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Topitsch A, Halstenbach T, Rothweiler R, Fretwurst T, Nelson K, Schilling O. Mass Spectrometry-Based Proteomics of Poly(methylmethacrylate)-Embedded Bone. J Proteome Res 2024; 23:1810-1820. [PMID: 38634750 DOI: 10.1021/acs.jproteome.4c00046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is a widely employed technique in proteomics research for studying the proteome biology of various clinical samples. Hard tissues, such as bone and teeth, are routinely preserved using synthetic poly(methyl methacrylate) (PMMA) embedding resins that enable histological, immunohistochemical, and morphological examination. However, the suitability of PMMA-embedded hard tissues for large-scale proteomic analysis remained unexplored. This study is the first to report on the feasibility of PMMA-embedded bone samples for LC-MS/MS analysis. Conventional workflows yielded merely limited coverage of the bone proteome. Using advanced strategies of prefractionation by high-pH reversed-phase liquid chromatography in combination with isobaric tandem mass tag labeling resulted in proteome coverage exceeding 1000 protein identifications. The quantitative comparison with cryopreserved samples revealed that each sample preparation workflow had a distinct impact on the proteomic profile. However, workflow replicates exhibited a high reproducibility for PMMA-embedded samples. Our findings further demonstrate that decalcification prior to protein extraction, along with the analysis of solubilization fractions, is not preferred for PMMA-embedded bone. The biological applicability of the proposed workflow was demonstrated using samples of human PMMA-embedded alveolar bone and the iliac crest, which revealed anatomical site-specific proteomic profiles. Overall, these results establish a crucial foundation for large-scale proteomics studies contributing to our knowledge of bone biology.
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Affiliation(s)
- Annika Topitsch
- Institute for Surgical Pathology, Faculty of Medicine, Medical Center - University of Freiburg, Breisacher Straße 115a, 79106 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstraße 19a, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
- Department of Oral and Maxillofacial Surgery/Translational Implantology, Faculty of Medicine, Medical Center - University of Freiburg, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - Tim Halstenbach
- Department of Oral and Maxillofacial Surgery/Translational Implantology, Faculty of Medicine, Medical Center - University of Freiburg, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - René Rothweiler
- Department of Oral and Maxillofacial Surgery/Translational Implantology, Faculty of Medicine, Medical Center - University of Freiburg, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - Tobias Fretwurst
- Department of Oral and Maxillofacial Surgery/Translational Implantology, Faculty of Medicine, Medical Center - University of Freiburg, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - Katja Nelson
- Department of Oral and Maxillofacial Surgery/Translational Implantology, Faculty of Medicine, Medical Center - University of Freiburg, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - Oliver Schilling
- Institute for Surgical Pathology, Faculty of Medicine, Medical Center - University of Freiburg, Breisacher Straße 115a, 79106 Freiburg, Germany
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Korchak JA, Jeffery ED, Bandyopadhyay S, Jordan BT, Lehe M, Watts EF, Fenix A, Wilhelm M, Sheynkman GM. IS-PRM-based peptide targeting informed by long-read sequencing for alternative proteome detection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.01.587549. [PMID: 38617311 PMCID: PMC11014528 DOI: 10.1101/2024.04.01.587549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Alternative splicing is a major contributor of transcriptomic complexity, but the extent to which transcript isoforms are translated into stable, functional protein isoforms is unclear. Furthermore, detection of relatively scarce isoform-specific peptides is challenging, with many protein isoforms remaining uncharted due to technical limitations. Recently, a family of advanced targeted MS strategies, termed internal standard parallel reaction monitoring (IS-PRM), have demonstrated multiplexed, sensitive detection of pre-defined peptides of interest. Such approaches have not yet been used to confirm existence of novel peptides. Here, we present a targeted proteogenomic approach that leverages sample-matched long-read RNA sequencing (LR RNAseq) data to predict potential protein isoforms with prior transcript evidence. Predicted tryptic isoform-specific peptides, which are specific to individual gene product isoforms, serve as "triggers" and "targets" in the IS-PRM method, Tomahto. Using the model human stem cell line WTC11, LR RNAseq data were generated and used to inform the generation of synthetic standards for 192 isoform-specific peptides (114 isoforms from 55 genes). These synthetic "trigger" peptides were labeled with super heavy tandem mass tags (TMT) and spiked into TMT-labeled WTC11 tryptic digest, predicted to contain corresponding endogenous "target" peptides. Compared to DDA mode, Tomahto increased detectability of isoforms by 3.6-fold, resulting in the identification of five previously unannotated isoforms. Our method detected protein isoform expression for 43 out of 55 genes corresponding to 54 resolved isoforms. This LR RNA seq-informed Tomahto targeted approach, called LRP-IS-PRM, is a new modality for generating protein-level evidence of alternative isoforms - a critical first step in designing functional studies and eventually clinical assays.
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Affiliation(s)
- Jennifer A. Korchak
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Erin D. Jeffery
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Saikat Bandyopadhyay
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Ben T. Jordan
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD USA
| | - Micah Lehe
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Emily F. Watts
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
| | - Aidan Fenix
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Mathias Wilhelm
- Computational Mass Spectrometry, Technical University of Munich (TUM), D-85354 Freising, Germany
| | - Gloria M. Sheynkman
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
- UVA Comprehensive Cancer Center, University of Virginia, Charlottesville, VA, USA
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Dey AK, Banarjee R, Boroumand M, Rutherford DV, Strassheim Q, Nyunt T, Olinger B, Basisty N. Translating Senotherapeutic Interventions into the Clinic with Emerging Proteomic Technologies. BIOLOGY 2023; 12:1301. [PMID: 37887011 PMCID: PMC10604147 DOI: 10.3390/biology12101301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/25/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023]
Abstract
Cellular senescence is a state of irreversible growth arrest with profound phenotypic changes, including the senescence-associated secretory phenotype (SASP). Senescent cell accumulation contributes to aging and many pathologies including chronic inflammation, type 2 diabetes, cancer, and neurodegeneration. Targeted removal of senescent cells in preclinical models promotes health and longevity, suggesting that the selective elimination of senescent cells is a promising therapeutic approach for mitigating a myriad of age-related pathologies in humans. However, moving senescence-targeting drugs (senotherapeutics) into the clinic will require therapeutic targets and biomarkers, fueled by an improved understanding of the complex and dynamic biology of senescent cell populations and their molecular profiles, as well as the mechanisms underlying the emergence and maintenance of senescence cells and the SASP. Advances in mass spectrometry-based proteomic technologies and workflows have the potential to address these needs. Here, we review the state of translational senescence research and how proteomic approaches have added to our knowledge of senescence biology to date. Further, we lay out a roadmap from fundamental biological discovery to the clinical translation of senotherapeutic approaches through the development and application of emerging proteomic technologies, including targeted and untargeted proteomic approaches, bottom-up and top-down methods, stability proteomics, and surfaceomics. These technologies are integral for probing the cellular composition and dynamics of senescent cells and, ultimately, the development of senotype-specific biomarkers and senotherapeutics (senolytics and senomorphics). This review aims to highlight emerging areas and applications of proteomics that will aid in exploring new senescent cell biology and the future translation of senotherapeutics.
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Affiliation(s)
| | | | | | | | | | | | | | - Nathan Basisty
- Translational Geroproteomics Unit, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA; (A.K.D.); (R.B.); (M.B.); (D.V.R.); (Q.S.); (T.N.); (B.O.)
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4
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Sheng Z, Guo A, Wang J, Chen X. Preparation, physicochemical properties and antimicrobial activity of chitosan from fly pupae. Heliyon 2022; 8:e11168. [PMID: 36303907 PMCID: PMC9593200 DOI: 10.1016/j.heliyon.2022.e11168] [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: 01/13/2022] [Revised: 03/14/2022] [Accepted: 08/05/2022] [Indexed: 11/06/2022] Open
Abstract
As an alternative chitosan source, edible insects have been proposed as an unconventional but viable option. Taking fly pupae as an example, this work performed chitosan extraction through a traditional chemical method with some modifications, and investigated its physicochemical properties and antimicrobial activity. The results showed that adding 0.5% sodium sulfite (Na2SO3, w/w, Na2SO3/fly pupae) synergized with sodium hydroxide (NaOH) for deproteinization was more effective than lye alone. Acid leaching was applied for desalination, and the optimal concentration of hydrochloric acid (HCl) was determined as 2 mol/L by ash content. For decoloration, the optimal decolorization oxidant was sodium hypochlorite (NaClO) with a concentration of 1.0%. For the deacetylation of chitin to chitosan, both the yield and degree of deacetylation (DD) using segmented treatment with alkali-NaOH were higher than those of traditional one-time deacetylation. The established physicochemical properties corresponded with the typical characteristics of chitosan. The determination of antimicrobial activity of chitosan by the turbidimetric method showed that chitosan exhibited notable activity in the order of Staphylococcus aureus > Escherichia coli > Saccharomyces cerevisiae, and this effect decreased with the increase in viscosity-average molecular weight (Mη). These results proved the viability of our improved method for the preparation of chitosan, a valuable antimicrobial agent, using an alternative natural source. Chitosan was prepared from fly pupae through an improved traditional method. The physicochemical properties corresponded with the characteristics of chitosan. Oligochitosan exhibited stronger antimicrobial activity than that of chitosan.
