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Lazebnik T, Bunimovich-Mendrazitsky S. Predicting lung cancer's metastats' locations using bioclinical model. Front Med (Lausanne) 2024; 11:1388702. [PMID: 38846148 PMCID: PMC11153684 DOI: 10.3389/fmed.2024.1388702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 05/13/2024] [Indexed: 06/09/2024] Open
Abstract
Background Lung cancer is a global leading cause of cancer-related deaths, and metastasis profoundly influences treatment outcomes. The limitations of conventional imaging in detecting small metastases highlight the crucial need for advanced diagnostic approaches. Methods This study developed a bioclinical model using three-dimensional CT scans to predict the spatial spread of lung cancer metastasis. Utilizing a three-layer biological model, we identified regions with a high probability of metastasis colonization and validated the model on real-world data from 10 patients. Findings The validated bioclinical model demonstrated a promising 74% accuracy in predicting metastasis locations, showcasing the potential of integrating biophysical and machine learning models. These findings underscore the significance of a more comprehensive approach to lung cancer diagnosis and treatment. Interpretation This study's integration of biophysical and machine learning models contributes to advancing lung cancer diagnosis and treatment, providing nuanced insights for informed decision-making.
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Affiliation(s)
- Teddy Lazebnik
- Department of Cancer Biology, Cancer Institute, University College London, London, United Kingdom
- Department of Mathematics, Ariel University, Ariel, Israel
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2
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Dogra P, Shinglot V, Ruiz-Ramírez J, Cave J, Butner JD, Schiavone C, Duda DG, Kaseb AO, Chung C, Koay EJ, Cristini V, Ozpolat B, Calin GA, Wang Z. Translational modeling-based evidence for enhanced efficacy of standard-of-care drugs in combination with anti-microRNA-155 in non-small-cell lung cancer. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.14.24304306. [PMID: 38559070 PMCID: PMC10980136 DOI: 10.1101/2024.03.14.24304306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Elevated microRNA-155 (miR-155) expression in non-small-cell lung cancer (NSCLC) promotes cisplatin resistance and negatively impacts treatment outcomes. However, miR-155 can also boost anti-tumor immunity by suppressing PD-L1 expression. We developed a multiscale mechanistic model, calibrated with in vivo data and then extrapolated to humans, to investigate the therapeutic effects of nanoparticle-delivered anti-miR-155 in NSCLC, alone or in combination with standard-of-care drugs. Model simulations and analyses of the clinical scenario revealed that monotherapy with anti-miR-155 at a dose of 2.5 mg/kg administered once every three weeks has substantial anti-cancer activity. It led to a median progression-free survival (PFS) of 6.7 months, which compared favorably to cisplatin and immune checkpoint inhibitors. Further, we explored the combinations of anti-miR-155 with standard-of-care drugs, and found strongly synergistic two- and three-drug combinations. A three-drug combination of anti-miR-155, cisplatin, and pembrolizumab resulted in a median PFS of 13.1 months, while a two-drug combination of anti-miR-155 and cisplatin resulted in a median PFS of 11.3 months, which emerged as a more practical option due to its simple design and cost-effectiveness. Our analyses also provided valuable insights into unfavorable dose ratios for drug combinations, highlighting the need for optimizing dose regimen to prevent antagonistic effects. Thus, this work bridges the gap between preclinical development and clinical translation of anti-miR-155 and unravels the potential of anti-miR-155 combination therapies in NSCLC.
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Affiliation(s)
- Prashant Dogra
- Mathematics in Medicine Program, Department of Medicine, Houston Methodist Research Institute, Houston, TX, USA
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA
| | - Vrushaly Shinglot
- Mathematics in Medicine Program, Department of Medicine, Houston Methodist Research Institute, Houston, TX, USA
| | | | - Joseph Cave
- Mathematics in Medicine Program, Department of Medicine, Houston Methodist Research Institute, Houston, TX, USA
- Physiology, Biophysics, and Systems Biology Program, Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Joseph D. Butner
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Carmine Schiavone
- Mathematics in Medicine Program, Department of Medicine, Houston Methodist Research Institute, Houston, TX, USA
- Department of Chemical, Materials and Industrial Production Engineering, University of Naples Federico II, Naples, Italy
| | - Dan G. Duda
- Edwin. L. Steele Laboratories for Tumor Biology, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Ahmed O. Kaseb
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Caroline Chung
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Eugene J. Koay
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Vittorio Cristini
- Mathematics in Medicine Program, Department of Medicine, Houston Methodist Research Institute, Houston, TX, USA
- Physiology, Biophysics, and Systems Biology Program, Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA
- Neal Cancer Center, Houston Methodist Research Institute, Houston, TX, USA
- Department of Imaging Physics, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Bulent Ozpolat
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX, USA
| | - George A. Calin
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zhihui Wang
- Mathematics in Medicine Program, Department of Medicine, Houston Methodist Research Institute, Houston, TX, USA
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA
- Neal Cancer Center, Houston Methodist Research Institute, Houston, TX, USA
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3
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Canciello A, Cerveró-Varona A, Peserico A, Mauro A, Russo V, Morrione A, Giordano A, Barboni B. "In medio stat virtus": Insights into hybrid E/M phenotype attitudes. Front Cell Dev Biol 2022; 10:1038841. [PMID: 36467417 PMCID: PMC9715750 DOI: 10.3389/fcell.2022.1038841] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 11/02/2022] [Indexed: 08/22/2023] Open
Abstract
Epithelial-mesenchymal plasticity (EMP) refers to the ability of cells to dynamically interconvert between epithelial (E) and mesenchymal (M) phenotypes, thus generating an array of hybrid E/M intermediates with mixed E and M features. Recent findings have demonstrated how these hybrid E/M rather than fully M cells play key roles in most of physiological and pathological processes involving EMT. To this regard, the onset of hybrid E/M state coincides with the highest stemness gene expression and is involved in differentiation of either normal and cancer stem cells. Moreover, hybrid E/M cells are responsible for wound healing and create a favorable immunosuppressive environment for tissue regeneration. Nevertheless, hybrid state is responsible of metastatic process and of the increasing of survival, apoptosis and therapy resistance in cancer cells. The present review aims to describe the main features and the emerging concepts regulating EMP and the formation of E/M hybrid intermediates by describing differences and similarities between cancer and normal hybrid stem cells. In particular, the comprehension of hybrid E/M cells biology will surely advance our understanding of their features and how they could be exploited to improve tissue regeneration and repair.
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Affiliation(s)
- Angelo Canciello
- Faculty of Bioscience and Technology for Food Agriculture and Environment, University of Teramo, Teramo, Italy
- Department of Biology, College of Science and Technology, Temple University, Philadelphia, PA, United States
| | - Adrián Cerveró-Varona
- Faculty of Bioscience and Technology for Food Agriculture and Environment, University of Teramo, Teramo, Italy
| | - Alessia Peserico
- Faculty of Bioscience and Technology for Food Agriculture and Environment, University of Teramo, Teramo, Italy
| | - Annunziata Mauro
- Faculty of Bioscience and Technology for Food Agriculture and Environment, University of Teramo, Teramo, Italy
| | - Valentina Russo
- Faculty of Bioscience and Technology for Food Agriculture and Environment, University of Teramo, Teramo, Italy
| | - Andrea Morrione
- Department of Biology, College of Science and Technology, Temple University, Philadelphia, PA, United States
| | - Antonio Giordano
- Department of Biology, College of Science and Technology, Temple University, Philadelphia, PA, United States
- Sbarro Health Research Organization (SHRO), Philadelphia, PA, United States
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Barbara Barboni
- Faculty of Bioscience and Technology for Food Agriculture and Environment, University of Teramo, Teramo, Italy
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4
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Dogra P, Ramírez JR, Butner JD, Peláez MJ, Chung C, Hooda-Nehra A, Pasqualini R, Arap W, Cristini V, Calin GA, Ozpolat B, Wang Z. Translational Modeling Identifies Synergy between Nanoparticle-Delivered miRNA-22 and Standard-of-Care Drugs in Triple-Negative Breast Cancer. Pharm Res 2022; 39:511-528. [PMID: 35294699 PMCID: PMC8986735 DOI: 10.1007/s11095-022-03176-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 01/21/2022] [Indexed: 12/29/2022]
Abstract
Purpose Downregulation of miRNA-22 in triple-negative breast cancer (TNBC) is associated with upregulation of eukaryotic elongation 2 factor kinase (eEF2K) protein, which regulates tumor growth, chemoresistance, and tumor immunosurveillance. Moreover, exogenous administration of miRNA-22, loaded in nanoparticles to prevent degradation and improve tumor delivery (termed miRNA-22 nanotherapy), to suppress eEF2K production has shown potential as an investigational therapeutic agent in vivo. Methods To evaluate the translational potential of miRNA-22 nanotherapy, we developed a multiscale mechanistic model, calibrated to published in vivo data and extrapolated to the human scale, to describe and quantify the pharmacokinetics and pharmacodynamics of miRNA-22 in virtual patient populations. Results Our analysis revealed the dose-response relationship, suggested optimal treatment frequency for miRNA-22 nanotherapy, and highlighted key determinants of therapy response, from which combination with immune checkpoint inhibitors was identified as a candidate strategy for improving treatment outcomes. More importantly, drug synergy was identified between miRNA-22 and standard-of-care drugs against TNBC, providing a basis for rational therapeutic combinations for improved response Conclusions The present study highlights the translational potential of miRNA-22 nanotherapy for TNBC in combination with standard-of-care drugs. Supplementary Information The online version contains supplementary material available at 10.1007/s11095-022-03176-3.
