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Guo H, Li J, Lu P. Systematic review and meta-analysis of mass spectrometry proteomics applied to ocular fluids to assess potential biomarkers of age-related macular degeneration. BMC Ophthalmol 2023; 23:507. [PMID: 38087257 PMCID: PMC10717315 DOI: 10.1186/s12886-023-03237-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Age-related macular degeneration (AMD) is a significant cause of severe vision loss. The main purpose of this study was to identify mass spectrometry proteomics-based potential biomarkers of AMD that contribute to understanding the mechanisms of disease and aiding in early diagnosis. METHODS This study retrieved studies that aim to detect differences relate to proteomics in AMD patients and healthy control groups by mass spectrometry (MS) proteomics approaches. The search process was accord with PRISMA guidelines (PROSPERO database: CRD42023388093). Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes Pathway Analysis (KEGG) were performed on differentially expressed proteins (DEPs) in the included articles using the DAVID database. DEPs were included in a meta-analysis when their effect size could be computed in at least two research studies. The effect size of measured proteins was transformed to the log2-fold change. Protein‒protein interaction (PPI) analysis was conducted on proteins that were statistically significant in the meta-analysis using the String online database. RESULTS Eleven studies fulfilled the inclusion criteria, and 161 DEPs were identified. The GO analysis showed that AMD is significantly related to proteolysis, extracellular exosome and protein binding. In KEGG, the most significant pathway was the complement and coagulation cascades. Meta-analysis results suggested that eight proteins were statistically significant, and according to PPI results, the most significant four proteins were serotransferrin (TF), apolipoprotein A1 (APOA1), complement C3 (C3) and lipocalin-1 (LCN1). CONCLUSIONS Four possible biomarkers, TF, APOA1, C3 and LCN1, were found to be significant in the pathogenesis of AMD and need to be further validated. Further studies should be performed to evaluate diagnostic and therapeutic value of these proteins.
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Affiliation(s)
- Hanmu Guo
- Department of Ophthalmology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jianqing Li
- Department of Ophthalmology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Peirong Lu
- Department of Ophthalmology, The First Affiliated Hospital of Soochow University, Suzhou, China.
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Lu F, Duan W, Cui Y, Zhang J, Zhu D, Zhang M, Yan Y. 2D-DIGE based proteome analysis of wheat-Thinopyrum intermedium 7XL/7DS translocation line under drought stress. BMC Genomics 2022; 23:369. [PMID: 35568798 PMCID: PMC9107758 DOI: 10.1186/s12864-022-08599-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 05/03/2022] [Indexed: 11/29/2022] Open
Abstract
Background Drought stress is the most limiting factor for plant growth and crop production worldwide. As a major cereal crop, wheat is susceptible to drought. Thus, discovering and utilizing drought-tolerant gene resources from related species are highly important for improving wheat drought resistance. In this study, the drought tolerance of wheat Zhongmai 8601-Thinopyrum intermedium 7XL/7DS translocation line YW642 was estimated under drought stress, and then two-dimensional difference gel electrophoresis (2D-DIGE) based proteome analysis of the developing grains was performed to uncover the drought-resistant proteins. Results The results showed that 7XL/7DS translocation possessed a better drought-tolerance compared to Zhongmai 8601. 2D-DIGE identified 146 differential accumulation protein (DAP) spots corresponding to 113 unique proteins during five grain developmental stages of YW642 under drought stress. Among them, 55 DAP spots corresponding to 48 unique proteins displayed an upregulated expression, which were mainly involved in stress/defense, energy metabolism, starch metabolism, protein metabolism/folding and transport. The cis-acting element analysis revealed that abundant stress-related elements were present in the promoter regions of the drought-responsive protein genes, which could play important roles in drought defense. RNA-seq and RT-qPCR analyses revealed that some regulated DAP genes also showed a high expression level in response to drought stress. Conclusions Our results indicated that Wheat-Th. intermedium 7XL/7DS translocation line carried abundant drought-resistant proteins that had potential application values for wheat drought tolerance improvement. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08599-1.
