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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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Bruschi M, Petretto A, Caicci F, Bartolucci M, Calzia D, Santucci L, Manni L, Ramenghi LA, Ghiggeri G, Traverso CE, Candiano G, Panfoli I. Proteome of Bovine Mitochondria and Rod Outer Segment Disks: Commonalities and Differences. J Proteome Res 2018; 17:918-925. [PMID: 29299929 DOI: 10.1021/acs.jproteome.7b00741] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The retinal rod outer segment (OS) is a stack of disks surrounded by the plasma membrane, housing proteins related to phototransduction, as well as mitochondrial proteins involved in oxidative phosphorylation (OxPhos). This prompted us to compare the proteome of bovine OS disks and mitochondria to assess the significant top gene signatures of each sample. The two proteomes, obtained by LTQ-Orbitrap Velos mass spectrometry, were compared by statistical analyses. In total, 4139 proteins were identified, 2045 of which overlapping in the two sets. Nonhierarchical Spearman's correlogram revealed that the groups were clearly discriminated. Partial least square discriminant plus support vector machine analysis identified the major discriminative proteins, implied in phototransduction and lipid metabolism, respectively. Gene Ontology analysis identified top gene signatures of the disk proteome, enriched in vesiculation, glycolysis, and OxPhos proteins. The tricarboxylic acid cycle and the electron transport proteins were similarly enriched in the two samples, but the latter was up regulated in disks. Data suggest that the mitochondrial OxPhos proteins may represent a true OS proteome component, outside the mitochondrion. This knowledge may help the scientific community in the further studies of retinal physiology and pathology.
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Affiliation(s)
| | | | - Federico Caicci
- Department of Biology, Università di Padova , 35121 Padova, Italy
| | | | - Daniela Calzia
- Dipartimento di Farmacia-DIFAR, Università di Genova , 16132 Genoa, Italy
| | | | - Lucia Manni
- Department of Biology, Università di Padova , 35121 Padova, Italy
| | | | | | - Carlo E Traverso
- Clinica Oculistica, (Di.N.O.G.M.I.) Università Department of Intensive Care di Genova, IRCCS Azienda Ospedaliera Universitaria San Martino-IST , 16132 Genoa, Italy
| | | | - Isabella Panfoli
- Dipartimento di Farmacia-DIFAR, Università di Genova , 16132 Genoa, Italy
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Han RX, Kim HR, Diao YF, Lee MG, Jin DI. Detection of early pregnancy-specific proteins in Holstein milk. J Proteomics 2012; 75:3221-9. [PMID: 22484055 DOI: 10.1016/j.jprot.2012.03.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Revised: 03/12/2012] [Accepted: 03/18/2012] [Indexed: 10/28/2022]
Abstract
Bovine pregnancy is commonly diagnosed by rectal palpation or ultrasonography and changes in progesterone concentration. To determine a simpler and less expensive diagnostic method, we sought to identify early pregnancy-specific proteins in bovine milk by comparing samples collected from pregnant and non-pregnant Holstein cattle. Of the 600-700 protein spots visible on 2-DE gel images, 39 were differentially expressed in milk from pregnant and non-pregnant cattle. Antibodies generated against synthetic peptides of milk whey proteins expressed specifically during pregnancy were used to confirm protein expression patterns. Western blot analysis showed that the levels of expression of lactoferrin (lactotransferrin) and alpha1G T-type calcium channel subunit (alpha-1G) were higher in samples from pregnant than non-pregnant cattle. These findings suggest that assays for pregnancy-specific milk proteins may be used to diagnose pregnancy in cattle.
