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Tian X, Permentier HP, Bischoff R. Chemical isotope labeling for quantitative proteomics. MASS SPECTROMETRY REVIEWS 2023; 42:546-576. [PMID: 34091937 PMCID: PMC10078755 DOI: 10.1002/mas.21709] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/22/2021] [Accepted: 05/17/2021] [Indexed: 05/05/2023]
Abstract
Advancements in liquid chromatography and mass spectrometry over the last decades have led to a significant development in mass spectrometry-based proteome quantification approaches. An increasingly attractive strategy is multiplex isotope labeling, which significantly improves the accuracy, precision and throughput of quantitative proteomics in the data-dependent acquisition mode. Isotope labeling-based approaches can be classified into MS1-based and MS2-based quantification. In this review, we give an overview of approaches based on chemical isotope labeling and discuss their principles, benefits, and limitations with the goal to give insights into fundamental questions and provide a useful reference for choosing a method for quantitative proteomics. As a perspective, we discuss the current possibilities and limitations of multiplex, isotope labeling approaches for the data-independent acquisition mode, which is increasing in popularity.
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Affiliation(s)
- Xiaobo Tian
- Department of Analytical Biochemistry and Interfaculty Mass Spectrometry Center, Groningen Research Institute of PharmacyUniversity of GroningenGroningenThe Netherlands
| | - Hjalmar P. Permentier
- Department of Analytical Biochemistry and Interfaculty Mass Spectrometry Center, Groningen Research Institute of PharmacyUniversity of GroningenGroningenThe Netherlands
| | - Rainer Bischoff
- Department of Analytical Biochemistry and Interfaculty Mass Spectrometry Center, Groningen Research Institute of PharmacyUniversity of GroningenGroningenThe Netherlands
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2
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Yerlikaya A, Zeren S. Molecular Pathways, Targeted Therapies, and Proteomic Investigations of Colorectal Cancer. Curr Mol Med 2023; 23:2-12. [PMID: 34951572 DOI: 10.2174/1566524022666211224120614] [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] [Received: 07/29/2021] [Revised: 11/11/2021] [Accepted: 11/25/2021] [Indexed: 12/16/2022]
Abstract
According to the GLOBOCAN 2020 data, colorectal cancer is the third most commonly diagnosed cancer and the second leading cause of cancer-related death. The risk factors for colorectal cancer include a diet abundant with fat, refined carbohydrates, animal protein, low fiber content, alcoholism, obesity, long-term cigarette smoking, low physical activity, and aging. Colorectal carcinomas are classified as adenocarcinoma, neuroendocrine, squamous cell, adenosquamous, spindle cell, and undifferentiated carcinomas. In addition, many variants of colorectal carcinomas have been recently distinguished based on histological, immunological, and molecular characteristics. Recently developed targeted molecules in conjunction with standard chemotherapeutics or immune checkpoint inhibitors provide promising treatment protocols for colorectal cancer. However, the benefit of targeted therapies is strictly dependent on the mutational status of signaling molecules (e.g., KRAS) or mismatch repair systems. Here it is aimed to provide a comprehensive view of colorectal cancer types, molecular pathways associated, recently developed targeted therapies, as well as proteomic investigations applied to colorectal cancer for the discovery of novel biomarkers and new targets for treatment protocols.
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Affiliation(s)
- Azmi Yerlikaya
- Department of Medical Biology, Faculty of Medicine, Kutahya Health Sciences University, Kutahya, Turkey
| | - Sezgin Zeren
- Department of General Surgery, Faculty of Medicine, Kutahya Health Sciences University, Kutahya, Turkey
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Bai Y, Li L, Dong B, Ma W, Chen H, Yu Y. Phosphorylation‐mediated PI3K‐Art
signalling pathway as a therapeutic mechanism in the
hydrogen‐induced
alleviation of brain injury in septic mice. J Cell Mol Med 2022; 26:5713-5727. [DOI: 10.1111/jcmm.17568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 09/13/2022] [Accepted: 09/17/2022] [Indexed: 11/30/2022] Open
Affiliation(s)
- Yuanyuan Bai
- Department of Anesthesiology Tianjin Institute of Anesthesiology, General Hospital of Tianjin Medical University Tianjin China
- Tianjin Research Institute of Anesthesiology Tianjin China
| | - Li Li
- Department of Anesthesiology, Huashan Hospital Fudan University Shanghai China
| | - Beibei Dong
- Department of Anesthesiology Tianjin Institute of Anesthesiology, General Hospital of Tianjin Medical University Tianjin China
- Tianjin Research Institute of Anesthesiology Tianjin China
| | - Wanjie Ma
- Department of Anesthesiology Tianjin Institute of Anesthesiology, General Hospital of Tianjin Medical University Tianjin China
- Tianjin Research Institute of Anesthesiology Tianjin China
| | - Hongguang Chen
- Department of Anesthesiology Tianjin Institute of Anesthesiology, General Hospital of Tianjin Medical University Tianjin China
- Tianjin Research Institute of Anesthesiology Tianjin China
| | - Yonghao Yu
- Department of Anesthesiology Tianjin Institute of Anesthesiology, General Hospital of Tianjin Medical University Tianjin China
- Tianjin Research Institute of Anesthesiology Tianjin China
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Sharma KB, Aggarwal S, Yadav AK, Vrati S, Kalia M. Studying Autophagy Using a TMT-Based Quantitative Proteomics Approach. Methods Mol Biol 2022; 2445:183-203. [PMID: 34972993 DOI: 10.1007/978-1-0716-2071-7_12] [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: 06/14/2023]
Abstract
Maintenance of cellular homeostasis through regulated degradation of proteins and organelles is a defining feature of autophagy. This process itself is tightly regulated in a series of well-defined biochemical reactions governed largely by the highly conserved ATG protein family. Given its crucial role in regulating protein levels under both basal and stress conditions such as starvation and infection, genetic or pharmacological perturbation of autophagy results in massive changes in the cellular proteome and impacts nearly every biological process. Therefore, studying autophagy perturbations at a global scale assumes prime importance. In recent years, quantitative mass spectrometry (MS)-based proteomics has emerged as a powerful approach to explore biological processes through global proteome quantification analysis. Tandem mass tag (TMT)-based MS proteomics is one such robust quantitative technique that can examine relative protein abundances in multiple samples (parallel multiplexing). Investigating autophagy through TMT-based MS approach can give great insights into autophagy-regulated biological processes, protein-protein interaction networks, spatiotemporal protein dynamics, and identification of new autophagy substrates. This chapter provides a detailed protocol for studying the impact of a dysfunctional autophagy pathway on the cellular proteome and pathways in a healthy vs. disease (virus infection) condition using a 16-plex TMT-based quantitative proteomics approach. We also provide a pipeline on data processing and analysis using available web-based tools.
