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Thorman AW, Reigle J, Chutipongtanate S, Yang J, Shamsaei B, Pilarczyk M, Fazel-Najafabadi M, Adamczak R, Kouril M, Bhatnagar S, Hummel S, Niu W, Morrow AL, Czyzyk-Krzeska MF, McCullumsmith R, Seibel W, Nassar N, Zheng Y, Hildeman DA, Medvedovic M, Herr AB, Meller J. Accelerating drug discovery and repurposing by combining transcriptional signature connectivity with docking. SCIENCE ADVANCES 2024; 10:eadj3010. [PMID: 39213358 PMCID: PMC11364105 DOI: 10.1126/sciadv.adj3010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 07/26/2024] [Indexed: 09/04/2024]
Abstract
We present an in silico approach for drug discovery, dubbed connectivity enhanced structure activity relationship (ceSAR). Building on the landmark LINCS library of transcriptional signatures of drug-like molecules and gene knockdowns, ceSAR combines cheminformatic techniques with signature concordance analysis to connect small molecules and their targets and further assess their biophysical compatibility using molecular docking. Candidate compounds are first ranked in a target structure-independent manner, using chemical similarity to LINCS analogs that exhibit transcriptomic concordance with a target gene knockdown. Top candidates are subsequently rescored using docking simulations and machine learning-based consensus of the two approaches. Using extensive benchmarking, we show that ceSAR greatly reduces false-positive rates, while cutting run times by multiple orders of magnitude and further democratizing drug discovery pipelines. We further demonstrate the utility of ceSAR by identifying and experimentally validating inhibitors of BCL2A1, an important antiapoptotic target in melanoma and preterm birth-associated inflammation.
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Affiliation(s)
- Alexander W. Thorman
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - James Reigle
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, USA
- Department of Biostatistics, Health Informatics and Data Sciences, University of Cincinnati, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Somchai Chutipongtanate
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, USA
- Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Juechen Yang
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, USA
- Department of Biostatistics, Health Informatics and Data Sciences, University of Cincinnati, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Behrouz Shamsaei
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, USA
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Marcin Pilarczyk
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Mehdi Fazel-Najafabadi
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Rafal Adamczak
- Department of Informatics, Faculty of Physics, Astronomy an Informatics, Nicolaus Copernicus University, Toruń, Poland
| | - Michal Kouril
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Surbhi Bhatnagar
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Computer Science, University of Cincinnati, Cincinnati, OH, USA
| | - Sarah Hummel
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Wen Niu
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Ardythe L. Morrow
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Maria F. Czyzyk-Krzeska
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Department of Veterans Affairs, Cincinnati Veteran Affairs Medical Center, Cincinnati, OH, USA
| | | | - William Seibel
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Nicolas Nassar
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Yi Zheng
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - David A. Hildeman
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Mario Medvedovic
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, USA
- Department of Biostatistics, Health Informatics and Data Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Andrew B. Herr
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Division of Infectious Diseases, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Jarek Meller
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, USA
- Department of Biostatistics, Health Informatics and Data Sciences, University of Cincinnati, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Informatics, Faculty of Physics, Astronomy an Informatics, Nicolaus Copernicus University, Toruń, Poland
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Department of Computer Science, University of Cincinnati, Cincinnati, OH, USA
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Ng MSY, Kaur G, Francis RS, Hawley CM, Johnson DW. Drug repurposing for glomerular diseases: an underutilized resource. Nat Rev Nephrol 2024:10.1038/s41581-024-00864-8. [PMID: 39085415 DOI: 10.1038/s41581-024-00864-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/17/2024] [Indexed: 08/02/2024]
Abstract
Drug repurposing in glomerular disease can deliver opportunities for steroid-free regimens, enable personalized multi-target options for resistant or relapsing disease and enhance treatment options for understudied populations (for example, children) and in resource-limited settings. Identification of drug-repurposing candidates can be data driven, which utilizes existing data on disease pathobiology, drug features and clinical outcomes, or experimental, which involves high-throughput drug screens. Information from databases of approved drugs, clinical trials and PubMed registries suggests that at least 96 drugs on the market cover 49 targets with immunosuppressive potential that could be candidates for drug repurposing in glomerular disease. Furthermore, evidence to support drug repurposing is available for 191 immune drug target-glomerular disease pairs. Non-immunological drug repurposing includes strategies to reduce haemodynamic overload, podocyte injury and kidney fibrosis. Recommended strategies to expand drug-repurposing capacity in glomerular disease include enriching drug databases with glomeruli-specific information, enhancing the accessibility of primary clinical trial data, biomarker discovery to improve participant selection into clinical trials and improve surrogate outcomes and initiatives to reduce patent, regulatory and organizational hurdles.
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Affiliation(s)
- Monica Suet Ying Ng
- Kidney Health Service, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia.
- Conjoint Internal Medicine Laboratory, Chemical Pathology, Pathology Queensland, Brisbane, Queensland, Australia.
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia.
- Department of Kidney and Transplant Services, Princess Alexandra Hospital, Brisbane, Queensland, Australia.
| | - Gursimran Kaur
- Department of Rheumatology, Saint Vincent's Hospital, Sydney, New South Wales, Australia
- Saint Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
- Rheumatology Department, Sunshine Coast University Hospital, Birtinya, Queensland, Australia
| | - Ross S Francis
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia
- Department of Kidney and Transplant Services, Princess Alexandra Hospital, Brisbane, Queensland, Australia
| | - Carmel M Hawley
- Department of Kidney and Transplant Services, Princess Alexandra Hospital, Brisbane, Queensland, Australia
- Translational Research Institute, Brisbane, Queensland, Australia
- Centre for Kidney Disease Research, University of Queensland, Brisbane, Queensland, Australia
| | - David W Johnson
- Department of Kidney and Transplant Services, Princess Alexandra Hospital, Brisbane, Queensland, Australia
- Translational Research Institute, Brisbane, Queensland, Australia
- Centre for Kidney Disease Research, University of Queensland, Brisbane, Queensland, Australia
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Truong TTT, Liu ZSJ, Panizzutti B, Kim JH, Dean OM, Berk M, Walder K. Network-based drug repurposing for schizophrenia. Neuropsychopharmacology 2024; 49:983-992. [PMID: 38321095 PMCID: PMC11039639 DOI: 10.1038/s41386-024-01805-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 01/10/2024] [Accepted: 01/12/2024] [Indexed: 02/08/2024]
Abstract
Despite recent progress, the challenges in drug discovery for schizophrenia persist. However, computational drug repurposing has gained popularity as it leverages the wealth of expanding biomedical databases. Network analyses provide a comprehensive understanding of transcription factor (TF) regulatory effects through gene regulatory networks, which capture the interactions between TFs and target genes by integrating various lines of evidence. Using the PANDA algorithm, we examined the topological variances in TF-gene regulatory networks between individuals with schizophrenia and healthy controls. This algorithm incorporates binding motifs, protein interactions, and gene co-expression data. To identify these differences, we subtracted the edge weights of the healthy control network from those of the schizophrenia network. The resulting differential network was then analysed using the CLUEreg tool in the GRAND database. This tool employs differential network signatures to identify drugs that potentially target the gene signature associated with the disease. Our analysis utilised a large RNA-seq dataset comprising 532 post-mortem brain samples from the CommonMind project. We constructed co-expression gene regulatory networks for both schizophrenia cases and healthy control subjects, incorporating 15,831 genes and 413 overlapping TFs. Through drug repurposing, we identified 18 promising candidates for repurposing as potential treatments for schizophrenia. The analysis of TF-gene regulatory networks revealed that the TFs in schizophrenia predominantly regulate pathways associated with energy metabolism, immune response, cell adhesion, and thyroid hormone signalling. These pathways represent significant targets for therapeutic intervention. The identified drug repurposing candidates likely act through TF-targeted pathways. These promising candidates, particularly those with preclinical evidence such as rimonabant and kaempferol, warrant further investigation into their potential mechanisms of action and efficacy in alleviating the symptoms of schizophrenia.
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Affiliation(s)
- Trang T T Truong
- Deakin University, IMPACT, The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Geelong, Australia
| | - Zoe S J Liu
- Deakin University, IMPACT, The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Geelong, Australia
| | - Bruna Panizzutti
- Deakin University, IMPACT, The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Geelong, Australia
| | - Jee Hyun Kim
- Deakin University, IMPACT, The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Geelong, Australia
- Florey Institute of Neuroscience and Mental Health, Parkville, Australia
| | - Olivia M Dean
- Deakin University, IMPACT, The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Geelong, Australia
- Florey Institute of Neuroscience and Mental Health, Parkville, Australia
| | - Michael Berk
- Deakin University, IMPACT, The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Geelong, Australia
- Orygen, The National Centre of Excellence in Youth Mental Health, Centre for Youth Mental Health, The Florey Institute for Neuroscience and Mental Health and the Department of Psychiatry, University of Melbourne, Parkville, 3010, Australia
| | - Ken Walder
- Deakin University, IMPACT, The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Geelong, Australia.
