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Odongo R, Demiroglu-Zergeroglu A, Çakır T. A network-based drug prioritization and combination analysis for the MEK5/ERK5 pathway in breast cancer. BioData Min 2024; 17:5. [PMID: 38378612 PMCID: PMC10880212 DOI: 10.1186/s13040-024-00357-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 02/12/2024] [Indexed: 02/22/2024] Open
Abstract
BACKGROUND Prioritizing candidate drugs based on genome-wide expression data is an emerging approach in systems pharmacology due to its holistic perspective for preclinical drug evaluation. In the current study, a network-based approach was proposed and applied to prioritize plant polyphenols and identify potential drug combinations in breast cancer. We focused on MEK5/ERK5 signalling pathway genes, a recently identified potential drug target in cancer with roles spanning major carcinogenesis processes. RESULTS By constructing and identifying perturbed protein-protein interaction networks for luminal A breast cancer, plant polyphenols and drugs from transcriptome data, we first demonstrated their systemic effects on the MEK5/ERK5 signalling pathway. Subsequently, we applied a pathway-specific network pharmacology pipeline to prioritize plant polyphenols and potential drug combinations for use in breast cancer. Our analysis prioritized genistein among plant polyphenols. Drug combination simulations predicted several FDA-approved drugs in breast cancer with well-established pharmacology as candidates for target network synergistic combination with genistein. This study also highlights the concept of target network enhancer drugs, with drugs previously not well characterised in breast cancer being prioritized for use in the MEK5/ERK5 pathway in breast cancer. CONCLUSION This study proposes a computational framework for drug prioritization and combination with the MEK5/ERK5 signaling pathway in breast cancer. The method is flexible and provides the scientific community with a robust method that can be applied to other complex diseases.
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Affiliation(s)
- Regan Odongo
- Department of Bioengineering, Faculty of Engineering, Gebze Technical University, Gebze, Kocaeli, 41400, Turkey.
| | - Asuman Demiroglu-Zergeroglu
- Department of Molecular Biology & Genetics, Faculty of Science, Gebze Technical University, Gebze, Kocaeli, 41400, Turkey
| | - Tunahan Çakır
- Department of Bioengineering, Faculty of Engineering, Gebze Technical University, Gebze, Kocaeli, 41400, Turkey
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Yenilmez Çiftçi G, Bayık N, Turhal G, Nermin Başlılar İ, Demiroglu-Zergeroglu A. The first mono anthraquinone substituted monospiro cyclotriphosphazene derivatives and their effects on non-small cell lung cancer cells. Inorganica Chim Acta 2022. [DOI: 10.1016/j.ica.2022.121002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Odongo R, Demiroglu-Zergeroglu A, Çakır T. A systems pharmacology approach based on oncogenic signalling pathways to determine the mechanisms of action of natural products in breast cancer from transcriptome data. BMC Complement Med Ther 2021; 21:181. [PMID: 34193143 PMCID: PMC8244196 DOI: 10.1186/s12906-021-03340-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 06/02/2021] [Indexed: 12/16/2022] Open
Abstract
Background Narrow spectrum of action through limited molecular targets and unforeseen drug-related toxicities have been the main reasons for drug failures at the phase I clinical trials in complex diseases. Most plant-derived compounds with medicinal values possess poly-pharmacologic properties with overall good tolerability, and, thus, are appropriate in the management of complex diseases, especially cancers. However, methodological limitations impede attempts to catalogue targeted processes and infer systemic mechanisms of action. While most of the current understanding of these compounds is based on reductive methods, it is increasingly becoming clear that holistic techniques, leveraging current improvements in omic data collection and bioinformatics methods, are better suited for elucidating their systemic effects. Thus, we developed and implemented an integrative systems