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Affiliation(s)
- Prashant Dogra
- Mathematics in Medicine Program, Houston Methodist Research Institute, Houston, Texas, 77030, USA
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, 10065, USA
| | - Javier Ruiz Ramírez
- Mathematics in Medicine Program, Houston Methodist Research Institute, Houston, Texas, 77030, USA
| | - Joseph D Butner
- Mathematics in Medicine Program, Houston Methodist Research Institute, Houston, Texas, 77030, USA
| | - Maria J Peláez
- Mathematics in Medicine Program, Houston Methodist Research Institute, Houston, Texas, 77030, USA
| | - Caroline Chung
- Department of Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, 77030, USA
| | - Anupama Hooda-Nehra
- Rutgers Cancer Institute of New Jersey, Newark, New Jersey, 07101, USA
- Department of Medicine, Division of Hematology/Oncology, Rutgers New Jersey Medical School, Newark, New Jersey, 07103, USA
| | - Renata Pasqualini
- Rutgers Cancer Institute of New Jersey, Newark, New Jersey, 07101, USA
- Department of Radiation Oncology, Division of Cancer Biology, Rutgers New Jersey Medical School, Newark, New Jersey, 07103, USA
| | - Wadih Arap
- Rutgers Cancer Institute of New Jersey, Newark, New Jersey, 07101, USA
- Department of Medicine, Division of Hematology/Oncology, Rutgers New Jersey Medical School, Newark, New Jersey, 07103, USA
| | - Vittorio Cristini
- Mathematics in Medicine Program, Houston Methodist Research Institute, Houston, Texas, 77030, USA
- Department of Imaging Physics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, 77230, USA
- Physiology, Biophysics, and Systems Biology Program, Graduate School of Medical Sciences, Weill Cornell Medicine, New York, New York, 10065, USA
| | - George A Calin
- Department of Translational Molecular Pathology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, 77030, USA
| | - Bulent Ozpolat
- Department of Experimental Therapeutics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas, 77030, USA
| | - Zhihui Wang
- Mathematics in Medicine Program, Houston Methodist Research Institute, Houston, Texas, 77030, USA.
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, 10065, USA.
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Li C, Chen L, Song W, Peng B, Zhu J, Fang L. DICER activates autophagy and promotes cisplatin resistance in non-small cell lung cancer by binding with let-7i-5p. Acta Histochem 2021; 123:151788. [PMID: 34543777 DOI: 10.1016/j.acthis.2021.151788] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 08/24/2021] [Accepted: 09/03/2021] [Indexed: 02/08/2023]
Abstract
OBJECTIVE Drug resistance is the main obstacle in the treatment of non-small cell lung cancer (NSCLC). This study aimed to explore the mechanism of DICER in NSCLC resistance and its downstream signaling pathways. METHODS The A549 cisplatin (DDP)-resistant strain A549/DDP was established. A549/DDP cells were transfected with DICER- and let-7i-5p-related vectors, and treated with autophagy activator rapamycin. The cell viability and apoptosis were tested by CCK-8 assay and flow cytometry, respectively. The formation of autophagosomes was observed with a transmission electron microscopy. RT-qPCR and Western blot assay were conducted to detect expression levels of DICER, let-7i-5p, autophagy-related proteins, and the PI3K/AKT/mTOR pathway-related proteins. The dual luciferase reporter gene assay was implemented to confirm the targeted binding of DICER and let-7i-5p. RESULTS DICER was highly expressed in DDP-resistant NSCLC tissues and cells, and DICER could target and negatively regulate the expression of let-7i-5p. DDP treatment could inhibit the viability and promote cell apoptosis of A549/DDP cells. Downregulation of DICER in A549/DDP cells exhibited a decrease of cell viability, a decreased ratio of LC3-II/LC3-I and autophagosomes, together with an elevation of cell apoptosis rate and the phosphorylation levels of PI3K/AKT/mTOR. Treatment of rapamycin and let-7i-5p inhibitor reversed the effects of downregulated DICER in cell viability, ratio of LC3-II/LC3-I, autophagosomes, cell apoptosis rate and the phosphorylation levels of PI3K/AKT/mTOR in A549/DDP cells. CONCLUSION Our research suggests that DICER promotes autophagy and DDP resistance in NSCLC through downregulating let-7i-5p, and inhibits the activation of PI3K/AKT/mTOR pathway.
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Lee J, Lee D, Kim Y. Mathematical model of STAT signalling pathways in cancer development and optimal control approaches. ROYAL SOCIETY OPEN SCIENCE 2021; 8:210594. [PMID: 34631119 PMCID: PMC8479343 DOI: 10.1098/rsos.210594] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 09/03/2021] [Indexed: 06/10/2023]
Abstract
In various diseases, the STAT family display various cellular controls over various challenges faced by the immune system and cell death programs. In this study, we investigate how an intracellular signalling network (STAT1, STAT3, Bcl-2 and BAX) regulates important cellular states, either anti-apoptosis or apoptosis of cancer cells. We adapt a mathematical framework to illustrate how the signalling network can generate a bi-stability condition so that it will induce either apoptosis or anti-apoptosis status of tumour cells. Then, we use this model to develop several anti-tumour strategies including IFN-β infusion. The roles of JAK-STATs signalling in regulation of the cell death program in cancer cells and tumour growth are poorly understood. The mathematical model unveils the structure and functions of the intracellular signalling and cellular outcomes of the anti-tumour drugs in the presence of IFN-β and JAK stimuli. We identify the best injection order of IFN-β and DDP among many possible combinations, which may suggest better infusion strategies of multiple anti-cancer agents at clinics. We finally use an optimal control theory in order to maximize anti-tumour efficacy and minimize administrative costs. In particular, we minimize tumour volume and maximize the apoptotic potential by minimizing the Bcl-2 concentration and maximizing the BAX level while minimizing total injection amount of both IFN-β and JAK2 inhibitors (DDP).
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Affiliation(s)
- Jonggul Lee
- Pierre Louis Institute of Epidemiology and Public Health, Paris 75012, France
| | - Donggu Lee
- Department of Mathematics, Konkuk University, Seoul 05029, Republic of Korea
| | - Yangjin Kim
- Department of Mathematics, Konkuk University, Seoul 05029, Republic of Korea
- Mathematical Biosciences Institute, Columbus, OH 43210, USA
- Department of Neurosurgery, Harvard Medical School & Brigham and Women’s Hospital, Boston MA 02115, USA
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7
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Al Bitar S, Ballouz T, Doughan S, Gali-Muhtasib H, Rizk N. Potential role of micro ribonucleic acids in screening for anal cancer in human papilloma virus and human immunodeficiency virus related malignancies. World J Gastrointest Pathophysiol 2021; 12:59-83. [PMID: 34354849 PMCID: PMC8316837 DOI: 10.4291/wjgp.v12.i4.59] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/24/2021] [Accepted: 05/19/2021] [Indexed: 02/06/2023] Open
Abstract
Despite advances in antiretroviral treatment (ART), human immunodeficiency virus (HIV) continues to be a major global public health issue owing to the increased mortality rates related to the prevalent oncogenic viruses among people living with HIV (PLWH). Human papillomavirus (HPV) is the most common sexually transmitted viral disease in both men and women worldwide. High-risk or oncogenic HPV types are associated with the development of HPV-related malignancies, including cervical, penile, and anal cancer, in addition to oral cancers. The incidence of anal squamous cell cancers is increasing among PLWH, necessitating the need for reliable screening methods in this population at risk. In fact, the currently used screening methods, including the Pap smear, are invasive and are neither sensitive nor specific. Investigators are interested in circulatory and tissue micro ribonucleic acids (miRNAs), as these small non-coding RNAs are ideal biomarkers for early detection and prognosis of cancer. Multiple miRNAs are deregulated during HIV and HPV infection and their deregulation contributes to the pathogenesis of disease. Here, we will review the molecular basis of HIV and HPV co-infections and focus on the pathogenesis and epidemiology of anal cancer in PLWH. The limitations of screening for anal cancer and the need for a reliable screening program that involves specific miRNAs with diagnostic and therapeutic values is also discussed.