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Affiliation(s)
- Fengkun Lu
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Science, Capital Normal University, Beijing, 100048, China
| | - Wenjing Duan
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Science, Capital Normal University, Beijing, 100048, China
| | - Yue Cui
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Science, Capital Normal University, Beijing, 100048, China
| | - Junwei Zhang
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Science, Capital Normal University, Beijing, 100048, China
| | - Dong Zhu
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Science, Capital Normal University, Beijing, 100048, China
| | - Ming Zhang
- College of Agricultural and Biological Engineering (College of Tree Peony), Heze University, 2269 Daxue Road, Heze, 274015, Shandong, China.
| | - Yueming Yan
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Science, Capital Normal University, Beijing, 100048, China.
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Shin JY, Lee J, Park J, Kim M, Chung H, Byeon SH. Association of Keratin 8 Level in Aqueous Humor With Outcomes of Intravitreal Ranibizumab Treatment for Neovascular Age-Related Macular Degeneration. Transl Vis Sci Technol 2022; 11:26. [PMID: 35040914 PMCID: PMC8764207 DOI: 10.1167/tvst.11.1.26] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Purpose To investigate keratin 8 (KRT8) level in the aqueous humor (AH) of patients with neovascular age-related macular degeneration (nAMD) and elucidate its association with intravitreal ranibizumab (IVR) treatment outcomes. Methods This prospective study involved 58 eyes of treatment-naïve nAMD patients treated with three IVR doses monthly and whose AH samples were collected at baseline and two months after the initial treatment. KRT8 level was determined using the enzyme-linked immunosorbent assay and compared with that of the control group, which comprised patients who underwent cataract surgery during the same period. The nAMD-affected eyes were classified into responder (dry) and poor responder (persistent fluid) groups, according to optical coherence tomography (OCT) findings at month three. Additionally, associations between the KRT8 level and IVR treatment outcomes were analyzed. Results The baseline KRT8 level was significantly higher in the AMD group than in the control group. In the AMD group, responders demonstrated significant differences between the KRT8 level at the baseline and month two, whereas poor responders exhibited no significant change. Regression analysis revealed that a higher KRT8 level at month two was significantly associated with persistent fluid upon OCT at months three and six. Conclusions Monitoring aqueous KRT8 level may facilitate early determination of the therapeutic effects of IVR in nAMD patients and reflect the conditions of retinal pigment epithelium during the disease course. Translational Relevance Monitoring aqueous KRT8 may aid early determination of therapeutic effects of IVR in neovascular AMD patients and reflect the health conditions of retinal pigment epithelium.
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Affiliation(s)
- Joo Youn Shin
- Department of Ophthalmology, Institute of Vision Research, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jonghyun Lee
- Department of Ophthalmology, Ilsan Paik Hospital, Inje University College of Medicine, Goyang, Republic of Korea
| | - Jinkyu Park
- Department of Ophthalmology, Institute of Vision Research, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Min Kim
- Department of Ophthalmology, Institute of Vision Research, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Hyewon Chung
- Department of Ophthalmology, Konkuk University School of Medicine, Konkuk University Medical Center, Seoul, Korea
| | - Suk Ho Byeon
- Department of Ophthalmology, Institute of Vision Research, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
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Baek JH, Lim D, Park KH, Chae JB, Jang H, Lee J, Chung H. Quantitative proteomic analysis of aqueous humor from patients with drusen and reticular pseudodrusen in age-related macular degeneration. BMC Ophthalmol 2018; 18:289. [PMID: 30404605 PMCID: PMC6222993 DOI: 10.1186/s12886-018-0941-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 10/12/2018] [Indexed: 01/12/2023] Open
Abstract
Background To identify novel biomarkers related to the pathogenesis of dry age-related macular degeneration (AMD), we adopted a human retinal pigment epithelial (RPE) cell culture model that mimics some features of dry AMD including the accumulation of intra- and sub-RPE deposits. Then, we investigated the aqueous humor (AH) proteome using a data-independent acquisition method (sequential window acquisition of all theoretical fragment ion mass spectrometry) for dry AMD patients and controls. Methods After uniformly pigmented polarized monolayers of human fetal primary RPE (hfRPE) cells were established, the cells were exposed to 4-hydroxy-2-nonenal (4-HNE), followed by Western blotting, immunofluorescence analysis and ELISA of cells or conditioned media for several proteins of interest. Data-dependent acquisition