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Poh QH, Rai A, Cross J, Greening DW. HB-EGF-loaded nanovesicles enhance trophectodermal spheroid attachment and invasion. Proteomics 2024; 24:e2200145. [PMID: 38214697 DOI: 10.1002/pmic.202200145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 01/13/2024]
Abstract
The ability of trophectodermal cells (outer layer of the embryo) to attach to the endometrial cells and subsequently invade the underlying matrix are critical stages of embryo implantation during successful pregnancy establishment. Extracellular vesicles (EVs) have been implicated in embryo-maternal crosstalk, capable of reprogramming endometrial cells towards a pro-implantation signature and phenotype. However, challenges associated with EV yield and direct loading of biomolecules limit their therapeutic potential. We have previously established generation of cell-derived nanovesicles (NVs) from human trophectodermal cells (hTSCs) and their capacity to reprogram endometrial cells to enhance adhesion and blastocyst outgrowth. Here, we employed a rapid NV loading strategy to encapsulate potent implantation molecules such as HB-EGF (NVHBEGF). We show these loaded NVs elicit EGFR-mediated effects in recipient endometrial cells, activating kinase phosphorylation sites that modulate their activity (AKT S124/129, MAPK1 T185/Y187), and downstream signalling pathways and processes (AKT signal transduction, GTPase activity). Importantly, they enhanced target cell attachment and invasion. The phosphoproteomics and proteomics approach highlight NVHBEGF-mediated short-term signalling patterns and long-term reprogramming capabilities on endometrial cells which functionally enhance trophectodermal-endometrial interactions. This proof-of-concept study demonstrates feasibility in enhancing the functional potency of NVs in the context of embryo implantation.
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Affiliation(s)
- Qi Hui Poh
- Molecular Proteomics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, Australia
- Department of Cardiovascular Research, Translation and Implementation, La Trobe University, Melbourne, Victoria, Australia
| | - Alin Rai
- Molecular Proteomics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Department of Cardiovascular Research, Translation and Implementation, La Trobe University, Melbourne, Victoria, Australia
- Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Jonathon Cross
- Molecular Proteomics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - David W Greening
- Molecular Proteomics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Department of Cardiovascular Research, Translation and Implementation, La Trobe University, Melbourne, Victoria, Australia
- Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Baker Department of Cardiometabolic Health, University of Melbourne, Melbourne, Victoria, Australia
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2
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Khojasteh Poor F, Keivan M, Ramazii M, Ghaedrahmati F, Anbiyaiee A, Panahandeh S, Khoshnam SE, Farzaneh M. Mini review: The FDA-approved prescription drugs that target the MAPK signaling pathway in women with breast cancer. Breast Dis 2021; 40:51-62. [PMID: 33896802 DOI: 10.3233/bd-201063] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Breast cancer (BC) is the most common cancer and the prevalent type of malignancy among women. Multiple risk factors, including genetic changes, biological age, dense breast tissue, and obesity are associated with BC. The mitogen-activated protein kinases (MAPK) signaling pathway has a pivotal role in regulating biological functions such as cell proliferation, differentiation, apoptosis, and survival. It has become evident that the MAPK pathway is associated with tumorigenesis and may promote breast cancer development. The MAPK/RAS/RAF cascade is closely associated with breast cancer. RAS signaling can enhance BC cell growth and progression. B-Raf is an important kinase and a potent RAF isoform involved in breast tumor initiation and differentiation. Depending on the reasons for cancer, there are different strategies for treatment of women with BC. Till now, several FDA-approved treatments have been investigated that inhibit the MAPK pathway and reduce metastatic progression in breast cancer. The most common breast cancer drugs that regulate or inhibit the MAPK pathway may include Farnesyltransferase inhibitors (FTIs), Sorafenib, Vemurafenib, PLX8394, Dabrafenib, Ulixertinib, Simvastatin, Alisertib, and Teriflunomide. In this review, we will discuss the roles of the MAPK/RAS/RAF/MEK/ERK pathway in BC and summarize the FDA-approved prescription drugs that target the MAPK signaling pathway in women with BC.