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Affiliation(s)
- Zhicun Sheng
- Jiangsu Agri-animal Husbandry Vocational College, Taizhou, Jiangsu, 225300, China,Tianjin University of Science and Technology, Tianjin, 300457, China,Corresponding author.
| | - Ainan Guo
- Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Jing Wang
- Jiangsu Agri-animal Husbandry Vocational College, Taizhou, Jiangsu, 225300, China
| | - Xiaolan Chen
- Jiangsu Agri-animal Husbandry Vocational College, Taizhou, Jiangsu, 225300, China
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5
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Madda R, Chen CM, Chen CF, Wang JY, Wu PK, Chen WM. Effect of Cryoablation Treatment on the Protein Expression Profile of Low-Grade Central Chondrosarcoma Identified by LC-ESI-MS/MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1469-1489. [PMID: 34003650 DOI: 10.1021/jasms.1c00068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The use of cryoablation/cryosurgery in treating solid tumors has been proven as a unique technique that uses lethal temperatures to destroy the tumors and impart better functions for the affected organs. This novel technique recently demonstrated the best clinical results in chondrosarcoma (CSA) with faster recovery, less recurrence, and metastasis. Due to the resistant nature of CSA to chemo and radiation therapy, cryoablation comes to light as the best alternative approach. Therefore, for the first time, we aimed to compare CSA-untreated with cryoablation treated samples to discover some potential markers that may provide various clues in terms of diagnosis and pathophysiology and may facilitate the development of novel methods to treat sarcoma efficiently. To find the altered proteins among both groups, a mass-based label-free approach was employed and identified a total of 160 significantly altered proteins. Among these, 138 proteins were dysregulated with <1- to -0.1-fold, 18 proteins were up-regulated with >3 folds, and four proteins were similarly expressed in the untreated group compared to the treated. Interestingly, the differential expressions of proteins from the untreated group showed contrast expressions in the treated group. Furthermore, the functional enrichment analysis revealed that most of the identified proteins from this study were associated with various significant pathways such as glycolysis, MAPK activation, PI3K-Akt signaling, extracellular matrix degradation, etc. In addition, two protein expressions, such as fibronectin and annexin-1, were validated by immunoblot analysis. Therefore, this study signifies the most comprehensive discovery of altered protein expressions to date and the first large-scale detection of protein profiles from CSA-cryoablation treated compared to untreated. This work may serve as the basis for future research to open novel treatment options for chondrosarcoma.
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Affiliation(s)
- Rashmi Madda
- Department of Orthopedics & Traumatology, Taipei Veterans General Hospital, Taipai 11217 Taiwan
- Department of orthopedics, Therapeutical and Musculoskeletal Tumor Research Center, Taipei Veterans General Hospital, Taipai 11217 Taiwan
- Orthopedic Department, School of Medicine, National Yang-Ming University, Taipai 11221 Taiwan
- Institute of Clinical Medicine, School of Medicine, National Yang-Ming University, Taipai 11221 Taiwan
| | - Chao-Ming Chen
- Department of Orthopedics & Traumatology, Taipei Veterans General Hospital, Taipai 11217 Taiwan
- Department of orthopedics, Therapeutical and Musculoskeletal Tumor Research Center, Taipei Veterans General Hospital, Taipai 11217 Taiwan
- Orthopedic Department, School of Medicine, National Yang-Ming University, Taipai 11221 Taiwan
- Institute of Clinical Medicine, School of Medicine, National Yang-Ming University, Taipai 11221 Taiwan
| | - Cheng-Fong Chen
- Department of Orthopedics & Traumatology, Taipei Veterans General Hospital, Taipai 11217 Taiwan
- Department of orthopedics, Therapeutical and Musculoskeletal Tumor Research Center, Taipei Veterans General Hospital, Taipai 11217 Taiwan
- Orthopedic Department, School of Medicine, National Yang-Ming University, Taipai 11221 Taiwan
| | - Jir-You Wang
- Department of Orthopedics & Traumatology, Taipei Veterans General Hospital, Taipai 11217 Taiwan
- Department of orthopedics, Therapeutical and Musculoskeletal Tumor Research Center, Taipei Veterans General Hospital, Taipai 11217 Taiwan
- Orthopedic Department, School of Medicine, National Yang-Ming University, Taipai 11221 Taiwan
- Institute of Clinical Medicine, School of Medicine, National Yang-Ming University, Taipai 11221 Taiwan
| | - Po-Kuei Wu
- Department of Orthopedics & Traumatology, Taipei Veterans General Hospital, Taipai 11217 Taiwan
- Department of orthopedics, Therapeutical and Musculoskeletal Tumor Research Center, Taipei Veterans General Hospital, Taipai 11217 Taiwan
- Orthopedic Department, School of Medicine, National Yang-Ming University, Taipai 11221 Taiwan
- Institute of Clinical Medicine, School of Medicine, National Yang-Ming University, Taipai 11221 Taiwan
| | - Wei-Ming Chen
- Department of Orthopedics & Traumatology, Taipei Veterans General Hospital, Taipai 11217 Taiwan
- Department of orthopedics, Therapeutical and Musculoskeletal Tumor Research Center, Taipei Veterans General Hospital, Taipai 11217 Taiwan
- Orthopedic Department, School of Medicine, National Yang-Ming University, Taipai 11221 Taiwan
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6
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Wang J, Jia X, Meng X, Li Y, Wu W, Zhang X, Xu H, Cui J. Annexin A3 may play an important role in ochratoxin-induced malignant transformation of human gastric epithelium cells. Toxicol Lett 2019; 313:150-158. [PMID: 31276768 DOI: 10.1016/j.toxlet.2019.07.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 06/24/2019] [Accepted: 07/01/2019] [Indexed: 10/26/2022]
Abstract
Ochratoxin A (OTA), one of the most abundant food-contaminating mycotoxins, is a possible carcinogen to humans. We previously demonstrated that long-term (40 weeks) OTA exposure induces the malignant transformation of human gastric epithelium cells (GES-1) in vitro. However, the specific mechanism underlying OTA-induced gastric carcinogenesis is complex. In the present study, we used 2-DE and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI/TOF MS) combined with bioinformatics and immunoblotting to investigate the differentially expressed proteins between GES-1 and OTA-malignant transformed GES-1 cells (OTA-GES-1T cells) in vitro. We found that four differentially expressed proteins were identified after malignant transformation, including actin, cytoplasmic 1 (ACTB), F-actin-capping protein subunit alpha-1 (CAPZA1), Annexin A3 (ANXA3), thioredoxin peroxidase B from red blood cells (TPx-B) and Fibrinogen beta B (Fibrinogen β). Among the differentially expressed proteins, the effect of Annexin A3 was analyzed by MTT assay, western blot, cell cycle analysis, wound healing assay, Transwell assay, and colony formation assay in OTA-GES-1T cells. The results showed that inhibition of Annexin A3 by siRNA effectively prevented the proliferation, migration, and invasion abilities of OTA-GES-1T cells. Collectively, the results of this study will guide future research on OTA carcinogenicity.
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Affiliation(s)
- Juan Wang
- Department of Pathology, The Second Hospital, Hebei Medical University, Shijiazhuang, China
| | - Xin Jia
- Department of Pathology, The Second Hospital, Hebei Medical University, Shijiazhuang, China
| | - Xinxing Meng
- Department of Pathology, The Second Hospital, Hebei Medical University, Shijiazhuang, China
| | - Yuehong Li
- Department of Pathology, The Second Hospital, Hebei Medical University, Shijiazhuang, China
| | - Wenxin Wu
- Department of Pathology, The Second Hospital, Hebei Medical University, Shijiazhuang, China
| | - Xianghong Zhang
- Department of Pathology, The Second Hospital, Hebei Medical University, Shijiazhuang, China
| | - Hong Xu
- Medical Research Center, North China University of Science and Technology, Tangshan, China
| | - Jinfeng Cui
- Department of Pathology, The Second Hospital, Hebei Medical University, Shijiazhuang, China.
