Expression of mRNA encoding extracellular matrix glycoproteins SPARC and SC1 is temporally and spatially regulated in the developing cochlea of the rat inner ear

Exome sequencing utility in defining the genetic landscape of hearing loss and novel-gene discovery in Iran

Hearing loss (HL) is one of the most common sensory defects affecting more than 466 million individuals worldwide. It is clinically and genetically heterogeneous with over 120 genes causing non-syndromic HL identified to date. Here, we performed exome sequencing (ES) on a cohort of Iranian families with no disease-causing variants in known deafness-associated genes after screening with a targeted gene panel. We identified likely causal variants in 20 out of 71 families screened. Fifteen families segregated variants in known deafness-associated genes. Eight families segregated variants in novel candidate genes for HL: DBH, TOP3A, COX18, USP31, TCF19, SCP2, TENM1, and CARMIL1. In the three of these families, intrafamilial locus heterogeneity was observed with variants in both known and novel candidate genes. In aggregate, we were able to identify the underlying genetic cause of HL in nearly 30% of our study cohort using ES. This study corroborates the observation that high-throughput DNA sequencing in populations with high rates of consanguineous marriages represents a more appropriate strategy to elucidate the genetic etiology of heterogeneous conditions such as HL.

Matricellular protein SPARC/osteonectin expression is regulated by DNA methylation in its core promoter region

BACKGROUND

SPARC/osteonectin is an evolutionarily conserved matricellular protein that modulates cell-matrix interaction and cell function. In all vertebrates, SPARC is dynamically expressed during embryogenesis. However, the precise function of SPARC and the regulatory elements required for its expression in particular during early embryogenesis are largely unknown.

RESULTS

The present study was undertaken to explore the molecular mechanisms that regulate sparc gene expression by in vivo functional characterization of the sparc promoter and identification of possible putative regulatory elements that govern basal promoter activity. We report here transient expression analyses of eGFP expression from transgenic zebrafish containing a Sparc-iTol2-eGFP-BAC and/or 7.25 kb-sparc-Tol2-eGFP constructs. eGFP expression was specifically found in the notochord, otic vesicle, fin fold, intermediate cell mass, and olfactory placode of BAC and Tol2 transposon vectors injected embryos. Deletion analysis revealed that promoter activity resides in the unique 5'-untranslated intronic region. Computer-based analysis revealed a putative CpG island immediately proximal to the translation start site within the intron sequence. Global inhibition of methylation with 5-Aza-2-deoxycytidine promoted sparc expression in association with decreasing CpG methylation.

CONCLUSIONS

Taken together, these data identify a contributory role for DNA methylation in regulating sparc expression in zebrafish embryogenesis.

Expression and function of scleraxis in the developing auditory system

A study of genes expressed in the developing inner ear identified the bHLH transcription factor Scleraxis (Scx) in the developing cochlea. Previous work has demonstrated an essential role for Scx in the differentiation and development of tendons, ligaments and cells of chondrogenic lineage. Expression in the cochlea has been shown previously, however the functional role for Scx in the cochlea is unknown. Using a Scx-GFP reporter mouse line we examined the spatial and temporal patterns of Scx expression in the developing cochlea between embryonic day 13.5 and postnatal day 25. Embryonically, Scx is expressed broadly throughout the cochlear duct and surrounding mesenchyme and at postnatal ages becomes restricted to the inner hair cells and the interdental cells of the spiral limbus. Deletion of Scx results in hearing impairment indicated by elevated auditory brainstem response (ABR) thresholds and diminished distortion product otoacoustic emission (DPOAE) amplitudes, across a range of frequencies. No changes in either gross cochlear morphology or expression of the Scx target genes Col2A, Bmp4 or Sox9 were observed in Scx(-/-) mutants, suggesting that the auditory defects observed in these animals may be a result of unidentified Scx-dependent processes within the cochlea.

SC1/hevin and reactive gliosis after transient ischemic stroke in young and aged rats

