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Horánszky A, Shashikadze B, Elkhateib R, Lombardo SD, Lamberto F, Zana M, Menche J, Fröhlich T, Dinnyés A. Proteomics and disease network associations evaluation of environmentally relevant Bisphenol A concentrations in a human 3D neural stem cell model. Front Cell Dev Biol 2023; 11:1236243. [PMID: 37664457 PMCID: PMC10472293 DOI: 10.3389/fcell.2023.1236243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 07/31/2023] [Indexed: 09/05/2023] Open
Abstract
Bisphenol A (BPA) exposure is associated with a plethora of neurodevelopmental abnormalities and brain disorders. Previous studies have demonstrated BPA-induced perturbations to critical neural stem cell (NSC) characteristics, such as proliferation and differentiation, although the underlying molecular mechanisms remain under debate. The present study evaluated the effects of a repeated-dose exposure of environmentally relevant BPA concentrations during the in vitro 3D neural induction of human induced pluripotent stem cells (hiPSCs), emulating a chronic exposure scenario. Firstly, we demonstrated that our model is suitable for NSC differentiation during the early stages of embryonic brain development. Our morphological image analysis showed that BPA exposure at 0.01, 0.1 and 1 µM decreased the average spheroid size by day 21 (D21) of the neural induction, while no effect on cell viability was detected. No alteration to the rate of the neural induction was observed based on the expression of key neural lineage and neuroectodermal transcripts. Quantitative proteomics at D21 revealed several differentially abundant proteins across all BPA-treated groups with important functions in NSC proliferation and maintenance (e.g., FABP7, GPC4, GAP43, Wnt-8B, TPPP3). Additionally, a network analysis demonstrated alterations to the glycolytic pathway, potentially implicating BPA-induced changes to glycolytic signalling in NSC proliferation impairments, as well as the pathophysiology of brain disorders including intellectual disability, autism spectrum disorders, and amyotrophic lateral sclerosis (ALS). This study enhances the current understanding of BPA-related NSC aberrations based mostly on acute, often high dose exposures of rodent in vivo and in vitro models and human GWAS data in a novel human 3D cell-based model with real-life scenario relevant prolonged and low-level exposures, offering further mechanistic insights into the ramifications of BPA exposure on the developing human brain and consequently, later life neurological disorders.
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Affiliation(s)
- Alex Horánszky
- BioTalentum Ltd., Gödöllő, Hungary
- Department of Physiology and Animal Health, Institute of Physiology and Animal Nutrition, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - Bachuki Shashikadze
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Munich, Germany
| | - Radwa Elkhateib
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Munich, Germany
| | - Salvo Danilo Lombardo
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria
- Department of Structural and Computational Biology, Center for Molecular Biology, University of Vienna, Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Federica Lamberto
- BioTalentum Ltd., Gödöllő, Hungary
- Department of Physiology and Animal Health, Institute of Physiology and Animal Nutrition, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | | | - Jörg Menche
- Max Perutz Labs, Vienna Biocenter Campus (VBC), Vienna, Austria
- Department of Structural and Computational Biology, Center for Molecular Biology, University of Vienna, Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Faculty of Mathematics, University of Vienna, Vienna, Austria
| | - Thomas Fröhlich
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Munich, Germany
| | - András Dinnyés
- BioTalentum Ltd., Gödöllő, Hungary
- Department of Physiology and Animal Health, Institute of Physiology and Animal Nutrition, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
- Department of Cell Biology and Molecular Medicine, University of Szeged, Szeged, Hungary
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Yu L, Su Y, Liu Y, Zeng X. Review of unsupervised pretraining strategies for molecules representation. Brief Funct Genomics 2021; 20:323-332. [PMID: 34342611 DOI: 10.1093/bfgp/elab036] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/07/2021] [Accepted: 07/08/2021] [Indexed: 11/14/2022] Open
Abstract
In recent years, the computer-assisted techniques make a great progress in the field of drug discovery. And, yet, the problem of limited labeled data problem is still challenging and also restricts the performance of these techniques in specific tasks, such as molecular property prediction, compound-protein interaction and de novo molecular generation. One effective solution is to utilize the experience and knowledge gained from other tasks to cope with related pursuits. Unsupervised pretraining is promising, due to its capability of leveraging a vast number of unlabeled molecules and acquiring a more informative molecular representation for the downstream tasks. In particular, models trained on large-scale unlabeled molecules can capture generalizable features, and this ability can be employed to improve the performance of specific downstream tasks. Many relevant pretraining works have been recently proposed. Here, we provide an overview of molecular unsupervised pretraining and related applications in drug discovery. Challenges and possible solutions are also summarized.