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Affiliation(s)
- Rong Xun Han
- Department of Animal Science & Biotechnology, Research Center for Transgenic and Cloned Pigs, Chungnam National University, Daejeon, South Korea
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Reidel B, Thompson JW, Farsiu S, Moseley MA, Skiba NP, Arshavsky VY. Proteomic profiling of a layered tissue reveals unique glycolytic specializations of photoreceptor cells. Mol Cell Proteomics 2010; 10:M110.002469. [PMID: 21173383 DOI: 10.1074/mcp.m110.002469] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The retina is a highly ordered tissue whose outermost layers are formed by subcellular compartments of photoreceptors generating light-evoked electrical responses. We studied protein distributions among individual photoreceptor compartments by separating the entire photoreceptor layer of a flat-mounted frozen retina into a series of thin tangential cryosections and analyzing protein compositions of each section by label-free quantitative mass spectrometry. Based on 5038 confidently identified peptides assigned to 896 protein database entries, we generated a quantitative proteomic database (a "map") correlating the distribution profiles of identified proteins with the profiles of marker proteins representing individual compartments of photoreceptors and adjacent cells. We evaluated the applicability of several common peptide-to-protein quantification algorithms in the context of our database and found that the highest reliability was obtained by summing the intensities of all peptides representing a given protein, using at least the 5-6 most intense peptides when applicable. We used this proteome map to investigate the distribution of glycolytic enzymes, critical in fulfilling the extremely high metabolic demands of photoreceptor cells, and obtained two major findings. First, unlike the majority of neurons rich in hexokinase I, but similar to other highly metabolically active cells, photoreceptors express hexokinase II. Hexokinase II has a very high catalytic activity when associated with mitochondria, and indeed we found it colocalized with mitochondria in photoreceptors. Second, photoreceptors contain very little triosephosphate isomerase, an enzyme converting dihydroxyacetone phosphate into glyceraldehyde-3-phosphate. This may serve as a functional adaptation because dihydroxyacetone phosphate is a major precursor in phospholipid biosynthesis, a process particularly active in photoreceptors because of the constant renewal of their light-sensitive membrane disc stacks. Overall, our approach for proteomic profiling of very small tissue amounts at a resolution of a few microns, combining cryosectioning and liquid chromatography-tandem MS, can be applied for quantitative investigation of proteomes where spatial resolution is paramount.
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Affiliation(s)
- Boris Reidel
- Albert Eye Research Institute, 2310 Erwin Road, Durham NC 27710, USA
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OKAMOTO H, UMEDA S, NOZAWA T, SUZUKI MT, YOSHIKAWA Y, MATSUURA ET, IWATA T. Comparative Proteomic Analyses of Macular and Peripheral Retina of Cynomolgus Monkeys (Macaca fascicularis). Exp Anim 2010; 59:171-82. [DOI: 10.1538/expanim.59.171] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Affiliation(s)
- Haru OKAMOTO
- Division of Molecular & Cellular Biology, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center
- Department of Advanced Biosciences, Ochanomizu University
| | - Shinsuke UMEDA
- Division of Molecular & Cellular Biology, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center
| | | | | | - Yasuhiro YOSHIKAWA
- Department of Biomedical Science, Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | | | - Takeshi IWATA
- Division of Molecular & Cellular Biology, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center
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Finnegan S, Robson JL, Wylie M, Healy A, Stitt AW, Curry WJ. Protein expression profiling during chick retinal maturation: a proteomics-based approach. Proteome Sci 2008; 6:34. [PMID: 19077203 PMCID: PMC2648947 DOI: 10.1186/1477-5956-6-34] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2008] [Accepted: 12/10/2008] [Indexed: 11/16/2022] Open
Abstract
Background The underlying pathways that drive retinal neurogenesis and synaptogenesis are still relatively poorly understood. Protein expression analysis can provide direct insight into these complex developmental processes. The aim of this study was therefore to employ proteomic analysis to study the developing chick retina throughout embryonic (E) development commencing at day 12 through 13, 17, 19 and post-hatch (P) 1 and 33 days. Results 2D proteomic and mass spectrometric analysis detected an average of 1514 spots per gel with 15 spots demonstrating either modulation or constitutive expression identified via MS. Proteins identified included alpha and beta-tubulin, alpha enolase, B-creatine kinase, gamma-actin, platelet-activating factor (PAF), PREDICTED: similar to TGF-beta interacting protein 1, capping protein (actin filament muscle Z line), nucleophosmin 1 (NPM1), dimethylarginine dimethylaminohydrolase, triosphoaphate isomerase, DJ1, stathmin, fatty acid binding protein 7 (FABP7/B-FABP), beta-synuclein and enhancer of rudimentary homologue. Conclusion This study builds upon previous proteomic investigations of retinal development and represents the addition of a unique data set to those previously reported. Based on reported bioactivity some of the identified proteins are most likely to be important to normal retinal development in the chick. Continued analysis of the dynamic protein populations present at the early stages and throughout retinal development will increase our understanding of the molecular events underpinning retinogenesis.
