Identification of preferentially expressed cochlear genes by systematic sequencing of a rat cochlea cDNA library

Positional cloning of deafness genes

The identification of the majority of the known causative genes involved in nonsyndromic sensorineural hearing loss (NSHL) started with linkage analysis as part of a positional cloning procedure. The human and mouse genome projects in combination with technical developments on genotyping, transcriptomics, proteomics, and the creation of animal models have greatly enhanced the speed of disease gene identification. In the present chapter, we first discuss the possibilities for exclusion of known NSHL loci and genes. Subsequently, methods are described to determine the genomic regions that contain the genetic defects. These include linkage analysis with genotyping and statistical evaluation and the determination of copy number variations. In the case of a large genomic region, candidate genes are selected and prioritized using gene expression analysis, protein network data, and phenotypes of animal models. A number of algorithms are described to automate the process of candidate gene selection. The novel high-throughput sequencing techniques might make gene selection and prioritization unnecessary in the near future. Once genetic variants are identified, questions on pathogenicity need to be addressed, which is the topic of the last section of this chapter.

Is otospiralin inner ear specific? Evidence for its expression in mouse brain

The small protein otospiralin has initially been identified as an inner ear specific molecule. However, compelling evidence from high throughput sequencing projects suggested that otospiralin is likely expressed in the central nervous system. Here, we tested this hypothesis using a combination of molecular biology, immunological, and histological techniques, and found that otospiralin is expressed in numerous regions of the central nervous system in mouse. In situ hybridization and immunohistochemistry revealed that otospiralin is widely expressed in neuronal cell bodies and glia. Ultrastructural observations in the cerebral cortex located the small protein in close proximity to membranous organelles in perikarya, the inner face of post-synaptic neuronal membranes, and in astrocytic processes. These results are in agreement with the predicted structure of the protein which revealed a single N-terminal transmembrane helix domain followed by a C-terminus cytosolic tail. Interestingly, 2 weeks after a mechanical trauma in the cerebral cortex, otospiralin expression increased in reactive astrocytes located within the vicinity of the site of injury, but not in neurons. Collectively, our observations suggest that otospiralin is possibly involved in signaling pathways, and could play a role in repair mechanisms subsequent to an injury in the central nervous system.

Coxsackie adenovirus receptor and alpha nu beta3/alpha nu beta5 integrins in adenovirus gene transfer of rat cochlea

This study was designed to determine whether Coxsackie adenovirus receptor (CAR) and alpha nu beta3/alpha nu beta5 integrin co-receptors are involved in adenovirus gene transfer in the rat cochlea. We find that CAR and integrin co-receptors are expressed in every cell subtype transduced by the adenoviral vector Ad5 DeltaE1-E3/cytomegalovirus/green fluorescent protein (GFP) on cochlear slices in vitro. The spiral ganglion neurons, which do not express CAR, were not transduced by the virus. Blocking these receptors by monoclonal antibodies decreased transgene expression, whereas disrupting tight junctions with ethylenediaminetetraacetic acid led to an increased transgene expression. However, sensory hair cells and strial cells also expressing CAR and alpha nu integrins were not transduced by the vector. GFP expression was also studied in vivo. Perilymphatic perfusion of adenovirus in vivo did not affect hearing and only cells lining the perilymphatic spaces were transduced. Endolymphatic perfusion resulted in low-frequency hearing loss and although some cells of the organ of Corti were efficiently transduced, the sensory and the strial cells were not. Transduced sensory and strial cells were occasionally observed in cochleas after single shot of adenovirus. Pretreatment with anti-CAR and anti-alpha nu antibodies decreases GFP expression in vivo, suggesting that the CAR/alpha nu integrin pathway is involved in adenovirus transduction in the cochlea.