biology pipeline to study these compounds and reveal their mechanism of actions on breast cancer cell lines. Methods Transcriptome data from compound-treated breast cancer cell lines, representing triple negative (TN), luminal A (ER+) and HER2+ tumour types, were mapped on human protein interactome to construct targeted subnetworks. The subnetworks were analysed for enriched oncogenic signalling pathways. Pathway redundancy was reduced by constructing pathway-pathway interaction networks, and the sets of overlapping genes were subsequently used to infer pathway crosstalk. The resulting filtered pathways were mapped on oncogenesis processes to evaluate their anti-carcinogenic effectiveness, and thus putative mechanisms of action. Results The signalling pathways regulated by Actein, Withaferin A, Indole-3-Carbinol and Compound Kushen, which are extensively researched compounds, were shown to be projected on a set of oncogenesis processes at the transcriptomic level in different breast cancer subtypes. The enrichment of well-known tumour driving genes indicate that these compounds indirectly dysregulate cancer driving pathways in the subnetworks. Conclusion The proposed framework infers the mechanisms of action of potential drug candidates from their enriched protein interaction subnetworks and oncogenic signalling pathways. It also provides a systematic approach for evaluating such compounds in polygenic complex diseases. In addition, the plant-based compounds used here show poly-pharmacologic mechanism of action by targeting subnetworks enriched with cancer driving genes. This network perspective supports the need for a systemic drug-target evaluation for lead compounds prior to efficacy experiments. Supplementary Information The online version contains supplementary material available at 10.1186/s12906-021-03340-z.
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Affiliation(s)
- Regan Odongo
- Department of Bioengineering, Gebze Technical University, Gebze, Kocaeli, Turkey.,Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, Kocaeli, Turkey
| | | | - Tunahan Çakır
- Department of Bioengineering, Gebze Technical University, Gebze, Kocaeli, Turkey.
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Demiroglu-Zergeroglu A, Turhal G, Topal H, Ceylan H, Donbaloglu F, Karadeniz Cerit K, Odongo RR. Anticarcinogenic effects of halofuginone on lung-derived cancer cells. Cell Biol Int 2020; 44:1934-1944. [PMID: 32437065 DOI: 10.1002/cbin.11399] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/04/2020] [Accepted: 05/18/2020] [Indexed: 02/06/2023]
Abstract
Malignant mesothelioma is a rare but aggressive form of malignancy, which is difficult to diagnose and is resistant to current chemotherapeutic treatment options. Molecular techniques have been used to investigate the mechanisms of action and the beneficial therapeutic effects of halofuginone (HF) in several cancers but not malignant mesotheliomas. In this study, the antiproliferative and apoptotic effects of HF were investigated through its ability to deregulate EGFR downstream signalling cascade proteins in the pathologically aggressive malignant mesothelioma and non-small-cell lung cancer cells. We showed that administration of HF at nanomolar concentrations induced a dose-dependent reduction in the viability of cancer cells, made cell cycle arrest, inhibited proliferation of cancer cells via STAT3 and ERK1/2 pathways and triggered the apoptotic cascade via p38MAPK. We demonstrated that the apoptotic cell death mechanism was mediated by enhanced activation of caspase-3 and concomitant PARP cleavage, downregulation of Bcl-2 and upregulation of Bax in both malignant mesothelioma and lung cancer cells. In particular, we demonstrated that cancer cells were more sensitive to HF treatment than normal mesothelial cells. Taken together, this study suggests that HF exerts its anticancer effects in lung-derived cancers by targeting signal transduction pathways mainly through deregulation of ERK1/2, STAT3 and p38MAPK to reduce cancer cell viability, induce cell cycle arrest and apoptotic cell death. Thus, HF might be considered as a potential agent against malignant mesothelioma and/or lung cancer cells.
