In silico analyses of mouse inner-ear transcripts

How your ears can tell what is hidden in your heart: wild-type transthyretin amyloidosis as potential cause of sensorineural hearing loss inelderly-AmyloDEAFNESS pilot study

BACKGROUND

Wild-type transthyretin amyloidosis (ATTRwt) is an age-related life-threatening condition. Prognosis is mainly dependent on cardiac involvement. Other organs and tissues may be affected. Their early recognition may increase awareness of physicians and positively affects the prognosis. Presbycusis is another age-related disorder. Whether this disease is associated to ATTRwt amyloidosis is unknown.

METHODS

Sixteen consecutive patients with confirmed diagnosis of ATTRwt amyloidosis at the Mondor Amyloidosis Network, France, underwent otoscopy and audiological tests including pure tone audiometry, speech reception threshold and speech discrimination score.

RESULTS

The mean age was 79 ± 5 years. All were male with an NYHA average of 2.5 ± 0.8. All the patients had sensorineural hearing loss that seemed to preexist to cardiac disorder with greater severity than expected for their age. For speech discrimination test, the mean speech reception threshold was 28 ± 15 dB and the mean speech discrimination score was 68 ± 16 at 40 dB. Ten patients (62.5%) failed to recognize 100% of the words. Compared to age-related expectations according to statistical distribution (ISO), hearing loss included all frequencies and was more severe in patients with ATTRwt amyloidosis.

CONCLUSIONS

These findings suggest that amyloid deposits could infiltrate the various anatomical structures of the inner ear. Description of specific audiologic pattern of ATTRwt amyloidosis might be proposed as a "red flag" and could help for early identification of patients who may be at high risk of ATTRwt amyloidosis as specific treatments are available.

Genome-wide analysis of binding sites and direct target genes of the orphan nuclear receptor NR2F1/COUP-TFI

Background

Identification of bona fide direct nuclear receptor gene targets has been challenging but essential for understanding regulation of organismal physiological processes.

Results

We describe a methodology to identify transcription factor binding sites and target genes in vivo by intersecting microarray data, computational binding site queries, and evolutionary conservation. We provide detailed experimental validation of each step and, as a proof of principle, utilize the methodology to identify novel direct targets of the orphan nuclear receptor NR2F1 (COUP-TFI). The first step involved validation of microarray gene expression profiles obtained from wild-type and COUP-TFI^−/− inner ear tissues. Secondly, we developed a bioinformatic tool to search for COUP-TFI DNA binding sites in genomes, using a classification-type Hidden Markov Model trained with 49 published COUP-TF response elements. We next obtained a ranked list of candidate in vivo direct COUP-TFI targets by integrating the microarray and bioinformatics analyses according to the degree of binding site evolutionary conservation and microarray statistical significance. Lastly, as proof-of-concept, 5 specific genes were validated for direct regulation. For example, the fatty acid binding protein 7 (Fabp7) gene is a direct COUP-TFI target in vivo because: i) we identified 2 conserved COUP-TFI binding sites in the Fabp7 promoter; ii) Fapb7 transcript and protein levels are significantly reduced in COUP-TFI^−/− tissues and in MEFs; iii) chromatin immunoprecipitation demonstrates that COUP-TFI is recruited to the Fabp7 promoter in vitro and in vivo and iv) it is associated with active chromatin having increased H3K9 acetylation and enrichment for CBP and SRC-1 binding in the newborn brain.

Conclusion

We have developed and validated a methodology to identify in vivo direct nuclear receptor target genes. This bioinformatics tool can be modified to scan for response elements of transcription factors, cis-regulatory modules, or any flexible DNA pattern.

Glucose transporter 5 is undetectable in outer hair cells and does not contribute to cochlear amplification

Glucose transporter 5 (Glut5) is a high-affinity fructose transporter. It was proposed to be a motor protein or part of the motor complex required for cochlear amplification in outer hair cells (OHCs). Here we show that, in contrast to previous reports, Glut5 is undetectable, and possibly absent, in OHCs harvested from wildtype mice. Further, Glut5-deficient mice display normal OHC morphology and motor function (i.e., nonlinear capacitance and electromotility) and normal cochlear sensitivity and frequency selectivity. We conclude that Glut5 is not required for OHC motility or cochlear amplification.

Ion channel gene expression in the inner ear

The ion channel genome is still being defined despite numerous publications on the subject. The ion channel transcriptome is even more difficult to assess. Using high-throughput computational tools, we surveyed all available inner ear cDNA libraries to identify genes coding for ion channels. We mapped over 100,000 expressed sequence tags (ESTs) derived from human cochlea, mouse organ of Corti, mouse and zebrafish inner ear, and rat vestibular end organs to Homo sapiens, Mus musculus, Danio rerio, and Rattus norvegicus genomes. A survey of EST data alone reveals that at least a third of the ion channel genome is expressed in the inner ear, with highest expression occurring in hair cell-enriched mouse organ of Corti and rat vestibule. Our data and comparisons with other experimental techniques that measure gene expression show that every method has its limitations and does not per se provide a complete coverage of the inner ear ion channelome. In addition, the data show that most genes produce alternative transcripts with the same spectrum across multiple organisms, no ion channel gene variants are unique to the inner ear, and many splice variants have yet to be annotated. Our high-throughput approach offers a qualitative computational and experimental analysis of ion channel genes in inner ear cDNA collections. A lack of data and incomplete gene annotations prevent both rigorous statistical analyses and comparisons of entire ion channelomes derived from different tissues and organisms.

