Deafness Genes in Mice and Men

tubby, tub, tub

deaf waddler, dfw, Atp2b2

waltzer, v, mdfw, ahl, Cdh23

Black Swiss, ahl5, Gipc3

Varitint-waddler, Va, Mcoln3

jackson circler, jc, Sobp

Tail-short, Ts, Rpl38

Hearing is one the five basic senses in mammalian organisms.  Historically, the mechanisms of auditory perception and processing have been studied using physiological and psycho-acoustic means.  Molecular biologic approaches have been largely absent from the field.  Only in 1995, applying a genetic positional cloning paradigm in human and mouse was the first gene relevant for hearing identified as myosin 7A.  Recognizing the accuracy of the mouse in modeling human deafness and realizing the enormous potential of forward-genetics in elucidating molecular mechanisms critical for basic function of hearing, research in my laboratory focused on the molecular genetics of mono- and oligogenic hearing loss in the mouse.

Since inception, my laboratory has identified six novel deafness genes: Atp2b2, Cdh23, Trpml3, Sobp, Rpl38, and Gipc3.  Through my collaborations with human geneticists and by others, four of these genes subsequently were also shown to have human disease homologs causing Usher syndrome type 1D, non-syndromic hearing loss (DFNB15/95), digenic hearing impairment and cognitive disability (MRAMS).

Research from my lab identified the age-related hearing loss locus ahl, which is largely responsible for the progressive hearing loss observed in many common inbred strains of mice.  More recently, we cloned a second quantitative trait locus in the mouse – ahl5 – responsible for progressive sensorineural hearing impairment and audiogenic seizures.  Additionally, we mapped several novel quantitative trait loci that control various forms of hearing deficits in common inbred, recombinant inbred and outbred strains of mice (ahl6, Snhl1-4, Hfhl1-3).  Our cumulative data suggest that a small number of rare risk alleles with small to moderate effects per each strain confer oligogenic hearing loss.  This is important because it may model the genetics of complex forms of human hearing loss, such as presbycusis and noise – induced hearing loss.

My research resulted in the first chromosomal location of a genetic modifier of hearing loss, mdfw, in the mouse, which I subsequently identified on the molecular level.  Our result provided a genetic paradigm that informs the clinical diagnostic and prognosis of some forms of hearing impairment in the human population.

In addition to its clinical relevance, research from my laboratory made significant advances towards a molecular understanding of basic auditory mechanisms.  In particular my discovery of the novel Cadherin 23 gene and my hypothesis that the protein “may function as hair bundle organizer perhaps by cross-linking stereocilia” ultimately led to the identification of the molecular component of stereocilia side links and the tip-link, a unique molecular structure thought to directly mediate mechano-transduction.

Lastly, my laboratory made collaborative contributions to important research on Vlgr1 and Usher syndrome type 2C, Gla (Fabry disease), ß-Spectrin 4, Pendrin (Pendred Syndrome) and others.


Genes involved in mono-genic Hearing Loss

1.    Atp2b2  -  The Ca2+ ATPase PMCA2 is critical for hearing in mammals.

At The Jackson Laboratory, I identified a second allele at the deaf waddler locus (dfw2J) causing ataxic gait and congenital deafness.  Additionally, I recognized and genetically mapped a genetic modifier of dfw (termed mdfw) that confers susceptibility to hearing loss in dfw2J heterozygotes.  In collaboration with Bruce Tempel, University of Washington, we identified a missense mutation (dfw) and a two-base pair deletion (dfw2J) in the Atp2b2 gene, which encodes a plasma membrane calcium ATPase (Pmca2).  We localized Pmca2 to the mechanosensitive stereocilia bundle at auditory hair cells and suggested Pmca2 as the main regulator of Ca2+ homeostasis in mammalian hair cell stereocilia.  Subsequent work by Carfoli and others identified mutations in the human gene of ATP2B2 associated with profound hearing loss.

Konrad Noben-Trauth, Qing Y. Zheng, Kenneth R. Johnson and Patsy M. Nishina (1997).  mdfw: a deafness susceptibility locus that interacts with deaf waddler (dfw).  Genomics 44, 266-272.

Valerie A. Street, Jennifer W. McKee-Johnson, Rosalia C. Fonseca, Bruce L. Tempel and Konrad Noben-Trauth (1998).  Mutations in a plasma membrane Ca2+-ATPase gene cause deafness in deafwaddler mice.  Nature Genetics 19, 390-394.