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Affiliation(s)
- Samar Al Bitar
- Department of Biology, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Tala Ballouz
- Department of Internal Medicine, American University of Beirut Medical Center, Beirut 1107 2020, Lebanon
| | - Samer Doughan
- Department of Surgery, American University of Beirut Medical Center, Beirut 1107 2020, Lebanon
| | - Hala Gali-Muhtasib
- Department of Biology and Center for Drug Discovery, American University of Beirut, Beirut 1107 2020, Lebanon
| | - Nesrine Rizk
- Department of Internal Medicine, American University of Beirut Medical Center, Beirut 1107 2020, Lebanon
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Sha Y, Wang S, Bocci F, Zhou P, Nie Q. Inference of Intercellular Communications and Multilayer Gene-Regulations of Epithelial-Mesenchymal Transition From Single-Cell Transcriptomic Data. Front Genet 2021; 11:604585. [PMID: 33488673 PMCID: PMC7820899 DOI: 10.3389/fgene.2020.604585] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 12/02/2020] [Indexed: 01/31/2023] Open
Abstract
Epithelial-to-mesenchymal transition (EMT) plays an important role in many biological processes during development and cancer. The advent of single-cell transcriptome sequencing techniques allows the dissection of dynamical details underlying EMT with unprecedented resolution. Despite several single-cell data analysis on EMT, how cell communicates and regulates dynamics along the EMT trajectory remains elusive. Using single-cell transcriptomic datasets, here we infer the cell-cell communications and the multilayer gene-gene regulation networks to analyze and visualize the complex cellular crosstalk and the underlying gene regulatory dynamics along EMT. Combining with trajectory analysis, our approach reveals the existence of multiple intermediate cell states (ICSs) with hybrid epithelial and mesenchymal features. Analyses on the time-series datasets from cancer cell lines with different inducing factors show that the induced EMTs are context-specific: the EMT induced by transforming growth factor B1 (TGFB1) is synchronous, whereas the EMTs induced by epidermal growth factor and tumor necrosis factor are asynchronous, and the responses of TGF-β pathway in terms of gene expression regulations are heterogeneous under different treatments or among various cell states. Meanwhile, network topology analysis suggests that the ICSs during EMT serve as the signaling in cellular communication under different conditions. Interestingly, our analysis of a mouse skin squamous cell carcinoma dataset also suggests regardless of the significant discrepancy in concrete genes between in vitro and in vivo EMT systems, the ICSs play dominant role in the TGF-β signaling crosstalk. Overall, our approach reveals the multiscale mechanisms coupling cell-cell communications and gene-gene regulations responsible for complex cell-state transitions.
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Affiliation(s)
- Yutong Sha
- Department of Mathematics, University of California, Irvine, Irvine, CA, United States
- The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, United States
| | - Shuxiong Wang
- Department of Mathematics, University of California, Irvine, Irvine, CA, United States
| | - Federico Bocci
- Department of Mathematics, University of California, Irvine, Irvine, CA, United States
- The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, United States
| | - Peijie Zhou
- Department of Mathematics, University of California, Irvine, Irvine, CA, United States
| | - Qing Nie
- Department of Mathematics, University of California, Irvine, Irvine, CA, United States
- The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, CA, United States
- Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, United States
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9
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Liu J, Feng Y, Zeng X, He M, Gong Y, Liu Y. Extracellular vesicles-encapsulated let-7i shed from bone mesenchymal stem cells suppress lung cancer via KDM3A/DCLK1/FXYD3 axis. J Cell Mol Med 2020; 25:1911-1926. [PMID: 33350586 PMCID: PMC7882949 DOI: 10.1111/jcmm.15866] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 07/23/2020] [Accepted: 08/21/2020] [Indexed: 12/24/2022] Open
Abstract
Accumulating evidence has suggested that extracellular vesicles (EVs) play a crucial role in lung cancer treatment. Thus, we aimed to investigate the modulatory role of bone marrow mesenchymal stem cell (BMSC)-EV-derived let-7i and their molecular mechanism in lung cancer progression. Microarray-based analysis was applied to predict lung cancer-related miRNAs and their downstream genes. RT-qPCR and Western blot analyses were conducted to determine Let-7i, lysine demethylase 3A (KDM3A), doublecortin-like kinase 1 (DCLK1) and FXYD domain-containing ion transport regulator 3 (FXYD3) expressions, after which dual-luciferase reporter gene assay and ChIP assay were used to identify the relationship among them. After loss- and gain-of-function assays, the effects of let-7i, KDM3A, DCLK1 and FXYD3 on the biological characteristics of lung cancer cells were assessed. Finally, tumour growth in nude mice was assessed by xenograft tumours in nude mice. Bioinformatics analysis screened out the let-7i and its downstream gene, that is KDM3A. The findings showed the presence of a high expression of KDM3A and DCLK1 and reduced expression of let-7i and FXYD3 in lung cancer. KDM3A elevated DCLK1 by removing the methylation of H3K9me2. Moreover, DCLK1 suppressed the FXYD3 expression. BMSC-EV-derived let-7i resulted in the down-regulation of KDM3A expression and reversed its promoting role in lung cancer development. Consistently, in vivo experiments in nude mice also confirmed that tumour growth was suppressed by the BMSC-EV-derived let-7i. In conclusion, our findings demonstrated that the BMSC-EV-derived let-7i possesses an inhibitory role in lung cancer progression through the KDM3A/DCLK1/FXYD3 axis, suggesting a new molecular target for lung cancer treatment.
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Affiliation(s)
- Jiefeng Liu
- Department of General Surgery, The Fourth Hospital of Changsha, Hunan Normal University, Changsha, China
| | - Yuhua Feng
- Department of Oncology, the Second Xiangya Hospital, Central South University, Changsha, China
| | - Xinyu Zeng
- Department of General Surgery, The Fourth Hospital of Changsha, Hunan Normal University, Changsha, China
| | - Miao He
- Department of General Surgery, The Fourth Hospital of Changsha, Hunan Normal University, Changsha, China
| | - Yujing Gong
- Department of General Surgery, The Fourth Hospital of Changsha, Hunan Normal University, Changsha, China
| | - Yiping Liu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, China
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10
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Abstract
Advances in molecular genetics have identified several species of RNA that fail to translate - hence the non-coding RNAs. The two major groups within this class of nucleic acids are microRNAs (miRNA) and long non-coding RNAs (lncRNA). There is growing body of evidence supporting the view that these molecules have regulatory effect on both DNA and RNA. The objective of this brief review is to explain the molecular genetic of these molecules, to summarize their potential as mediators of disease, and to highlight their value as diagnostic markers and as tools in disease management.
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Affiliation(s)
- P Waller
- Department of Biomedical Sciences, University of Kingston, London, UK
| | - A D Blann
- Institute of Biomedical Science, London, UK
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11
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Grau Ribes A, De Decker Y, Rongy L. Connecting gene expression to cellular movement: A transport model for cell migration. Phys Rev E 2019; 100:032412. [PMID: 31639952 DOI: 10.1103/physreve.100.032412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Indexed: 12/13/2022]
Abstract
The adhesion properties and the mobility of biological cells play key roles in the propagation of cancer. These properties are expected to depend on intracellular processes and on the concentrations of chemicals inside the cell. While most existing reaction-diffusion models for cell migration consider that cell mobility and proliferation rate are constant or depend on an external diffusing species, they do not include the gene expression dynamics taking place in moving cells that affect cellular transport. In this work, we propose a multiscale model where mobility and proliferation depend explicitly on the cell's internal state. We focus more specifically on the case of cellular mobility in epithelial tissues. Wound-healing experiments have demonstrated that the loss of a key protein, E-cadherin, results in a significant increase in both mobility and invasiveness of epithelial cells, with dramatic consequences on cancer progression. We can reproduce the results of these experiments under various genetic conditions with a single set of parameters.
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Affiliation(s)
- Alexis Grau Ribes
- Nonlinear Physical Chemistry Unit, Faculté des Sciences, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Yannick De Decker
- Nonlinear Physical Chemistry Unit, Faculté des Sciences, Université libre de Bruxelles (ULB), Brussels, Belgium
| | - Laurence Rongy
- Nonlinear Physical Chemistry Unit, Faculté des Sciences, Université libre de Bruxelles (ULB), Brussels, Belgium
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12
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Khafaei M, Rezaie E, Mohammadi A, Shahnazi Gerdehsang P, Ghavidel S, Kadkhoda S, Zorrieh Zahra A, Forouzanfar N, Arabameri H, Tavallaie M. miR-9: From function to therapeutic potential in cancer. J Cell Physiol 2019; 234:14651-14665. [PMID: 30693512 DOI: 10.1002/jcp.28210] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 01/10/2019] [Indexed: 01/24/2023]
Abstract
Malignant neoplasms are regarded as the main cause of death around the world; hence, many research studies were conducted to further perceive molecular mechanisms, treatment, and cancer prognosis. Cancer is known as a major factor for health-related problems in the world. The main challenges associated with these diseases are prompt diagnosis, disease remission classification and treatment status forecast. Therefore, progressing in such areas by developing new and optimized methods with the help of minimally invasive biological markers such as circular microRNAs (miRNAs) can be considered important. miRNA interactions with target genes have specified their role in development, apoptosis, differentiation, and proliferation and also, confirm direct miRNA function in cancer. Different miRNAs expression levels in various types of malignant neoplasms have been observed to be associated with prognosis of various carcinomas. miR-9 seems to implement opposite practices in different tissues or under various cancer incidences by influencing different genes. Aberrant miR-9 levels have been observed in many cancer types. Therefore, we intended to investigate the precise role of miR-9 in patients with malignant neoplasms. To this end, in this study, we attempted to examine different studies to clarify the overall role of miR-9 as a prognostic marker in several human tumors. The presented data in this study can help us to find the novel therapeutic avenues for treatment of human cancers.
