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Wang R, Ren C, Gao T, Li H, Bo X, Zhu D, Zhang D, Chen H, Zhang Y. SEPDB: a database of secreted proteins. Database (Oxford) 2024; 2024:baae007. [PMID: 38345567 PMCID: PMC10878045 DOI: 10.1093/database/baae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 12/14/2023] [Accepted: 01/24/2024] [Indexed: 02/15/2024]
Abstract
Detecting changes in the dynamics of secreted proteins in serum has been a challenge for proteomics. Enter secreted protein database (SEPDB), an integrated secretory proteomics database offering human, mouse and rat secretory proteomics datasets collected from serum, exosomes and cell culture media. SEPDB compiles secreted protein information from secreted protein database, UniProt and Human Protein Atlas databases to annotate secreted proteomics data based on protein subcellular localization and disease markers. SEPDB integrates the latest predictive modeling techniques to measure deviations in the distribution of signal peptide structures of secreted proteins, extends signal peptide sequence prediction by excluding transmembrane structural domain proteins and updates the validation analysis pipeline for secreted proteins. To establish tissue-specific profiles, we have also created secreted proteomics datasets associated with different human tissues. In addition, we provide information on heterogeneous receptor network organizational relationships, reflective of the complex functional information inherent in the molecular structures of secreted proteins that serve as ligands. Users can take advantage of the Refreshed Search, Analyze, Browse and Download functions of SEPDB, which is available online at https://sysomics.com/SEPDB/. Database URL: https://sysomics.com/SEPDB/.
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Affiliation(s)
- Ruiqing Wang
- The State Key Laboratory of Complex, Severe, and Rare Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, #5 Dong Dan San Tiao, Beijing 100005, China
- Experimental Center, Shandong University of Traditional Chinese Medicine, Key Laboratory of Traditional Chinese Medicine Classical Theory, Ministry of Education, Shandong University of Traditional Chinese Medicine, #4655 Daxue Road, Changqing District, Jinan, Shandong Province 250355, China
| | - Chao Ren
- Institute of Health Service and Transfusion Medicine, #27 Taiping Road, Haidian District, Beijing 100850, China
| | - Tian Gao
- The State Key Laboratory of Complex, Severe, and Rare Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, #5 Dong Dan San Tiao, Beijing 100005, China
- Experimental Center, Shandong University of Traditional Chinese Medicine, Key Laboratory of Traditional Chinese Medicine Classical Theory, Ministry of Education, Shandong University of Traditional Chinese Medicine, #4655 Daxue Road, Changqing District, Jinan, Shandong Province 250355, China
| | - Hao Li
- Institute of Health Service and Transfusion Medicine, #27 Taiping Road, Haidian District, Beijing 100850, China
| | - Xiaochen Bo
- Institute of Health Service and Transfusion Medicine, #27 Taiping Road, Haidian District, Beijing 100850, China
| | - Dahai Zhu
- The State Key Laboratory of Complex, Severe, and Rare Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, #5 Dong Dan San Tiao, Beijing 100005, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), #96 South Xingdao Ring Road, Haizhu District, Guangzhou 510005, China
| | - Dan Zhang
- Experimental Center, Shandong University of Traditional Chinese Medicine, Key Laboratory of Traditional Chinese Medicine Classical Theory, Ministry of Education, Shandong University of Traditional Chinese Medicine, #4655 Daxue Road, Changqing District, Jinan, Shandong Province 250355, China
| | - Hebing Chen
- Institute of Health Service and Transfusion Medicine, #27 Taiping Road, Haidian District, Beijing 100850, China
| | - Yong Zhang
- The State Key Laboratory of Complex, Severe, and Rare Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, #5 Dong Dan San Tiao, Beijing 100005, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), #96 South Xingdao Ring Road, Haizhu District, Guangzhou 510005, China
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Scebba F, Tognotti D, Presciuttini G, Gabellieri E, Cioni P, Angeloni D, Basso B, Morelli E. A SELDI-TOF approach to ecotoxicology: comparative profiling of low molecular weight proteins from a marine diatom exposed to CdSe/ZnS quantum dots. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2016; 123:45-52. [PMID: 26323371 DOI: 10.1016/j.ecoenv.2015.08.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 08/19/2015] [Accepted: 08/21/2015] [Indexed: 06/04/2023]
Abstract
Quantum dots (QDs), namely semiconductor nanocrystals, due to their particular optical and electronic properties, have growing applications in device technology, biotechnology and biomedical fields. Nevertheless, the possible threat to human health and the environment have attracted increasing attention as the production and applications of QDs increases rapidly while standard evaluation of safety lags. In the present study we performed proteomic analyses, by means of 2D gel electrophoresis and Surface Enhanced Laser Desorption Ionization-Time of Flight-Mass Spectrometry (SELDI-TOF-MS). We aimed to identify potential biomarkers of exposure to CdSe/ZnS quantum dots. The marine diatom Phaeodactylum tricornutum exposed to 2.5nM QDs was used as a model system. Both 2DE and SELDI showed the presence of differentially expressed proteins. By Principal Component Analysis (PCA) we were able to show that the differentially expressed proteins can discriminate between exposed and not exposed cells. Furthermore, a protein profile specific for exposed cells was obtained by SELDI analysis. To our knowledge, this is the first example of the application of SELDI technology to the analysis of microorganisms used as biological sentinel model of marine environmental pollution.
