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Fu Q, Vegesna M, Sundararaman N, Damoc E, Arrey TN, Pashkova A, Mengesha E, Debbas P, Joung S, Li D, Cheng S, Braun J, McGovern DPB, Murray C, Xuan Y, Eyk JEV. Paradigm shift in biomarker translation: a pipeline to generate clinical grade biomarker candidates from DIA-MS discovery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.20.586018. [PMID: 38562888 PMCID: PMC10983901 DOI: 10.1101/2024.03.20.586018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Clinical biomarker development has been stymied by inaccurate protein quantification from mass spectrometry (MS) discovery data and a prolonged validation process. To mitigate these issues, we created the Targeted Extraction Assessment of Quantification (TEAQ) software package. This innovative tool uses the discovery cohort analysis to select precursors, peptides, and proteins that adhere to established targeted assay criteria. TEAQ was applied to Data-Independent Acquisition MS data from plasma samples acquired on an Orbitrap™ Astral™ MS. Identified precursors were evaluated for linearity, specificity, repeatability, reproducibility, and intra-protein correlation from 11-point loading curves under three throughputs, to develop a resource for clinical-grade targeted assays. From a clinical cohort of individuals with inflammatory bowel disease (n=492), TEAQ successfully identified 1116 signature peptides for 327 quantifiable proteins from 1180 identified proteins. Embedding stringent selection criteria adaptable to targeted assay development into the analysis of discovery data will streamline the transition to validation and clinical studies.
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Chen YT, Liao WR, Wang HT, Chen HW, Chen SF. Targeted protein quantitation in human body fluids by mass spectrometry. MASS SPECTROMETRY REVIEWS 2023; 42:2379-2403. [PMID: 35702881 DOI: 10.1002/mas.21788] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 01/11/2022] [Accepted: 04/08/2022] [Indexed: 06/15/2023]
Abstract
Human body fluids (biofluids) contain various proteins, some of which reflect individuals' physiological conditions or predict diseases. Therefore, the analysis of biofluids can provide substantial information on novel biomarkers for clinical diagnosis and prognosis. In the past decades, mass spectrometry (MS)-based technologies have been developed as proteomic strategies not only for the identification of protein biomarkers but also for biomarker verification/validation in body fluids for clinical applications. The main advantage of targeted MS-based methodologies is the accurate and specific simultaneous quantitation of multiple biomarkers with high sensitivity. Here, we review MS-based methodologies that are currently used for the targeted quantitation of protein components in human body fluids, especially in plasma, urine, cerebrospinal fluid, and saliva. In addition, the currently used MS-based methodologies are summarized with a specific focus on applicable clinical sample types, MS configurations, and acquisition modes.
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Affiliation(s)
- Yi-Ting Chen
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Nephrology, Kidney Research Center, Linkou Medical Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Molecular and Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Wan-Rou Liao
- Department of Chemistry, National Taiwan Normal University, Taipei, Taiwan
| | - Hsueh-Ting Wang
- Instrumentation Center, National Taiwan Normal University, Taipei, Taiwan
| | - Hsiao-Wei Chen
- Molecular and Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Sung-Fang Chen
- Department of Chemistry, National Taiwan Normal University, Taipei, Taiwan
- Instrumentation Center, National Taiwan Normal University, Taipei, Taiwan
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Sivanesan I, Gopal J, Hasan N, Muthu M. A systematic assessment of matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) application for rapid identification of pathogenic microbes that affect food crops: delivered and future deliverables. RSC Adv 2023; 13:17297-17314. [PMID: 37304772 PMCID: PMC10251190 DOI: 10.1039/d3ra01633a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/20/2023] [Indexed: 06/13/2023] Open
Abstract
MALDI-TOF MS has decades of experience in the detection and identification of microbial pathogens. This has now become a valuable analytical tool when it comes to the identification and detection of clinical microbial pathogens. This review gives a brief synopsis of what has been achieved using MALDI-TOF MS in clinical microbiology. The major focus, however, is on summarizing and highlighting the effectiveness of MALDI-TOF MS as a novel tool for rapid identification of food crop microbial pathogens. The methods used and the sample preparation methodologies reported thus far have been highlighted and the challenges and gaps and recommendations for fine tuning the technique have been put forth. In an era where anything close to the health and welfare of humanity has been considered as the top priority, this review pitches on one such relevant research topics.
