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Baxi AB, Nemes P, Moody SA. Time-resolved quantitative proteomic analysis of the developing Xenopus otic vesicle reveals putative congenital hearing loss candidates. iScience 2023; 26:107665. [PMID: 37670778 PMCID: PMC10475516 DOI: 10.1016/j.isci.2023.107665] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/16/2023] [Accepted: 08/14/2023] [Indexed: 09/07/2023] Open
Abstract
Over 200 genes are known to underlie human congenital hearing loss (CHL). Although transcriptomic approaches have identified candidate regulators of otic development, little is known about the abundance of their protein products. We used a multiplexed quantitative mass spectrometry-based proteomic approach to determine protein abundances over key stages of Xenopus otic morphogenesis to reveal a dynamic expression of cytoskeletal, integrin signaling, and extracellular matrix proteins. We correlated these dynamically expressed proteins to previously published lists of putative downstream targets of human syndromic hearing loss genes: SIX1 (BOR syndrome), CHD7 (CHARGE syndrome), and SOX10 (Waardenburg syndrome). We identified transforming growth factor beta-induced (Tgfbi), an extracellular integrin-interacting protein, as a putative target of Six1 that is required for normal otic vesicle formation. Our findings demonstrate the application of this Xenopus dataset to understanding the dynamic regulation of proteins during otic development and to discovery of additional candidates for human CHL.
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Affiliation(s)
- Aparna B. Baxi
- Department of Anatomy and Cell Biology, The George Washington University School of Medicine and Health Sciences, Washington, DC 20052, USA
| | - Peter Nemes
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
| | - Sally A. Moody
- Department of Anatomy and Cell Biology, The George Washington University School of Medicine and Health Sciences, Washington, DC 20052, USA
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2
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Jones M, Kovacevic B, Ionescu CM, Wagle SR, Quintas C, Wong EYM, Mikov M, Mooranian A, Al-Salami H. The applications of Targeted Delivery for Gene Therapies in Hearing Loss. J Drug Target 2023:1-22. [PMID: 37211674 DOI: 10.1080/1061186x.2023.2216900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 12/07/2022] [Accepted: 04/09/2023] [Indexed: 05/23/2023]
Abstract
Gene therapies are becoming more abundantly researched for use in a multitude of potential treatments, including for hearing loss. Hearing loss is a condition which impacts an increasing number of the population each year, with significant burdens associated. As such, this review will present the concept that delivering a gene effectively to the inner ear may assist in expanding novel treatment options and improving patient outcomes. Historically, several drawbacks have been associated with the use of gene therapies, some of which may be overcome via targeted delivery. Targeted delivery has the potential to alleviate off-target effects and permit a safer delivery profile. Viral vectors have often been described as a delivery method, however, there is an emerging depiction of the potential for nanotechnology to be used. Resulting nanoparticles may also be tuned to allow for targeted delivery. Therefore, this review will focus on hearing loss, gene delivery techniques and inner ear targets, including highlighting promising research. Targeted delivery is a key concept to permitting gene delivery in a safe effective manner, however, further research is required, both in the determination of genes to use in functional hearing recovery and formulating nanoparticles for targeted delivery.