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Affiliation(s)
- Francesca Scebba
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127 Pisa, Italy.
| | - Danika Tognotti
- National Research Council - Institute of Biophysics, Section of Pisa, Via Moruzzi, 1, 56124 Pisa, Italy
| | - Gianluca Presciuttini
- National Research Council - Institute of Biophysics, Section of Pisa, Via Moruzzi, 1, 56124 Pisa, Italy
| | - Edi Gabellieri
- National Research Council - Institute of Biophysics, Section of Pisa, Via Moruzzi, 1, 56124 Pisa, Italy
| | - Patrizia Cioni
- National Research Council - Institute of Biophysics, Section of Pisa, Via Moruzzi, 1, 56124 Pisa, Italy
| | - Debora Angeloni
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127 Pisa, Italy
| | - Barbara Basso
- National Research Council - Institute of Biophysics, Section of Pisa, Via Moruzzi, 1, 56124 Pisa, Italy
| | - Elisabetta Morelli
- National Research Council - Institute of Biophysics, Section of Pisa, Via Moruzzi, 1, 56124 Pisa, Italy
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Jiang J, Wolters JEJ, van Breda SG, Kleinjans JC, de Kok TM. Development of novel tools for the in vitro investigation of drug-induced liver injury. Expert Opin Drug Metab Toxicol 2015; 11:1523-37. [PMID: 26155718 DOI: 10.1517/17425255.2015.1065814] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
INTRODUCTION Due to its complex mechanisms and unpredictable occurrence, drug-induced liver injury (DILI) complicates drug identification and classification. Since species-specific differences in metabolism and pharmacokinetics exist, data obtained from animal studies may not be sufficient to predict DILI in humans. AREAS COVERED Over the last few decades, numerous in vitro models have been developed to replace animal testing. The advantages and disadvantages of commonly used liver-derived in vitro models (e.g., cell lines, hepatocyte models, liver slices, three-dimensional (3D) hepatospheres, etc.) are discussed. Toxicogenomics-based methodologies (genomics, epigenomics, transcriptomics, proteomics and metabolomics) and next-generation sequencing have also been used to enhance the reliability of DILI prediction. This review presents an overview of the currently used alternative toxicological models and of the most advanced approaches in the field of DILI research. EXPERT OPINION It seems unlikely that a single in vitro system will be able to mimic the complex interactions in the human liver. Three-dimensional multicellular systems may bridge the gap between conventional 2D models and in vivo clinical studies in humans and provide a reliable basis for hepatic toxicity assay development. Next-generation sequencing technologies, in comparison to microarray-based technologies, may overcome the current limitations and are promising for the development of predictive models in the near future.