for identification of the AH proteome and SWATH-based mass spectrometry were performed for 11 dry AMD patients according to their phenotypes (including soft drusen and reticular pseudodrusen [RPD]) and 2 controls (3 groups). Results Increased intra- and sub-RPE deposits were observed in 4-HNE-treated hfRPE cells compared with control cultures based on APOA1, cathepsin D, and clusterin immunoreactivity. Additionally, the differential abundance of proteins in apical and basal chambers with or without 4-HNE treatment confirmed the polarized secretion of proteins from hfRPE cells. A total of 119 proteins were quantified in dry AMD patients and controls by SWATH-MS. Sixty-five proteins exhibited significantly altered abundance among the three groups. A two-dimensional principal component analysis plot was generated to identify typical proteins related to the pathogenesis of dry AMD. Among the identified proteins, eight proteins, including APOA1, CFHR2, and CLUS, were previously considered major components or regulators of drusen. Three proteins (SERPINA4, LUM, and KERA proteins) have not been previously described as components of drusen or as being related to dry AMD. Interestingly, the LUM and KERA proteins, which are related to extracellular matrix organization, were upregulated in both RPD and soft drusen. Conclusions Differential protein expression in the AH between patients with drusen and RPD was quantified using SWATH-MS in the present study. Detailed proteomic analyses of dry AMD patients might provide insights into the in vivo biology of drusen and RPD. Electronic supplementary material The online version of this article (10.1186/s12886-018-0941-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Je-Hyun Baek
- R&D Center for Clinical Mass Spectrometry, Seegene Medical Foundation, Seoul, 04805, South Korea
| | - Daehan Lim
- Department of Ophthalmology, Konkuk University School of Medicine, Konkuk University Medical Center, 120-1 Neungdong-ro, Gwangjin-gu, Seoul, Republic of Korea
| | - Kyu Hyung Park
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam, 13620, South Korea
| | - Jae-Byoung Chae
- Department of Ophthalmology, Konkuk University School of Medicine, Konkuk University Medical Center, 120-1 Neungdong-ro, Gwangjin-gu, Seoul, Republic of Korea
| | - Hyoik Jang
- Department of Ophthalmology, Konkuk University School of Medicine, Konkuk University Medical Center, 120-1 Neungdong-ro, Gwangjin-gu, Seoul, Republic of Korea
| | - Jonghyun Lee
- Department of Ophthalmology, Ilsan Paik Hospital, Inje University College of Medicine, Goyang, 10380, South Korea
| | - Hyewon Chung
- Department of Ophthalmology, Konkuk University School of Medicine, Konkuk University Medical Center, 120-1 Neungdong-ro, Gwangjin-gu, Seoul, Republic of Korea.
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iTRAQ-based proteomics monitors the withering dynamics in postharvest leaves of tea plant (Camellia sinensis). Mol Genet Genomics 2017; 293:45-59. [DOI: 10.1007/s00438-017-1362-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 08/20/2017] [Indexed: 12/12/2022]
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Kersten E, Paun CC, Schellevis RL, Hoyng CB, Delcourt C, Lengyel I, Peto T, Ueffing M, Klaver CCW, Dammeier S, den Hollander AI, de Jong EK. Systemic and ocular fluid compounds as potential biomarkers in age-related macular degeneration. Surv Ophthalmol 2017; 63:9-39. [PMID: 28522341 DOI: 10.1016/j.survophthal.2017.05.003] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 05/09/2017] [Accepted: 05/09/2017] [Indexed: 12/15/2022]
Abstract
Biomarkers can help unravel mechanisms of disease and identify new targets for therapy. They can also be useful in clinical practice for monitoring disease progression, evaluation of treatment efficacy, and risk assessment in multifactorial diseases, such as age-related macular degeneration (AMD). AMD is a highly prevalent progressive retinal disorder for which multiple genetic and environmental risk factors have been described, but the exact etiology is not yet fully understood. Many compounds have been evaluated for their association with AMD. We performed an extensive literature review of all compounds measured in serum, plasma, vitreous, aqueous humor, and urine of AMD patients. Over 3600 articles were screened, resulting in more than 100 different compounds analyzed in AMD studies, involved in neovascularization, immunity, lipid metabolism, extracellular matrix, oxidative stress, diet, hormones, and comorbidities (such as kidney disease). For each compound, we provide a short description of its function and discuss the results of the studies in relation to its usefulness as AMD biomarker. In addition, biomarkers identified by hypothesis-free techniques, including metabolomics, proteomics, and epigenomics, are covered. In summary, compounds belonging to the oxidative stress pathway, the complement system, and lipid metabolism are the most promising biomarker candidates for AMD. We hope that this comprehensive survey of the literature on systemic and ocular fluid compounds as potential biomarkers in AMD will provide a stepping stone for future research and possible implementation in clinical practice.
