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Gholizadeh E, Karbalaei R, Khaleghian A, Salimi M, Gilany K, Soliymani R, Tanoli Z, Rezadoost H, Baumann M, Jafari M, Tang J. Identification of Celecoxib-Targeted Proteins Using Label-Free Thermal Proteome Profiling on Rat Hippocampus. Mol Pharmacol 2021; 99:308-318. [PMID: 33632781 DOI: 10.1124/molpharm.120.000210] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/10/2021] [Indexed: 12/25/2022] Open
Abstract
Celecoxib, or Celebrex, a nonsteroidal anti-inflammatory drug, is one of the most common medicines for treating inflammatory diseases. Recently, it has been shown that celecoxib is associated with implications in complex diseases, such as Alzheimer disease and cancer as well as with cardiovascular risk assessment and toxicity, suggesting that celecoxib may affect multiple unknown targets. In this project, we detected targets of celecoxib within the nervous system using a label-free thermal proteome profiling method. First, proteins of the rat hippocampus were treated with multiple drug concentrations and temperatures. Next, we separated the soluble proteins from the denatured and sedimented total protein load by ultracentrifugation. Subsequently, the soluble proteins were analyzed by nano-liquid chromatography tandem mass spectrometry to determine the identity of the celecoxib-targeted proteins based on structural changes by thermal stability variation of targeted proteins toward higher solubility in the higher temperatures. In the analysis of the soluble protein extract at 67°C, 44 proteins were uniquely detected in drug-treated samples out of all 478 identified proteins at this temperature. Ras-associated binding protein 4a, 1 out of these 44 proteins, has previously been reported as one of the celecoxib off targets in the rat central nervous system. Furthermore, we provide more molecular details through biomedical enrichment analysis to explore the potential role of all detected proteins in the biologic systems. We show that the determined proteins play a role in the signaling pathways related to neurodegenerative disease-and cancer pathways. Finally, we fill out molecular supporting evidence for using celecoxib toward the drug-repurposing approach by exploring drug targets. SIGNIFICANCE STATEMENT: This study determined 44 off-target proteins of celecoxib, a nonsteroidal anti-inflammatory and one of the most common medicines for treating inflammatory diseases. It shows that these proteins play a role in the signaling pathways related to neurodegenerative disease and cancer pathways. Finally, the study provides molecular supporting evidence for using celecoxib toward the drug-repurposing approach by exploring drug targets.
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Affiliation(s)
- Elham Gholizadeh
- Department of Biochemistry, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran (E.G., A.K.);Department of Psychology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania (R.K.); Physiology and Pharmacology Department, Pasteur Institute of Iran, Tehran, Iran (M.S.); Reproductive Immunology Research Center, Avicenna Research Institute, and Integrative Oncology Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran (K.G.); Medicum, Biochemistry/Developmental Biology and HiLIFE, Meilahti Clinical Proteomics Core Facility (R.S., M.B.), and Research Program in Systems Oncology, Faculty of Medicine (Z.T., M.J., J.T.), University of Helsinki, Helsinki, Finland; and Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, Tehran, Iran (H.R.)
| | - Reza Karbalaei
- Department of Biochemistry, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran (E.G., A.K.);Department of Psychology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania (R.K.); Physiology and Pharmacology Department, Pasteur Institute of Iran, Tehran, Iran (M.S.); Reproductive Immunology Research Center, Avicenna Research Institute, and Integrative Oncology Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran (K.G.); Medicum, Biochemistry/Developmental Biology and HiLIFE, Meilahti Clinical Proteomics Core Facility (R.S., M.B.), and Research Program in Systems Oncology, Faculty of Medicine (Z.T., M.J., J.T.), University of Helsinki, Helsinki, Finland; and Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, Tehran, Iran (H.R.)