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Abd-Elsalam KA, Kasem K, Almoammar H. Carbon nanomaterials (CNTs) phytotoxicity: Quo vadis? CARBON NANOMATERIALS FOR AGRI-FOOD AND ENVIRONMENTAL APPLICATIONS 2020:557-581. [DOI: 10.1016/b978-0-12-819786-8.00024-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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Pan L, Lee YM, Lim TK, Lin Q, Xu X. Quantitative Proteomics Study Reveals Changes in the Molecular Landscape of Human Embryonic Stem Cells with Impaired Stem Cell Differentiation upon Exposure to Titanium Dioxide Nanoparticles. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:e1800190. [PMID: 29741810 DOI: 10.1002/smll.201800190] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 03/27/2018] [Indexed: 06/08/2023]
Abstract
The increasing number of nanoparticles (NPs) being used in various industries has led to growing concerns of potential hazards that NP exposure can incur on human health. However, its global effects on humans and the underlying mechanisms are not systemically studied. Human embryonic stem cells (hESCs), with the ability to differentiate to any cell types, provide a unique system to assess cellular, developmental, and functional toxicity in vitro within a single system highly relevant to human physiology. Here, the quantitative proteomics approach is adopted to evaluate the molecular consequences of titanium dioxide NPs (TiO2 NPs) exposure in hESCs. The study identifies ≈328 unique proteins significantly affected by TiO2 NPs exposure. Proteomics analysis highlights that TiO2 NPs can induce DNA damage, elevated oxidative stress, apoptotic responses, and cellular differentiation. Furthermore, in vivo analysis demonstrates remarkable reduction in the ability of hESCs in teratoma formation after TiO2 NPs exposure, suggesting impaired pluripotency. Subsequently, it is found that TiO2 NPs can disrupt hESC mesoderm differentiation into cardiomyocytes. The study unveils comprehensive changes in the molecular landscape of hESCs by TiO2 NPs and identifies the impact which TiO2 NPs can have on the pluripotency and differentiation properties of human stem cells.
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Affiliation(s)
- Lei Pan
- Institute of Stem Cell and Regenerative Medicine, Medical College, Xiamen University, Chengzhi Building, Xiang'an Campus, Xiamen, Fujian Province, 361100, P. R. China
| | - Yew Mun Lee
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore
| | - Teck Kwang Lim
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore
| | - Qingsong Lin
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore
| | - Xiuqin Xu
- Institute of Stem Cell and Regenerative Medicine, Medical College, Xiamen University, Chengzhi Building, Xiang'an Campus, Xiamen, Fujian Province, 361100, P. R. China
- Shenzhen Research Institute of Xiamen University, Shenzhen, Guangdong Province, 518000, P. R. China
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Organotypic three-dimensional cancer cell cultures mirror drug responses in vivo: lessons learned from the inhibition of EGFR signaling. Oncotarget 2017; 8:107423-107440. [PMID: 29296175 PMCID: PMC5746077 DOI: 10.18632/oncotarget.22475] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 10/27/2017] [Indexed: 01/07/2023] Open
Abstract
Complex three-dimensional (3D) in vitro models that recapitulate human tumor biology are essential to understand the pathophysiology of the disease and to aid in the discovery of novel anti-cancer therapies. 3D organotypic cultures exhibit intercellular communication, nutrient and oxygen gradients, and cell polarity that is lacking in two-dimensional (2D) monolayer cultures. In the present study, we demonstrate that 2D and 3D cancer models exhibit different drug sensitivities towards both targeted inhibitors of EGFR signaling and broad acting cytotoxic agents. Changes in the kinase activities of ErbB family members and differential expression of apoptosis- and survival-associated genes before and after drug treatment may account for the differential drug sensitivities. Importantly, EGFR oncoprotein addiction was evident only in the 3D cultures mirroring the effect of EGFR inhibition in the clinic. Furthermore, targeted drug efficacy was strongly increased when incorporating cancer-associated fibroblasts into the 3D cultures. Taken together, we provide conclusive evidence that complex 3D cultures are more predictive of the clinical outcome than their 2D counterparts. In the future, 3D cultures will be instrumental for understanding the mode of action of drugs, identifying genotype-drug response relationships and developing patient-specific and personalized cancer treatments.