2.    Cdh23  -  Mutations in a novel cadherin cause deafness in mouse and human.

The identification of the waltzer (v) locus was undertaken based upon the assumption that mdfw and v are allelic variants at the same locus.  Through positional cloning, my laboratory identified a novel cadherin (Cdh23) gene encoding a 3354 amino acid protein.  In this study, we were the first to suggest that cadherin 23 “may function as a hair bundle organizer, perhaps by cross-linking stereocilia”.  In collaboration we showed that Cdh23 is a side-link in developing cochlear stereocilia.  My hypothesis ultimately led to the identification of Cdh23 as a molecular component of the tip-link, a unique molecular structure thought to gate the mechano-transduction channel.  My work on Cdh23 also gave raise to the collaborative discovery with Hanno Bolz and Christian Kubisch of mutations in the human gene (CDH23) underlying Usher Syndrome type 1D and non-syndromic hearing loss.  As of today, mutations in CDH23 are a leading cause of hearing loss in the human population.

Elizabeth C. Bryda, Hung J. Kim, Marie E. Legare, Wayne Frankel and Konrad Noben-Trauth (2001).  High-resolution genetic and physical mapping of modifier-of-deafwaddler (mdfw) and waltzer (Cdh23v).  Genomics 73, 338-342.

Federica Di Palma, Ralph H. Holme, Elizabeth C. Bryda, Inna A. Belyantseva, Richard Pellegrino, Bechara Kachar, Karen P. Steel and Konrad Noben-Trauth (2001).  Mutations in Cdh23, encoding a new type of cadherin, cause stereocilia disorganization in waltzer, the mouse model for Usher syndrome type 1D.  Nature Genetics 27, 103-107.

Federica Di Palma, Richard Pellegrino and Konrad Noben-Trauth (2001).  Genomic structure, alternative splice forms and normal and mutant alleles of cadherin-23 (Cdh23).  Gene 28, 31-41.

Agnieszka K. Rzadzinska, Adam Derr, Bechara Kachar and Konrad Noben-Trauth (2005). Sustained cadherin 23 expression in young and adult cochlea of normal and hearing impaired mice.  Hearing Research 208, 114-121.

3.    Trpml3  -  Dominant mutations in a TRP channel cause deafness in mice.

This study identified a member of the large family of transient-receptor-potential (TRP) channels (Mcoln3, also named TRPML3) as the cause of pigmentation anomalies, embryonic lethality and endocochlear and sensorineural hearing loss.  Dominant mutations disrupt the structure of the stereocilia bundle during development and in the adult lead to hair cell degeneration and hearing loss.  Our subsequent immuno-localization positioned Trpml3 to the ankle link region near the base of stereocilia.  In a collaborative study, we demonstrated reduced mechano-electrical transducer currents and an inwardly rectifying leak conductance in Varitint-waddler cochlear hair cells, which explains the hair cell degeneration and hearing loss.

Hung J. Kim, Torrance Jackson and Konrad Noben-Trauth (2002).  Genetic analyses of the mouse deafness mutations varitint-waddler (Va) and jerker (Espnje).  J. Assoc. Res. Otolaryngology 4, 83-90.

Federica Di Palma, Inna Belyantseva, Hung J. Kim, Thomas F. Vogt, Bechara Kachar and Konrad Noben-Trauth (2002).  Mutations in Mcoln3 associated with deafness and pigmentation defects in varitint-waddler (Va) mice.  Proc. Natl. Acad. Sci. USA 99, 14994-14999 (2002).

Feng Qian and Konrad Noben-Trauth (2005).  Cellular and molecular function of mucolipins (TRPML) and polycystin 2 (TRPP2).  Pflügers Archiv European Journal of Physiology 451, 277-285.

Margaret Atiba-Davis and Konrad Noben-Trauth (2007).  TRPML3 and hearing loss in the varitint-waddler mouse.  Biochimica et Biophysica Acta 1772, 1028-1031.

Alex F.J. van Anken, Margaret Atiba-Davies, Walter Marcotti, Richard Goodyear, Jane E. Bryant, Guy P. Richardson, Konrad Noben-Trauth and Corné J. Kros (2008).  TRPML3 mutations cause impaired mechano-electrical transduction and depolarization by an inward-rectifier cation current in auditory hair cells of varitint-waddler mice.  Journal of Physiology 586, 5403-5418.

