bottom-up-shotgun-proteomics-to-identify-comprehensive-cochlear

Bottom-up and Shotgun Proteomics to Identify a Comprehensive Cochlear Proteome

Proteomics is a commonly used approach that can provide insights into complex biological systems. The cochlear sensory epithelium contains receptors that ...

University of South Florida

Signal coding by the receptor and neuronal cells of the auditory system involves various ion channels that modulate a sound stimulus. The genes that encode a number of these ion channels and their accessory subunits are presently unknown for channels found in the sensory epithelium and cochlear nerve. Among these genes are those that encode delayed rectifier and transient type potassium channels found in both the sensory cells and the ganglion. Here, we report the cloning and developmental expression of Shaker family members that include cKv1.2, cKv1.3, cKv1.5, and the Shaker-related cGMP-gated potassium channel cKCNA10. Clones were obtained by screening a chicken embryonic cochlea cDNA library using, as a probe, a mixture of two DNA fragments of cKv1.2 and cKv1.3 obtained by the reverse transcription polymerase chain reaction (RT-PCR). Sequence analysis revealed chicken homologues of Kv1.2, Kv1.3, Kv1.5 and cGMP-gated potassium channels with a deduced amino acid homology of 96-98%, 82-84%, 67-71% and 67-79% to correspondent mammalian homologues. During development of chicken inner ear, RT-PCR studies show expression of cKv1.2, cKv1.3 and cKv1.5 as early as Embryonic Day (ED) 3, while cKCNA10 was detected at low levels beginning on ED6 and was highly expressed by ED9. Additionally, analysis of expression in different parts of the cochlea showed that these genes were co-expressed in different regions of the cochlea, including the cochlear ganglion, sensory epithelium, lagena, and tegmentum. This expression pattern suggests the potential for the formation of heteromeric channels from the corresponding alpha-subunits in these various tissues.

Cloning and developmental expression of Shaker potassium channels in the cochlea of the chicken.

Receptor cells of the auditory and vestibular end organs of vertebrates acquire various types of potassium channels during development. Their expression and kinetics can differ along the tonotopic axis as well as in different cell types of the sensory epithelium. These variations can play a crucial role in modulating sensory transduction and cochlear tuning. Whole-cell tight-seal recordings of isolated hair cells revealed the presence of an arachidonic acid-sensitive A-type channel in the short (outer) hair cells of the chicken cochlea. This polyunsaturated fatty acid blocked the A-current, thereby increasing the amplitude and duration of the voltage response in these cells. We identified the gene encoding this channel as belonging to a member of the Shal subfamily, Kv4.2. Expression of the recombinant channel shows half-activation and inactivation potentials shifted to more positive values relative to native channels, suggesting that the native channel is coexpressed with an accessory subunit. RT-PCR revealed that transcription begins early in development, whereas in situ hybridization showed mRNA expression limited to the intermediate and short hair cells located in specific regions of the adult cochlea. Additional localization, using immunofluorescent staining, revealed clustering in apical-lateral regions of the receptor cell as well as in the cochlear ganglion. These experiments provide evidence that in addition to membrane proteins modulating excitation in these receptor cells, fatty acids contribute to the coding of auditory stimuli via these channels.

Identification and localization of an arachidonic acid-sensitive potassium channel in the cochlea.

The acquisition of ion channels is critical to the formation of neuronal pathways in the peripheral and central nervous systems. This study describes the different types of inward currents (Ii) recorded from the soma of isolated cochleovestibular ganglion (CVG) cells of the embryonic chicken, Gallus gallus. Cells were isolated for whole-cell tight-seal recording from embryonic day (ED) 3, an age when the CVG is a cell cluster, to ED 9, an age when the cochlear and vestibular ganglia (CG, VG) are distinct structures. Results show Na+ and Ca2+ currents (INa and ICa) are acquired by ED 3, although INa dominates with greater density levels that peak by ED 6-7 in VG neurons. In the CG, INa acquisition is slower, reaching peak values by ED 8-9. Isolation of ICa, using Ba2+ as the charge carrier, showed both transient (IBaT)- and sustained (IBaL)-type currents on ED 3. Unlike INa, IBa density varied with age and ganglion. Total IBa increased steadily, showing a decline only in CG cells on ED 8-9 as a result of a decrease in IBaT. IBaL density increased over time, reaching a maximum on ED 6-7 in VG cells, followed by a decline on ED 8-9. In comparison, IBaL in CG neurons, did not increase significantly beyond mean values measured on ED 5. The early onset of these currents and the variations in Ca2+ channel expression between the ganglia suggests that intracellular signals relevant to phenotypic differentiation begin within these early time frames.