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Li M, Hu T, Tie C, Qu L, Zheng H, Zhang J. Quantitative Proteomics and Targeted Fatty Acids Analysis Reveal the Damage of Triptolide in Liver and Kidney. Proteomics 2017; 17. [DOI: 10.1002/pmic.201700001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 08/25/2017] [Indexed: 12/30/2022]
Affiliation(s)
- Menglin Li
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; Institute of Materia Medica; Chinese Academy of Medical Sciences and Peking Union Medical College; Beijing P. R. China
| | - Ting Hu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; Institute of Materia Medica; Chinese Academy of Medical Sciences and Peking Union Medical College; Beijing P. R. China
| | - Cai Tie
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; Institute of Materia Medica; Chinese Academy of Medical Sciences and Peking Union Medical College; Beijing P. R. China
| | - Liang Qu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; Institute of Materia Medica; Chinese Academy of Medical Sciences and Peking Union Medical College; Beijing P. R. China
- Pharmaron Beijing Co., Ltd.; BDA; Beijing P.R. China
| | - Hao Zheng
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; Institute of Materia Medica; Chinese Academy of Medical Sciences and Peking Union Medical College; Beijing P. R. China
| | - Jinlan Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines; Institute of Materia Medica; Chinese Academy of Medical Sciences and Peking Union Medical College; Beijing P. R. China
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Abstract
Although safety of drug candidates is carefully monitored in preclinical and clinical studies using a variety of approaches, drug toxicity may still occur in clinical practice. Therefore, novel approaches are needed to complement the current drug safety evaluation system. Metabolomics comprehensively analyzes the metabolites altered by drug exposure, which can therefore be used to profile drug metabolism, endobiotic metabolism, and drug-microbiota interactions. The information from metabolomic analysis can be used to determine the off-targets of a drug candidate, and thus provide a mechanistic understanding of drug toxicity. We herein discuss the opportunities of metabolomics in drug safety evaluation.
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Suman S, Mishra S, Shukla Y. Toxicoproteomics in human health and disease: an update. Expert Rev Proteomics 2016; 13:1073-1089. [DOI: 10.1080/14789450.2016.1252676] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Shankar Suman
- Proteomics and Environmental Carcinogenesis Laboratory, Food, Drug and Chemical Toxicology Group, CSIR-Indian Institute of Toxicology Research, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Lucknow, India
| | - Sanjay Mishra
- Proteomics and Environmental Carcinogenesis Laboratory, Food, Drug and Chemical Toxicology Group, CSIR-Indian Institute of Toxicology Research, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Lucknow, India
| | - Yogeshwer Shukla
- Proteomics and Environmental Carcinogenesis Laboratory, Food, Drug and Chemical Toxicology Group, CSIR-Indian Institute of Toxicology Research, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Lucknow, India
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Gao Y, Cao Z, Yang X, Abdelmegeed MA, Sun J, Chen S, Beger RD, Davis K, Salminen WF, Song BJ, Mendrick DL, Yu LR. Proteomic analysis of acetaminophen-induced hepatotoxicity and identification of heme oxygenase 1 as a potential plasma biomarker of liver injury. Proteomics Clin Appl 2016; 11. [PMID: 27634590 DOI: 10.1002/prca.201600123] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 09/02/2016] [Accepted: 09/13/2016] [Indexed: 02/06/2023]