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.

Predicting candidate genes for human deafness disorders: a bioinformatics approach

BACKGROUND

There are more than 50 genes for autosomal dominant and autosomal recessive nonsyndromic hereditary deafness that are yet to be cloned. The human genome sequence and expression profiles of transcripts in the inner ear have aided positional cloning approaches. The knowledge of protein interactions offers additional advantages in selecting candidate genes within a mapped region.

RESULTS

We have employed a bioinformatic approach to assemble the genes encoded by genomic regions that harbor various deafness loci. The genes were then in silico analyzed for their candidacy by expression pattern and ability to interact with other proteins. Such analyses have narrowed a list of 2400 genes from suspected regions of the genome to a manageable number of about 140 for further analysis.

CONCLUSION

We have established a list of strong candidate genes encoded by the regions linked to various nonsyndromic hereditary hearing loss phenotypes by using a novel bioinformatic approach. The candidates presented here provide a starting point for mutational analysis in well-characterized families along with genetic linkage to refine the loci. The advantages and shortcomings of this bioinformatic approach are discussed.

In silico assessment of gene function involved in cysteine biosynthesis in Arabidopsis: expression analysis of multiple isoforms of serine acetyltransferase

In plants, the inorganic sulfur is first fixed into cysteine by the cysteine biosynthetic pathway. This biosynthetic pathway of cysteine involves several enzymatic reactions. In Arabidopsis thaliana, multiple isoforms seem to participate in each enzymatic step for cysteine biosynthesis. To obtain more insights on the specific role of each isoform involved in the cysteine biosynthesis, in silico analysis of these isoforms using Arabidopsis expressed sequence tags (EST) database was carried out. This EST database analysis revealed distinct population distribution of ESTs among multiple isoforms, suggesting that each isoform has its particular expression pattern, presumably associated with its specific role in cysteine biosynthesis. As another in silico analysis, co-expression analysis of genes involved in sulfur metabolism in Arabidopsis was performed using a public transcriptome database of DNA microarrays. This co-expression analysis also suggested specific function and co-regulation of some isoform genes for cysteine biosynthesis by consideration on the clustering of co-expressed genes. From the results of sensitivity to feedback regulation, subcellular localization and expression of mRNA analyses, each serine acetyltransferase (SATase) isoform seems to have its specific role for cysteine biosynthesis. Similar expression patterns were observed between the experimental results of expression data for SATase isoforms and the in silico results of "digital northern" analysis using EST database.

Assessment of differential gene expression in vestibular epithelial cell types using microarray analysis

Current global gene expression techniques allow the evaluation and comparison of the expression of thousands of genes in a single experiment, providing a tremendous amount of information. However, the data generated by these techniques are context-dependent, and minor differences in the individual biological samples, methodologies for RNA acquisition, amplification, hybridization protocol and gene chip preparation, as well as hardware and analysis software, lead to poor correlation between the results. One of the significant difficulties presently faced is the standardization of the protocols for the meaningful comparison of results. In the inner ear, the acquisition of RNA from individual cell populations remains a challenge due to the high density of the different cell types and the paucity of tissue. Consequently, laser capture microdissection was used to selectively collect individual cells and regions of cells from cristae ampullares followed by extraction of total RNA and amplification to amounts sufficient for high throughput analysis. To demonstrate hair cell-specific gene expression, myosin VIIA, calmodulin and alpha9 nicotinic acetylcholine receptor subunit mRNAs were amplified using reverse transcription-polymerase chain reaction (RT-PCR). To demonstrate supporting cell-specific gene expression, cyclin-dependent kinase inhibitor p27kip1 mRNA was amplified using RT-PCR. Subsequent experiments with alpha9 RT-PCR demonstrated phenotypic differences between type I and type II hair cells, with expression only in type II hair cells. Using the laser capture microdissection technique, microarray expression profiling demonstrated 408 genes with more than a five-fold difference in expression between the hair cells and supporting cells, of these 175 were well annotated. There were 97 annotated genes with greater than a five-fold expression difference in the hair cells relative to the supporting cells, and 78 annotated genes with greater than a five-fold expression difference in the supporting cells relative to the hair cells.

Selective acquisition of individual cell types in the vestibular periphery for molecular biology studies

OBJECTIVES

To develop a method for characterizing the transcriptome of individual cell types in the inner ear sensory epithelia.

STUDY DESIGN

We employed the technique of laser capture microdissection to obtain enriched populations of hair cells and supporting cells. The respective mRNAs were extracted, reverse transcribed, and amplified using PCR.