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Affiliation(s)
- Kiran Bala Sharma
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Suruchi Aggarwal
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Amit Kumar Yadav
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Sudhanshu Vrati
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, Haryana, India.
| | - Manjula Kalia
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, Haryana, India.
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Sharaireh A, Tierney AL, Unwin RD. Global Proteomic Profiling of Embryonic Stem Cells Using iTRAQ Isobaric Tags with LC-MS/MS Quantification. Methods Mol Biol 2022; 2490:157-177. [PMID: 35486245 DOI: 10.1007/978-1-0716-2281-0_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
In this methods chapter, we describe the use of isobaric tags for relative and absolute quantification (iTRAQ) for the differential expression analysis of global proteins between embryonic stem cell samples. This protocol describes how proteins are collected from cell culture, digested and prepared so that peptides are labeled with these isobaric tags. Labeled digests are pooled, fractionated offline, and quantified using liquid chromatography-mass spectrometry (LC-MS). This offline fractionation allows for a greater separation and thus increased identification/quantification of peptides. This combined method enables large-scale, deep penetration into the proteome of embryonic stem cells. During quantification, the relative intensities of label-derived reporter ions represent the relative amount of peptide in each sample. Using search algorithms that integrate the generated data for the identified and quantified peptides allows the relative quantification of proteins in the samples. The isobaric tags can be used in a 4 or 8 multiplexed manner; however, using an 8-plex experimental setup allows for the simultaneous analysis of biological and technical replicates within the same mass spectrometry run, thus minimizing experimental variation and increasing the confidence in any identified expression differences.
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Affiliation(s)
- Aseel Sharaireh
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK.
- Department of Conservative Dentistry, School of Dentistry, University of Jordan, Amman, Jordan.
| | - Anna L Tierney
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Richard D Unwin
- Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
- Stoller Biomarker Discovery Centre, Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
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Liu Y, Qiu Y, Yin Q, Li X, Bai Q, Li Y, Xiao H. iTRAQ-based quantitative proteomic reveals proteomic changes in Serratia sp. CM01 and mechanism of Cr(Ⅵ) resistance. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 228:112899. [PMID: 34823212 DOI: 10.1016/j.ecoenv.2021.112899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 09/29/2021] [Accepted: 10/11/2021] [Indexed: 06/13/2023]
Abstract
OBJECTIVE Serratia sp. CM01 is a wild strain with the resistance and reduction ability of chromium(Ⅵ). The aim of this study it to investigate the underlying mechanisms of the Cr(Ⅵ) tolerance and reduction of strain CM01, and to explore its response to environmental pollution pressure at the molecular level. METHODS The iTRAQ technique was utilized to investigate the differentially expressed protein patterns related to the Cr(Ⅵ)-resistance in wild-type strain CM01 and domesticated CM01. RT-qPCR was used to verify the expression levels of several functional genes. The cell surface hydrophobicity and autoaggregation, the intracellular glucose content, and the total superoxide dismutase (SOD) activity were determined. RESULTS In total, 2750 proteins were detected and identified in WT CM01 and domesticated CM01. Compared with WT CM01, the iTRAQ results of 646 proteins were found to be significantly differentially expressed in domesticated CM01. There were 343 up-regulated and 303 down-regulated proteins, which mainly related to carbohydrate metabolism, stress responses, amino acid metabolism and some other systems. RT-qPCR results showed that the expression level of seven genes in domesticated CM01 were consistent with the iTRAQ proteomic profiles. The cell surface hydrophobicity, self-aggregation, intracellular glucose content and total SOD activity of domesticated CM01 with Cr(Ⅵ) treatment were significantly higher than without Cr(Ⅵ) treatment. CONCLUSION Domesticated CM01 displayed a complex biological network to exhibit the tolerance of Cr(Ⅵ), which may be attributed to the following aspects: (a) CM01 reduced the consumption of glucose by inhibiting the metabolism of carbohydrates, which was an energy-saving survival mode. (b) The inositol phosphate metabolism pathway played an important role. (c) Oxidative stress proteins enhanced the adaptability. (d) CM01 enhanced biosynthesis of hydrophobic amino acids to resistance to Cr(Ⅵ). (e) Several key systems and proteins, such as UvrABC system, Lon protease, porin OmpC, also may play an important role.