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Ahn SH, Kim JH. Factor-specific generative pattern from large-scale drug-induced gene expression profile. Sci Rep 2023; 13:6339. [PMID: 37072452 PMCID: PMC10113368 DOI: 10.1038/s41598-023-33061-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 04/06/2023] [Indexed: 05/03/2023] Open
Abstract
Drug discovery is a complex and interdisciplinary field that requires the identification of potential drug targets for specific diseases. In this study, we present FacPat, a novel approach that identifies the optimal factor-specific pattern explaining the drug-induced gene expression profile. FacPat uses a genetic algorithm based on pattern distance to mine the optimal factor-specific pattern for each gene in the LINCS L1000 dataset. We applied Benjamini-Hochberg correction to control the false discovery rate and identified significant and interpretable factor-specific patterns consisting of 480 genes, 7 chemical compounds, and 38 human cell lines. Using our approach, we identified genes that show context-specific effects related to chemical compounds and/or human cell lines. Furthermore, we performed functional enrichment analysis to characterize biological features. We demonstrate that FacPat can be used to reveal novel relationships among drugs, diseases, and genes.
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Affiliation(s)
- Se Hwan Ahn
- Department of Biomedical Sciences, Seoul National University Biomedical Informatics (SNUBI), Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Ju Han Kim
- Department of Biomedical Sciences, Seoul National University Biomedical Informatics (SNUBI), Seoul National University College of Medicine, Seoul, Republic of Korea.
- Division of Biomedical Informatics, Seoul National University Biomedical Informatics (SNUBI), Seoul National University College of Medicine, Seoul, Republic of Korea.
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Truong TTT, Panizzutti B, Kim JH, Walder K. Repurposing Drugs via Network Analysis: Opportunities for Psychiatric Disorders. Pharmaceutics 2022; 14:1464. [PMID: 35890359 PMCID: PMC9319329 DOI: 10.3390/pharmaceutics14071464] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/30/2022] [Accepted: 07/12/2022] [Indexed: 02/04/2023] Open
Abstract
Despite advances in pharmacology and neuroscience, the path to new medications for psychiatric disorders largely remains stagnated. Drug repurposing offers a more efficient pathway compared with de novo drug discovery with lower cost and less risk. Various computational approaches have been applied to mine the vast amount of biomedical data generated over recent decades. Among these methods, network-based drug repurposing stands out as a potent tool for the comprehension of multiple domains of knowledge considering the interactions or associations of various factors. Aligned well with the poly-pharmacology paradigm shift in drug discovery, network-based approaches offer great opportunities to discover repurposing candidates for complex psychiatric disorders. In this review, we present the potential of network-based drug repurposing in psychiatry focusing on the incentives for using network-centric repurposing, major network-based repurposing strategies and data resources, applications in psychiatry and challenges of network-based drug repurposing. This review aims to provide readers with an update on network-based drug repurposing in psychiatry. We expect the repurposing approach to become a pivotal tool in the coming years to battle debilitating psychiatric disorders.
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Affiliation(s)
- Trang T. T. Truong
- IMPACT, The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin University, Geelong 3220, Australia; (T.T.T.T.); (B.P.); (J.H.K.)
| | - Bruna Panizzutti
- IMPACT, The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin University, Geelong 3220, Australia; (T.T.T.T.); (B.P.); (J.H.K.)
| | - Jee Hyun Kim
- IMPACT, The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin University, Geelong 3220, Australia; (T.T.T.T.); (B.P.); (J.H.K.)
- Mental Health Theme, The Florey Institute of Neuroscience and Mental Health, Parkville 3010, Australia
| | - Ken Walder
- IMPACT, The Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin University, Geelong 3220, Australia; (T.T.T.T.); (B.P.); (J.H.K.)
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Application of network link prediction in drug discovery. BMC Bioinformatics 2021; 22:187. [PMID: 33845763 PMCID: PMC8042985 DOI: 10.1186/s12859-021-04082-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 03/16/2021] [Indexed: 11/10/2022] Open
Abstract
Background Technological and research advances have produced large volumes of biomedical data. When represented as a network (graph), these data become useful for modeling entities and interactions in biological and similar complex systems. In the field of network biology and network medicine, there is a particular interest in predicting results from drug–drug, drug–disease, and protein–protein interactions to advance the speed of drug discovery. Existing data and modern computational methods allow to identify potentially beneficial and harmful interactions, and therefore, narrow drug trials ahead of actual clinical trials. Such automated data-driven investigation relies on machine learning techniques. However, traditional machine learning approaches require extensive preprocessing of the data that makes them impractical for large datasets. This study presents wide range of machine learning methods for predicting outcomes from biomedical interactions and evaluates the performance of the traditional methods with more recent network-based approaches. Results We applied a wide range of 32 different network-based machine learning models to five commonly available biomedical datasets, and evaluated their performance based on three important evaluations metrics namely AUROC, AUPR, and F1-score. We achieved this by converting link prediction problem as binary classification problem. In order to achieve this we have considered the existing links as positive example and randomly sampled negative examples from non-existant set. After experimental evaluation we found that Prone, ACT and \documentclass[12pt]{minimal}
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\begin{document}$$LRW_5$$\end{document}LRW5 are the top 3 best performers on all five datasets. Conclusions This work presents a comparative evaluation of network-based machine learning algorithms for predicting network links, with applications in the prediction of drug-target and drug–drug interactions, and applied well known network-based machine learning methods. Our work is helpful in guiding researchers in the appropriate selection of machine learning methods for pharmaceutical tasks. Supplementary Information The online version supplementary material available at 10.1186/s12859-021-04082-y.
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Jarada TN, Rokne JG, Alhajj R. A review of computational drug repositioning: strategies, approaches, opportunities, challenges, and directions. J Cheminform 2020; 12:46. [PMID: 33431024 PMCID: PMC7374666 DOI: 10.1186/s13321-020-00450-7] [Citation(s) in RCA: 146] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 07/13/2020] [Indexed: 01/13/2023] Open
Abstract
Drug repositioning is the process of identifying novel therapeutic potentials for existing drugs and discovering therapies for untreated diseases. Drug repositioning, therefore, plays an important role in optimizing the pre-clinical process of developing novel drugs by saving time and cost compared to the traditional de novo drug discovery processes. Since drug repositioning relies on data for existing drugs and diseases the enormous growth of publicly available large-scale biological, biomedical, and electronic health-related data along with the high-performance computing capabilities have accelerated the development of computational drug repositioning approaches. Multidisciplinary researchers and scientists have carried out numerous attempts, with different degrees of efficiency and success, to computationally study the potential of repositioning drugs to identify alternative drug indications. This study reviews recent advancements in the field of computational drug repositioning. First, we highlight different drug repositioning strategies and provide an overview of frequently used resources. Second, we summarize computational approaches that are extensively used in drug repositioning studies. Third, we present different computing and experimental models to validate computational methods. Fourth, we address prospective opportunities, including a few target areas. Finally, we discuss challenges and limitations encountered in computational drug repositioning and conclude with an outline of further research directions.
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Affiliation(s)
- Tamer N Jarada
- Department of Computer Science, University of Calgary, Calgary, Alberta, Canada
| | - Jon G Rokne
- Department of Computer Science, University of Calgary, Calgary, Alberta, Canada
| | - Reda Alhajj
- Department of Computer Science, University of Calgary, Calgary, Alberta, Canada.
- Department of Computer Engineering, Istanbul Medipol University, Istanbul, Turkey.
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Moridi M, Ghadirinia M, Sharifi-Zarchi A, Zare-Mirakabad F. The assessment of efficient representation of drug features using deep learning for drug repositioning. BMC Bioinformatics 2019; 20:577. [PMID: 31726977 PMCID: PMC6854697 DOI: 10.1186/s12859-019-3165-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 10/21/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND De novo drug discovery is a time-consuming and expensive process. Nowadays, drug repositioning is utilized as a common strategy to discover a new drug indication for existing drugs. This strategy is mostly used in cases with a limited number of candidate pairs of drugs and diseases. In other words, they are not scalable to a large number of drugs and diseases. Most of the in-silico methods mainly focus on linear approaches while non-linear models are still scarce for new indication predictions. Therefore, applying non-linear computational approaches can offer an opportunity to predict possible drug repositioning candidates. RESULTS In this study, we present a non-linear method for drug repositioning. We extract four drug features and two disease features to find the semantic relations between drugs and diseases. We utilize deep learning to extract an efficient representation for each feature. These representations reduce the dimension and heterogeneity of biological data. Then, we assess the performance of different combinations of drug features to introduce a pipeline for drug repositioning. In the available database, there are different numbers of known drug-disease associations corresponding to each combination of drug features. Our assessment shows that as the numbers of drug features increase, the numbers of available drugs decrease. Thus, the proposed method with large numbers of drug features is as accurate as small numbers. CONCLUSION Our pipeline predicts new indications for existing drugs systematically, in a more cost-effective way and shorter timeline. We assess the pipeline to discover the potential drug-disease associations based on cross-validation experiments and some clinical trial studies.
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Affiliation(s)
- Mahroo Moridi
- Department of Mathematics and Computer Science, Amirkabir University of Technology, (Tehran Polytechnic), Tehran, Iran
| | - Marzieh Ghadirinia
- Department of Computer Engineering, Sharif University of Technology, Tehran, Iran
| | - Ali Sharifi-Zarchi
- Department of Computer Engineering, Sharif University of Technology, Tehran, Iran
| | - Fatemeh Zare-Mirakabad
- Department of Mathematics and Computer Science, Amirkabir University of Technology, (Tehran Polytechnic), Tehran, Iran.
