1
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Mishra A, Vasanthan M, Malliappan SP. Drug Repurposing: A Leading Strategy for New Threats and Targets. ACS Pharmacol Transl Sci 2024; 7:915-932. [PMID: 38633585 PMCID: PMC11019736 DOI: 10.1021/acsptsci.3c00361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 03/01/2024] [Accepted: 03/06/2024] [Indexed: 04/19/2024]
Abstract
Less than 6% of rare illnesses have an appropriate treatment option. Repurposed medications for new indications are a cost-effective and time-saving strategy that results in excellent success rates, which may significantly lower the risk associated with therapeutic development for rare illnesses. It is becoming a realistic alternative to repurposing "conventional" medications to treat joint and rare diseases considering the significant failure rates, high expenses, and sluggish stride of innovative medication advancement. This is due to delisted compounds, cheaper research fees, and faster development time frames. Repurposed drug competitors have been developed using strategic decisions based on data analysis, interpretation, and investigational approaches, but technical and regulatory restrictions must also be considered. Combining experimental and computational methodologies generates innovative new medicinal applications. It is a one-of-a-kind strategy for repurposing human-safe pharmaceuticals to treat uncommon and difficult-to-treat ailments. It is a very effective method for discovering and creating novel medications. Several pharmaceutical firms have developed novel therapies by repositioning old medications. Repurposing drugs is practical, cost-effective, and speedy and generally involves lower risks when compared to developing a new drug from the beginning.
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Affiliation(s)
- Ashish
Sriram Mishra
- Department
of Pharmaceutics, SRM College of Pharmacy, SRM Institute of Science and Technology, Kattankulathur, 603202, Tamil Nadu, India
| | - Manimaran Vasanthan
- Department
of Pharmaceutics, SRM College of Pharmacy, SRM Institute of Science and Technology, Kattankulathur, 603202, Tamil Nadu, India
| | - Sivakumar Ponnurengam Malliappan
- School
of Medicine and Pharmacy, Duy Tan University, Da Nang Vietnam, Institute
of Research and Development, Duy Tan University, Da Nang 550000, Vietnam
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2
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Mannarino L, Ravasio N, D’Incalci M, Marchini S, Masseroli M. In-Silico Identification of Novel Pharmacological Synergisms: The Trabectedin Case. Int J Mol Sci 2024; 25:2059. [PMID: 38396735 PMCID: PMC10888651 DOI: 10.3390/ijms25042059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/06/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
The in-silico strategy of identifying novel uses for already existing drugs, known as drug repositioning, has enhanced drug discovery. Previous studies have shown a positive correlation between expression changes induced by the anticancer agent trabectedin and those caused by irinotecan, a topoisomerase I inhibitor. Leveraging the availability of transcriptional datasets, we developed a general in-silico drug-repositioning approach that we applied to investigate novel trabectedin synergisms. We set a workflow allowing the identification of genes selectively modulated by a drug and possible novel drug interactions. To show its effectiveness, we selected trabectedin as a case-study drug. We retrieved eight transcriptional cancer datasets including controls and samples treated with trabectedin or its analog lurbinectedin. We compared gene signature associated with each dataset to the 476,251 signatures from the Connectivity Map database. The most significant connections referred to mitomycin-c, topoisomerase II inhibitors, a PKC inhibitor, a Chk1 inhibitor, an antifungal agent, and an antagonist of the glutamate receptor. Genes coherently modulated by the drugs were involved in cell cycle, PPARalpha, and Rho GTPases pathways. Our in-silico approach for drug synergism identification showed that trabectedin modulates specific pathways that are shared with other drugs, suggesting possible synergisms.
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Affiliation(s)
- Laura Mannarino
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, 20072 Milan, Italy;
- Laboratory of Cancer Pharmacology, IRCCS Humanitas Research Hospital, Via Manzoni 56, Rozzano, 20089 Milan, Italy;
| | - Nicholas Ravasio
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, 20133 Milan, Italy; (N.R.); (M.M.)
| | - Maurizio D’Incalci
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, Pieve Emanuele, 20072 Milan, Italy;
- Laboratory of Cancer Pharmacology, IRCCS Humanitas Research Hospital, Via Manzoni 56, Rozzano, 20089 Milan, Italy;
| | - Sergio Marchini
- Laboratory of Cancer Pharmacology, IRCCS Humanitas Research Hospital, Via Manzoni 56, Rozzano, 20089 Milan, Italy;
| | - Marco Masseroli
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, 20133 Milan, Italy; (N.R.); (M.M.)
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3
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Chai B, Efstathiou C, Yue H, Draviam VM. Opportunities and challenges for deep learning in cell dynamics research. Trends Cell Biol 2023:S0962-8924(23)00228-3. [PMID: 38030542 DOI: 10.1016/j.tcb.2023.10.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/30/2023] [Accepted: 10/13/2023] [Indexed: 12/01/2023]
Abstract
The growth of artificial intelligence (AI) has led to an increase in the adoption of computer vision and deep learning (DL) techniques for the evaluation of microscopy images and movies. This adoption has not only addressed hurdles in quantitative analysis of dynamic cell biological processes but has also started to support advances in drug development, precision medicine, and genome-phenome mapping. We survey existing AI-based techniques and tools, as well as open-source datasets, with a specific focus on the computational tasks of segmentation, classification, and tracking of cellular and subcellular structures and dynamics. We summarise long-standing challenges in microscopy video analysis from a computational perspective and review emerging research frontiers and innovative applications for DL-guided automation in cell dynamics research.
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Affiliation(s)
- Binghao Chai
- School of Biological and Behavioural Sciences, Queen Mary University of London (QMUL), London E1 4NS, UK
| | - Christoforos Efstathiou
- School of Biological and Behavioural Sciences, Queen Mary University of London (QMUL), London E1 4NS, UK
| | - Haoran Yue
- School of Biological and Behavioural Sciences, Queen Mary University of London (QMUL), London E1 4NS, UK
| | - Viji M Draviam
- School of Biological and Behavioural Sciences, Queen Mary University of London (QMUL), London E1 4NS, UK; The Alan Turing Institute, London NW1 2DB, UK.
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4
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Dang D, Efstathiou C, Sun D, Yue H, Sastry NR, Draviam VM. Deep learning techniques and mathematical modeling allow 3D analysis of mitotic spindle dynamics. J Cell Biol 2023; 222:213913. [PMID: 36880744 PMCID: PMC9998659 DOI: 10.1083/jcb.202111094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/03/2022] [Accepted: 01/31/2023] [Indexed: 03/08/2023] Open
Abstract
Time-lapse microscopy movies have transformed the study of subcellular dynamics. However, manual analysis of movies can introduce bias and variability, obscuring important insights. While automation can overcome such limitations, spatial and temporal discontinuities in time-lapse movies render methods such as 3D object segmentation and tracking difficult. Here, we present SpinX, a framework for reconstructing gaps between successive image frames by combining deep learning and mathematical object modeling. By incorporating expert feedback through selective annotations, SpinX identifies subcellular structures, despite confounding neighbor-cell information, non-uniform illumination, and variable fluorophore marker intensities. The automation and continuity introduced here allows the precise 3D tracking and analysis of spindle movements with respect to the cell cortex for the first time. We demonstrate the utility of SpinX using distinct spindle markers, cell lines, microscopes, and drug treatments. In summary, SpinX provides an exciting opportunity to study spindle dynamics in a sophisticated way, creating a framework for step changes in studies using time-lapse microscopy.
