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Licier R, Miranda E, Serrano H. A Quantitative Proteomics Approach to Clinical Research with Non-Traditional Samples. Proteomes 2016; 4:proteomes4040031. [PMID: 28248241 PMCID: PMC5260964 DOI: 10.3390/proteomes4040031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 09/19/2016] [Accepted: 09/21/2016] [Indexed: 01/13/2023] Open
Abstract
The proper handling of samples to be analyzed by mass spectrometry (MS) can guarantee excellent results and a greater depth of analysis when working in quantitative proteomics. This is critical when trying to assess non-traditional sources such as ear wax, saliva, vitreous humor, aqueous humor, tears, nipple aspirate fluid, breast milk/colostrum, cervical-vaginal fluid, nasal secretions, bronco-alveolar lavage fluid, and stools. We intend to provide the investigator with relevant aspects of quantitative proteomics and to recognize the most recent clinical research work conducted with atypical samples and analyzed by quantitative proteomics. Having as reference the most recent and different approaches used with non-traditional sources allows us to compare new strategies in the development of novel experimental models. On the other hand, these references help us to contribute significantly to the understanding of the proportions of proteins in different proteomes of clinical interest and may lead to potential advances in the emerging field of precision medicine.
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Affiliation(s)
- Rígel Licier
- Department of Medicine, San Juan Bautista School of Medicine, Caguas 00727, Puerto Rico.
- Quantitative Proteomics Laboratory, Comprehensive Cancer Center of Puerto Rico, San Juan 00936, Puerto Rico.
| | - Eric Miranda
- Quantitative Proteomics Laboratory, Comprehensive Cancer Center of Puerto Rico, San Juan 00936, Puerto Rico.
- Department of Internal Medicine, University of Puerto Rico, Medical Sciences Campus, San Juan 00936, Puerto Rico.
| | - Horacio Serrano
- Quantitative Proteomics Laboratory, Comprehensive Cancer Center of Puerto Rico, San Juan 00936, Puerto Rico.
- Department of Internal Medicine, University of Puerto Rico, Medical Sciences Campus, San Juan 00936, Puerto Rico.
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Murthy KR, Dammalli M, Pinto SM, Murthy KB, Nirujogi RS, Madugundu AK, Dey G, Subbannayya Y, Mishra UK, Nair B, Gowda H, Prasad TK. A Comprehensive Proteomics Analysis of the Human Iris Tissue: Ready to Embrace Postgenomics Precision Medicine in Ophthalmology? OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2016; 20:510-9. [DOI: 10.1089/omi.2016.0100] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Krishna R. Murthy
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- Amrita School of Biotechnology, Amrita VishwaVidyapeetham, Kollam, India
- Vittala International Institute of Ophthalmology, Bangalore, India
| | - Manjunath Dammalli
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- Department of Biotechnology, Siddaganga Institute of Technology, Tumkur, India
| | - Sneha M. Pinto
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore, India
| | | | - Raja Sekhar Nirujogi
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Anil K. Madugundu
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Gourav Dey
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- Manipal University, Manipal, India
| | - Yashwanth Subbannayya
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore, India
| | | | - Bipin Nair
- Amrita School of Biotechnology, Amrita VishwaVidyapeetham, Kollam, India
| | - Harsha Gowda
- Institute of Bioinformatics, International Tech Park, Bangalore, India
| | - T.S. Keshava Prasad
- Institute of Bioinformatics, International Tech Park, Bangalore, India
- YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore, India
- NIMHANS-IOB Bioinformatics and Proteomics Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences, Bangalore, India
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Yu-Wai-Man C, Khaw PT. Personalized Medicine in Ocular Fibrosis: Myth or Future Biomarkers. Adv Wound Care (New Rochelle) 2016; 5:390-402. [PMID: 27679750 PMCID: PMC5028906 DOI: 10.1089/wound.2015.0677] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Accepted: 02/04/2016] [Indexed: 02/06/2023] Open