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Abstract
Fibrosis is the abnormal deposition of extracellular matrix, which can lead to organ dysfunction, morbidity, and death. The disease burden caused by fibrosis is substantial, and there are currently no therapies that can prevent or reverse fibrosis. Metabolic alterations are increasingly recognized as an important pathogenic process that underlies fibrosis across many organ types. As a result, metabolically targeted therapies could become important strategies for fibrosis reduction. Indeed, some of the pathways targeted by antifibrotic drugs in development - such as the activation of transforming growth factor-β and the deposition of extracellular matrix - have metabolic implications. This Review summarizes the evidence to date and describes novel opportunities for the discovery and development of drugs for metabolic reprogramming, their associated challenges, and their utility in reducing fibrosis. Fibrotic therapies are potentially relevant to numerous common diseases such as cirrhosis, non-alcoholic steatohepatitis, chronic renal disease, heart failure, diabetes, idiopathic pulmonary fibrosis, and scleroderma.
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Musa A, Tripathi S, Dehmer M, Yli-Harja O, Kauffman SA, Emmert-Streib F. Systems Pharmacogenomic Landscape of Drug Similarities from LINCS data: Drug Association Networks. Sci Rep 2019; 9:7849. [PMID: 31127155 PMCID: PMC6534546 DOI: 10.1038/s41598-019-44291-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 05/08/2019] [Indexed: 02/01/2023] Open
Abstract
Modern research in the biomedical sciences is data-driven utilizing high-throughput technologies to generate big genomic data. The Library of Integrated Network-based Cellular Signatures (LINCS) is an example for a large-scale genomic data repository providing hundred thousands of high-dimensional gene expression measurements for thousands of drugs and dozens of cell lines. However, the remaining challenge is how to use these data effectively for pharmacogenomics. In this paper, we use LINCS data to construct drug association networks (DANs) representing the relationships between drugs. By using the Anatomical Therapeutic Chemical (ATC) classification of drugs we demonstrate that the DANs represent a systems pharmacogenomic landscape of drugs summarizing the entire LINCS repository on a genomic scale meaningfully. Here we identify the modules of the DANs as therapeutic attractors of the ATC drug classes.
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Affiliation(s)
- Aliyu Musa
- Predictive Society and Data Analytics Lab, Tampere University, Tampere, Korkeakoulunkatu 10, 33720, Tampere, Finland
- Institute of Biosciences and Medical Technology, Tampere University, Tampere, Korkeakoulunkatu 10, 33720, Tampere, Finland
| | - Shailesh Tripathi
- Predictive Society and Data Analytics Lab, Tampere University, Tampere, Korkeakoulunkatu 10, 33720, Tampere, Finland
- Institute for Intelligent Production, Faculty for Management, University of Applied Sciences Upper Austria, Wehrgrabengasse 1-3, 4400, Steyr, Austria
| | - Matthias Dehmer
- Department for Biomedical Computer Science and Mechatronics, UMIT - The Health and Lifesciences University, Eduard Wallnoefer Zentrum 1, 6060, Hall in Tyrol, Austria
- College of Computer and Control Engineering, Nankai University, Tianjin, 300350, P.R. China
- Institute for Intelligent Production, Faculty for Management, University of Applied Sciences Upper Austria, Wehrgrabengasse 1-3, 4400, Steyr, Austria
| | - Olli Yli-Harja
- Institute of Biosciences and Medical Technology, Tampere University, Tampere, Korkeakoulunkatu 10, 33720, Tampere, Finland
- Computational Systems Biology Lab, Tampere University of Technology, Korkeakoulunkatu 10, 33720, Tampere, Finland
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | | | - Frank Emmert-Streib
- Predictive Society and Data Analytics Lab, Tampere University, Tampere, Korkeakoulunkatu 10, 33720, Tampere, Finland.
- Institute of Biosciences and Medical Technology, Tampere University, Tampere, Korkeakoulunkatu 10, 33720, Tampere, Finland.
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Forés-Martos J, Catalá-López F, Sánchez-Valle J, Ibáñez K, Tejero H, Palma-Gudiel H, Climent J, Pancaldi V, Fañanás L, Arango C, Parellada M, Baudot A, Vogt D, Rubenstein JL, Valencia A, Tabarés-Seisdedos R. Transcriptomic metaanalyses of autistic brains reveals shared gene expression and biological pathway abnormalities with cancer. Mol Autism 2019; 10:17. [PMID: 31007884 PMCID: PMC6454734 DOI: 10.1186/s13229-019-0262-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 02/19/2019] [Indexed: 12/27/2022] Open
Abstract
Background Epidemiological and clinical evidence points to cancer as a comorbidity in people with autism spectrum disorders (ASD). A significant overlap of genes and biological processes between both diseases has also been reported. Methods Here, for the first time, we compared the gene expression profiles of ASD frontal cortex tissues and 22 cancer types obtained by differential expression meta-analysis and report gene, pathway, and drug set-based overlaps between them. Results Four cancer types (brain, thyroid, kidney, and pancreatic cancers) presented a significant overlap in gene expression deregulations in the same direction as ASD whereas two cancer types (lung and prostate cancers) showed differential expression profiles significantly deregulated in the opposite direction from ASD. Functional enrichment and LINCS L1000 based drug set enrichment analyses revealed the implication of several biological processes and pathways that were affected jointly in both diseases, including impairments of the immune system, and impairments in oxidative phosphorylation and ATP synthesis among others. Our data also suggest that brain and kidney cancer have patterns of transcriptomic dysregulation in the PI3K/AKT/MTOR axis that are similar to those found in ASD. Conclusions Comparisons of ASD and cancer differential gene expression meta-analysis results suggest that brain, kidney, thyroid, and pancreatic cancers are candidates for direct comorbid associations with ASD. On the other hand, lung and prostate cancers are candidates for inverse comorbid associations with ASD. Joint perturbations in a set of specific biological processes underlie these associations which include several pathways previously implicated in both cancer and ASD encompassing immune system alterations, impairments of energy metabolism, cell cycle, and signaling through PI3K and G protein-coupled receptors among others. These findings could help to explain epidemiological observations pointing towards direct and inverse comorbid associations between ASD and specific cancer types and depict a complex scenario regarding the molecular patterns of association between ASD and cancer. Electronic supplementary material The online version of this article (10.1186/s13229-019-0262-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jaume Forés-Martos
- 1Biomedical Research Networking Center of Mental Health (CIBERSAM), Madrid, Spain
| | - Ferrán Catalá-López
- 1Biomedical Research Networking Center of Mental Health (CIBERSAM), Madrid, Spain.,2Teaching Unit of Psychiatry and Psychological Medicine, Department of Medicine, University of Valencia, Blasco-Ibañez 15, 46010 Valencia, Spain.,3INCLIVA Health Research Institute, Valencia, Spain.,4Department of Health Planning and Economics, National School of Public Health/IMIENS, Institute of Health Carlos III, Madrid, Spain
| | | | | | - Héctor Tejero
- 7Structural Biology Program, Spanish National Cancer Research Program (CNIO), Madrid, Spain
| | - Helena Palma-Gudiel
- 1Biomedical Research Networking Center of Mental Health (CIBERSAM), Madrid, Spain.,8Anthropology Section, Department of Evolutionary Biology, Ecology and Environmental Sciences, Biomedicine Institute (IBUB), University of Barcelona (UB), Barcelona, Spain
| | - Joan Climent
- 3INCLIVA Health Research Institute, Valencia, Spain.,9Departamento de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Cardenal Herrera-CEU, CEU Universities, Calle Ramon y Cajal s/n 46115 Alfara del Patriarca, Valencia, Spain
| | - Vera Pancaldi
- 5Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Lourdes Fañanás
- 1Biomedical Research Networking Center of Mental Health (CIBERSAM), Madrid, Spain.,8Anthropology Section, Department of Evolutionary Biology, Ecology and Environmental Sciences, Biomedicine Institute (IBUB), University of Barcelona (UB), Barcelona, Spain
| | - Celso Arango
- 1Biomedical Research Networking Center of Mental Health (CIBERSAM), Madrid, Spain.,Department of Child and Adolescent Psychiatry, Hospital General Universitario Gregorio Marañón, IiSGM, School of Medicine, Universidad Complutense, Madrid, Spain
| | - Mara Parellada
- 1Biomedical Research Networking Center of Mental Health (CIBERSAM), Madrid, Spain.,Department of Child and Adolescent Psychiatry, Hospital General Universitario Gregorio Marañón, IiSGM, School of Medicine, Universidad Complutense, Madrid, Spain
| | - Anaïs Baudot
- 11Aix-Marseille Univ, Inserm, MMG, Marseille Medical Genetics, Marseille, France
| | - Daniel Vogt
- 12Department of Pediatrics and Human Development, Michigan State University, East Lansing, MI 48824 USA
| | - John L Rubenstein
- 13Nina Ireland Laboratory of Developmental Neurobiology, University of California, San Francisco, CA 94158 USA.,14Department of Psychiatry, University of California, San Francisco, CA 94158 USA
| | - Alfonso Valencia
- 5Barcelona Supercomputing Center (BSC), Barcelona, Spain.,15Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Rafael Tabarés-Seisdedos
- 1Biomedical Research Networking Center of Mental Health (CIBERSAM), Madrid, Spain.,2Teaching Unit of Psychiatry and Psychological Medicine, Department of Medicine, University of Valencia, Blasco-Ibañez 15, 46010 Valencia, Spain.,3INCLIVA Health Research Institute, Valencia, Spain
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12
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Küçük McGinty H, Visser U, Schürer S. How to Develop a Drug Target Ontology: KNowledge Acquisition and Representation Methodology (KNARM). Methods Mol Biol 2019; 1939:49-69. [PMID: 30848456 PMCID: PMC7257161 DOI: 10.1007/978-1-4939-9089-4_4] [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] [Indexed: 09/06/2023]
Abstract
Technological advancements in many fields have led to huge increases in data production, including data volume, diversity, and the speed at which new data is becoming available. In accordance with this, there is a lack of conformity in the ways data is interpreted. This era of "big data" provides unprecedented opportunities for data-driven research and "big picture" models. However, in-depth analyses-making use of various data types and data sources and extracting knowledge-have become a more daunting task. This is especially the case in life sciences where simplification and flattening of diverse data types often lead to incorrect predictions. Effective applications of big data approaches in life sciences require better, knowledge-based, semantic models that are suitable as a framework for big data integration, while avoiding oversimplifications, such as reducing various biological data types to the gene level. A huge hurdle in developing such semantic knowledge models, or ontologies, is the knowledge acquisition bottleneck. Automated methods are still very limited, and significant human expertise is required. In this chapter, we describe a methodology to systematize this knowledge acquisition and representation challenge, termed KNowledge Acquisition and Representation Methodology (KNARM). We then describe application of the methodology while implementing the Drug Target Ontology (DTO). We aimed to create an approach, involving domain experts and knowledge engineers, to build useful, comprehensive, consistent ontologies that will enable big data approaches in the domain of drug discovery, without the currently common simplifications.