SC1 is a member of the SPARC family of glycoproteins that regulate cell-matrix interactions in the developing brain. SC1 is expressed in astrocytes, but nothing is known about the expression in the aged or after stroke. We found that after focal striatal ischemic infarction in adult rats, SC1 increased in astrocytes surrounding the infarct and in the glial scar, but in aged rats, SC1 was lower at the lesion edge. Glial fibrillary acidic protein (GFAP) also increased, but it was less prominent in reactive astrocytes further from the lesion in the aged rats. On the basis of their differential expression of several molecules, 2 types of reactive astrocytes with differing spatiotemporal distributions were identified. On Days 3 and 7, SC1 was prevalent in cells expressing markers of classic reactive astrocytes (GFAP, vimentin, nestin, S100β), as well as apoliprotein E (ApoE), interleukin 1β, aggrecanase 1 (ADAMTS4), and heat shock protein 25 (Hsp25). Adjacent to the lesion on Days 1 and 3, astrocytes with low GFAP levels and a "starburst" SC1 pattern expressed S100β, ApoE, and Hsp32 but not vimentin, nestin, interleukin 1β, ADAMTS4, or Hsp25. Neither cell type was immunoreactive for NG2,CC-1, CD11b, or ionized calcium-binding adapter-1. Their differing expression of inflammation-related and putatively protective molecules suggests different roles for starburst and classic reactive astrocytes in the early glial responses to ischemia.

A novel mutation within the MIR96 gene causes non-syndromic inherited hearing loss in an Italian family by altering pre-miRNA processing

The miR-96, miR-182 and miR-183 microRNA (miRNA) family is essential for differentiation and function of the vertebrate inner ear. Recently, point mutations within the seed region of miR-96 were reported in two Spanish families with autosomal dominant non-syndromic sensorineural hearing loss (NSHL) and in a mouse model of NSHL. We screened 882 NSHL patients and 836 normal-hearing Italian controls and identified one putative novel mutation within the miR-96 gene in a family with autosomal dominant NSHL. Although located outside the mature miR-96 sequence, the detected variant replaces a highly conserved nucleotide within the companion miR-96*, and is predicted to reduce the stability of the pre-miRNA hairpin. To evaluate the effect of the detected mutation on miR-96/mir-96* biogenesis, we investigated the maturation of miR-96 by transient expression in mammalian cells, followed by real-time reverse-transcription polymerase chain reaction (PCR). We found that both miR-96 and miR-96* levels were significantly reduced in the mutant, whereas the precursor levels were unaffected. Moreover, miR-96 and miR-96* expression levels could be restored by a compensatory mutation that reconstitutes the secondary structure of the pre-miR-96 hairpin, demonstrating that the mutation hinders precursor processing, probably interfering with Dicer cleavage. Finally, even though the mature miR-96 sequence is not altered, we demonstrated that the identified mutation significantly impacts on miR-96 regulation of selected targets. In conclusion, we provide further evidence of the involvement of miR-96 mutations in human deafness and demonstrate that a quantitative defect of this miRNA may contribute to NSHL.

Expression, functional, and structural analysis of proteins critical for otoconia development

Otoconia, developed during late gestation and perinatal stages, couple mechanic force to the sensory hair cells in the vestibule for motion detection and bodily balance. In the present work, we have investigated whether compensatory deposition of another protein(s) may have taken place to partially alleviate the detrimental effects of Oc90 deletion by analyzing a comprehensive list of plausible candidates, and have found a drastic increase in the deposition of Sparc-like 1 (aka Sc1 or hevin) in Oc90 null versus wt otoconia. We show that such up-regulation is specific to Sc1, and that stable transfection of Oc90 and Sc1 full-length expression constructs in NIH/3T3 cells indeed promotes matrix calcification. Analysis and modeling of Oc90 and Sc1 protein structures show common features that may be critical requirements for the otoconial matrix backbone protein. Such information will serve as the foundation for future regenerative purposes.

Sparc (Osteonectin) functions in morphogenesis of the pharyngeal skeleton and inner ear

Sparc (Osteonectin), a matricellular glycoprotein expressed by many differentiated cells, is a major non-collagenous constituent of vertebrate bones. Recent studies indicate that Sparc expression appears early in development, although its function and regulation during embryogenesis are largely unknown. We cloned zebrafish sparc and investigated its role during development, using a mo rpholino antisense oligonucleotide-based knockdown approach. Consistent with its strong expression in the otic vesicle and developing pharyngeal cartilages, knockdown of Sparc function resulted in specific inner ear and cartilage defects that are highlighted by changes in gene expression, morphology and behavior. We rescued the knockdown phenotypes by co-injecting sparc mRNA, providing evidence that the knockdown phenotype is due specifically to impairment of Sparc function. A comparison of the phenotypes of Sparc knockdown and known zebrafish mutants with similar defects places Sparc downstream of sox9 in the genetic network that regulates development of the pharyngeal skeleton and inner ear of vertebrates.