| | - Ali Khaleghian
- Department of Biochemistry, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran (E.G., A.K.);Department of Psychology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania (R.K.); Physiology and Pharmacology Department, Pasteur Institute of Iran, Tehran, Iran (M.S.); Reproductive Immunology Research Center, Avicenna Research Institute, and Integrative Oncology Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran (K.G.); Medicum, Biochemistry/Developmental Biology and HiLIFE, Meilahti Clinical Proteomics Core Facility (R.S., M.B.), and Research Program in Systems Oncology, Faculty of Medicine (Z.T., M.J., J.T.), University of Helsinki, Helsinki, Finland; and Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, Tehran, Iran (H.R.)
| | - Mona Salimi
- Department of Biochemistry, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran (E.G., A.K.);Department of Psychology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania (R.K.); Physiology and Pharmacology Department, Pasteur Institute of Iran, Tehran, Iran (M.S.); Reproductive Immunology Research Center, Avicenna Research Institute, and Integrative Oncology Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran (K.G.); Medicum, Biochemistry/Developmental Biology and HiLIFE, Meilahti Clinical Proteomics Core Facility (R.S., M.B.), and Research Program in Systems Oncology, Faculty of Medicine (Z.T., M.J., J.T.), University of Helsinki, Helsinki, Finland; and Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, Tehran, Iran (H.R.)
| | - Kambiz Gilany
- Department of Biochemistry, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran (E.G., A.K.);Department of Psychology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania (R.K.); Physiology and Pharmacology Department, Pasteur Institute of Iran, Tehran, Iran (M.S.); Reproductive Immunology Research Center, Avicenna Research Institute, and Integrative Oncology Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran (K.G.); Medicum, Biochemistry/Developmental Biology and HiLIFE, Meilahti Clinical Proteomics Core Facility (R.S., M.B.), and Research Program in Systems Oncology, Faculty of Medicine (Z.T., M.J., J.T.), University of Helsinki, Helsinki, Finland; and Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, Tehran, Iran (H.R.)
| | - Rabah Soliymani
- Department of Biochemistry, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran (E.G., A.K.);Department of Psychology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania (R.K.); Physiology and Pharmacology Department, Pasteur Institute of Iran, Tehran, Iran (M.S.); Reproductive Immunology Research Center, Avicenna Research Institute, and Integrative Oncology Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran (K.G.); Medicum, Biochemistry/Developmental Biology and HiLIFE, Meilahti Clinical Proteomics Core Facility (R.S., M.B.), and Research Program in Systems Oncology, Faculty of Medicine (Z.T., M.J., J.T.), University of Helsinki, Helsinki, Finland; and Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, Tehran, Iran (H.R.)
| | - Ziaurrehman Tanoli
- Department of Biochemistry, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran (E.G., A.K.);Department of Psychology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania (R.K.); Physiology and Pharmacology Department, Pasteur Institute of Iran, Tehran, Iran (M.S.); Reproductive Immunology Research Center, Avicenna Research Institute, and Integrative Oncology Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran (K.G.); Medicum, Biochemistry/Developmental Biology and HiLIFE, Meilahti Clinical Proteomics Core Facility (R.S., M.B.), and Research Program in Systems Oncology, Faculty of Medicine (Z.T., M.J., J.T.), University of Helsinki, Helsinki, Finland; and Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, Tehran, Iran (H.R.)
| | - Hassan Rezadoost
- Department of Biochemistry, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran (E.G., A.K.);Department of Psychology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania (R.K.); Physiology and Pharmacology Department, Pasteur Institute of Iran, Tehran, Iran (M.S.); Reproductive Immunology Research Center, Avicenna Research Institute, and Integrative Oncology Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran (K.G.); Medicum, Biochemistry/Developmental Biology and HiLIFE, Meilahti Clinical Proteomics Core Facility (R.S., M.B.), and Research Program in Systems Oncology, Faculty of Medicine (Z.T., M.J., J.T.), University of Helsinki, Helsinki, Finland; and Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, Tehran, Iran (H.R.)
