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Prokai L, Zaman K, Prokai-Tatrai K. Mass spectrometry-based retina proteomics. MASS SPECTROMETRY REVIEWS 2023; 42:1032-1062. [PMID: 35670041 PMCID: PMC9730434 DOI: 10.1002/mas.21786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 06/15/2023]
Abstract
A subfield of neuroproteomics, retina proteomics has experienced a transformative growth since its inception due to methodological advances in enabling chemical, biochemical, and molecular biology techniques. This review focuses on mass spectrometry's contributions to facilitate mammalian and avian retina proteomics to catalog and quantify retinal protein expressions, determine their posttranslational modifications, as well as its applications to study the proteome of the retina in the context of biology, health and diseases, and therapy developments.
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Affiliation(s)
- Laszlo Prokai
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Khadiza Zaman
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Katalin Prokai-Tatrai
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, Texas, USA
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2
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Huang Y, Chen X, Zhuang J, Yu K. The Role of Retinal Dysfunction in Myopia Development. Cell Mol Neurobiol 2022:10.1007/s10571-022-01309-1. [DOI: 10.1007/s10571-022-01309-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 11/16/2022] [Indexed: 11/27/2022]
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Shan SSW, Wang PF, Cheung JKW, Yu F, Zheng H, Luo S, Yip SP, To CH, LAM C. Transcriptional profiling of the chick retina identifies down-regulation of VIP and UTS2B genes during early lens-induced myopia. Mol Omics 2022; 18:449-459. [DOI: 10.1039/d1mo00407g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Gene expression of the chick retina was examined during the early development of lens-induced myopia (LIM) using whole transcriptome sequencing. Monocular treatment of the right eyes with −10 diopter (D)...
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Basak M, Mitra S, Agnihotri SK, Jain A, Vyas A, Bhatt MLB, Sachan R, Sachdev M, Nemade HB, Bandyopadhyay D. Noninvasive Point-of-Care Nanobiosensing of Cervical Cancer as an Auxiliary to Pap-Smear Test. ACS APPLIED BIO MATERIALS 2021; 4:5378-5390. [PMID: 35007017 DOI: 10.1021/acsabm.1c00470] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A potential cancer antigen (Ag), protein-phosphatase-1-gamma-2 (PP1γ2), with a restricted expression in testis and sperms has been identified as a biomarker specific to cervical cancer (CaCx). Detection of this cancer biomarker antigen (NCB-Ag) in human urine opens up the possibility of noninvasive detection of CaCx to supplement the dreaded and invasive Pap-smear test. A colorimetric response of an assembly of gold nanoparticles (Au NPs) has been employed for the quantitative, noninvasive, and point-of-care-testing of CaCx in the urine. In order to fabricate the immunosensor, Au NPs of sizes ∼5-20 nm have been chemically modified with a linker, 3,3'-di-thio-di-propionic-acid-di(n-hydroxy-succinimide-ester) (DTSP) to attach the antibody (Ab) specific to the NCB-Ag. Interestingly, the addition of Ag to the composite of Ab-DTSP-Au NPs leads to a significant hypsochromic shift due to a localized surface plasmon resonance phenomenon, which originates from the specific epitope-paratope interaction between the NCB-Ag and Ab-DTSP-Au NPs. The variations in the absorbance and wavelength shift during such attachments of different concentrations of NCB-Ag on the Ab-DTSP-Au NPs composite have been employed as a calibration to identify NCB-Ag in human urine. An in-house prototype has been assembled by integrating a light-emitting diode of a narrow range wavelength in one side of a cuvette in which the reaction has been performed while a sensitive photodetector to the other side to transduce the transmitted signal associated with the loading of NCB-Ag in the Ab-DTSP-Au NPs composite. The proposed immunosensing platform has been tested against other standard proteins to ensure noninterference alongside proving the proof-for-specificity of the NCB detection.
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Affiliation(s)
- Mitali Basak
- Centre for Nanotechnology, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Shirsendu Mitra
- Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Saurabh Kumar Agnihotri
- Endocrinology, Division, CSIR-Central Drug Research Institute Lucknow, Lucknow, Uttar Pradesh 226 031, India
| | - Ankita Jain
- Endocrinology, Division, CSIR-Central Drug Research Institute Lucknow, Lucknow, Uttar Pradesh 226 031, India
| | - Akanksha Vyas
- Endocrinology, Division, CSIR-Central Drug Research Institute Lucknow, Lucknow, Uttar Pradesh 226 031, India
| | | | - Rekha Sachan
- King George's Medical University, Lucknow, Uttar Pradesh 226 003, India
| | - Monika Sachdev
- Endocrinology, Division, CSIR-Central Drug Research Institute Lucknow, Lucknow, Uttar Pradesh 226 031, India
| | - Harshal B Nemade
- Centre for Nanotechnology, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Dipankar Bandyopadhyay
- Centre for Nanotechnology, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India.,Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
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Bian J, Sze YH, Tse DYY, To CH, McFadden SA, Lam CSY, Li KK, Lam TC. SWATH Based Quantitative Proteomics Reveals Significant Lipid Metabolism in Early Myopic Guinea Pig Retina. Int J Mol Sci 2021; 22:4721. [PMID: 33946922 PMCID: PMC8124159 DOI: 10.3390/ijms22094721] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/22/2021] [Accepted: 04/25/2021] [Indexed: 12/14/2022] Open
Abstract
Most of the previous myopic animal studies employed a single-candidate approach and lower resolution proteomics approaches that were difficult to detect minor changes, and generated limited systems-wide biological information. Hence, a complete picture of molecular events in the retina involving myopic development is lacking. Here, to investigate comprehensive retinal protein alternations and underlying molecular events in the early myopic stage, we performed a data-independent Sequential Window Acquisition of all Theoretical Mass Spectra (SWATH) based proteomic analysis coupled with different bioinformatics tools in pigmented guinea pigs after 4-day lens-induced myopia (LIM). Myopic eyes compared to untreated contralateral control eyes caused significant changes in refractive error and choroid thickness (p < 0.05, n = 5). Relative elongation of axial length and the vitreous chamber depth were also observed. Using pooled samples from all individuals (n = 10) to build a species-specific retinal ion library for SWATH analysis, 3202 non-redundant proteins (with 24,616 peptides) were identified at 1% global FDR. For quantitative analysis, the 10 individual retinal samples (5 pairs) were analyzed using a high resolution Triple-TOF 6600 mass spectrometry (MS) with technical replicates. In total, 37 up-regulated and 21 down-regulated proteins were found significantly changed after LIM treatment (log2 ratio (T/C) > 0.26 or < -0.26; p ≤ 0.05). Data are accepted via ProteomeXchange with identifier PXD025003. Through Ingenuity Pathways Analysis (IPA), "lipid metabolism" was found as the top function associated with the differentially expressed proteins. Based on the protein abundance and peptide sequences, expression patterns of two regulated proteins (SLC6A6 and PTGES2) identified in this pathway were further successfully validated with high confidence (p < 0.05) using a novel Multiple Reaction Monitoring (MRM) assay on a QTRAP 6500+ MS. In summary, through an integrated discovery and targeted proteomic approach, this study serves as the first report to detect and confirm novel retinal protein changes and significant biological functions in the early LIM mammalian guinea pigs. The study provides new workflow and insights for further research to myopia control.