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Affiliation(s)
- David Dang
- School of Biological and Behavioural Sciences, Queen Mary University of London , London, UK.,Department of Informatics, King's College London , London, UK
| | | | - Dijue Sun
- School of Biological and Behavioural Sciences, Queen Mary University of London , London, UK
| | - Haoran Yue
- School of Biological and Behavioural Sciences, Queen Mary University of London , London, UK
| | | | - Viji M Draviam
- School of Biological and Behavioural Sciences, Queen Mary University of London , London, UK
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5
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Torricelli F, Sauta E, Manicardi V, Mandato VD, Palicelli A, Ciarrocchi A, Manzotti G. An Innovative Drug Repurposing Approach to Restrain Endometrial Cancer Metastatization. Cells 2023; 12:cells12050794. [PMID: 36899930 PMCID: PMC10001006 DOI: 10.3390/cells12050794] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/22/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
BACKGROUND Endometrial cancer (EC) is the most common gynecologic tumor and the world's fourth most common cancer in women. Most patients respond to first-line treatments and have a low risk of recurrence, but refractory patients, and those with metastatic cancer at diagnosis, remain with no treatment options. Drug repurposing aims to discover new clinical indications for existing drugs with known safety profiles. It provides ready-to-use new therapeutic options for highly aggressive tumors for which standard protocols are ineffective, such as high-risk EC. METHODS Here, we aimed at defining new therapeutic opportunities for high-risk EC using an innovative and integrated computational drug repurposing approach. RESULTS We compared gene-expression profiles, from publicly available databases, of metastatic and non-metastatic EC patients being metastatization the most severe feature of EC aggressiveness. A comprehensive analysis of transcriptomic data through a two-arm approach was applied to obtain a robust prediction of drug candidates. CONCLUSIONS Some of the identified therapeutic agents are already successfully used in clinical practice to treat other types of tumors. This highlights the potential to repurpose them for EC and, therefore, the reliability of the proposed approach.
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Affiliation(s)
- Federica Torricelli
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Viale Risorgimento 80, 42123 Reggio Emilia, Italy
| | - Elisabetta Sauta
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Viale Risorgimento 80, 42123 Reggio Emilia, Italy
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, 27100 Pavia, Italy
| | - Veronica Manicardi
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Viale Risorgimento 80, 42123 Reggio Emilia, Italy
- Department of Electrical, Computer and Biomedical Engineering, University of Pavia, 27100 Pavia, Italy
- Clinical and Experimental Medicine PhD Program, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Vincenzo Dario Mandato
- Unit of Obstetrics and Gynaecology, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
| | - Andrea Palicelli
- Pathology Unit, Department of Oncology and Advanced Technologies, Azienda USL-IRCCS di Reggio Emilia, 42123 Reggio Emilia, Italy
| | - Alessia Ciarrocchi
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Viale Risorgimento 80, 42123 Reggio Emilia, Italy
| | - Gloria Manzotti
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Viale Risorgimento 80, 42123 Reggio Emilia, Italy
- Correspondence: ; Tel.: +39-05-2229-5477
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6
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Liu Z, Yang H, Chen Z, Jing C. A novel chromatin regulator-related immune checkpoint related gene prognostic signature and potential candidate drugs for endometrial cancer patients. Hereditas 2022; 159:40. [PMID: 36253800 PMCID: PMC9578220 DOI: 10.1186/s41065-022-00253-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 09/22/2022] [Indexed: 11/14/2022] Open
Abstract
Background Endometrial cancer (EC) is the most common gynecologic malignancy in developed countries and its prevalence is increasing. As an emerging therapy with a promising efficacy, immunotherapy has been extensively applied in the treatment of solid tumors. In addition, chromatin regulators (CRs), as essential upstream regulators of epigenetics, play a significant role in tumorigenesis and cancer development. Methods CRs and immune checkpoint-related genes (ICRGs) were obtained from the previous top research. The Genome Cancer Atlas (TCGA) was utilized to acquire the mRNA expression and clinical information of patients with EC. Correlation analysis was utilized for screen CRs-related ICRGs (CRRICRGs). By Cox regression and least absolute shrinkage and selection operator (LASSO) analysis, prognosis related CRRICRGs were screened out and risk model was constructed. The Kaplan–Meier curve was used to estimate the prognosis between high- and low-risk group. By comparing the IC50 value, the drugs sensitivity difference was explored. We obtained small molecule drugs for the treatment of UCEC patients based on CAMP dataset. Results We successfully constructed a 9 CRRICRs-based prognostic signature for patients with UCEC and found the riskscore was an independent prognostic factor. The results of functional analysis suggested that CRRICRGs may be involved in immune processes associated with cancer. Immune characteristics analysis provided further evidence that the CRRICRGs-based model was correlated with immune cells infiltration and immune checkpoint. Eight small molecule drugs that may be effective for the treatment of UCEC patients were screened. Effective drugs identified by drug sensitivity profiling in high- and low-risk groups. Conclusion In summary, our study provided novel insights into the function of CRRICRGs in UCEC. We also developed a reliable prognostic panel for the survival of patients with UCEC. Supplementary Information The online version contains supplementary material available at 10.1186/s41065-022-00253-w.
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Affiliation(s)
- Zesi Liu
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Dalian Medical University, Dalian, 116000, Liaoning Province, China
| | - Hongxia Yang
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Dalian Medical University, Dalian, 116000, Liaoning Province, China
| | - Ziyu Chen
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Dalian Medical University, Dalian, 116000, Liaoning Province, China
| | - Chunli Jing
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Dalian Medical University, Dalian, 116000, Liaoning Province, China.
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7
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Zareifi DS, Chaliotis O, Chala N, Meimetis N, Sofotasiou M, Zeakis K, Pantiora E, Vezakis A, Matsopoulos GK, Fragulidis G, Alexopoulos LG. A network-based computational and experimental framework for repurposing compounds towards the treatment of Non-Alcoholic Fatty Liver Disease. iScience 2022; 25:103890. [PMID: 35252807 PMCID: PMC8889147 DOI: 10.1016/j.isci.2022.103890] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 01/11/2022] [Accepted: 02/04/2022] [Indexed: 11/29/2022] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is among the most common liver pathologies, however, none approved condition-specific therapy yet exists. The present study introduces a drug repositioning (DR) approach that combines in vitro steatosis models with a network-based computational platform, constructed upon genomic data from diseased liver biopsies and compound-treated cell lines, to propose effectively repositioned therapeutic compounds. The introduced in silico approach screened 20′000 compounds, while complementary in vitro and proteomic assays were developed to test the efficacy of the 46 in silico predictions. This approach successfully identified six compounds, including the known anti-steatogenic drugs resveratrol and sirolimus. In short, gallamine triethiotide, diflorasone, fenoterol, and pralidoxime ameliorate steatosis similarly to resveratrol/sirolimus. The implementation holds great potential in reducing screening time in the early drug discovery stages and in delivering promising compounds for in vivo testing. A computational and experimental drug-screening platform for NAFLD was created This framework evaluates in silico and validates in vitro a great number of compounds 20′000 compounds were screened in silico and 21 were selected for validation Six compounds reversed fully or partially the steatotic phenotype