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Affiliation(s)
- Melissa Jones
- The Biotechnology and Drug Development Research Laboratory, Curtin Medical School & Curtin Health Innovation Research Institute, Curtin University, Bentley 6102, Perth, Western Australia, Australia
- Hearing Therapeutics Department, Ear Science Institute Australia, Queen Elizabeth II Medical Centre, Nedlands 6009, Perth, Western Australia, Australia
| | - Bozica Kovacevic
- The Biotechnology and Drug Development Research Laboratory, Curtin Medical School & Curtin Health Innovation Research Institute, Curtin University, Bentley 6102, Perth, Western Australia, Australia
- Hearing Therapeutics Department, Ear Science Institute Australia, Queen Elizabeth II Medical Centre, Nedlands 6009, Perth, Western Australia, Australia
| | - Corina Mihaela Ionescu
- The Biotechnology and Drug Development Research Laboratory, Curtin Medical School & Curtin Health Innovation Research Institute, Curtin University, Bentley 6102, Perth, Western Australia, Australia
- Hearing Therapeutics Department, Ear Science Institute Australia, Queen Elizabeth II Medical Centre, Nedlands 6009, Perth, Western Australia, Australia
| | - Susbin Raj Wagle
- The Biotechnology and Drug Development Research Laboratory, Curtin Medical School & Curtin Health Innovation Research Institute, Curtin University, Bentley 6102, Perth, Western Australia, Australia
- Hearing Therapeutics Department, Ear Science Institute Australia, Queen Elizabeth II Medical Centre, Nedlands 6009, Perth, Western Australia, Australia
| | - Christina Quintas
- School of human sciences, University of Western Australia, Crawley 6009, Perth, Western Australia, Australia
| | - Elaine Y M Wong
- Hearing Therapeutics Department, Ear Science Institute Australia, Queen Elizabeth II Medical Centre, Nedlands 6009, Perth, Western Australia, Australia
| | - Momir Mikov
- Department of Pharmacology, Toxicology and Clinical Pharmacology, Faculty of Medicine, University of Novi Sad, Hajduk Veljkova 3, 21101 Novi Sad, Serbia
| | - Armin Mooranian
- The Biotechnology and Drug Development Research Laboratory, Curtin Medical School & Curtin Health Innovation Research Institute, Curtin University, Bentley 6102, Perth, Western Australia, Australia
- Hearing Therapeutics Department, Ear Science Institute Australia, Queen Elizabeth II Medical Centre, Nedlands 6009, Perth, Western Australia, Australia
- School of Pharmacy, University of Otago, Dunedin, Otago, New Zealand
| | - Hani Al-Salami
- The Biotechnology and Drug Development Research Laboratory, Curtin Medical School & Curtin Health Innovation Research Institute, Curtin University, Bentley 6102, Perth, Western Australia, Australia
- Hearing Therapeutics Department, Ear Science Institute Australia, Queen Elizabeth II Medical Centre, Nedlands 6009, Perth, Western Australia, Australia
- Medical School, University of Western Australia, Perth, Western Australia, Australia
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3
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Honda T, Kawasaki N, Yanagihara R, Tamura R, Murakami K, Ichimiya T, Matsumoto N, Nishihara S, Yamamoto K. Involvement of cochlin binding to sulfated heparan sulfate/heparin in the pathophysiology of autosomal dominant late-onset hearing loss (DFNA9). PLoS One 2022; 17:e0268485. [PMID: 35901072 PMCID: PMC9333281 DOI: 10.1371/journal.pone.0268485] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 05/01/2022] [Indexed: 11/30/2022] Open
Abstract
Late-onset non-syndromic autosomal dominant hearing loss 9 (DFNA9) is a hearing impairment caused by mutations in the coagulation factor C homology gene (COCH). COCH encodes for cochlin, a major component of the cochlear extracellular matrix. Though biochemical and genetic studies have characterized the properties of wild-type and mutated cochlins derived from DFNA9, little is known about the underlying pathogenic mechanism. In this study, we established a cochlin reporter cell, which allowed us to monitor the interaction of cochlin with its ligand(s) by means of a β-galactosidase assay. We found a class of highly sulfated glycosaminoglycans (GAGs), heparin, that were selectively bound to cochlin. The interaction was distinctly abrogated by N-desulfation, but not by 2-O- or 6-O-desulfation. The binding of cochlin to GAG was diminished by all of the point mutations found in DFNA9 patients. Through GAG composition analysis and immunostaining using mouse cochlin/immunoglobulin-Fc fusion protein, we identified moderately sulfated GAGs in mouse cochlea tissue; this implies that cochlin binds to such sulfated GAGs in the cochlea. Since GAGs play an important role in cell growth and survival as co-receptors of signal transduction mechanisms, the interaction of cochlin with GAGs in the extracellular matrix could aid the pathological research of autosomal dominant late-onset hearing loss in DFNA9.
