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Nissa MU, Pinto N, Varshnay A, Goswami M, Srivastava S. Ecological Monitoring and Omics: A Comprehensive Comparison of Workflows for Mass Spectrometry-Based Quantitative Proteomics of Fish ( Labeo rohita) Liver Tissue. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2022; 26:489-503. [PMID: 36036978 DOI: 10.1089/omi.2022.0086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Introduction: The liver is highly sensitive to the environmental factors. Liver tissue, particularly from fish, is often used as a biological target in ecological monitoring, disease research, and stress response studies. Labeo rohita (rohu) is a fish with a significant role in the global aquaculture economy. Methods: Bottom-up proteomics relies on efficient sample preparation for performing mass spectrometric analysis of the liver tissue. Optimization of protein solubilization and digestion strategies is the key step to obtain reliable data for a successful proteomics experiment. Because the goal of extraction is to acquire the optimum protein quality and yield, the first step should be to choose an appropriate extraction method based on the type of sample. Solubilization buffers containing sodium dodecyl sulfate (SDS) or urea, and digestion methods such as filter-aided sample preparation (FASP), suspension trap (S-Trap) and in-solution are often used in proteomics but are in need of comparative evaluation with an eye to protocol optimization. Experiment: We applied two different solubilization buffers (one containing SDS, and other containing urea) and three digestion methods (FASP, S-Trap, and in-solution) to the proteomic analysis of the fish (L. rohita) liver tissue. Label-free quantification analysis was performed to analyze the similarities and differences in the results with each method. Gene ontology-based functional analysis was performed for the identified proteome across the experimental conditions to overview their protein classes, molecular functions, and biological processes. Results: SDS lysis followed by S-Trap digestion outperformed the other combinations of lysis and digestion in terms of higher protein coverage, consistency in the results and repeatability. Filter-based methods provided comparatively better results than in-solution digestion. Discussion: This protocol presents new insights on ways to optimize discovery and targeted proteomic analyses of liver tissue using the fish L. rohita as a case study. Other tissues can also be evaluated in the future drawing from the results in this study. This would help the scientific community with hypothesis-driven studies on topics ranging from basic biology to applied aquaculture research and ecological monitoring. This is particularly relevant in the current era of ecological crises and environmental pollution, where advances and optimization in research protocols can contribute to in-depth studies of ecosystems and planetary health.
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Affiliation(s)
- Mehar Un Nissa
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
| | - Nevil Pinto
- Central Institute of Fisheries Education, Indian Council of Agricultural Research, Mumbai, Maharashtra, India
| | | | - Mukunda Goswami
- Central Institute of Fisheries Education, Indian Council of Agricultural Research, Mumbai, Maharashtra, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
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Lizano-Fallas V, Carrasco Del Amor A, Cristobal S. Systematic analysis of chemical-protein interactions from zebrafish embryo by proteome-wide thermal shift assay, bridging the gap between molecular interactions and toxicity pathways. J Proteomics 2021; 249:104382. [PMID: 34555547 DOI: 10.1016/j.jprot.2021.104382] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 09/15/2021] [Indexed: 02/06/2023]
Abstract
The molecular interaction between chemicals and proteins often promotes alteration of cellular function. One of the challenges of the toxicology is to predict the impact of exposure to chemicals. Assessing the impact of exposure implies to understand their mechanism of actions starting from identification of specific protein targets of the interaction. Current methods can mainly predict effects of characterized chemicals with knowledge of its targets, and mechanism of actions. Here, we show that proteome-wide thermal shift methods can identify chemical-protein interactions and the protein targets from bioactive chemicals. We analyzed the identified targets from a soluble proteome extracted from zebrafish embryo, that is a model system for toxicology. To evaluate the utility to predict mechanism of actions, we discussed the applicability in four cases: single chemicals, chemical mixtures, novel chemicals, and novel drugs. Our results showed that this methodology could identify the protein targets, discriminate between protein increasing and decreasing in solubility, and offering additional data to complement the map of intertwined mechanism of actions. We anticipate that the proteome integral solubility alteration (PISA) assay, as it is defined here for the unbiased identification of protein targets of chemicals could bridge the gap between molecular interactions and toxicity pathways. SIGNIFICANCE: One of the challenges of the environmental toxicology is to predict the impact of exposure to chemicals on environment and human health. Our phenotype should be explained by our genotype and the environmental exposure. Genomic methodologies can offer a deep analysis of human genome that alone cannot explain our risks of disease. We are starting to understand the key role of exposure to chemicals on our health and risks of disease. Here, we present a proteomic-based method for the identification of soluble proteins interacting with chemicals in zebrafish embryo and discuss the opportunities to complement the map of toxicity pathway perturbations. We anticipate that this PISA assay could bridge the gap between molecular interactions and toxicity pathways.