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Affiliation(s)
- Asuman Demiroglu-Zergeroglu
- Department of Molecular Biology & Genetics, Faculty of Science, Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Gulseren Turhal
- Department of Molecular Biology & Genetics, Faculty of Science, Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Halime Topal
- Department of Molecular Biology & Genetics, Faculty of Science, Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Hurmuz Ceylan
- Department of Molecular Biology & Genetics, Faculty of Science, Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Fadime Donbaloglu
- Department of Molecular Biology & Genetics, Faculty of Science, Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Kivilcim Karadeniz Cerit
- Department of Pediatric Surgery, School of Medicine, Marmara University, Pendik, Istanbul, Turkey
| | - Ronald R Odongo
- Department of Molecular Biology & Genetics, Faculty of Science, Gebze Technical University, Gebze, Kocaeli, Turkey
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Yenilmez Çiftçi G, Tanrıverdi Eçik E, Goler O, Yuksel F, Duygulu E, Donbaloglu F, Turhal G, Demiroglu-Zergeroglu A. Thiazole substituted dispiromonoansa and monospiro cyclotriphosphazenes: Design, synthesis and biological activity. Inorganica Chim Acta 2019. [DOI: 10.1016/j.ica.2019.119158] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Demiroglu-Zergeroglu A, Ayvali N, Turhal G, Ceylan H, Nacak Baytas S. Investigation of potent anticarcinogenic activity of 1, 3-diarylpyrazole acrylamide derivatives in vitro. J Pharm Pharmacol 2018; 70:1619-1629. [PMID: 30198567 DOI: 10.1111/jphp.13012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 08/10/2018] [Indexed: 02/06/2023]
Abstract
OBJECTIVES Pyrazole derivatives are pharmacologically powerful agents pointing at new horizons in the development of anticancer therapies. In this study, anticarcinogenic potential of a series of pyrazole-acrylamide derivatives has been investigated in mesothelial, malignant mesothelioma and lung cancer cell lines. METHODS The effect of compounds on the viability of cells and the distribution of cell cycle were examined through MTS assay and PI staining, respectively. Apoptosis was evaluated via caspase-3 enzymatic assay and AO/EB staining. Proteins involved in proliferation, survival and apoptosis were analysed by immunoblotting. KEY FINDINGS Twelve compounds of 21 (4a-4v) reduced the viability of cells but, only the subset of five (4f, 4i, 4j, 4k and 4v) induced the caspase-3 activity. Among five, only one compound (4k) significantly suppressed phosphorylation and expression of ERK1/2 and AKT proteins in 24 h. Exposing cancer cells to successive concentrations of 4k gave rise to dose- and time-dependent G2/M phase arrest and apoptosis. CONCLUSIONS 4k has revealed its potent antiproliferative activity by decreasing viability and inhibiting proliferation and survival signals of cancer cells. Moreover, 4k has exposed cytostatic and apoptotic effect especially, on cancer cells. Therefore, it may be necessary to examine the biological actions of 4k in vivo as well.
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Affiliation(s)
| | - Nurettin Ayvali
- Department of Molecular Biology & Genetics, Gebze Technical University, Gebze/Kocaeli, Turkey
| | - Gulseren Turhal
- Department of Molecular Biology & Genetics, Gebze Technical University, Gebze/Kocaeli, Turkey
| | - Hurmuz Ceylan
- Department of Molecular Biology & Genetics, Gebze Technical University, Gebze/Kocaeli, Turkey
| | - Sultan Nacak Baytas
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Gazi University, Ankara, Turkey
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Demiroglu-Zergeroglu A, Candemir G, Turhanlar E, Sagir F, Ayvali N. EGFR-dependent signalling reduced and p38 dependent apoptosis required by Gallic acid in Malignant Mesothelioma cells. Biomed Pharmacother 2016; 84:2000-2007. [PMID: 27847212 DOI: 10.1016/j.biopha.2016.11.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 11/02/2016] [Accepted: 11/02/2016] [Indexed: 12/25/2022] Open
Abstract
The unrestrained EGFR signalling contributes to malignant phenotype in a number of cancers including Malignant Mesotheliomas. Present study was designed to evaluate EGFR-dependent anti-proliferative and apoptotic effects of Gallic acid in transformed Mesothelial (MeT-5A) and Malignant Mesothelioma (SPC212) cells. Gallic acid reduced the viability of Malignant Mesothelioma cells in a concentration and time-dependent manner. However, viability of mesothelial cells reduced only at high concentration and longer time periods. Gallic acid restrained the activation of EGFR, ERK1/2 and AKT proteins and down regulated expression of Cyclin D and Bcl-2 genes, but upregulated the expression of p21 gene in EGF-induced SPC212 cells. GA-induced transitory G1 arrest and triggered mitochondrial and death receptor mediated apoptosis, which requires p38MAPK activation. The data provided here indicate that GA is able to inhibit EGFR dependent proliferation and survival signals and induces p38 pathway dependent apoptosis in Malignant Mesothelioma cells. On the basis of these experimental findings it is worthwhile to investigate further the biological activity of Gallic acid on other Mesothelioma cell lines harbouring aberrant EGFR signals.