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Affiliation(s)
- Iyyakkannu Sivanesan
- Department of Bioresources and Food Science, Institute of Natural Science and Agriculture, Konkuk University 1 Hwayang-dong, Gwangjin-gu Seoul 05029 Korea
| | - Judy Gopal
- Department of Research and Innovation, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS) Thandalam Chennai 602105 Tamil Nadu India +91 44 2681 1009 +91 44 66726677
| | - Nazim Hasan
- Department of Chemistry, Faculty of Science, Jazan University P.O. Box 114 Jazan Saudi Arabia
| | - Manikandan Muthu
- Department of Research and Innovation, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences (SIMATS) Thandalam Chennai 602105 Tamil Nadu India +91 44 2681 1009 +91 44 66726677
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Deng T, Liu Y, Gael A, Fu X, Deng X, Liu Y, Wu Y, Wu Y, Wang H, Deng Y, Lai J, Fu Q. Study on Proteomics-Based Aortic Dissection Molecular Markers Using iTRAQ Combined With Label Free Techniques. Front Physiol 2022; 13:862732. [PMID: 35910577 PMCID: PMC9335284 DOI: 10.3389/fphys.2022.862732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Aortic dissection refers to the separation of aortic media and extension along the long axis to form the true and false chambers of the aortic wall. 65–70% of the patients died of cardiac tamponade, arrhythmia, dissection rupture, etc. At present, echocardiography, computed tomography angiography (CTA), etc. are the main diagnosis tools for aortic dissection. To date, there is no rapid serum molecular marker that can be used for differential diagnosis and risk assessment.Objectives: To screen serum molecular markers systematically amid aortic dissection and acute coronary syndrome and to preliminarily identify the pathogenesis of acute aortic dissection.Methods: Related disputes cases of all hospitals were statistically analyzed for the AAD medical disputes ratio, early death ratio and misdiagnosis ratio from the database of Guangdong Province Medical Disputes Coordination Committee from 2013 to 2017. Serum and Aortic tissues samples were respectively quantified by iTRAQ and label-free analysis, further validated by ELISA and protein verified by immunofluorescence and Western blot from AAD and control patients enrolled from the Zhujiang Hospital of Southern Medical University and Guangdong Province people's Hospital from 2016 to 2018.Results: AAD cases ratio accounted for 15.29% in all 150 cardiovascular disputes, 59.26% in all cardiovascular death less than 24 h, and 88.89% in the patients who remained undiagnosed at the time of death, 84 proteins (66 and 18 upregulated and downregulated, respectively) were identified by iTRAQ and 16 proteins (9 and 7 upregulated and downregulated, respectively) by Label-free. Nine proteins (Lumican, FGL1, PI16, MMP9, FBN1, MMP2, VWF, MMRN1, and PF4) related to the pathogenesis of aortic dissection were identified by David /Ease and String techniques as candidate biomarkers for verification test. Four proteins (Lumican, FGL1, PI16, and MMP9) were found to be statistically different after ELISA verification. The expression of FGL1, PI16, and MMP9 proteins was pathologically significantly increased except for Lumican. Histologically, TGF-β1, α-SMA, and Collagen1 were also significantly higher in the aortic group.Conclusion: Lumican, FGL1, PI16, and MMP9 may be potential biomarkers in AAD patients, and the Lumican-mediated TGF-β1 pathway is likely to be involved in the pathogenesis of aortic dissection.