Abstract
PURPOSE Overdose of acetaminophen (APAP) is a major cause of acute liver failure. This study was aimed to identify pathways related to hepatotoxicity and potential biomarkers of liver injury. EXPERIMENTAL DESIGN Rats were treated with low (100 mg/kg) and high (1250 mg/kg) doses of APAP, and liver tissues at 6 and 24 h post-treatment were analyzed using a proteomic approach of 16O/18O labeling and 2D-LC-MS/MS. RESULTS Molecular pathways evolved progressively from scattered and less significant perturbations to more focused and significant alterations in a dose- and time-dependent manner upon APAP treatment. Imbalanced expression of hemeoxygenase 1 (HMOX1) and biliverdin reductase A (BLVRA) was associated with hepatotoxicity. Protein abundance changes of a total of 31 proteins were uniquely correlated to liver damage, among which a dramatic increase of HMOX1 levels in plasma was observed. Liver injury-associated significant elevation of plasma HMOX1 was further validated in mice treated with APAP. CONCLUSIONS AND CLINICAL RELEVANCE This study unveiled molecular changes associated with APAP-induced liver toxicity at the pathway levels and identified HMOX1 as a potential plasma biomarker of liver injury.
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Affiliation(s)
- Yuan Gao
- Division of Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - Zhijun Cao
- Division of Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - Xi Yang
- Division of Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - Mohamed A Abdelmegeed
- Laboratory of Membrane Biochemistry and Biophysics, National Institute on Alcohol Abuse and Alcoholism, Bethesda, MD, USA
| | - Jinchun Sun
- Division of Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - Si Chen
- Division of Biochemical Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - Richard D Beger
- Division of Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - Kelly Davis
- Toxicologic Pathology Associates, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - William F Salminen
- Division of Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - Byoung-Joon Song
- Laboratory of Membrane Biochemistry and Biophysics, National Institute on Alcohol Abuse and Alcoholism, Bethesda, MD, USA
| | - Donna L Mendrick
- Division of Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - Li-Rong Yu
- Division of Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
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Beger RD, Bhattacharyya S, Yang X, Gill PS, Schnackenberg LK, Sun J, James LP. Translational biomarkers of acetaminophen-induced acute liver injury. Arch Toxicol 2015; 89:1497-522. [PMID: 25983262 PMCID: PMC4551536 DOI: 10.1007/s00204-015-1519-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 04/21/2015] [Indexed: 12/17/2022]
Abstract
Acetaminophen (APAP) is a commonly used analgesic drug that can cause liver injury, liver necrosis and liver failure. APAP-induced liver injury is associated with glutathione depletion, the formation of APAP protein adducts, the generation of reactive oxygen and nitrogen species and mitochondrial injury. The systems biology omics technologies (transcriptomics, proteomics and metabolomics) have been used to discover potential translational biomarkers of liver injury. The following review provides a summary of the systems biology discovery process, analytical validation of biomarkers and translation of omics biomarkers from the nonclinical to clinical setting in APAP-induced liver injury.