Deafness and cochlear fibrocyte alterations in mice deficient for the inner ear protein otospiralin

In the cochlea, the mammalian auditory organ, fibrocytes of the mesenchymal nonsensory regions play important roles in cochlear physiology, including the maintenance of ionic and hydric components in the endolymph. Occurrence of human deafness in fibrocyte alterations underlines their critical roles in auditory function. We recently described a novel gene, Otos, which encodes otospiralin, a small protein of unknown function that is produced by the fibrocytes of the cochlea and vestibule. We now have generated mice with deletion of Otos and found that they show moderate deafness, with no frequency predominance. Histopathology revealed a degeneration of type II and IV fibrocytes, while hair cells and stria vascularis appeared normal. Together, these findings suggest that impairment of fibrocytes caused by the loss in otospiralin leads to abnormal cochlear physiology and auditory function. This moderate dysfunction may predispose to age-related hearing loss.

Isolation from cochlea of a novel human intronless gene with predominant fetal expression

We have cloned a novel human gene, designated PFET1 (predominantly fetal expressed T1 domain) (HUGO-approved symbol KCTD12 or C13orf2), by subtractive hybridization and differential screening of human fetal cochlear cDNA clones. Also, we have identified the mouse homolog, designated Pfet1. PFET1/Pfet1 encode a single transcript of approximately 6 kb in human, and three transcripts of approximately 4, 4.5, and 6 kb in mouse with a 70% GC-rich open reading frame (ORF) consisting of 978 bp in human and 984 bp in mouse. Both genes have unusually long 3' untranslated (3' UTR) regions (4996 bp in human PFET1, 3700 bp in mouse Pfet1) containing 12 and 5 putative polyadenylation consensus sequences, respectively. Pfetin, the protein encoded by PFET1/Pfet1, is predicted to have 325 amino acids in human and 327 amino acids in mouse and to contain a voltage-gated potassium (K+) channel tetramerization (T1) domain. Otherwise, to date these genes have no significant homology to any known gene. PFET1 maps to the long arm of human chromosome 13, in band q21 as shown by FISH analysis and STS mapping. Pfet1 maps to mouse chromosome 14 near the markers D14Mit8, D14Mit93, and D14Mit145.1. The human 6 kb transcript is present in a variety of fetal organs, with highest expression levels in the cochlea and brain and, in stark contrast, is detected only at extremely low levels in adult organs, such as brain and lung. Immunohistochemistry with a polyclonal antibody raised against a synthetic peptide to PFET1 sequence (pfetin) reveals immunostaining in a variety of cell types in human, monkey, mouse, and guinea pig cochleas and the vestibular system, including type I vestibular hair cells.

Cloning, characterization, and mRNA expression analysis of novel human fetal cochlear cDNAs☆

To identify novel genes that are expressed specifically or preferentially in the cochlea, we constructed a cDNA library enriched for human cochlear cDNAs using a suppression subtractive hybridization technique. We analyzed 2640 clones by sequencing and BLAST similarity searches. One hundred and fifty-five different cDNA fragments mapped in nonsyndromic hearing impairment loci for which the causative gene has not been cloned yet. Approximately 30% of the clones show no similarity to any known human gene or expressed sequence tag (EST). Clones mapping in nonsyndromic deafness loci and a selection of clones that represent novel ESTs were analyzed by reverse transcriptase-polymerase chain reaction (RT-PCR) of RNA derived from 12 human fetal tissues. Our data suggest that a quarter of the novel genes in our library are preferentially expressed in fetal cochlea. These may play a physiologically important role in the hearing process and represent candidate genes for hereditary hearing impairment.

Gene structure, chromosomal localization, and mutation screening of the human gene for the inner ear protein otospiralin

Otospiralin is a novel protein of unknown function that is produced by non-sensory cells (fibrocytes) of the inner ear (cochlea and vestibule). We showed that downregulation of otospiralin in guinea pigs leads to deafness and we therefore hypothesized that genetic defects in the otospiralin gene could also cause deafness in humans. In this study, we cloned and localized OTOSP, the human gene for otospiralin. OTOSP spans 1630 nucleotides, contains four exons and codes for a 567-nucleotide cDNA. By fluorescence in situ hybridization and hybrid panel mapping we localized OTOSP on chromosome 2 at position q37.3. There is currently no deafness family linked to this region. We screened OTOSP for mutations in 410 unrelated patients exhibiting various levels of hearing loss. Beside intronic polymorphisms, a rare variant (Pro7Leu) was found in 4 deafness patients and 3 control individuals, indicating that this change is not involved in this condition and excluding OTOSP as a major gene for genetic deafness.