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Affiliation(s)
- Sorcha Finnegan
- Centre for Vision Sciences, Queen's University of Belfast, Institute of Clinical Sciences, Royal Victoria Hospital, Belfast, Northern Ireland.
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Panfoli I, Musante L, Bachi A, Ravera S, Calzia D, Cattaneo A, Bruschi M, Bianchini P, Diaspro A, Morelli A, Pepe IM, Tacchetti C, Candiano G. Proteomic analysis of the retinal rod outer segment disks. J Proteome Res 2008; 7:2654-69. [PMID: 18489131 DOI: 10.1021/pr7006939] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The initial events of vision at low light take place in vertebrate retinal rods. The rod outer segment consists of a stack of flattened disks surrounded by the plasma membrane. A list of the proteins that reside in disks has not been achieved yet. We present the first comprehensive proteomic analysis of purified rod disks, obtained by combining the results of two-dimensional gel electrophoresis separation of disk proteins to MALDI-TOF or nLC-ESI-MS/MS mass spectrometry techniques. Intact disks were isolated from bovine retinal rod outer segments by a method that minimizes contamination from inner segment. Out of a total of 187 excised spots, 148 proteins were unambiguously identified. An additional set of 61 proteins (partially overlapping with the previous ones) was generated by one-dimensional (1D) gel nLC-ESI-MS/MS method. Proteins involved in vision as well as in aerobic metabolism were found, among which are the five complexes of oxidative phosphorylation. Results from biochemical, Western blot, and confocal laser scanning microscopy immunochemistry experiments suggest that F 1F o-ATP synthase is located and catalytically active in ROS disk membranes. This study represents a step toward a global physiological characterization of the disk proteome and provides information necessary for future studies on energy supply for phototransduction.
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Affiliation(s)
- Isabella Panfoli
- Department of Biology, University of Genoa, V.le Benedetto XV 3, 16132 Genova, Italy. ,
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Haniu H, Komori N, Takemori N, Singh A, Ash JD, Matsumoto H. Proteomic trajectory mapping of biological transformation: Application to developmental mouse retina. Proteomics 2006; 6:3251-61. [PMID: 16673440 DOI: 10.1002/pmic.200500813] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
In this report we introduce a new concept "proteomic trajectory mapping" for the investigation of a complex phenomenon underlying biological transformation and transition. We define proteomic trajectory to be the kinetic trace of protein expression and present a successful proteomic trajectory mapping of complex molecular events underlying postnatal development of mouse retina. Cluster analysis of the trajectory data using a two-state model identified four proteomic trajectory types: two distinct trajectory types accounting for the decline or the rise of protein molecules actively expressed in the juvenile stage (J-type) or in the adult stage (A-type), a class of transient trajectories that mediate the transformation from the juvenile to the adult stage (T-type), and the steady trajectories throughout the entire process of transformation (C-type). The dominance of particular protein categories expressed in each trajectory characterizes the stage of retinal development. Proteomic trajectory mapping will be a powerful tool to study the systematic changes of protein expression caused by physiological, genetic, or pathological agents and the reverse of such changes to the norm by a treatment. The proteomic trajectory mapping is applicable to any biological transformation and, therefore, will be a powerful tool in biomedical sciences.