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7
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Rusconi B, Good M, Warner BB. The Microbiome and Biomarkers for Necrotizing Enterocolitis: Are We Any Closer to Prediction? J Pediatr 2017; 189:40-47.e2. [PMID: 28669607 PMCID: PMC5614810 DOI: 10.1016/j.jpeds.2017.05.075] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 04/24/2017] [Accepted: 05/26/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Brigida Rusconi
- Division of Gastroenterology, Hepatology & Nutrition, Pathobiology Research Unit, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Misty Good
- Division of Newborn Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Barbara B. Warner
- Division of Newborn Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
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8
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Yan F, Mo X, Liu J, Ye S, Zeng X, Chen D. Thymic function in the regulation of T cells, and molecular mechanisms underlying the modulation of cytokines and stress signaling (Review). Mol Med Rep 2017; 16:7175-7184. [PMID: 28944829 PMCID: PMC5865843 DOI: 10.3892/mmr.2017.7525] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 05/12/2017] [Indexed: 01/08/2023] Open
Abstract
The thymus is critical in establishing and maintaining the appropriate microenvironment for promoting the development and selection of T cells. The function and structure of the thymus gland has been extensively studied, particularly as the thymus serves an important physiological role in the lymphatic system. Numerous studies have investigated the morphological features of thymic involution. Recently, research attention has increasingly been focused on thymic proteins as targets for drug intervention. Omics approaches have yielded novel insights into the thymus and possible drug targets. The present review addresses the signaling and transcriptional functions of the thymus, including the molecular mechanisms underlying the regulatory functions of T cells and their role in the immune system. In addition, the levels of cytokines secreted in the thymus have a significant effect on thymic functions, including thymocyte migration and development, thymic atrophy and thymic recovery. Furthermore, the regulation and molecular mechanisms of stress-mediated thymic atrophy and involution were investigated, with particular emphasis on thymic function as a potential target for drug development and discovery using proteomics.
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Affiliation(s)
- Fenggen Yan
- Department of Dermatology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, Guangdong 510120, P.R. China
| | - Xiumei Mo
- Department of Dermatology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, Guangdong 510120, P.R. China
| | - Junfeng Liu
- Department of Dermatology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, Guangdong 510120, P.R. China
| | - Siqi Ye
- Department of Dermatology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, Guangdong 510120, P.R. China
| | - Xing Zeng
- Department of Dermatology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, Guangdong 510120, P.R. China
| | - Dacan Chen
- Department of Dermatology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, Guangdong 510120, P.R. China
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Duan L, Cao Z, Yobas L. Continuous-Flow Electrophoresis of DNA and Proteins in a Two-Dimensional Capillary-Well Sieve. Anal Chem 2017; 89:10022-10028. [DOI: 10.1021/acs.analchem.7b02484] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lian Duan
- Department
of Electronic and Computer Engineering, and ‡Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR, China
| | - Zhen Cao
- Department
of Electronic and Computer Engineering, and ‡Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR, China
| | - Levent Yobas
- Department
of Electronic and Computer Engineering, and ‡Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR, China
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10
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Identification of Tengfu Jiangya Tablet Target Biomarkers with Quantitative Proteomic Technique. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2017; 2017:7594805. [PMID: 28408942 PMCID: PMC5376940 DOI: 10.1155/2017/7594805] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 02/08/2017] [Indexed: 12/21/2022]
Abstract
Tengfu Jiangya Tablet (TJT) is a well accepted antihypertension drug in China and its major active components were Uncaria total alkaloids and Semen Raphani soluble alkaloid. To further explore treatment effects mechanism of TJT on essential hypertension, a serum proteomic study was performed. Potential biomarkers were quantified in serum of hypertension individuals before and after taking TJT with isobaric tags for relative and absolute quantitation (iTRAQ) coupled two-dimensional liquid chromatography followed electrospray ionization-tandem mass spectrometry (2D LC-MS/MS) proteomics technique. Among 391 identified proteins with high confidence, 70 proteins were differentially expressed (fold variation criteria, >1.2 or <0.83) between two groups (39 upregulated and 31 downregulated). Combining with Gene Ontology annotation, KEGG pathway analysis, and literature retrieval, 5 proteins were chosen as key target biomarkers during TJT therapeutic process. And the alteration profiles of these 5 proteins were verified by ELISA and Western Blot. Proteins Kininogen 1 and Keratin 1 are members of Kallikrein system, while Myeloperoxidase, Serum Amyloid protein A, and Retinol binding protein 4 had been reported closely related to vascular endothelial injury. Our study discovered 5 target biomarkers of the compound Chinese medicine TJT. Secondly, this research initially revealed the antihypertension therapeutic mechanism of this drug from a brand-new aspect.
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11
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Funke S, Perumal N, Bell K, Pfeiffer N, Grus FH. The potential impact of recent insights into proteomic changes associated with glaucoma. Expert Rev Proteomics 2017; 14:311-334. [PMID: 28271721 DOI: 10.1080/14789450.2017.1298448] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
INTRODUCTION Glaucoma, a major ocular neuropathy, is still far from being understood on a molecular scale. Proteomic workflows revealed glaucoma associated alterations in different eye components. By using state-of-the-art mass spectrometric (MS) based discovery approaches large proteome datasets providing important information about glaucoma related proteins and pathways could be generated. Corresponding proteomic information could be retrieved from various ocular sample species derived from glaucoma experimental models or from original human material (e.g. optic nerve head or aqueous humor). However, particular eye tissues with the potential for understanding the disease's molecular pathomechanism remains underrepresented. Areas covered: The present review provides an overview of the analysis depth achieved for the glaucomatous eye proteome. With respect to different eye regions and biofluids, proteomics related literature was found using PubMed, Scholar and UniProtKB. Thereby, the review explores the potential of clinical proteomics for glaucoma research. Expert commentary: Proteomics will provide important contributions to understanding the molecular processes associated with glaucoma. Sensitive discovery and targeted MS approaches will assist understanding of the molecular interplay of different eye components and biofluids in glaucoma. Proteomic results will drive the comprehension of glaucoma, allowing a more stringent disease hypothesis within the coming years.
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Affiliation(s)
- Sebastian Funke
- a Experimental Ophthalmology , University Medical Center , Mainz , Germany
| | - Natarajan Perumal
- a Experimental Ophthalmology , University Medical Center , Mainz , Germany
| | - Katharina Bell
- a Experimental Ophthalmology , University Medical Center , Mainz , Germany
| | - Norbert Pfeiffer
- a Experimental Ophthalmology , University Medical Center , Mainz , Germany
| | - Franz H Grus
- a Experimental Ophthalmology , University Medical Center , Mainz , Germany
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12
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Rice SJ, Liu X, Miller B, Joshi M, Zhu J, Caruso C, Gilbert C, Toth J, Reed M, Rassaei N, Das A, Barochia A, El-Bayoumy K, Belani CP. Proteomic profiling of human plasma identifies apolipoprotein E as being associated with smoking and a marker for squamous metaplasia of the lung. Proteomics 2015; 15:3267-77. [DOI: 10.1002/pmic.201500029] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 04/23/2015] [Accepted: 06/04/2015] [Indexed: 12/25/2022]
Affiliation(s)
- Shawn J. Rice
- Penn State Hershey Cancer Institute; Penn State College of Medicine; Hershey PA USA
| | - Xin Liu
- Penn State Hershey Cancer Institute; Penn State College of Medicine; Hershey PA USA
| | - Bruce Miller
- Penn State Hershey Cancer Institute; Penn State College of Medicine; Hershey PA USA
| | - Monika Joshi
- Penn State Hershey Cancer Institute; Penn State College of Medicine; Hershey PA USA
| | - Junjia Zhu
- Penn State Hershey Cancer Institute; Penn State College of Medicine; Hershey PA USA
| | - Carla Caruso
- Department of Pathology; Penn State College of Medicine; Hershey PA USA
| | - Chris Gilbert
- Department of Pulmonary Medicine; Penn State College of Medicine; Hershey PA USA
| | - Jennifer Toth
- Department of Pulmonary Medicine; Penn State College of Medicine; Hershey PA USA
| | - Michael Reed
- Penn State Heart and Vascular Institute and Cardiothoracic Surgery; Penn State College of Medicine; Hershey PA USA
| | - Negar Rassaei
- Department of Pulmonary Medicine; Penn State College of Medicine; Hershey PA USA
| | - Arun Das
- Department of Biochemistry and Molecular Biology; Penn State College of Medicine; Hershey PA USA
| | - Amit Barochia
- Penn State Hershey Cancer Institute; Penn State College of Medicine; Hershey PA USA
| | - Karam El-Bayoumy
- Department of Biochemistry and Molecular Biology; Penn State College of Medicine; Hershey PA USA
| | - Chandra P. Belani
- Penn State Hershey Cancer Institute; Penn State College of Medicine; Hershey PA USA
- Department of Biochemistry and Molecular Biology; Penn State College of Medicine; Hershey PA USA
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Fert-Bober J, Giles JT, Holewinski RJ, Kirk JA, Uhrigshardt H, Crowgey EL, Andrade F, Bingham CO, Park JK, Halushka MK, Kass DA, Bathon JM, Van Eyk JE. Citrullination of myofilament proteins in heart failure. Cardiovasc Res 2015; 108:232-42. [PMID: 26113265 DOI: 10.1093/cvr/cvv185] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 06/17/2015] [Indexed: 11/12/2022] Open
Abstract
AIMS Citrullination, the post-translational conversion of arginine to citrulline by the enzyme family of peptidylarginine deiminases (PADs), is associated with several diseases, and specific citrullinated proteins have been shown to alter function while others act as auto-antigens. In this study, we identified citrullinated proteins in human myocardial samples, from healthy and heart failure patients, and determined several potential functional consequences. Further we investigated PAD isoform cell-specific expression in the heart. METHODS AND RESULTS A citrullination-targeted proteomic strategy using data-independent (SWATH) acquisition method was used to identify the modified cardiac proteins. Citrullinated-induced sarcomeric proteins were validated using two-dimensional gel electrophoresis and investigated using biochemical and functional assays. Myocardial PAD isoforms were confirmed by RT-PCR with PAD2 being the major isoform in myocytes. In total, 304 citrullinated sites were identified that map to 145 proteins among the three study groups: normal, ischaemia, and dilated cardiomyopathy. Citrullination of myosin (using HMM fragment) decreased its intrinsic ATPase activity and inhibited the acto-HMM-ATPase activity. Citrullinated TM resulted in stronger F-actin binding and inhibited the acto-HMM-ATPase activity. Citrullinated TnI did not alter the binding to F-actin or acto-HMM-ATPase activity. Overall, citrullination of sarcomeric proteins caused a decrease in Ca(2+) sensitivity in skinned cardiomyocytes, with no change in maximal calcium-activated force or hill coefficient. CONCLUSION Citrullination unique to the cardiac proteome was identified. Our data indicate important structural and functional alterations to the cardiac sarcomere and the contribution of protein citrullination to this process.