Abstract
Significance: Fibrosis-related events play a part in the pathogenesis or failure of treatment of virtually all the blinding diseases around the world, and also account for over 40% of all deaths. It is well established that the eye and other tissues of some group of patients, for example Afro-Caribbean people, scar worse than others. However, there is a current lack of reliable biomarkers to stratify the risk of scarring and postsurgical fibrosis in the eye. Recent Advances: Recent studies using genomics, proteomics, metabolomics, clinical phenotyping, and high-resolution in vivo imaging techniques have revealed potential novel biomarkers to identify and stratify patients at risk of scarring in different fibrotic eye diseases. Critical Issues: Most of the studies, to date, have been done in animals or small cohorts of patients and future research is needed to validate these results in large longitudinal human studies. Detailed clinical phenotyping and effective biobanking of patient tissues will also be critical for future biomarker research in ocular fibrosis. Future Directions: The ability to predict the risk of scarring and to tailor the antifibrotic treatment regimen to each individual patient will be an extremely useful tool clinically to prevent undertreating, or exposing patients to unnecessary treatments with potential side effects. An exciting future prospect will be to use new advances in genotyping, namely next-generation whole genome sequencing like RNA-Seq, to develop a customized gene chip in ocular fibrosis. Successful translation of future biomarkers to benefit patient care will also ultimately require a strong collaboration between academics, pharmaceutical, and biotech companies.
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Affiliation(s)
- Cynthia Yu-Wai-Man
- National Institute for Health Research (NIHR) Biomedical Research Centre at Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, United Kingdom
| | - Peng Tee Khaw
- National Institute for Health Research (NIHR) Biomedical Research Centre at Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, United Kingdom
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54
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Lam MPY, Venkatraman V, Xing Y, Lau E, Cao Q, Ng DCM, Su AI, Ge J, Van Eyk JE, Ping P. Data-Driven Approach To Determine Popular Proteins for Targeted Proteomics Translation of Six Organ Systems. J Proteome Res 2016; 15:4126-4134. [PMID: 27356587 DOI: 10.1021/acs.jproteome.6b00095] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Amidst the proteomes of human tissues lie subsets of proteins that are closely involved in conserved pathophysiological processes. Much of biomedical research concerns interrogating disease signature proteins and defining their roles in disease mechanisms. With advances in proteomics technologies, it is now feasible to develop targeted proteomics assays that can accurately quantify protein abundance as well as their post-translational modifications; however, with rapidly accumulating number of studies implicating proteins in diseases, current resources are insufficient to target every protein without judiciously prioritizing the proteins with high significance and impact for assay development. We describe here a data science method to prioritize and expedite assay development on high-impact proteins across research fields by leveraging the biomedical literature record to rank and normalize proteins that are popularly and preferentially published by biomedical researchers. We demonstrate this method by finding priority proteins across six major physiological systems (cardiovascular, cerebral, hepatic, renal, pulmonary, and intestinal). The described method is data-driven and builds upon the collective knowledge of previous publications referenced on PubMed to lend objectivity to target selection. The method and resulting popular protein lists may also be useful for exploring biological processes associated with various physiological systems and research topics, in addition to benefiting ongoing efforts to facilitate the broad translation of proteomics technologies.