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Affiliation(s)
- Hisao Haniu
- Department of Biochemistry and Molecular Biology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
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Lu Z, Poliakov E, Redmond TM. Identification of a KRAB-zinc finger protein binding to the Rpe65 gene promoter. Curr Eye Res 2006; 31:457-66. [PMID: 16714237 DOI: 10.1080/02713680600678059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
PURPOSE We wish to identify transcriptional factors involved in regulation binding to the proximal promoter region of the RPE65 gene that confers RPE-specific expression. METHODS We incubated human D407 RPE cell nuclear extract with double-stranded (sense 5-prime biotinylated) oligonucleotides, based on the RPE65 proximal gene promoter, bound to streptavidin-Dynabeads. Bound nuclear proteins were eluted, separated on SDS-PAGE, and analyzed by mass spectrometry. Peptide sequence was used to identify cDNA clones that were subcloned into pCDNA3.1 for expression and co-transfection into D407 cells to assess transcriptional activation of mouse Rpe65 gene promoter/reporter constructs. SiRNA interference was used to suppress ZNF492 expression. RESULTS We identified a D407 nuclear protein binding to biotinylated-DNA/streptavidin beads as the product of clone KIAA1473 encoding a protein named ZNF492. ZNF492 has an open reading frame of 531 amino acids with a truncated N-terminus and lacks the usual Krüppel-associated box-A (KRAB-A) while KRAB-B remains intact and has 12 C2H2 zinc-fingers in tandem arrangement. Co-expression in D407 cells of ZNF492 protein did not activate TR1, a mouse Rpe65 gene promoter/reporter construct with 49-bp 5-prime flanking sequence, but did activate construct TR2, containing 188-bp 5-prime flanking sequence, by 2.5-fold, and the longer constructs TR4, containing 655-bp 5-prime flanking sequence, and TR5, containing 1240-bp 5-prime flanking sequence, by about 2-fold. SiRNA-mediated suppression of ZNF492 in D407 resulted in decreased Rpe65 promoter activity. CONCLUSIONS We have identified ZNF492, a KRAB-zinc finger protein, by its interaction with immobilized RPE65 promoter DNA sequence. This KRAB-zinc finger protein serves as a moderate transcriptional factor for Rpe65 gene upregulation. In ZNF492, absence of KRAB-A might reduce or prevent co-repressor binding to account for the modest upregulation of Rpe65 gene expression.
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Affiliation(s)
- Zhongjian Lu
- Laboratory of Retinal Cell and Molecular Biology, National Eye Institute/NIH, 7 Memorial Drive, Bethesda, MD 20892, USA
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Bowes Rickman C, Ebright JN, Zavodni ZJ, Yu L, Wang T, Daiger SP, Wistow G, Boon K, Hauser MA. Defining the human macula transcriptome and candidate retinal disease genes using EyeSAGE. Invest Ophthalmol Vis Sci 2006; 47:2305-16. [PMID: 16723438 PMCID: PMC2813776 DOI: 10.1167/iovs.05-1437] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE To develop large-scale, high-throughput annotation of the human macula transcriptome and to identify and prioritize candidate genes for inherited retinal dystrophies, based on ocular-expression profiles using serial analysis of gene expression (SAGE). METHODS Two human retina and two retinal pigment epithelium (RPE)/choroid SAGE libraries made from matched macula or midperipheral retina and adjacent RPE/choroid of morphologically normal 28- to 66-year-old donors and a human central retina longSAGE library made from 41- to 66-year-old donors were generated. Their transcription profiles were entered into a relational database, EyeSAGE, including microarray expression profiles of retina and publicly available normal human tissue SAGE libraries. EyeSAGE was used to identify retina- and RPE-specific and -associated genes, and candidate genes for retina and RPE disease loci. Differential and/or cell-type specific expression was validated by quantitative and single-cell RT-PCR. RESULTS Cone photoreceptor-associated gene expression was elevated in the macula transcription profiles. Analysis of the longSAGE retina tags enhanced tag-to-gene mapping and revealed alternatively spliced genes. Analysis of candidate gene expression tables for the identified Bardet-Biedl syndrome disease gene (BBS5) in the BBS5 disease region table yielded BBS5 as the top candidate. Compelling candidates for inherited retina diseases were identified. CONCLUSIONS The EyeSAGE database, combining three different gene-profiling platforms including the authors' multidonor-derived retina/RPE SAGE libraries and existing single-donor retina/RPE libraries, is a powerful resource for definition of the retina and RPE transcriptomes. It can be used to identify retina-specific genes, including alternatively spliced transcripts and to prioritize candidate genes within mapped retinal disease regions.
