Induction of cell proliferation and beta-catenin expression in rat utricles in vitro

Toward a systems biology of mouse inner ear organogenesis: gene expression pathways, patterns and network analysis

We describe the most comprehensive study to date on gene expression during mouse inner ear (IE) organogenesis. Samples were microdissected from mouse embryos at E9-E15 in half-day intervals, a period that spans all of IE organogenesis. These included separate dissections of all discernible IE substructures such as the cochlea, utricle, and saccule. All samples were analyzed on high density expression microarrays under strict statistical filters. Extensive confirmatory tests were performed, including RNA in situ hybridizations. More than 5000 genes significantly varied in expression according to developmental stage, tissue, or both and defined 28 distinct expression patterns. For example, upregulation of 315 genes provided a clear-cut "signature" of early events in IE specification. Additional, clear-cut, gene expression signatures marked specific structures such as the cochlea, utricle, or saccule throughout late IE development. Pathway analysis identified 53 signaling cascades enriched within the 28 patterns. Many novel pathways, not previously implicated in IE development, including beta-adrenergic, amyloid, estrogen receptor, circadian rhythm, and immune system pathways, were identified. Finally, we identified positional candidate genes in 54 uncloned nonsyndromic human deafness intervals. This detailed analysis provides many new insights into the spatial and temporal genetic specification of this complex organ system.

Thyroid hormone receptor alpha1 directly controls transcription of the beta-catenin gene in intestinal epithelial cells

Thyroid hormones, T3 and T4, are known regulators of intestine development. The best characterized example is the remodeling of the gastrointestinal tract during amphibian metamorphosis. Thyroid hormones act via nuclear receptors, the TRs, which are T3-dependent transcription factors. We previously showed that intestinal epithelial cell proliferation is controlled by thyroid hormones and the TRalpha gene. To analyze the mechanisms responsible, we studied the expression of genes belonging to and/or activated by the Wnt/beta-catenin pathway, a major actor in the control of physiological and pathological epithelial proliferation in the intestine. We show that T3-TRalpha1 controls the transcription of the beta-catenin gene in an epithelial cell-autonomous way. This is parallel to positive regulation of proliferation-controlling genes such as type D cyclins and c-myc, known targets of the Wnt/beta-catenin. In addition, we show that the regulation of the beta-catenin gene is direct, as TR binds in vitro and in chromatin in vivo to a specific thyroid hormone-responsive element present in intron 1 of this gene. This is the first report concerning in vivo transcriptional control of the beta-catenin gene. As Wnt/beta-catenin plays a crucial role in intestinal tumorigenesis, our observations open a new perspective on the study of TRs as potential tumor inducers.

Disruption and restoration of cell-cell junctions in mouse vestibular epithelia following aminoglycoside treatment

The intracellular junction complexes, which consist of tight junctions (TJ), adherens junctions (AJ), and desmosomes, mediate cell-cell adhesion in epithelial cells. E-cadherin, which is a major component of AJ, plays a role not only in the maintenance of cell-cell junctions, but also in repressing cell proliferation. In this study, we examined changes of E-cadherin expression in mouse vestibular epithelia following local application of neomycin using immunohistochemistry and western blotting, and morphology of cell-cell junctions by transmission electron microscopy (TEM). Immunohistochemistry and western blotting revealed down-expression of E-cadherin and its consecutive recovery. TEM demonstrated temporal disruption of cell-cell junctions. Morphology of cell-cell junctions was more rapidly restored than recovery of E-cadherin expression. Transient disruption of cell-cell junctions and down-expression of E-cadherin is a rational response for the deletion of dying hair cells, and may be associated with a limited capacity for cell proliferations in mammalian vestibular epithelia following their rapid restoration.

In silico analysis of 2085 clones from a normalized rat vestibular periphery 3' cDNA library

The inserts from 2400 cDNA clones isolated from a normalized Rattus norvegicus vestibular periphery cDNA library were sequenced and characterized. The Wackym-Soares vestibular 3' cDNA library was constructed from the saccular and utricular maculae, the ampullae of all three semicircular canals and Scarpa's ganglia containing the somata of the primary afferent neurons, microdissected from 104 male and female rats. The inserts from 2400 randomly selected clones were sequenced from the 5' end. Each sequence was analyzed using the BLAST algorithm compared to the Genbank nonredundant, rat genome, mouse genome and human genome databases to search for high homology alignments. Of the initial 2400 clones, 315 (13%) were found to be of poor quality and did not yield useful information, and therefore were eliminated from the analysis. Of the remaining 2085 sequences, 918 (44%) were found to represent 758 unique genes having useful annotations that were identified in databases within the public domain or in the published literature; these sequences were designated as known characterized sequences. 1141 sequences (55%) aligned with 1011 unique sequences had no useful annotations and were designated as known but uncharacterized sequences. Of the remaining 26 sequences (1%), 24 aligned with rat genomic sequences, but none matched previously described rat expressed sequence tags or mRNAs. No significant alignment to the rat or human genomic sequences could be found for the remaining 2 sequences. Of the 2085 sequences analyzed, 86% were singletons. The known, characterized sequences were analyzed with the FatiGO online data-mining tool (http://fatigo.bioinfo.cnio.es/) to identify level 5 biological process gene ontology (GO) terms for each alignment and to group alignments with similar or identical GO terms. Numerous genes were identified that have not been previously shown to be expressed in the vestibular system. Further characterization of the novel cDNA sequences may lead to the identification of genes with vestibular-specific functions. Continued analysis of the rat vestibular periphery transcriptome should provide new insights into vestibular function and generate new hypotheses. Physiological studies are necessary to further elucidate the roles of the identified genes and novel sequences in vestibular function.

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.