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Affiliation(s)
- Hande Küçük McGinty
- Department of Computer Science, University of Miami, Coral Gables, FL, USA
- Collaborative Drug Discovery, Inc., Burlingame, CA, USA
| | - Ubbo Visser
- Department of Computer Science, University of Miami, Coral Gables, FL, USA
| | - Stephan Schürer
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL, USA.
- Center for Computational Science, University of Miami, Coral Gables, FL, USA.
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13
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Monks A, Zhao Y, Hose C, Hamed H, Krushkal J, Fang J, Sonkin D, Palmisano A, Polley EC, Fogli LK, Konaté MM, Miller SB, Simpson MA, Voth AR, Li MC, Harris E, Wu X, Connelly JW, Rapisarda A, Teicher BA, Simon R, Doroshow JH. The NCI Transcriptional Pharmacodynamics Workbench: A Tool to Examine Dynamic Expression Profiling of Therapeutic Response in the NCI-60 Cell Line Panel. Cancer Res 2018; 78:6807-6817. [PMID: 30355619 PMCID: PMC6295263 DOI: 10.1158/0008-5472.can-18-0989] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 07/24/2018] [Accepted: 10/16/2018] [Indexed: 12/31/2022]
Abstract
: The intracellular effects and overall efficacies of anticancer therapies can vary significantly by tumor type. To identify patterns of drug-induced gene modulation that occur in different cancer cell types, we measured gene-expression changes across the NCI-60 cell line panel after exposure to 15 anticancer agents. The results were integrated into a combined database and set of interactive analysis tools, designated the NCI Transcriptional Pharmacodynamics Workbench (NCI TPW), that allows exploration of gene-expression modulation by molecular pathway, drug target, and association with drug sensitivity. We identified common transcriptional responses across agents and cell types and uncovered gene-expression changes associated with drug sensitivity. We also demonstrated the value of this tool for investigating clinically relevant molecular hypotheses and identifying candidate biomarkers of drug activity. The NCI TPW, publicly available at https://tpwb.nci.nih.gov, provides a comprehensive resource to facilitate understanding of tumor cell characteristics that define sensitivity to commonly used anticancer drugs. SIGNIFICANCE: The NCI Transcriptional Pharmacodynamics Workbench represents the most extensive compilation to date of directly measured longitudinal transcriptional responses to anticancer agents across a thoroughly characterized ensemble of cancer cell lines.
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Affiliation(s)
- Anne Monks
- Molecular Pharmacology Group, Frederick National Laboratory for Cancer Research sponsored by the NCI, Frederick, Maryland
| | - Yingdong Zhao
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, NCI, NIH, Rockville, Maryland
| | - Curtis Hose
- Molecular Pharmacology Group, Frederick National Laboratory for Cancer Research sponsored by the NCI, Frederick, Maryland
| | - Hossein Hamed
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, NCI, NIH, Rockville, Maryland
| | - Julia Krushkal
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, NCI, NIH, Rockville, Maryland
| | - Jianwen Fang
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, NCI, NIH, Rockville, Maryland
| | - Dmitriy Sonkin
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, NCI, NIH, Rockville, Maryland
| | - Alida Palmisano
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, NCI, NIH, Rockville, Maryland
| | - Eric C Polley
- Division of Cancer Treatment and Diagnosis, NCI, NIH, Bethesda, Maryland
| | - Laura K Fogli
- Division of Cancer Treatment and Diagnosis, NCI, NIH, Bethesda, Maryland
| | - Mariam M Konaté
- Division of Cancer Treatment and Diagnosis, NCI, NIH, Bethesda, Maryland
| | - Sarah B Miller
- Division of Cancer Treatment and Diagnosis, NCI, NIH, Bethesda, Maryland
| | - Melanie A Simpson
- Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research sponsored by the NCI, Frederick, Maryland
| | - Andrea Regier Voth
- Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research sponsored by the NCI, Frederick, Maryland
| | - Ming-Chung Li
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, NCI, NIH, Rockville, Maryland
| | - Erik Harris
- Molecular Pharmacology Group, Frederick National Laboratory for Cancer Research sponsored by the NCI, Frederick, Maryland
| | - Xiaolin Wu
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research sponsored by the NCI, Frederick, Maryland
| | - John W Connelly
- Molecular Pharmacology Group, Frederick National Laboratory for Cancer Research sponsored by the NCI, Frederick, Maryland
| | - Annamaria Rapisarda
- Molecular Pharmacology Group, Frederick National Laboratory for Cancer Research sponsored by the NCI, Frederick, Maryland
| | - Beverly A Teicher
- Division of Cancer Treatment and Diagnosis, NCI, NIH, Bethesda, Maryland
| | - Richard Simon
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, NCI, NIH, Rockville, Maryland
| | - James H Doroshow
- Division of Cancer Treatment and Diagnosis, NCI, NIH, Bethesda, Maryland.
- Center for Cancer Research, NCI, NIH, Bethesda, Maryland
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14
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Busonero C, Leone S, Bianchi F, Acconcia F. In silico screening for ERα down modulators identifies thioridazine as an anti-proliferative agent in primary, 4OH-tamoxifen-resistant and Y537S ERα-expressing breast cancer cells. Cell Oncol (Dordr) 2018; 41:677-686. [PMID: 30182339 DOI: 10.1007/s13402-018-0400-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2018] [Indexed: 02/07/2023] Open
Abstract
PURPOSE Most breast cancers (BCs) express estrogen receptor α (ERα) and are treated with the endocrine therapy (ET) drugs 4OH-tamoxifen (Tam) and fulvestrant (ICI 182,780; ICI). Unfortunately, a high fraction of ET treated women relapses and becomes resistant to ET. Therefore, additional anti-BC drugs are needed. Recently, we proposed that the identification of novel anti-BC drugs can be achieved using modulation of the intracellular ERα content in BC cells as a pharmacological target. Here, we searched for Food and Drug Administration (FDA)-approved drugs that potentially modify the ERα content in BC cells. METHODS We screened in silico more than 60,000 compounds to identify FDA-approved drugs with a gene signature similar to that of ICI. We identified mitoxantrone and thioridazine and tested them in primary, Tam-resistant and genome-edited Y537S ERα-expressing BC cells. RESULTS We found that mitoxantrone and thioridazine induced ERα downmodulation and prevented MCF-7 BC cell proliferation. Interestingly, while mitoxantrone was found to be toxic for normal breast epithelial cells, thioridazine showed a preferential activity towards BC cells. Thioridazine also reduced the ERα content and prevented cell proliferation in primary, Tam-resistant and genome-edited Y537S ERα expressing BC cells. CONCLUSIONS We suggest that modulation of the intracellular ERα concentration in BC cells can be exploited in in silico screens to identify anti-BC drugs and uncover a re-purposing opportunity for thioridazine in the treatment of primary and metastatic ET resistant BCs.
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Affiliation(s)
- Claudia Busonero
- Department of Sciences, Section Biomedical Sciences and Technology, University Roma Tre, Viale Guglielmo Marconi, 446, I-00146, Rome, Italy
| | - Stefano Leone
- Department of Sciences, Section Biomedical Sciences and Technology, University Roma Tre, Viale Guglielmo Marconi, 446, I-00146, Rome, Italy
| | - Fabrizio Bianchi
- ISBREMIT, Institute for Stem-cell Biology, Regenerative Medicine and Innovative Therapies, IRCCS Casa Sollievo della Sofferenza, Viale Padre Pio, 7, 71013, San Giovanni Rotondo (FG), Italy
| | - Filippo Acconcia
- Department of Sciences, Section Biomedical Sciences and Technology, University Roma Tre, Viale Guglielmo Marconi, 446, I-00146, Rome, Italy.