Gene expression profiling analysis of the inner ear

Recent developments in molecular genetics, including progress in the human genome project, have allowed identification of genes at an unprecedented rate. To date gene expression profiling studies have focused on identifying transcripts that are specifically or preferentially enriched within the inner ear on the assumption that they are more likely to be important for auditory and vestibular function. It is now apparent that some genes preferentially expressed in the cochleo-vestibular system are not crucial for hearing or balance or their functions are compensated for by other genes. In addition, transcripts expressed at low abundance in the inner ear are generally under-represented in gene profiling studies. In this review, we highlight the limitations of current gene expression profiling strategies as a discovery tool for genes involved in cochleo-vestibular development and function. We argue that expression profiling based on hierarchical clustering of transcripts by gene ontology, combined with tissue enrichment data, is more effective for inner ear gene discovery. This approach also provides a framework to assist and direct the functional characterization of gene products.

Gene expression changes during step-wise differentiation of embryonic stem cells along the inner ear hair cell pathway

CONCLUSION

Our study outlines an alternative approach for the selection and investigation of genes involved in inner ear function.

OBJECTIVE

To gain understanding of the gene pathways involved in the development of the normal cochlea.

MATERIALS AND METHODS

Microarray technology currently offers the most efficient approach to investigate gene expression and identify pathways involved in cell differentiation. Epidermal growth factor (EGF) induces cultures derived from the organ of Corti to proliferate and produce new hair cells. Since pluripotent embryonic stem (ES) cells have the capacity to generate all tissues, we induced murine ES cells to differentiate towards ectodermal and neuroectodermal cell types and from there investigated their commitment towards the hair cell lineage in the presence of EGF. Cells were collected at three points along the differentiation pathway and their expression profiles were determined using the Soares NMIE mouse inner ear cDNA library printed in microarray format.

RESULTS

Three genes up-regulated after addition of EGF (serine (or cysteine) proteinase inhibitor, clade H, member 1 (Serpinh1), solute carrier family 2 (facilitated glucose transporter), member 10 (Slc2a10) and secreted acidic cysteine-rich glycoprotein (Sparc)) were selected for further analysis and characterization. Of the three genes, Serpinh1 and Slc2a10 have never been implicated in the hearing process.

Matricellular hevin regulates decorin production and collagen assembly

Matricellular proteins such as SPARC, thrombospondin 1 and 2, and tenascin C and X subserve important functions in extracellular matrix synthesis and cellular adhesion to extracellular matrix. By virtue of its reported interaction with collagen I and deadhesive activity on cells, we hypothesized that hevin, a member of the SPARC gene family, regulates dermal extracellular matrix and collagen fibril formation. We present evidence for an altered collagen matrix and levels of the proteoglycan decorin in the normal dermis and dermal wound bed of hevin-null mice. The dermal elastic modulus was also enhanced in hevin-null animals. The levels of decorin protein secreted by hevin-null dermal fibroblasts were increased by exogenous hevin in vitro, data indicating that hevin might regulate both decorin and collagen fibrillogenesis. We also report a decorin-independent function for hevin in collagen fibrillogenesis. In vitro fibrillogenesis assays indicated that hevin enhanced fibril formation kinetics. Furthermore, cell adhesion assays indicated that cells adhered differently to collagen fibrils formed in the presence of hevin. Our observations support the capacity of hevin to modulate the structure of dermal extracellular matrix, specifically by its regulation of decorin levels and collagen fibril assembly.

Age-related changes in cochlear gene expression in normal and shaker 2 mice

The vertebrate cochlea is a complex organ optimized for sound transduction. Auditory hair cells, with their precisely arranged stereocilia bundles, transduce sound waves to electrical signals that are transmitted to the brain. Mutations in the unconventional myosin XV cause deafness in both human DFNB3 families and in shaker 2 (sh2) mice as a result of defects in stereocilia. In these mutant mice, hair cells have relatively normal spatial organization of stereocilia bundles but lack the graded, stair-step organization. We used sh2 mice as an experimental model to investigate the molecular consequences of the sh2 mutation in the Myo15 gene. Gene expression profiling with Affymetrix GeneChips in deaf homozygous (sh2/sh2) mice at 3 weeks and 3 months of age, and in age-matched, normal-hearing heterozygotes (+/sh2) identified only a few genes whose expression was affected by genotype, but a large number with age-associated changes in expression in both normal mice and sh2/sh2 homozygotes. Microarray data analyzed using Robust Multiarray Average identified Aim1, Dbi, and Tm4sf3 as genes with increased expression in sh2/sh2 homozygotes. These increases were confirmed by quantitative reverse transcription-polymerase chain reaction. Genes exhibiting altered expression with age encoded collagens and proteins involved in collagen maturation, extracellular matrix, and bone mineralization. These results identified potential cellular pathways associated with myosin XV defects, and age-associated molecular events that are likely to be involved in maturation of the cochlea and auditory function.