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Affiliation(s)
- Veronica Lizano-Fallas
- Department of Biomedical and Clinical Sciences, Cell Biology, Medical Faculty, Linköping University, Linköping 581 85, Sweden
| | - Ana Carrasco Del Amor
- Department of Biomedical and Clinical Sciences, Cell Biology, Medical Faculty, Linköping University, Linköping 581 85, Sweden
| | - Susana Cristobal
- Department of Biomedical and Clinical Sciences, Cell Biology, Medical Faculty, Linköping University, Linköping 581 85, Sweden.; Ikerbasque, Basque Foundation for Science, Department of Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), Barrio Sarriena, s/n, Leioa 48940, Spain..
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Pan L, Yuan Z, Farouk MH, Qin G, Bao N. Isolation and analysation of soybean agglutinin-specific binding proteins for erythrocyte membrane in different animal species. ITALIAN JOURNAL OF ANIMAL SCIENCE 2021. [DOI: 10.1080/1828051x.2020.1869600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Li Pan
- Key Laboratory of Animal Production, Product Quality and Security, Ministry of Education, Key Laboratory of Animal Nutrition and Feed Science, College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Zhijie Yuan
- Key Laboratory of Animal Production, Product Quality and Security, Ministry of Education, Key Laboratory of Animal Nutrition and Feed Science, College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Mohammed Hamdy Farouk
- Animal Production Department, Faculty of Agriculture, Al-Azhar University, Cairo, Egypt
| | - Guixin Qin
- Key Laboratory of Animal Production, Product Quality and Security, Ministry of Education, Key Laboratory of Animal Nutrition and Feed Science, College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Nan Bao
- Key Laboratory of Animal Production, Product Quality and Security, Ministry of Education, Key Laboratory of Animal Nutrition and Feed Science, College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
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Hou HT, Wang J, Zhang X, Wang ZQ, Chen TN, Zhang JL, Yang Q, He GW. Endothelial nitric oxide synthase enhancer AVE3085 reverses endothelial dysfunction induced by homocysteine in human internal mammary arteries. Nitric Oxide 2018; 81:21-27. [PMID: 30300735 DOI: 10.1016/j.niox.2018.10.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 09/07/2018] [Accepted: 10/04/2018] [Indexed: 12/23/2022]
Abstract
Homocysteine (Hcy) is an independent risk factor for endothelial dysfunction in cardiovascular diseases. We hypothesized that the eNOS transcription enhancer AVE3085 may protect the endothelial function damaged by Hcy in the human internal mammary artery (IMA). Cumulative concentration-relaxation curves to acetylcholine (-10 to -4.5 log mol/L) or sodium nitroprusside were established in IMA from patients undergoing coronary artery surgery precontracted by U46619 (-8 log mol/L) in the absence/presence of Hcy (100 μmol/L) with/without AVE3085 (30 μmol/L) in vitro in a myograph. RT-qPCR and ELISA were used to quantify the mRNA and protein levels of eNOS. Colorimetric assay method was used to detect the production of nitric oxide (NO). Maximal relaxation was significantly attenuated by Hcy in human IMA. Co-incubation with AVE3085 protected endothelium from the impairment by Hcy and increased the production of NO. Exposure to Hcy for 24 h downregulated eNOS protein expression (P < 0.05) whereas it upregulated the expression of eNOS at mRNA levels (P < 0.05). The presence of AVE3085 in addition to Hcy significantly increased the eNOS protein (P < 0.05) and slightly decreased the mRNA level. The study for the first time revealed that in the human blood vessels (IMA) the clinically-relevant high concentration of Hcy directly causes endothelial dysfunction by downregulating eNOS protein that may be reversed by AVE3085. These findings not only provide new direction for protecting endothelium during coronary artery bypass grafting and improving long-term patency of the grafts, but also provide evidence to the use of eNOS enhancer in the patients with endothelial dysfunction in various pathological conditions.