| | - Marc Baumann
- Department of Biochemistry, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran (E.G., A.K.);Department of Psychology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania (R.K.); Physiology and Pharmacology Department, Pasteur Institute of Iran, Tehran, Iran (M.S.); Reproductive Immunology Research Center, Avicenna Research Institute, and Integrative Oncology Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran (K.G.); Medicum, Biochemistry/Developmental Biology and HiLIFE, Meilahti Clinical Proteomics Core Facility (R.S., M.B.), and Research Program in Systems Oncology, Faculty of Medicine (Z.T., M.J., J.T.), University of Helsinki, Helsinki, Finland; and Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, Tehran, Iran (H.R.)
| | - Mohieddin Jafari
- Department of Biochemistry, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran (E.G., A.K.);Department of Psychology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania (R.K.); Physiology and Pharmacology Department, Pasteur Institute of Iran, Tehran, Iran (M.S.); Reproductive Immunology Research Center, Avicenna Research Institute, and Integrative Oncology Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran (K.G.); Medicum, Biochemistry/Developmental Biology and HiLIFE, Meilahti Clinical Proteomics Core Facility (R.S., M.B.), and Research Program in Systems Oncology, Faculty of Medicine (Z.T., M.J., J.T.), University of Helsinki, Helsinki, Finland; and Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, Tehran, Iran (H.R.)
| | - Jing Tang
- Department of Biochemistry, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran (E.G., A.K.);Department of Psychology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania (R.K.); Physiology and Pharmacology Department, Pasteur Institute of Iran, Tehran, Iran (M.S.); Reproductive Immunology Research Center, Avicenna Research Institute, and Integrative Oncology Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran (K.G.); Medicum, Biochemistry/Developmental Biology and HiLIFE, Meilahti Clinical Proteomics Core Facility (R.S., M.B.), and Research Program in Systems Oncology, Faculty of Medicine (Z.T., M.J., J.T.), University of Helsinki, Helsinki, Finland; and Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, Tehran, Iran (H.R.)
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Barneh F, Mirzaie M, Nickchi P, Tan TZ, Thiery JP, Piran M, Salimi M, Goshadrou F, Aref AR, Jafari M. Integrated use of bioinformatic resources reveals that co-targeting of histone deacetylases, IKBK and SRC inhibits epithelial-mesenchymal transition in cancer. Brief Bioinform 2020; 20:717-731. [PMID: 29726962 DOI: 10.1093/bib/bby030] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 03/04/2018] [Indexed: 02/07/2023] Open
Abstract
With the advent of high-throughput technologies leading to big data generation, increasing number of gene signatures are being published to predict various features of diseases such as prognosis and patient survival. However, to use these signatures for identifying therapeutic targets, use of additional bioinformatic tools is indispensible part of research. Here, we have generated a pipeline comprised of nearly 15 bioinformatic tools and enrichment statistical methods to propose and validate a drug combination strategy from already approved drugs and present our approach using published pan-cancer epithelial-mesenchymal transition (EMT) signatures as a case study. We observed that histone deacetylases were critical targets to tune expression of multiple epithelial versus mesenchymal genes. Moreover, SRC and IKBK were the principal intracellular kinases regulating multiple signaling pathways. To confirm the anti-EMT efficacy of the proposed target combination in silico, we validated expression of targets in mesenchymal versus epithelial subtypes of ovarian cancer. Additionally, we inhibited the pinpointed proteins in vitro using an invasive lung cancer cell line. We found that whereas low-dose mono-therapy failed to limit cell dispersion from collagen spheroids in a microfluidic device as a metric of EMT, the combination fully inhibited dissociation and invasion of cancer cells toward cocultured endothelial cells. Given the approval status and safety profiles of the suggested drugs, the proposed combination set can be considered in clinical trials.