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Affiliation(s)
- Ting Deng
- Department of Cardiovascular Disease, First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Cardiology, Laboratory of Heart Center, Heart Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Guangdong Provincial Biomedical Engineering Technology, Research Center for Cardiovascular Disease, Guangdong, China
- Sino-Japanese Cooperation Platform for Translational Research in the Heart Failure, Guangzhou, China
| | - Yongguang Liu
- Department of Organ Transplantation, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Akindavyi Gael
- Department of Cardiology, Laboratory of Heart Center, Heart Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Guangdong Provincial Biomedical Engineering Technology, Research Center for Cardiovascular Disease, Guangdong, China
- Sino-Japanese Cooperation Platform for Translational Research in the Heart Failure, Guangzhou, China
- Department of Cardiology, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Xiaohua Fu
- Department of Invasive Technology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Xiaofang Deng
- Department of Neonatology, Guangdong Provincial People’s Hospital, Guangzhou, China
| | - Yunfeng Liu
- Department of Cardiology, Laboratory of Heart Center, Heart Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Guangdong Provincial Biomedical Engineering Technology, Research Center for Cardiovascular Disease, Guangdong, China
- Sino-Japanese Cooperation Platform for Translational Research in the Heart Failure, Guangzhou, China
| | - Yizhang Wu
- Department of Cardiology, Laboratory of Heart Center, Heart Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Guangdong Provincial Biomedical Engineering Technology, Research Center for Cardiovascular Disease, Guangdong, China
- Sino-Japanese Cooperation Platform for Translational Research in the Heart Failure, Guangzhou, China
| | - Yingzhi Wu
- Department of Cardiology, Laboratory of Heart Center, Heart Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Guangdong Provincial Biomedical Engineering Technology, Research Center for Cardiovascular Disease, Guangdong, China
- Sino-Japanese Cooperation Platform for Translational Research in the Heart Failure, Guangzhou, China
| | - Huimin Wang
- Department of Cardiology, Laboratory of Heart Center, Heart Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Guangdong Provincial Biomedical Engineering Technology, Research Center for Cardiovascular Disease, Guangdong, China
- Sino-Japanese Cooperation Platform for Translational Research in the Heart Failure, Guangzhou, China
| | - Yuying Deng
- Department of Cardiology, Laboratory of Heart Center, Heart Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Guangdong Provincial Biomedical Engineering Technology, Research Center for Cardiovascular Disease, Guangdong, China
- Sino-Japanese Cooperation Platform for Translational Research in the Heart Failure, Guangzhou, China
| | - Jun Lai
- Department of Cardiology, Laboratory of Heart Center, Heart Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Guangdong Provincial Biomedical Engineering Technology, Research Center for Cardiovascular Disease, Guangdong, China
- Sino-Japanese Cooperation Platform for Translational Research in the Heart Failure, Guangzhou, China
| | - Qiang Fu
- Department of Cardiology, Laboratory of Heart Center, Heart Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Guangdong Provincial Biomedical Engineering Technology, Research Center for Cardiovascular Disease, Guangdong, China
- Sino-Japanese Cooperation Platform for Translational Research in the Heart Failure, Guangzhou, China
- Department of Cardiology, Shenzhen Hospital, Southern Medical University, Shenzhen, China
- *Correspondence: Qiang Fu,
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Kulyyassov A, Fresnais M, Longuespée R. Targeted liquid chromatography-tandem mass spectrometry analysis of proteins: Basic principles, applications, and perspectives. Proteomics 2021; 21:e2100153. [PMID: 34591362 DOI: 10.1002/pmic.202100153] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/08/2021] [Accepted: 09/24/2021] [Indexed: 12/25/2022]
Abstract
Liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) is now the main analytical method for the identification and quantification of peptides and proteins in biological samples. In modern research, identification of biomarkers and their quantitative comparison between samples are becoming increasingly important for discovery, validation, and monitoring. Such data can be obtained following specific signals after fragmentation of peptides using multiple reaction monitoring (MRM) and parallel reaction monitoring (PRM) methods, with high specificity, accuracy, and reproducibility. In addition, these methods allow measurement of the amount of post-translationally modified forms and isoforms of proteins. This review article describes the basic principles of MRM assays, guidelines for sample preparation, recent advanced MRM-based strategies, applications and illustrative perspectives of MRM/PRM methods in clinical research and molecular biology.