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Affiliation(s)
| | - Vidya Venkatraman
- Advanced Clinical Biosystems Research Institute, Department of Medicine and The Heart Institute, Cedars-Sinai Medical Center , Los Angeles, California 90048, United States
| | | | | | - Quan Cao
- Department of Cardiology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University , Shanghai, 200433, China
| | | | - Andrew I Su
- Department of Molecular and Experimental Medicine, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Junbo Ge
- Department of Cardiology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University , Shanghai, 200433, China
| | - Jennifer E Van Eyk
- Advanced Clinical Biosystems Research Institute, Department of Medicine and The Heart Institute, Cedars-Sinai Medical Center , Los Angeles, California 90048, United States
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55
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Liu Y, Bouhenni RA, Dufresne CP, Semba RD, Edward DP. Differential Expression of Vitreous Proteins in Young and Mature New Zealand White Rabbits. PLoS One 2016; 11:e0153560. [PMID: 27089221 PMCID: PMC4835093 DOI: 10.1371/journal.pone.0153560] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 03/31/2016] [Indexed: 02/06/2023] Open
Abstract
Different anatomical regions have been defined in the vitreous humor including central vitreous, basal vitreous, vitreous cortex, vitreoretinal interface and zonule. In this study we sought to characterize changes in the proteome of vitreous humor (VH) related to compartments or age in New Zealand white rabbits (NZW). Vitreous humor was cryo-collected from young and mature New Zealand white rabbit eyes, and dissected into anterior and posterior compartments. All samples were divided into 4 groups: Young Anterior (YA), Young Posterior (YP), Mature Anterior (MA) and Mature Posterior (MP) vitreous. Tryptic digests of total proteins were analyzed by liquid chromatography followed by tandem mass spectrometry. Spectral count was used to determine the relative protein abundances and identify proteins with statistical differences between compartment and age groups. Western blotting was performed to validate some of the differentially expressed proteins. Our results showed that 231, 375, 273 and 353 proteins were identified in the YA, YP, MA and MP respectively. Fifteen proteins were significantly differentially expressed between YA and YP, and 11 between MA and MP. Carbonic anhydrase III, lambda crystallin, alpha crystallin A and B, beta crystallin B1 and B2 were more abundant in the anterior region, whereas vimentin was less abundant in the anterior region. For comparisons between age groups, 4 proteins were differentially expressed in both YA relative to MA and YP relative to MP. Western blotting confirmed the differential expression of carbonic anhydrase III, alpha crystallin B and beta crystallin B2. The protein profiles of the vitreous humor showed age- and compartment-related differences. This differential protein profile provides a baseline for understanding the vitreous compartmentalization in the rabbit and suggests that further studies profiling proteins in different compartments of the vitreous in other species may be warranted.
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Affiliation(s)
- Ying Liu
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, United States of America
- Changsha Aier Eye Hospital, Changsha, China
| | | | - Craig P. Dufresne
- Thermo Fisher Scientific, West Palm Beach, Florida, United States of America
| | - Richard D. Semba
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, United States of America
| | - Deepak P. Edward
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, United States of America
- King Khaled Eye Specialist Hospital, Riyadh, Saudi Arabia
- * E-mail:
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56
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Zhang P, Kirby D, Dufresne C, Chen Y, Turner R, Ferri S, Edward DP, Van Eyk JE, Semba RD. Defining the proteome of human iris, ciliary body, retinal pigment epithelium, and choroid. Proteomics 2016; 16:1146-53. [PMID: 26834087 DOI: 10.1002/pmic.201500188] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 11/19/2015] [Accepted: 01/25/2016] [Indexed: 11/09/2022]
Abstract
The iris is a fine structure that controls the amount of light that enters the eye. The ciliary body controls the shape of the lens and produces aqueous humor. The retinal pigment epithelium and choroid (RPE/choroid) are essential in supporting the retina and absorbing light energy that enters the eye. Proteins were extracted from iris, ciliary body, and RPE/choroid tissues of eyes from five individuals and fractionated using SDS-PAGE. After in-gel digestion, peptides were analyzed using LC-MS/MS on an Orbitrap Elite mass spectrometer. In iris, ciliary body, and RPE/choroid, we identified 2959, 2867, and 2755 nonredundant proteins with peptide and protein false-positive rates of <0.1% and <1%, respectively. Forty-three unambiguous protein isoforms were identified in iris, ciliary body, and RPE/choroid. Four "missing proteins" were identified in ciliary body based on ≥2 proteotypic peptides. The mass spectrometric proteome database of the human iris, ciliary body, and RPE/choroid may serve as a valuable resource for future investigations of the eye in health and disease. The MS proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifiers PXD001424 and PXD002194.