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Affiliation(s)
- Jingfang Bian
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (J.B.); (Y.-H.S.); (D.Y.-Y.T.); (C.-H.T.); (C.S.-Y.L.); (K.-K.L.)
| | - Ying-Hon Sze
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (J.B.); (Y.-H.S.); (D.Y.-Y.T.); (C.-H.T.); (C.S.-Y.L.); (K.-K.L.)
| | - Dennis Yan-Yin Tse
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (J.B.); (Y.-H.S.); (D.Y.-Y.T.); (C.-H.T.); (C.S.-Y.L.); (K.-K.L.)
- Centre for Eye and Vision Research (CEVR), 17W Hong Kong Science Park, Hong Kong, China
| | - Chi-Ho To
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (J.B.); (Y.-H.S.); (D.Y.-Y.T.); (C.-H.T.); (C.S.-Y.L.); (K.-K.L.)
- Centre for Eye and Vision Research (CEVR), 17W Hong Kong Science Park, Hong Kong, China
| | - Sally A. McFadden
- School of Psychology, College of Engineering, Science and the Environment, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Carly Siu-Yin Lam
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (J.B.); (Y.-H.S.); (D.Y.-Y.T.); (C.-H.T.); (C.S.-Y.L.); (K.-K.L.)
- Centre for Eye and Vision Research (CEVR), 17W Hong Kong Science Park, Hong Kong, China
| | - King-Kit Li
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (J.B.); (Y.-H.S.); (D.Y.-Y.T.); (C.-H.T.); (C.S.-Y.L.); (K.-K.L.)
| | - Thomas Chuen Lam
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (J.B.); (Y.-H.S.); (D.Y.-Y.T.); (C.-H.T.); (C.S.-Y.L.); (K.-K.L.)
- Centre for Eye and Vision Research (CEVR), 17W Hong Kong Science Park, Hong Kong, China
- Shenzhen Research Institute, The Hong Kong Polytechnic University, Shenzhen 518052, China
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RNA-seq and GSEA identifies suppression of ligand-gated chloride efflux channels as the major gene pathway contributing to form deprivation myopia. Sci Rep 2021; 11:5280. [PMID: 33674625 PMCID: PMC7935918 DOI: 10.1038/s41598-021-84338-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 01/15/2021] [Indexed: 12/13/2022] Open
Abstract
Currently there is no consensus regarding the aetiology of the excessive ocular volume that characterizes high myopia. Thus, we aimed to test whether the gene pathways identified by gene set enrichment analysis of RNA-seq transcriptomics refutes the predictions of the Retinal Ion Driven Efflux (RIDE) hypothesis when applied to the induction of form-deprivation myopia (FDM) and subsequent recovery (post-occluder removal). We found that the induction of profound FDM led to significant suppression in the ligand-gated chloride ion channel transport pathway via suppression of glycine, GABAA and GABAC ionotropic receptors. Post-occluder removal for short term recovery from FDM of 6 h and 24 h, induced significant upregulation of the gene families linked to cone receptor phototransduction, mitochondrial energy, and complement pathways. These findings support a model of form deprivation myopia as a Cl− ion driven adaptive fluid response to the modulation of the visual signal cascade by form deprivation that in turn affects the resultant ionic environment of the outer and inner retinal tissues, axial and vitreal elongation as predicted by the RIDE model. Occluder removal and return to normal light conditions led to return to more normal upregulation of phototransduction, slowed growth rate, refractive recovery and apparent return towards physiological homeostasis.
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Abstract
Myopia is a globally emerging issue, with multiple medical and socio-economic burdens and no well-established causal treatment thus far. A better insight into altered biochemical pathways and underlying pathogenesis might facilitate early diagnosis and treatment of myopia, ultimately leading to the development of more effective preventive and therapeutic measures. In this review, we summarize current data about the metabolomics and proteomics of myopia in humans and present various experimental approaches and animal models, along with their strengths and weaknesses. We also discuss the potential applicability of these findings to medical practice and suggest directions for future research.