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Affiliation(s)
- Yuan Liu
- Department of Health Laboratory Technology, School of Public Health and Management, Chongqing Medical University, No. 1 Yixueyuan Road, Yuzhong District, Chongqing 400016, China; Center for Disease Control and Prevention, Chongqing 400010, China
| | - Yanlun Qiu
- Center for Disease Control and Prevention, Beibei District, Chongqing 400700, China
| | - Qi Yin
- Department of Health Laboratory Technology, School of Public Health and Management, Chongqing Medical University, No. 1 Yixueyuan Road, Yuzhong District, Chongqing 400016, China
| | - Xinglong Li
- Department of Health Laboratory Technology, School of Public Health and Management, Chongqing Medical University, No. 1 Yixueyuan Road, Yuzhong District, Chongqing 400016, China
| | - Qunhua Bai
- Department of Health Laboratory Technology, School of Public Health and Management, Chongqing Medical University, No. 1 Yixueyuan Road, Yuzhong District, Chongqing 400016, China
| | - Yingli Li
- Department of Health Laboratory Technology, School of Public Health and Management, Chongqing Medical University, No. 1 Yixueyuan Road, Yuzhong District, Chongqing 400016, China
| | - Hong Xiao
- Department of Health Laboratory Technology, School of Public Health and Management, Chongqing Medical University, No. 1 Yixueyuan Road, Yuzhong District, Chongqing 400016, China.
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Chen X, Sun Y, Zhang T, Shu L, Roepstorff P, Yang F. Quantitative Proteomics Using Isobaric Labeling: A Practical Guide. GENOMICS, PROTEOMICS & BIOINFORMATICS 2021; 19:689-706. [PMID: 35007772 PMCID: PMC9170757 DOI: 10.1016/j.gpb.2021.08.012] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 05/19/2021] [Accepted: 09/27/2021] [Indexed: 01/09/2023]
Abstract
In the past decade, relative proteomic quantification using isobaric labeling technology has developed into a key tool for comparing the expression of proteins in biological samples. Although its multiplexing capacity and flexibility make this a valuable technology for addressing various biological questions, its quantitative accuracy and precision still pose significant challenges to the reliability of its quantification results. Here, we give a detailed overview of the different kinds of isobaric mass tags and the advantages and disadvantages of the isobaric labeling method. We also discuss which precautions should be taken at each step of the isobaric labeling workflow, to obtain reliable quantification results in large-scale quantitative proteomics experiments. In the last section, we discuss the broad applications of the isobaric labeling technology in biological and clinical studies, with an emphasis on thermal proteome profiling and proteogenomics.
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Affiliation(s)
- Xiulan Chen
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100149, China.
| | - Yaping Sun
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100149, China
| | - Tingting Zhang
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100149, China
| | - Lian Shu
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100149, China
| | - Peter Roepstorff
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Fuquan Yang
- Key Laboratory of Protein and Peptide Pharmaceuticals & Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100149, China.
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8
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Aggarwal S, Tolani P, Gupta S, Yadav AK. Posttranslational modifications in systems biology. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021; 127:93-126. [PMID: 34340775 DOI: 10.1016/bs.apcsb.2021.03.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The biological complexity cannot be captured by genes or proteins alone. The protein posttranslational modifications (PTMs) impart functional diversity to the proteome and regulate protein structure, activity, localization and interactions. Their dynamics drive cellular signaling, growth and development while their dysregulation causes many diseases. Mass spectrometry based quantitative profiling of PTMs and bioinformatics analysis tools allow systems level insights into their network architecture. High-resolution profiling of PTM networks will advance disease understanding and precision medicine. It can accelerate the discovery of biomarkers and drug targets. This requires better tools for unbiased, high-throughput and accurate PTM identification, site localization and automated annotation on a systems level.
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Affiliation(s)
- Suruchi Aggarwal
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India; Department of Molecular Biology and Biotechnology, Cotton University, Guwahati, Assam, India
| | - Priya Tolani
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Srishti Gupta
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India; School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Amit Kumar Yadav
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India.
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Zhang D, Dong X, Liu X, Ye L, Li S, Zhu R, Ye Y, Jiang Y. Proteomic Analysis of Brain Regions Reveals Brain Regional Differences and the Involvement of Multiple Keratins in Chronic Alcohol Neurotoxicity. Alcohol Alcohol 2020; 55:147-156. [PMID: 32047899 DOI: 10.1093/alcalc/agaa007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/22/2019] [Accepted: 01/13/2020] [Indexed: 12/29/2022] Open
Abstract
AIMS Alcohol abuse has attracted public attention and chronic alcohol exposure can result in irreversible structural changes in the brain. The molecular mechanisms underlying alcohol neurotoxicity are complex, mandating comprehensive mining of spatial protein expression profile. METHODS In this study, mice models of chronic alcohol intoxication were established after 95% alcohol vapor administration for 30 consecutive days. On Day 30, striatum (the dorsal and ventral striatum) and hippocampus, the two major brain regions responsible for learning and memorizing while being sensitive to alcohol toxicity, were collected. After that, isobaric tags for relative and absolute quantitation -based quantitative proteomic analysis were carried out for further exploration of the novel mechanisms underlying alcohol neurotoxicity. RESULTS Proteomic results showed that in the striatum, 29 proteins were significantly up-regulated and 17 proteins were significantly down-regulated. In the hippocampus, 72 proteins were significantly up-regulated, while 2 proteins were significantly down-regulated. Analysis of the overlay proteins revealed that a total of 102 proteins were consistently altered (P < 0.05) in both hippocampus and striatum regions, including multiple keratins such as Krt6a, Krt17 and Krt5. Ingenuity pathway analysis revealed that previously reported diseases/biofunctions such as dermatological diseases and developmental disorders were enriched in those proteins. Interestingly, the glucocorticoid receptor (GR) signaling was among the top enriched pathways in both brain regions, while multiple keratins from the GR signaling such as Krt1 and Krt17 exhibited significantly opposite expression patterns in the two brain nuclei. Moreover, there are several other involved pathways significantly differed between the hippocampus and striatum. CONCLUSIONS Our data revealed brain regional differences upon alcohol consumption and indicated the critical involvement of keratins from GR signaling in alcohol neurotoxicity. The differences in proteomic results between the striatum and hippocampus suggested a necessity of taking into consideration brain regional differences and intertwined signaling pathways rather than merely focusing on single nuclei or molecule during the study of drug-induced neurotoxicity in the future.