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Affiliation(s)
- Pingbo Zhang
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - David Kirby
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Yan Chen
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Randi Turner
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sara Ferri
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Deepak P Edward
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,King Khaled Eye Specialist Hospital, Riyadh, Kingdom of Saudi Arabia
| | - Jennifer E Van Eyk
- Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA.,Department of Medicine, The Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Richard D Semba
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Yee KMP, Feener EP, Madigan M, Jackson NJ, Gao BB, Ross-Cisneros FN, Provis J, Aiello LP, Sadun AA, Sebag J. Proteomic Analysis of Embryonic and Young Human Vitreous. Invest Ophthalmol Vis Sci 2016; 56:7036-42. [PMID: 26529037 DOI: 10.1167/iovs.15-16809] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
PURPOSE The proteomic profile of vitreous from second-trimester human embryos and young adults was characterized using mass spectrometry and analyzed for changes in protein levels that may relate to structural changes occurring during this time. This vitreous proteome was compared to previous reports to confirm proteins already identified and reveal novel ones. METHODS Vitreous from 17 human embryos aged 14 to 20 weeks gestation (WG) and from a 12-, a 14-, a 15-, and a 28-year-old was individually analyzed using tandem mass spectrometry-based proteomics. Peptide spectral count associations with embryonic age were assessed using a general linear model of fold changes and Spearman's rank correlation. Differences between embryonic and young adult vitreous proteomes were also compared. Immunohistochemistry was used to evaluate three proteins in five additional fetal (10-18 WG) human eyes. RESULTS There were 1217 proteins identified in fetal and young adult human vitreous, 206 after quantile normalization and variance filtering. In embryos, the peptide counts of 37 proteins changed significantly from 14 to 20 WG: 75.7% increased, 24.3% decreased. Immunohistochemistry confirmed the absence of clusterin and cadherin in 10 and 14 WG eyes and their presence at 18 WG. Comparing embryonic to young adult vitreous, 47 proteins were significantly higher or lower. A total of 768 proteins not previously identified in the literature are presented. CONCLUSIONS Proteins previously unreported in the human vitreous were identified. The human vitreous proteome undergoes significant changes during embryogenesis and young adulthood. A number of protein levels change considerably during the second trimester, with the majority decreasing.
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Affiliation(s)
- Kenneth M P Yee
- VMR Institute for Vitreous Macula Retina, Huntington Beach, California, United States 2Doheny Eye Institute, Los Angeles, California, United States
| | - Edward P Feener
- Beetham Eye Institute, Joslin Diabetes Center, Boston, Massachusetts, United States
| | - Michele Madigan
- School of Optometry and Vision Science, University of New South Wales, Sydney, Australia 5Save Sight Institute, University of Sydney, Sydney, Australia
| | - Nicholas J Jackson
- Department of Medicine Statistics Core, David Geffen School of Medicine at UCLA, Los Angeles, California, United States
| | - Ben-Bo Gao
- Beetham Eye Institute, Joslin Diabetes Center, Boston, Massachusetts, United States
| | | | - Jan Provis
- John Curtin School of Medical Research, Canberra, Australia 8Australian National University, Canberra, Australia
| | - Lloyd Paul Aiello
- Beetham Eye Institute, Joslin Diabetes Center, Boston, Massachusetts, United States 9Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, United States
| | - Alfredo A Sadun
- Doheny Eye Institute, Los Angeles, California, United States 10Department of Ophthalmology, David Geffen School of Medicine at UCLA, Los Angeles, California, United States
| | - J Sebag
- VMR Institute for Vitreous Macula Retina, Huntington Beach, California, United States 2Doheny Eye Institute, Los Angeles, California, United States
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Poulsen ET, Nielsen NS, Jensen MM, Nielsen E, Hjortdal J, Kim EK, Enghild JJ. LASIK surgery of granular corneal dystrophy type 2 patients leads to accumulation and differential proteolytic processing of transforming growth factor beta-induced protein (TGFBIp). Proteomics 2016; 16:539-43. [DOI: 10.1002/pmic.201500287] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 09/29/2015] [Accepted: 11/09/2015] [Indexed: 11/11/2022]
Affiliation(s)
| | | | - Morten M. Jensen
- Department of Molecular Biology and Genetics; Aarhus University; Aarhus Denmark
| | - Esben Nielsen
- Department of Ophthalmology; Aarhus University Hospital; Aarhus Denmark
| | - Jesper Hjortdal
- Department of Ophthalmology; Aarhus University Hospital; Aarhus Denmark
| | - Eung Kweon Kim
- Department of Ophthalmology; Corneal Dystrophy Research Institute; Yonsei University College of Medicine; Seoul South Korea