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Affiliation(s)
- Mostafa Khafaei
- Human Genetics Research Center, Baqiyatallah Medical Science University, Tehran, Iran
| | - Ehsan Rezaie
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Science, Tehran, Iran
| | - Ali Mohammadi
- Human Genetics Research Center, Baqiyatallah Medical Science University, Tehran, Iran
| | | | - Sara Ghavidel
- Department Cell and Molecular Biology, Tonekabon Branch, Islamic Azad University, Tehran, Iran
| | - Sepideh Kadkhoda
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Atieh Zorrieh Zahra
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Narjes Forouzanfar
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hossein Arabameri
- Human Genetics Research Center, Baqiyatallah Medical Science University, Tehran, Iran
| | - Mahmood Tavallaie
- Human Genetics Research Center, Baqiyatallah Medical Science University, Tehran, Iran
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13
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MicroRNA-9 enhanced radiosensitivity and its mechanism of DNA methylation in non-small cell lung cancer. Gene 2019; 710:178-185. [PMID: 31158449 DOI: 10.1016/j.gene.2019.05.050] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/17/2019] [Accepted: 05/25/2019] [Indexed: 12/30/2022]
Abstract
In order to improve the therapeutic effect of non-small cell lung cancer (NSCLC), it is critical to combine radiation and gene therapy. Our study found that the activation of microRNA-9 (miR-9) conferred ionizing radiation (IR) sensitivity in cancer cells. Furthermore, increased microRNA-9 promoter methylation level was observed after IR. Our study combined the IR and microRNA-9 overexpression treatment which leads to a significant enhancement in the therapeutic efficiency in lung cancer both in vitro and in vivo. Therefore, it is plausible that microRNA-9 can be used as a novel therapeutic strategy of NSCLC. MTT assay was performed to detect the effect of microRNA-9 on the survival and growth of NSCLC cells. Flow cytometry results showed that microRNA-9 enhanced the apoptosis of NSCLC cells. Wound healing assay found that microRNA-9 can inhibit the migration of NSCLC cells and enhance the effect of radiation on the migration of NSCLC cells. In addition, bisulfate sequencing PCR was performed to analyze the methylation status of the microRNA-9 promoter. In order to determine the effect of microRNA-9 and its promoter methylation status on proliferation and radio-sensitivity in vivo, a subcutaneous tumor formation assay in nude mice was performed. Results have shown that microRNA-9 overexpression increased the radiosensitivity of A549 cells by inhibiting cell activity and migration, and by increasing apoptosis. In addition, the promoter methylation status of the microRNA-9 gene increased in response to ionizing radiation. Our study demonstrated that microRNA-9 enhanced radiosensitivity in NSCLC and this effect is highly regulated by its promoter methylation status. These results will help to clarify regulatory mechanisms of radiation resistance thus stimulate new methods for improving radiotherapy for NSCLC.
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14
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Sethi S, Sethi S, Bluth MH. Clinical Implication of MicroRNAs in Molecular Pathology: An Update for 2018. Clin Lab Med 2019; 38:237-251. [PMID: 29776629 DOI: 10.1016/j.cll.2018.02.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
MicroRNAs (miRNAs) are poised to provide diagnostic, prognostic, and therapeutic targets for several diseases including malignancies for precision medicine applications. The miRNAs have immense potential in the clinical arena because they can be detected in the blood, serum, tissues (fresh and formalin-fixed paraffin-embedded), and fine-needle aspirate specimens. The most attractive feature of miRNA-based therapy is that a single miRNA could be useful for targeting multiple genes that are deregulated in cancers, which can be further investigated through systems biology and network analysis that may provide cancer-specific personalized therapy.
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Affiliation(s)
- Seema Sethi
- Department of Pathology, University of Michigan and VA Hospital, E300, 2215 Fuller Road, Ann Arbor, MI 48105, USA.
| | - Sajiv Sethi
- Department of Gastroenterology, University of South Florida, 12901 Bruce B. Downs Boulevard, MDC 82, Tampa, FL 33612, USA
| | - Martin H Bluth
- Department of Pathology, Wayne State University, School of Medicine, 540 East Canfield Street, Detroit, MI 48201, USA; Pathology Laboratories, Michigan Surgical Hospital, 21230 Dequindre Road, Warren, MI 48091, USA
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15
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Zhao C, Zhang Y, Popel AS. Mechanistic Computational Models of MicroRNA-Mediated Signaling Networks in Human Diseases. Int J Mol Sci 2019; 20:E421. [PMID: 30669429 PMCID: PMC6358731 DOI: 10.3390/ijms20020421] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Revised: 01/14/2019] [Accepted: 01/15/2019] [Indexed: 12/17/2022] Open
Abstract
MicroRNAs (miRs) are endogenous non-coding RNA molecules that play important roles in human health and disease by regulating gene expression and cellular processes. In recent years, with the increasing scientific knowledge and new discovery of miRs and their gene targets, as well as the plentiful experimental evidence that shows dysregulation of miRs in a wide variety of human diseases, the computational modeling approach has emerged as an effective tool to help researchers identify novel functional associations between differential miR expression and diseases, dissect the phenotypic expression patterns of miRs in gene regulatory networks, and elucidate the critical roles of miRs in the modulation of disease pathways from mechanistic and quantitative perspectives. Here we will review the recent systems biology studies that employed different kinetic modeling techniques to provide mechanistic insights relating to the regulatory function and therapeutic potential of miRs in human diseases. Some of the key computational aspects to be discussed in detail in this review include (i) models of miR-mediated network motifs in the regulation of gene expression, (ii) models of miR biogenesis and miR⁻target interactions, and (iii) the incorporation of such models into complex disease pathways in order to generate mechanistic, molecular- and systems-level understanding of pathophysiology. Other related bioinformatics tools such as computational platforms that predict miR-disease associations will also be discussed, and we will provide perspectives on the challenges and opportunities in the future development and translational application of data-driven systems biology models that involve miRs and their regulatory pathways in human diseases.
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Affiliation(s)
- Chen Zhao
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Yu Zhang
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Aleksander S Popel
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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16
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Guinde J, Frankel D, Perrin S, Delecourt V, Lévy N, Barlesi F, Astoul P, Roll P, Kaspi E. Lamins in Lung Cancer: Biomarkers and Key Factors for Disease Progression through miR-9 Regulation? Cells 2018; 7:E78. [PMID: 30012957 PMCID: PMC6071028 DOI: 10.3390/cells7070078] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 07/06/2018] [Accepted: 07/09/2018] [Indexed: 02/08/2023] Open
Abstract
Lung cancer represents the primary cause of cancer death in the world. Malignant cells identification and characterization are crucial for the diagnosis and management of patients with primary or metastatic cancers. In this context, the identification of new biomarkers is essential to improve the differential diagnosis between cancer subtypes, to select the most appropriate therapy, and to establish prognostic correlations. Nuclear abnormalities are hallmarks of carcinoma cells and are used as cytological diagnostic criteria of malignancy. Lamins (divided into A- and B-types) are localized in the nuclear matrix comprising nuclear lamina, where they act as scaffolding protein, involved in many nuclear functions, with regulatory effects on the cell cycle and differentiation, senescence and apoptosis. Previous studies have suggested that lamins are involved in tumor development and progression with opposite results concerning their prognostic role. This review provides an overview of lamins expression in lung cancer and the relevance of these findings for disease diagnosis and prognosis. Furthermore, we discuss the link between A-type lamins expression in lung carcinoma cells and nuclear deformability, epithelial to mesenchymal transition, and metastatic potential, and which mechanisms could regulate A-type lamins expression in lung cancer, such as the microRNA miR-9.
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Affiliation(s)
- Julien Guinde
- Aix Marseille Université, INSERM, MMG, 13385 Marseille, France.
- APHM, Hôpital Nord, Department of Thoracic Oncology-Pleural Diseases-Interventional Pulmonology, CEDEX 5, 13385 Marseille, France.
| | - Diane Frankel
- Aix Marseille Université, APHM, INSERM, MMG, Hôpital la Timone, Service de Biologie Cellulaire, 13385 Marseille, France.
| | - Sophie Perrin
- Aix Marseille Université, INSERM, MMG, 13385 Marseille, France.
- ProGeLife, 13385 Marseille, France.
| | | | - Nicolas Lévy
- Aix Marseille Université, APHM, INSERM, MMG, Hôpital la Timone, Département de Génétique Médicale, 13385 Marseille, France.
| | - Fabrice Barlesi
- Aix Marseille Université, APHM, CNRS, INSERM, CRCM, Multidisciplinary Oncology & Therapeutic Innovations Department, 13385 Marseille, France.
| | - Philippe Astoul
- APHM, Hôpital Nord, Department of Thoracic Oncology-Pleural Diseases-Interventional Pulmonology, CEDEX 5, 13385 Marseille, France.
| | - Patrice Roll
- Aix Marseille Université, APHM, INSERM, MMG, Hôpital la Timone, Service de Biologie Cellulaire, 13385 Marseille, France.
| | - Elise Kaspi
- Aix Marseille Université, APHM, INSERM, MMG, Hôpital la Timone, Service de Biologie Cellulaire, 13385 Marseille, France.