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Cairoli F, Battocchio M, Veronesi MC, Brambilla D, Conserva F, Eberini I, Wait R, Gianazza E. Serum protein pattern during cow pregnancy: Acute-phase proteins increase in the peripartum period. Electrophoresis 2006; 27:1617-25. [PMID: 16548048 DOI: 10.1002/elps.200500742] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Serum collected in a time-course mode during the pregnancy of a group of heifers was analyzed by 2-DE under various experimental conditions to optimize resolution of all protein spots. Changes in the levels of some components were detected during the last phase of pregnancy and early postpartum. These included a decrease of alpha2-HS-glycoprotein, an increase of alpha1-antichymotrypsin and, with a much larger and more abrupt variation, of orosomucoid and haptoglobin. These findings associate the weeks preceding calving with an acute-phase reaction. Analysis of individual animal's sera by 1-DE demonstrated a higher level of orosomucoid in the sera of cows developing postpartum endometritis during the 2 wk after calving (i.e., in the course of the infection) but a lower level during the 2 wk before calving. This observation could represent an important tool for the prepartum detection of animals prone to develop postpartum endometritis and lead to a more accurate peripartum management of those animals.
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Affiliation(s)
- Fausto Cairoli
- Dipartimento di Scienze Cliniche Veterinarie - Sezione di Clinica Ostetrica e Ginecologica Veterinaria, Facoltà di Medicina Veterinaria, Università degli Studi di Milano, Milano, Italia
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Nakanishi T, Koyama R, Ikeda T, Shimizu A. Catalogue of soluble proteins in the human vitreous humor: comparison between diabetic retinopathy and macular hole. J Chromatogr B Analyt Technol Biomed Life Sci 2002; 776:89-100. [PMID: 12127329 DOI: 10.1016/s1570-0232(02)00078-8] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Two-dimensional gel electrophoresis and mass spectrometry were used to make a catalogue of soluble proteins in the human vitreous humor (VH). Fifty-one different proteins were identified on silver-stained two-dimensional (2D) gel patterns with VH proteins obtained from diabetic retinopathy and macular hole. Thirty of these have not been listed in the reported 2D profiles of plasma. Immunoglobulin (Ig), alpha1-antitrypsin, alpha2-HS glycoprotein,and complement C(4) fragment showed stronger spots in VH with diabetic retinopathy patient samples than those with macular hole. Pigment epithelium-derived factor, a potent inhibitor of angiogenesis in the cornea and vitreous, was clearly detected in VH with diabetes. It is impressive that the inhibitor increases in the vitreous with proliferative angiogenesis.
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Affiliation(s)
- Toyofumi Nakanishi
- Department of Clinical Pathology, Osaka Medical College, 2-7 Daigakucho, Takatsuki, Osaka 569-8686, Japan
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Kennedy S. The role of proteomics in toxicology: identification of biomarkers of toxicity by protein expression analysis. Biomarkers 2002; 7:269-90. [PMID: 12171755 DOI: 10.1080/13547500210127318] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Proteomics, i.e. the high throughput separation, display and identification of proteins, has the potential to be a powerful tool in drug development. It could increase the predictability of early drug development and identify non-invasive biomarkers of toxicity or efficacy. This review provides an introduction to modern proteomics, with particular reference to applications in toxicology. A literature search was carried out to identify studies in two broad classes: screening/predictive toxicology, and mechanistic toxicology. The strengths and limitations of current methods and the likely impact of techniques in drug development are also considered. Proteomics can increase the speed and sensitivity of toxicological screening by identifying protein markers of toxicity. Proteomics studies have already provided insights into the mechanisms of action of a wide range of substances, from metals to peroxisome proliferators. Current limitations involving speed of throughput are being overcome by increasing automation and the development of new techniques. The isotope-coded affinity tag (ICAT) method appears particularly promising. The application of proteomics to drug development has given rise to the new field of pharmacoproteomics. New associations between proteins and toxicopathological effects are constantly being identified, and major progress is on the horizon as we move into the post-genomic era.