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Affiliation(s)
- Richard D Beger
- Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, USA,
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Rabilloud T, Lescuyer P. Proteomics in mechanistic toxicology: History, concepts, achievements, caveats, and potential. Proteomics 2014; 15:1051-74. [DOI: 10.1002/pmic.201400288] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 07/25/2014] [Accepted: 08/25/2014] [Indexed: 12/19/2022]
Affiliation(s)
- Thierry Rabilloud
- Laboratory of Chemistry and Biology of Metals; CNRS UMR; 5249 Grenoble France
- Laboratory of Chemistry and Biology of Metals; Université Grenoble Alpes; Grenoble France
- Laboratory of Chemistry and Biology of Metals; CEA Grenoble; iRTSV/CBM; Grenoble France
| | - Pierre Lescuyer
- Department of Human Protein Sciences; Clinical Proteomics and Chemistry Group; Geneva University; Geneva Switzerland
- Toxicology and Therapeutic Drug Monitoring Laboratory; Department of Genetic and Laboratory Medicine; Geneva University Hospitals; Geneva Switzerland
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Acosta-Martin AE, Lane L. Combining bioinformatics and MS-based proteomics: clinical implications. Expert Rev Proteomics 2014; 11:269-84. [PMID: 24720436 DOI: 10.1586/14789450.2014.900446] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Clinical proteomics research aims at i) discovery of protein biomarkers for screening, diagnosis and prognosis of disease, ii) discovery of protein therapeutic targets for improvement of disease prevention, treatment and follow-up, and iii) development of mass spectrometry (MS)-based assays that could be implemented in clinical chemistry, microbiology or hematology laboratories. MS has been increasingly applied in clinical proteomics studies for the identification and quantification of proteins. Bioinformatics plays a key role in the exploitation of MS data in several aspects such as the generation and curation of protein sequence databases, the development of appropriate software for MS data treatment and integration with other omics data and the establishment of adequate standard files for data sharing. In this article, we discuss the main MS approaches and bioinformatics solutions that are currently applied to accomplish the objectives of clinical proteomic research.
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Issa NT, Byers SW, Dakshanamurthy S. Big data: the next frontier for innovation in therapeutics and healthcare. Expert Rev Clin Pharmacol 2014; 7:293-8. [PMID: 24702684 DOI: 10.1586/17512433.2014.905201] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Advancements in genomics and personalized medicine not only effect healthcare delivery from patient and provider standpoints, but also reshape biomedical discovery. We are in the era of the '-omics', wherein an individual's genome, transcriptome, proteome and metabolome can be scrutinized to the finest resolution to paint a personalized biochemical fingerprint that enables tailored treatments, prognoses, risk factors, etc. Digitization of this information parlays into 'big data' informatics-driven evidence-based medical practice. While individualized patient management is a key beneficiary of next-generation medical informatics, this data also harbors a wealth of novel therapeutic discoveries waiting to be uncovered. 'Big data' informatics allows for networks-driven systems pharmacodynamics whereby drug information can be coupled to cellular- and organ-level physiology for determining whole-body outcomes. Patient '-omics' data can be integrated for ontology-based data-mining for the discovery of new biological associations and drug targets. Here we highlight the potential of 'big data' informatics for clinical pharmacology.
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Affiliation(s)
- Naiem T Issa
- Department of Oncology, Lombardi Cancer Center, Georgetown University Medical Center, Washington, DC USA
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14
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Liu Y, Guo M. Chemical proteomic strategies for the discovery and development of anticancer drugs. Proteomics 2014; 14:399-411. [DOI: 10.1002/pmic.201300261] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Revised: 09/26/2013] [Accepted: 10/11/2013] [Indexed: 11/07/2022]
Affiliation(s)
- Yuanzhen Liu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture; Wuhan Botanical Garden; Chinese Academy of Sciences; Wuhan P. R. China
| | - Mingquan Guo
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture; Wuhan Botanical Garden; Chinese Academy of Sciences; Wuhan P. R. China
- The Keck School of Medicine; University of Southern California; Los Angeles CA USA
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Xiong Q, Ge F. Identification and evaluation of a panel of serum biomarkers for predicting response to thalidomide in multiple myeloma patients. Expert Rev Proteomics 2014; 8:439-42. [DOI: 10.1586/epr.11.42] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Gu Q, Yu LR. Proteomics quality and standard: from a regulatory perspective. J Proteomics 2013; 96:353-9. [PMID: 24316359 DOI: 10.1016/j.jprot.2013.11.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2012] [Revised: 11/07/2013] [Accepted: 11/22/2013] [Indexed: 12/30/2022]
Abstract
Proteomics has emerged as a rapidly expanding field dealing with large-scale protein analyses. It is anticipated that proteomics data will be increasingly submitted to the U.S. Food and Drug Administration (FDA) for biomarker qualification or in conjunction with applications for the approval of drugs, medical devices, and other FDA-regulated consumer products. To date, however, no established guideline has been available regarding the generation, submission and assessment of the quality of proteomics data that will be reviewed by regulatory agencies for decision making. Therefore, this commentary is aimed at provoking some thoughts and debates towards developing a framework which can guide future proteomics data submission. The ultimate goal is to establish quality control standards for proteomics data generation and evaluation, and to prepare government agencies such as the FDA to meet future obligations utilizing proteomics data to support regulatory decision.