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Affiliation(s)
| | - Margaux Fresnais
- Department of Clinical Pharmacology and Pharmacoepidemiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Rémi Longuespée
- Department of Clinical Pharmacology and Pharmacoepidemiology, Heidelberg University Hospital, Heidelberg, Germany
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Wang X, Song T, Sun Y, Men L, Gu Y, Zhang S, Chen X. Proteomic Analysis Reveals the Effect of Trichostatin A and Bone Marrow-Derived Dendritic Cells on the Fatty Acid Metabolism of NIH3T3 Cells under Oxygen-Glucose Deprivation Conditions. J Proteome Res 2020; 20:960-971. [PMID: 33226813 DOI: 10.1021/acs.jproteome.0c00713] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fibroblasts mediate acute wound healing and long-term tissue remodeling with scarring after tissue injury. Following myocardial infarction (MI), necrotized cardiomyocytes become replaced by secreted extracellular matrix proteins produced by fibroblasts. Dendritic cells (DCs) can migrate from the bone marrow to the infarct areas and infarct border areas to mediate collagen accumulation after MI. Trichostatin A (TSA) is known to regulate apoptosis and proliferation in fibroblasts and affect the functions of DCs under oxygen-glucose deprivation (OGD) conditions. In this study, we used label-free quantitative proteomics to investigate the effects of TSA and bone marrow-derived dendritic cells (BMDCs) on NIH3T3 fibroblasts under OGD conditions. The results showed that the fatty acid degradation pathway was significantly upregulated in NIH3T3 cells under OGD conditions and that the fatty acid synthesis pathway was significantly downregulated in NIH3T3 cells treated with conditioned media (CM) from BMDCs treated with TSA under OGD conditions [BMDCs-CM(TSA)]. In addition, BMDCs-CM(TSA) significantly decreased the levels of triglycerides and free fatty acids and mediated fatty acid metabolism-related proteins in NIH3T3 cells under OGD conditions. In summary, this proteomics analysis showed that TSA and BMDCs affect fatty acid metabolism in NIH3T3 cells under OGD conditions.
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Affiliation(s)
- Xuan Wang
- Department of Pharmacology, College of Basic Medical Sciences, Jilin University, Changchun 130000, China
| | - Tongtong Song
- Department of Pharmacology, College of Basic Medical Sciences, Jilin University, Changchun 130000, China
| | - Yunpeng Sun
- Cardiac Surgery Department, The First Hospital of Jilin University, Changchun 130000, China
| | - Lihui Men
- Department of Pharmacology, College of Basic Medical Sciences, Jilin University, Changchun 130000, China
| | - Yiwen Gu
- Department of Pharmacology, College of Basic Medical Sciences, Jilin University, Changchun 130000, China
| | - Siwei Zhang
- Department of Pharmacology, College of Basic Medical Sciences, Jilin University, Changchun 130000, China
| | - Xia Chen
- Department of Pharmacology, College of Basic Medical Sciences, Jilin University, Changchun 130000, China
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Chen H, Wu M, Jiang W, Liu X, Zhang J, Yu C. iTRAQ‑based quantitative proteomics analysis of the potential application of secretoneurin gene therapy for cardiac hypertrophy induced by DL‑isoproterenol hydrochloride in mice. Int J Mol Med 2020; 45:793-804. [PMID: 31985029 PMCID: PMC7015125 DOI: 10.3892/ijmm.2020.4472] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 12/17/2019] [Indexed: 02/05/2023] Open
Abstract
A previous study by our group demonstrated a protective role of the neuropeptide secretoneurin (SN) in DL‑isoproterenol hydrochloride (ISO)‑induced cardiac hypertrophy in mice. To further characterize the molecular mechanism of SN treatment, an isobaric tags for relative and absolute quantification (iTRAQ)‑based quantitative proteomic analysis was applied to identify putative target proteins and molecular pathways. An SN expression vector was injected into the myocardial tissues of mice, and the animals were then subcutaneously injected with ISO (5 mg/kg/day) for 7 days to induce cardiac hypertrophy. The results of echocardiography and hemodynamic measurements indicated that the function of the heart impaired by ISO treatment was significantly ameliorated via SN gene injection. The investigation of heart proteomics was performed by iTRAQ‑based liquid chromatography‑tandem mass spectrometry analysis. A total of 2,044 quantified proteins and 15 differentially expressed proteins were associated with SN overexpression in mice with cardiac hypertrophy. Functional enrichment analysis demonstrated that these effects were possibly associated with metabolic processes. A protein‑protein interaction network analysis was constructed and the data indicated that apolipoprotein C‑III (Apoc3) was associated with the positive effect of SN on the induction of cardiac hypertrophy in mice. The present study proposed a potential mechanism of SN action on Apoc3 upregulation that may contribute to the amelioration of cardiac hypertrophy. These findings can aid the clinical application of SN in patients with cardiac hypertrophy.