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Affiliation(s)
- Sandy Kennedy
- Oxford GlycoSciences (UK) Ltd, The Forum, 86 Milton Park, Abingdon, Oxfordshire OX14 4RY, UK.
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Abstract
The hormone melatonin is synthesized by pinealocytes and retinal photoreceptors with a diurnal rhythm. Melatonin produced in the retina at night is thought to exert local modulatory effects by binding to specific receptors in several different retinal cell types. The mechanisms by which melatonin influences circadian activity in retinal cells is poorly understood. Suppression of cyclic AMP synthesis appears to be a major signaling pathway in response to melatonin receptor binding in many tissues. A potential downstream consequence of melatonin-induced changes in cyclic AMP concentrations and protein phosphorylation is the up- or down-regulation of expression of specific genes. In this report, we examined the changes in expression levels of specific proteins in the neural retina and retinal pigment epithelium (RPE) in response to melatonin treatment, because both of these tissues express melatonin receptors. Neural retina and RPE isolated from the eyes of Xenopus laevis were treated with or without 1 microM melatonin for 6 hr, then the rapidly synthesized tissue proteins were radiolabeled by a 15 min incubation with 35S-methionine, and the proteins were subsequently analyzed by two-dimensional gel electrophoresis and autoradiography. In both the neural retina and RPE, the densities of some specific proteins were altered in response to melatonin treatment, and the few protein spots that were altered were distinct between the two tissues. These results support the concept that one function of melatonin may be to regulate the expression of specific genes and the consequent protein levels, and that the target genes may differ according to the cell or tissue type.
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Affiliation(s)
- Allan F Wiechmann
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City 73190, USA.
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Niwayama S, Kurono S, Matsumoto H. Synthesis of d-labeled N-alkylmaleimides and application to quantitative peptide analysis by isotope differential mass spectrometry. Bioorg Med Chem Lett 2001; 11:2257-61. [PMID: 11527710 DOI: 10.1016/s0960-894x(01)00452-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
d-Labeled N-alkylmaleimides have been prepared for specific modification of the terminal SH groups of cysteine residues in proteins or peptides. These reagents are useful tools for quantitative analysis of peptides by stable isotope differential mass spectrometry.
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Affiliation(s)
- S Niwayama
- Department of Chemistry, Oklahoma State University, Stillwater, OK 74078-3071, USA.
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16
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Pourcho RG, Qin P, Goebel DJ. Cellular and subcellular distribution of NMDA receptor subunit NR2B in the retina. J Comp Neurol 2001; 433:75-85. [PMID: 11283950 DOI: 10.1002/cne.1126] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Immunocytochemical studies showed the presence of staining for the N-methyl-D-aspartate (NMDA)-R2B glutamate receptor subunit at multiple sites in the cat retina. Reaction product in photoreceptor cells was localized at the inner/outer segment junction and in the axon terminals. Staining within the inner retina was limited to ganglion cells and their dendrites ramifying throughout the inner plexiform layer. These cells were seen to receive synaptic input from cone bipolar cells in both sublaminae. As with other glutamate receptor subunits, this immunoreactivity was typically confined to a single postsynaptic element at a cone bipolar dyad complex. Immunocytochemical localization of the NMDA-R1 subunit, considered to be an essential component of functional receptors, showed a widespread distribution across the retina including all the sites where NMDA-R2B staining was seen. Immunoprecipitation and Western blot analysis were used to confirm the presence of the NR2B receptor protein and its association with the NR1 subunit in both proximal and distal retinal layers. The findings suggest that NMDA-R2B subunits are positioned for multiple functions within the retina.
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Affiliation(s)
- R G Pourcho
- Department of Anatomy and Cell Biology, School of Medicine, Wayne State University, 540 East Canfield Avenue, Detroit, MI 48201, USA.