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Affiliation(s)
- Dingang Zhang
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Xiaoru Dong
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Xiaochen Liu
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Lin Ye
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Shuhao Li
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Rongzhe Zhu
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Yonghong Ye
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Yan Jiang
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
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Jiang Y, Bian Y, Lian N, Wang Y, Xie K, Qin C, Yu Y. iTRAQ-Based Quantitative Proteomic Analysis of Intestines in Murine Polymicrobial Sepsis with Hydrogen Gas Treatment. DRUG DESIGN DEVELOPMENT AND THERAPY 2020; 14:4885-4900. [PMID: 33209018 PMCID: PMC7670176 DOI: 10.2147/dddt.s271191] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/10/2020] [Indexed: 12/11/2022]
Abstract
Objective Sepsis-associated intestinal injury has a higher morbidity and mortality in patients with sepsis, but there is still no effective treatment. Our research team has proven that inhaling 2% hydrogen gas (H2) can effectively improve sepsis and related organ damage, but the specific molecular mechanism of its role is not clear. In this study, isobaric tags for relative and absolute quantitation (iTRAQ)-based quantitative proteomics analysis was used for studying the effect of H2 on intestinal injury in sepsis. Methods Male C57BL/6J mice were used to prepare a sepsis model by cecal ligation and puncture (CLP). The 7-day survival rates of mice were measured. 4-kd fluorescein isothiocyanate-conjugated Dextran (FITC-dextran) blood concentration measurement, combined with hematoxylin-eosinstain (HE) staining and Western blotting, was used to study the effect of H2 on sepsis-related intestinal damage. iTRAQ-based liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis was used for studying the proteomics associated with H2 for the treatment of intestinal injury. Results H2 can significantly improve the 7-day survival rates of sepsis mice. The load of blood and peritoneal lavage bacteria was increased, and H2 treatment can significantly reduce it. CLP mice had significant intestinal damage, and inhalation of 2% hydrogen could significantly reduce this damage. All 4194 proteins were quantified, of which 199 differentially expressed proteins were associated with the positive effect of H2 on sepsis. Functional enrichment analysis indicated that H2 may reduce intestinal injury in septic mice through the effects of thyroid hormone synthesis and nitrogen metabolism signaling pathway. Western blot showed that H2 was reduced by down-regulating the expressions of deleted in malignant brain tumors 1 protein (DMBT1), insulin receptor substrate 2 (IRS2), N-myc downregulated gene 1 (NDRG1) and serum amyloid A-1 protein (SAA1) intestinal damage in sepsis mice. Conclusion A total of 199 differential proteins were related with H2 in the intestinal protection of sepsis. H2-related differential proteins were notably enriched in the following signaling pathways, including thyroid hormone synthesis signaling pathway, nitrogen metabolism signaling pathways, digestion and absorption signaling pathways (vitamins, proteins and fats). H2 reduced intestinal injury in septic mice by down-regulating the expressions of SAA1, NDRG1, DMBT1 and IRS2.
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Affiliation(s)
- Yi Jiang
- Department of Anesthesiology, Tianjin Medical University General Hospital, Tianjin, People's Republic of China.,Tianjin Institute of Anesthesiology, Tianjin, People's Republic of China
| | - Yingxue Bian
- Department of Anesthesiology, Tianjin Union Medical Center, Tianjin, People's Republic of China
| | - Naqi Lian
- Department of Anesthesiology, Tianjin Medical University General Hospital, Tianjin, People's Republic of China.,Tianjin Institute of Anesthesiology, Tianjin, People's Republic of China
| | - Yaoqi Wang
- Department of Anesthesiology, Tianjin Medical University General Hospital, Tianjin, People's Republic of China.,Tianjin Institute of Anesthesiology, Tianjin, People's Republic of China
| | - Keliang Xie
- Department of Anesthesiology, Tianjin Medical University General Hospital, Tianjin, People's Republic of China.,Tianjin Institute of Anesthesiology, Tianjin, People's Republic of China
| | - Chao Qin
- Department of Anesthesiology, Tianjin Medical University General Hospital, Tianjin, People's Republic of China.,Tianjin Institute of Anesthesiology, Tianjin, People's Republic of China
| | - Yonghao Yu
- Department of Anesthesiology, Tianjin Medical University General Hospital, Tianjin, People's Republic of China.,Tianjin Institute of Anesthesiology, Tianjin, People's Republic of China
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11
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Xie K, Lian N, Kan Y, Yang M, Pan J, Yu Y, Yu Y. iTRAQ-based quantitative proteomic analysis of the therapeutic effects of 2% hydrogen gas inhalation on brain injury in septic mice. Brain Res 2020; 1746:147003. [PMID: 32603701 DOI: 10.1016/j.brainres.2020.147003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 05/24/2020] [Accepted: 06/23/2020] [Indexed: 12/22/2022]
Abstract
Sepsis encephalopathy (SAE) has a high incidence and mortality rate in patients with sepsis; however, there is currently no effective treatment. Our previous studies have reported that 2% hydrogen (H2) gas inhalation had a protective effect on sepsis and SAE; however, the specific mechanism have not been fully elucidated. In the current study, male Institute of Cancer Research mice were either used to create the cecal ligation and puncture (CLP) model or for sham surgery, followed by 2% H2 gas inhalation for 60 min beginning at 1 and 6 h following sham or CLP surgeries. The isobaric tags for relative and absolute quantitation (iTRAQ)-based quantitative proteomics combined with liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis, hematoxylin and eosin (H&E) staining, Nissl staining, and western blot analysis were used to investigate the effects of H2 on brain injury in mice with sepsis. The results of the H&E, and Nissl staining indicated that the CLP mice had a significant brain injury, which was characterized by aggravated pathological damage and was alleviated by 2% H2 inhalation. Quantitative proteomics based on iTRAQ combined with LC-MS/MS analysis quantified a total of 5317 proteins, of which 39 were connected with the protective mechanism of H2. In addition, H2 could regulate the immune and the coagulation systems. Furthermore, western blot analysis revealed that H2 decreased SAE in septic mice by downregulating the protein expression levels of SMAD4, DPYS, PTGDS and upregulating the expression level of CUL4A. These results provide insights into the mechanism of the positive effect of H2 on SAE and contribute to the clinical application of H2 in patients with sepsis.