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Affiliation(s)
- Danae Stella Zareifi
- School of Mechanical Engineering, National Technical University of Athens, Iroon Polytechneiou 9, Zografou, 15780 Athens, Greece
| | - Odysseas Chaliotis
- School of Mechanical Engineering, National Technical University of Athens, Iroon Polytechneiou 9, Zografou, 15780 Athens, Greece
| | - Nafsika Chala
- School of Mechanical Engineering, National Technical University of Athens, Iroon Polytechneiou 9, Zografou, 15780 Athens, Greece
| | - Nikos Meimetis
- School of Mechanical Engineering, National Technical University of Athens, Iroon Polytechneiou 9, Zografou, 15780 Athens, Greece
| | - Maria Sofotasiou
- School of Mechanical Engineering, National Technical University of Athens, Iroon Polytechneiou 9, Zografou, 15780 Athens, Greece
| | - Konstantinos Zeakis
- School of Electrical Engineering, National Technical University of Athens, 15780 Athens, Greece
| | - Eirini Pantiora
- 2nd Department of Surgery, Aretaieio Hospital, University of Athens, School of Medicine, 11528, Athens, Greece
| | - Antonis Vezakis
- 2nd Department of Surgery, Aretaieio Hospital, University of Athens, School of Medicine, 11528, Athens, Greece
| | - George K. Matsopoulos
- School of Electrical Engineering, National Technical University of Athens, 15780 Athens, Greece
| | - Georgios Fragulidis
- 2nd Department of Surgery, Aretaieio Hospital, University of Athens, School of Medicine, 11528, Athens, Greece
| | - Leonidas G. Alexopoulos
- School of Mechanical Engineering, National Technical University of Athens, Iroon Polytechneiou 9, Zografou, 15780 Athens, Greece
- ProtATonce Ltd, Patriarchou Grigoriou & Neapoleos Demokritos Science Park, Building#27, Agia Paraskevi GR15343, Greece
- Corresponding author
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8
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Song X, Conti D, Shrestha RL, Braun D, Draviam VM. Counteraction between Astrin-PP1 and Cyclin-B-CDK1 pathways protects chromosome-microtubule attachments independent of biorientation. Nat Commun 2021; 12:7010. [PMID: 34853300 PMCID: PMC8636589 DOI: 10.1038/s41467-021-27131-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 11/02/2021] [Indexed: 02/08/2023] Open
Abstract
Defects in chromosome-microtubule attachment can cause chromosomal instability (CIN), frequently associated with infertility and aggressive cancers. Chromosome-microtubule attachment is mediated by a large macromolecular structure, the kinetochore. Sister kinetochores of each chromosome are pulled by microtubules from opposing spindle-poles, a state called biorientation which prevents chromosome missegregation. Kinetochore-microtubule attachments that lack the opposing-pull are detached by Aurora-B/Ipl1. It is unclear how mono-oriented attachments that precede biorientation are spared despite the lack of opposing-pull. Using an RNAi-screen, we uncover a unique role for the Astrin-SKAP complex in protecting mono-oriented attachments. We provide evidence of domains in the microtubule-end associated protein that sense changes specific to end-on kinetochore-microtubule attachments and assemble an outer-kinetochore crescent to stabilise attachments. We find that Astrin-PP1 and Cyclin-B-CDK1 pathways counteract each other to preserve mono-oriented attachments. Thus, CIN prevention pathways are not only surveying attachment defects but also actively recognising and stabilising mature attachments independent of biorientation. Chromosome instability frequently occurs due to issues with chromosome-microtubule attachments. Here the authors show that the Astrin-PP1 and Cyclin-B-CDK1 pathways counteract each other to protect chromosome-microtubule attachments independent of biorientation.
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Affiliation(s)
- Xinhong Song
- School of Biological and Chemical Sciences, Queen Mary, University of London, London, E1 4NS, UK
| | - Duccio Conti
- School of Biological and Chemical Sciences, Queen Mary, University of London, London, E1 4NS, UK.,Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Straße 11, 44227, Dortmund, Germany
| | - Roshan L Shrestha
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK.,Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Dominique Braun
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| | - Viji M Draviam
- School of Biological and Chemical Sciences, Queen Mary, University of London, London, E1 4NS, UK. .,Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK.
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9
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Wang F, Ding Y, Lei X, Liao B, Wu FX. Human Protein Complex-Based Drug Signatures for Personalized Cancer Medicine. IEEE J Biomed Health Inform 2021; 25:4079-4088. [PMID: 34665747 DOI: 10.1109/jbhi.2021.3120933] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Disease signature-based drug repositioning approaches typically first identify a disease signature from gene expression profiles of disease samples to represent a particular disease. Then such a disease signature is connected with the drug-induced gene expression profiles to find potential drugs for the particular disease. In order to obtain reliable disease signatures, the size of disease samples should be large enough, which is not always a single case in practice, especially for personalized medicine. On the other hand, the sample sizes of drug-induced gene expression profiles are generally large. In this study, we propose a new drug repositioning approach (HDgS), in which the drug signature is first identified from drug-induced gene expression profiles, and then connected to the gene expression profiles of disease samples to find the potential drugs for patients. In order to take the dependencies among genes into account, the human protein complexes (HPC) are used to define the drug signature. The proposed HDgS is applied to the drug-induced gene expression profiles in LINCS and several types of cancer samples. The results indicate that the HPC-based drug signature can effectively find drug candidates for patients and that the proposed HDgS can be applied for personalized medicine with even one patient sample.
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10
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Chen F, Shi Q, Pei F, Vogt A, Porritt RA, Garcia G, Gomez AC, Cheng MH, Schurdak ME, Liu B, Chan SY, Arumugaswami V, Stern AM, Taylor DL, Arditi M, Bahar I. A systems-level study reveals host-targeted repurposable drugs against SARS-CoV-2 infection. Mol Syst Biol 2021; 17:e10239. [PMID: 34339582 PMCID: PMC8328275 DOI: 10.15252/msb.202110239] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 12/22/2022] Open
Abstract
Understanding the mechanism of SARS-CoV-2 infection and identifying potential therapeutics are global imperatives. Using a quantitative systems pharmacology approach, we identified a set of repurposable and investigational drugs as potential therapeutics against COVID-19. These were deduced from the gene expression signature of SARS-CoV-2-infected A549 cells screened against Connectivity Map and prioritized by network proximity analysis with respect to disease modules in the viral-host interactome. We also identified immuno-modulating compounds aiming at suppressing hyperinflammatory responses in severe COVID-19 patients, based on the transcriptome of ACE2-overexpressing A549 cells. Experiments with Vero-E6 cells infected by SARS-CoV-2, as well as independent syncytia formation assays for probing ACE2/SARS-CoV-2 spike protein-mediated cell fusion using HEK293T and Calu-3 cells, showed that several predicted compounds had inhibitory activities. Among them, salmeterol, rottlerin, and mTOR inhibitors exhibited antiviral activities in Vero-E6 cells; imipramine, linsitinib, hexylresorcinol, ezetimibe, and brompheniramine impaired viral entry. These novel findings provide new paths for broadening the repertoire of compounds pursued as therapeutics against COVID-19.