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Affiliation(s)
| | - Mingjun Wu
- Institute of Life Science, Chongqing Medical University, Chongqing 400016
| | - Wei Jiang
- State Key Laboratory of Biotherapy, Molecular Medicine Research Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Xiang Liu
- Institute of Life Science, Chongqing Medical University, Chongqing 400016
| | - Jun Zhang
- Institute of Life Science, Chongqing Medical University, Chongqing 400016
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Guan W, Liu Y, Liu Y, Wang Q, Ye HL, Cheng YG, Kuang HX, Jiang XC, Yang BY. Proteomics Research on the Protective Effect of Mangiferin on H9C2 Cell Injury Induced by H 2O 2. Molecules 2019; 24:molecules24101911. [PMID: 31109015 PMCID: PMC6572523 DOI: 10.3390/molecules24101911] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 05/06/2019] [Accepted: 05/15/2019] [Indexed: 12/12/2022] Open
Abstract
Cardiovascular disease is one of the leading causes of morbidity and mortality worldwide. Mangiferin is a natural glucosylxanthone with antioxidant and anti-inflammatory properties, which has been confirmed to protect cardiac cells from myocardial infarction and myocardial ischemia reperfusion injury (MIRI); however, the underlying mechanism is still unclear. As oxidative stress is a major pathogenesis of MIRI, an H9C2 cell injury induced by hydrogen peroxide (H2O2) was established to simulate MIRI in vitro. Herein, the protective effect of mangiferin against MIRI was evaluated and the isobaric tags for relative and absolute quantitation (iTRAQ)-based proteomics was applied to explore the underlying molecular mechanism. In this research, mangiferin markedly ameliorated the oxidative imbalance by increasing the antioxidative capacity of the H9C2 cell. Moreover, proteomics analysis revealed that mangiferin pretreatment brought twenty differently-expressed proteins back to normal, most of which were related to glucose and fatty acid metabolism. Glycolysis, citrate cycle, and fatty acid degradation pathways were highlighted by Kyoto Encyclopedia of Gene and Genomes (KEGG) analysis. Western blot validation of six cardiac metabolism-related proteins were consistent with the proteomics analysis. Taken together, mangiferin protected the cardiomyocytes from MIRI by enhancing the antioxidant capacity and increasing the activities of glycolysis, citrate cycle, and fatty acid degradation pathways.
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Affiliation(s)
- Wei Guan
- Key Laboratory of Chinese Materia Medica, Ministry of Education of Heilongjiang University of Chinese Medicine, Harbin 150040, China.
| | - Yan Liu
- Key Laboratory of Chinese Materia Medica, Ministry of Education of Heilongjiang University of Chinese Medicine, Harbin 150040, China.
| | - Yuan Liu
- Key Laboratory of Chinese Materia Medica, Ministry of Education of Heilongjiang University of Chinese Medicine, Harbin 150040, China.
| | - Qi Wang
- Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, Harbin 150036, China.
| | - Hong-Liang Ye
- Key Laboratory of Chinese Materia Medica, Ministry of Education of Heilongjiang University of Chinese Medicine, Harbin 150040, China.
| | - Yan-Gang Cheng
- Key Laboratory of Chinese Materia Medica, Ministry of Education of Heilongjiang University of Chinese Medicine, Harbin 150040, China.
| | - Hai-Xue Kuang
- Key Laboratory of Chinese Materia Medica, Ministry of Education of Heilongjiang University of Chinese Medicine, Harbin 150040, China.
| | - Xi-Cheng Jiang
- Key Laboratory of Chinese Materia Medica, Ministry of Education of Heilongjiang University of Chinese Medicine, Harbin 150040, China.
| | - Bing-You Yang
- Key Laboratory of Chinese Materia Medica, Ministry of Education of Heilongjiang University of Chinese Medicine, Harbin 150040, China.