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Affiliation(s)
- Keliang Xie
- Department of Anesthesia, Tianjin Medical University General Hospital, Tianjin, China; Tianjin Institute of Anesthesiology, Tianjin, China
| | - Naqi Lian
- Department of Anesthesia, Tianjin Medical University General Hospital, Tianjin, China; Tianjin Institute of Anesthesiology, Tianjin, China
| | - Yufei Kan
- Department of Anesthesiology of Grade 2016, Tianjin Medical University, Tianjin, China
| | - Man Yang
- Department of Anesthesia, Tianjin Medical University General Hospital, Tianjin, China; Tianjin Institute of Anesthesiology, Tianjin, China
| | - Jiacheng Pan
- Department of Anesthesia, Tianjin Medical University General Hospital, Tianjin, China; Tianjin Institute of Anesthesiology, Tianjin, China
| | - Yang Yu
- Department of Anesthesia, Tianjin Medical University General Hospital, Tianjin, China; Tianjin Institute of Anesthesiology, Tianjin, China.
| | - Yonghao Yu
- Department of Anesthesia, Tianjin Medical University General Hospital, Tianjin, China.
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Aggarwal S, Kumar A, Jamwal S, Midha MK, Talukdar NC, Yadav AK. HyperQuant-A Computational Pipeline for Higher Order Multiplexed Quantitative Proteomics. ACS OMEGA 2020; 5:10857-10867. [PMID: 32455206 PMCID: PMC7240821 DOI: 10.1021/acsomega.0c00515] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 04/09/2020] [Indexed: 06/11/2023]
Abstract
Quantitative proteomics has evolved considerably over the last decade with the advent of higher order multiplexing (HOM) techniques. With the development of methods such as-multitagging, cPILOT, hyperplexing, BONPlex, and MITNCAT, the HOM technique is rapidly taking the center stage in multiplexed quantitative proteomics. These studies combined MS1 and MS2 labels in a single experiment enabling higher sample throughput. While HOM is highly promising, the computational analysis is still a big challenge, as the available tools cannot harness its power completely. We have developed a new quantitative pipeline, HyperQuant to aid in accurately quantitating complex HOM data. The pipeline uses identification results from either MaxQuant or any other search engine and quantitation results from QuantWizIQ. The Mapper and Combiner modules of HyperQuant allow facile integration of the labeled data, along with peptide spectrum match (PSM) intensity/ratio integration for proteins, respectively, for each PSM label combination. This also includes appropriate combination of replicates/fractions before summarizing the protein intensity/ratio, leading to robust quantitation. To the best of our knowledge, this is the first tool for the quantitation of HOM data with flexibility for any combination of MS1 and MS2 labels. We demonstrate its utility in analyzing two 18-plex data sets from the hyperplexing and the BONplex studies. The tool is open source and freely available for noncommercial use. HyperQuant is a highly valuable tool that will help in advancing the field of multiplexed quantitative proteomics.