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Lam C, Li KK, Do CW, Chan H, To CH, Kwong JMK. Quantitative profiling of regional protein expression in rat retina after partial optic nerve transection using fluorescence difference two‑dimensional gel electrophoresis. Mol Med Rep 2019; 20:2734-2742. [PMID: 31524249 PMCID: PMC6691257 DOI: 10.3892/mmr.2019.10525] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 05/14/2019] [Indexed: 12/17/2022] Open
Abstract
To examine the difference between primary and secondary retinal ganglion cell (RGC) degeneration, the protein expression at four regions of retina including superior, temporal, inferior and nasal quadrant in a rat model of partial optic nerve transection (pONT) using 2-D Fluorescence Difference Gel Electrophoresis (DIGE) were investigated. Unilateral pONT was performed on the temporal side of optic nerves of adult Wistar rats to separate primary and secondary RGC loss. Topographical quantification of RGCs labeled by Rbpms antibody and analysis of axonal injury by grading of optic nerve damage at 1 week (n=8) and 8 weeks (n=15) after pONT demonstrated early RGC loss at temporal region, which is considered as primary RGC degeneration and progressing RGC loss at nasal region, which is considered as secondary RGC degeneration. Early protein expression in each retinal quadrant (n=4) at 2 weeks after pONT was compared with the corresponding quadrant in the contralateral control eye by DIGE. For all comparisons, 24 differentially expressed proteins (>1.2-fold; P<0.05; ≥3 non-duplicated peptide matches) were identified by mass spectrometry (MS). Interestingly, in the nasal retina, serum albumin and members of crystallin family, including αA, αB, βA2, βA3, βB2 and γS indicating stress response were upregulated. By contrast, only αB and βA2 crystallin proteins were altered in temporal quadrant. In the superior and inferior quadrants, βB2 crystallin, keratin type I, S-arrestin and lamin-B1 were upregulated, while heat shock cognate 71 kDa protein and heterogeneous nuclear ribonucleoproteins A2/B1 were downregulated. In summary, the use of DIGE followed by MS is useful to detect early regional protein regulation in the retina after localized optic nerve injury.
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Affiliation(s)
- Chuen Lam
- School of Optometry, Hong Kong Polytechnic University, Hong Kong 999077, SAR, P.R. China
| | - King Kit Li
- School of Optometry, Hong Kong Polytechnic University, Hong Kong 999077, SAR, P.R. China
| | - Chi Wai Do
- School of Optometry, Hong Kong Polytechnic University, Hong Kong 999077, SAR, P.R. China
| | - Henry Chan
- School of Optometry, Hong Kong Polytechnic University, Hong Kong 999077, SAR, P.R. China
| | - Chi Ho To
- School of Optometry, Hong Kong Polytechnic University, Hong Kong 999077, SAR, P.R. China
| | - Jacky Man Kwong Kwong
- Department of Ophthalmology, Stein Eye Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
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Shan SW, Tse DYY, Zuo B, To CH, Liu Q, McFadden SA, Chun RKM, Bian J, Li KK, Lam TC. Data on differentially expressed proteins in retinal emmetropization process in guinea pig using integrated SWATH-based and targeted-based proteomics. Data Brief 2018; 21:1750-1755. [PMID: 30505911 PMCID: PMC6249517 DOI: 10.1016/j.dib.2018.08.119] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 08/24/2018] [Indexed: 11/20/2022] Open
Abstract
Myopia is generally regarded as a failure of normal emmetropization process, however, its underlying molecular mechanisms are unclear. Retinal protein profile changes using integrated SWATH and MRM-HR MS were studied in guinea pigs at 3- and 21-days of age, where the axial elongation was significantly detected. Differential proteins expressions were identified, and related to pathways which are important in postnatal development in retina, proliferation, breakdown of glycogen-energy and visual phototransduction. These results are significant as key retinal protein players and pathways that underlying emmetropization can be discovered. All raw data generated from IDA and SWATH acquisitions were accepted and published in the Peptide Atlas public repository (http://www.peptideatlas.org/) for general release (Data ID PASS00746). A more comprehensive analysis of this data can be obtained in the article “Integrated SWATH-based and targeted-based proteomics provide insights into the retinal emmetropization process in guinea pig” in Journal of Proteomics (Shan et al., 2018) [1].