- Institute of Vision Research; Severance Biomedical Science Institute; Brain Korea 21 Plus Project for Medical Science; Yonsei University College of Medicine; Seoul South Korea
| | - Jan J. Enghild
- Department of Molecular Biology and Genetics; Aarhus University; Aarhus Denmark
- Interdisciplinary Nanoscience Center; Aarhus University; Aarhus Denmark
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Bottom–up protein identifications from microliter quantities of individual human tear samples. Important steps towards clinical relevance. EUPA OPEN PROTEOMICS 2015. [DOI: 10.1016/j.euprot.2015.06.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Semba RD, Lam M, Sun K, Zhang P, Schaumberg DA, Ferrucci L, Ping P, Van Eyk JE. Priorities and trends in the study of proteins in eye research, 1924-2014. Proteomics Clin Appl 2015; 9:1105-22. [PMID: 26123431 PMCID: PMC4695326 DOI: 10.1002/prca.201500006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 03/26/2015] [Accepted: 06/25/2015] [Indexed: 11/12/2022]
Abstract
PURPOSE To identify the proteins that are relevant to eye research and develop assays for the study of a set of these proteins. EXPERIMENTAL DESIGN We conducted a bibliometric analysis by merging gene lists for human and mouse from the National Center for Biotechnology Information FTP site and combining them with PubMed references that were retrieved with the search terms "eye" [MeSH Terms] OR "eye" [All Fields] OR "eyes" [All Fields]. RESULTS For human and mouse eye studies, respectively, the total number of publications was 13,525 and 23,895 and the total number of proteins was 4050 and 4717. For proteins in human and mouse eye studies, respectively, 88.7 and 81.7% had five or fewer citations. The top 50 most intensively studied proteins for human and mouse eye studies were generally in the areas of photoreceptors and phototransduction, inflammation, and angiogenesis, neurodevelopment, lens transparency, and cell-cycle and cellular processes. We proposed selected reaction monitoring assays that were developed in silico for the top fifty most intensively studied proteins in human and mouse eye research. CONCLUSIONS AND CLINICAL RELEVANCE We conclude that scientists engaged in eye research tend to focus on the same proteins. Newer resources and tools in proteomics can expand the investigations to lesser-known proteins of the eye.
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Affiliation(s)
- Richard D. Semba
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Maggie Lam
- Cardiac Proteomics and Signaling Laboratory, Department of Physiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
| | - Kai Sun
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Pingbo Zhang
- Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Debra A. Schaumberg
- Center for Translational Medicine, Moran Eye Center, University of Utah School of Medicine, Salt Lake City, UT
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA
| | - Luigi Ferrucci
- National Institute on Aging, National Institutes of Health, Baltimore, MD
| | - Peipei Ping
- Cardiac Proteomics and Signaling Laboratory, Department of Physiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
| | - Jennifer E. Van Eyk
- Advanced Clinical BioSystems Research Institute, The Heart Institute and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA
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62
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Zhang P, Dufresne C, Turner R, Ferri S, Venkatraman V, Karani R, Lutty GA, Van Eyk JE, Semba RD. The proteome of human retina. Proteomics 2015; 15:836-40. [PMID: 25407473 DOI: 10.1002/pmic.201400397] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 10/14/2014] [Accepted: 11/14/2014] [Indexed: 01/07/2023]
Abstract
The retina is a delicate tissue that detects light, converts photochemical energy into neural signals, and transmits the signals to the visual cortex of the brain. A detailed protein inventory of the proteome of the normal human eye may provide a foundation for new investigations into both the physiology of the retina and the pathophysiology of retinal diseases. To provide an inventory, proteins were extracted from five retinas of normal eyes and fractionated using SDS-PAGE. After in-gel digestion, peptides were analyzed in duplicate using LC-MS/MS on an Orbitrap Elite mass spectrometer. A total of 3436 nonredundant proteins were identified in the human retina, including 20 unambiguous protein isoforms, of which eight have not previously been demonstrated to exist at the protein level. The proteins identified in the retina included most of the enzymes involved in the visual cycle and retinoid metabolism. One hundred and fifty-eight proteins that have been associated with age-related macular degeneration were identified in the retina. The MS proteome database of the human retina may serve as a valuable resource for future investigations of retinal biology and disease. All MS data have been deposited in the ProteomeXchange with identifier PXD001242 (http://proteomecentral.proteomexchange.org/dataset/PXD001242).