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Preece RL, Han SYS, Bahn S. Proteomic approaches to identify blood-based biomarkers for depression and bipolar disorders. Expert Rev Proteomics 2018; 15:325-340. [DOI: 10.1080/14789450.2018.1444483] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Rhian Lauren Preece
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Sung Yeon Sarah Han
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Sabine Bahn
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
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Wang Q, Guo L, Strawser CJ, Hauser LA, Hwang WT, Snyder NW, Lynch DR, Mesaros C, Blair IA. Low apolipoprotein A-I levels in Friedreich's ataxia and in frataxin-deficient cells: Implications for therapy. PLoS One 2018; 13:e0192779. [PMID: 29447225 PMCID: PMC5813973 DOI: 10.1371/journal.pone.0192779] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Accepted: 01/30/2018] [Indexed: 12/21/2022] Open
Abstract
Friedreich's ataxia (FA) is an autosomal recessive neurodegenerative disorder, which results primarily from reduced expression of the mitochondrial protein frataxin. FA has an estimated prevalence of one in 50,000 in the population, making it the most common hereditary ataxia. Paradoxically, mortality arises most frequently from cardiomyopathy and cardiac failure rather than from neurological effects. Decreased high-density lipoprotein (HDL) and apolipoprotein A-I (ApoA-l) levels in the general population are associated with an increased risk of mortality from cardiomyopathy and heart failure. However, the pathophysiology of heart disease in FA is non-vascular and there are conflicting data on HDL-cholesterol in FA. Two studies have shown a decrease in HDL-cholesterol compared with controls and two have shown there was no difference between FA and controls. One also showed that there was no difference in serum Apo-A-I levels in FA when compared with controls. Using a highly specific stable isotope dilution mass spectrometry-based assay, we demonstrated a 21.6% decrease in serum ApoA-I in FA patients (134.8 mg/dL, n = 95) compared with non-affected controls (172.1 mg/dL, n = 95). This is similar to the difference in serum ApoA-I levels between non-smokers and tobacco smokers. Knockdown of frataxin by > 70% in human hepatoma HepG2 cells caused a 20% reduction in secreted ApoA-I. Simvastatin, a 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) reductase inhibitor caused a 200% increase in HMG-CoA in the control HepG2 cells with a similar increase in the frataxin knockdown HepG2 cells, back to levels found in the control cells. There was a concomitant 20% increase in secreted ApoA-I to levels found in the control cells that were treated with simvastatin. This study provides compelling evidence that ApoA-I levels are reduced in FA patients compared with controls and suggest that statin treatment would normalize the ApoA-I levels.
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Affiliation(s)
- QingQing Wang
- Penn/CHOP Center of Excellence in Friedreich’s Ataxia, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Penn SRP Center and Center of Excellence in Environmental Toxicology Center, Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Lili Guo
- Penn SRP Center and Center of Excellence in Environmental Toxicology Center, Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Cassandra J. Strawser
- Penn/CHOP Center of Excellence in Friedreich’s Ataxia, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Division of Neurology, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Lauren A. Hauser
- Penn/CHOP Center of Excellence in Friedreich’s Ataxia, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Division of Neurology, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Wei-Ting Hwang
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Nathaniel W. Snyder
- AJ Drexel Autism Institute, Drexel University, Philadelphia, Pennsylvania, United States of America
| | - David R. Lynch
- Penn/CHOP Center of Excellence in Friedreich’s Ataxia, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Division of Neurology, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Clementina Mesaros
- Penn/CHOP Center of Excellence in Friedreich’s Ataxia, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Penn SRP Center and Center of Excellence in Environmental Toxicology Center, Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Ian A. Blair
- Penn/CHOP Center of Excellence in Friedreich’s Ataxia, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Penn SRP Center and Center of Excellence in Environmental Toxicology Center, Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania Philadelphia, Philadelphia, Pennsylvania, United States of America
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11
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Hsiao YC, Chu LJ, Chen YT, Chi LM, Chien KY, Chiang WF, Chang YT, Chen SF, Wang WS, Chuang YN, Lin SY, Chien CY, Chang KP, Chang YS, Yu JS. Variability Assessment of 90 Salivary Proteins in Intraday and Interday Samples from Healthy Donors by Multiple Reaction Monitoring-Mass Spectrometry. Proteomics Clin Appl 2018; 12. [PMID: 29350471 DOI: 10.1002/prca.201700039] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 12/11/2017] [Indexed: 12/19/2022]
Abstract
PURPOSE Saliva is an attractive sample source for the biomarker-based testing of several diseases, especially oral cancer. Here, we sought to apply multiplexed LC-MRM-MS to precisely quantify 90 disease-related proteins and assess their intra- and interindividual variability in saliva samples from healthy donors. EXPERIMENTAL DESIGN We developed two multiplexed LC-MRM-MS assays for 122 surrogate peptides representing a set of disease-related proteins. Saliva samples were collected from 10 healthy volunteers at three different time points (Day 1 morning and afternoon, and Day 2 morning). Each sample was spiked with a constant amount of a 15 N-labeled protein and analyzed by MRM-MS in triplicate. Quantitative results from LC-MRM-MS were calculated by single-point quantification with reference to a known amount of internal standard (heavy peptide). RESULTS The CVs for assay reproducibility and technical variation were 13 and 11%, respectively. The average concentrations of the 99 successfully quantified proteins ranged from 0.28 ± 0.58 ng mL-1 for profilin-2 (PFN2) to 8.55 ±8.96 μg mL-1 for calprotectin (S100A8). For the 90 proteins detectable in >50% of samples, the average CVs for intraday, interday, intraindividual, and interindividual samples were 38%, 43%, 45%, and 69%, respectively. The fluctuations of most target proteins in individual subjects were found to be within ± twofold. CONCLUSIONS AND CLINICAL RELEVANCE Our study elucidated the intra- and interindividual variability of 90 disease-related proteins in saliva samples from healthy donors. The findings may facilitate the further development of salivary biomarkers for oral and systemic diseases.