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Affiliation(s)
- Sze Wan Shan
- Laboratory of Experimental Optometry, Centre for Myopia Research, School of Optometry, the Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Dennis Yan-Yin Tse
- Laboratory of Experimental Optometry, Centre for Myopia Research, School of Optometry, the Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Bing Zuo
- Laboratory of Experimental Optometry, Centre for Myopia Research, School of Optometry, the Hong Kong Polytechnic University, Kowloon, Hong Kong.,State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
| | - Chi Ho To
- Laboratory of Experimental Optometry, Centre for Myopia Research, School of Optometry, the Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Quan Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
| | - Sally A McFadden
- School of Psychology, Faculty of Science, University of Newcastle, Callaghan, New South Wales, Australia
| | - Rachel Ka-Man Chun
- Laboratory of Experimental Optometry, Centre for Myopia Research, School of Optometry, the Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Jingfang Bian
- Laboratory of Experimental Optometry, Centre for Myopia Research, School of Optometry, the Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - King Kit Li
- Laboratory of Experimental Optometry, Centre for Myopia Research, School of Optometry, the Hong Kong Polytechnic University, Kowloon, Hong Kong
| | - Thomas Chuen Lam
- Laboratory of Experimental Optometry, Centre for Myopia Research, School of Optometry, the Hong Kong Polytechnic University, Kowloon, Hong Kong
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Riddell N, Faou P, Crewther SG. Short term optical defocus perturbs normal developmental shifts in retina/RPE protein abundance. BMC DEVELOPMENTAL BIOLOGY 2018; 18:18. [PMID: 30157773 PMCID: PMC6116556 DOI: 10.1186/s12861-018-0177-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 08/16/2018] [Indexed: 02/06/2023]
Abstract
BACKGROUND Myopia (short-sightedness) affects approximately 1.4 billion people worldwide, and prevalence is increasing. Animal models induced by defocusing lenses show striking similarity with human myopia in terms of morphology and the implicated genetic pathways. Less is known about proteome changes in animals. Thus, the present study aimed to improve understanding of protein pathway responses to lens defocus, with an emphasis on relating expression changes to no lens control development and identifying bidirectional and/or distinct pathways across myopia and hyperopia (long-sightedness) models. RESULTS Quantitative label-free proteomics and gene set enrichment analysis (GSEA) were used to examine protein pathway expression in the retina/RPE of chicks following 6 h and 48 h of myopia induction with - 10 dioptre (D) lenses, hyperopia induction with +10D lenses, or normal no lens rearing. Seventy-one pathways linked to cell development and neuronal maturation were differentially enriched between 6 and 48 h in no lens chicks. The majority of these normal developmental changes were disrupted by lens-wear (47 of 71 pathways), however, only 11 pathways displayed distinct expression profiles across the lens conditions. Most notably, negative lens-wear induced up-regulation of proteins involved in ATP-driven ion transport, calcium homeostasis, and GABA signalling between 6 and 48 h, while the same proteins were down-regulated over time in normally developing chicks. Glutamate and bicarbonate/chloride transporters were also down-regulated over time in normally developing chicks, and positive lens-wear inhibited this down-regulation. CONCLUSIONS The chick retina/RPE proteome undergoes extensive pathway expression shifts during normal development. Most of these pathways are further disrupted by lens-wear. The identified expression patterns suggest close interactions between neurotransmission (as exemplified by increased GABA receptor and synaptic protein expression), cellular ion homeostasis, and associated energy resources during myopia induction. We have also provided novel evidence for changes to SLC-mediated transmembrane transport during hyperopia induction, with potential implications for signalling at the photoreceptor-bipolar synapse. These findings reflect a key role for perturbed neurotransmission and ionic homeostasis in optically-induced refractive errors, and are predicted by our Retinal Ion Driven Efflux (RIDE) model.
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Affiliation(s)
- Nina Riddell
- Department of Psychology and Counselling, School of Psychology and Public Health, La Trobe University, Plenty Rd., Bundoora, Melbourne, VIC, 3083, Australia.
| | - Pierre Faou
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Sciences, La Trobe University, Melbourne, VIC, Australia
| | - Sheila G Crewther
- Department of Psychology and Counselling, School of Psychology and Public Health, La Trobe University, Plenty Rd., Bundoora, Melbourne, VIC, 3083, Australia
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Zhou YY, Chun RKM, Wang JC, Zuo B, Li KK, Lam TC, Liu Q, To CH. Proteomic analysis of chick retina during early recovery from lens‑induced myopia. Mol Med Rep 2018; 18:59-66. [PMID: 29749514 PMCID: PMC6059693 DOI: 10.3892/mmr.2018.8954] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 03/06/2018] [Indexed: 12/13/2022] Open
Abstract
Myopia development has been extensively studied from different perspectives. Myopia recovery is also considered important for understanding the development of myopia. However, despite several previous studies, retinal proteomics during recovery from myopia is still relatively unknown. Therefore, the aim of the present study was to investigate the changes in protein profiles of chicken retinas during early recovery from lens-induced myopia to evaluate the signals involved in the adjustment of this refractive disorder. Three-day old chickens wore glasses for 7 days (−10D lens over the right eye and a plano lens as control over the left eye), followed by 24 h without lenses. Protein expression in the retina was measured by two-dimensional fluorescence difference gel electrophoresis (2D-DIGE). Pro-Q Diamond phosphoprotein staining 2D gel electrophoresis was used to analyze phosphoprotein profiles. Protein spots with significant differences (P<0.05) were analyzed by mass spectrometry. The minus lens-treated eye became myopic, however following 24 h recovery, less myopia was observed. 2D-DIGE proteomic analysis demonstrated that three identified protein spots were upregulated at least 1.2-fold in myopic recovery retinas compared with those of the controls, Ras related protein Rab-11B, S-antigen retina and pineal gland and 26S proteasome non-ATPase regulatory subunit 14. Pro-Q Diamond images further revealed three protein spots with significant changes (at least 1.8-fold): β-tubulin was downregulated, while peroxiredoxin 4 and ubiquitin carboxyl-terminal hydrolase-L1 were upregulated in the recovery retinas compared with the control eye retinas. The present study detected previously unreported protein changes in recovering eyes, therefore revealing their potential involvement in retinal remodeling during eye ball reforge.