Calcium deposition and expression of bone modelling markers in the tympanic membrane following acute otitis media

BACKGROUND AND OBJECTIVES

In accordance with clinical findings, myringosclerosis develops after otitis media (OM) and paracentesis in an experimental setting. The pathogenesis of this phenomenon of calcification is poorly understood. As the calcification process and the sclerotic plaques of the drum mimics features of bone tissue, this study explores tympanic membrane calcium deposition in association with the expression of three bone modelling markers: osteopontin (OPN), osteoprotegerin (OPG) and osteonectin (ON). OPN is secreted by osteoblasts and is found at calcification sites, e.g. during pathological calcification in chronic OM. The cytokine OPG is an inhibitor of bone resorption and consequently bone remodelling. ON is a calcium binding glycoprotein necessary for the maintenance of bone mass and remodelling. It is found in bone matrix and synthesized by osteoblasts.

METHOD

A rat model of acute otitis media (AOM) caused by non-typeable Haemophilus influenzae was used. Four days following middle ear inoculation, a myringotomy was performed in six animals. Another group of ten animals was inoculated only. The drum was dissected in two animals from each group on day 4, 7, 14 and 28 post-inoculation, and the expression of OPN, OPG and ON was determined by immunohistochemistry. von Kossa staining determined the deposition of calcium and immune staining for CD68 identified macrophages.

RESULTS

Calcium depositions were initially accumulated in the cytoplasm of macrophages and dispersed in the connective tissue layers of the pars flaccida and tensa. Late accumulation occurred in the lamina propria of pars tensa, more extensively in myringotomized ears. OPN expression was found early in inflammatory cells including especially macrophages and late in pars tensa fibrocytes. OPG expression was initially located to inflammatory cells and late to pars tensa fibrocytes and the inner basal membrane of pars flaccida. Some ears displayed a marked pars flaccida expression of ON in the connective tissue matrix on early days and at the inner basal membrane on later days. The latter cases were from myringotomized ears. Otherwise, no apparent differences of marker expression occurred between myringotomized and non-myringotomized animals.

CONCLUSION

We conclude that osteopontin, osteoprotegerin and osteonectin are expressed by different cell types in the tympanic membrane during calcification in association with AOM, with or without myringotomy. These molecules may accordingly play a role in the pathogenesis of myringosclerosis, in which macrophages and fibrocytes appear as potential major players.

Entorhinal deafferentation induces upregulation of SPARC in the mouse hippocampus

SPARC is a matricellular protein that modulates cell-cell and cell-matrix interactions by virtue of its antiproliferative and counteradhesive properties. Here, we report the denervation-induced upregulation of SPARC mRNA and protein in the mouse hippocampus following transections of the entorhinal afferents. Northern blot analysis showed that SPARC mRNA was upregulated in a transient manner in the deafferented mouse hippocampus. In situ hybridization and immunohistochemistry confirmed the temporal upregulation of both SPARC mRNA and protein specifically in the denervated areas, which initiated at 7 days postlesion, reached the maximum at 15 as well as 30 days postlesion, and subsided towards normal levels by 60 days postlesion. Double labeling by either a combination of in situ hybridization for SPARC mRNA with immunohistochemistry for glial fibrillary acidic protein or double immunofluorescence staining for both proteins in the hippocampus revealed that SPARC-expressing cells are reactive astrocytes. In respect to the spatiotemporal alterations of SPARC expression in the denervated hippocampus, we suggest that SPARC may be involved in modulation of the denervation-induced plasticity processes such as glial cell proliferation, axonal sprouting and subsequent synaptogenesis in the hippocampus following entorhinal deafferentation.

Matricellular homologs in the foreign body response: hevin suppresses inflammation, but hevin and SPARC together diminish angiogenesis

Implanted foreign materials, used to restore or assist tissue function, elicit an initial acute inflammatory response followed by chronic fibrosis that leads to the entrapment of the biomaterial in a thick, poorly vascularized collagenous capsule. Matricellular proteins, secreted macromolecules that interact with extracellular matrix proteins but do not in themselves serve structural roles, have been identified as important mediators of the foreign body response that includes inflammation, angiogenesis, and collagen synthesis and assembly. In this report we delineate functions of hevin and SPARC, two homologs of the SPARC family of matricellular proteins, in the foreign body response. Despite their sequence similarity, hevin and SPARC mediate different aspects of this fibrotic response. Using mice with targeted gene deletions, we show that hevin is central to the progression of biomaterial-induced inflammation whereas SPARC regulates the formation of the collagenous capsule. Although vascular density within the capsule is unaltered in the absence of either protein, SPARC-hevin double-null capsules show substantially increased numbers of vessels, indicating compensatory functions for these two proteins in the inhibition of angiogenesis. These results provide important information for further development of implant technology.