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15
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Musa A, Tripathi S, Kandhavelu M, Dehmer M, Emmert-Streib F. Harnessing the biological complexity of Big Data from LINCS gene expression signatures. PLoS One 2018; 13:e0201937. [PMID: 30157183 PMCID: PMC6114505 DOI: 10.1371/journal.pone.0201937] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 07/24/2018] [Indexed: 01/02/2023] Open
Abstract
Gene expression profiling using transcriptional drug perturbations are useful for many biomedical discovery studies including drug repurposing and elucidation of drug mechanisms (MoA) and many other pharmacogenomic applications. However, limited data availability across cell types has severely hindered our capacity to progress in these areas. To fill this gap, recently, the LINCS program generated almost 1.3 million profiles for over 40,000 drug and genetic perturbations for over 70 different human cell types, including meta information about the experimental conditions and cell lines. Unfortunately, Big Data like the ones generated from the ongoing LINCS program do not enable easy insights from the data but possess considerable challenges toward their analysis. In this paper, we address some of these challenges. Specifically, first, we study the gene expression signature profiles from all cell lines and their perturbagents in order to obtain insights in the distributional characteristics of available conditions. Second, we investigate the differential expression of genes for all cell lines obtaining an understanding of condition dependent differential expression manifesting the biological complexity of perturbagents. As a result, our analysis helps the experimental design of follow-up studies, e.g., by selecting appropriate cell lines.
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Affiliation(s)
- Aliyu Musa
- Predictive Medicine and Data Analytics Lab, Department of Signal Processing, Tampere University of Technology, Tampere, Finland
- Molecular Signaling Lab, Faculty of Biomedical Sciences and Engineering, Tampere University of Technology, Tampere, Finland
| | - Shailesh Tripathi
- Predictive Medicine and Data Analytics Lab, Department of Signal Processing, Tampere University of Technology, Tampere, Finland
- University of Applied Sciences Upper Austria, Steyr, Austria
| | - Meenakshisundaram Kandhavelu
- Molecular Signaling Lab, Faculty of Biomedical Sciences and Engineering, Tampere University of Technology, Tampere, Finland
- BioMediTech Institute, Tampere University of Technology, Tampere, Finland
| | - Matthias Dehmer
- University of Applied Sciences Upper Austria, Steyr, Austria
- Institute for Bioinformatics and Translational Research, UMIT- The Health and Life Sciences University, Hall in Tyrol, Austria
| | - Frank Emmert-Streib
- Predictive Medicine and Data Analytics Lab, Department of Signal Processing, Tampere University of Technology, Tampere, Finland
- Molecular Signaling Lab, Faculty of Biomedical Sciences and Engineering, Tampere University of Technology, Tampere, Finland
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16
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Alexander-Dann B, Pruteanu LL, Oerton E, Sharma N, Berindan-Neagoe I, Módos D, Bender A. Developments in toxicogenomics: understanding and predicting compound-induced toxicity from gene expression data. Mol Omics 2018; 14:218-236. [PMID: 29917034 PMCID: PMC6080592 DOI: 10.1039/c8mo00042e] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 05/08/2018] [Indexed: 12/12/2022]
Abstract
The toxicogenomics field aims to understand and predict toxicity by using 'omics' data in order to study systems-level responses to compound treatments. In recent years there has been a rapid increase in publicly available toxicological and 'omics' data, particularly gene expression data, and a corresponding development of methods for its analysis. In this review, we summarize recent progress relating to the analysis of RNA-Seq and microarray data, review relevant databases, and highlight recent applications of toxicogenomics data for understanding and predicting compound toxicity. These include the analysis of differentially expressed genes and their enrichment, signature matching, methods based on interaction networks, and the analysis of co-expression networks. In the future, these state-of-the-art methods will likely be combined with new technologies, such as whole human body models, to produce a comprehensive systems-level understanding of toxicity that reduces the necessity of in vivo toxicity assessment in animal models.
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Affiliation(s)
- Benjamin Alexander-Dann
- University of Cambridge
, Centre for Molecular Informatics
, Department of Chemistry
,
Lensfield Road
, Cambridge CB2 1EW
, UK
.
;
| | - Lavinia Lorena Pruteanu
- University of Cambridge
, Centre for Molecular Informatics
, Department of Chemistry
,
Lensfield Road
, Cambridge CB2 1EW
, UK
.
;
- Babeş-Bolyai University
, Institute for Doctoral Studies
,
1 Kogălniceanu Street
, Cluj-Napoca 400084
, Romania
- University of Medicine and Pharmacy “Iuliu Haţieganu”
, MedFuture Research Centre for Advanced Medicine
,
23 Marinescu Street/4-6 Pasteur Street
, Cluj-Napoca 400337
, Romania
| | - Erin Oerton
- University of Cambridge
, Centre for Molecular Informatics
, Department of Chemistry
,
Lensfield Road
, Cambridge CB2 1EW
, UK
.
;
| | - Nitin Sharma
- University of Cambridge
, Centre for Molecular Informatics
, Department of Chemistry
,
Lensfield Road
, Cambridge CB2 1EW
, UK
.
;
| | - Ioana Berindan-Neagoe
- University of Medicine and Pharmacy “Iuliu Haţieganu”
, MedFuture Research Centre for Advanced Medicine
,
23 Marinescu Street/4-6 Pasteur Street
, Cluj-Napoca 400337
, Romania
- University of Medicine and Pharmacy “Iuliu Haţieganu”
, Research Center for Functional Genomics
, Biomedicine and Translational Medicine
,
23 Marinescu Street
, Cluj-Napoca 400337
, Romania
- The Oncology Institute “Prof. Dr Ion Chiricuţă”
, Department of Functional Genomics and Experimental Pathology
,
34-36 Republicii Street
, Cluj-Napoca 400015
, Romania
| | - Dezső Módos
- University of Cambridge
, Centre for Molecular Informatics
, Department of Chemistry
,
Lensfield Road
, Cambridge CB2 1EW
, UK
.
;
| | - Andreas Bender
- University of Cambridge
, Centre for Molecular Informatics
, Department of Chemistry
,
Lensfield Road
, Cambridge CB2 1EW
, UK
.
;
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17
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Ferrero E, Agarwal P. Connecting genetics and gene expression data for target prioritisation and drug repositioning. BioData Min 2018; 11:7. [PMID: 29881461 PMCID: PMC5984374 DOI: 10.1186/s13040-018-0171-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 05/14/2018] [Indexed: 12/18/2022] Open
Abstract
Developing new drugs continues to be a highly inefficient and costly business. By repurposing an existing compound for a different indication, drug repositioning offers an attractive alternative to traditional drug discovery. Most of these approaches work by matching transcriptional disease signatures to anti-correlated gene expression profiles of drug perturbations. Genome-wide association studies (GWASs) are of great interest to researchers in the pharmaceutical industry because drug programmes with supporting genetic evidence are more likely to successfully progress through the drug discovery pipeline. Here, we present a systematic approach to generate drug repositioning hypothesis based on disease genetics by mining public repositories of GWAS data and drug transcriptomic profiles. We find that genes genetically associated with a certain disease are more likely to be differentially expressed in the same disease (p-value = 1.54e-17 and AUC = 0.75) and that, in existing drug - disease combinations, genes significantly up- or down-regulated after drug treatment are enriched for genes genetically associated with that disease (p-value = 1.1e-79 and AUC = 0.64). Finally, we use this framework to generate and rank novel GWAS-driven drug repositioning predictions.
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Affiliation(s)
- Enrico Ferrero
- Computational Biology, Target Sciences, GSK, Gunnels Wood Road, Stevenage, SG1 2NY UK
- Present Address: Autoimmunity, Transplantation and Inflammation, Novartis Institutes for Biomedical Research, Fabrikstrasse 2, Basel, 4056 Switzerland
| | - Pankaj Agarwal
- Computational Biology, Target Sciences, GSK, 1250 S. Collegeville Road, UP12-100, Collegeville, PA 19426-0989 USA
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18
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Musa A, Ghoraie LS, Zhang SD, Glazko G, Yli-Harja O, Dehmer M, Haibe-Kains B, Emmert-Streib F. A review of connectivity map and computational approaches in pharmacogenomics. Brief Bioinform 2018; 19:506-523. [PMID: 28069634 PMCID: PMC5952941 DOI: 10.1093/bib/bbw112] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Large-scale perturbation databases, such as Connectivity Map (CMap) or Library of Integrated Network-based Cellular Signatures (LINCS), provide enormous opportunities for computational pharmacogenomics and drug design. A reason for this is that in contrast to classical pharmacology focusing at one target at a time, the transcriptomics profiles provided by CMap and LINCS open the door for systems biology approaches on the pathway and network level. In this article, we provide a review of recent developments in computational pharmacogenomics with respect to CMap and LINCS and related applications.
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Affiliation(s)
- Aliyu Musa
- Predictive Medicine and Analytics Lab, Department of Signal Processing, Tampere University of Technology, Tampere, Finland
| | - Laleh Soltan Ghoraie
- Bioinformatics and Computational Genomics Laboratory, Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada
| | - Shu-Dong Zhang
- Northern Ireland Centre for Stratified Medicine, Biomedical Sciences Research Institute, University of Ulster, C-TRIC Building, Altnagelvin Area Hospital, Glenshane Road, Derry/Londonderry, Northern Ireland, UK
| | - Galina Glazko
- University of Rochester Department of Biostatistics and Computational Biology, Rochester, New York, USA
| | - Olli Yli-Harja
- Computational Systems Biology, Department of Signal Processing, Tampere University of Technology, Tampere, Finland
| | - Matthias Dehmer
- Institute for Bioinformatics and Translational Research, UMIT- The Health and Life Sciences University, Eduard Wallnoefer Zentrum 1, Hall in Tyrol, Austria
| | - Benjamin Haibe-Kains
- Bioinformatics and Computational Genomics Laboratory, Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
- Ontario Institute of Cancer Research, Toronto, ON, Canada
| | - Frank Emmert-Streib
- Predictive Medicine and Analytics Lab, Department of Signal Processing, Tampere University of Technology, Tampere, Finland
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19
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Musa A, Ghoraie LS, Zhang SD, Glazko G, Yli-Harja O, Dehmer M, Haibe-Kains B, Emmert-Streib F. A review of connectivity map and computational approaches in pharmacogenomics. Brief Bioinform 2018. [PMID: 28069634 DOI: 10.1093/bib] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023] Open
Abstract
Large-scale perturbation databases, such as Connectivity Map (CMap) or Library of Integrated Network-based Cellular Signatures (LINCS), provide enormous opportunities for computational pharmacogenomics and drug design. A reason for this is that in contrast to classical pharmacology focusing at one target at a time, the transcriptomics profiles provided by CMap and LINCS open the door for systems biology approaches on the pathway and network level. In this article, we provide a review of recent developments in computational pharmacogenomics with respect to CMap and LINCS and related applications.