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Affiliation(s)
- Yung-Chin Hsiao
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Liver Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Lichieh Julie Chu
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Liver Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Yi-Ting Chen
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Nephrology, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Lang-Ming Chi
- Clinical Proteomics Core Laboratory, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Kun-Yi Chien
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Wei-Fan Chiang
- Department of Oral and Maxillofacial Surgery, Chi-Mei Medical Center, Tainan, Taiwan.,School of Dentistry, National Yang Ming University, Taipei, Taiwan
| | - Ya-Ting Chang
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Szu-Fan Chen
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Wei-Shun Wang
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Yao-Ning Chuang
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Shih-Yu Lin
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Chih-Yen Chien
- Department of Otolaryngology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Kai-Ping Chang
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Departments of Otolaryngology, Head and Neck Surgery, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Yu-Sun Chang
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Departments of Otolaryngology, Head and Neck Surgery, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Jau-Song Yu
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Liver Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan.,Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Cell and Molecular Biology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
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Conti M, Poppi I, Cavedagna TM, Zamagni E, Leone O, Corti B, Milandri A, Bacci F, Ramazzotti E, Mancini R, Cavo M, Quarta CC, Rapezzi C. A targeted proteomics approach to amyloidosis typing. CLINICAL MASS SPECTROMETRY 2018. [DOI: 10.1016/j.clinms.2018.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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iTRAQ analysis of a mouse acute myocardial infarction model reveals that vitamin D binding protein promotes cardiomyocyte apoptosis after hypoxia. Oncotarget 2017; 9:1969-1979. [PMID: 29416745 PMCID: PMC5788613 DOI: 10.18632/oncotarget.23025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 09/03/2017] [Indexed: 12/16/2022] Open
Abstract
The proteome profile changes after acute myocardial infarction (AMI) and the roles played by important protein species remain poorly understood. Here, we constructed a mouse AMI model by ligating the left coronary artery of male C57B/6J mice to investigate the molecular changes after AMI on the protein level. Total proteins of the left ventricle were extracted and quantitatively analyzed by isobaric tags using relative and absolute quantitation (iTRAQ) technologies. The transcript and protein levels of important genes were further validated using quantitative polymerase chain reaction and western blot. An oxygen and glucose deprivation/reperfusion cell model was constructed using H9C2 cells to further validate the expression patterns and functions of important proteins after hypoxia. Seven hundred seventy-six proteins were identified as differentially abundant proteins after AMI, of which 406 were accumulated, and 370 were reduced. Gene ontology enrichment analysis showed that the most enriched molecular function category terms were binding, including calcium ion biding, GTP binding, actin binding and lipid binding. The expression levels of vitamin D binding protein (VDBP) and its related proteins were increased in both left ventricular tissue and H9C2 cells after ischemia-hypoxia. Overexpression of VDBP in H9C2 cells reduced vitamin D receptor and promoted the cell apoptosis rate after hypoxia. Our data provided new insights into proteome profile changes after AMI and indicated that VDBP could promote cardiomyocyte apoptosis after hypoxia.
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Manikandan M, Deenadayalan A, Vimala A, Gopal J, Chun S. Clinical MALDI mass spectrometry for tuberculosis diagnostics: Speculating the methodological blueprint and contemplating the obligation to improvise. Trends Analyt Chem 2017. [DOI: 10.1016/j.trac.2017.06.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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