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Affiliation(s)
- Fangyuan Chen
- Department of Computational and Systems BiologySchool of MedicineUniversity of PittsburghPittsburghPAUSA
- School of MedicineTsinghua UniversityBeijingChina
| | - Qingya Shi
- Department of Computational and Systems BiologySchool of MedicineUniversity of PittsburghPittsburghPAUSA
- School of MedicineTsinghua UniversityBeijingChina
| | - Fen Pei
- Department of Computational and Systems BiologySchool of MedicineUniversity of PittsburghPittsburghPAUSA
- University of Pittsburgh Drug Discovery InstitutePittsburghPAUSA
| | - Andreas Vogt
- Department of Computational and Systems BiologySchool of MedicineUniversity of PittsburghPittsburghPAUSA
- University of Pittsburgh Drug Discovery InstitutePittsburghPAUSA
| | - Rebecca A Porritt
- Department of PediatricsDivision of Pediatric Infectious Diseases and ImmunologyCedars‐Sinai Medical CenterLos AngelesCAUSA
- Biomedical Sciences, Infectious and Immunologic Diseases Research CenterCedars‐Sinai Medical CenterLos AngelesCAUSA
| | - Gustavo Garcia
- Department of Molecular and Medical PharmacologyDavid Geffen School of MedicineUniversity of CaliforniaLos AngelesCAUSA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell ResearchUniversity of CaliforniaLos AngelesCAUSA
| | - Angela C Gomez
- Department of PediatricsDivision of Pediatric Infectious Diseases and ImmunologyCedars‐Sinai Medical CenterLos AngelesCAUSA
| | - Mary Hongying Cheng
- Department of Computational and Systems BiologySchool of MedicineUniversity of PittsburghPittsburghPAUSA
| | - Mark E Schurdak
- Department of Computational and Systems BiologySchool of MedicineUniversity of PittsburghPittsburghPAUSA
- University of Pittsburgh Drug Discovery InstitutePittsburghPAUSA
| | - Bing Liu
- Department of Computational and Systems BiologySchool of MedicineUniversity of PittsburghPittsburghPAUSA
| | - Stephen Y Chan
- Pittsburgh Heart, Lung, Blood, and Vascular Medicine InstituteUniversity of Pittsburgh Medical CenterPittsburghPAUSA
- Division of CardiologyDepartment of MedicineUniversity of Pittsburgh Medical CenterPittsburghPAUSA
| | - Vaithilingaraja Arumugaswami
- Department of Molecular and Medical PharmacologyDavid Geffen School of MedicineUniversity of CaliforniaLos AngelesCAUSA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell ResearchUniversity of CaliforniaLos AngelesCAUSA
| | - Andrew M Stern
- Department of Computational and Systems BiologySchool of MedicineUniversity of PittsburghPittsburghPAUSA
- University of Pittsburgh Drug Discovery InstitutePittsburghPAUSA
| | - D Lansing Taylor
- Department of Computational and Systems BiologySchool of MedicineUniversity of PittsburghPittsburghPAUSA
- University of Pittsburgh Drug Discovery InstitutePittsburghPAUSA
| | - Moshe Arditi
- Department of PediatricsDivision of Pediatric Infectious Diseases and ImmunologyCedars‐Sinai Medical CenterLos AngelesCAUSA
- Biomedical Sciences, Infectious and Immunologic Diseases Research CenterCedars‐Sinai Medical CenterLos AngelesCAUSA
| | - Ivet Bahar
- Department of Computational and Systems BiologySchool of MedicineUniversity of PittsburghPittsburghPAUSA
- University of Pittsburgh Drug Discovery InstitutePittsburghPAUSA
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11
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Multinucleation associated DNA damage blocks proliferation in p53-compromised cells. Commun Biol 2021; 4:451. [PMID: 33837239 PMCID: PMC8035210 DOI: 10.1038/s42003-021-01979-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 03/11/2021] [Indexed: 02/06/2023] Open
Abstract
Nuclear atypia is one of the hallmarks of cancers. Here, we perform single-cell tracking studies to determine the immediate and long-term impact of nuclear atypia. Tracking the fate of newborn cells exhibiting nuclear atypia shows that multinucleation, unlike other forms of nuclear atypia, blocks proliferation in p53-compromised cells. Because ~50% of cancers display compromised p53, we explored how multinucleation blocks proliferation. Multinucleation increases 53BP1-decorated nuclear bodies (DNA damage repair platforms), along with a heterogeneous reduction in transcription and protein accumulation across the multi-nucleated compartments. Multinucleation Associated DNA Damage associated with 53BP1-bodies remains unresolved for days, despite an intact NHEJ machinery that repairs laser-induced DNA damage within minutes. Persistent DNA damage, a DNA replication block, and reduced phospho-Rb, reveal a novel replication stress independent cell cycle arrest caused by mitotic lesions. These findings call for segregating protective and prohibitive nuclear atypia to inform therapeutic approaches aimed at limiting tumour heterogeneity. Hart et al. track newborn single cells by live microscopy after inducing a variety of nuclear atypia by CENP-E inhibitor treatment. They find that that multinucleation, unlike other forms of nuclear atypia, blocks proliferation independently of p53 and is associated with persistent 53BP1 DNA damage foci, thus providing insights into the consequences of multinucleation, often observed in disease states.
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12
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Identification of metastasis and prognosis-associated genes for serous ovarian cancer. Biosci Rep 2021; 40:225195. [PMID: 32510146 PMCID: PMC7317593 DOI: 10.1042/bsr20194324] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 05/21/2020] [Accepted: 06/03/2020] [Indexed: 12/19/2022] Open
Abstract
Serous ovarian cancer is one of the most fatal gynecological tumors with an extremely low 5-year survival rate. Most patients are diagnosed at an advanced stage with wide metastasis. The dysregulation of genes serves an important role in the metastasis progression of ovarian cancer. Differentially expressed genes (DEGs) between primary tumors and metastases of serous ovarian cancer were screened out in the gene expression profile of GSE73168 from Gene Expression Omnibus (GEO). Cytoscape plugin cytoHubba and weighted gene co-expression network analysis (WGCNA) were utilized to select hub genes. Univariate and multivariate Cox regression analyses were used to screen out prognosis-associated genes. Furthermore, the Oncomine validation, prognostic analysis, methylation mechanism, gene set enrichment analysis (GSEA), TIMER database analysis and administration of candidate molecular drugs were conducted for hub genes. Nine hundred and fifty-seven DEGs were identified in the gene expression profile of GSE73168. After using Cytoscape plugin cytoHubba, 83 genes were verified. In co-expression network, the blue module was most closely related to tumor metastasis. Furthermore, the genes in Cytoscape were analyzed, showing that the blue module and screened 17 genes were closely associated with tumor metastasis. Univariate and multivariate Cox regression revealed that the age, stage and STMN2 were independent prognostic factors. The Cancer Genome Atlas (TCGA) suggested that the up-regulated expression of STMN2 was related to poor prognosis of ovarian cancer. Thus, STMN2 was considered as a new key gene after expression validation, survival analysis and TIMER database validation. GSEA confirmed that STMN2 was probably involved in ECM receptor interaction, focal adhesion, TGF beta signaling pathway and MAPK signaling pathway. Furthermore, three candidate small molecule drugs for tumor metastasis (diprophylline, valinomycin and anisomycin) were screened out. The quantitative reverse transcription-polymerase chain reaction (qRT-PCR) and western blot showed that STMN2 was highly expressed in ovarian cancer tissue and ovarian cancer cell lines. Further studies are needed to investigate these prognosis-associated genes for new therapy target.
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13
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Talikka M, Belcastro V, Boué S, Marescotti D, Hoeng J, Peitsch MC. Applying Systems Toxicology Methods to Drug Safety. SYSTEMS MEDICINE 2021. [DOI: 10.1016/b978-0-12-801238-3.11522-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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14
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Valli D, Gruszka AM, Alcalay M. Has Drug Repurposing Fulfilled its Promise in Acute Myeloid Leukaemia? J Clin Med 2020; 9:E1892. [PMID: 32560371 PMCID: PMC7356362 DOI: 10.3390/jcm9061892] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/11/2020] [Accepted: 06/15/2020] [Indexed: 12/16/2022] Open
Abstract
Drug repurposing is a method of drug discovery that consists of finding a new therapeutic context for an old drug. Compound identification arises from screening of large libraries of active compounds, through interrogating databases of cell line gene expression response upon treatment or by merging several types of information concerning disease-drug relationships. Although, there is a general consensus on the potential and advantages of this drug discovery modality, at the practical level to-date no non-anti-cancer repurposed compounds have been introduced into standard acute myeloid leukaemia (AML) management, albeit that preclinical validation yielded several candidates. The review presents the state-of-the-art drug repurposing approach in AML and poses the question of what has to be done in order to take a full advantage of it, both at the stage of screening design and later when progressing from the preclinical to the clinical phases of drug development. We argue that improvements are needed to model and read-out systems as well as to screening technologies, but also to more funding and trust in drug repurposing strategies.
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Affiliation(s)
- Debora Valli
- Department of Experimental Oncology, Istituto Europeo di Oncologia IRCCS, Via Adamello 16, 20 139 Milan, Italy; (D.V.); (M.A.)
| | - Alicja M. Gruszka
- Department of Experimental Oncology, Istituto Europeo di Oncologia IRCCS, Via Adamello 16, 20 139 Milan, Italy; (D.V.); (M.A.)
| | - Myriam Alcalay
- Department of Experimental Oncology, Istituto Europeo di Oncologia IRCCS, Via Adamello 16, 20 139 Milan, Italy; (D.V.); (M.A.)