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Affiliation(s)
- Aliyu Musa
- Predictive Medicine and Analytics Lab, Department of Signal Processing, Tampere University of Technology, Tampere, Finland
| | - Laleh Soltan Ghoraie
- Bioinformatics and Computational Genomics Laboratory, Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada
| | - Shu-Dong Zhang
- Northern Ireland Centre for Stratified Medicine, Biomedical Sciences Research Institute, University of Ulster, C-TRIC Building, Altnagelvin Area Hospital, Glenshane Road, Derry/Londonderry BT47 6SB, Northern Ireland, UK
| | - Galina Glazko
- University of Rochester Department of Biostatistics and Computational Biology, Rochester, New York 14642, USA
| | - Olli Yli-Harja
- Computational Systems Biology, Department of Signal Processing, Tampere University of Technology, Tampere, Finland
| | - Matthias Dehmer
- Institute for Bioinformatics and Translational Research, UMIT- The Health and Life Sciences University, Eduard Wallnoefer Zentrum 1, 6060 Hall in Tyrol, Austria
| | - Benjamin Haibe-Kains
- Bioinformatics and Computational Genomics Laboratory, Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
- Ontario Institute of Cancer Research, Toronto, ON, Canada
| | - Frank Emmert-Streib
- Predictive Medicine and Analytics Lab, Department of Signal Processing, Tampere University of Technology, Tampere, Finland
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20
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Ching T, Himmelstein DS, Beaulieu-Jones BK, Kalinin AA, Do BT, Way GP, Ferrero E, Agapow PM, Zietz M, Hoffman MM, Xie W, Rosen GL, Lengerich BJ, Israeli J, Lanchantin J, Woloszynek S, Carpenter AE, Shrikumar A, Xu J, Cofer EM, Lavender CA, Turaga SC, Alexandari AM, Lu Z, Harris DJ, DeCaprio D, Qi Y, Kundaje A, Peng Y, Wiley LK, Segler MHS, Boca SM, Swamidass SJ, Huang A, Gitter A, Greene CS. Opportunities and obstacles for deep learning in biology and medicine. J R Soc Interface 2018; 15:20170387. [PMID: 29618526 PMCID: PMC5938574 DOI: 10.1098/rsif.2017.0387] [Citation(s) in RCA: 811] [Impact Index Per Article: 135.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 03/07/2018] [Indexed: 11/12/2022] Open
Abstract
Deep learning describes a class of machine learning algorithms that are capable of combining raw inputs into layers of intermediate features. These algorithms have recently shown impressive results across a variety of domains. Biology and medicine are data-rich disciplines, but the data are complex and often ill-understood. Hence, deep learning techniques may be particularly well suited to solve problems of these fields. We examine applications of deep learning to a variety of biomedical problems-patient classification, fundamental biological processes and treatment of patients-and discuss whether deep learning will be able to transform these tasks or if the biomedical sphere poses unique challenges. Following from an extensive literature review, we find that deep learning has yet to revolutionize biomedicine or definitively resolve any of the most pressing challenges in the field, but promising advances have been made on the prior state of the art. Even though improvements over previous baselines have been modest in general, the recent progress indicates that deep learning methods will provide valuable means for speeding up or aiding human investigation. Though progress has been made linking a specific neural network's prediction to input features, understanding how users should interpret these models to make testable hypotheses about the system under study remains an open challenge. Furthermore, the limited amount of labelled data for training presents problems in some domains, as do legal and privacy constraints on work with sensitive health records. Nonetheless, we foresee deep learning enabling changes at both bench and bedside with the potential to transform several areas of biology and medicine.
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Affiliation(s)
- Travers Ching
- Molecular Biosciences and Bioengineering Graduate Program, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Daniel S Himmelstein
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Brett K Beaulieu-Jones
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alexandr A Kalinin
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | | | - Gregory P Way
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Enrico Ferrero
- Computational Biology and Stats, Target Sciences, GlaxoSmithKline, Stevenage, UK
| | | | - Michael Zietz
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael M Hoffman
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Wei Xie
- Electrical Engineering and Computer Science, Vanderbilt University, Nashville, TN, USA
| | - Gail L Rosen
- Ecological and Evolutionary Signal-processing and Informatics Laboratory, Department of Electrical and Computer Engineering, Drexel University, Philadelphia, PA, USA
| | - Benjamin J Lengerich
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Johnny Israeli
- Biophysics Program, Stanford University, Stanford, CA, USA
| | - Jack Lanchantin
- Department of Computer Science, University of Virginia, Charlottesville, VA, USA
| | - Stephen Woloszynek
- Ecological and Evolutionary Signal-processing and Informatics Laboratory, Department of Electrical and Computer Engineering, Drexel University, Philadelphia, PA, USA
| | - Anne E Carpenter
- Imaging Platform, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Avanti Shrikumar
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Jinbo Xu
- Toyota Technological Institute at Chicago, Chicago, IL, USA
| | - Evan M Cofer
- Department of Computer Science, Trinity University, San Antonio, TX, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Christopher A Lavender
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Srinivas C Turaga
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA, USA
| | - Amr M Alexandari
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Zhiyong Lu
- National Center for Biotechnology Information and National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - David J Harris
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL, USA
| | | | - Yanjun Qi
- Department of Computer Science, University of Virginia, Charlottesville, VA, USA
| | - Anshul Kundaje
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Yifan Peng
- National Center for Biotechnology Information and National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Laura K Wiley
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Marwin H S Segler
- Institute of Organic Chemistry, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Simina M Boca
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC, USA
| | - S Joshua Swamidass
- Department of Pathology and Immunology, Washington University in Saint Louis, St Louis, MO, USA
| | - Austin Huang
- Department of Medicine, Brown University, Providence, RI, USA
| | - Anthony Gitter
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA
- Morgridge Institute for Research, Madison, WI, USA
| | - Casey S Greene
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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21
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Tan SK, Jermakowicz A, Mookhtiar AK, Nemeroff CB, Schürer SC, Ayad NG. Drug Repositioning in Glioblastoma: A Pathway Perspective. Front Pharmacol 2018; 9:218. [PMID: 29615902 PMCID: PMC5864870 DOI: 10.3389/fphar.2018.00218] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 02/27/2018] [Indexed: 12/27/2022] Open
Abstract
Glioblastoma multiforme (GBM) is the most malignant primary adult brain tumor. The current standard of care is surgical resection, radiation, and chemotherapy treatment, which extends life in most cases. Unfortunately, tumor recurrence is nearly universal and patients with recurrent glioblastoma typically survive <1 year. Therefore, new therapies and therapeutic combinations need to be developed that can be quickly approved for use in patients. However, in order to gain approval, therapies need to be safe as well as effective. One possible means of attaining rapid approval is repurposing FDA approved compounds for GBM therapy. However, candidate compounds must be able to penetrate the blood-brain barrier (BBB) and therefore a selection process has to be implemented to identify such compounds that can eliminate GBM tumor expansion. We review here psychiatric and non-psychiatric compounds that may be effective in GBM, as well as potential drugs targeting cell death pathways. We also discuss the potential of data-driven computational approaches to identify compounds that induce cell death in GBM cells, enabled by large reference databases such as the Library of Integrated Network Cell Signatures (LINCS). Finally, we argue that identifying pathways dysregulated in GBM in a patient specific manner is essential for effective repurposing in GBM and other gliomas.