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Affiliation(s)
- Pingbo Zhang
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Aebersold R, Bader GD, Edwards AM, van Eyk J, Kussman M, Qin J, Omenn GS. Highlights of B/D-HPP and HPP Resource Pillar Workshops at 12th Annual HUPO World Congress of Proteomics: September 14-18, 2013, Yokohama, Japan. Proteomics 2014; 14:975-88. [PMID: 24596128 DOI: 10.1002/pmic.201400041] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 02/20/2014] [Indexed: 12/24/2022]
Abstract
At the 12th Annual HUPO World Congress of Proteomics in Japan, the Human Proteome Project (HPP) presented 16 scientific workshop sessions. Here we summarize highlights of ten workshops from the Biology and Disease-driven HPP (B/D-HPP) teams and three from the HPP Resource Pillars. Highlights of the three Chromosome-centric HPP sessions appeared in the many articles of the 2014 C-HPP special issue of the Journal of Proteome Research .
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Saraygord-Afshari N, Naderi-Manesh H, Naderi M. Increasing proteome coverage for gel-based human tear proteome maps: towards a more comprehensive profiling. Biomed Chromatogr 2014; 29:1056-67. [DOI: 10.1002/bmc.3392] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2014] [Revised: 09/29/2014] [Accepted: 10/20/2014] [Indexed: 01/25/2023]
Affiliation(s)
- Neda Saraygord-Afshari
- Department of Biophysics, Faculty of Biological Sciences; Tarbiat Modares University; Tehran Iran
| | - Hossein Naderi-Manesh
- Department of Biophysics, Faculty of Biological Sciences; Tarbiat Modares University; Tehran Iran
| | - Mostafa Naderi
- Department of Ophthalmology; Bina eye hospital; Tehran Iran
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65
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Rocha AS, Santos FM, Monteiro JP, Castro-de-Sousa JP, Queiroz JA, Tomaz CT, Passarinha LA. Trends in proteomic analysis of human vitreous humor samples. Electrophoresis 2014; 35:2495-508. [DOI: 10.1002/elps.201400049] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 05/02/2014] [Accepted: 05/02/2014] [Indexed: 12/17/2022]
Affiliation(s)
- Ana S. Rocha
- CICS-UBI - Health Sciences Research Centre; University of Beira Interior; Covilhã Portugal
- Chemistry Department; Faculty of Sciences, University of Beira Interior; Covilhã Portugal
| | - Fátima M. Santos
- CICS-UBI - Health Sciences Research Centre; University of Beira Interior; Covilhã Portugal
- Chemistry Department; Faculty of Sciences, University of Beira Interior; Covilhã Portugal
| | - João P. Monteiro
- CICS-UBI - Health Sciences Research Centre; University of Beira Interior; Covilhã Portugal
| | - João P. Castro-de-Sousa
- Medical Sciences Department; Faculty of Health sciences; University of Beira Interior; Covilhã Portugal
- Ophthalmology Service; Leiria-Pombal Hospital Center; Pombal Portugal
| | - João A. Queiroz
- CICS-UBI - Health Sciences Research Centre; University of Beira Interior; Covilhã Portugal
- Chemistry Department; Faculty of Sciences, University of Beira Interior; Covilhã Portugal
| | - Cândida T. Tomaz
- CICS-UBI - Health Sciences Research Centre; University of Beira Interior; Covilhã Portugal
- Chemistry Department; Faculty of Sciences, University of Beira Interior; Covilhã Portugal
| | - Luís A. Passarinha
- CICS-UBI - Health Sciences Research Centre; University of Beira Interior; Covilhã Portugal
- Medical Sciences Department; Faculty of Health sciences; University of Beira Interior; Covilhã Portugal
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Elsobky S, Crane AM, Margolis M, Carreon TA, Bhattacharya SK. Review of application of mass spectrometry for analyses of anterior eye proteome. World J Biol Chem 2014; 5:106-114. [PMID: 24921002 PMCID: PMC4050106 DOI: 10.4331/wjbc.v5.i2.106] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 01/16/2014] [Accepted: 03/04/2014] [Indexed: 02/05/2023] Open