Transient expression of the t-isoform of plastins/fimbrin in the stereocilia of developing auditory hair cells

The transduction of auditory signals by cochlear hair cells depends upon the integrity of hair cell stereociliary bundles. Stereocilia contain a central core of actin filaments, cross-linked by actin bundling proteins. In the cochlea, the two proteins described to date as responsible for the spatial arrangement of actin filaments in sterocilia are fimbrin and the recently discovered espin. Fimbrin (the chick homolog of human I-plastin) belongs to the plastins/fimbrin family that includes two additional isoforms of plastins, T- and L-plastin. In the present study, we used isoform specific antibodies to investigate the presence of the T- and L-isoforms of plastin/fimbrin in the adult and developing rat cochlea. We found that T-plastin, but not L-plastin, is expressed in the rat cochlea. During postnatal development of the rat organ of Corti, T-plastin can be detected in the core of stereocilia from early stages of hair cell differentiation, and its expression gradually increases in stereocilia as hair cells mature. However, as opposed to other actin-binding proteins expressed in stereocilia, T-plastin is absent from the stereocilia of mature hair cells. Such temporally restricted expression strengthens the idea of functional differences between plastins isoforms, and suggests that T-plastin could have a specific role in stereocilia formation.

Molecular screens for inner ear genes

Identification of the genes that encode proteins that are important for proper function of specific inner ear cell types is central to our understanding of the molecular basis of hearing and balance. Whereas the combination of electrophysiology and biophysics has resulted in an exquisite understanding of inner ear function, little is known about the proteins that confer these properties at the cellular level. Furthermore, the genes that control inner ear development, susceptibility to wear and tear, regeneration from damage, and age-related degeneration, are largely unknown. This review discusses tools that have been developed during the past few years to address this imbalance between a thorough physiologic characterization of inner ear function and a detailed understanding at a molecular level of the proteins involved in these functions. Creation of inner ear cDNA libraries has laid the foundation for the discovery of genes that are specifically expressed by cell types of the inner ear and that encode proteins that are important for molecular processes in these cells. In conjunction with expressed sequence tag database analysis, cDNA subtraction, and DNA arrays, functionally important genes, whose specific expression patterns are usually verified by gene expression analysis, can be identified. Discussion of these techniques takes into account the specific characteristics of the inner ear in relation to its study using molecular biological approaches.

Identification of preferentially expressed mRNAs in retina and cochlea

To search for genes that could be involved in genetic disorders primarily involving the retina and the cochlea, we tried to identify mRNAs preferentially expressed in retina and cochlea and to establish their chromosomal localization. Two approaches were employed. First, a mouse subtracted library (retina + cochlea against liver + brain) was generated. Randomly selected cDNA clones were sequenced and compared to databases. Tissue expression of some of them was analyzed by RT-PCR. Using radiation hybrid cell lines, the mouse chromosomal localization was determined for those showing the highest level in the retina and the cochlea. Second, human Expressed Sequence Tags (ESTs) with preferential expression in the retina and the cochlea were searched for in databases, and chromosomal localization was also established. From 171 sequenced clones, 73 were classified as known genes (with 17 clones coding for 6 genes), 86 were homologous to ESTs, and 12 were unidentified. Of 108 selected clones, 22 (18.5%) had the highest level of expression in the retina and/or the cochlea, while expression was higher in another tissue or ubiquitous for 60 (55.5%) and 22 (20.4%) of them, respectively. By RT-PCR, one clone similar to the mouse Asic3 cDNA (proton-gated channel) was found mainly in the retina and cochlea, but its human ortholog was widely expressed. We selected 17 ESTs from the UniGene database with restricted expression including in the retina and cochlea. We mapped 10 of these ESTs as well as four mouse clones from the subtracted library. Some of them localized to morbid intervals. The combined information from expression analysis and chromosomal localization allowed for the identification of potential candidate genes for retinal diseases (CORD8, CORD9) and syndromic blindness/deafness/renal defects.