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Affiliation(s)
- Tomoko Honda
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Norihito Kawasaki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Rei Yanagihara
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Ryo Tamura
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Karin Murakami
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Tomomi Ichimiya
- Department of Bioinformatics, Graduate School of Engineering, Soka University, Hachioji, Tokyo, Japan
| | - Naoki Matsumoto
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Shoko Nishihara
- Department of Bioinformatics, Graduate School of Engineering, Soka University, Hachioji, Tokyo, Japan
- Glycan & Life System Integration Center (GaLSIC), Soka University, Hachioji, Tokyo, Japan
| | - Kazuo Yamamoto
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
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4
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Kaderbay A, Berger F, Bouamrani A, Bidart M, Petre G, Baguant A, Giraud L, Schmerber S. Perilymph metabolomic and proteomic MALDI-ToF profiling with porous silicon chips: a proof-of-concept study. Hear Res 2022; 417:108457. [DOI: 10.1016/j.heares.2022.108457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 01/16/2022] [Accepted: 01/27/2022] [Indexed: 11/30/2022]
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5
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Darville LNF, Sokolowski BHA. Label-free quantitative mass spectrometry analysis of differential protein expression in the developing cochlear sensory epithelium. Proteome Sci 2018; 16:15. [PMID: 30127667 PMCID: PMC6091194 DOI: 10.1186/s12953-018-0144-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 07/26/2018] [Indexed: 12/27/2022] Open
Abstract
Background The sensory epithelium of the inner ear converts the mechanical energy of sound to electro-chemical energy recognized by the central nervous system. This process is mediated by receptor cells known as hair cells that express proteins in a timely fashion with the onset of hearing. Methods The proteomes of 3, 14, and 30 day-old mice cochlear sensory epithelia were revealed, using label-free quantitative mass spectrometry (LTQ-Orbitrap). Statistical analysis using a one-way ANOVA followed by Bonferroni’s post-hoc test was used to show significant differences in protein expression. Ingenuity Pathway Analysis was used to observe networks of differentially expressed proteins, their biological processes, and associated diseases, while Cytoscape software was used to determine putative interactions with select biomarker proteins. These candidate biomarkers were further verified using Western blotting, while coimmunoprecipitation was used to verify putative partners determined using bioinformatics. Results We show that a comparison across all three proteomes shows that there are 447 differentially expressed proteins, with 387 differentially expressed between postnatal day 3 and 30. Ingenuity Pathway Analysis revealed ~ 62% of postnatal day 3 downregulated proteins are involved in neurological diseases. Several proteins are expressed exclusively on P3, including Parvin α, Drebrin1 (Drb1), Secreted protein acidic and cysteine rich (SPARC), Transmembrane emp24 domain-containing protein 10 (Tmed10). Coimmunoprecipitations showed that Parvin and SPARC interact with integrin-linked protein kinase and the large conductance calcium-activated potassium channel, respectively. Conclusions Quantitative mass spectrometry revealed the identification of numerous differentially regulated proteins over three days of postnatal development. These data provide insights into functional pathways regulating normal sensory and supporting cell development in the cochlea that include potential biomarkers. Interacting partners of two of these markers suggest the importance of these complexes in regulating cellular structure and synapse development. Electronic supplementary material The online version of this article (10.1186/s12953-018-0144-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lancia N F Darville
- Morsani College of Medicine, Department of Otolaryngology-HNS, University of South Florida, 12901 Bruce B. Downs Blvd, Tampa, FL 33612 USA
| | - Bernd H A Sokolowski
- Morsani College of Medicine, Department of Otolaryngology-HNS, University of South Florida, 12901 Bruce B. Downs Blvd, Tampa, FL 33612 USA
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6
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Shao Y, Yin X, Kang D, Shen B, Zhu Z, Li X, Li H, Xie L, Wang G, Liang Y. An integrated strategy for the quantitative analysis of endogenous proteins: A case of gender-dependent expression of P450 enzymes in rat liver microsome. Talanta 2017; 170:514-522. [DOI: 10.1016/j.talanta.2017.04.050] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Revised: 04/14/2017] [Accepted: 04/21/2017] [Indexed: 12/17/2022]
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7
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Schmitt HA, Pich A, Schröder A, Scheper V, Lilli G, Reuter G, Lenarz T. Proteome Analysis of Human Perilymph Using an Intraoperative Sampling Method. J Proteome Res 2017; 16:1911-1923. [DOI: 10.1021/acs.jproteome.6b00986] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Heike A. Schmitt
- Department
of Otolaryngology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
- Cluster
of Excellence of the German Research Foundation (DFG; “Deutsche
Forschungsgemeinschaft”) “Hearing4all”, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Andreas Pich
- Core