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Affiliation(s)
- Jian Jiang
- a 1 Maastricht University, GROW School for Oncology and Developmental Biology, Department of Toxicogenomics , Maastricht, The Netherlands +31 43 3881090 ; +31 43 3884146 ;
| | - Jarno E J Wolters
- b 2 Maastricht University, GROW School for Oncology and Developmental Biology, Department of Toxicogenomics , Maastricht, The Netherlands
| | - Simone G van Breda
- b 2 Maastricht University, GROW School for Oncology and Developmental Biology, Department of Toxicogenomics , Maastricht, The Netherlands
| | - Jos C Kleinjans
- b 2 Maastricht University, GROW School for Oncology and Developmental Biology, Department of Toxicogenomics , Maastricht, The Netherlands
| | - Theo M de Kok
- b 2 Maastricht University, GROW School for Oncology and Developmental Biology, Department of Toxicogenomics , Maastricht, The Netherlands
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Ramm S, Morissey B, Hernandez B, Rooney C, Pennington SR, Mally A. Application of a discovery to targeted LC-MS proteomics approach to identify deregulated proteins associated with idiosyncratic liver toxicity in a rat model of LPS/diclofenac co-administration. Toxicology 2015; 331:100-11. [PMID: 25772430 DOI: 10.1016/j.tox.2015.03.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 02/25/2015] [Accepted: 03/09/2015] [Indexed: 12/30/2022]
Abstract
Increasing experimental and clinical evidence suggest a contribution of non-drug related risk factors (e.g., underlying disease, bacterial/viral infection) to idiosyncratic drug reactions (IDR). Our previous work showed that co-treatment with bacterial endotoxin (LPS) and therapeutic doses of diclofenac (Dcl), an analgesic associated with drug idiosyncrasy in patients, induced severe hepatotoxicity in rats. Here, we used an integrated discovery to targeted LC-MS proteomics approach to identify mechanistically relevant liver and plasma proteins modulated by LPS/Dcl treatment, potentially applicable as early markers for IDRs. Based on pre-screening results and their role in liver toxicity, 47 liver and 15 plasma proteins were selected for targeted LC-MS analysis. LPS alone significantly changed the levels of 19 and 3 of these proteins, respectively. T-kininogen-1, previously suggested as a marker of drug-induced liver injury, was markedly elevated in plasma after repeated Dcl treatment in the absence of hepatotoxicity, possibly indicating clinically silent stress. Dcl both alone and in combination with LPS, caused up-regulation of the ATP synthase subunits (ATP5J, ATPA, and ATPB), suggesting that Dcl may sensitize cells against additional stress factors, such as LPS through generation of mitochondrial stress. Additionally, depletion of plasma fibrinogen was observed in the co-treatment group, consistent with an increased hepatic fibrin deposition and suspected contribution of the hemostatic system to IDRs. In contrast, several proteins previously suggested as liver biomarkers, such as clusterin, did not correlate with liver injury in this model. Taken together, these analyses revealed proteomic changes in a rat model of LPS/Dcl co-administration that could offer mechanistic insight and may serve as biomarkers or safety alert for a drug's potential to cause IDRs.
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Affiliation(s)
- S Ramm
- Department of Toxicology, University of Würzburg, Würzburg, Germany
| | - B Morissey
- UCD School of Medicine and Medical Science, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - B Hernandez
- UCD School of Medicine and Medical Science, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - C Rooney
- UCD School of Medicine and Medical Science, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - S R Pennington
- UCD School of Medicine and Medical Science, UCD Conway Institute, University College Dublin, Dublin, Ireland
| | - A Mally
- Department of Toxicology, University of Würzburg, Würzburg, Germany.
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Yamazaki M, Miyake M, Sato H, Masutomi N, Tsutsui N, Adam KP, Alexander DC, Lawton KA, Milburn MV, Ryals JA, Wulff JE, Guo L. Perturbation of bile acid homeostasis is an early pathogenesis event of drug induced liver injury in rats. Toxicol Appl Pharmacol 2013; 268:79-89. [PMID: 23360887 DOI: 10.1016/j.taap.2013.01.018] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Revised: 01/03/2013] [Accepted: 01/18/2013] [Indexed: 12/28/2022]
Abstract
Drug-induced liver injury (DILI) is a significant consideration for drug development. Current preclinical DILI assessment relying on histopathology and clinical chemistry has limitations in sensitivity and discordance with human. To gain insights on DILI pathogenesis and identify potential biomarkers for improved DILI detection, we performed untargeted metabolomic analyses on rats treated with thirteen known hepatotoxins causing various types of DILI: necrosis (acetaminophen, bendazac, cyclosporine A, carbon tetrachloride, ethionine), cholestasis (methapyrilene and naphthylisothiocyanate), steatosis (tetracycline and ticlopidine), and idiosyncratic (carbamazepine, chlorzoxasone, flutamide, and nimesulide) at two doses and two time points. Statistical analysis and pathway mapping of the nearly 1900 metabolites profiled in the plasma, urine, and liver revealed diverse time and dose dependent metabolic cascades leading to DILI by the hepatotoxins. The most consistent change induced by the hepatotoxins, detectable even at the early time point/low dose, was the significant elevations of a panel of bile acids in the plasma and urine, suggesting that DILI impaired hepatic bile acid uptake from the circulation. Furthermore, bile acid amidation in the hepatocytes was altered depending on the severity of the hepatotoxin-induced oxidative stress. The alteration of the bile acids was most evident by the necrosis and cholestasis hepatotoxins, with more subtle effects by the steatosis and idiosyncratic hepatotoxins. Taking together, our data suggest that the perturbation of bile acid homeostasis is an early event of DILI. Upon further validation, selected bile acids in the circulation could be potentially used as sensitive and early DILI preclinical biomarkers.