- Department of Oncology and Hemato-Oncology, University of Milan, Via Festa del Perdono 7, 20 122 Milan, Italy
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15
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Ceddia G, Pinoli P, Ceri S, Masseroli M. Matrix Factorization-based Technique for Drug Repurposing Predictions. IEEE J Biomed Health Inform 2020; 24:3162-3172. [PMID: 32365039 DOI: 10.1109/jbhi.2020.2991763] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Classical drug design methodologies are hugely costly and time-consuming, with approximately 85% of the new proposed molecules failing in the first three phases of the FDA drug approval process. Thus, strategies to find alternative indications for already approved drugs that leverage computational methods are of crucial relevance. We previously demonstrated the efficacy of the Non-negative Matrix Tri-Factorization, a method that allows exploiting both data integration and machine learning, to infer novel indications for approved drugs. In this work, we present an innovative enhancement of the NMTF method that consists of a shortest-path evaluation of drug-protein pairs using the protein-to-protein interaction network. This approach allows inferring novel protein targets that were never considered as drug targets before, increasing the information fed to the NMTF method. Indeed, this novel advance enables the investigation of drug-centric predictions, simultaneously identifying therapeutic classes, protein targets and diseases associated with a particular drug. To test our methodology, we applied the NMTF and shortest-path enhancement methods to an outdated collection of data and compared the predictions against the most updated version, obtaining very good performance, with an Average Precision Score of 0.82. The data enhancement strategy allowed increasing the number of putative protein targets from 3,691 to 15,295, while the predictive performance of the method is slightly increased. Finally, we also validated our top-scored predictions according to the literature, finding relevant confirmation of predicted interactions between drugs and protein targets, as well as of predicted annotations between drugs and both therapeutic classes and diseases.
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16
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Conti D, Gul P, Islam A, Martín-Durán JM, Pickersgill RW, Draviam VM. Kinetochores attached to microtubule-ends are stabilised by Astrin bound PP1 to ensure proper chromosome segregation. eLife 2019; 8:49325. [PMID: 31808746 PMCID: PMC6930079 DOI: 10.7554/elife.49325] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 12/01/2019] [Indexed: 12/12/2022] Open
Abstract
Microtubules segregate chromosomes by attaching to macromolecular kinetochores. Only microtubule-end attached kinetochores can be pulled apart; how these end-on attachments are selectively recognised and stabilised is not known. Using the kinetochore and microtubule-associated protein, Astrin, as a molecular probe, we show that end-on attachments are rapidly stabilised by spatially-restricted delivery of PP1 near the C-terminus of Ndc80, a core kinetochore-microtubule linker. PP1 is delivered by the evolutionarily conserved tail of Astrin and this promotes Astrin’s own enrichment creating a highly-responsive positive feedback, independent of biorientation. Abrogating Astrin:PP1-delivery disrupts attachment stability, which is not rescued by inhibiting Aurora-B, an attachment destabiliser, but is reversed by artificially tethering PP1 near the C-terminus of Ndc80. Constitutive Astrin:PP1-delivery disrupts chromosome congression and segregation, revealing a dynamic mechanism for stabilising attachments. Thus, Astrin-PP1 mediates a dynamic ‘lock’ that selectively and rapidly stabilises end-on attachments, independent of biorientation, and ensures proper chromosome segregation.
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Affiliation(s)
- Duccio Conti
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom.,Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Parveen Gul
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Asifa Islam
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - José M Martín-Durán
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Richard W Pickersgill
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Viji M Draviam
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom.,Department of Genetics, University of Cambridge, Cambridge, United Kingdom
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17
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Keenan AB, Wojciechowicz ML, Wang Z, Jagodnik KM, Jenkins SL, Lachmann A, Ma'ayan A. Connectivity Mapping: Methods and Applications. Annu Rev Biomed Data Sci 2019. [DOI: 10.1146/annurev-biodatasci-072018-021211] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Connectivity mapping resources consist of signatures representing changes in cellular state following systematic small-molecule, disease, gene, or other form of perturbations. Such resources enable the characterization of signatures from novel perturbations based on similarity; provide a global view of the space of many themed perturbations; and allow the ability to predict cellular, tissue, and organismal phenotypes for perturbagens. A signature search engine enables hypothesis generation by finding connections between query signatures and the database of signatures. This framework has been used to identify connections between small molecules and their targets, to discover cell-specific responses to perturbations and ways to reverse disease expression states with small molecules, and to predict small-molecule mimickers for existing drugs. This review provides a historical perspective and the current state of connectivity mapping resources with a focus on both methodology and community implementations.
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Affiliation(s)
- Alexandra B. Keenan
- Department of Pharmacological Sciences and Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Megan L. Wojciechowicz
- Department of Pharmacological Sciences and Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zichen Wang
- Department of Pharmacological Sciences and Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kathleen M. Jagodnik
- Department of Pharmacological Sciences and Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sherry L. Jenkins
- Department of Pharmacological Sciences and Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alexander Lachmann
- Department of Pharmacological Sciences and Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Avi Ma'ayan
- Department of Pharmacological Sciences and Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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18
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Yang X, Wang Y, Byrne R, Schneider G, Yang S. Concepts of Artificial Intelligence for Computer-Assisted Drug Discovery. Chem Rev 2019; 119:10520-10594. [PMID: 31294972 DOI: 10.1021/acs.chemrev.8b00728] [Citation(s) in RCA: 343] [Impact Index Per Article: 68.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Artificial intelligence (AI), and, in particular, deep learning as a subcategory of AI, provides opportunities for the discovery and development of innovative drugs. Various machine learning approaches have recently (re)emerged, some of which may be considered instances of domain-specific AI which have been successfully employed for drug discovery and design. This review provides a comprehensive portrayal of these machine learning techniques and of their applications in medicinal chemistry. After introducing the basic principles, alongside some application notes, of the various machine learning algorithms, the current state-of-the art of AI-assisted pharmaceutical discovery is discussed, including applications in structure- and ligand-based virtual screening, de novo drug design, physicochemical and pharmacokinetic property prediction, drug repurposing, and related aspects. Finally, several challenges and limitations of the current methods are summarized, with a view to potential future directions for AI-assisted drug discovery and design.
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Affiliation(s)
- Xin Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital , Sichuan University , Chengdu , Sichuan 610041 , China
| | - Yifei Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital , Sichuan University , Chengdu , Sichuan 610041 , China
| | - Ryan Byrne
- ETH Zurich , Department of Chemistry and Applied Biosciences , Vladimir-Prelog-Weg 4 , CH-8093 Zurich , Switzerland
| | - Gisbert Schneider
- ETH Zurich , Department of Chemistry and Applied Biosciences , Vladimir-Prelog-Weg 4 , CH-8093 Zurich , Switzerland
| | - Shengyong Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital , Sichuan University , Chengdu , Sichuan 610041 , China
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19
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Liu J, Nie S, Liang J, Jiang Y, Wan Y, Zhou S, Cheng W. Competing endogenous RNA network of endometrial carcinoma: A comprehensive analysis. J Cell Biochem 2019; 120:15648-15660. [PMID: 31056798 DOI: 10.1002/jcb.28831] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 02/23/2019] [Accepted: 02/28/2019] [Indexed: 12/18/2022]
Abstract
Competing endogenous RNA (ceRNA) network is dysregulated in the initiation and progression of tumors. In the present study, we explored the regulatory mechanism of ceRNA in endometrial carcinoma (EC) and the potential key molecules with potential value in the diagnosis, treatment, and prognosis of EC. The long noncoding RNAs (lncRNAs) and messenger RNAs (mRNAs) expression profiles (552 EC tissues and 35 nontumor tissues) and microRNAs (miRNAs) expression profiles (546 EC tissues and 33 nontumor tissues) were downloaded from The Cancer Genome Atlas database to identify differentially expressed RNAs (DERNAs) in EC. An integrated bioinformatics analysis was used to construct an EC-specific ceRNA network and select key molecules. As a result, 96 differentially expressed lncRNAs (DElncRNAs), 29 differentially expressed miRNAs (DEmiRNAs), and 77 differentially expressed mRNAs (DEmRNAs) were identified. An EC-specific ceRNA network was built based on nine DElncRNAs significantly associated with overall survival. CCNB1 was found as a key gene in EC through the weighted gene coexpression network analysis and protein-protein interaction network analysis. Our ceRNA network showed C2orf48 and LINC00483 might upregulate CCNB1 via competing with miR-183. In addition, we found a subnetwork which contained survival-associated DERNAs (AC110491.1, LINC00483-miR-192-GRHL1). The results of reverse transcription quantitative polymerase chain reaction supported the relative expressions of C2orf48, LINC00483 were upregulated and that of AC110491.1 was downregulated in EC. We further found C2orf48 was upregulated in serous EC, endometrioid EC, and mixed serous and endometrioid EC. LINC00483 was upregulated in mixed serous and endometrioid EC compared with that in the normal tissues according to UALCAN database. In addition, candidate small molecular drugs were screened out by ConnectivityMap based on the 77 DEmRNAs in the ceRNA network. Eventually, C2orf48, LINC00483, and AC110491.1 were identified as three key lncRNAs in EC.