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Affiliation(s)
- Farnaz Barneh
- Department of Basic Sciences, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Drug Design and Bioinformatics Unit, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mehdi Mirzaie
- Department of Applied Mathematics, Faculty of Mathematical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Payman Nickchi
- Drug Design and Bioinformatics Unit, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.,Department of Statistics and Actuarial Science, Simon Fraser University, Burnaby, BC, Canada
| | - Tuan Zea Tan
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore, Translational Centre for Development and Research, National University Health System, MD11, #03-10, 10 Medical Drive, Singapore 117597, Singapore
| | - Jean Paul Thiery
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore.,Institut Gustave Roussy, Inserm Unit 1186 Comprehensive Cancer Center, Villejuif, France.,CNRS UMR 7057 Matter and Complex Systems, University Paris Denis Diderot, Paris, France
| | - Mehran Piran
- Drug Design and Bioinformatics Unit, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mona Salimi
- Department of Physiology and Pharmacology, Pasteur Institute of Iran, Tehran, Iran
| | - Fatemeh Goshadrou
- Department of Basic Sciences, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amir R Aref
- Department of Medical Oncology, Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston 02215, USA
| | - Mohieddin Jafari
- Drug Design and Bioinformatics Unit, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
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Barneh F, Salimi M, Goshadrou F, Ashtiani M, Mirzaie M, Zali H, Jafari M. Valproic acid inhibits the protective effects of stromal cells against chemotherapy in breast cancer: Insights from proteomics and systems biology. J Cell Biochem 2018; 119:9270-9283. [PMID: 29953653 DOI: 10.1002/jcb.27196] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 05/24/2018] [Indexed: 12/14/2022]
Abstract
Interaction between tumor and stromal cells is beginning to be decoded as a contributor to chemotherapy resistance. Here, we aim to take a system-level approach to explore a mechanism by which stromal cells induce chemoresistance in cancer cells and subsequently identify a drug that can inhibit such interaction. Using a proteomic dataset containing quantitative data on secretome of stromal cells, we performed multivariate analyses and found that bone-marrow mesenchymal stem cells (BM-MSCs) play the most protective role against chemotherapeutics. Pathway enrichment tests showed that secreted cytokines from BM-MSCs activated 4 signaling pathways including Janus kinase-signal transducer and activator of transcription, phosphatidylinositol 3-kinase-protein kinase B, and mitogen-activated protein kinase, transforming growth factor-β in cancer cells collectively leading to nuclear factor kappa-light-chain-enhancer of activated B cells (NF-kB) transcription factor activation. Based on the data from integrated Library of Integrated Network-Based Cellular Signatures (iLINCs) program, we found that among different drugs, valproic acid (VA) affected the expression of 34 genes within the identified pathways that are activated by stromal cells. Our in vitro experiments confirmed that VA inhibits NF-kB activation in cancer cells. In addition, analyzing gene expression data in patients taking oral VA showed that this drug decreased expression of antioxidant enzymes culminating in increased oxidative stress in tumor cells. These results suggest that VA confines the protective role of stromal cells by inhibiting the adaptation mechanisms toward oxidative stress which is potentiated by stromal cells. Since VA is an already prescribed drug manifesting anticancer effects, this study provides a mechanistic insight for combination of VA with chemotherapy in the clinical setting.
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Affiliation(s)
- Farnaz Barneh
- Department of Basic Sciences, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Physiology and Pharmacology Department, Pasteur Institute of Iran, Tehran, Iran.,Drug Design and Bioinformatics Unit, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mona Salimi
- Physiology and Pharmacology Department, Pasteur Institute of Iran, Tehran, Iran
| | - Fatemeh Goshadrou
- Department of Basic Sciences, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Minoo Ashtiani
- Drug Design and Bioinformatics Unit, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.,Department of Computer Science and Statistics, Faculty of Mathematics, K. N. Toosi University of Technology, Tehran, Iran
| | - Mehdi Mirzaie
- Department of Applied Mathematics, Faculty of Mathematical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Hakimeh Zali
- School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical sciences, Tehran, Iran
| | - Mohieddin Jafari
- Drug Design and Bioinformatics Unit, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
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