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Affiliation(s)
- Qiang Gu
- Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, USA
| | - Li-Rong Yu
- Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, USA.
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Lionetto L, Gentile G, Bellei E, Capi M, Sabato D, Marsibilio F, Simmaco M, Pini LA, Martelletti P. The omics in migraine. J Headache Pain 2013; 14:55. [PMID: 23815568 PMCID: PMC3727988 DOI: 10.1186/1129-2377-14-55] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 06/22/2013] [Indexed: 12/29/2022] Open
Abstract
The term omics consist of three main areas of molecular biology, such as genomics, proteomics and metabolomics. The omics synergism recognise migraine as an ideal study model, due to its multifactorial nature. In this review, the plainly research data featuring in this complex network are reported and analyzed, as single or multiple factor in pathophysiology of migraine. The future of migraine biomolecular research shall be focused on networking among these different and hierarchical disciplines. We have to look for its Ariadne’s tread, in order to see the whole painting of migraine molecular biology.
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Affiliation(s)
- Luana Lionetto
- Sant'Andrea Hospital, Advanced Molecular Diagnostics Unit, Via di Grottarossa 1035 - 1039, Rome 00189, Italy.
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Guo M, Huang BX. Integration of phosphoproteomic, chemical, and biological strategies for the functional analysis of targeted protein phosphorylation. Proteomics 2013; 13:424-37. [PMID: 23125184 DOI: 10.1002/pmic.201200274] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2012] [Revised: 09/04/2012] [Accepted: 09/20/2012] [Indexed: 12/20/2022]
Abstract
Reversible phosphorylation, tightly controlled by protein kinases and phosphatases, plays a central role in mediating biological processes, such as protein-protein interactions, subcellular translocation, and activation of cellular enzymes. MS-based phosphoproteomics has now allowed the detection and quantification of tens of thousands of phosphorylation sites from a typical biological sample in a single experiment, which has posed new challenges in functional analysis of each and every phosphorylation site on specific signaling phosphoproteins of interest. In this article, we review recent advances in the functional analysis of targeted phosphorylation carried out by various chemical and biological approaches in combination with the MS-based phosphoproteomics. This review focuses on three types of strategies, including forward functional analysis, defined for the result-driven phosphoproteomics efforts in determining the substrates of a specific protein kinase; reverse functional analysis, defined for tracking the kinase(s) for specific phosphosite(s) derived from the discovery-driven phosphoproteomics efforts; and MS-based analysis on the structure-function relationship of phosphoproteins. It is expected that this review will provide a state-of-the-art overview of functional analysis of site-specific phosphorylation and explore new perspectives and outline future challenges.
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Affiliation(s)
- Mingquan Guo
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.