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Affiliation(s)
- Yun Yun Zhou
- Refractive Surgery Department, State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat‑sen University, Guangzhou, Guangdong 510060, P.R. China
| | - Rachel Ka Man Chun
- Laboratory of Experimental Optometry, Centre for Myopia Research, School of Optometry, Hong Kong Polytechnic University, Hong Kong 999077, SAR, P.R. China
| | - Jian Chao Wang
- Department of Ophthalmology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shanxi 710049, P.R. China
| | - Bing Zuo
- Laboratory of Experimental Optometry, Centre for Myopia Research, School of Optometry, Hong Kong Polytechnic University, Hong Kong 999077, SAR, P.R. China
| | - King Kit Li
- Laboratory of Experimental Optometry, Centre for Myopia Research, School of Optometry, Hong Kong Polytechnic University, Hong Kong 999077, SAR, P.R. China
| | - Thomas Chuen Lam
- Laboratory of Experimental Optometry, Centre for Myopia Research, School of Optometry, Hong Kong Polytechnic University, Hong Kong 999077, SAR, P.R. China
| | - Quan Liu
- Refractive Surgery Department, State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat‑sen University, Guangzhou, Guangdong 510060, P.R. China
| | - Chi-Ho To
- Refractive Surgery Department, State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat‑sen University, Guangzhou, Guangdong 510060, P.R. China
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Integrated SWATH-based and targeted-based proteomics provide insights into the retinal emmetropization process in guinea pig. J Proteomics 2018; 181:1-15. [PMID: 29572162 DOI: 10.1016/j.jprot.2018.03.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 03/12/2018] [Accepted: 03/19/2018] [Indexed: 01/13/2023]
Abstract
Myopia is generally regarded as a failure of normal emmetropization process, however, its underlying molecular mechanisms are unclear. To investigate the retinal protein profile changes during emmetropization, we studied differential protein expressions of ocular growth in young guinea pigs at 3 and 21 days old respectively, when significant axial elongation was detected (P < 0.001, n = 10). Independent pooled retinal samples of both eyes were subjected to SWATH mass spectrometry (MS) followed by bioinformatics analysis using cloud-based platforms. A comprehensive retina SWATH ion-library consisting of 3138 (22,871) unique proteins (peptides) at 1% FDR was constructed. 40 proteins were found to be significantly up-regulated and 8 proteins down-regulated during emmetropization (≥log2 of 0.43 with ≥2 peptides matched per protein; P < 0.05). Using pathway analysis, the most significant pathway identifiable was 'phototransduction' (P = 1.412e-4). Expression patterns of 7 proteins identified in this pathway were further validated and confirmed (P < 0.05) with high-resolution Multiple Reaction Monitoring (MRM-HR) MS. Combining discovery and targeted proteomics approaches, this study for the first time comprehensively profiled protein changes in the guinea pig retina during normal emmetropization-associated eye growth. The findings of this study are also relevant to the myopia development, which is the result of failed emmetropization. SIGNIFICANCE Myopia is considered as a failure of emmetropization. However, the underlying biochemical mechanism of emmetropization, a visually guided process in which eye grows towards the optimal optical state of clear vision during early development, is not well understood. Retina is known as the key tissue to regulate this active eye growth. we studied eye growth of young guinea pigs and harvested their retinal tissues. A comprehensive SWATH ion library with identification of a total 3138 unique proteins were established, in which 48 proteins exhibited significant differential expressions between 3 and 21 days old. After MRM-HR confirmation, 'phototransduction' were found as the most active pathway during emmetropic eye growth. This study is the first in discovering key retinal protein players and pathways which are presumably orchestrated by biological mechanism(s) underlying emmetropization.
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13
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Wu Y, Lam CSY, Tse DYY, To CH, Liu Q, McFadden SA, Chun RKM, Li KK, Bian J, Lam C. Early quantitative profiling of differential retinal protein expression in lens-induced myopia in guinea pig using fluorescence difference two-dimensional gel electrophoresis. Mol Med Rep 2018; 17:5571-5580. [PMID: 29436656 PMCID: PMC5865996 DOI: 10.3892/mmr.2018.8584] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 11/13/2017] [Indexed: 12/14/2022] Open
Abstract
The current study aimed to investigate the differential protein expression in guinea pig retinas in response to lens-induced myopia (LIM) before fully compensated eye growth. Four days old guinea pigs (n=5) were subjected to −4D LIM for 8 days. Refractive errors were measured before and at the end of the lens wear period. Ocular dimensions were also recorded using high-frequency A-scan ultrasonography. After the LIM treatment, retinas of both eyes were harvested and soluble proteins were extracted. Paired retinal protein expressions in each animal were profiled and compared using a sensitive fluorescence difference two-dimensional gel electrophoresis. The quantitative retinal proteomes of myopic and control eye were analysed using computerised DeCyder software. Those proteins that were consistently changed with at least 1.2-fold difference (P<0.05) in the same direction in all five animals were extracted, trypsin digested and identified by tandem mass spectrometry. Significant myopia was induced in guinea pigs after 8 days of lens wear. The vitreous chamber depth in lens-treated eyes was found to be significantly elongated. Typically, more than 1,000 protein spots could be detected from each retina. Thirty-two of them showed differential expression between myopic and untreated retina. Among these proteins, 21 spots were upregulated and 11 were downregulated. Eight protein spots could be successfully identified which included β-actin, enolase 1, cytosolic malate dehydrogenase, Ras-related protein Rab-11B, protein-L-isoaspartate (D-aspartate) O-methyltransferase, PKM2 protein, X-linked eukaryotic translation initiation factor 1A and ACP1 protein. The present study serves as the first report to uncover the retinal 2D proteome expressions in mammalian guinea pig myopia model using a top-down fluorescent dyes labelling gel approach. The results showed a downregulation in glycolytic enzymes that may suggest a significant alteration of glycolysis during myopia development. Other protein candidates also suggested multiple pathways which could provide new insights for further study of the myopic eye growth.