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17
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Grau Ribes A, De Decker Y, Gérard C, Rongy L. Modelling the propagation of a dynamical signature in gene expression mediated by the transport of extracellular microRNAs. MOLECULAR BIOSYSTEMS 2018; 13:2379-2391. [PMID: 28953276 DOI: 10.1039/c7mb00509a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Extracellular microRNAs (miRNAs) carried by exosomes can play a key role in cell-to-cell communication. Deregulation of miRNA expression and exosome secretion have been related to pathological conditions such as cancer. While it is known that circulating miRNAs can alter gene expression in recipient cells, it remains unclear how significant the dynamical impact of these extracellular miRNAs is. To shed light on this issue, we propose a model for the spatio-temporal evolution of the protein expression in a cell tissue altered by abnormal miRNA expression in a donor cell. This results in a nonhomogeneous cellular response in the tissue, which we quantify by studying the range of action of the donor cell on the surrounding cells. Key model parameters that control the range of action are identified. Based on a model for a heterogeneous cell population, we show that the dynamics of gene expression in the tissue is robust to random changes of the parameter values. Furthermore, we study the propagation of gene expression oscillations in a tissue induced by extracellular miRNAs. In the donor cell, the miRNA inhibits its own transcription which can give rise to local oscillations in gene expression. The resulting oscillations of the concentration of extracellular miRNA induce oscillations of the protein concentration in recipient cells. We analyse the nonmonotonic spatial evolution of the oscillation amplitude of the protein concentration in the tissue which may have implications for the propagation of oscillations in biological rhythms such as the circadian clock.
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Affiliation(s)
- Alexis Grau Ribes
- Nonlinear Physical Chemistry Unit, Faculté des Sciences, Université libre de Bruxelles (ULB), Brussels, Belgium.
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18
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Chen J, An T, Ma Y, Situ B, Chen D, Xu Y, Zhang L, Dai Z, Zou X. Isothermal Amplification on a Structure-Switchable Symmetric Toehold Dumbbell-Template: A Strategy Enabling MicroRNA Analysis at the Single-Cell Level with Ultrahigh Specificity and Accuracy. Anal Chem 2017; 90:859-865. [DOI: 10.1021/acs.analchem.7b03713] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jun Chen
- School
of Chemistry, Sun Yat−Sen University, Guangzhou 510275, PR China
| | - Taixue An
- Department
of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Yingjun Ma
- School
of Chemistry, Sun Yat−Sen University, Guangzhou 510275, PR China
| | - Bo Situ
- Department
of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
- Guangdong Engineering and Technology Research Center for Rapid Diagnostic Biosensors, Guangzhou 510515, China
| | - Danping Chen
- School
of Chemistry, Sun Yat−Sen University, Guangzhou 510275, PR China
| | - Yuzhi Xu
- School
of Chemistry, Sun Yat−Sen University, Guangzhou 510275, PR China
| | - Li Zhang
- School
of Chemistry, Sun Yat−Sen University, Guangzhou 510275, PR China
| | - Zong Dai
- School
of Chemistry, Sun Yat−Sen University, Guangzhou 510275, PR China
- Guangdong Engineering and Technology Research Center for Rapid Diagnostic Biosensors, Guangzhou 510515, China
| | - Xiaoyong Zou
- School
of Chemistry, Sun Yat−Sen University, Guangzhou 510275, PR China
- Guangdong Engineering and Technology Research Center for Rapid Diagnostic Biosensors, Guangzhou 510515, China
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19
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Proctor CJ, Smith GR. Computer simulation models as a tool to investigate the role of microRNAs in osteoarthritis. PLoS One 2017; 12:e0187568. [PMID: 29095952 PMCID: PMC5695613 DOI: 10.1371/journal.pone.0187568] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 10/23/2017] [Indexed: 12/21/2022] Open
Abstract
The aim of this study was to show how computational models can be used to increase our understanding of the role of microRNAs in osteoarthritis (OA) using miR-140 as an example. Bioinformatics analysis and experimental results from the literature were used to create and calibrate models of gene regulatory networks in OA involving miR-140 along with key regulators such as NF-κB, SMAD3, and RUNX2. The individual models were created with the modelling standard, Systems Biology Markup Language, and integrated to examine the overall effect of miR-140 on cartilage homeostasis. Down-regulation of miR-140 may have either detrimental or protective effects for cartilage, indicating that the role of miR-140 is complex. Studies of individual networks in isolation may therefore lead to different conclusions. This indicated the need to combine the five chosen individual networks involving miR-140 into an integrated model. This model suggests that the overall effect of miR-140 is to change the response to an IL-1 stimulus from a prolonged increase in matrix degrading enzymes to a pulse-like response so that cartilage degradation is temporary. Our current model can easily be modified and extended as more experimental data become available about the role of miR-140 in OA. In addition, networks of other microRNAs that are important in OA could be incorporated. A fully integrated model could not only aid our understanding of the mechanisms of microRNAs in ageing cartilage but could also provide a useful tool to investigate the effect of potential interventions to prevent cartilage loss.
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Affiliation(s)
- Carole J. Proctor
- Newcastle University Institute for Ageing, Newcastle University, Newcastle upon Tyne, United Kingdom
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
- * E-mail:
| | - Graham R. Smith
- Newcastle University Institute for Ageing, Newcastle University, Newcastle upon Tyne, United Kingdom
- Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne, United Kingdom
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20
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Lai X, Friedman A. Exosomal microRNA concentrations in colorectal cancer: A mathematical model. J Theor Biol 2017; 415:70-83. [DOI: 10.1016/j.jtbi.2016.12.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 12/06/2016] [Accepted: 12/10/2016] [Indexed: 12/19/2022]
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21
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Lai X, Friedman A. Exosomal miRs in Lung Cancer: A Mathematical Model. PLoS One 2016; 11:e0167706. [PMID: 28002496 PMCID: PMC5176278 DOI: 10.1371/journal.pone.0167706] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 11/18/2016] [Indexed: 01/11/2023] Open
Abstract
Lung cancer, primarily non-small-cell lung cancer (NSCLC), is the leading cause of cancer deaths in the United States and worldwide. While early detection significantly improves five-year survival, there are no reliable diagnostic tools for early detection. Several exosomal microRNAs (miRs) are overexpressed in NSCLC, and have been suggested as potential biomarkers for early detection. The present paper develops a mathematical model for early stage of NSCLC with emphasis on the role of the three highest overexpressed miRs, namely miR-21, miR-205 and miR-155. Simulations of the model provide quantitative relationships between the tumor volume and the total mass of each of the above miRs in the tumor. Because of the positive correlation between these miRs in the tumor tissue and in the blood, the results of the paper may be viewed as a first step toward establishing a combination of miRs 21, 205, 155 and possibly other miRs as serum biomarkers for early detection of NSCLC.
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Affiliation(s)
- Xiulan Lai
- Institute for Mathematical Sciences, Renmin University of China, Beijing, P. R. China
| | - Avner Friedman
- Mathematical Bioscience Institute & Department of Mathematics, Ohio State University, Columbus, OH, United States of America
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22
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Lai X, Wolkenhauer O, Vera J. Understanding microRNA-mediated gene regulatory networks through mathematical modelling. Nucleic Acids Res 2016; 44:6019-35. [PMID: 27317695 PMCID: PMC5291278 DOI: 10.1093/nar/gkw550] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 06/06/2016] [Indexed: 12/19/2022] Open
Abstract
The discovery of microRNAs (miRNAs) has added a new player to the regulation of gene expression. With the increasing number of molecular species involved in gene regulatory networks, it is hard to obtain an intuitive understanding of network dynamics. Mathematical modelling can help dissecting the role of miRNAs in gene regulatory networks, and we shall here review the most recent developments that utilise different mathematical modelling approaches to provide quantitative insights into the function of miRNAs in the regulation of gene expression. Key miRNA regulation features that have been elucidated via modelling include: (i) the role of miRNA-mediated feedback and feedforward loops in fine-tuning of gene expression; (ii) the miRNA–target interaction properties determining the effectiveness of miRNA-mediated gene repression; and (iii) the competition for shared miRNAs leading to the cross-regulation of genes. However, there is still lack of mechanistic understanding of many other properties of miRNA regulation like unconventional miRNA–target interactions, miRNA regulation at different sub-cellular locations and functional miRNA variant, which will need future modelling efforts to deal with. This review provides an overview of recent developments and challenges in this field.