Abstract
Proteins have important functional roles in the body, which can be altered in disease states. The eye is a complex organ rich in proteins; in particular, the anterior eye is very sophisticated in function and is most commonly involved in ophthalmic diseases. Proteomics, the large scale study of proteins, has greatly impacted our knowledge and understanding of gene function in the post-genomic period. The most significant breakthrough in proteomics has been mass spectrometric identification of proteins, which extends analysis far beyond the mere display of proteins that classical techniques provide. Mass spectrometry functions as a “mass analyzer” which simplifies the identification and quantification of proteins extracted from biological tissue. Mass spectrometric analysis of the anterior eye proteome provides a differential display for protein comparison of normal and diseased tissue. In this article we present the key proteomic findings in the recent literature related to the cornea, aqueous humor, trabecular meshwork, iris, ciliary body and lens. Through this we identified unique proteins specific to diseases related to the anterior eye.
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Abstract
The human eye proteome is the latest addition to the HUPO Human Proteome Project (HPP). Semba et al. (The Human Eye Proteome Project: Perspectives on an emerging proteome. Proteomics 2013, 13, 2500-2511) establish a provisional baseline for the proteomes of the many anatomical compartments of the eye, based on literature review. As part of the Biology and Disease-driven HPP, they and their colleagues will generate fresh data and meet the stringent guidelines for protein identification and characterization as established by the HPP.
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Affiliation(s)
- Gilbert S Omenn
- Center for Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109-2218, USA.
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Semba RD, Huang H, Lutty GA, Van Eyk JE, Hart GW. The role of O-GlcNAc signaling in the pathogenesis of diabetic retinopathy. Proteomics Clin Appl 2014; 8:218-31. [PMID: 24550151 DOI: 10.1002/prca.201300076] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Revised: 09/24/2013] [Accepted: 10/04/2013] [Indexed: 12/14/2022]
Abstract
Diabetic retinopathy is a leading cause of blindness worldwide. Despite laser and surgical treatments, antiangiogenic and other therapies, and strict metabolic control, many patients progress to visual impairment and blindness. New insights are needed into the pathophysiology of diabetic retinopathy in order to develop new methods to improve the detection and treatment of disease and the prevention of blindness. Hyperglycemia and diabetes result in increased flux through the hexosamine biosynthetic pathway, which, in turn, results in increased PTM of Ser/Thr residues of proteins by O-linked β-N-acetylglucosamine (O-GlcNAc). O-GlcNAcylation is involved in regulation of many nuclear and cytoplasmic proteins in a manner similar to protein phosphorylation. Altered O-GlcNAc signaling has been implicated in the pathogenesis of diabetes and may play an important role in the pathogenesis of diabetic retinopathy. The goal of this review is to summarize the biology of the hexosamine biosynthesis pathway and O-GlcNAc signaling, to present the current evidence for the role of O-GlcNAc signaling in diabetes and diabetic retinopathy, and to discuss future directions for research on O-GlcNAc in the pathogenesis of diabetic retinopathy.
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Affiliation(s)
- Richard D Semba
- Wilmer Eye Institute, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
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