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Affiliation(s)
- Justyna Fert-Bober
- The Heart Institute and Department of Medicine, Cedars-Sinai Medical Center, Advanced Clinical BioSystems Research Institute, Advanced Health Science Building, 9229, Los Angeles, CA, USA Bayview Proteomics Center, Division of Cardiology, Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - John T Giles
- Division of Rheumatology, Department of Medicine, Columbia University, New York, NY, USA
| | - Ronald J Holewinski
- The Heart Institute and Department of Medicine, Cedars-Sinai Medical Center, Advanced Clinical BioSystems Research Institute, Advanced Health Science Building, 9229, Los Angeles, CA, USA
| | - Jonathan A Kirk
- Division of Cardiology, Department of Medicine, The Johns Hopkins University Medical Institutions, Baltimore, MD, USA
| | - Helge Uhrigshardt
- Bayview Proteomics Center, Division of Cardiology, Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Erin L Crowgey
- The Heart Institute and Department of Medicine, Cedars-Sinai Medical Center, Advanced Clinical BioSystems Research Institute, Advanced Health Science Building, 9229, Los Angeles, CA, USA
| | - Felipe Andrade
- Division of Cardiology, Department of Medicine, The Johns Hopkins University Medical Institutions, Baltimore, MD, USA
| | - Clifton O Bingham
- Division of Rheumatology, Department of Medicine, Johns Hopkins University, Baltimore, MD, USA Division of Rheumatology, Department of Medicine, Seoul National University Hospital, Seoul, Korea
| | - Jin Kyun Park
- Division of Rheumatology, Department of Medicine, Johns Hopkins University, Baltimore, MD, USA Division of Rheumatology, Department of Medicine, Seoul National University Hospital, Seoul, Korea
| | - Marc K Halushka
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - David A Kass
- Division of Cardiology, Department of Medicine, The Johns Hopkins University Medical Institutions, Baltimore, MD, USA
| | - Joan M Bathon
- Division of Rheumatology, Department of Medicine, Columbia University, New York, NY, USA
| | - Jennifer E Van Eyk
- The Heart Institute and Department of Medicine, Cedars-Sinai Medical Center, Advanced Clinical BioSystems Research Institute, Advanced Health Science Building, 9229, Los Angeles, CA, USA Bayview Proteomics Center, Division of Cardiology, Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
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The Potential of Proteomics in Understanding Neurodegeneration. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2015; 121:25-58. [DOI: 10.1016/bs.irn.2015.05.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Plouffe BD, Murthy SK, Lewis LH. Fundamentals and application of magnetic particles in cell isolation and enrichment: a review. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2015; 78:016601. [PMID: 25471081 PMCID: PMC4310825 DOI: 10.1088/0034-4885/78/1/016601] [Citation(s) in RCA: 177] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Magnetic sorting using magnetic beads has become a routine methodology for the separation of key cell populations from biological suspensions. Due to the inherent ability of magnets to provide forces at a distance, magnetic cell manipulation is now a standardized process step in numerous processes in tissue engineering, medicine, and in fundamental biological research. Herein we review the current status of magnetic particles to enable isolation and separation of cells, with a strong focus on the fundamental governing physical phenomena, properties and syntheses of magnetic particles and on current applications of magnet-based cell separation in laboratory and clinical settings. We highlight the contribution of cell separation to biomedical research and medicine and detail modern cell-separation methods (both magnetic and non-magnetic). In addition to a review of the current state-of-the-art in magnet-based cell sorting, we discuss current challenges and available opportunities for further research, development and commercialization of magnetic particle-based cell-separation systems.
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Affiliation(s)
- Brian D Plouffe
- Department of Chemical Engineering, Northeastern University, Boston, MA 02115, USA. The Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, MA 02115, USA
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MIĘKUS NATALIA, OLĘDZKA ILONA, PLENIS ALINA, WOŹNIAK ZOFIA, LEWCZUK ANNA, KOSZAŁKA PATRYCJA, SEROCZYŃSKA BARBARA, BĄCZEK TOMASZ. Gel electrophoretic separation of proteins from cultured neuroendocrine tumor cell lines. Mol Med Rep 2014; 11:1407-15. [DOI: 10.3892/mmr.2014.2864] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 06/05/2014] [Indexed: 11/05/2022] Open
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Shen S, Loo RRO, Wanner IB, Loo JA. Addressing the needs of traumatic brain injury with clinical proteomics. Clin Proteomics 2014; 11:11. [PMID: 24678615 PMCID: PMC3976360 DOI: 10.1186/1559-0275-11-11] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 02/10/2014] [Indexed: 12/15/2022] Open
Abstract
Background Neurotrauma or injuries to the central nervous system (CNS) are a serious public health problem worldwide. Approximately 75% of all traumatic brain injuries (TBIs) are concussions or other mild TBI (mTBI) forms. Evaluation of concussion injury today is limited to an assessment of behavioral symptoms, often with delay and subject to motivation. Hence, there is an urgent need for an accurate chemical measure in biofluids to serve as a diagnostic tool for invisible brain wounds, to monitor severe patient trajectories, and to predict survival chances. Although a number of neurotrauma marker candidates have been reported, the broad spectrum of TBI limits the significance of small cohort studies. Specificity and sensitivity issues compound the development of a conclusive diagnostic assay, especially for concussion patients. Thus, the neurotrauma field currently has no diagnostic biofluid test in clinical use. Content We discuss the challenges of discovering new and validating identified neurotrauma marker candidates using proteomics-based strategies, including targeting, selection strategies and the application of mass spectrometry (MS) technologies and their potential impact to the neurotrauma field. Summary Many studies use TBI marker candidates based on literature reports, yet progress in genomics and proteomics have started to provide neurotrauma protein profiles. Choosing meaningful marker candidates from such ‘long lists’ is still pending, as only few can be taken through the process of preclinical verification and large scale translational validation. Quantitative mass spectrometry targeting specific molecules rather than random sampling of the whole proteome, e.g., multiple reaction monitoring (MRM), offers an efficient and effective means to multiplex the measurement of several candidates in patient samples, thereby omitting the need for antibodies prior to clinical assay design. Sample preparation challenges specific to TBI are addressed. A tailored selection strategy combined with a multiplex screening approach is helping to arrive at diagnostically suitable candidates for clinical assay development. A surrogate marker test will be instrumental for critical decisions of TBI patient care and protection of concussion victims from repeated exposures that could result in lasting neurological deficits.
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Affiliation(s)
| | | | | | - Joseph A Loo
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA 90095, USA.