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Affiliation(s)
- Xin Lai
- Laboratory of Systems Tumour Immunology, Department of Dermatology, Erlangen University Hospital and Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, 91054, Germany
| | - Olaf Wolkenhauer
- Department of Systems Biology & Bioinformatics, University of Rostock, Rostock, 18051, Germany Stellenbosch Institute for Advanced Study, Wallenberg Research Centre at Stellenbosch University, 7600, South Africa
| | - Julio Vera
- Laboratory of Systems Tumour Immunology, Department of Dermatology, Erlangen University Hospital and Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, 91054, Germany
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23
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Chen J, Zhou X, Ma Y, Lin X, Dai Z, Zou X. Asymmetric exponential amplification reaction on a toehold/biotin featured template: an ultrasensitive and specific strategy for isothermal microRNAs analysis. Nucleic Acids Res 2016; 44:e130. [PMID: 27257058 PMCID: PMC5009742 DOI: 10.1093/nar/gkw504] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 05/21/2016] [Indexed: 12/19/2022] Open
Abstract
The sensitive and specific analysis of microRNAs (miRNAs) without using a thermal cycler instrument is significant and would greatly facilitate biological research and disease diagnostics. Although exponential amplification reaction (EXPAR) is the most attractive strategy for the isothermal analysis of miRNAs, its intrinsic limitations of detection efficiency and inevitable non-specific amplification critically restrict its use in analytical sensitivity and specificity. Here, we present a novel asymmetric EXPAR based on a new biotin/toehold featured template. A biotin tag was used to reduce the melting temperature of the primer/template duplex at the 5′ terminus of the template, and a toehold exchange structure acted as a filter to suppress the non-specific trigger of EXPAR. The asymmetric EXPAR exhibited great improvements in amplification efficiency and specificity as well as a dramatic extension of dynamic range. The limit of detection for the let-7a analysis was decreased to 6.02 copies (0.01 zmol), and the dynamic range was extended to 10 orders of magnitude. The strategy enabled the sensitive and accurate analysis of let-7a miRNA in human cancer tissues with clearly better precision than both standard EXPAR and RT-qPCR. Asymmetric EXPAR is expected to have an important impact on the development of simple and rapid molecular diagnostic applications for short oligonucleotides.
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Affiliation(s)
- Jun Chen
- School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, China
| | - Xueqing Zhou
- School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yingjun Ma
- School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, China
| | - Xiulian Lin
- College of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Zong Dai
- School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, China
| | - Xiaoyong Zou
- School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, China SYSU-CMU Shunde International Joint Research Institute, Shunde, Guangdong 528300, China
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24
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Liu X, Luo Z, Peng H, Jiang H, Xu L. Prognostic role of miR-9 expression in various human malignant neoplasms: a meta-analysis. Onco Targets Ther 2016; 9:3039-47. [PMID: 27284255 PMCID: PMC4883817 DOI: 10.2147/ott.s98923] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Emerging evidence has shown that aberrant microRNA expression has the potential to be used for predicting survival and treatment response of malignant neoplasms. In recent years, the role of miR-9 had been investigated in various types of cancers, and it was found that the results were inconsistent and inconclusive. Hence, in this study, a meta-analysis was conducted to assess the prognostic value of miR-9 in various types of tumors. Eligible studies were identified through a systematic search in PubMed and EMBASE and then were assessed by further quality evaluation. Pooled hazard ratios (HRs) with 95% confidence intervals for overall survival (OS) were calculated to investigate the association between miR-9 expression and cancer prognosis. The pooled results of eight published studies showed that elevated miR-9 was a predictor of poor survival of various carcinomas, with pooled HR of 3.04 (95% confidence interval: 1.96–4.73) for OS. Subgroup analysis on the basis of tumor type, sample size, and HR estimate also showed that high levels of miR-9 were also significantly correlated with OS. In addition, when the subgroup analyses were grouped by follow-up time, it was found that the elevated expression of miR-9 was associated with a lower long-term survival when the follow-up time was >60 months, but there was no correlation between the outcomes and those patients whose follow-up time was <60 months. Funnel plots and Egger’s tests revealed that there was no obvious publication bias risk in the meta-analysis. In conclusion, our results demonstrated that higher expression level of miR-9 significantly predicted worse OS in various carcinomas and that miR-9 may act as a novel biomarker in the prognosis of malignant neoplasms.
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Affiliation(s)
- Xiaodan Liu
- Division of Birth Cohort Study, Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Ziyan Luo
- Division of Birth Cohort Study, Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Hongxia Peng
- Division of Birth Cohort Study, Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Hua Jiang
- Department of Hematology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Ling Xu
- Department of Hematology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
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25
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Tugay K, Guay C, Marques AC, Allagnat F, Locke JM, Harries LW, Rutter GA, Regazzi R. Role of microRNAs in the age-associated decline of pancreatic beta cell function in rat islets. Diabetologia 2016; 59:161-169. [PMID: 26474776 PMCID: PMC4670458 DOI: 10.1007/s00125-015-3783-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 09/23/2015] [Indexed: 11/03/2022]
Abstract
AIMS/HYPOTHESIS Ageing can lead to reduced insulin sensitivity and loss of pancreatic beta cell function, predisposing individuals to the development of diabetes. The aim of this study was to assess the contribution of microRNAs (miRNAs) to age-associated beta cell dysfunction. METHODS The global mRNA and miRNA profiles of 3- and 12-month-old rat islets were collected by microarray. The functional impact of age-associated differences in miRNA expression was investigated by mimicking the observed changes in primary beta cells from young animals. RESULTS Beta cells from 12-month-old rats retained normal insulin content and secretion, but failed to proliferate in response to mitotic stimuli. The islets of these animals displayed modifications at the level of several miRNAs, including upregulation of miR-34a, miR-124a and miR-383, and downregulation of miR-130b and miR-181a. Computational analysis of the transcriptomic modifications observed in the islets of 12-month-old rats revealed that the differentially expressed genes were enriched for miR-34a and miR-181a targets. Indeed, the induction of miR-34a and reduction of miR-181a in the islets of young animals mimicked the impaired beta cell proliferation observed in old animals. mRNA coding for alpha-type platelet-derived growth factor receptor, which is critical for compensatory beta cell mass expansion, is directly inhibited by miR34a and is likely to be at least partly responsible for the effects of this miRNA. CONCLUSIONS/INTERPRETATION Changes in the level of specific miRNAs that occur during ageing affect the proliferative capacity of beta cells. This might reduce their ability to expand under conditions of increased insulin demand, favouring the development of type 2 diabetes.
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Affiliation(s)
- Ksenia Tugay
- Department of Fundamental Neurosciences, University of Lausanne, Rue du Bugnon 9, CH-1005, Lausanne, Switzerland
| | - Claudiane Guay
- Department of Fundamental Neurosciences, University of Lausanne, Rue du Bugnon 9, CH-1005, Lausanne, Switzerland
| | - Ana C Marques
- Department of Physiology, University of Lausanne, Lausanne, Switzerland
| | - Florent Allagnat
- Department of Physiology, University of Lausanne, Lausanne, Switzerland
| | - Jonathan M Locke
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Lorna W Harries
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Guy A Rutter
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Imperial College London, London, UK
| | - Romano Regazzi
- Department of Fundamental Neurosciences, University of Lausanne, Rue du Bugnon 9, CH-1005, Lausanne, Switzerland.
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Nie JH, Chen ZH, Shao CL, Pei WW, Zhang J, Zhang SY, Jiao Y, Tong J. Analysis of the miRNA-mRNA networks in malignant transformation BEAS-2B cells induced by alpha-particles. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2016; 79:427-435. [PMID: 27267825 DOI: 10.1080/15287394.2016.1176628] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The aim of this study was to determine the toxicity induced by irradiation with alpha-particles on malignant transformation of immortalized human bronchial epithelial cells (BEAS-2B) using miRNA-mRNA networks. The expression of BEAS-2B cells was determined by measuring colony formation, mtDNA, mitochondrial membrane potential (MMP), and ROS levels. Changes in BEAS-2B cell gene expression were observed and quantified using microarrays that included an increase in 157 mRNA and 20 miRNA expression and a decrease in 77 mRNA and 48 miRNA. Bioinformatic software was used to analyze these different mRNA and miRNA, which indicated that miR-107 and miR-494 play an important role in alpha-particles-mediated cellular malignant transformation processes. The pathways related to systemic lupus erythematosus, cytokine-cytokine receptor interaction, MAPK signaling pathway, regulation of actin cytoskeleton, and cell adhesion molecules (CAMs) were stimulated, while those of ribosome, transforming growth factor (TGF)-beta signaling pathway, and metabolic pathways were inhibited. Data suggest that miRNA and mRNA play a crucial role in alpha-particles-mediated malignant transformation processes. It is worth noting that three target genes associated with lung cancer were identified and upregulated PEG 10 (paternally expressed gene 10), ARHGAP26, and IRS1.