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Affiliation(s)
- Suruchi Aggarwal
- Translational
Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad−Gurgaon
Expressway, Faridabad 121001, Haryana, India
- Division
of Life Sciences, Institute of Advanced
Study in Science and Technology, Vigyan Path, Paschim Boragaon, Garchuk, Guwahati, Assam 781035, India
- Department
of Molecular Biology and Biotechnology, Cotton University, Panbazar, Guwahati, Assam 781001, India
| | - Ajay Kumar
- Translational
Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad−Gurgaon
Expressway, Faridabad 121001, Haryana, India
| | - Shilpa Jamwal
- Translational
Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad−Gurgaon
Expressway, Faridabad 121001, Haryana, India
| | - Mukul Kumar Midha
- Translational
Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad−Gurgaon
Expressway, Faridabad 121001, Haryana, India
| | - Narayan Chandra Talukdar
- Division
of Life Sciences, Institute of Advanced
Study in Science and Technology, Vigyan Path, Paschim Boragaon, Garchuk, Guwahati, Assam 781035, India
- Department
of Molecular Biology and Biotechnology, Cotton University, Panbazar, Guwahati, Assam 781001, India
| | - Amit Kumar Yadav
- Translational
Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad−Gurgaon
Expressway, Faridabad 121001, Haryana, India
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13
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Ning H, Cui Y, Song X, Chen L, Yin Z, Hua L, Ren F, Suo Y, Wang X, Zhang H, Hu D, Ge Y. iTRAQ-based proteomic analysis reveals key proteins affecting cardiac function in broilers that died of sudden death syndrome. Poult Sci 2020; 98:6472-6482. [PMID: 31509194 PMCID: PMC8913949 DOI: 10.3382/ps/pez532] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 08/31/2019] [Indexed: 12/26/2022] Open
Abstract
Sudden death syndrome (SDS), which is a cardiac-related condition commonly observed in chickens selected for rapid growth, causes significant economic losses to the global poultry industry. Its pathogenesis in broilers is poorly understood, and little is known about the proteome of the heart tissue of SDS broilers. A quantitative proteomic approach using isobaric tags for relative and absolute quantification labeling of peptides was used to characterize the protein expression profiles in the left ventricle of SDS broilers. These proteins were further analyzed by bioinformatics, and two proteins were validated by western blot analysis. We identified 186 differentially expressed proteins (DEPs), of which 72 were upregulated, and 114 were downregulated in the SDS group. Functional annotation suggested that 7 DEPs were related to cardiac muscle contraction, and another 7 DEPs were related to cardiac energy metabolism. Protein interaction network predictions indicated that differences in cardiac muscle contraction between SDS and healthy groups were regulated by troponin T, tropomyosin alpha-1 chain, fast myosin heavy chain HCIII, myosin-1B, coronin, and myoglobin, whereas differences in cardiac energy metabolism and biosynthesis of amino acids were regulated by gamma-enolase, phosphoglycerate mutase, NADH-ubiquinone oxidoreductase chain 2, serine/threonine-protein kinase, myoglobin, and alpha-amylase. Our expression profiles provide useful information and new insights into key proteins to elucidate SDS for further studies.
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Affiliation(s)
- Hongmei Ning
- College of Animal Science and Technology, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Yunli Cui
- College of Animal Science and Technology, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Xiaochao Song
- College of Animal Science and Technology, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Lingli Chen
- College of Animal Science and Technology, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Zhihong Yin
- College of Animal Science and Technology, Henan Institute of Science and Technology, Xinxiang 453003, China.,Postdoctoral Research and Development Base, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Liushuai Hua
- College of Animal Science and Technology, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Fei Ren
- College of Animal Science and Technology, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Yu Suo
- College of Animal Science and Technology, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Xinrui Wang
- College of Animal Science and Technology, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Hongli Zhang
- College of Animal Science and Technology, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Dongfang Hu
- College of Animal Science and Technology, Henan Institute of Science and Technology, Xinxiang 453003, China.,Postdoctoral Research and Development Base, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Yaming Ge
- College of Animal Science and Technology, Henan Institute of Science and Technology, Xinxiang 453003, China
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14
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Zhang Y, Yang J, Chen Y, Lv J, Zhang J, Zhang Y, Zhao X, Fang H, Liu C, Zhang Q, Cui X, Wang X, Gao F. iTRAQ-Based Proteomics Analysis of Plasma of Myasthenia Gravis Patients Treated with Jia Wei Bu Zhong Yi Qi Decoction. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2019; 2019:9147072. [PMID: 31915455 PMCID: PMC6930785 DOI: 10.1155/2019/9147072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 09/04/2019] [Accepted: 10/01/2019] [Indexed: 11/18/2022]
Abstract
Myasthenia gravis (MG) is an autoimmune disease. A proportion of MG patients did not get satisfactory results after treatment with pyridostigmine and prednisone. Jia Wei Bu Zhong Yi Qi (Jia Wei BZYQ) decoction, a water extract from multiple herbs, has been demonstrated to be effective in the treatment of multiple "Qi deficiency type" diseases including MG in China. In this text, we investigated protein alterations in the plasma from healthy volunteers (C), MG patients without any treatment (T1), MG patients with routine western medical treatment (T2), and MG patients with combined treatments of Jia Wei BZYQ decoction and routine western medicines (T3) and identified some potential proteins involved in the pathogenesis and treatment of MG. iTRAQ (isobaric tags for relative and absolute quantitation) and 2D-LC-MS/MS (two-dimensional liquid chromatography-tandem mass spectrometry technologies) were employed to screen differentially expressed proteins. The identification, quantification, functional annotation, and interaction of proteins were analyzed by matching software and databases. In our project, 618 proteins were identified, among which 447 proteins had quantitative data. The number of differentially expressed proteins was 110, 117, 143, 115, 86, and 158 in T1 vs. C, T2 vs. C, T2 vs. T1, T3 vs. C, T3 vs. T1, and T3 vs. T2 groups, respectively. Functional annotation results showed that many differentially expressed proteins were closely associated with immune responses. For instance, some key proteins such as C-reactive protein, apolipoprotein C-III, apolipoprotein A-II, alpha-actinin-1, and thrombospondin-1 have been found to be abnormally expressed in T3 group compared to T1 group or T2 group. Interaction network analyses also provided some potential biomarkers or targets for MG management.