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Polkinghorne VR, Standeven KF, Schroeder V, Carter AM. Role of proteomic technologies in understanding risk of arterial thrombosis. Expert Rev Proteomics 2014; 6:539-50. [DOI: 10.1586/epr.09.75] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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New insight into neurodegeneration: the role of proteomics. Mol Neurobiol 2013; 49:1181-99. [PMID: 24323427 DOI: 10.1007/s12035-013-8590-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 11/06/2013] [Indexed: 12/11/2022]
Abstract
Recent advances within the field of proteomics, including both upstream and downstream protocols, have fuelled a transition from simple protein identification to functional analysis. A battery of proteomics approaches is now being employed for the analysis of protein expression levels, the monitoring of cellular activities and for gaining an increased understanding into biochemical pathways. Combined, these approaches are changing the way we study disease by allowing accurate and targeted, large scale protein analysis, which will provide invaluable insight into disease pathogenesis. Neurodegenerative disorders, including Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD), amyotrophic lateral sclerosis (ALS), prion disease, and other diseases that affect the neuromuscular system, are a leading cause of disability in the aging population. There are no effective intervention strategies for these disorders and diagnosis is challenging as it relies primarily on clinical symptomatic features, which often overlap at early stages of disease. There is, therefore, an urgent need to develop reliable biomarkers to improve early and specific diagnosis, to track disease progression, to measure molecular responses towards treatment regimes and ultimately devise new therapeutic strategies. To accomplish this, a better understanding of disease mechanisms is needed. In this review we summarize recent advances in the field of proteomics applicable to neurodegenerative disorders, and how these advances are fueling our understanding, diagnosis, and treatment of these complex disorders.
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Stein DR, Hu X, McCorrister SJ, Westmacott GR, Plummer FA, Ball TB, Carpenter MS. High pH reversed-phase chromatography as a superior fractionation scheme compared to off-gel isoelectric focusing for complex proteome analysis. Proteomics 2013; 13:2956-66. [DOI: 10.1002/pmic.201300079] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2013] [Revised: 06/10/2013] [Accepted: 07/10/2013] [Indexed: 11/08/2022]
Affiliation(s)
- Derek R. Stein
- Department of Medical Microbiology; University of Manitoba; Winnipeg MB Canada
| | - Xiaojie Hu
- Section of Viral Diseases; Public Health Agency of Canada; Winnipeg MB Canada
| | - Stuart J. McCorrister
- Mass Spectrometry and Proteomics Core Facility; Public Health Agency of Canada; Winnipeg MB Canada
| | - Garrett R. Westmacott
- National HIV and Retrovirology Laboratories; Public Health Agency of Canada; Winnipeg MB Canada
| | - Francis A. Plummer
- Department of Medical Microbiology; University of Manitoba; Winnipeg MB Canada
- National HIV and Retrovirology Laboratories; Public Health Agency of Canada; Winnipeg MB Canada
| | - Terry B. Ball
- Department of Medical Microbiology; University of Manitoba; Winnipeg MB Canada
- National HIV and Retrovirology Laboratories; Public Health Agency of Canada; Winnipeg MB Canada
- Department of Immunology; University of Manitoba; Winnipeg MB Canada
| | - Michael S. Carpenter
- Department of Medical Microbiology; University of Manitoba; Winnipeg MB Canada
- Section of Viral Diseases; Public Health Agency of Canada; Winnipeg MB Canada
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Biomarker discovery in transplantation—proteomic adventure or mission impossible? Clin Biochem 2013; 46:497-505. [DOI: 10.1016/j.clinbiochem.2012.10.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 10/09/2012] [Accepted: 10/11/2012] [Indexed: 01/10/2023]
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24
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Tezel G. A proteomics view of the molecular mechanisms and biomarkers of glaucomatous neurodegeneration. Prog Retin Eye Res 2013; 35:18-43. [PMID: 23396249 DOI: 10.1016/j.preteyeres.2013.01.004] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 01/25/2013] [Accepted: 01/28/2013] [Indexed: 02/07/2023]
Abstract
Despite improving understanding of glaucoma, key molecular players of neurodegeneration that can be targeted for treatment of glaucoma, or molecular biomarkers that can be useful for clinical testing, remain unclear. Proteomics technology offers a powerful toolbox to accomplish these important goals of the glaucoma research and is increasingly being applied to identify molecular mechanisms and biomarkers of glaucoma. Recent studies of glaucoma using proteomics analysis techniques have resulted in the lists of differentially expressed proteins in human glaucoma and animal models. The global analysis of protein expression in glaucoma has been followed by cell-specific proteome analysis of retinal ganglion cells and astrocytes. The proteomics data have also guided targeted studies to identify post-translational modifications and protein-protein interactions during glaucomatous neurodegeneration. In addition, recent applications of proteomics have provided a number of potential biomarker candidates. Proteomics technology holds great promise to move glaucoma research forward toward new treatment strategies and biomarker discovery. By reviewing the major proteomics approaches and their applications in the field of glaucoma, this article highlights the power of proteomics in translational and clinical research related to glaucoma and also provides a framework for future research to functionally test the importance of specific molecular pathways and validate candidate biomarkers.
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Affiliation(s)
- Gülgün Tezel
- Department of Ophthalmology & Visual Sciences, University of Louisville School of Medicine, Louisville, KY, USA.
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25
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Rivera-Burgos D, Regnier FE. Disparities between immobilized enzyme and solution based digestion of transferrin with trypsin. J Sep Sci 2012; 36:454-60. [PMID: 23281316 DOI: 10.1002/jssc.201200740] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Revised: 10/11/2012] [Accepted: 10/12/2012] [Indexed: 11/10/2022]
Affiliation(s)
| | - Fred E. Regnier
- Department of Chemistry; Purdue University; West Lafayette IN USA
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26
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Tezel G, Thornton IL, Tong MG, Luo C, Yang X, Cai J, Powell DW, Soltau JB, Liebmann JM, Ritch R. Immunoproteomic analysis of potential serum biomarker candidates in human glaucoma. Invest Ophthalmol Vis Sci 2012; 53:8222-31. [PMID: 23150628 DOI: 10.1167/iovs.12-10076] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
PURPOSE Evidence supporting the immune system involvement in glaucoma includes increased titers of serum antibodies to retina and optic nerve proteins, although their pathogenic importance remains unclear. This study using an antibody-based proteomics approach aimed to identify disease-related antigens as candidate biomarkers of glaucoma. METHODS Serum samples were collected from 111 patients with primary open-angle glaucoma and an age-matched control group of 49 healthy subjects without glaucoma. For high-throughput characterization of antigens, serum IgG was eluted from five randomly selected glaucomatous samples and analyzed by linear ion trap mass spectrometry (LC-MS/MS). Serum titers of selected biomarker candidates were then measured by specific ELISAs in the whole sample pool (including an additional control group of diabetic retinopathy). RESULTS LC-MS/MS analysis of IgG elutes revealed a complex panel of proteins, including those detectable only in glaucomatous samples. Interestingly, many of these antigens corresponded to upregulated retinal proteins previously identified in glaucomatous donors (or that exhibited increased methionine oxidation). Moreover, additional analysis detected a greater immunoreactivity of the patient sera to glaucomatous retinal proteins (or to oxidatively stressed cell culture proteins), thereby suggesting the importance of disease-related protein modifications in autoantibody production/reactivity. As a narrowing-down strategy for selection of initial biomarker candidates, we determined the serum proteins overlapping with the retinal proteins known to be up-regulated in glaucoma. Four of the selected 10 candidates (AIF, cyclic AMP-responsive element binding protein, ephrin type-A receptor, and huntingtin) exhibited higher ELISA titers in the glaucomatous sera. CONCLUSIONS A number of serum proteins identified by this immunoproteomic study of human glaucoma may represent diseased tissue-related antigens and serve as candidate biomarkers of glaucoma.
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Affiliation(s)
- Gülgün Tezel
- Department of Ophthalmology & Visual Sciences, University of Louisville School of Medicine, Louisville, Kentucky 40202, USA.
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Savino R, Paduano S, Preianò M, Terracciano R. The proteomics big challenge for biomarkers and new drug-targets discovery. Int J Mol Sci 2012. [PMID: 23203042 PMCID: PMC3509558 DOI: 10.3390/ijms131113926] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
In the modern process of drug discovery, clinical, functional and chemical proteomics can converge and integrate synergies. Functional proteomics explores and elucidates the components of pathways and their interactions which, when deregulated, lead to a disease condition. This knowledge allows the design of strategies to target multiple pathways with combinations of pathway-specific drugs, which might increase chances of success and reduce the occurrence of drug resistance. Chemical proteomics, by analyzing the drug interactome, strongly contributes to accelerate the process of new druggable targets discovery. In the research area of clinical proteomics, proteome and peptidome mass spectrometry-profiling of human bodily fluid (plasma, serum, urine and so on), as well as of tissue and of cells, represents a promising tool for novel biomarker and eventually new druggable targets discovery. In the present review we provide a survey of current strategies of functional, chemical and clinical proteomics. Major issues will be presented for proteomic technologies used for the discovery of biomarkers for early disease diagnosis and identification of new drug targets.