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Affiliation(s)
- Fatemeh Khojasteh Poor
- Department of Obstetrics and Gynecology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Mona Keivan
- Fertility and Infertility Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran.,Fertility, Infertility and Perinatology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mohammad Ramazii
- Kerman University of Medical Sciences, University of Kerman, Kerman, Iran
| | - Farhoodeh Ghaedrahmati
- Department of Immunology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Amir Anbiyaiee
- Department of Surgery, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Samira Panahandeh
- School of Health, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Seyed Esmaeil Khoshnam
- Persian Gulf Physiology Research Center, Medical Basic Sciences Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Maryam Farzaneh
- Fertility, Infertility and Perinatology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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3
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Interactions between Ligand-Bound EGFR and VEGFR2. J Mol Biol 2021; 433:167006. [PMID: 33891904 DOI: 10.1016/j.jmb.2021.167006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/25/2021] [Accepted: 04/15/2021] [Indexed: 11/21/2022]
Abstract
In this work, we put forward the provocative hypothesis that the active, ligand-bound RTK dimers from unrelated subfamilies can associate into heterooligomers with novel signaling properties. This hypothesis is based on a quantitative FRET study that monitors the interactions between EGFR and VEGFR2 in the plasma membrane of live cells in the absence of ligand, in the presence of either EGF or VEGF, and in the presence of both ligands. We show that direct interactions occur between EGFR and VEGFR2 in the absence of ligand and in the presence of the two cognate ligands. However, there are not significant heterointeractions between EGFR and VEGFR2 when only one of the ligands is present. Since RTK dimers and RTK oligomers are believed to signal differently, this finding suggests a novel mechanism for signal diversification.
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4
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Zacarías-Lara OJ, Méndez-Luna D, Martínez-Ruíz G, García-Sanchéz JR, Fragoso-Vázquez MJ, Bello M, Becerra-Martínez E, García-Vázquez JB, Correa-Basurto J. Synthesis and In Vitro Evaluation of Tetrahydroquinoline Derivatives as Antiproliferative Compounds of Breast Cancer via Targeting the GPER. Anticancer Agents Med Chem 2020; 19:760-771. [PMID: 30451119 DOI: 10.2174/1871520618666181119094144] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 07/03/2018] [Accepted: 11/04/2018] [Indexed: 02/06/2023]
Abstract
BACKGROUND Some reports have demonstrated the role of the G Protein-coupled Estrogen Receptor (GPER) in growth and proliferation of breast cancer cells. OBJECTIVE In an effort to develop new therapeutic strategies against breast cancer, we employed an in silico study to explore the binding modes of tetrahydroquinoline 2 and 4 to be compared with the reported ligands G1 and G1PABA. METHODS This study aimed to design and filter ligands by in silico studies determining their Lipinski's rule, toxicity and binding properties with GPER to achieve experimental assays as anti-proliferative compounds of breast cancer cell lines. RESULTS In silico studies suggest as promissory two tetrahydroquinoline 2 and 4 which contain a carboxyl group instead of the acetyl group (as is needed for G1 synthesis), which add low (2) and high hindrance (4) chemical moieties to explore the polar, hydrophobic and hindrance effects. Docking and molecular dynamics simulations of the target compounds were performed with GPER to explore their binding mode and free energy values. In addition, the target small molecules were synthesized and assayed in vitro using breast cancer cells (MCF-7 and MDA-MB-231). Experimental assays showed that compound 2 decreased cell proliferation, showing IC50 values of 50µM and 25µM after 72h of treatment of MCF-7 and MDA-MB-231 cell lines, respectively. Importantly, compound 2 showed a similar inhibitory effect on proliferation as G1 compound in MDA-MB-231 cells, suggesting that both ligands reach the GPER-binding site in a similar way, as was demonstrated through in silico studies. CONCLUSION A concentration-dependent inhibition of cell proliferation occurred with compound 2 in the two cell lines regardless of GPER.