RESULTS

We were able to isolate RNAs with good integrity from enriched cell populations obtained with laser capture microscopy and amplify specific mRNA targets.

CONCLUSIONS

We can now investigate the molecular differences between the different cell types in the inner ear sensory epithelia as identified by morphological criteria.

SIGNIFICANCE

Analysis of gene expression profiles in the inner ear cell types has been hampered by the small size of this tissue and by the compact histoarchitecture of the sensory epithelia; however, the present technique offers new possibilities for the analysis of transcriptomes in the vestibular periphery using available high-throughput gene expression analysis methods.

Targeting hearing genes in mice

The rate of identification of genes for hearing has clearly outpaced the rate of determination of the functions of these genes' products. The use of transgenic and knock-out mouse models is a powerful approach to the elucidation of gene function in the ear. A large number of gene-targeted mice with auditory defects have recently been created and characterized, and nine independent mouse lines in which Cre recombinase activity begins to be expressed during early embryonic development of the ear or is specifically expressed in hair cells during postnatal development will be useful for ear-specific gene manipulation when combined with mouse lines that have loxP sites flanking the genes of interest. Existing gene-trapped embryonic stem (ES) cells and existing targeting constructs are readily available; new targeting constructs can easily be created by modifying bacterial artificial chromosomes and using them to directly transfect and screen ES cells; and N-ethyl-N-nitrosourea mutagenesis of ES cells can create point mutations in specific genes. To minimize variation in hearing phenotypes and avoid undesired hearing defects, mutant mice in the common gene-targeting background strains (129 and C57BL/6) should be transferred into congenic CBA/CaJ, a strain with "gold standard" normal hearing. Valuable mutant strains can be maintained, distributed, and cryopreserved in one of four NIH-sponsored Mutant Mouse Regional Resource Centers. Targeting hearing genes in mice will provide unprecedented opportunities for collaboration and new directions in the hearing research community.

Identification of unique transcripts from a mouse full-length, subtracted inner ear cDNA library

A small-scale full-length library construction approach was developed to facilitate production of a mouse full-length cDNA encyclopedia representing approximately 250 enriched, normalized, and/or subtracted cDNA libraries. One library produced using this approach was a subtracted adult mouse inner ear cDNA library (sIEa). The average size of the inserts was approximately 2.5 kb, with the majority ranging from 0.5 to 7.0 kb. From this library 22,574 sequence reads were obtained from 15,958 independent clones. Sequencing and chromosomal localization established 5240 clusters, with 1302 clusters being unique and 359 representing new ESTs. Our sIEa library contributed 56.1% of the 7773 nonredundant Unigene clusters associated with the four mouse inner ear libraries in the NCBI dbEST. Based on homologous chromosomal regions between human and mouse, we identified 1018 UniGene clusters associated with the deafness locus critical regions. Of these, 59 clusters were found only in our sIEa library and represented approximately 50% of the identified critical regions.

An in silico assessment of gene function and organization of the phenylpropanoid pathway metabolic networks in Arabidopsis thaliana and limitations thereof

The Arabidopsis genome sequencing in 2000 gave to science the first blueprint of a vascular plant. Its successful completion also prompted the US National Science Foundation to launch the Arabidopsis 2010 initiative, the goal of which is to identify the function of each gene by 2010. In this study, an exhaustive analysis of The Institute for Genomic Research (TIGR) and The Arabidopsis Information Resource (TAIR) databases, together with all currently compiled EST sequence data, was carried out in order to determine to what extent the various metabolic networks from phenylalanine ammonia lyase (PAL) to the monolignols were organized and/or could be predicted. In these databases, there are some 65 genes which have been annotated as encoding putative enzymatic steps in monolignol biosynthesis, although many of them have only very low homology to monolignol pathway genes of known function in other plant systems. Our detailed analysis revealed that presently only 13 genes (two PALs, a cinnamate-4-hydroxylase, a p-coumarate-3-hydroxylase, a ferulate-5-hydroxylase, three 4-coumarate-CoA ligases, a cinnamic acid O-methyl transferase, two cinnamoyl-CoA reductases) and two cinnamyl alcohol dehydrogenases can be classified as having a bona fide (definitive) function; the remaining 52 genes currently have undetermined physiological roles. The EST database entries for this particular set of genes also provided little new insight into how the monolignol pathway was organized in the different tissues and organs, this being perhaps a consequence of both limitations in how tissue samples were collected and in the incomplete nature of the EST collections. This analysis thus underscores the fact that even with genomic sequencing, presumed to provide the entire suite of putative genes in the monolignol-forming pathway, a very large effort needs to be conducted to establish actual catalytic roles (including enzyme versatility), as well as the physiological function(s) for each member of the (multi)gene families present and the metabolic networks that are operative. Additionally, one key to identifying physiological functions for many of these (and other) unknown genes, and their corresponding metabolic networks, awaits the development of technologies to comprehensively study molecular processes at the single cell level in particular tissues and organs, in order to establish the actual metabolic context.