Konrad Noben-Trauth (2011).  The TRPML3 channel: from gene to function.  In: Transient Receptor Potential Channels, Advances in Experimental Medicine and Biology 704, 229-237.

4.    Sobp  -  Cochlea patterning defects in mice and mental disability in humans.

Initiation of the study of the Jackson circler (jc) mouse mutant was guided by the observation that erratic circling behavior oftentimes results from cellular defects of the sensory epithelia of cochlea and vestibule.  In homozygous jc mice, we identified a profound congenital hearing loss, accompanied by severe cochlear patterning defects that included a shortened cochlea, supernumerary outer hair cells, ectopic expression of vestibular-like hair cells in Kolliker’s organ and mirror-image duplication of the apical part of the organ of Corti.  On the molecular level, we traced these defects to a small intragenic deletion in the Sobp (sine oculis-binding protein) gene.  Motif analyses, evolutionary comparisons, and in vitro localization studies suggest that Sobp functions as nuclear FCS-type zinc-finger protein acting perhaps as suppressor of gene transcription.  Following our discovery, Lina Basel at University of Tel Aviv and colleagues identified a truncating mutation in the human SOBP gene underlying mental disabilities, anterior maxillary protrusion and strabismus syndrome (MRAMS) in a human pedigree.

Alfredo Calderon, Adam Derr, Barden B. Stagner, Kenneth R. Johnson, Glen Martin and Konrad Noben-Trauth (2006).  Cochlear developmental defect and background-dependent hearing thresholds in the Jackson circler (jc) mutant mouse.  Hearing Research 221, 44-58.

Zheng Chen, Mireille Montcouquiol, Alfredo Calderon, Nancy A. Jenkins, Neal G. Copeland, Matthew W. Kelley and Konrad Noben-Trauth (2008).  Jxc1/Sobp, encoding a nuclear zinc finger protein, is critical for cochlear growth, cell fate, and patterning of the organ of Corti.  Journal of Neuroscience 28, 6633-6641 (2008).

Efrat Birk, Adi Har-Zahav, Chiara M. Manzini, Metsada Pasmanik-Chor, Liora Kornreich, Christopher A.Walsh, Konrad Noben-Trauth, Adi Albin, Amos J. Simon, Laurence Colleaux, Yair Morad, Limor Rainshtein, David J. Tischfield, Peter Wang, Nurit Magal, Idit Maya, Noa Shoshani, Gidon Rehavi, Doron Gothelf, Gal Maydan, Mordechai Shohat and Lina Basel-Vanagaite (2010).  SOBP is mutated in syndromic and nonsyndromic intellectual disability and is highly expressed in the brain limbic system.  Am. J. Hum. Genet. 87, 694-700.

5.    Rpl38  -  Deletion of ribosomal protein L38 associated with chronic otitis media and conductive hearing loss in mice.

The Tail-short mutation is characterized by skeletal abnormalities, embryonic lethality and transient anemia.  Since skeletal malformations can be associated with hearing impairment, we studied the morphology and physiology of the ear.  We found that Ts mice develop several - probably interrelated - pathologies in the middle ear: (1) massive ectopic bone deposition onto the round window ridge extending from the round window up to the apex of the cochlea; (2) production of large amounts of cholesterol crystals and cholesterol granulomas in the middle ear cavity; (3) development of a chronic otitis media with effusion and (4) enlargement of the Eustachian tube.  This leads to a conductive hearing loss by three weeks of age.  On the molecular level, we showed that the pathosis is the result of a large-scale deletion of the gene Rpl38, encoding a ribosomal protein of the large subunit.  Our work suggests Rpl38 as a risk factor for chronic otitis media in humans.

Konrad Noben-Trauth and Joseph P. Latoche (2011).  Ectopic mineralization in the middle ear and chronic otitis media with effusion caused by Rpl38 deficiency in the Tail short (Ts) mouse.  J. Biol. Chem. 286, 3079-3093.

  1. 6.    Tubby  -  Sensorineural degeneration and obesity.