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Affiliation(s)
- Oscar J Zacarías-Lara
- Laboratorio de Diseno y Desarrollo de Nuevos Farmacos e Innovacion Biotecnologica (Laboratory for the Design and Development of New Drugs and Biotechnological Innovation), Escuela Superior de Medicina, Instituto Politecnico Nacional, Plan de San Luis y Diaz Miron, 11340 Mexico, CDMX, Mexico
| | - David Méndez-Luna
- Laboratorio de Diseno y Desarrollo de Nuevos Farmacos e Innovacion Biotecnologica (Laboratory for the Design and Development of New Drugs and Biotechnological Innovation), Escuela Superior de Medicina, Instituto Politecnico Nacional, Plan de San Luis y Diaz Miron, 11340 Mexico, CDMX, Mexico
| | - Gustavo Martínez-Ruíz
- Unidad de Investigacion en Enfermedades Oncologicas, Hospital Infantil de Mexico, Federico Gomez, Mexico
| | - José R García-Sanchéz
- Laboratorio de Oncologia Molecular y Estres Oxidativo, Seccion de Estudios de Posgrado e Investigacion, Escuela Superior de Medicina, Instituto Politecnico Nacional, Plan de San Luis y Diaz Miron, 11340 Mexico, CDMX, Mexico
| | - Manuel J Fragoso-Vázquez
- Laboratorio de Diseno y Desarrollo de Nuevos Farmacos e Innovacion Biotecnologica (Laboratory for the Design and Development of New Drugs and Biotechnological Innovation), Escuela Superior de Medicina, Instituto Politecnico Nacional, Plan de San Luis y Diaz Miron, 11340 Mexico, CDMX, Mexico.,Departamento de Química Orgánica, Escuela Nacional de Ciencias, Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala, México, CDMX., 11340 México
| | - Martiniano Bello
- Laboratorio de Diseno y Desarrollo de Nuevos Farmacos e Innovacion Biotecnologica (Laboratory for the Design and Development of New Drugs and Biotechnological Innovation), Escuela Superior de Medicina, Instituto Politecnico Nacional, Plan de San Luis y Diaz Miron, 11340 Mexico, CDMX, Mexico
| | - Elvia Becerra-Martínez
- Laboratorio de RMN, Centro de Nanociencias y Micro y Nanotecnologias, Instituto Politecnico Nacional, Calle Luis Enrique Erro s/n, Unidad Profesional Adolfo Lopez Mateos, Gustavo A, Madero, 07738 Mexico, Ciudad de Mexico, Mexico
| | - Juan B García-Vázquez
- Laboratorio de Diseno y Desarrollo de Nuevos Farmacos e Innovacion Biotecnologica (Laboratory for the Design and Development of New Drugs and Biotechnological Innovation), Escuela Superior de Medicina, Instituto Politecnico Nacional, Plan de San Luis y Diaz Miron, 11340 Mexico, CDMX, Mexico
| | - José Correa-Basurto
- Laboratorio de Diseno y Desarrollo de Nuevos Farmacos e Innovacion Biotecnologica (Laboratory for the Design and Development of New Drugs and Biotechnological Innovation), Escuela Superior de Medicina, Instituto Politecnico Nacional, Plan de San Luis y Diaz Miron, 11340 Mexico, CDMX, Mexico
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5
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Braicu C, Buse M, Busuioc C, Drula R, Gulei D, Raduly L, Rusu A, Irimie A, Atanasov AG, Slaby O, Ionescu C, Berindan-Neagoe I. A Comprehensive Review on MAPK: A Promising Therapeutic Target in Cancer. Cancers (Basel) 2019; 11:cancers11101618. [PMID: 31652660 PMCID: PMC6827047 DOI: 10.3390/cancers11101618] [Citation(s) in RCA: 476] [Impact Index Per Article: 95.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 10/13/2019] [Accepted: 10/16/2019] [Indexed: 02/07/2023] Open
Abstract
The mitogen-activated protein kinase (MAPK) pathway is an important bridge in the switch from extracellular signals to intracellular responses. Alterations of signaling cascades are found in various diseases, including cancer, as a result of genetic and epigenetic changes. Numerous studies focused on both the homeostatic and the pathologic conduct of MAPK signaling; however, there is still much to be deciphered in terms of regulation and action models in both preclinical and clinical research. MAPK has implications in the response to cancer therapy, particularly the activation of the compensatory pathways in response to experimental MAPK inhibition. The present paper discusses new insights into MAPK as a complex cell signaling pathway with roles in the sustenance of cellular normal conduit, response to cancer therapy, and activation of compensatory pathways. Unfortunately, most MAPK inhibitors trigger resistance due to the activation of compensatory feed-back loops in tumor cells and tumor microenvironment components. Therefore, novel combinatorial therapies have to be implemented for cancer management in order to restrict the possibility of alternative pathway activation, as a perspective for developing novel therapies based on integration in translational studies.
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Affiliation(s)
- Cornelia Braicu
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Mihail Buse
- MEDFUTURE-Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Constantin Busuioc
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Rares Drula
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Diana Gulei
- MEDFUTURE-Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Lajos Raduly
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | | | - Alexandru Irimie
- Department of Surgery, The Oncology Institute "Prof. Dr. Ion Chiricuta", 40015 Cluj-Napoca, Romania.
- Department of Surgical Oncology and Gynecological Oncology, Iuliu Hatieganu University of Medicine and Pharmacy, 40015 Cluj-Napoca, Romania.
| | - Atanas G Atanasov
- Department of Pharmacognosy, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria.
- Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, Jastrzebiec, 05-552 Magdalenka, Poland.