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Affiliation(s)
- Jinhui Liu
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Sipei Nie
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Junya Liang
- Hypertension Research Center, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Yi Jiang
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yicong Wan
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Shulin Zhou
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Wenjun Cheng
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
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20
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Liu J, Nie S, Gao M, Jiang Y, Wan Y, Ma X, Zhou S, Cheng W. Identification of EPHX2 and RMI2 as two novel key genes in cervical squamous cell carcinoma by an integrated bioinformatic analysis. J Cell Physiol 2019; 234:21260-21273. [PMID: 31041817 DOI: 10.1002/jcp.28731] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 04/05/2019] [Accepted: 04/11/2019] [Indexed: 12/27/2022]
Abstract
Cervical cancer is the fourth most common malignancy in women worldwide and cervical squamous cell carcinoma (CESC) is the most common histological type of cervical cancer. The dysregulation of genes plays a significant role in cancer. In the present study, we screened out differentially expressed genes (DEGs) of CESC in the GSE63514 data set from the Gene Expression Omnibus database. An integrated bioinformatics analysis was used to select hub genes, as well as to investigate their related prognostic signature, functional annotation, methylation mechanism, and candidate molecular drugs. As a result, a total of 1907 DEGs were identified (944 were upregulated and 963 were downregulated). In the protein-protein interaction network, three hub modules and 30 hub genes were identified. And two hub modules and 116 hub genes were screened out from four CESC-related modules by the weighted gene coexpression network analysis. The gene ontology term enrichment analysis and Kyoto encyclopedia of genes and genomes pathway analysis were performed to better understand functions and pathways. Genes with a significant prognostic value were found by prognostic signature analysis. And there were five genes (EPHX2, CHAF1B, KIAA1524, CDC45, and RMI2) identified as significant CESC-associated genes after expression validation and survival analysis. Among them, EPHX2 and RMI2 were noted as two novel key genes for the CESC-associated methylation and expression. In addition, four candidate small molecule drugs for CESC (camptothecin, resveratrol, vorinostat, and trichostatin A) were defined. Further studies are required to explore these significant CESC-associated genes for their potentiality in diagnosis, prognosis, and targeted therapy.
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Affiliation(s)
- Jinhui Liu
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Sipei Nie
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Mei Gao
- Department of Anesthesiology and Perioperative Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yi Jiang
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yicong Wan
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xiaoling Ma
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Shulin Zhou
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Wenjun Cheng
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
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21
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22
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Srivastava PK, van Eyll J, Godard P, Mazzuferi M, Delahaye-Duriez A, Van Steenwinckel J, Gressens P, Danis B, Vandenplas C, Foerch P, Leclercq K, Mairet-Coello G, Cardenas A, Vanclef F, Laaniste L, Niespodziany I, Keaney J, Gasser J, Gillet G, Shkura K, Chong SA, Behmoaras J, Kadiu I, Petretto E, Kaminski RM, Johnson MR. A systems-level framework for drug discovery identifies Csf1R as an anti-epileptic drug target. Nat Commun 2018; 9:3561. [PMID: 30177815 PMCID: PMC6120885 DOI: 10.1038/s41467-018-06008-4] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 08/03/2018] [Indexed: 01/14/2023] Open
Abstract
The identification of drug targets is highly challenging, particularly for diseases of the brain. To address this problem, we developed and experimentally validated a general computational framework for drug target discovery that combines gene regulatory information with causal reasoning (“Causal Reasoning Analytical Framework for Target discovery”—CRAFT). Using a systems genetics approach and starting from gene expression data from the target tissue, CRAFT provides a predictive framework for identifying cell membrane receptors with a direction-specified influence over disease-related gene expression profiles. As proof of concept, we applied CRAFT to epilepsy and predicted the tyrosine kinase receptor Csf1R as a potential therapeutic target. The predicted effect of Csf1R blockade in attenuating epilepsy seizures was validated in three pre-clinical models of epilepsy. These results highlight CRAFT as a systems-level framework for target discovery and suggest Csf1R blockade as a novel therapeutic strategy in epilepsy. CRAFT is applicable to disease settings other than epilepsy. The identification of new drug targets is highly challenging, particularly for diseases of the brain. This study describes a general computational gene regulatory framework called CRAFT for drug target discovery, and the authors use CRAFT to identify the microglial membrane receptor Csf1R as a potential therapeutic target for epilepsy.
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Affiliation(s)
| | - Jonathan van Eyll
- UCB Pharma, Avenue de l'industrie, Braine-l'Alleud, R9, B-1420, Belgium
| | - Patrice Godard
- Clarivate Analytics (formerly the IP & Science Business of Thomson Reuters), 5901 Priestly Drive, #200, Carlsbad, CA, 92008, USA
| | - Manuela Mazzuferi
- UCB Pharma, Avenue de l'industrie, Braine-l'Alleud, R9, B-1420, Belgium
| | - Andree Delahaye-Duriez
- Division of Brain Sciences, Imperial College London, London, W12 0NN, UK.,UFR de Santé, Médecine et Biologie Humaine, Sorbonne Paris Cité, Université Paris 13, Bobigny, France.,PROTECT, INSERM, Sorbonne Paris Cité, Université Paris Diderot, Paris, France
| | | | - Pierre Gressens
- PROTECT, INSERM, Sorbonne Paris Cité, Université Paris Diderot, Paris, France.,School of Biomedical Engineering & Imaging Sciences, Centre for the Developing Brain, King's College London, St. Thomas' Hospital, London, SE1 7EH, UK
| | - Benedicte Danis
- UCB Pharma, Avenue de l'industrie, Braine-l'Alleud, R9, B-1420, Belgium
| | | | - Patrik Foerch
- UCB Pharma, Avenue de l'industrie, Braine-l'Alleud, R9, B-1420, Belgium
| | - Karine Leclercq
- UCB Pharma, Avenue de l'industrie, Braine-l'Alleud, R9, B-1420, Belgium
| | | | - Alvaro Cardenas
- UCB Pharma, Avenue de l'industrie, Braine-l'Alleud, R9, B-1420, Belgium
| | - Frederic Vanclef
- UCB Pharma, Avenue de l'industrie, Braine-l'Alleud, R9, B-1420, Belgium
| | - Liisi Laaniste
- Division of Brain Sciences, Imperial College London, London, W12 0NN, UK
| | | | - James Keaney
- UCB Pharma, Avenue de l'industrie, Braine-l'Alleud, R9, B-1420, Belgium
| | - Julien Gasser
- UCB Pharma, Avenue de l'industrie, Braine-l'Alleud, R9, B-1420, Belgium
| | - Gaelle Gillet
- UCB Pharma, Avenue de l'industrie, Braine-l'Alleud, R9, B-1420, Belgium
| | - Kirill Shkura
- Division of Brain Sciences, Imperial College London, London, W12 0NN, UK
| | - Seon-Ah Chong
- UCB Pharma, Avenue de l'industrie, Braine-l'Alleud, R9, B-1420, Belgium
| | - Jacques Behmoaras
- Centre for Complement and Inflammation Research, Imperial College London, London, W12 0NN, UK
| | - Irena Kadiu
- UCB Pharma, Avenue de l'industrie, Braine-l'Alleud, R9, B-1420, Belgium
| | - Enrico Petretto
- Duke-NUS Medical School, Centre for Computational Biology, 8 College Road, Singapore, 169857, Republic of Singapore. .,Faculty of Medicine, MRC Clinical Sciences Centre, Imperial College London, London, W12 0NN, UK.
| | - Rafal M Kaminski
- UCB Pharma, Avenue de l'industrie, Braine-l'Alleud, R9, B-1420, Belgium.
| | - Michael R Johnson
- Division of Brain Sciences, Imperial College London, London, W12 0NN, UK.