Expression of members of Wnt and Frizzled gene families in the postnatal rat cochlea

The functioning of the mammalian cochlea is entirely based on its mechanical properties, which are supported by a highly complex tissue architecture resulting from the precise arrangement of sensory hair cells and non-sensory supporting cells. Growing evidence indicates that evolutionary conserved signaling pathways are involved in inner ear development and in the differentiation of its diverse cell types. We investigated whether members of the Wnt and Frizzled gene families, which play key roles in a wide variety of cellular and developmental processes, are expressed in the postnatal rat cochlea. A PCR screening of a rat cochlea cDNA library performed with degenerate primers allowed us to isolate five members of the Wnt gene family (RWnt-2B, -4, -5A, -5B, and -7A) and six members of the Frizzled gene family (Rfz1, Rfz2, Rfz3, Rfz4, Rfz6, Rfz9). In situ hybridization and immunocytochemistry experiments demonstrated that RWnt-4, -5B, -7A have distinct, although partly overlapping, expression patterns in the juvenile rat cochlea. These results suggest that the Wnt-Frizzled signaling pathway could be involved in several aspects of late cochlear differentiation and/or auditory function.

Downregulation of otospiralin, a novel inner ear protein, causes hair cell degeneration and deafness

Mesenchymal nonsensory regions of the inner ear are important structures surrounding the neurosensory epithelium that are believed to participate in the ionic homeostasis of the cochlea and vestibule. We report here the discovery of otospiralin, an inner ear-specific protein that is produced by fibrocytes from these regions, including the spiral ligament and spiral limbus in the cochlea and the maculae and semicircular canals in the vestibule. Otospiralin is a novel 6.4 kDa protein of unknown function that shares a protein motif with the gag p30 core shell nucleocapsid protein of type C retroviruses. To evaluate its functional importance, we downregulated otospiralin by cochlear perfusion of antisense oligonucleotides in guinea pigs. This led to a rapid threshold elevation of the compound action potentials and irreversible deafness. Cochlear examination by transmission electron microscopy revealed hair cell loss and degeneration of the organ of Corti. This demonstrates that otospiralin is essential for the survival of the neurosensory epithelium.

In vivo transfer of antisense oligonucleotide against urinary kininase blunts deoxycorticosterone acetate-salt hypertension in rats

We have previously reported that the renal kallikrein-kinin system suppressed the development of deoxycorticosterone acetate (DOCA)-salt hypertension. Kinins were degraded in the kidney mainly by carboxypeptidase Y (CPY)-like kininase. Blockade of renal kinin degradation may reduce hypertension in the developmental stage. We constructed an antisense oligonucleotide against rat CPY homologue (5'-CAT-CTC-TGC-TTC-CTT-GTG-TC-3', AS) and its randomized control oligonucleotide (5'-TCC-TTC-CTG-CTT-GAG-TTC-CT-3', RC), and prepared an HVJ-liposome complex that prolongs and increases the effectiveness of the antisense oligonucleotide. Antisense oligonucleotide was transfected (25 nmole rat(-1), in terms of nucleotide) into the kidney from the renal artery. Blood pressure was measured through a catheter inserted into the abdominal aorta. Mean blood pressure (MBP) in DOCA-salt treated (for 2 weeks) Sprague Dawley strain rats was 130+/-3 mmHg (n=11), and was reduced significantly (P<0.05) more by AS transfection (122+/-4 mmHg, n=6) than by RC treatment (137+/-6 mmHg, n=5) 4 days after the transfection. This reduction in MBP was accompanied by increased urinary sodium excretion (AS, 8.4+/-1.5 mmole day(-1); RC, 4.6+/-0.5 mmole day(-1), P<0.05) and a reduction in urinary CPY-like kininase activity. Ebelactone B (5 mg kg(-1), twice a day, p.o.), an inhibitor for urinary CPY-like kininase, also reduced MBP and induced natriuresis to the same degree as AS. Lisinopril, an inhibitor for angiotensin converting enzyme (ACE) failed to reduce the elevated MBP. These results suggest that CPY-like kininase may have more contribution than ACE to degrade kinin in the kidney, and that knockdown of CPY-like kininase in the kidney may partly prevent rat DOCA-salt hypertension.

