing research field because of the mouse's tiny ear size...
  28. pmc Mouse models for human otitis media
    Dennis R Trune
    Oregon Hearing Research Center, Mail Code NRC04, Oregon Health and Science University, 3181 S W Sam Jackson Park Road, Portland, OR 97239 3098, USA
    Brain Res 1277:90-103. 2009
    ..Furthermore, the completion of the mouse genome sequence has offered a powerful set of tools for investigating gene function and is generating a rich resource of mouse mutants for studying the genetic factors underlying OM...
  29. pmc Vestibular evoked myogenic potentials in normal mice and Phex mice with spontaneous endolymphatic hydrops
    Kianoush Sheykholeslami
    Department of Otolaryngology Head and Neck Surgery, Case Medical Center University Hospitals of Cleveland, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, USA
    Otol Neurotol 30:535-44. 2009
    ..Evaluation of the sacculocollic pathway via VEMPs in mice can set the stage for future evaluations of mutant mice that now play an important role in research regarding human auditory and vestibular dysfunction...
  30. pmc Otitis media in a mouse model for Down syndrome
    Fengchan Han
    Department of Otolaryngology HNS, Case Western Reserve University, Cleveland, OH 44106, USA
    Int J Exp Pathol 90:480-8. 2009
    ..Bacteria of pathogenic importance to humans also were identified in the Ts65Dn mice. This is the first report of otitis media in the Ts65Dn mouse as a model characteristic of human Down syndrome...
  31. pmc Role for Toll-like receptor 2 in the immune response to Streptococcus pneumoniae infection in mouse otitis media
    Fengchan Han
    Department of Otolaryngology HNS, Case Western Reserve University, Cleveland, Ohio 44106, USA
    Infect Immun 77:3100-8. 2009
    ..This study provides evidence that TLR2 is important in the molecular pathogenesis and host response to otitis media...