Facility Proteomics, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Anke Schröder
- Core
Facility Proteomics, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Verena Scheper
- Department
of Otolaryngology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
- Cluster
of Excellence of the German Research Foundation (DFG; “Deutsche
Forschungsgemeinschaft”) “Hearing4all”, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Giorgio Lilli
- Department
of Otolaryngology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
- Cluster
of Excellence of the German Research Foundation (DFG; “Deutsche
Forschungsgemeinschaft”) “Hearing4all”, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Günter Reuter
- Department
of Otolaryngology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
- Cluster
of Excellence of the German Research Foundation (DFG; “Deutsche
Forschungsgemeinschaft”) “Hearing4all”, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Thomas Lenarz
- Department
of Otolaryngology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
- Cluster
of Excellence of the German Research Foundation (DFG; “Deutsche
Forschungsgemeinschaft”) “Hearing4all”, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
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8
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Global Analysis of Protein Expression of Inner Ear Hair Cells. J Neurosci 2016; 37:1320-1339. [PMID: 28039372 DOI: 10.1523/jneurosci.2267-16.2016] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Revised: 11/29/2016] [Accepted: 12/19/2016] [Indexed: 11/21/2022] Open
Abstract
The mammalian inner ear (IE) subserves auditory and vestibular sensations via highly specialized cells and proteins. Sensory receptor hair cells (HCs) are necessary for transducing mechanical inputs and stimulating sensory neurons by using a host of known and as yet unknown protein machinery. To understand the protein composition of these unique postmitotic cells, in which irreversible protein degradation or damage can lead to impaired hearing and balance, we analyzed IE samples by tandem mass spectrometry to generate an unbiased, shotgun-proteomics view of protein identities and abundances. By using Pou4f3/eGFP-transgenic mice in which HCs express GFP driven by Pou4f3, we FACS purified a population of HCs to analyze and compare the HC proteome with other IE subproteomes from sensory epithelia and whole IE. We show that the mammalian HC proteome comprises hundreds of uniquely or highly expressed proteins. Our global proteomic analysis of purified HCs extends the existing HC transcriptome, revealing previously undetected gene products and isoform-specific protein expression. Comparison of our proteomic data with mouse and human databases of genetic auditory/vestibular impairments confirms the critical role of the HC proteome for normal IE function, providing a cell-specific pool of candidates for novel, important HC genes. Several proteins identified exclusively in HCs by proteomics and verified by immunohistochemistry map to human genetic deafness loci, potentially representing new deafness genes. SIGNIFICANCE STATEMENT Hearing and balance rely on specialized sensory hair cells (HCs) in the inner ear (IE) to convey information about sound, acceleration, and orientation to the brain. Genetically and environmentally induced perturbations to HC proteins can result in deafness and severe imbalance. We used transgenic mice with GFP-expressing HCs, coupled with FACS sorting and tandem mass spectrometry, to define the most complete HC and IE proteome to date. We show that hundreds of proteins are uniquely identified or enriched in HCs, extending previous gene expression analyses to reveal novel HC proteins and isoforms. Importantly, deafness-linked proteins were significantly enriched in HCs, suggesting that this in-depth proteomic analysis of IE sensory cells may hold potential for deafness gene discovery.
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Smith ME, Rajadinakaran G. The Transcriptomics to Proteomics of Hair Cell Regeneration: Looking for a Hair Cell in a Haystack. MICROARRAYS 2016; 2. [PMID: 24416530 PMCID: PMC3886832 DOI: 10.3390/microarrays2030186] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Mature mammals exhibit very limited capacity for regeneration of auditory hair cells, while all non-mammalian vertebrates examined can regenerate them. In an effort to find therapeutic targets for deafness and balance disorders, scientists have examined gene expression patterns in auditory tissues under different developmental and experimental conditions. Microarray technology has allowed the large-scale study of gene expression profiles (transcriptomics) at whole-genome levels, but since mRNA expression does not necessarily correlate with protein expression, other methods, such as microRNA analysis and proteomics, are needed to better understand the process of hair cell regeneration. These technologies and some of the results of them are discussed in this review. Although there is a considerable amount of variability found between studies owing to different species, tissues and treatments, there is some concordance between cellular pathways important for hair cell regeneration. Since gene expression and proteomics data is now commonly submitted to centralized online databases, meta-analyses of these data may provide a better picture of pathways that are common to the process of hair cell regeneration and lead to potential therapeutics. Indeed, some of the proteins found to be regulated in the inner ear of animal models (e.g., IGF-1) have now gone through human clinical trials.