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Affiliation(s)
- Yi Wu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat‑Sen University, Guangzhou, Guangdong 510060, P.R. China
| | - Carly Siu-Yin Lam
- Laboratory of Experimental Optometry, Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Hong Kong, SAR, P.R. China
| | - Dennis Yan-Yin Tse
- Laboratory of Experimental Optometry, Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Hong Kong, SAR, P.R. China
| | - Chi Ho To
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat‑Sen University, Guangzhou, Guangdong 510060, P.R. China
| | - Quan Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat‑Sen University, Guangzhou, Guangdong 510060, P.R. China
| | - Sally A McFadden
- School of Psychology, Faculty of Science and IT, The University of Newcastle, Callaghan, NSW 2308, Australia
| | - Rachel Ka-Man Chun
- Laboratory of Experimental Optometry, Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Hong Kong, SAR, P.R. China
| | - King Kit Li
- Laboratory of Experimental Optometry, Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Hong Kong, SAR, P.R. China
| | - Jianfang Bian
- Laboratory of Experimental Optometry, Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Hong Kong, SAR, P.R. China
| | - Chuen Lam
- Laboratory of Experimental Optometry, Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Hong Kong, SAR, P.R. China
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Iwamoto N, Shimada T. Recent advances in mass spectrometry-based approaches for proteomics and biologics: Great contribution for developing therapeutic antibodies. Pharmacol Ther 2017; 185:147-154. [PMID: 29274706 DOI: 10.1016/j.pharmthera.2017.12.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Since the turn of the century, mass spectrometry (MS) technologies have continued to improve dramatically, and advanced strategies that were impossible a decade ago are increasingly becoming available. The basic characteristics behind these advancements are MS resolution, quantitative accuracy, and information science for appropriate data processing. The spectral data from MS contain various types of information. The benefits of improving the resolution of MS data include accurate molecular structural-derived information, and as a result, we can obtain a refined biomolecular structure determination in a sequential and large-scale manner. Moreover, in MS data, not only accurate structural information but also the generated ion amount plays an important rule. This progress has greatly contributed a research field that captures biological events as a system by comprehensively tracing the various changes in biomolecular dynamics. The sequential changes of proteome expression in biological pathways are very essential, and the amounts of the changes often directly become the targets of drug discovery or indicators of clinical efficacy. To take this proteomic approach, it is necessary to separate the individual MS spectra derived from each biomolecule in the complexed biological samples. MS itself is not so infinite to perform the all peak separation, and we should consider improving the methods for sample processing and purification to make them suitable for injection into MS. The above-described characteristics can only be achieved using MS with any analytical instrument. Moreover, MS is expected to be applied and expand into many fields, not only basic life sciences but also forensic medicine, plant sciences, materials, and natural products. In this review, we focus on the technical fundamentals and future aspects of the strategies for accurate structural identification, structure-indicated quantitation, and on the challenges for pharmacokinetics of high-molecular-weight protein biopharmaceuticals.
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Affiliation(s)
- Noriko Iwamoto
- Leading Technology of Bioanalysis and Protein Chemistry, SHIMADZU Corporation, Kyoto, Japan
| | - Takashi Shimada
- Leading Technology of Bioanalysis and Protein Chemistry, SHIMADZU Corporation, Kyoto, Japan.
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Yu FJ, Lam TC, Liu LQ, Chun RKM, Cheung JKW, Li KK, To CH. Isotope-coded protein label based quantitative proteomic analysis reveals significant up-regulation of apolipoprotein A1 and ovotransferrin in the myopic chick vitreous. Sci Rep 2017; 7:12649. [PMID: 28978931 PMCID: PMC5627271 DOI: 10.1038/s41598-017-12650-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 09/13/2017] [Indexed: 02/05/2023] Open
Abstract
This study used isotope-coded protein label (ICPL) quantitative proteomics and bioinformatics analysis to examine changes in vitreous protein content and associated pathways during lens-induced eye growth. First, the vitreous protein profile of normal 7-day old chicks was characterized by nano-liquid chromatography electrospray ionization tandem mass spectrometry. A total of 341 unique proteins were identified. Next, myopia and hyperopia were induced in the same chick by attaching -10D lenses to the right eye and +10D lenses to the left eye, for 3 and 7 days. Protein expression in lens-induced ametropic eyes was analyzed using the ICPL approach coupled to LCMS. Four proteins (cystatin, apolipoprotein A1, ovotransferrin, and purpurin) were significantly up-regulated in the vitreous after 3 days of wearing -10D lenses relative to +10D lens contralateral eyes. The differences in protein expression were less pronounced after 7 days when the eyes approached full compensation. In a different group of chicks, western blot confirmed the up-regulation of apolipoprotein A1 and ovotransferrin in the myopic vitreous relative to both contralateral lens-free eyes and hyperopic eyes in separate animals wearing +10D lenses. Bioinformatics analysis suggested oxidative stress and lipid metabolism as pathways involved in compensated ocular elongation.
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Affiliation(s)
- Feng-Juan Yu
- Laboratory of Experimental Optometry, Centre for Myopia Research, School of Optometry, the Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Thomas Chuen Lam
- Laboratory of Experimental Optometry, Centre for Myopia Research, School of Optometry, the Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong.
| | - Long-Qian Liu
- Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
| | - Rachel Ka-Man Chun
- Laboratory of Experimental Optometry, Centre for Myopia Research, School of Optometry, the Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Jimmy Ka-Wai Cheung
- Laboratory of Experimental Optometry, Centre for Myopia Research, School of Optometry, the Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - King-Kit Li
- Laboratory of Experimental Optometry, Centre for Myopia Research, School of Optometry, the Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Chi-Ho To
- Laboratory of Experimental Optometry, Centre for Myopia Research, School of Optometry, the Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
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Chen BJ, Lam TC, Liu LQ, To CH. Post-translational modifications and their applications in eye research (Review). Mol Med Rep 2017; 15:3923-3935. [PMID: 28487982 DOI: 10.3892/mmr.2017.6529] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Accepted: 02/22/2017] [Indexed: 02/05/2023] Open
Abstract
Gene expression is the process by which genetic information is used for the synthesis of a functional gene product, and ultimately regulates cell function. The increase of biological complexity from genome to proteome is vast, and the post-translational modification (PTM) of proteins contribute to this complexity. The study of protein expression and PTMs has attracted attention in the post‑genomic era. Due to the limited capability of conventional biochemical techniques in the past, large‑scale PTM studies were technically challenging. The introduction of effective protein separation methods, specific PTM purification strategies and advanced mass spectrometers has enabled the global profiling of PTMs and the identification of a targeted PTM within the proteome. The present review provides an overview of current proteomic technologies being applied in eye research, with a particular focus on studies of PTMs in ocular tissues and ocular diseases.