- Institute of Neurobiology, Bulgarian Academy of Sciences, 23 Acad. G. Bonchev str., 1113 Sofia, Bulgaria.
| | - Ondrej Slaby
- Central European Institute of Technology, Masaryk University, 601 77 Brno, Czech Republic.
- Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute, 601 77 Brno, Czech Republic.
| | - Calin Ionescu
- th Surgical Department, Municipal Hospital, 400139, Cluj-Napoca, Romania.
- Department of Surgery, Iuliu Hatieganu University of Medicine and Pharmacy, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
| | - Ioana Berindan-Neagoe
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
- MEDFUTURE-Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 23 Marinescu Street, 40015 Cluj-Napoca, Romania.
- Department of Functional Genomics and Experimental Pathology, The Oncology Institute Prof. Dr. Ion Chiricuta, Republicii 34 Street, 400015 Cluj-Napoca, Romania.
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6
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Lill D, Rukhlenko OS, Mc Elwee AJ, Kashdan E, Timmer J, Kholodenko BN. Mapping connections in signaling networks with ambiguous modularity. NPJ Syst Biol Appl 2019; 5:19. [PMID: 31149348 PMCID: PMC6533310 DOI: 10.1038/s41540-019-0096-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 04/24/2019] [Indexed: 12/16/2022] Open
Abstract
Modular Response Analysis (MRA) is a suite of methods that under certain assumptions permits the precise reconstruction of both the directions and strengths of connections between network modules from network responses to perturbations. Standard MRA assumes that modules are insulated, thereby neglecting the existence of inter-modular protein complexes. Such complexes sequester proteins from different modules and propagate perturbations to the protein abundance of a downstream module retroactively to an upstream module. MRA-based network reconstruction detects retroactive, sequestration-induced connections when an enzyme from one module is substantially sequestered by its substrate that belongs to a different module. Moreover, inferred networks may surprisingly depend on the choice of protein abundances that are experimentally perturbed, and also some inferred connections might be false. Here, we extend MRA by introducing a combined computational and experimental approach, which allows for a computational restoration of modular insulation, unmistakable network reconstruction and discrimination between solely regulatory and sequestration-induced connections for a range of signaling pathways. Although not universal, our approach extends MRA methods to signaling networks with retroactive interactions between modules arising from enzyme sequestration effects.
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Affiliation(s)
- Daniel Lill
- Institute of Physics, University of Freiburg, Freiburg, Germany
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
| | | | | | - Eugene Kashdan
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
- School of Mathematics and Statistics, University College Dublin, Dublin, Ireland
| | - Jens Timmer
- Institute of Physics, University of Freiburg, Freiburg, Germany
- BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany
| | - Boris N. Kholodenko
- Systems Biology Ireland, University College Dublin, Dublin, Ireland
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin, Ireland
- School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT USA
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7
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Gao S, Wang J, Tian S, Luo J. miR‑9 depletion suppresses the proliferation of osteosarcoma cells by targeting p16. Int J Oncol 2019; 54:1921-1932. [PMID: 31081054 PMCID: PMC6521929 DOI: 10.3892/ijo.2019.4783] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 10/13/2019] [Indexed: 12/21/2022] Open
Abstract
Osteosarcoma (OS) is a common primary malignancy in adolescents and children. MicroRNAs (miRNAs or miRs) can regulate the progression of OS. Herein, we explored the target genes and effects of miR-9 in OS. Cell growth, colony formation and cell cycle were respectively examined using a cell counting kit-8 (CCK-8), crystal violet staining and flow cytometry. The target gene of miR-9 was predicted according to the MicroRNA.org website. Luciferase activity was examined using a dual luciferase reporter gene assay kit. The corresponding factors levels were analyzed by carrying out reverse transcription-quantitative PCR (RT-qPCR) and western blot analysis. A mouse model of OS was also established and the volume and weight of the tumors of the mice with OS were measured. The levels of p16 in the mice with OS were detected by immunohistochemistry (IHC). The data revealed a high expression of miR-9 and a low expression of p16 in the OS tissue. p16 was found to be the target gene for miR-9 in OS. miR-9 depletion decreased the proliferation and colony formation of Saos-2 cells by arresting the cells at the G1 phase, accompanied by the downregulation of cyclin A, cyclin D1 and c-Myc expression levels. Moreover, miR-9 depletion inhibited the phosphorylation of p38, c-Jun N-terminal kinase (JNK) and extracellular signal-regulated kinase (ERK). In vivo, miR-9 depletion decreased the tumor volume and weight and increased p16 expression in the mouse tumor tissues. Nevertheless, p16 silencing reversed the suppressive effects of miR-9 inhibitors on OS cells. On the whole, the findings of this study substantiate that miR-9 depletion suppresses cell proliferation by targeting p16 in OS and by mediating the activation of the ERK/p38/JNK pathway.