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23
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Zulkipli I, Clark J, Hart M, Shrestha RL, Gul P, Dang D, Kasichiwin T, Kujawiak I, Sastry N, Draviam VM. Spindle rotation in human cells is reliant on a MARK2-mediated equatorial spindle-centering mechanism. J Cell Biol 2018; 217:3057-3070. [PMID: 29941476 PMCID: PMC6122980 DOI: 10.1083/jcb.201804166] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 05/18/2018] [Accepted: 05/24/2018] [Indexed: 12/11/2022] Open
Abstract
Unlike man-made wheels that are centered and rotated via an axle, the mitotic spindle of a human cell is rotated by external cortical pulling mechanisms. Zulkipli et al. identify MARK2’s role in equatorial spindle centering and astral microtubule length, which in turn control spindle rotation. The plane of cell division is defined by the final position of the mitotic spindle. The spindle is pulled and rotated to the correct position by cortical dynein. However, it is unclear how the spindle’s rotational center is maintained and what the consequences of an equatorially off centered spindle are in human cells. We analyzed spindle movements in 100s of cells exposed to protein depletions or drug treatments and uncovered a novel role for MARK2 in maintaining the spindle at the cell’s geometric center. Following MARK2 depletion, spindles glide along the cell cortex, leading to a failure in identifying the correct division plane. Surprisingly, spindle off centering in MARK2-depleted cells is not caused by excessive pull by dynein. We show that MARK2 modulates mitotic microtubule growth and length and that codepleting mitotic centromere-associated protein (MCAK), a microtubule destabilizer, rescues spindle off centering in MARK2-depleted cells. Thus, we provide the first insight into a spindle-centering mechanism needed for proper spindle rotation and, in turn, the correct division plane in human cells.
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Affiliation(s)
- Ihsan Zulkipli
- Department of Genetics, University of Cambridge, Cambridge, England, UK
| | - Joanna Clark
- Department of Genetics, University of Cambridge, Cambridge, England, UK
| | - Madeleine Hart
- School of Biological and Chemical Sciences, Queen Mary University of London, London, England, UK
| | - Roshan L Shrestha
- Department of Genetics, University of Cambridge, Cambridge, England, UK
| | - Parveen Gul
- School of Biological and Chemical Sciences, Queen Mary University of London, London, England, UK
| | - David Dang
- School of Biological and Chemical Sciences, Queen Mary University of London, London, England, UK.,Department of Informatics, King's College, London, England, UK
| | - Tami Kasichiwin
- School of Biological and Chemical Sciences, Queen Mary University of London, London, England, UK
| | - Izabela Kujawiak
- Department of Genetics, University of Cambridge, Cambridge, England, UK
| | - Nishanth Sastry
- Department of Informatics, King's College, London, England, UK
| | - Viji M Draviam
- School of Biological and Chemical Sciences, Queen Mary University of London, London, England, UK .,Department of Genetics, University of Cambridge, Cambridge, England, UK
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24
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Ravikumar B, Aittokallio T. Improving the efficacy-safety balance of polypharmacology in multi-target drug discovery. Expert Opin Drug Discov 2017; 13:179-192. [DOI: 10.1080/17460441.2018.1413089] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Balaguru Ravikumar
- Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Helsinki, Finland
| | - Tero Aittokallio
- Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Helsinki, Finland
- Department of Mathematics and Statistics, University of Turku, Turku, Finland
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25
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Shrestha RL, Conti D, Tamura N, Braun D, Ramalingam RA, Cieslinski K, Ries J, Draviam VM. Aurora-B kinase pathway controls the lateral to end-on conversion of kinetochore-microtubule attachments in human cells. Nat Commun 2017; 8:150. [PMID: 28751710 PMCID: PMC5532248 DOI: 10.1038/s41467-017-00209-z] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 06/12/2017] [Indexed: 12/29/2022] Open
Abstract
Human chromosomes are captured along microtubule walls (lateral attachment) and then tethered to microtubule-ends (end-on attachment) through a multi-step end-on conversion process. Upstream regulators that orchestrate this remarkable change in the plane of kinetochore-microtubule attachment in human cells are not known. By tracking kinetochore movements and using kinetochore markers specific to attachment status, we reveal a spatially defined role for Aurora-B kinase in retarding the end-on conversion process. To understand how Aurora-B activity is counteracted, we compare the roles of two outer-kinetochore bound phosphatases and find that BubR1-associated PP2A, unlike KNL1-associated PP1, plays a significant role in end-on conversion. Finally, we uncover a novel role for Aurora-B regulated Astrin-SKAP complex in ensuring the correct plane of kinetochore-microtubule attachment. Thus, we identify Aurora-B as a key upstream regulator of end-on conversion in human cells and establish a late role for Astrin-SKAP complex in the end-on conversion process.Human chromosomes are captured along microtubule walls and then tethered to microtubule-ends through a multi-step end-on conversion process. Here the authors show that Aurora-B regulates end-on conversion in human cells and establish a late role for Astrin-SKAP complex in the end-on conversion process.
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Affiliation(s)
- Roshan L Shrestha
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Duccio Conti
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Naoka Tamura
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
- Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Dominique Braun
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| | - Revathy A Ramalingam
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Konstanty Cieslinski
- European Molecular Biology Laboratory, Cell Biology and Biophysics Unit, Meyerhofstrasse 1, Heidelberg, Germany
| | - Jonas Ries
- European Molecular Biology Laboratory, Cell Biology and Biophysics Unit, Meyerhofstrasse 1, Heidelberg, Germany
| | - Viji M Draviam
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK.
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK.
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26
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Wen Q, Dunne PD, O’Reilly PG, Li G, Bjourson AJ, McArt DG, Hamilton PW, Zhang SD. KRAS mutant colorectal cancer gene signatures identified angiotensin II receptor blockers as potential therapies. Oncotarget 2017; 8:3206-3225. [PMID: 27965461 PMCID: PMC5356876 DOI: 10.18632/oncotarget.13884] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Accepted: 11/30/2016] [Indexed: 01/13/2023] Open
Abstract
Colorectal cancer (CRC) is a life-threatening disease with high prevalence and mortality worldwide. The KRAS oncogene is mutated in approximately 40% of CRCs. While antibody based EGFR inhibitors (cetuximab and panitumumab) represent a major treatment strategy for advanced KRAS wild type (KRAS-WT) CRCs, there still remains no effective therapeutic course for advanced KRAS mutant (KRAS-MT) CRC patients.In this study, we employed a novel and comprehensive approach of gene expression connectivity mapping (GECM) to identify candidate compounds to target KRAS-MT tumors. We first created a combined KRAS-MT gene signature with 248 ranked significant genes using 677 CRC clinical samples. A series of 248 sub-signatures was then created containing an increasing number of the top ranked genes. As an input to GECM analysis, each sub-signature was translated into a statistically significant therapeutic drugs list, which was finally combined to obtain a single list of significant drugs.We identify four antihypertensive angiotensin II receptor blockers (ARBs) within the top 30 significant drugs indicating that these drugs have a mechanism of action that can alter the KRAS-MT CRC oncogenic signaling. A hypergeometric test (p-value = 6.57 × 10-6) confirmed that ARBs are significantly enriched in our results. These findings support the hypothesis that ARB antihypertensive drugs may directly block KRAS signaling resulting in improvement in patient outcome or, through a reversion to a KRAS wild-type phenotype, improve the response to anti-EGFR treatment. Antihypertensive angiotensin II receptor blockers are therefore worth further investigation as potential therapeutic candidates in this difficult category of advanced colorectal cancers.