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Affiliation(s)
- Bing-Jie Chen
- Department of Optometry and Visual Science, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Thomas Chuen Lam
- Laboratory of Experimental Optometry, Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, SAR, P.R. China
| | - Long-Qian Liu
- Department of Optometry and Visual Science, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Chi-Ho To
- Laboratory of Experimental Optometry, Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, SAR, P.R. China
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Barathi VA, Chaurasia SS, Poidinger M, Koh SK, Tian D, Ho C, Iuvone PM, Beuerman RW, Zhou L. Involvement of GABA transporters in atropine-treated myopic retina as revealed by iTRAQ quantitative proteomics. J Proteome Res 2014; 13:4647-58. [PMID: 25211393 PMCID: PMC4227558 DOI: 10.1021/pr500558y] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Atropine,
a muscarinic antagonist, is known to inhibit myopia progression
in several animal models and humans. However, the mode of action is
not established yet. In this study, we compared quantitative iTRAQ
proteomic analysis in the retinas collected from control and lens-induced
myopic (LIM) mouse eyes treated with atropine. The myopic group received
a (−15D) spectacle lens over the right eye on postnatal day
10 with or without atropine eye drops starting on postnatal day 24.
Axial length was measured by optical low coherence interferometry
(OLCI), AC-Master, and refraction was measured by automated infrared
photorefractor at postnatal 24, 38, and 52 days. Retinal tissue samples
were pooled from six eyes for each group. The experiments were repeated
twice, and technical replicates were also performed for liquid chromatography–tandem
mass spectrometry (LC–MS/MS) analysis. MetaCore was used to
perform protein profiling for pathway analysis. We identified a total
of 3882 unique proteins with <1% FDR by analyzing the samples in
replicates for two independent experiments. This is the largest number
of mouse retina proteome reported to date. Thirty proteins were found
to be up-regulated (ratio for myopia/control > global mean ratio
+
1 standard deviation), and 28 proteins were down-regulated (ratio
for myopia/control < global mean ratio - 1 standard deviation)
in myopic eyes as compared with control retinas. Pathway analysis
using MetaCore revealed regulation of γ-aminobutyric acid (GABA)
levels in the myopic eyes. Detailed analysis of the quantitative proteomics
data showed that the levels of GABA transporter 1 (GAT-1) were elevated
in myopic retina and significantly reduced after atropine treatment.
These results were further validated with immunohistochemistry and
Western blot analysis. In conclusion, this study provides a comprehensive
quantitative proteomic analysis of atropine-treated mouse retina and
suggests the involvement of GABAergic signaling in the antimyopic
effects of atropine in mouse eyes. The GABAergic transmission in the
neural retina plays a pivotal role in the maintenance of axial eye
growth in mammals.
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Affiliation(s)
- Veluchamy A Barathi
- Singapore Eye Research Institute , 11 Third Hospital Avenue, Singapore 168751, Singapore
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Abstract
Proteomics, a highly sophisticated way to study the protein profile of various biological tissues or fluids, has hitherto had a relatively limited role ophthalmic science. Of the few proteomic studies that have been performed, liquid chromatography, electrophoresis gel separation and mass spectrometry have been utilized to investigate the proteome of several different eye structures and fluids from both humans and animal models. Ophthalmic proteomic studies have so far attempted to identify proteins unique to the eye, to investigate protein changes due to the onset of various diseases and to identify proteins that could act as markers of disease. Proteomics has the potential to improve the way in which eye disease is diagnosed and potentially even treated by identifying novel pathogenic pathways that may be susceptible to therapeutic manipulation. The aim of this review is to give an overview the current and potential application of proteomic science to ophthalmic research.
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Affiliation(s)
- Narelle L Jay
- Save Sight Institute and The University of Sydney, 8 Macquarie St, Sydney, NSW 2001, Australia
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Frost MR, Norton TT. Alterations in protein expression in tree shrew sclera during development of lens-induced myopia and recovery. Invest Ophthalmol Vis Sci 2012; 53:322-36. [PMID: 22039233 DOI: 10.1167/iovs.11-8354] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE During the development of, and recovery from, negative lens-induced myopia there is regulated remodeling of the scleral extracellular matrix (ECM) that controls the extensibility of the sclera. Difference gel electrophoresis (DIGE) was used to identify and categorize proteins whose levels are altered in this process. METHODS Two groups of five tree shrews started monocular lens wear 24 days after eye opening (days of visual experience [VE]). The lens-induced myopia (LIM) group wore a -5 D lens for 4 days. The recovery (REC) group wore a -5 D lens for 11 days and then recovered for 4 days. Two normal groups (28 and 39 days of VE; n = 5 each) were also examined, age-matched to each of the treatment groups. Refractive and A-scan measures confirmed the effect of the treatments. Scleral proteins were isolated and resolved by DIGE. Proteins that differed in abundance were identified by mass spectrometry. Ingenuity pathway analysis was used to investigate potential biological pathway interactions. RESULTS During normal development (28-39 days of VE), eight proteins decreased and one protein increased in relative abundance. LIM-treated eyes were myopic and longer than control eyes; LIM-control eyes were slightly myopic compared with 28N eyes, indicating a yoking effect. In both the LIM-treated and the LIM-control eyes, there was a general downregulation from normal of proteins involved in transcription, cell adhesion, and protein synthesis. Additional proteins involved in cell adhesion, actin cytoskeleton, transcriptional regulation, and ECM structural proteins differed in the LIM-treated eyes versus normal but did not differ in the control eyes versus normal. REC-treated eyes were recovering from the induced myopia. REC-control eye refractions were not significantly different from the 39N eyes, and few proteins differed from age-matched normal eyes. The balance of protein expression in the REC-treated eyes, compared with normal eyes and REC-control eyes, shifted toward upregulation or a return to normal levels of proteins involved in cell adhesion, cell division, cytoskeleton, and ECM structural proteins, including upregulation of several cytoskeleton-related proteins not affected during myopia development. CONCLUSIONS The DIGE procedure revealed new proteins whose abundance is altered during myopia development and recovery. Many of these are involved in cell-matrix adhesions, cytoskeleton, and transcriptional regulation and extend our understanding of the remodeling that controls the extensibility of the sclera. Reductions in these proteins during minus lens wear may produce the increased scleral viscoelasticity that results in faster axial elongation. Recovery is not a mirror image of lens-induced myopia-many protein levels, decreased during LIM, returned to normal, or slightly above normal, and additional cytoskeleton proteins were upregulated. However, no single protein or pathway appeared to be responsible for the scleral changes during myopia development or recovery.