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Affiliation(s)
- Song Gao
- Department of Orthopedics, Henan Provincial People's Hospital, Zhengzhou, Henan 450003, P.R. China
| | - Jianchao Wang
- Department of Orthopedics, Henan Provincial People's Hospital, Zhengzhou, Henan 450003, P.R. China
| | - Shujian Tian
- Department of Orthopedics, Henan Provincial People's Hospital, Zhengzhou, Henan 450003, P.R. China
| | - Jianping Luo
- Department of Orthopedics, Henan Provincial People's Hospital, Zhengzhou, Henan 450003, P.R. China
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8
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Thomaseth C, Fey D, Santra T, Rukhlenko OS, Radde NE, Kholodenko BN. Impact of measurement noise, experimental design, and estimation methods on Modular Response Analysis based network reconstruction. Sci Rep 2018; 8:16217. [PMID: 30385767 PMCID: PMC6212399 DOI: 10.1038/s41598-018-34353-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 10/16/2018] [Indexed: 11/16/2022] Open
Abstract
Modular Response Analysis (MRA) is a method to reconstruct signalling networks from steady-state perturbation data which has frequently been used in different settings. Since these data are usually noisy due to multi-step measurement procedures and biological variability, it is important to investigate the effect of this noise onto network reconstruction. Here we present a systematic study to investigate propagation of noise from concentration measurements to network structures. Therefore, we design an in silico study of the MAPK and the p53 signalling pathways with realistic noise settings. We make use of statistical concepts and measures to evaluate accuracy and precision of individual inferred interactions and resulting network structures. Our results allow to derive clear recommendations to optimize the performance of MRA based network reconstruction: First, large perturbations are favorable in terms of accuracy even for models with non-linear steady-state response curves. Second, a single control measurement for different perturbation experiments seems to be sufficient for network reconstruction, and third, we recommend to execute the MRA workflow with the mean of different replicates for concentration measurements rather than using computationally more involved regression strategies.
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Affiliation(s)
- Caterina Thomaseth
- University of Stuttgart, Institute for Systems Theory and Automatic Control, Stuttgart, Germany
| | - Dirk Fey
- University College Dublin, Systems Biology Ireland, UCD School of Medicine, Dublin, Ireland
| | - Tapesh Santra
- University College Dublin, Systems Biology Ireland, UCD School of Medicine, Dublin, Ireland
| | - Oleksii S Rukhlenko
- University College Dublin, Systems Biology Ireland, UCD School of Medicine, Dublin, Ireland
| | - Nicole E Radde
- University of Stuttgart, Institute for Systems Theory and Automatic Control, Stuttgart, Germany.
| | - Boris N Kholodenko
- University College Dublin, Systems Biology Ireland, UCD School of Medicine, Dublin, Ireland.,Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
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9
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Santra T, Rukhlenko O, Zhernovkov V, Kholodenko BN. Reconstructing static and dynamic models of signaling pathways using Modular Response Analysis. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.coisb.2018.02.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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10
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Abstract
STAT3 plays a central role in oncogenesis by mediating cell survival, growth, and differentiation. It is constitutively activated in breast cancer. We investigated the role of STAT3 in tumor development by knocking down STAT3 levels in MDA-MB-231 triple negative breast cancer cells using short hairpin RNA. The tumor forming potential of these STAT3-depleted cells was assessed by xenografts in immunocompromised NOD SCID mice. Contrary to its accepted tumor promoting role, we found STAT3 to be a negative regulator of growth in MDA-MB-231- derived tumors. Although similar observations have been made in thyroid carcinoma and lung adenocarcinoma xenograft studies, our novel results showed for the first time that the role of STAT3 in promoting tumorigenesis may be context-specific, and that STAT3 may actually be a negative regulator of certain breast-cancer types. Studies to identify the mechanisms of STAT3's negative regulatory role may be useful in developing STAT3-based therapeutics.
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Affiliation(s)
- Kasturi Banerjee
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA, USA
| | - Cindy Pru
- Department of Animal Sciences, Center for Reproductive Biology, Washington State University, Pullman, WA, USA
| | - James K Pru
- Department of Animal Sciences, Center for Reproductive Biology, Washington State University, Pullman, WA, USA
| | - Haluk Resat
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA, USA
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