Survey of inward ionic currents acquired by the cochleovestibular ganglion of the early-aged embryonic chick.

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.

Ion channel gene expression in the inner ear.

The structural phenotype of neural connections in the auditory brainstem is sculpted by spontaneous and stimulus-induced neural activities during development. However, functional and molecular mechanisms of spontaneous action potentials (SAPs) in the developing cochlea are unknown. Additionally, it is unclear how regenerating hair cells establish their neural ranking in the constellation of neurons in the brainstem. We have demonstrated that a transient Ca(2+) current produced by the Ca(v)3.1 channel is expressed early in development to initiate spontaneous Ca(2+) spikes. Ca(v)1.3 currents, typical of mature hair cells, appeared later in development. Moreover, there is a surprising disappearance of the Ca(v)3.1 current that coincides with the attenuation of the transient Ca(2+) current as the electrical properties of hair cells transition to the mature phenotype. Remarkably, this process is recapitulated during hair-cell regeneration, suggesting that the transient expression of Ca(v)3.1 and the ensuing SAPs are signatures of hair cell development and regeneration.

Development and regeneration of hair cells share common functional features.

Functional proteomics comprises a wide range of technologies for the identification of novel protein-protein interactions and biological markers. Studies of protein-protein interactions have gained from the development of techniques and technologies such as immunoprecipitation, preparative two-dimensional (2-D) gel electrophoresis for peptide mass fingerprinting (PMF), using matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry, and liquid chromatography-tandem mass spectrometry (LC-MS/MS). These applications enabled the discovery of putative protein partners without a priori knowledge of which one(s) might be relevant. Here, we report the methods by which membrane proteins are isolated from cochlear tissues and prepared for identification by mass spectrometry techniques.

The use of 2-D gels to identify novel protein-protein interactions in the cochlea.

Genomics has provided us with vast amounts of data and thus, the challenge to identify and characterize gene products. Proteomics analysis, using methods such as yeast two-hybrid screenings, isoelectric focusing, and mass spectroscopy, generate potentially useful information. To determine functional relationships between and among proteins, however, the initial data for putative protein interactions must first be validated. One technique, which is considered the gold standard, is coimmunoprecipitation.

In vivo verification of protein interactions in the inner ear by coimmunoprecipitation.

Proteomic analysis of sensory organs such as the cochlea is challenging due to its small size and difficulties with membrane protein isolation. Mass spectrometry in conjunction with separation methods can provide a more comprehensive proteome, because of the ability to enrich protein samples, detect hydrophobic proteins, and identify low abundant proteins by reducing the proteome dynamic range. GELFrEE as well as different separation and digestion techniques were combined with FASP and nanoLC-MS/MS to obtain an in-depth proteome analysis of cochlear sensory epithelium from 30-day-old mice. Digestion with LysC/trypsin followed by SCX fractionation and multiple nanoLC-MS/MS analyses identified 3773 proteins with a 1% FDR. Of these, 694 protein IDs were in the plasmalemma. Protein IDs obtained by combining outcomes from GELFrEE/LysC/trypsin with GELFrEE/trypsin/trypsin generated 2779 proteins, of which 606 additional proteins were identified using the GELFrEE/LysC/trypsin approach. Combining results from the different techniques resulted in a total of 4620 IDs, including a number of previously unreported proteins. GO analyses showed high expression of binding and catalytic proteins as well as proteins associated with metabolism. The results show that the application of multiple techniques is needed to provide an exhaustive proteome of the cochlear sensory epithelium that includes many membrane proteins. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium with the data set identifier PXD000231.

Article	Year
Cloning and developmental expression of Shaker potassium channels in the cochlea of the chicken. Brain research. Molecular brain research\| PubMed ID: 14969738	2004
Identification and localization of an arachidonic acid-sensitive potassium channel in the cochlea. The Journal of neuroscience : the official journal of the Society for Neuroscience\| PubMed ID: 15254081	2004
Survey of inward ionic currents acquired by the cochleovestibular ganglion of the early-aged embryonic chick. Journal of neuroscience research\| PubMed ID: 16447282	2006
Ion channel gene expression in the inner ear. Journal of the Association for Research in Otolaryngology : JARO\| PubMed ID: 17541769	2007
Development and regeneration of hair cells share common functional features. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 18025474	2007
The use of 2-D gels to identify novel protein-protein interactions in the cochlea. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 18839353	2009
In vivo verification of protein interactions in the inner ear by coimmunoprecipitation. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 18839355	2009
In-depth proteomic analysis of mouse cochlear sensory epithelium by mass spectrometry. Journal of proteome research\| PubMed ID: 23721421	2013

Bernd H.A. Sokolowski

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