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Affiliation(s)
- Yunke Zhang
- School of Rehabilitation Medicine, Henan University of Chinese Medicine, No. 156 Jinshui East Road, Zhengzhou City, Henan Province 450008, China
| | - Junhong Yang
- Department of Neurology, The First Affiliated Hospital of Henan University of Chinese Medicine, No. 19, Renmin Road, Zhengzhou City, Henan Province 450000, China
| | - Yingzhe Chen
- Department of Neurology, Pingdingshan Traditional Chinese Medicine Hospital, Henan No. 4 Courtyard, North Section of Zhongxing Road, Pingdingshan City 467000, China
| | - Jie Lv
- Department of Neuroimmunology Research, Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Henan, No. 40, University Road, Zhengzhou City, Henan Province 450052, China
| | - Jing Zhang
- Department of Neuroimmunology Research, Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Henan, No. 40, University Road, Zhengzhou City, Henan Province 450052, China
| | - Yingna Zhang
- Department of Neuroimmunology Research, Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Henan, No. 40, University Road, Zhengzhou City, Henan Province 450052, China
| | - Xue Zhao
- Department of Neuroimmunology Research, Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Henan, No. 40, University Road, Zhengzhou City, Henan Province 450052, China
| | - Hua Fang
- Department of Neuroimmunology Research, Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Henan, No. 40, University Road, Zhengzhou City, Henan Province 450052, China
| | - Chongchong Liu
- Beijing University of Chinese Medicine, No. 11, North Third Ring Road, Chaoyang District, Beijing 100029, China
| | - Qingyong Zhang
- Myasthenia Gravis Comprehensive Diagnosis and Treatment Center, Henan Provincial People's Hospital, No. 7, Weiwu Road, Zhengzhou City, Henan Province 450003, China
| | - Xinzheng Cui
- Myasthenia Gravis Comprehensive Diagnosis and Treatment Center, Henan Provincial People's Hospital, No. 7, Weiwu Road, Zhengzhou City, Henan Province 450003, China
| | - Xiaohan Wang
- Henan University of Chinese Medicine, No. 156 Jinshui East Road, Zhengzhou City, Henan Province 450008, China
| | - Feng Gao
- Department of Neuroimmunology Research, Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Henan, No. 40, University Road, Zhengzhou City, Henan Province 450052, China
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15
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Adipose-Derived Mesenchymal Stem Cells Enhance Ovarian Cancer Growth and Metastasis by Increasing Thymosin Beta 4X-Linked Expression. Stem Cells Int 2019; 2019:9037197. [PMID: 31781249 PMCID: PMC6855023 DOI: 10.1155/2019/9037197] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Revised: 04/17/2019] [Accepted: 08/06/2019] [Indexed: 12/11/2022] Open
Abstract
As shown in our previous studies, growth and metastasis of ovarian cancer can be regulated by adipose-derived mesenchymal stem cells (ADSCs). However, the underlying mechanism has not yet been revealed. In this study, a proteomics analysis was performed to compare protein expression treated with and without ADSCs in ovarian cancer cells. Protein levels were altered in ovarian cancer cells due to the treatment of ADSCs. Thymosin beta 4 X-linked (TMSB4X) levels changed dramatically, and this protein was identified as one of the most important candidate molecules contributing to the tumour-promoting effects of ADSCs. Compared with the cells that are cultured in the normal growth medium, the TMSB4X levels cultured in ADSC-conditioned medium increased significantly in ovarian cancer cells. Furthermore, the growth and invasion of cancer cells were decreased, even in the ADSC-conditioned medium treatment group (P < 0.05), by the inhibition of TMSB4X. As shown in the bioluminescence images captured in vivo, increased ovarian cancer's growth and metastasis, along with elevated TMSB4X expression, were observed in the group of ADSC-conditioned medium, and the tumour-promoting effect of ADSCs was attenuated by the inhibition of TMSB4X. Based on our findings, increased TMSB4X expression may play a role in accelerating the ADSC-mediated proliferation, invasion, and migration of ovarian cancers.
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16
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Aggarwal S, Talukdar NC, Yadav AK. Advances in Higher Order Multiplexing Techniques in Proteomics. J Proteome Res 2019; 18:2360-2369. [DOI: 10.1021/acs.jproteome.9b00228] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Suruchi Aggarwal
- Drug Discovery Research Centre, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Third Milestone, Faridabad − Gurgaon Expressway, Faridabad, Haryana 121001, India
- Division of Life Sciences, Institute of Advanced Study in Science and Technology, Vigyan Path, Paschim Boragaon, Garchuk, Guwahati, Assam 781035, India
- Department of Molecular Biology and Biotechnology, Cotton University, Panbazar, Guwahati, Assam 781001, India
| | - Narayan C. Talukdar
- Division of Life Sciences, Institute of Advanced Study in Science and Technology, Vigyan Path, Paschim Boragaon, Garchuk, Guwahati, Assam 781035, India
- Department of Molecular Biology and Biotechnology, Cotton University, Panbazar, Guwahati, Assam 781001, India
| | - Amit K. Yadav
- Drug Discovery Research Centre, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Third Milestone, Faridabad − Gurgaon Expressway, Faridabad, Haryana 121001, India
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17
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Cheruiyot C, Pataki Z, Ramratnam B, Li M. Proteomic Analysis of Exosomes and Its Application in HIV-1 Infection. Proteomics Clin Appl 2018; 12:e1700142. [PMID: 29687643 DOI: 10.1002/prca.201700142] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 03/23/2018] [Indexed: 12/21/2022]
Abstract
Exosomes are 30-100 nm extracellular vesicles secreted from late endosomes by various types of cells. Numerous studies have suggested that exosomes play significant roles in human immunodeficiency virus 1 (HIV-1) biogenesis. Proteomics coupled with exosome fractionation has been successfully used to identify various exosomal proteins and helped to uncover the interactions between exosomes and HIV-1. To inform the current progress in the intersection of exosome, proteomics, and HIV-1, this review is focused on: i) analyzing different exosome isolation, purification methods, and their implications in HIV-1 studies; ii) evaluating the roles of various proteomic techniques in defining exosomal contents; iii) discussing the research and clinical applications of proteomics and exosome in HIV-1 biology.