Characterization of novel and identified genes in guinea pig organ of corti

A number of proteins are expressed in the organ of Corti and are considered to be responsible for hearing. However, most of them have not been identified. Therefore, to achieve a better understanding of the genetic factors influencing these traits, the first step is to characterize the genes expressed in the organ of Corti. In the present study, a cDNA library was constructed from the guinea pig organ of Corti. After sequencing isolated clones, 196 expressed sequence tags (ESTs) were identified with FASTA analysis: 65 ESTs showed significant sequence homology to previously identified genes in guinea pig, human or other species, and 131 ESTs showed no significant matches to sequences already present in the DNA database DDBJ/GenBank/EMBL. A variety of matching sequences, some of which were known to be cochlea-specific, were found through FASTA analysis of the 65 clones. RT-PCR with a panel of 10 different tissue mRNA revealed the restricted expression of 13 unknown clones. The results of our analysis allowed the establishment of a list of genes expressed in the guinea pig organ of Corti.

Nucleotide sequence databases: a gold mine for biologists

The rapid expansion of nucleotide sequence data available in public databases is revolutionizing biomedical research. These databases have a variety of uses, including the discovery of novel genes, identification of homologous genes, analysis of alternative splicing, chromosomal localization of genes, and detection of polymorphisms. Data sets such as the human transcript map will undoubtedly accelerate identification of candidate genes in positional-cloning approaches. Careful in silico analysis can significantly reduce the amount of lab work required. Approximately half of all human genes are represented in these databases; therefore, one need not wait for the entire human genome to be sequenced before performing genome-wide studies.

Expression pattern of mammalian cochlea outer hair cell (OHC) mRNA: screening of a rat OHC cDNA library

The aim of this study was to characterize the mRNA content of mammalian cochlear outer hair cells (OHCs) and to search for specific genes possibly involved in their unique properties. Indeed, OHCs, which feature high-frequency electromotility, are responsible for the exquisite sensitivity and frequency selectivity of the cochlea. Damage to these cells, which occurs in various conditions, causes a reduction in the cochlear sensitivity by about 50 dB and the alteration of frequency discrimination. Total RNA was extracted from about 2000 mechanically dissociated OHCs, and a polymerase chain reaction (PCR) amplified cDNA library was constructed. The presence of the alpha-9 acetylcholine receptor subunit, preferentially expressed in OHCs, was found by direct PCR amplification of the library. A systematic sequencing of 218 clones showed 78% known genes, 11% EST-related sequences, and 11% unknown genes. The known-gene group was characterized by two main features: a large proportion (55%) of mitochondrial transcripts and an abundance in calcium-binding proteins, such as calmodulin and calbindin, for which expression has already been demonstrated in OHCs. Another protein, the oncomodulin recently shown to be OHC specific, was also found, and its mRNA expression was confirmed by in situ hybridization. Among the 24 unknown genes, 7 were expressed in a restricted pattern, including one expressed in cochlea and spleen and, to a lesser extent, in lungs.

Genetic causes of hearing loss

In the past year, genes involved in the branchio-oto-renal and Treacher-Collins syndromes were cloned. Myosin 7A, a gene previously implicated in Usher syndrome type 1B, was also found to be mutated in non-syndromic hearing loss. Likewise, linkage studies in Pendred syndrome and Usher syndrome type 1D suggest that allelic mutations can cause syndromic and non-syndromic forms of deafness. In patients with X-linked deafness type 3, a hotspot for deletions was found 900 kb proximal to the causal gene POU3F4. Most importantly, the connexin 26 gene is mutated in approximately 50% of all recessive deafness families, enabling early diagnosis and carrier detection.

Identification and cloning of differentially expressed genes

Only a few of the methods currently used for identification of differentially expressed genes take advantage of the fact that (near) complete sets of cDNA clones and sequences representing all human and mouse genes will be available for high throughput survey of gene expression. Accordingly, strategies based on hybridization of complex (cDNA or RNA) probes to cDNA microarrays, either on glass slides or on chips, are likely to become increasingly more advantageous. Recognizing, however, that the power of these methods depends upon the availability of such resources, strategies are being pursued to facilitate completion of the ongoing efforts to identify all human and mouse genes.