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Affiliation(s)
- Rocco Savino
- Department of Health Sciences, Laboratory of Mass Spectrometry and Proteomics, University "Magna Græcia", Catanzaro, University Campus, Europa Avenue, 88100 Catanzaro, Italy.
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Lai JH, She TF, Juang YM, Tsay YG, Huang AH, Yu SL, Chen JJW, Lai CC. Comparative proteomic profiling of human lung adenocarcinoma cells (CL 1-0) expressing miR-372. Electrophoresis 2012; 33:675-88. [PMID: 22451061 DOI: 10.1002/elps.201100329] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Lung cancer is a common malignancy and has a poor overall prognosis. Widespread metastasis is a common phenomenon in non-small cell lung cancer (NSCLC). It has been demonstrated that cancer relapse and survival can be predicted by the presence of a five-microRNA (miRNA) signature independent of stage or histologic type in NSCLC patients. Among the five miRNAs in the signature, miR-372 has been shown to play a significant role in metastasis and in the development of human testicular germ cell tumors. In addition, there is evidence that miR-372 posttranscriptionally downregulates large tumor suppressor, homolog 2 (Lats2), resulting in tumorigenesis and proliferation. To further investigate the cellular mechanisms involved in miR-372-induced silencing, we conducted a comparative proteomic analysis of NSCLC CL 1-0 cells expressing miRNA-372 and/or vector only by using two-dimensional gel electrophoresis (2DE), two-dimensional difference gel electrophoresis (2D-DIGE), and LC/MS/MS. Proteins identified as being up- or downregulated were further classified according to their biological functions. Many of the proteins identified in our study may be potential diagnostic biomarkers of NSCLC, particularly phosphorylated eIF4A-I.
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Affiliation(s)
- Juo-Hsin Lai
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan
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Antberg L, Cifani P, Sandin M, Levander F, James P. Critical Comparison of Multidimensional Separation Methods for Increasing Protein Expression Coverage. J Proteome Res 2012; 11:2644-52. [DOI: 10.1021/pr201257y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Linn Antberg
- Protein Technology,
Department of Immunotechnology,
CREATE Health, Lund University, Sweden
| | - Paolo Cifani
- Protein Technology,
Department of Immunotechnology,
CREATE Health, Lund University, Sweden
| | - Marianne Sandin
- Protein Technology,
Department of Immunotechnology,
CREATE Health, Lund University, Sweden
| | - Fredrik Levander
- Protein Technology,
Department of Immunotechnology,
CREATE Health, Lund University, Sweden
| | - Peter James
- Protein Technology,
Department of Immunotechnology,
CREATE Health, Lund University, Sweden
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Donovan LE, Higginbotham L, Dammer EB, Gearing M, Rees H, Xia Q, Duong D, Seyfried NT, Lah JJ, Levey AI. Analysis of a membrane-enriched proteome from postmortem human brain tissue in Alzheimer's disease. Proteomics Clin Appl 2012; 6:201-11. [PMID: 22532456 PMCID: PMC3338199 DOI: 10.1002/prca.201100068] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Accepted: 12/19/2011] [Indexed: 12/29/2022]
Abstract
PURPOSE The present study is a discovery mode proteomics analysis of the membrane-enriched fraction of postmortem brain tissue from Alzheimer's disease (AD) and control cases. This study aims to validate a method to identify new proteins that could be involved in the pathogenesis of AD and potentially serve as disease biomarkers. EXPERIMENTAL DESIGN Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to analyze the membrane-enriched fraction of human postmortem brain tissue from five AD and five control cases of similar age. Biochemical validation of specific targets was performed by immunoblotting. RESULTS One thousand seven hundred and nine proteins were identified from the membrane-enriched fraction of frontal cortex. Label-free quantification by spectral counting and G-test analysis identified 13 proteins that were significantly changed in disease. In addition to Tau (MAPT), two additional proteins found to be enriched in AD, ubiquitin carboxy-terminal hydrolase 1 (UCHL1), and syntaxin-binding protein 1 (Munc-18), were validated through immunoblotting. DISCUSSION AND CLINICAL RELEVANCE: Proteomic analysis of the membrane-enriched fraction of postmortem brain tissue identifies proteins biochemically altered in AD. Further analysis of this subproteome may help elucidate mechanisms behind AD pathogenesis and provide new sources of biomarkers.
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Affiliation(s)
- Laura E. Donovan
- Departments of Neurology, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Lenora Higginbotham
- Departments of Neurology, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Eric B. Dammer
- Human Genetics, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Marla Gearing
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, Georgia 30322
- Experimental Pathology, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Howard Rees
- Departments of Neurology, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Qiangwei Xia
- Human Genetics, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Duc Duong
- Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
- Neuroscience Proteomics Core Facility. Emory University School of Medicine, Atlanta, Georgia 30322
| | - Nicholas T. Seyfried
- Departments of Neurology, Emory University School of Medicine, Atlanta, Georgia 30322
- Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
- Neuroscience Proteomics Core Facility. Emory University School of Medicine, Atlanta, Georgia 30322
| | - James J. Lah
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, Georgia 30322
- Departments of Neurology, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Allan I. Levey
- Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, Georgia 30322
- Departments of Neurology, Emory University School of Medicine, Atlanta, Georgia 30322
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North SH, Shriver-Lake LC, Taitt CR, Ligler FS. Rapid analytical methods for on-site triage for traumatic brain injury. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2012; 5:35-56. [PMID: 22462400 DOI: 10.1146/annurev-anchem-062011-143105] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Traumatic brain injury (TBI) results from an event that causes rapid acceleration and deceleration of the brain or penetration of the skull with an object. Responses to stimuli and questions, loss of consciousness, and altered behavior are symptoms currently used to justify brain imaging for diagnosis and therapeutic guidance. Tests based on such symptoms are susceptible to false-positive and false-negative results due to stress, fatigue, and medications. Biochemical markers of neuronal damage and the physiological response to that damage are being identified. Biosensors capable of rapid measurement of such markers in the circulation offer a solution for on-site triage, as long as three criteria are met: (a) Recognition reagents can be identified that are sufficiently sensitive and specific, (b) the biosensor can provide quantitative assessment of multiple markers rapidly and simultaneously, and (c) both the sensor and reagents are designed for use outside the laboratory.
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Affiliation(s)
- Stella H North
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, DC 20375-5348, USA.
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Guerrier L, Fortis F, Boschetti E. Solid-phase fractionation strategies applied to proteomics investigations. Methods Mol Biol 2012; 818:11-33. [PMID: 22083813 DOI: 10.1007/978-1-61779-418-6_2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Methods for protein fractionation in the proteomics investigation field are relatively numerous. They apply to the prefractionation of the sample to obtain less complex protein mixtures for an easier analysis; they are also used as a means to evidence specific proteins or protein classes otherwise impossible to detect. They involve depletion of high-abundance proteins suppressing the signal of dilute species; they are also capable to enhance the detectability of low-abundance species while concomitantly decreasing the concentration of abundant proteins such as albumin in serum and hemoglobin in red blood cell lysates. Fractionation of proteomes is also used for the isolation of targeted species that are selected for their different expression under certain pathological conditions and that are detected by mass spectrometry. Two unconventional methods of large interest in proteomics due to the low level of protein redundancy between fractions are also reported.All these methods are reviewed and detailed method given to allow specialists of proteomics investigation to access selected separation methods generally dispersed on different technical reviews or books.
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Affiliation(s)
- Luc Guerrier
- Bio-Rad Laboratories, Marnes la Coquette, France
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Abstract
Systems biology, with its associated technologies of proteomics, genomics, and metabolomics, is driving the evolution of our understanding of cardiovascular physiology. Rather than studying individual molecules or even single reactions, a systems approach allows integration of orthogonal data sets from distinct tiers of biological data, including gene, RNA, protein, metabolite, and other component networks. Together these networks give rise to emergent properties of cellular function, and it is their reprogramming that causes disease. We present 5 observations regarding how systems biology is guiding a revisiting of the central dogma: (1) It deemphasizes the unidirectional flow of information from genes to proteins; (2) it reveals the role of modules of molecules as opposed to individual proteins acting in isolation; (3) it enables discovery of novel emergent properties; (4) it demonstrates the importance of networks in biology; and (5) it adds new dimensionality to the study of biological systems.
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Affiliation(s)
- Sarah Franklin
- Department of Anesthesiology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA.