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Hayashi F, Matsuura I, Kachi S, Maeda T, Yamamoto M, Fujii Y, Liu H, Yamazaki M, Usukura J, Yamazaki A. Phosphorylation by cyclin-dependent protein kinase 5 of the regulatory subunit of retinal cGMP phosphodiesterase. II. Its role in the turnoff of phosphodiesterase in vivo. J Biol Chem 2000; 275:32958-65. [PMID: 10884379 DOI: 10.1074/jbc.m000703200] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Retinal cGMP phosphodiesterase (PDE) is regulated by Pgamma, the regulatory subunit of PDE, and GTP/Talpha, the GTP-bound alpha subunit of transducin. In the accompanying paper (Matsuura, I., Bondarenko, V. A., Maeda, T., Kachi, S., Yamazaki, M., Usukura, J., Hayashi, F., and Yamazaki, A. (2000) J. Biol. Chem. 275, 32950-32957), we have shown that all known Pgammas contain a specific phosphorylation motif for cyclin-dependent protein kinase 5 (Cdk5) and that the unknown kinase is Cdk5 complexed with its activator. Here, using frog rod photoreceptor outer segments (ROS) isolated by a new method, we show that Cdk5 is involved in light-dependent Pgamma phosphorylation in vivo. Under dark conditions only negligible amounts of Pgamma were phosphorylated. However, under illumination that bleached less than 0.3% of the rhodopsin, approximately 4% of the total Pgamma was phosphorylated in less than 10 s. Pgamma dephosphorylation occurred in less than 1 s after the light was turned off. Analysis of the phosphorylated amino acid, inhibition of Pgamma phosphorylation by Cdk inhibitors in vivo and in vitro, and two-dimensional peptide map analysis of Pgamma phosphorylated in vivo and in vitro indicate that Cdk5 phosphorylates a Pgamma threonine in the same manner in vivo and in vitro. These observations, together with immunological data showing the presence of Cdk5 in ROS, suggest that Cdk5 is involved in light-dependent Pgamma phosphorylation in ROS and that the phosphorylation is significant and reversible. In an homogenate of frog ROS, PDE activated by light/guanosine 5'-O-(3-thiotriphosphate) (GTPgammaS) was inhibited by Pgamma alone, but not by Pgamma complexed with GDP/Talpha or GTPgammaS/Talpha. Under these conditions, Pgamma phosphorylated by Cdk5 inhibited the light/GTPgammaS-activated PDE even in the presence of GTPgammaS/Talpha. These observations suggest that phosphorylated Pgamma interacts with and inhibits light/GTPgammaS-activated PDE, but does not interact with GTPgammaS/Talpha in the homogenate. Together, our results strongly suggest that after activation of PDE by light/GTP, Pgamma is phosphorylated by Cdk5 and the phosphorylated Pgamma inhibits GTP/Talpha-activated PDE, even in the presence of GTP/Talpha in ROS.
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Affiliation(s)
- F Hayashi
- Department of Biology, Faculty of Science, Kobe University, Kobe 657, Japan.
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Abstract
The goal of molecular ophthalmology is the early detection and therapeutic treatment of eye disease. Genomic technologies have profoundly enhanced the discovery of ocular disease candidate genes. Proteomics, the protein cognate of genomic technology, offers a means to monitor changes in the expression of a given ocular protein(s) and its post-translational modification, identify novel therapeutic targets and evaluate pharmacological effects on a given metabolic pathway. Using both tissue and cultured cells, numerous laboratories have begun to catalogue changes in ocular protein expression in normal, diseased and ageing subjects. Herein, we review published proteomic literature in the broad context of ophthalmic diseases involving various tissues of the eye.
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Affiliation(s)
- H T Steely
- Alcon Research Ltd, Fort Worth, TX 76134, USA.
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Matsumoto H, Komori N. Ocular proteomics: cataloging photoreceptor proteins by two-dimensional gel electrophoresis and mass spectrometry. Methods Enzymol 2000; 316:492-511. [PMID: 10800697 DOI: 10.1016/s0076-6879(00)16745-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- H Matsumoto
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City 73190, USA
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