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Affiliation(s)
- Sze Kiat Tan
- Department of Psychiatry and Behavioral Sciences, Center for Therapeutic Innovation, Miami Project to Cure Paralysis, Sylvester Comprehensive Cancer Center, University of Miami Brain Tumor Initiative, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Anna Jermakowicz
- Department of Psychiatry and Behavioral Sciences, Center for Therapeutic Innovation, Miami Project to Cure Paralysis, Sylvester Comprehensive Cancer Center, University of Miami Brain Tumor Initiative, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Adnan K Mookhtiar
- Department of Psychiatry and Behavioral Sciences, Center for Therapeutic Innovation, Miami Project to Cure Paralysis, Sylvester Comprehensive Cancer Center, University of Miami Brain Tumor Initiative, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Charles B Nemeroff
- Department of Psychiatry and Behavioral Sciences and Center on Aging, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Stephan C Schürer
- Department of Molecular Pharmacology, Center for Computational Sciences, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Nagi G Ayad
- Department of Psychiatry and Behavioral Sciences, Center for Therapeutic Innovation, Miami Project to Cure Paralysis, Sylvester Comprehensive Cancer Center, University of Miami Brain Tumor Initiative, University of Miami Miller School of Medicine, Miami, FL, United States
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22
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Almugbel R, Hung LH, Hu J, Almutairy A, Ortogero N, Tamta Y, Yeung KY. Reproducible Bioconductor workflows using browser-based interactive notebooks and containers. J Am Med Inform Assoc 2018; 25:4-12. [PMID: 29092073 PMCID: PMC6381817 DOI: 10.1093/jamia/ocx120] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 08/31/2017] [Accepted: 09/28/2017] [Indexed: 11/14/2022] Open
Abstract
Objective Bioinformatics publications typically include complex software workflows that are difficult to describe in a manuscript. We describe and demonstrate the use of interactive software notebooks to document and distribute bioinformatics research. We provide a user-friendly tool, BiocImageBuilder, that allows users to easily distribute their bioinformatics protocols through interactive notebooks uploaded to either a GitHub repository or a private server. Materials and methods We present four different interactive Jupyter notebooks using R and Bioconductor workflows to infer differential gene expression, analyze cross-platform datasets, process RNA-seq data and KinomeScan data. These interactive notebooks are available on GitHub. The analytical results can be viewed in a browser. Most importantly, the software contents can be executed and modified. This is accomplished using Binder, which runs the notebook inside software containers, thus avoiding the need to install any software and ensuring reproducibility. All the notebooks were produced using custom files generated by BiocImageBuilder. Results BiocImageBuilder facilitates the publication of workflows with a point-and-click user interface. We demonstrate that interactive notebooks can be used to disseminate a wide range of bioinformatics analyses. The use of software containers to mirror the original software environment ensures reproducibility of results. Parameters and code can be dynamically modified, allowing for robust verification of published results and encouraging rapid adoption of new methods. Conclusion Given the increasing complexity of bioinformatics workflows, we anticipate that these interactive software notebooks will become as necessary for documenting software methods as traditional laboratory notebooks have been for documenting bench protocols, and as ubiquitous.
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Affiliation(s)
- Reem Almugbel
- Institute of Technology, University of Washington, Tacoma, WA, USA
| | - Ling-Hong Hung
- Institute of Technology, University of Washington, Tacoma, WA, USA
| | - Jiaming Hu
- Institute of Technology, University of Washington, Tacoma, WA, USA
| | - Abeer Almutairy
- Institute of Technology, University of Washington, Tacoma, WA, USA
| | - Nicole Ortogero
- Department of Clinical Investigation, Madigan Army Medical Center, Tacoma, WA, USA
| | - Yashaswi Tamta
- Institute of Technology, University of Washington, Tacoma, WA, USA
| | - Ka Yee Yeung
- Institute of Technology, University of Washington, Tacoma, WA, USA
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23
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Young WC, Raftery AE, Yeung KY. Model-Based Clustering With Data Correction For Removing Artifacts In Gene Expression Data. Ann Appl Stat 2017; 11:1998-2026. [PMID: 30740193 DOI: 10.1214/17-aoas1051] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The NIH Library of Integrated Network-based Cellular Signatures (LINCS) contains gene expression data from over a million experiments, using Luminex Bead technology. Only 500 colors are used to measure the expression levels of the 1,000 landmark genes measured, and the data for the resulting pairs of genes are deconvolved. The raw data are sometimes inadequate for reliable deconvolution, leading to artifacts in the final processed data. These include the expression levels of paired genes being flipped or given the same value, and clusters of values that are not at the true expression level. We propose a new method called model-based clustering with data correction (MCDC) that is able to identify and correct these three kinds of artifacts simultaneously. We show that MCDC improves the resulting gene expression data in terms of agreement with external baselines, as well as improving results from subsequent analysis.
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Affiliation(s)
- William Chad Young
- Department of Statistics, University of Washington, Box 354322, Seattle, WA 98195
| | - Adrian E Raftery
- Department of Statistics, University of Washington, Box 354322, Seattle, WA 98195
| | - Ka Yee Yeung
- Institute of Technology, University of Washington Tacoma, Campus Box 358426, 1900 Commerce Street, Tacoma, WA 98402
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24
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Lin Y, Mehta S, Küçük-McGinty H, Turner JP, Vidovic D, Forlin M, Koleti A, Nguyen DT, Jensen LJ, Guha R, Mathias SL, Ursu O, Stathias V, Duan J, Nabizadeh N, Chung C, Mader C, Visser U, Yang JJ, Bologa CG, Oprea TI, Schürer SC. Drug target ontology to classify and integrate drug discovery data. J Biomed Semantics 2017; 8:50. [PMID: 29122012 PMCID: PMC5679337 DOI: 10.1186/s13326-017-0161-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 10/17/2017] [Indexed: 11/12/2022] Open
Abstract
Background One of the most successful approaches to develop new small molecule therapeutics has been to start from a validated druggable protein target. However, only a small subset of potentially druggable targets has attracted significant research and development resources. The Illuminating the Druggable Genome (IDG) project develops resources to catalyze the development of likely targetable, yet currently understudied prospective drug targets. A central component of the IDG program is a comprehensive knowledge resource of the druggable genome. Results As part of that effort, we have developed a framework to integrate, navigate, and analyze drug discovery data based on formalized and standardized classifications and annotations of druggable protein targets, the Drug Target Ontology (DTO). DTO was constructed by extensive curation and consolidation of various resources. DTO classifies the four major drug target protein families, GPCRs, kinases, ion channels and nuclear receptors, based on phylogenecity, function, target development level, disease association, tissue expression, chemical ligand and substrate characteristics, and target-family specific characteristics. The formal ontology was built using a new software tool to auto-generate most axioms from a database while supporting manual knowledge acquisition. A modular, hierarchical implementation facilitate ontology development and maintenance and makes use of various external ontologies, thus integrating the DTO into the ecosystem of biomedical ontologies. As a formal OWL-DL ontology, DTO contains asserted and inferred axioms. Modeling data from the Library of Integrated Network-based Cellular Signatures (LINCS) program illustrates the potential of DTO for contextual data integration and nuanced definition of important drug target characteristics. DTO has been implemented in the IDG user interface Portal, Pharos and the TIN-X explorer of protein target disease relationships. Conclusions DTO was built based on the need for a formal semantic model for druggable targets including various related information such as protein, gene, protein domain, protein structure, binding site, small molecule drug, mechanism of action, protein tissue localization, disease association, and many other types of information. DTO will further facilitate the otherwise challenging integration and formal linking to biological assays, phenotypes, disease models, drug poly-pharmacology, binding kinetics and many other processes, functions and qualities that are at the core of drug discovery. The first version of DTO is publically available via the website http://drugtargetontology.org/, Github (http://github.com/DrugTargetOntology/DTO), and the NCBO Bioportal (http://bioportal.bioontology.org/ontologies/DTO). The long-term goal of DTO is to provide such an integrative framework and to populate the ontology with this information as a community resource. Electronic supplementary material The online version of this article (10.1186/s13326-017-0161-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yu Lin
- Center for Computational Science, University of Miami, Coral Gables, FL, USA
| | - Saurabh Mehta
- Center for Computational Science, University of Miami, Coral Gables, FL, USA.,Department of Applied Chemistry, Delhi Technological University, Delhi, India
| | - Hande Küçük-McGinty
- Center for Computational Science, University of Miami, Coral Gables, FL, USA.,Department of Computer Science, University of Miami, Coral Gables, FL, USA
| | - John Paul Turner
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Dusica Vidovic
- Center for Computational Science, University of Miami, Coral Gables, FL, USA.,Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Michele Forlin
- Center for Computational Science, University of Miami, Coral Gables, FL, USA.,Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Amar Koleti
- Center for Computational Science, University of Miami, Coral Gables, FL, USA
| | - Dac-Trung Nguyen
- National Center for Advancing Translational Science, Rockville, MD, USA
| | - Lars Juhl Jensen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rajarshi Guha
- National Center for Advancing Translational Science, Rockville, MD, USA
| | - Stephen L Mathias
- Department of Internal Medicine, Translational Informatics Division, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Oleg Ursu
- Department of Internal Medicine, Translational Informatics Division, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Vasileios Stathias
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Jianbin Duan
- Center for Computational Science, University of Miami, Coral Gables, FL, USA.,Department of Computer Science, University of Miami, Coral Gables, FL, USA
| | - Nooshin Nabizadeh
- Center for Computational Science, University of Miami, Coral Gables, FL, USA
| | - Caty Chung
- Center for Computational Science, University of Miami, Coral Gables, FL, USA
| | - Christopher Mader
- Center for Computational Science, University of Miami, Coral Gables, FL, USA
| | - Ubbo Visser
- Department of Computer Science, University of Miami, Coral Gables, FL, USA
| | - Jeremy J Yang
- Department of Internal Medicine, Translational Informatics Division, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Cristian G Bologa
- Department of Internal Medicine, Translational Informatics Division, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Tudor I Oprea
- Department of Internal Medicine, Translational Informatics Division, University of New Mexico School of Medicine, Albuquerque, NM, USA.
| | - Stephan C Schürer
- Center for Computational Science, University of Miami, Coral Gables, FL, USA. .,Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, FL, USA.