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Affiliation(s)
- Makoto Yamazaki
- Mitsubishi Tanabe Pharma Corporation, Kisarazu, Chiba, Japan
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Gianazza E, Wait R, Eberini I, Sensi C, Sironi L, Miller I. Proteomics of rat biological fluids — The tenth anniversary update. J Proteomics 2012; 75:3113-28. [DOI: 10.1016/j.jprot.2012.03.053] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2012] [Revised: 03/26/2012] [Accepted: 03/28/2012] [Indexed: 01/29/2023]
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Collins BC, Miller CA, Sposny A, Hewitt P, Wells M, Gallagher WM, Pennington SR. Development of a pharmaceutical hepatotoxicity biomarker panel using a discovery to targeted proteomics approach. Mol Cell Proteomics 2012; 11:394-410. [PMID: 22527513 DOI: 10.1074/mcp.m111.016493] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
There is a pressing and continued need for improved predictive power in preclinical pharmaceutical toxicology assessment as substantial numbers of drugs are still removed from the market, or from late-stage development, because of unanticipated issues of toxicity. In recent years a number of consortia have been formed with a view to integrating -omics molecular profiling strategies to increase the sensitivity and predictive power of preclinical toxicology evaluation. In this study we report on the LC-MS based proteomic analysis of the effects of the hepatotoxic compound EMD 335823 on liver from rats using an integrated discovery to targeted proteomics approach. This compound was one of a larger panel studied by a variety of molecular profiling techniques as part of the InnoMed PredTox Consortium. Label-free LC-MS analysis of hepatotoxicant EMD 335823 treated animals revealed only moderate correlation of individual protein expression with changes in mRNA expression observed by transcriptomic analysis of the same liver samples. Significantly however, analysis of the protein and transcript changes at the pathway level revealed they were in good agreement. This higher level analysis was also consistent with the previously suspected PPARα activity of the compound. Subsequently, a panel of potential biomarkers of liver toxicity was assembled from the label-free LC-MS proteomics discovery data, the previously acquired transcriptomics data and selected candidates identified from the literature. We developed and then deployed optimized selected reaction monitoring assays to undertake multiplexed measurement of 48 putative toxicity biomarkers in liver tissue. The development of the selected reaction monitoring assays was facilitated by the construction of a peptide MS/MS spectral library from pooled control and treated rat liver lysate using peptide fractionation by strong cation exchange and off-gel electrophoresis coupled to LC-MS/MS. After iterative optimization and quality control of the selected reaction monitoring assay panel, quantitative measurements of 48 putative biomarkers in the liver of EMD 335823 treated rats were carried out and this revealed that the panel is highly enriched for proteins modulated significantly on drug treatment/hepatotoxic insult. This proof-of-principle study provides a roadmap for future large scale pre-clinical toxicology biomarker verification studies whereby putative toxicity biomarkers assembled from multiple disparate sources can be evaluated at medium-high throughput by targeted MS.
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Affiliation(s)
- Ben C Collins
- UCD School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
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Suter L, Schroeder S, Meyer K, Gautier JC, Amberg A, Wendt M, Gmuender H, Mally A, Boitier E, Ellinger-Ziegelbauer H, Matheis K, Pfannkuch F. EU Framework 6 Project: Predictive Toxicology (PredTox)—overview and outcome. Toxicol Appl Pharmacol 2011; 252:73-84. [DOI: 10.1016/j.taap.2010.10.008] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2010] [Revised: 10/06/2010] [Accepted: 10/09/2010] [Indexed: 11/16/2022]
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