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Affiliation(s)
| | - Gulsife Candemir
- Gebze Technical University, Department of Molecular Biology & Genetics, Gebze/Kocaeli, Turkey
| | - Ebru Turhanlar
- Gebze Technical University, Department of Molecular Biology & Genetics, Gebze/Kocaeli, Turkey
| | - Fatma Sagir
- Gebze Technical University, Department of Molecular Biology & Genetics, Gebze/Kocaeli, Turkey
| | - Nurettin Ayvali
- Gebze Technical University, Department of Molecular Biology & Genetics, Gebze/Kocaeli, Turkey
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Zhang X, De Milito A, Demiroglu-Zergeroglu A, Gullbo J, D'Arcy P, Linder S. Eradicating Quiescent Tumor Cells by Targeting Mitochondrial Bioenergetics. Trends Cancer 2016; 2:657-663. [PMID: 28741504 DOI: 10.1016/j.trecan.2016.10.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 10/06/2016] [Accepted: 10/12/2016] [Indexed: 01/08/2023]
Abstract
The presence of quiescent cell populations in solid tumors represents a major challenge for disease eradication. Such cells are generally present in poorly vascularized tumor areas, show limited sensitivity to traditional chemotherapeutical drugs, and tend to resume proliferation, resulting in tumor reseeding and growth. There is growing recognition of the importance of developing therapies that target these quiescent cell populations to achieve long-lasting remission. Recent studies have shown that the combination of hypoxia and reduced nutrient availability in poorly vascularized areas results in limited tumor metabolic plasticity coupled with an increased sensitivity to perturbations in mitochondrial flux. Targeting of mitochondrial bioenergetics in these quiescent cell tumor populations may enable tumor eradication and improve the prognosis of patients with cancer.
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Affiliation(s)
- Xiaonan Zhang
- Department of Medical and Health Sciences, Linköping University, SE-581 83 Linköping, Sweden; Department of Oncology-Pathology, Karolinska Institute, SE-171 76 Stockholm, Sweden
| | - Angelo De Milito
- Department of Oncology-Pathology, Karolinska Institute, SE-171 76 Stockholm, Sweden
| | | | - Joachim Gullbo
- Department of Immunology, Genetics and Pathology, Section of Oncology, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Padraig D'Arcy
- Department of Medical and Health Sciences, Linköping University, SE-581 83 Linköping, Sweden
| | - Stig Linder
- Department of Medical and Health Sciences, Linköping University, SE-581 83 Linköping, Sweden; Department of Oncology-Pathology, Karolinska Institute, SE-171 76 Stockholm, Sweden.
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Demiroglu-Zergeroglu A, Pelin B, Attar R, Karatekelioglu E, Attar E, Bulun S. Sodium butyrate (NaBu) decreases proliferation of stromal cells derived from endometriosis and Ishikawa cells in culture. Fertil Steril 2007. [DOI: 10.1016/j.fertnstert.2007.07.706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Demiroglu-Zergeroglu A, Balcik P, Attar R, Basara B, Cemal H, Attar E. Sodium butyrate (NaBu) inhibits proliferation of CO25 myoblast cells bearing a human steroid-inducible N-ras oncogene. Fertil Steril 2007. [DOI: 10.1016/j.fertnstert.2007.07.742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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