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Affiliation(s)
- Michael E. Smith
- Bioinformatics and Information Science Center, Department of Biology, Western Kentucky University, Bowling Green, KY 42101, USA
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-270-745-2405; Fax: +1-270-745-6856
| | - Gopinath Rajadinakaran
- Department of Genetics and Developmental Biology, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT 06030, USA; E-Mail:
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Alawieh A, Mondello S, Kobeissy F, Shibbani K, Bassim M. Proteomics studies in inner ear disorders: pathophysiology and biomarkers. Expert Rev Proteomics 2015; 12:185-96. [PMID: 25795149 DOI: 10.1586/14789450.2015.1024228] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Although proteomics has been exploited in a wide range of diseases for identification of biomarkers and pathophysiological mechanisms, there are still biomedical disciplines such as otology where proteomics platforms are underused due to technical challenges and/or complex features of the disease. Thus, in the past few years, healthcare and scientific agencies have advocated the development and adoption of proteomic technologies in otological research. However, few studies have been conducted and limited literature is available in this area. Here, we present the state of the art of proteomics in otology, discussing the substantial evidence from recent experimental models and clinical studies in inner-ear conditions. We also delineate a series of critical issues including minute size of the inner ear, delicacy and poor accessibility of tissue that researchers face while undertaking otology proteomics research. Furthermore, we provide perspective to enhance the impact and lead to the clinical implementation of these proteomics-based strategies.
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Affiliation(s)
- Ali Alawieh
- Department of Neurosciences, Medical University of South Carolina, Charleston, SC 29425, USA
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11
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Darville LNF, Sokolowski BHA. Bottom-up and shotgun proteomics to identify a comprehensive cochlear proteome. J Vis Exp 2014:51186. [PMID: 24638115 PMCID: PMC4144434 DOI: 10.3791/51186] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Proteomics is a commonly used approach that can provide insights into complex biological systems. The cochlear sensory epithelium contains receptors that transduce the mechanical energy of sound into an electro-chemical energy processed by the peripheral and central nervous systems. Several proteomic techniques have been developed to study the cochlear inner ear, such as two-dimensional difference gel electrophoresis (2D-DIGE), antibody microarray, and mass spectrometry (MS). MS is the most comprehensive and versatile tool in proteomics and in conjunction with separation methods can provide an in-depth proteome of biological samples. Separation methods combined with MS has the ability to enrich protein samples, detect low molecular weight and hydrophobic proteins, and identify low abundant proteins by reducing the proteome dynamic range. Different digestion strategies can be applied to whole lysate or to fractionated protein lysate to enhance peptide and protein sequence coverage. Utilization of different separation techniques, including strong cation exchange (SCX), reversed-phase (RP), and gel-eluted liquid fraction entrapment electrophoresis (GELFrEE) can be applied to reduce sample complexity prior to MS analysis for protein identification.
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Affiliation(s)
- Lancia N F Darville
- Department of Otolaryngology, Morsani College of Medicine, University of South Florida
| | - Bernd H A Sokolowski
- Department of Otolaryngology, Morsani College of Medicine, University of South Florida;
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12
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Darville LN, Sokolowski BH. In-depth proteomic analysis of mouse cochlear sensory epithelium by mass spectrometry. J Proteome Res 2013; 12:3620-30. [PMID: 23721421 PMCID: PMC3777728 DOI: 10.1021/pr4001338] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
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.
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Affiliation(s)
- Lancia N.F. Darville
- University of South Florida, Morsani College of Medicine, 12901 Bruce B. Downs Blvd. Department of Otolaryngology – HNS, Otology Laboratory, MDC83, Tampa FL 33647
| | - Bernd H.A. Sokolowski
- University of South Florida, Morsani College of Medicine, 12901 Bruce B. Downs Blvd. Department of Otolaryngology – HNS, Otology Laboratory, MDC83, Tampa FL 33647
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