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Affiliation(s)
- Qing Wen
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK
| | - Philip D. Dunne
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK
| | - Paul G. O’Reilly
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK
| | - Gerald Li
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK
| | - Anthony J. Bjourson
- Northern Ireland Centre for Stratified Medicine, Biomedical Sciences Research Institute, Ulster University, C-TRIC, Londonderry, UK
| | - Darragh G. McArt
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK
| | - Peter W. Hamilton
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK
| | - Shu-Dong Zhang
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK
- Northern Ireland Centre for Stratified Medicine, Biomedical Sciences Research Institute, Ulster University, C-TRIC, Londonderry, UK
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27
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Wooden B, Goossens N, Hoshida Y, Friedman SL. Using Big Data to Discover Diagnostics and Therapeutics for Gastrointestinal and Liver Diseases. Gastroenterology 2017; 152:53-67.e3. [PMID: 27773806 PMCID: PMC5193106 DOI: 10.1053/j.gastro.2016.09.065] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 09/15/2016] [Accepted: 09/25/2016] [Indexed: 12/13/2022]
Abstract
Technologies such as genome sequencing, gene expression profiling, proteomic and metabolomic analyses, electronic medical records, and patient-reported health information have produced large amounts of data from various populations, cell types, and disorders (big data). However, these data must be integrated and analyzed if they are to produce models or concepts about physiological function or mechanisms of pathogenesis. Many of these data are available to the public, allowing researchers anywhere to search for markers of specific biological processes or therapeutic targets for specific diseases or patient types. We review recent advances in the fields of computational and systems biology and highlight opportunities for researchers to use big data sets in the fields of gastroenterology and hepatology to complement traditional means of diagnostic and therapeutic discovery.
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Affiliation(s)
- Benjamin Wooden
- Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Nicolas Goossens
- Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York; Division of Gastroenterology and Hepatology, Department of Medical Specialties, Geneva University Hospital, Geneva, Switzerland
| | - Yujin Hoshida
- Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York.
| | - Scott L Friedman
- Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
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28
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Kibble M, Khan SA, Saarinen N, Iorio F, Saez-Rodriguez J, Mäkelä S, Aittokallio T. Transcriptional response networks for elucidating mechanisms of action of multitargeted agents. Drug Discov Today 2016; 21:1063-75. [PMID: 26979547 DOI: 10.1016/j.drudis.2016.03.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 02/15/2016] [Accepted: 03/04/2016] [Indexed: 01/08/2023]
Abstract
Drug discovery is moving away from the single target-based approach towards harnessing the potential of polypharmacological agents that modulate the activity of multiple nodes in the complex networks of deregulations underlying disease phenotypes. Computational network pharmacology methods that use systems-level drug-response phenotypes, such as those originating from genome-wide transcriptomic profiles, have proved particularly effective for elucidating the mechanisms of action of multitargeted compounds. Here, we show, via the case study of the natural product pinosylvin, how the combination of two complementary network-based methods can provide novel, unexpected mechanistic insights. This case study also illustrates that elucidating the mechanism of action of multitargeted natural products through transcriptional response-based approaches is a challenging endeavor, often requiring multiple computational-experimental iterations.
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Affiliation(s)
- Milla Kibble
- Institute for Molecular Medicine Finland (FIMM), Biomedicum Helsinki 2U, Tukholmankatu 8, University of Helsinki, Helsinki 00014, Finland.
| | - Suleiman A Khan
- Institute for Molecular Medicine Finland (FIMM), Biomedicum Helsinki 2U, Tukholmankatu 8, University of Helsinki, Helsinki 00014, Finland
| | - Niina Saarinen
- Institute of Biomedicine, Turku Center for Disease Modeling & Functional Foods Forum, University of Turku, Turku 20014, Finland
| | - Francesco Iorio
- European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK
| | - Julio Saez-Rodriguez
- European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK; Joint Research Centre for Computational Biomedicine (JRC-COMBINE) - RWTH Aachen University, Faculty of Medicine, D-52074 Aachen, Germany
| | - Sari Mäkelä
- Institute of Biomedicine, Turku Center for Disease Modeling & Functional Foods Forum, University of Turku, Turku 20014, Finland
| | - Tero Aittokallio
- Institute for Molecular Medicine Finland (FIMM), Biomedicum Helsinki 2U, Tukholmankatu 8, University of Helsinki, Helsinki 00014, Finland; Department of Mathematics and Statistics, Quantum, University of Turku, Turku 20014, Finland
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29
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Lee H, Kang S, Kim W. Drug Repositioning for Cancer Therapy Based on Large-Scale Drug-Induced Transcriptional Signatures. PLoS One 2016; 11:e0150460. [PMID: 26954019 PMCID: PMC4783079 DOI: 10.1371/journal.pone.0150460] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 02/15/2016] [Indexed: 11/18/2022] Open
Abstract
An in silico chemical genomics approach is developed to predict drug repositioning (DR) candidates for three types of cancer: glioblastoma, lung cancer, and breast cancer. It is based on a recent large-scale dataset of ~20,000 drug-induced expression profiles in multiple cancer cell lines, which provides i) a global impact of transcriptional perturbation of both known targets and unknown off-targets, and ii) rich information on drug's mode-of-action. First, the drug-induced expression profile is shown more effective than other information, such as the drug structure or known target, using multiple HTS datasets as unbiased benchmarks. Particularly, the utility of our method was robustly demonstrated in identifying novel DR candidates. Second, we predicted 14 high-scoring DR candidates solely based on expression signatures. Eight of the fourteen drugs showed significant anti-proliferative activity against glioblastoma; i.e., ivermectin, trifluridine, astemizole, amlodipine, maprotiline, apomorphine, mometasone, and nortriptyline. Our DR score strongly correlated with that of cell-based experimental results; the top seven DR candidates were positive, corresponding to an approximately 20-fold enrichment compared with conventional HTS. Despite diverse original indications and known targets, the perturbed pathways of active DR candidates show five distinct patterns that form tight clusters together with one or more known cancer drugs, suggesting common transcriptome-level mechanisms of anti-proliferative activity.
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Affiliation(s)
- Haeseung Lee
- Ewha Research Center for Systems Biology, Division of Molecular & Life Sciences, Ewha Womans University, Seoul, Korea
| | - Seungmin Kang
- Ewha Research Center for Systems Biology, Division of Molecular & Life Sciences, Ewha Womans University, Seoul, Korea
| | - Wankyu Kim
- Ewha Research Center for Systems Biology, Division of Molecular & Life Sciences, Ewha Womans University, Seoul, Korea
- * E-mail:
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30
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Chen B, Butte AJ. Leveraging big data to transform target selection and drug discovery. Clin Pharmacol Ther 2016; 99:285-97. [PMID: 26659699 PMCID: PMC4785018 DOI: 10.1002/cpt.318] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 12/02/2015] [Indexed: 02/06/2023]
Abstract
The advances of genomics, sequencing, and high throughput technologies have led to the creation of large volumes of diverse datasets for drug discovery. Analyzing these datasets to better understand disease and discover new drugs is becoming more common. Recent open data initiatives in basic and clinical research have dramatically increased the types of data available to the public. The past few years have witnessed successful use of big data in many sectors across the whole drug discovery pipeline. In this review, we will highlight the state of the art in leveraging big data to identify new targets, drug indications, and drug response biomarkers in this era of precision medicine.
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Affiliation(s)
- B Chen
- Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, California, USA
| | - A J Butte
- Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, California, USA
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