Tubby is a spontaneous recessive mutation that causes cochlear and retinal degeneration together with maturity-onset obesity and insulin resistance.   To better understand onset and pathology of obesity on the molecular level, Patsy Nishina and Jurgen Naggert at The Jackson Laboratory set out to clone this mutation.  Joining this group as postdoctoral fellow, we identified a loss-of-function mutation in a novel gene - tub - in the tubby locus.  Tub has a few additional homologs (Tulp1-3), of which Tulp1 underlies retinitis pigmentosa in humans.  On the molecular level, Tub associates with G-proteins at the plasma membrane and translocates to the nucleus.  However, a more detailed molecular and cellular understanding of its function is still absent.  In particular, the relationship of the sensory degeneration and obesity remains enigmatic.  Tub also genetically interacts with a structural protein - Mtap1 - in the cochlea, where both proteins co-localize to spiral ganglions.   A polymorphic isoform of Mtap1 accelerates hearing loss in tubby mice.

Michael A. North, Jürgen K. Naggert, Yingzhuo Yan, Konrad Noben-Trauth and Patsy M. Nishina (1997).  Molecular characterization of TUB, TULP1 and TULP2, members of the novel tubby gene family and their possible relation to ocular diseases.  Proc. Natl. Acad. Sci. USA 94, 3128-3133.

Konrad Noben-Trauth, Jürgen K. Naggert, Mike A. North and Patsy M. Nishina (1996).  A candidate gene for the mouse mutation tubby.  Nature 380, 534-538.

Genetic modification and oligogenic hearing loss

1.    Cdh23753A -  A single nucleotide polymorphism in Cdh23 is a genetic modifier and controls susceptibility to sensorineural hearing loss in common inbred strains.

Age-related hearing loss, also called presbycusis, affects a large fraction of the elderly population.  Age-related hearing loss is also a common phenotype in inbred strains.  Specifically, the C57BL/6J strain exhibits late-onset progressive sensorineural hearing loss, not unlike that observed in the human population.  In this project, we showed that a splice variant in the Cdh23 gene accounts for a large genetic fraction of hearing loss in C57BL/6J and many other inbred strains.  Hence, a single variant with strong effect is sufficient to induce presbycusis in animal models.  We also demonstrate that the Cdh23 splice variant accelerates the hearing loss in mice that are heterozygous for a mutation in Atp2b2 acting as a genetic modifier.  This study provides a genetic paradigm for late-onset hearing loss and genetic modification of hearing loss with implications for the diagnosis of hearing loss in the human population.

Konrad Noben-Trauth, Qing Y. Zheng and Kenneth R. Johnson (2003).  Association of cadherin 23 with polygenic inheritance and genetic modification of sensorineural hearing loss.  Nature Genetics 35, 21-23.

  1. 2.   Gipc3  -  Progressive hearing impairment and audiogenic seizures in mice and non-syndromic hearing loss in humans.

This study followed my interest on genetic modifiers and the interactions of genes in controlling hearing function.  In a screen of heterogeneous stocks, we found that many outbred strains show a remarkably diverse spectrum of hearing impairment.  One such strain, Black Swiss, develops an early-onset and moderate but slowly progressing hearing loss.  By genetic means, we identified a mutation in the PDZ-containing protein Gipc3 that causes stereocilia bundle defects, reduced mechano-transduction currents, increased membrane depolarizations of inner hair cells, elevated hearing thresholds and absent distortion product otoacoustic emissions in the presence of a normal endocochlear potential.  Black Swiss mice are also hypersensitive to noise, undergoing transient audiogenic seizures upon acoustic stimulation.  We showed that this sensitivity correlates with abnormally high amplitudes of afferent cochlear nerve fibers at the inner hair cell synapse.  This amplitude declines rapidly and concomitantly the mice become resistant to audiogenic stimulation.  Clinically, audiogenic seizures are a form of reflex epilepsies.  In this context, we showed in collaboration with Richard Smith, University of Iowa, and Hannie Kremer, Radboud University, that mutations in GIPC3 also cause sensorineural hearing loss DFNB15/95 in the human population.  Our work suggests Black Swiss mice as a model for acoustic hypersensitivity such as hyperacusis, tinnitus, and hyperacute hearing in autism.

Meghan Drayton and Konrad Noben-Trauth (2006).  Mapping quantitative trait loci for hearing loss in Black Swiss mice.  Hearing Research 212, 128-139.