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Kossowska B, Dudka I, Gancarz R, Antonowicz-Juchniewicz J. Application of classic epidemiological studies and proteomics in research of occupational and environmental exposure to lead, cadmium and arsenic. Int J Hyg Environ Health 2013; 216:1-7. [DOI: 10.1016/j.ijheh.2012.03.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Revised: 02/16/2012] [Accepted: 03/07/2012] [Indexed: 10/28/2022]
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Cho YE, Kim SH, Baek MC. Proteome profiling of tolbutamide-treated rat primary hepatocytes using nano LC-MS/MS and label-free protein quantitation. Electrophoresis 2012; 33:2806-17. [PMID: 22911336 DOI: 10.1002/elps.201200193] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Revised: 05/10/2012] [Accepted: 05/15/2012] [Indexed: 11/06/2022]
Abstract
Tolbutamide is used as a first line oral antihyperglycemic drug for type 2 diabetes. One side effect of this drug, hepatotoxicity, is well recognized; however, the precise mechanisms underlying tolbutamide-induced hepatotoxicity remain unclear. In this respect, proteomics techniques were used to gain further insight into the mechanistic processes of the hepatotoxicity induced by this drug. In this study, we aimed to identify molecular pathways based on proteins responding to cellular toxicity in tolbutamide-treated primary hepatocytes, using nano UPLC-MS/MS analysis. Rat primary hepatocytes were treated with an IC(20) concentration for 24 h to study the hepatotoxic effects of tolbutamide. For high-throughput label-free quantitation, tryptic-digested peptides of proteins from cell lysates were analyzed using LC-MS/MS and quantitated using the IDEAL-Q software, in which several parameters, such as assisted sequence, elution time, and mass-to-charge ratio were included. We quantified a total of 330 distinct proteins from the tolbutamide-treated hepatocytes and identified 55 upregulated and 82 downregulated proteins with expression changes. Among these differentially expressed proteins, we focused mainly on the 18 upregulated proteins belonging to xenobiotic cytochrome P450 (CYP), drug metabolism/detoxification, oxidative stress/antioxidant response, and cell damage pathway. CYP2D1, CYP2C11, UDP-glucuronosyltransferase 2B (UGT2B), superoxide dismutase 2 (SOD2), 60 kDa heat shock protein (HSPD1), heat shock protein 90 (HSP90), and catalase (CAT) were confirmed by Western blot analysis. In addition, various xenobiotic CYP proteins upregulated in the tolbutamide-treated group, CYP2D1, CYP2C13, and CYP2C11 were confirmed by reverse transcriptase-PCR analysis. Our results offer important new insights into the molecular mechanisms of tolbutamide-induced hepatotoxicity.
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Affiliation(s)
- Young-Eun Cho
- Department of Molecular Medicine, Kyungpook National University, Daegu, Republic of Korea
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Redox proteomics and drug development. J Proteomics 2011; 74:2575-95. [DOI: 10.1016/j.jprot.2011.01.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Revised: 12/22/2010] [Accepted: 01/09/2011] [Indexed: 01/06/2023]
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Yu LR. Pharmacoproteomics and toxicoproteomics: The field of dreams. J Proteomics 2011; 74:2549-53. [DOI: 10.1016/j.jprot.2011.10.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2011] [Accepted: 10/03/2011] [Indexed: 01/09/2023]
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Andersen ME, Al-Zoughool M, Croteau M, Westphal M, Krewski D. The future of toxicity testing. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART B, CRITICAL REVIEWS 2010; 13:163-196. [PMID: 20574896 DOI: 10.1080/10937404.2010.483933] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
In 2007, the U.S. National Research Council (NRC) released a report, "Toxicity Testing in the 21st Century: A Vision and a Strategy," that proposes a paradigm shift for toxicity testing of environmental agents. The vision is based on the notion that exposure to environmental agents leads to adverse health outcomes through the perturbation of toxicity pathways that are operative in humans. Implementation of the NRC vision will involve a fundamental change in the assessment of toxicity of environmental agents, moving away from adverse health outcomes observed in experimental animals to the identification of critical perturbations of toxicity pathways. Pathway perturbations will be identified using in vitro assays and quantified for dose response using methods in computational toxicology and other recent scientific advances in basic biology. Implementation of the NRC vision will require a major research effort, not unlike that required to successfully map the human genome, extending over 10 to 20 years, involving the broad scientific community to map important toxicity pathways operative in humans. This article provides an overview of the scientific tools and technologies that will form the core of the NRC vision for toxicity testing. Of particular importance will be the development of rapidly performed in vitro screening assays using human cells and cell lines or human tissue surrogates to efficiently identify environmental agents producing critical pathway perturbations. In addition to the overview of the NRC vision, this study documents the reaction by a number of stakeholder groups since 2007, including the scientific, risk assessment, regulatory, and animal welfare communities.
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Affiliation(s)
- Melvin E Andersen
- Hamner Institutes for Health Sciences, Research Triangle Park, North Carolina, USA
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