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Affiliation(s)
- Ji-Hua Nie
- a School of Public Health , Medical College of Soochow University , Suzhou , China
- b Jiangsu Key Laboratory of Preventive and Translational Medicine for Genetic Diseases , Suzhou , China
- c School of Radiation Medicine and Protection and Jiangsu Provincial Key Laboratory of Radiation Medicine and Protection , Medical College of Soochow University , Suzhou , China
| | - Zhi-Hai Chen
- a School of Public Health , Medical College of Soochow University , Suzhou , China
- b Jiangsu Key Laboratory of Preventive and Translational Medicine for Genetic Diseases , Suzhou , China
| | - Chun-Lin Shao
- e Institute of Radiation Medicine , Fudan University , Shanghai , China
| | - Wei-Wei Pei
- a School of Public Health , Medical College of Soochow University , Suzhou , China
- b Jiangsu Key Laboratory of Preventive and Translational Medicine for Genetic Diseases , Suzhou , China
| | - Jie Zhang
- a School of Public Health , Medical College of Soochow University , Suzhou , China
| | - Shu-Yu Zhang
- c School of Radiation Medicine and Protection and Jiangsu Provincial Key Laboratory of Radiation Medicine and Protection , Medical College of Soochow University , Suzhou , China
- d Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions and School for Radiological and Interdisciplinary Sciences (RAD-X) , Soochow University , Suzhou , China
| | - Yang Jiao
- c School of Radiation Medicine and Protection and Jiangsu Provincial Key Laboratory of Radiation Medicine and Protection , Medical College of Soochow University , Suzhou , China
- d Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions and School for Radiological and Interdisciplinary Sciences (RAD-X) , Soochow University , Suzhou , China
| | - Jian Tong
- a School of Public Health , Medical College of Soochow University , Suzhou , China
- b Jiangsu Key Laboratory of Preventive and Translational Medicine for Genetic Diseases , Suzhou , China
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27
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Diagnosis of Lung Cancer by Fractal Analysis of Damaged DNA. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2015; 2015:242695. [PMID: 26539245 PMCID: PMC4619900 DOI: 10.1155/2015/242695] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 03/24/2015] [Indexed: 12/17/2022]
Abstract
Cancer starts when cells in a part of the body start to grow out of control. In fact cells become cancer cells because of DNA damage. A DNA walk of a genome represents how the frequency of each nucleotide of a pairing nucleotide couple changes locally. In this research in order to study the cancer genes, DNA walk plots of genomes of patients with lung cancer were generated using a program written in MATLAB language. The data so obtained was checked for fractal property by computing the fractal dimension using a program written in MATLAB. Also, the correlation of damaged DNA was studied using the Hurst exponent measure. We have found that the damaged DNA sequences are exhibiting higher degree of fractality and less correlation compared with normal DNA sequences. So we confirmed this method can be used for early detection of lung cancer. The method introduced in this research not only is useful for diagnosis of lung cancer but also can be applied for detection and growth analysis of different types of cancers.
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Ni R, Huang Y, Wang J. miR-98 targets ITGB3 to inhibit proliferation, migration, and invasion of non-small-cell lung cancer. Onco Targets Ther 2015; 8:2689-97. [PMID: 26445551 PMCID: PMC4590683 DOI: 10.2147/ott.s90998] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Background Accumulating evidence has emphasized causative links between aberrant microRNA (miR) expression patterns and cancer development. Abnormally expressed miRNA-98 (miR-98) was found in certain types of human cancers. The biological roles of miR-98 in lung cancer, however, remain largely undefined. Methods We evaluated the expression of miR-98 in normal lung tissues, lung cancer tissues, normal human bronchial epithelial cells, and lung cancer cells using quantitative real-time polymerase chain reaction. Effect of miR-98 on proliferation of lung cancer cells was investigated using MTT assay and colony formation assay. Transwell assay was used to assess the effects of miR-98 on migration and invasion of lung cancer cells. Whether miR-98 targets the 3′-untranslated region (3′-UTR) of integrin β3 (ITGB3) coding gene ITGB3 mRNA was ascertained using luciferase reporter assay. Finally, we transplanted miR-98 expressing A549 cells into nude mice to observe the effect of miR-98 on tumor growth in vivo. Results We confirmed that miR-98 was frequently low expressed in lung cancer tissues and human lung cancer cells. Reintroduction of miR-98 into lung cancer cells inhibited cell proliferation, migration, and invasion in vitro and suppressed tumor formation in a nude mouse model. Furthermore, we identified that miR-98 exerted inhibitory roles by directly binding to 3′-UTR of ITGB3 mRNA, thus negatively regulated the expression of ITGB3. Interestingly, upon restoring the expression of ITGB3, the effect of miR-98 on cell proliferation was partially reversed. Conclusion Our findings suggest that miR-98 prevents proliferation, migration, and invasion of lung cancer cells by directly binding to the 3′-UTR of ITGB3 mRNA and could be a promising treatment option in anticancer therapy.
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Affiliation(s)
- Ran Ni
- Department of Respiration Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Yongjie Huang
- Department of Geriatric Respiration and Sleep, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, People's Republic of China
| | - Jing Wang
- Department of Respiration Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, People's Republic of China
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29
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Lu M, Jolly MK, Onuchic J, Ben-Jacob E. Toward decoding the principles of cancer metastasis circuits. Cancer Res 2015; 74:4574-87. [PMID: 25183783 DOI: 10.1158/0008-5472.can-13-3367] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Understanding epithelial-mesenchymal transitions (EMT) during cancer metastasis remains a major challenge in modern biology. Recent observations of cell behavior together with progress in mapping the underlying regulatory genetic networks led to new understandings of carcinoma metastasis. It is now established that the genetic network that regulates the EMT also enables an epithelial-mesenchymal hybrid phenotype. These hybrid cells possess mixed carcinoma epithelial and mesenchymal characteristics that enable specialized capabilities such as collective cell migration. On the gene network perspective, a four-component decision unit composed of two highly interconnected chimeric modules--the miR34/SNAIL and the miR200/ZEB mutual-inhibition feedback circuits--regulates the coexistence of and transitions between the different phenotypes. Here, we present a new tractable theoretical framework to model and decode the underlying principles governing the operation of the regulatory unit. Our approach connects the knowledge about intracellular pathways with observations of cellular behavior and advances toward understanding the logic of cancer decision-making. We found that the miR34/SNAIL module acts as an integrator while the miR200/ZEB module acts as a three-way switch. Consequently, the combined unit can give rise to three phenotypes (stable states): (i) a high miR200 and low ZEB, or (1, 0) state; (ii) a low miR200 and high ZEB, or (0, 1) state; and (iii) a medium miR200 and medium ZEB, or (½, ½) state. We associate these states with the epithelial, mesenchymal, and hybrid phenotypes, respectively. We reflect on the consistency between our theoretical predictions and recent observations in several types of carcinomas and suggest new testable predictions. See all articles in this Cancer Research section,
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Affiliation(s)
- Mingyang Lu
- Center for Theoretical Biological Physics, Departments of
| | - Mohit Kumar Jolly
- Center for Theoretical Biological Physics, Departments of Bioengineering
| | - Jose' Onuchic
- Center for Theoretical Biological Physics, Departments of Physics and Astronomy, Chemistry, and Biochemistry and Cell Biology, Rice University, Houston, Texas;
| | - Eshel Ben-Jacob
- Center for Theoretical Biological Physics, Departments of Biochemistry and Cell Biology, Rice University, Houston, Texas; School of Physics and Astronomy; and The Sagol School of Neuroscience, Tel-Aviv University, Tel-Aviv, Israel
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30
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Mitra R, Edmonds MD, Sun J, Zhao M, Yu H, Eischen CM, Zhao Z. Reproducible combinatorial regulatory networks elucidate novel oncogenic microRNAs in non-small cell lung cancer. RNA (NEW YORK, N.Y.) 2014; 20:1356-68. [PMID: 25024357 PMCID: PMC4138319 DOI: 10.1261/rna.042754.113] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Accepted: 05/01/2014] [Indexed: 06/03/2023]
Abstract
While previous studies reported aberrant expression of microRNAs (miRNAs) in non-small cell lung cancer (NSCLC), little is known about which miRNAs play central roles in NSCLC's pathogenesis and its regulatory mechanisms. To address this issue, we presented a robust computational framework that integrated matched miRNA and mRNA expression profiles in NSCLC using feed-forward loops. The network consists of miRNAs, transcription factors (TFs), and their common predicted target genes. To discern the biological meaning of their associations, we introduced the direction of regulation. A network edge validation strategy using three independent NSCLC expression profiling data sets pinpointed reproducible biological regulations. Reproducible regulation, which may reflect the true molecular interaction, has not been applied to miRNA-TF co-regulatory network analyses in cancer or other diseases yet. We revealed eight hub miRNAs that connected to a higher proportion of targets validated by independent data sets. Network analyses showed that these miRNAs might have strong oncogenic characteristics. Furthermore, we identified a novel miRNA-TF co-regulatory module that potentially suppresses the tumor suppressor activity of the TGF-β pathway by targeting a core pathway molecule (TGFBR2). Follow-up experiments showed two miRNAs (miR-9-5p and miR-130b-3p) in this module had increased expression while their target gene TGFBR2 had decreased expression in a cohort of human NSCLC. Moreover, we demonstrated these two miRNAs directly bind to the 3' untranslated region of TGFBR2. This study enhanced our understanding of miRNA-TF co-regulatory mechanisms in NSCLC. The combined bioinformatics and validation approach we described can be applied to study other types of diseases.