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Affiliation(s)
- Michael R Frost
- Department of Vision Sciences, School of Optometry, University of Alabama at Birmingham, Birmingham, Alabama 35294-4390, USA.
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Mandal N, Heegaard S, Prause JU, Honoré B, Vorum H. Ocular proteomics with emphasis on two-dimensional gel electrophoresis and mass spectrometry. Biol Proced Online 2009; 12:56-88. [PMID: 21406065 PMCID: PMC3055252 DOI: 10.1007/s12575-009-9019-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2009] [Accepted: 09/28/2009] [Indexed: 01/30/2023] Open
Abstract
The intention of this review is to provide an overview of current methodologies employed in the rapidly developing field of ocular proteomics with emphasis on sample preparation, two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and mass spectrometry (MS). Appropriate sample preparation for the diverse range of cells and tissues of the eye is essential to ensure reliable results. Current methods of protein staining for 2D-PAGE, protein labelling for two-dimensional difference gel electrophoresis, gel-based expression analysis and protein identification by MS are summarised. The uses of gel-free MS-based strategies (MuDPIT, iTRAQ, ICAT and SILAC) are also discussed. Proteomic technologies promise to shed new light onto ocular disease processes that could lead to the discovery of strong novel biomarkers and therapeutic targets useful in many ophthalmic conditions.
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Affiliation(s)
- Nakul Mandal
- Eye Pathology Section, Department of Neuroscience and Pharmacology, University of Copenhagen, Copenhagen, Denmark
- Department of Medical Biochemistry, Aarhus University, Aarhus, Denmark
| | - Steffen Heegaard
- Eye Pathology Section, Department of Neuroscience and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Jan Ulrik Prause
- Eye Pathology Section, Department of Neuroscience and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Bent Honoré
- Department of Medical Biochemistry, Aarhus University, Aarhus, Denmark
| | - Henrik Vorum
- Department of Medical Biochemistry, Aarhus University, Aarhus, Denmark
- Department of Ophthalmology, Aalborg Hospital, Aarhus University Hospital, Aalborg, Denmark
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Wu Y, Zhou J, Zhang X, Zheng X, Jiang X, Shi L, Yin W, Wang J. Optimized sample preparation for two-dimensional gel electrophoresis of soluble proteins from chicken bursa of Fabricius. Proteome Sci 2009; 7:38. [PMID: 19814785 PMCID: PMC2770044 DOI: 10.1186/1477-5956-7-38] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2009] [Accepted: 10/08/2009] [Indexed: 01/10/2024] Open
Abstract
BACKGROUND Two-dimensional gel electrophoresis (2-DE) is a powerful method to study protein expression and function in living organisms and diseases. This technique, however, has not been applied to avian bursa of Fabricius (BF), a central immune organ. Here, optimized 2-DE sample preparation methodologies were constructed for the chicken BF tissue. Using the optimized protocol, we performed further 2-DE analysis on a soluble protein extract from the BF of chickens infected with virulent avibirnavirus. To demonstrate the quality of the extracted proteins, several differentially expressed protein spots selected were cut from 2-DE gels and identified by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). RESULTS An extraction buffer containing 7 M urea, 2 M thiourea, 2% (w/v) 3-[(3-cholamidopropyl)-dimethylammonio]-1-propanesulfonate (CHAPS), 50 mM dithiothreitol (DTT), 0.2% Bio-Lyte 3/10, 1 mM phenylmethylsulfonyl fluoride (PMSF), 20 U/ml Deoxyribonuclease I (DNase I), and 0.25 mg/ml Ribonuclease A (RNase A), combined with sonication and vortex, yielded the best 2-DE data. Relative to non-frozen immobilized pH gradient (IPG) strips, frozen IPG strips did not result in significant changes in the 2-DE patterns after isoelectric focusing (IEF). When the optimized protocol was used to analyze the spleen and thymus, as well as avibirnavirus-infected bursa, high quality 2-DE protein expression profiles were obtained. 2-DE maps of BF of chickens infected with virulent avibirnavirus were visibly different and many differentially expressed proteins were found. CONCLUSION These results showed that method C, in concert extraction buffer IV, was the most favorable for preparing samples for IEF and subsequent protein separation and yielded the best quality 2-DE patterns. The optimized protocol is a useful sample preparation method for comparative proteomics analysis of chicken BF tissues.
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22
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Reprint of “The role of the lens in refractive development of the eye: Animal models of ametropia” [Experimental Eye Research 87 (2008) 3–8]. Exp Eye Res 2009. [DOI: 10.1016/s0014-4835(08)00458-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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23
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The role of the lens in refractive development of the eye: Animal models of ametropia. Exp Eye Res 2008; 87:3-8. [DOI: 10.1016/j.exer.2008.03.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2007] [Revised: 02/29/2008] [Accepted: 03/03/2008] [Indexed: 11/23/2022]
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