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Affiliation(s)
- Eveline Kersten
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Constantin C Paun
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Rosa L Schellevis
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Carel B Hoyng
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Cécile Delcourt
- Université de Bordeaux, ISPED, Bordeaux, France; INSERM, U1219-Bordeaux Population Health Research Center, Bordeaux, France
| | - Imre Lengyel
- Centre for Experimental Medicine, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, Northern Ireland, United Kingdom
| | - Tunde Peto
- Centre for Public Health, School of Medicine, Dentistry and Biomedical Science, Queen's University Belfast, Northern Ireland, United Kingdom
| | - Marius Ueffing
- Department for Ophthalmology and Medical Bioanalytics Centre Tübingen, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Caroline C W Klaver
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands; Department of Ophthalmology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Sascha Dammeier
- Department for Ophthalmology and Medical Bioanalytics Centre Tübingen, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Anneke I den Hollander
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands; Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Eiko K de Jong
- Department of Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands.
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Cehofski LJ, Honoré B, Vorum H. A Review: Proteomics in Retinal Artery Occlusion, Retinal Vein Occlusion, Diabetic Retinopathy and Acquired Macular Disorders. Int J Mol Sci 2017; 18:ijms18050907. [PMID: 28452939 PMCID: PMC5454820 DOI: 10.3390/ijms18050907] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 03/08/2017] [Accepted: 04/05/2017] [Indexed: 01/26/2023] Open
Abstract
Retinal artery occlusion (RAO), retinal vein occlusion (RVO), diabetic retinopathy (DR) and age-related macular degeneration (AMD) are frequent ocular diseases with potentially sight-threatening outcomes. In the present review we discuss major findings of proteomic studies of RAO, RVO, DR and AMD, including an overview of ocular proteome changes associated with anti-vascular endothelial growth factor (VEGF) treatments. Despite the severe outcomes of RAO, the proteome of the disease remains largely unstudied. There is also limited knowledge about the proteome of RVO, but proteomic studies suggest that RVO is associated with remodeling of the extracellular matrix and adhesion processes. Proteomic studies of DR have resulted in the identification of potential therapeutic targets such as carbonic anhydrase-I. Proliferative diabetic retinopathy is the most intensively studied stage of DR. Proteomic studies have established VEGF, pigment epithelium-derived factor (PEDF) and complement components as key factors associated with AMD. The aim of this review is to highlight the major milestones in proteomics in RAO, RVO, DR and AMD. Through large-scale protein analyses, proteomics is bringing new important insights into these complex pathological conditions.
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Affiliation(s)
- Lasse Jørgensen Cehofski
- Department of Ophthalmology, Aalborg University Hospital, Hobrovej 18-22, 9000 Aalborg, Denmark.
- Department of Clinical Medicine, Aalborg University, Søndre Skovvej 15, 9000 Aalborg, Denmark.
| | - Bent Honoré
- Department of Clinical Medicine, Aalborg University, Søndre Skovvej 15, 9000 Aalborg, Denmark.
- Department of Biomedicine, Aarhus University, Ole Worms Allé 3, Building 1182, 024, 8000 Aarhus C, Denmark.
| | - Henrik Vorum
- Department of Ophthalmology, Aalborg University Hospital, Hobrovej 18-22, 9000 Aalborg, Denmark.
- Department of Clinical Medicine, Aalborg University, Søndre Skovvej 15, 9000 Aalborg, Denmark.
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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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