Nikoletta Charizopoulou, Andrea Lelli, Margit Schraders, Kausik Ray, Michael S. Hildebrand, Arabandi Ramesh, C.R. Srikumari Srisailapathy, Jaap Oostrik, Ronald J.C. Admiraal, Harold R. Neely, Joseph R. Latoche, Richard J.H. Smith, John K. Northup, Hannie Kremer, Jeffrey R. Holt and Konrad Noben-Trauth (2011).  Gipc3 mutations associated with audiogenic seizures and sensorineural hearing loss in mouse and human. Nature Communications 2: 201.

3.    Snhl2-4  -  Oligogenic hearing loss and organ of Corti patterning defects in ALR/LtJ mice

This study was undertaken to investigate the complex genetics of hearing loss in the ALR/LtJ strain.  We found that ALR/LtJ mice develop early-onset profound sensorineural hearing loss as evidenced by high-to-low frequency hearing threshold shifts, absent distortion-product otoacoustic emissions, and normal endocochlear potentials.  Linkage analyses of a segregating backcross revealed three novel quantitative trait loci named sensorineural hearing loss (Snhl) -2, -3, and -4.  The QTLs achieved very high LOD scores with markers on chromosome 1 (Snhl2, LOD: 12), chromosome 6 (Snhl3, LOD: 24) and chromosome 10 (Snhl4, LOD: 11).  Together, they explained 90% of the phenotypic variance.  While Snhl2 and Snhl3 affected hearing thresholds across a broad range of test frequencies, Snhl4 caused primarily high-frequency hearing loss.  The hearing impairment is accompanied by an organ of Corti patterning defect that is characterized by the ectopic expression of supernumerary outer hair cells organized in additional rows along the abneural site of the sensory epithelium in the presence of unaltered planar polarity and otherwise normal cochlear duct morphology.  Whole-exome sequencing of the ALR/LtJ strain is under way and will provide candidate polymorphisms for further analyses in mouse strains and humans with sensorineural deafness, such as DFNB62.

Joseph R. Latoche, Harold R. Neely and Konrad Noben-Trauth (2011).  Polygenic sensorineural hearing loss (Snhl2, -3, and -4) and organ of Corti patterning defect in the ALR/LtJ strain.  Hearing Research 275, 150-159.

  1. 4.Hfhl1-3  -  High-frequency hearing loss in NIH Swiss mice

NIH Swiss mice are outbred, which is to say that they are phenotypically and genetically heterogeneous.  We showed that mice of this strain express various forms of sensorineural hearing impairment ranging from moderate to severe and affecting a variable range of hearing frequencies or only a subset.  This phenotypic variability on a genetic diverse background allows for the selective breeding of a chosen phenotype.  By  doing so we generated a mouse line with hearing loss mostly at the high frequency spectrum.  In contrast to all other mouse models, the high-frequency hearing loss is highly penetrant and non-progressive, neither spectral nor temporal.  Using linkage mapping we identified three novel quantitative trait loci - Hfhl1, Hfhl2 and Hfhl3 - on chromosome 8, 7, and 9, respectively.  They are of small effect and interestingly effect specific frequency regions on the tonotopic map.  Our study identifies QTLs with precise frequency-specific effects.  It suggests that frequency-specific hearing loss results from gene expression differences along the cochlear duct and it outlines a roadmap towards a molecular-based tonotopic map the the cochlea.

James M. Keller and Konrad Noben-Trauth (2012).  Genome-wide linkage analyses identify Hfhl1 and Hfhl3 loci with frequency-specific effects at the high frequency hearing spectrum in NIH Swiss mice.  BMC Genetics 13:32 (2012).

James M. Keller, Harold R. Neely, Joseph R. Latoche and Konrad Noben-Trauth (2011).  High-frequency sensorineural hearing loss and its underlying genetics (Hfhl1 and Hfhl2) in NIH Swiss mice. J. Assoc. Res. Otolaryngol. 12, 617-631.

Deafness Genes in Mice and Men

tubby, tub, tub

deaf waddler, dfw, Atp2b2

waltzer, v, mdfw, ahl, Cdh23

Black Swiss, ahl5, Gipc3

Varitint-waddler, Va, Mcoln3

jackson circler, jc, Sobp

Tail-short, Ts, Rpl38