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Selvaraju S, Rassi ZE. Liquid-phase-based separation systems for depletion, prefractionation and enrichment of proteins in biological fluids and matrices for in-depth proteomics analysis--an update covering the period 2008-2011. Electrophoresis 2012; 33:74-88. [PMID: 22125262 PMCID: PMC3516880 DOI: 10.1002/elps.201100431] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Revised: 09/05/2011] [Accepted: 09/06/2011] [Indexed: 11/08/2022]
Abstract
This review article expands on the previous one (Jmeian, Y. and El Rassi, Z. Electrophoresis 2009, 30, 249-261) by reviewing pertinent literature in the period extending from early 2008 to the present. Similar to the previous review article, the present one is concerned with proteomic sample preparation (e.g. depletion of high-abundance proteins, reduction of the protein dynamic concentration range, enrichment of a particular subproteome), and the subsequent chromatographic and/or electrophoretic prefractionation prior to peptide separation and identification by LC-MS/MS. This review article differs from the first version published in Electrophoresis 2009, 30, 249-261 by expanding on capturing/enriching subglycoproteomics by lectin affinity chromatography. Ninety-eight articles published in the period extending from early 2008 to the present have been reviewed. By no means is this review article exhaustive: its aim is to give a concise report on the latest developments in the field.
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Affiliation(s)
| | - Ziad El Rassi
- Department of Chemistry, Oklahoma State University, Stillwater, OK 74078-3071
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Proteomics—A Blessing or a Curse? Application of Proteomics Technology to Transplant Medicine. Transplantation 2011; 92:499-509. [DOI: 10.1097/tp.0b013e3182265358] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Govorun VM, Ivanov VT. [Proteomics and peptidomics in fundamental and applied medical studies]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2011; 37:199-215. [PMID: 21721253 DOI: 10.1134/s1068162011020063] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The review is focused on current issues of biomedical proteomics and peptidomics. The main attention is paid to modem proteomics technologies applied in medical research--extraction, detection and data analysis techniques. The use of chromatography, mass spectrometry and chromato mass spectrometry in proteogenomic, biomedical studies and biomarker discovery is discussed in detail.
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Boschetti E, Righetti PG. Mixed-bed chromatography as a way to resolve peculiar protein fractionation situations. J Chromatogr B Analyt Technol Biomed Life Sci 2011; 879:827-35. [DOI: 10.1016/j.jchromb.2011.03.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2010] [Revised: 02/28/2011] [Accepted: 03/03/2011] [Indexed: 11/26/2022]
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Meighan MM, Vasquez J, Dziubcynski L, Hews S, Hayes MA. Investigation of Electrophoretic Exclusion Method for the Concentration and Differentiation of Proteins. Anal Chem 2010; 83:368-73. [DOI: 10.1021/ac1025495] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Michelle M. Meighan
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States, and Department of Mathematics and Statistics, Swarthmore College, Swarthmore, Pennsylvania 19081, United States
| | - Jared Vasquez
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States, and Department of Mathematics and Statistics, Swarthmore College, Swarthmore, Pennsylvania 19081, United States
| | - Luke Dziubcynski
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States, and Department of Mathematics and Statistics, Swarthmore College, Swarthmore, Pennsylvania 19081, United States
| | - Sarah Hews
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States, and Department of Mathematics and Statistics, Swarthmore College, Swarthmore, Pennsylvania 19081, United States
| | - Mark A. Hayes
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287, United States, and Department of Mathematics and Statistics, Swarthmore College, Swarthmore, Pennsylvania 19081, United States
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Tomar AK, Saraswat M, Chhikara N, Kumar S, Yadav VK, Sooch BS, Singh TP, Yadav S. Differential proteomics of sperm: insights, challenges and future prospects. Biomark Med 2010; 4:905-10. [DOI: 10.2217/bmm.10.100] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Male factors account for 40% of infertility cases and most are caused by low sperm count, poor sperm quality or both. Defects in sperm are directly linked to reproductive malfunctions, and these defects may be caused by genetic mutations, environmental factors and exposure to free radicals, for example. Almost half of the male infertility cases have no known cause, indicating the lack of sensitive tests for the diagnosis of infertility. Proteomics has evolved as a major research field in biology and medicine, to identify and validate potent targets, at the molecular level, for development of more sensitive diagnostic tools. The recent advances in this field focus on the identification of differentially expressed proteins and analyzing their functional aspects for better understanding of the biological pathways. It not only provides a platform to discover biomarkers of infertility, but may also help in the design of effective male contraceptives. This article discusses various insights of proteomics for exploring biomarkers of male infertility in sperm. It also discusses the enhanced understanding of reproductive physiology offered by data produced by proteomic studies of spermatozoa.
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Affiliation(s)
- Anil Kumar Tomar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Mayank Saraswat
- Center for Bioanalytical Sciences, School of Biotechnology, Dublin City University, Dublin, Ireland
| | - Nirmal Chhikara
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Sanjay Kumar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | - Vikash Kumar Yadav
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
| | | | - Tej P Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
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Xavier T, Ganesan TS, Menon KN. A simple and efficient method for processing of cell lysates for two-dimensional gel electrophoresis. Electrophoresis 2010; 31:2429-35. [PMID: 20564265 DOI: 10.1002/elps.200900644] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Sample preparation is one of the major issues in 2-DE for the separation of proteins. Although a 100% representation of cellular proteins onto a 2-DE is virtually impossible, maximum representation of cellular proteins compared with the original cell lysate is important in the subsequent analysis. We demonstrate that lysis of cells in urea/thiourea solution with subsequent sonication to disrupt the nucleic acids and concentration of the lysate using centri-con led to enrichment of proteins. The procedure resulted in minimal nucleic acid contamination with better resolution of spots. 2-DE spot patterns of proteins prepared using urea-thiourea solubilization/centri-con method to other protein enrichment methods such as phenol/chloroform/isoamyl alcohol extraction, methanol/ammonium acetate precipitation, acetone precipitation and ethanol precipitation were compared. Urea-thiourea solubilization combined with centri-con method of protein enrichment represented higher number/unique spots particularly in the 50-250 kDa M(r) compared with others. Lysis of cells in urea/thiourea from the beginning of lysate preparation preserves the proteins from protease activity due to denaturation of proteases. Thus, we demonstrate that the centri-con methodology is simple and effective for the preparation of high-quality sample that can be used for a qualitative representation of cellular proteins on a 2-DE for proteomic analysis.
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Affiliation(s)
- Tessy Xavier
- Division of Molecular Medicine, Amrita Research Institute, Amrita Institute for Medical Sciences, Ponekkara, Kochi, India
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Merchant ML, Klein JB. Proteomic discovery of diabetic nephropathy biomarkers. Adv Chronic Kidney Dis 2010; 17:480-6. [PMID: 21044770 PMCID: PMC2987606 DOI: 10.1053/j.ackd.2010.09.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Accepted: 09/14/2010] [Indexed: 02/07/2023]
Abstract
Diabetes mellitus (DM) is a complex systemic disease with complications that result from both genetic predisposition and dysregulated metabolic pathways. It is highly prevalent, with current estimates stating that there are 17.5 million diagnosed and 6.6 million undiagnosed patients with diabetes in the United States. DM and its complications impose a significant societal and economic burden. The medical costs of common microvascular complications of uncontrolled DM, diabetic nephropathy (DN) and diabetic retinopathy account for 29% and 15%, respectively, of the $116 billion worth expenditures associated with diabetes. A substantial gap exists in our knowledge related to the understanding of these complications. To advance therapy and decrease the societal burden of DM, there is a clear need for biomarkers that can diagnose DN at an early stage and predict its course. Proteomics has evolved into a high-throughput, analytical discipline used to analyze complex biological data sets. These open-ended, hypothesis-generating approaches, when appropriately designed and interpreted, are well suited to the study of the pathogenic mechanisms of diabetic microvascular disease and the identification of biomarkers of DN. In this study, we review the evolving role played by proteomics in expanding our understanding of the diagnosis and pathogenesis of DN.