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.

Gene expression profile of the mouse organ of Corti at the onset of hearing

We describe the generation of an expressed sequence tag (EST) database of the mouse organ of Corti (OC). Over 20,000 independent clones were isolated, analyzed, and grouped into 8690 unique gene clusters. A large pool of novel genes unique to the OC was identified. Sequence alignments frequently revealed alternatively spliced forms of known genes potentially relevant in the OC function. We have also electronically mapped a subset of OC mouse ESTs to several syntenic regions associated with human autosomal and recessive deafness, which may prove useful for the identification of new positional candidates for these human diseases. The EST dataset is available as an interactive Web-based public database at. This resource provides both a view of the profile of gene expression in the OC at the onset of hearing and a tool to identify novel genes of importance in hearing.

Hevin/SC1, a matricellular glycoprotein and potential tumor-suppressor of the SPARC/BM-40/Osteonectin family

Hevin is an extracellular matrix-associated, secreted glycoprotein belonging to the secreted protein acidic and rich in cysteine (SPARC) family of matricellular proteins. It contains three conserved structural domains that are implicated in the regulation of cell adhesion, migration, and proliferation. Hevin is expressed during embryogenesis and tissue remodeling and is especially prominent in brain and vasculature. Its down-regulation in a number of cancers and the possibility of its functional compensation by SPARC has led to recent interest in hevin as a tumor suppressor and regulator of angiogenesis.

Mutations in the gene encoding KIAA1199 protein, an inner-ear protein expressed in Deiters' cells and the fibrocytes, as the cause of nonsyndromic hearing loss

We report three possibly disease-causing point mutations in one of the inner-ear-specific genes, KIAA1199. We identified an R187C mutation in one family, an R187H mutation in two unrelated families, and an H783Y mutation in one sporadic case of nonsyndromic hearing loss. In situ hybridization indicated that the murine homolog of KIAA1199 mRNA is expressed specifically in Deiters' cells in the organ of Corti at postnatal day zero (P n) P0 before the onset of hearing, but expression in those cells disappears by day P7. The signal of KIAA1199 was also observed in fibrocytes of the spiral ligament and the spiral limbus through to P21, when the murine cochlea matures. Thus, the gene product may be involved in uptake of potassium ions or trophic factors with a particular role in auditory development. Although the R187C and R187H mutations did not appear to affect subcellular localization of the gene product in vitro, the H783Y mutation did present an unusual cytoplasmic distribution pattern that could underlie the molecular mechanism of hearing impairment. Our data bring attention to a novel candidate for hearing loss and indicate that screening of mutations in inner-ear-specific genes is likely to be an efficient approach to finding genetic elements responsible for deafness.

Cell adhesion molecules during inner ear and hair cell development, including notch and its ligands

Cellular adhesion plays a key role in a number of unique developmental events, including proliferation, cell fate, morphogenesis, neurite outgrowth, fasciculation, and synaptogensis. The number of families of molecules that can mediate cell adhesion and the number of members of each of those families has continued to increase over time. Moreover, the potential for the formation of different pairs of heterodimers with different binding specificities, and for both homo- and hetero-dimeric interactions suggest that a vast number of specific signaling events can be mediated through the expression of different combinations of adhesion factors at different developmental time points. By comparison with the number of known adhesion molecules and their potential effects, our understanding of the role of adhesion in ear development is extremely limited. The patterns of expression for some adhesion molecules have been determined for some aspects of inner ear development. Similarly, with a few exceptions, functional data to indicate the roles of these adhesion molecules are also lacking. However, a consideration of even the limited existing data must lead to the conclusion that adhesion molecules play key roles in all aspects of the development of the auditory system. Unique expression domains for different groups of adhesion molecules within the developing otocyst and ear strongly suggest a role in the determination of different cellular domains. Similarly, the specific expression of adhesion molecules on developing neurites and their target hair cells, suggests a key role for adhesion in the establishment of neuronal connections and possible the development of tonotopy. Finally, the recent demonstration that Cdh23 and Pcdh15 play specific roles in the formation of the hair cell stereociliary bundle provides compelling evidence for the importance of adhesion molecules in the development of stereocilia. With the imminent completion of the mouse genome, it seems likely that the number of adhesion molecules can soon be fixed and that it will then be possible to generate a more comprehensive map of expression of these molecules within the developing inner ear. At the same time, the generation of new transgenic and molecular technologies promises to provide researchers with new tools to examine the specific effects of different adhesion molecules during inner ear development.

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.