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Affiliation(s)
- Collins Cheruiyot
- Department of Medicine, Division of Infectious Diseases, Laboratory of Retrovirology, Alpert Medical School of Brown University, Providence, RI, 02903, USA
| | - Zemplen Pataki
- Department of Medicine, Division of Infectious Diseases, Laboratory of Retrovirology, Alpert Medical School of Brown University, Providence, RI, 02903, USA
| | - Bharat Ramratnam
- Department of Medicine, Division of Infectious Diseases, Laboratory of Retrovirology, Alpert Medical School of Brown University, Providence, RI, 02903, USA.,Centers of Biomedical Research Excellence, Center for Cancer Research, Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, RI, 02903, USA.,Clinical Research Center of Lifespan, Providence, RI, 02903, USA
| | - Ming Li
- Department of Medicine, Division of Infectious Diseases, Laboratory of Retrovirology, Alpert Medical School of Brown University, Providence, RI, 02903, USA
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18
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Identification of Potential Biomarkers for Rhegmatogenous Retinal Detachment Associated with Choroidal Detachment by Vitreous iTRAQ-Based Proteomic Profiling. Int J Mol Sci 2016; 17:ijms17122052. [PMID: 27941623 PMCID: PMC5187852 DOI: 10.3390/ijms17122052] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 11/24/2016] [Accepted: 11/30/2016] [Indexed: 12/16/2022] Open
Abstract
Rhegmatogenous retinal detachment associated with choroidal detachment (RRDCD) is a complicated and serious type of rhegmatogenous retinal detachment (RRD). In this study, we identified differentially expressed proteins in the vitreous humors of RRDCD and RRD using isobaric tags for relative and absolute quantitation (iTRAQ) combined with nano-liquid chromatography-electrospray ion trap-mass spectrometry-mass spectrometry (nano-LC-ESI-MS/MS) and bioinformatic analysis. Our result shows that 103 differentially expressed proteins, including 54 up-regulated and 49 down-regulated proteins were identified in RRDCD. Gene ontology (GO) analysis suggested that most of the differentially expressed proteins were extracellular.The Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis suggested that proteins related to complement and coagulation cascades were significantly enriched. iTRAQ-based proteomic profiling reveals that complement and coagulation cascades and inflammation may play important roles in the pathogenesis of RRDCD. This study may provide novel insights into the pathogenesis of RRDCD and offer potential opportunities for the diagnosis and treatment of RRDCD.
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19
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Kumar A, Jamwal S, Midha MK, Hamza B, Aggarwal S, Yadav AK, Rao KVS. Dataset generated using hyperplexing and click chemistry to monitor temporal dynamics of newly synthesized macrophage secretome post infection by mycobacterial strains. Data Brief 2016; 9:349-54. [PMID: 27672675 PMCID: PMC5030312 DOI: 10.1016/j.dib.2016.08.055] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 08/24/2016] [Accepted: 08/29/2016] [Indexed: 12/02/2022] Open
Abstract
Here we provide data for SILAC and iTRAQ based hyperplexing combined with BONCAT based click chemistry for selective enrichment of newly synthesized proteins secreted by THP1 macrophages at various time points after infection with four different strains of Mycobacterium tuberculosis. The macrophages were infected with H37Ra, H37Rv, BND433 and JAL2287 strains of M. tuberculosis. Newly-synthesized secreted host proteins were observed, starting from six hours post-infection till 26 h, at 4 h intervals. We have combined BONCAT with hyperplexing (18-plex), which blends SILAC and iTRAQ, for the first time. Two sets of triplex SILAC were used to encode the strains of M. tuberculosis - H37Ra & H37Rv in one and BND433 & JAL2287 in another with a control in each. BONCAT was used to enrich the secretome for newly synthesized proteins while 6-plex iTRAQ labeling was employed to quantify the temporal changes in the captured proteome. Each set of 18-plex was run in 4 MS replicates with two linear and two non-linear separation modes. This new variant of hyperplexing method, combining triplex SILAC with 6-plex iTRAQ, achieves 18-plex quantitation in a single MS run. Hyperplexing enables large scale spatio-temporal systems biology studies where large number of samples can be processed simultaneously and in quantitative manner. Data are available via ProteomeXchange with identifier ProteomeXchange: PXD004281.
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Affiliation(s)
- Ajay Kumar
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Shilpa Jamwal
- Drug Discovery Research Center, Translational Health Science and Technology Institute (THSTI), NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad 121001, Haryana, India
| | - Mukul Kumar Midha
- Drug Discovery Research Center, Translational Health Science and Technology Institute (THSTI), NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad 121001, Haryana, India
| | - Baseerat Hamza
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Suruchi Aggarwal
- Drug Discovery Research Center, Translational Health Science and Technology Institute (THSTI), NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad 121001, Haryana, India
| | - Amit Kumar Yadav
- Drug Discovery Research Center, Translational Health Science and Technology Institute (THSTI), NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad 121001, Haryana, India
| | - Kanury V S Rao
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India; Drug Discovery Research Center, Translational Health Science and Technology Institute (THSTI), NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad 121001, Haryana, India
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