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Salinas K, Hemmer M, Serrano J, Higgins L, Anderson L, Benninghoff A, Williams D, Walker C. Identification of estrogen-responsive vitelline envelope protein fragments from rainbow trout (Oncorhynchus mykiss) plasma using mass spectrometry. Mol Reprod Dev 2010; 77:963-70. [DOI: 10.1002/mrd.21244] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2010] [Accepted: 08/28/2010] [Indexed: 11/06/2022]
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Jansen van Vuuren B, Read T, Olkhov RV, Shaw AM. Human serum albumin interference on plasmon-based immunokinetic assay for antibody screening in model blood sera. Anal Biochem 2010; 405:114-20. [DOI: 10.1016/j.ab.2010.05.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2010] [Revised: 05/17/2010] [Accepted: 05/20/2010] [Indexed: 12/12/2022]
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Sub-proteomic fractionation, iTRAQ, and OFFGEL-LC-MS/MS approaches to cardiac proteomics. J Proteomics 2010; 73:1551-61. [PMID: 20394843 DOI: 10.1016/j.jprot.2010.03.016] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Revised: 03/22/2010] [Accepted: 03/25/2010] [Indexed: 12/11/2022]
Abstract
Using an in solution based approach with a sub-proteomic fraction enriched in cardiac sarcomeric proteins; we identified protein abundance in ischemic and non-ischemic regions of rat hearts stressed by acute myocardial ischemia by ligating the left-anterior descending coronary artery in vivo for 1h without reperfusion. Sub-cellular fractionation permitted more in depth analysis of the proteome by reducing the sample complexity. A series of differential centrifugations produced nuclear, mitochondrial, cytoplasmic, microsomal, and sarcomeric enriched fractions of ischemic and non-ischemic tissues. The sarcomeric enriched fractions were labeled with isobaric tags for relative quantitation (iTRAQ), and then fractionated with an Agilent 3100 OFFGEL fractionator. The OFFGEL fractions were run on a Dionex U-3000 nano LC coupled to a ThermoFinnigan LTQ running in PQD (pulsed Q dissociation) mode. The peptides were analyzed using two search engines MASCOT (MatrixScience), and MassMatrix with false discovery rate of <5%. Compared to no fractionation prior to LC-MS/MS, fractionation with OFFGEL improved the identification of proteins approximately four-fold. We found that approximately 22 unique proteins in the sarcomeric enriched fraction had changed at least 20%. Our workflow provides an approach for discovery of unique biomarkers or changes in the protein profile of tissue in disorders of the heart.
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Ulukaya E, Yilmaz Y, Moshkovskii S, Karpova M, Pyatnitskiy M, Atug O, Dolar E. Proteomic analysis of serum in patients with non-alcoholic steatohepatitis using matrix-assisted laser desorption ionization time-of-flight mass spectrometry. Scand J Gastroenterol 2010; 44:1471-6. [PMID: 19883279 DOI: 10.3109/00365520903353379] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
OBJECTIVE We sought to investigate whether serum proteomic pattern analysis obtained using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI TOF-MS) may help to diagnose non-alcoholic steatohepatitis (NASH) in the setting of non-alcoholic fatty liver disease (NAFLD). MATERIAL AND METHODS We enrolled 80 patients with biopsy-proven NAFLD and 19 healthy comparison subjects. Patients with NAFLD were classified according to their liver histology as having definite NASH (n = 48), borderline NASH (n = 22) or simple steatosis (n = 10). Liver ultrasound scanning was performed to assess the degree of steatosis. Mass spectra of serum samples were obtained using a Ultraflex II mass spectrometer. RESULTS The highest accuracy for NASH diagnostics was reached using 15 peaks. Corresponding sensitivity and specificity values were 73.95% +/- 3.38% and 88.71% +/- 1.39%, respectively. However, mass spectra did not allow us to distinguish NASH from simple steatosis. CONCLUSIONS We conclude that proteomic analyses of serum samples from NAFLD patients by MALDI TOF-MS do not seem to have a major clinical value for diagnosing NASH. However, the identification of 15 peaks in our study may help to further elucidate the pathophysiology of NASH and merits further investigation.
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Affiliation(s)
- Engin Ulukaya
- Department of Biochemistry, Uludag University Medical School, Bursa, Turkey
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Candiano G, Santucci L, Petretto A, Bruschi M, Dimuccio V, Urbani A, Bagnasco S, Ghiggeri GM. 2D-electrophoresis and the urine proteome map: Where do we stand? J Proteomics 2010; 73:829-44. [DOI: 10.1016/j.jprot.2009.12.003] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2009] [Revised: 11/30/2009] [Accepted: 12/02/2009] [Indexed: 12/19/2022]
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Challenges for biomarker discovery in body fluids using SELDI-TOF-MS. J Biomed Biotechnol 2009; 2010:906082. [PMID: 20029632 PMCID: PMC2793423 DOI: 10.1155/2010/906082] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2009] [Accepted: 09/01/2009] [Indexed: 01/17/2023] Open
Abstract
Protein profiling using SELDI-TOF-MS has gained over the past few years an increasing interest in the field of biomarker discovery. The technology presents great potential if some parameters, such as sample handling, SELDI settings, and data analysis, are strictly controlled. Practical considerations to set up a robust and sensitive strategy for biomarker discovery are presented. This paper also reviews biological fluids generally available including a description of their peculiar properties and the preanalytical challenges inherent to sample collection and storage. Finally, some new insights for biomarker identification and validation challenges are provided.
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Merchant ML, Powell DW, Wilkey DW, Cummins TD, Deegens JK, Rood IM, McAfee KJ, Fleischer C, Klein E, Klein JB. Microfiltration isolation of human urinary exosomes for characterization by MS. Proteomics Clin Appl 2009; 4:84-96. [PMID: 21137018 DOI: 10.1002/prca.200800093] [Citation(s) in RCA: 152] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2008] [Revised: 09/14/2009] [Accepted: 09/28/2009] [Indexed: 12/12/2022]
Abstract
PURPOSE The purpose of this study was to address the hypothesis that small vesicular urinary particles known as exosomes could be selectively microfiltered using low protein-binding size exclusion filters, thereby simplifying their use in clinical biomarker discovery studies. EXPERIMENTAL DESIGN We characterized a microfiltration approach using a low protein binding, hydrophilized polyvinylidene difluoride membrane to easily and efficiently isolate urinary exosomes from fresh, room temperature or 4°C urine, with a simultaneous depletion of abundant urinary proteins. Using LC-MS, immunoblot analysis, and electron microscopy methods, we demonstrate this method to isolate intact exosomes and thereby enrich for a low abundant urinary proteome. RESULTS In comparison to other standard methods of exosome isolation including ultracentrifugation and nanofiltration, we demonstrate equivalent enrichment of the exosome proteome with reduced co-purification of abundant urinary proteins. CONCLUSION AND CLINICAL RELEVANCE In conclusion, we demonstrate a microfiltration isolation method that preserves the exosome structure, reduces contamination from higher abundant urinary proteins, and can be easily implemented into mass spectrometry analysis for biomarker discovery efforts or incorporation into routine clinical laboratory applications to yield higher sample throughput.
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Matt P, Huso DL, Habashi J, Holm T, Doyle J, Schoenhoff F, Liu G, Black J, Van Eyk JE, Dietz HC. Murine model of surgically induced acute aortic dissection type A. J Thorac Cardiovasc Surg 2009; 139:1041-7. [PMID: 19910001 DOI: 10.1016/j.jtcvs.2009.08.039] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2009] [Revised: 07/12/2009] [Accepted: 08/09/2009] [Indexed: 11/17/2022]
Abstract
OBJECTIVES This study aimed at developing a murine model of surgically induced acute aortic dissection type A for investigation of the formation and progression of acute aortic dissection and to test whether this system could be used for biomarker discovery. METHODS Adult fibrillin-1 deficient, Fbn1(C1039G/+) mice and wild-type mice were anesthetized, ventilated, and the ascending aorta exposed via hemisternotomy. We hypothesized that acute aortic dissection could be induced either by injecting autologous blood into the aortic wall or by injury to the wall with aortic clamping. Echocardiography was done preoperatively, and serum samples were collected before and 30 minutes after the operation and analyzed by enzyme-linked immunosorbent assay. RESULTS Echocardiography revealed larger aortic root diameters in Fbn1(C1039G/+) compared with wild-type mice (P = .001). Histologic examination showed that aortic clamp injury but not injection of blood leads to large intimal tears, disruption of aortic wall structures, and localized dissection of the aortic media in Fbn1(C1039G/+) mice. Acute aortic dissection developed in 4 of 5 Fbn1(C1039G/+) mice versus 0 of 5 wild-type mice after aortic clamping (P < .01). Elastin staining showed higher elastic fiber fragmentation and disarray in Fbn1(C1039G/+) compared with wild-type mice. Enzyme-linked immunosorbent assay analysis revealed elevated circulating transforming growth factor beta1 concentrations after induction of acute aortic dissection in Fbn1(C1039G/+) mice (P = .02, 150 +/- 61 ng/mL vs 456 +/- 97 ng/mL), but not in wild-type or sham-operated mice. CONCLUSIONS Aortic clamp injury can induce AAD in Fbn1(C1039G/+), but not in wild-type mice. This murine model of surgically induced acute aortic dissection is highly reproducible and nonlethal in the short term. Using this system, we revealed that circulating transforming growth factor beta1 is a promising biomarker for acute aortic dissection.
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Affiliation(s)
- Peter Matt
- Division of Cardiac Surgery, University Hospital Basel/Berne, Spitalstrasse 21, CH-4031 Basel, Switzerland.
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The use of omic technologies for biomarker development to trace functions of anabolic agents. J Chromatogr A 2009; 1216:8192-9. [DOI: 10.1016/j.chroma.2009.01.094] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2009] [Revised: 01/27/2009] [Accepted: 01/30/2009] [Indexed: 12/25/2022]
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