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Affiliation(s)
- Hai-Tao Hou
- Department of Cardiovascular Surgery & Center for Basic Medical Research, TEDA International Cardiovascular Hospital, Chinese Academy of Medical Sciences, Tianjin, China; The Affiliated Hospital of Hangzhou Normal University& Zhejiang University, Hangzhou, China
| | - Jun Wang
- Department of Cardiovascular Surgery & Center for Basic Medical Research, TEDA International Cardiovascular Hospital, Chinese Academy of Medical Sciences, Tianjin, China
| | - Xi Zhang
- Department of Cardiovascular Surgery & Center for Basic Medical Research, TEDA International Cardiovascular Hospital, Chinese Academy of Medical Sciences, Tianjin, China
| | - Zheng-Qing Wang
- Department of Cardiovascular Surgery & Center for Basic Medical Research, TEDA International Cardiovascular Hospital, Chinese Academy of Medical Sciences, Tianjin, China
| | - Tie-Nan Chen
- Department of Cardiovascular Surgery & Center for Basic Medical Research, TEDA International Cardiovascular Hospital, Chinese Academy of Medical Sciences, Tianjin, China
| | - Jian-Liang Zhang
- Department of Cardiovascular Surgery & Center for Basic Medical Research, TEDA International Cardiovascular Hospital, Chinese Academy of Medical Sciences, Tianjin, China
| | - Qin Yang
- Department of Cardiovascular Surgery & Center for Basic Medical Research, TEDA International Cardiovascular Hospital, Chinese Academy of Medical Sciences, Tianjin, China
| | - Guo-Wei He
- Department of Cardiovascular Surgery & Center for Basic Medical Research, TEDA International Cardiovascular Hospital, Chinese Academy of Medical Sciences, Tianjin, China; The Affiliated Hospital of Hangzhou Normal University& Zhejiang University, Hangzhou, China; Department of Surgery, Oregon Health and Science University, Portland, OR, USA.
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Drug Target Identification Using an iTRAQ-Based Quantitative Chemical Proteomics Approach—Based on a Target Profiling Study of Andrographolide. Methods Enzymol 2017; 586:291-309. [DOI: 10.1016/bs.mie.2016.09.049] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Target identification of natural and traditional medicines with quantitative chemical proteomics approaches. Pharmacol Ther 2016; 162:10-22. [DOI: 10.1016/j.pharmthera.2016.01.010] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Hou HT, Wang J, Wang ZQ, Liu XC, Marinko M, Novakovic A, Yang Q, He GW. Effect of Benidipine in Human Internal Mammary Artery and Clinical Implications. Ann Thorac Surg 2016; 101:1789-95. [DOI: 10.1016/j.athoracsur.2015.10.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 09/08/2015] [Accepted: 10/12/2015] [Indexed: 01/18/2023]
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Wang J, Zhang J, Zhang CJ, Wong YK, Lim TK, Hua ZC, Liu B, Tannenbaum SR, Shen HM, Lin Q. In situ Proteomic Profiling of Curcumin Targets in HCT116 Colon Cancer Cell Line. Sci Rep 2016; 6:22146. [PMID: 26915414 PMCID: PMC4768257 DOI: 10.1038/srep22146] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 02/08/2016] [Indexed: 01/02/2023] Open
Abstract
To date, the exact targets and mechanism of action of curcumin, a natural product with anti-inflammatory and anti-cancer properties, remain elusive. Here we synthesized a cell permeable curcumin probe (Cur-P) with an alkyne moiety, which can be tagged with biotin for affinity enrichment, or with a fluorescent dye for visualization of the direct-binding protein targets of curcumin in situ. iTRAQTM quantitative proteomics approach was applied to distinguish the specific binding targets from the non-specific ones. In total, 197 proteins were confidently identified as curcumin binding targets from HCT116 colon cancer cell line. Gene Ontology analysis showed that the targets are broadly distributed and enriched in the nucleus, mitochondria and plasma membrane, and they are involved in various biological functions including metabolic process, regulation, response to stimulus and cellular process. Ingenuity Pathway AnalysisTM (IPA) suggested that curcumin may exert its anticancer effects over multiple critical biological pathways including the EIF2, eIF4/p70S6K, mTOR signaling and mitochondrial dysfunction pathways. Functional validations confirmed that curcumin downregulates cellular protein synthesis, and induces autophagy, lysosomal activation and increased ROS production, thus leading to cell death.
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Affiliation(s)
- Jigang Wang
- Interdisciplinary Research Group in Infectious Diseases, Singapore-MIT Alliance for Research &Technology (SMART), 138602, Singapore.,Department of Biological Sciences, National University of Singapore, 117543, Singapore.,The State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Jianbin Zhang
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore
| | - Chong-Jing Zhang
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 117585, Singapore
| | - Yin Kwan Wong
- Department of Biological Sciences, National University of Singapore, 117543, Singapore
| | - Teck Kwang Lim
- Department of Biological Sciences, National University of Singapore, 117543, Singapore
| | - Zi-Chun Hua
- The State Key Laboratory of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Bin Liu
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 117585, Singapore
| | - Steven R Tannenbaum
- Interdisciplinary Research Group in Infectious Diseases, Singapore-MIT Alliance for Research &Technology (SMART), 138602, Singapore.,Departments of Biological Engineering &Chemistry, Massachusetts Institute of Technology, 02139, United States of America
| | - Han-Ming Shen
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore
| | - Qingsong Lin
- Department of Biological Sciences, National University of Singapore, 117543, Singapore
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