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Affiliation(s)
- Ramkrishna Mitra
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Mick D Edmonds
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Jingchun Sun
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Min Zhao
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Hui Yu
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Christine M Eischen
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
| | - Zhongming Zhao
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, Tennessee 37212, USA Center for Quantitative Sciences, Vanderbilt University, Nashville, Tennessee 37232, USA
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31
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You J, Li Y, Fang N, Liu B, Zu L, Chang R, Li X, Zhou Q. MiR-132 suppresses the migration and invasion of lung cancer cells via targeting the EMT regulator ZEB2. PLoS One 2014; 9:e91827. [PMID: 24626466 PMCID: PMC3953608 DOI: 10.1371/journal.pone.0091827] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 02/15/2014] [Indexed: 11/18/2022] Open
Abstract
MicroRNAs (miRNAs) are small, non-coding RNAs which can function as oncogenes or tumor suppressor genes in human cancers. Emerging evidence reveals that deregulation of miRNAs contributes to the human non-small cell lung cancer (NSCLC). In the present study, we demonstrated that the expression levels of miR-132 were dramatically decreased in examined NSCLC cell lines and clinical NSCLC tissue samples. Then, we found that introduction of miR-132 significantly suppressed the migration and invasion of lung cancer cells in vitro, suggesting that miR-132 may be a novel tumor suppressor. Further studies indicated that the EMT-related transcription factor ZEB2 was one direct target genes of miR-132, evidenced by the direct binding of miR-132 with the 3' untranslated region (3' UTR) of ZEB2. Further, miR-132 could decrease the expression of ZEB2 at the levels of mRNA and protein. Notably, the EMT marker E-cadherin or vimentin, a downstream of ZEB2, was also down-regulated or up-regulated upon miR-132 treatment. Additionally, over-expressing or silencing ZEB2 was able to elevate or inhibit the migration and invasion of lung cancer cells, parallel to the effect of miR-132 on the lung cancer cells. Meanwhile, knockdown of ZEB2 reversed the enhanced migration and invasion mediated by anti-miR-132. These results indicate that miR-132 suppresses the migration and invasion of NSCLC cells through targeting ZEB2 involving the EMT process. Thus, our finding provides new insight into the mechanism of NSCLC progression. Therapeutically, miR-132 may serve as a potential target in the treatment of human lung cancer.
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Affiliation(s)
- Jiacong You
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
- * E-mail: (JCY); (QZ)
| | - Yang Li
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Nianzhen Fang
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Bin Liu
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Lingling Zu
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Rui Chang
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Xuebing Li
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Qinghua Zhou
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin, China
- * E-mail: (JCY); (QZ)
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Gomez GG, Volinia S, Croce CM, Zanca C, Li M, Emnett R, Gutmann DH, Brennan CW, Furnari FB, Cavenee WK. Suppression of microRNA-9 by mutant EGFR signaling upregulates FOXP1 to enhance glioblastoma tumorigenicity. Cancer Res 2014; 74:1429-39. [PMID: 24436148 DOI: 10.1158/0008-5472.can-13-2117] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The EGF receptor (EGFR) is amplified and mutated in glioblastoma, in which its common mutation (ΔEGFR, also called EGFRvIII) has a variety of activities that promote growth and inhibit death, thereby conferring a strong tumor-enhancing effect. This range of activities suggested to us that ΔEGFR might exert its influence through pleiotropic effectors, and we hypothesized that microRNAs might serve such a function. Here, we report that ΔEGFR specifically suppresses one such microRNA, namely miR-9, through the Ras/PI3K/AKT axis that it is known to activate. Correspondingly, expression of miR-9 antagonizes the tumor growth advantage conferred by ΔEGFR. Silencing of FOXP1, a miR-9 target, inhibits ΔEGFR-dependent tumor growth and, conversely, de-repression of FOXP1, as a consequence of miR-9 inhibition, increases tumorigenicity. FOXP1 was sufficient to increase tumor growth in the absence of oncogenic ΔEGFR signaling. The significance of these findings is underscored by our finding that high FOXP1 expression predicts poor survival in a cohort of 131 patients with glioblastoma. Collectively, these data suggest a novel regulatory mechanism by which ΔEGFR suppression of miR-9 upregulates FOXP1 to increase tumorigenicity.
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Affiliation(s)
- German G Gomez
- Authors' Affiliations: Ludwig Institute for Cancer Research, University of California San Diego, La Jolla, California; Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio; Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, Virginia; Department of Neurology, Washington University School of Medicine, St. Louis, Missouri; and Department of Neurosurgery, Memorial Sloan-Kettering Cancer Center, New York, New York
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Sethi S, Ali S, Kong D, Philip PA, Sarkar FH. Clinical Implication of MicroRNAs in Molecular Pathology. Clin Lab Med 2013; 33:773-86. [DOI: 10.1016/j.cll.2013.08.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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34
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Chen QY, Jiao DM, Wu YQ, Wang L, Hu HZ, Song J, Yan J, Wu LJ. Functional and pathway enrichment analysis for integrated regulatory network of high- and low-metastatic lung cancer. MOLECULAR BIOSYSTEMS 2013; 9:3080-90. [PMID: 24077187 DOI: 10.1039/c3mb70288j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Metastasis is a common feature of lung cancer, involving relationships between genes, proteins and miRNAs. However, lack of early detection and limited options for targeted therapies are weaknesses that cantribute to the dismal statistics observed in lung cancer metastasis. In this paper, gene expression profiling analysis for genes differentially expressed between high- (95D) and low-metastatic lung cancer cell lines (95C) was performed using gene annotation, pathway analysis, literature mining, and the integrated regulatory network as well as motif analysis of miRNA-DEG and TF-DEG. In addition, the expression of EGR-1 (early growth reponse-1) in surgically resected lung squamous carcinomas, adenocarcinomas and normal lung tissue was detected by immunohistochemistry to reveal the relationships between EGR-1 and lung cancer metastasis. A total of 570 different expressed genes (DEGs) were screened, the vast majority of up-regulated DEGs were connected to cell adhesion and focal adhesion. EGR-1 was observed in the center node of the regulatory network, which seems to play a role in the process of cancer metastasis, and further immunohistochemistry detection confirmed this reasoning. Besides EGR-1, several significant module-related DEGs were enriched in the pathway within cancer and focal adhesion according to KEGG pathway enrichment analysis of network modules. The construction of an integrated regulatory network and the functional prediction of EGR-1 provided us with the cytological basis of lung cancer metastasis research and an understanding of the mechanism of metastasis in lung cancer. EGR-1 should be considered as a potential target gene in therapeutic agent for lung cancer metastasis.
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Affiliation(s)
- Qing-yong Chen
- Department of Respiratory Disease, The 117th Hospital of PLA, Hangzhou, Zhejiang 310013, P.R. China.
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Clinical advances in molecular biomarkers for cancer diagnosis and therapy. Int J Mol Sci 2013; 14:14771-84. [PMID: 23863689 PMCID: PMC3742272 DOI: 10.3390/ijms140714771] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Revised: 06/28/2013] [Accepted: 07/03/2013] [Indexed: 12/20/2022] Open
Abstract
Cancer diagnosis is currently undergoing a paradigm shift with the incorporation of molecular biomarkers as part of routine diagnostic panel. The molecular alteration ranges from those involving the DNA, RNA, microRNAs (miRNAs) and proteins. The miRNAs are recently discovered small non-coding endogenous single-stranded RNAs that critically regulates the development, invasion and metastasis of cancers. They are altered in cancers and have the potential to serve as diagnostic markers for cancer. Moreover, deregulating their activity offers novel cancer therapeutic approaches. The availability of high throughput techniques for the identification of altered cellular molecules allowed their use in cancer diagnosis. Their application to a variety of body specimens from blood to tissues has been helpful for appreciating their use in the clinical context. The development of innovative antibodies for immunohistochemical detection of proteins also assists in diagnosis and risk stratification. Overall, the novel cancer diagnostic tools have extended their application as prognostic risk factors and can be used as targets for personalized medicine.
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36
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The Tumor Suppressor Roles of miR-433 and miR-127 in Gastric Cancer. Int J Mol Sci 2013; 14:14171-84. [PMID: 23880861 PMCID: PMC3742237 DOI: 10.3390/ijms140714171] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Revised: 06/26/2013] [Accepted: 06/27/2013] [Indexed: 12/27/2022] Open
Abstract
The discovery of microRNAs (miRNAs) provides a new and powerful tool for studying the mechanism, diagnosis and treatment of human cancers. Currently, the methylation epigenetic silencing of miRNAs with tumor suppressor features by CpG island hypermethylation is emerging as a common hallmark of different tumors. Here we showed that miR-433 and miR-127 were significantly down-regulated in gastric cancer (GC) tissues compared with the adjacent normal regions in 86 paired samples. Moreover, the lower level of miR-433 and miR-127 was associated with pM or pTNM stage in clinical gastric cancer patients. The restored expression of miR-433 and miR-127 in GC cells upon 5-Aza-CdR and TSA treatment suggested the loss of miR-433 and miR-127 was at least partly regulated by epigenetic modification in GC. Furthermore, the ectopic expression of miR-433 and miR-127 in gastric cancer cell lines HGC-27 inhibits cell proliferation, cell cycle progression, cell migration and invasion by directly interacting with the mRNA encoding oncogenic factors KRAS and MAPK4 respectively. Taken together, our results showed that miR-433 and miR-127 might act as tumor suppressors in GC, and it may provide novel diagnostic and therapeutic options for human GC clinical operation in the near future.
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