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25
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Peng S, Yang S, Bo X, Li F. paraGSEA: a scalable approach for large-scale gene expression profiling. Nucleic Acids Res 2017; 45:e155. [PMID: 28973463 PMCID: PMC5737394 DOI: 10.1093/nar/gkx679] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Accepted: 07/27/2017] [Indexed: 12/28/2022] Open
Abstract
More studies have been conducted using gene expression similarity to identify functional connections among genes, diseases and drugs. Gene Set Enrichment Analysis (GSEA) is a powerful analytical method for interpreting gene expression data. However, due to its enormous computational overhead in the estimation of significance level step and multiple hypothesis testing step, the computation scalability and efficiency are poor on large-scale datasets. We proposed paraGSEA for efficient large-scale transcriptome data analysis. By optimization, the overall time complexity of paraGSEA is reduced from O(mn) to O(m+n), where m is the length of the gene sets and n is the length of the gene expression profiles, which contributes more than 100-fold increase in performance compared with other popular GSEA implementations such as GSEA-P, SAM-GS and GSEA2. By further parallelization, a near-linear speed-up is gained on both workstations and clusters in an efficient manner with high scalability and performance on large-scale datasets. The analysis time of whole LINCS phase I dataset (GSE92742) was reduced to nearly half hour on a 1000 node cluster on Tianhe-2, or within 120 hours on a 96-core workstation. The source code of paraGSEA is licensed under the GPLv3 and available at http://github.com/ysycloud/paraGSEA.
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Affiliation(s)
- Shaoliang Peng
- College of Computer Science and Electronic Engineering & National Supercomputer Centre in Changsha, Hunan University, Changsha 410082, China.,School of Computer Science, National University of Defense Technology, Changsha 410073, China
| | - Shunyun Yang
- School of Computer Science, National University of Defense Technology, Changsha 410073, China
| | - Xiaochen Bo
- Department of biotechnology, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Fei Li
- Department of biotechnology, Beijing Institute of Radiation Medicine, Beijing 100850, China
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26
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Ru GQ, Han Y, Wang W, Chen Y, Wang HJ, Xu WJ, Ma J, Ye M, Chen X, He XL, Győrffy B, Zhao ZS, Huang D. CEACAM6 is a prognostic biomarker and potential therapeutic target for gastric carcinoma. Oncotarget 2017; 8:83673-83683. [PMID: 29137373 PMCID: PMC5663545 DOI: 10.18632/oncotarget.19415] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 03/30/2017] [Indexed: 12/13/2022] Open
Abstract
This study aims to investigate the prognostic power of carcinoembryonic antigen-related cell adhesion molecule 6 (CEACAM6) in gastric cancer (GC) and its potential role in cancer development and progression. Data mining results show that CEACAM6 is overexpressed in gastric cancer and is correlated with lymph node metastasis. Subsequently, immunohistochemical staining was performed to determine CEACAM6 protein levels in paraffin gastric tumor specimens. Real-time reverse-transcription-polymerase chain reaction (RT-PCR) was conducted to detect CEACAM6 mRNA levels in fresh GC samples. CEACAM6 protein and mRNA levels were significantly up regulated in GC compared with paired normal mucosa. The IHC staining intensity of CEACAM6 was positively correlated with tumor size, Lauren's classification, vascular invasion, lymph node metastasis, distant metastasis, and TNM stage. CEACAM6 expression was inversely correlated with the five-year survival rate of GC patients. Cox multivariate analysis results demonstrated that the overall survival was independently correlated with CEACAM6 expression. A significant association was observed between CEACAM6 and distant metastases. Network analysis of downstream gene signatures revealed several hub genes such as SRC and DNM1L etc. which may mediating tumor promoting functions of CEACAM6. Further data mining discovered that Tamoxifen etc. could be therapeutic alternatives for gastric patients with CEACAM6 overexpression. Collectively, CEACAM6 overexpression is a common characteristic of GC and is associated with poor 5 year survival rate in GC. Besides, potential molecular mechanisms and treatment options were also provided.
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Affiliation(s)
- Guo-Qing Ru
- Department of Pathology, Zhejiang Provincial People's Hospital, Hangzhou, Zhejiang, PR China
| | - Yong Han
- Clinical Research Institute, Zhejiang Provincial People's Hospital, Hangzhou, Zhejiang, PR China
| | - Wei Wang
- Department of Pathology, Zhejiang Provincial People's Hospital, Hangzhou, Zhejiang, PR China
| | - Yuan Chen
- Department of Pathology, Zhejiang Provincial People's Hospital, Hangzhou, Zhejiang, PR China
| | - Hui-Ju Wang
- Clinical Research Institute, Zhejiang Provincial People's Hospital, Hangzhou, Zhejiang, PR China
| | - Wen-Juan Xu
- Department of Pathology, Zhejiang Provincial People's Hospital, Hangzhou, Zhejiang, PR China
| | - Jie Ma
- Department of Pathology, Zhejiang Provincial People's Hospital, Hangzhou, Zhejiang, PR China
| | - Meihua Ye
- Department of Pathology, Zhejiang Provincial People's Hospital, Hangzhou, Zhejiang, PR China
| | - Xi Chen
- VIP Medical Center, Zhejiang Provincial People's Hospital, Hangzhou, Zhejiang, PR China
| | - Xiang-Lei He
- Department of Pathology, Zhejiang Provincial People's Hospital, Hangzhou, Zhejiang, PR China
| | - Balázs Győrffy
- Momentum Cancer Biomarker Research Group, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary.,Second Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Zhong-Sheng Zhao
- Department of Pathology, Zhejiang Provincial People's Hospital, Hangzhou, Zhejiang, PR China
| | - Dongsheng Huang
- Clinical Research Institute, Zhejiang Provincial People's Hospital, Hangzhou, Zhejiang, PR China
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27
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Chen B, Ma L, Paik H, Sirota M, Wei W, Chua MS, So S, Butte AJ. Reversal of cancer gene expression correlates with drug efficacy and reveals therapeutic targets. Nat Commun 2017; 8:16022. [PMID: 28699633 PMCID: PMC5510182 DOI: 10.1038/ncomms16022] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 05/17/2017] [Indexed: 02/07/2023] Open
Abstract
The decreasing cost of genomic technologies has enabled the molecular characterization of large-scale clinical disease samples and of molecular changes upon drug treatment in various disease models. Exploring methods to relate diseases to potentially efficacious drugs through various molecular features is critically important in the discovery of new therapeutics. Here we show that the potency of a drug to reverse cancer-associated gene expression changes positively correlates with that drug's efficacy in preclinical models of breast, liver and colon cancers. Using a systems-based approach, we predict four compounds showing high potency to reverse gene expression in liver cancer and validate that all four compounds are effective in five liver cancer cell lines. The in vivo efficacy of pyrvinium pamoate is further confirmed in a subcutaneous xenograft model. In conclusion, this systems-based approach may be complementary to the traditional target-based approach in connecting diseases to potentially efficacious drugs.
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Affiliation(s)
- Bin Chen
- Department of Pediatrics, Institute for Computational Health Sciences, University of California, San Francisco, 550 16th Street, San Francisco, California 94143, USA
| | - Li Ma
- Department of Surgery, Asian Liver Center, School of Medicine, Stanford University, 1201 Welch Road, Stanford, California 94305, USA
| | - Hyojung Paik
- Department of Pediatrics, Institute for Computational Health Sciences, University of California, San Francisco, 550 16th Street, San Francisco, California 94143, USA.,Biomedical HPC Technology Research Center, Korea Institute of Science and Technology Information, 245, Daehak-ro, Yuseong-gu, Daejeon 34141, South Korea
| | - Marina Sirota
- Department of Pediatrics, Institute for Computational Health Sciences, University of California, San Francisco, 550 16th Street, San Francisco, California 94143, USA
| | - Wei Wei
- Department of Surgery, Asian Liver Center, School of Medicine, Stanford University, 1201 Welch Road, Stanford, California 94305, USA
| | - Mei-Sze Chua
- Department of Surgery, Asian Liver Center, School of Medicine, Stanford University, 1201 Welch Road, Stanford, California 94305, USA
| | - Samuel So
- Department of Surgery, Asian Liver Center, School of Medicine, Stanford University, 1201 Welch Road, Stanford, California 94305, USA
| | - Atul J Butte
- Department of Pediatrics, Institute for Computational Health Sciences, University of California, San Francisco, 550 16th Street, San Francisco, California 94143, USA
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28
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Vogrinc D, Kunej T. Drug repositioning: computational approaches and research examples classified according to the evidence level. Discoveries (Craiova) 2017; 5:e75. [PMID: 32309593 PMCID: PMC6941545 DOI: 10.15190/d.2017.5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 06/28/2017] [Accepted: 06/29/2017] [Indexed: 01/04/2023] Open
Abstract
Increasing need for novel drugs and their application for treating diseases are the main reasons for the development of bioinformatics platforms for drug repositioning. The use of existing approved drugs for treating other diseases reduces cost and time needed for a drug to come to clinical use. Different strategies for drug repositioning have been reported. The use of several omics types is becoming increasingly important in drug repositioning. Although there are several public databases intended for drug repositioning, not many successful cases of novel use of drugs have been reported in the literature and transferred to clinical use. Additionally, the study approaches in published literature are very heterogeneous. A classification scheme - Drug Repositioning Evidence Level (DREL) - for drug repositioning projects, according to the level of scientific evidence has been proposed previously. In the present study, we have reviewed main databases and bioinformatics approaches enabling drug repositioning studies. We also reviewed six published studies and evaluated them according to the DREL classification. The evaluated cases used drug repositioning approach for therapy of rheumatoid arthritis, cancer, coronary artery disease, diabetes, and gulf war illness. The drug repositioning study field could benefit from clearer definition in published articles therefore including drug repositioning DREL classification scheme could be included in published original and review studies. Novel bioinformatics approaches to improve prediction of drug-target interactions, continuous updating of the databases, and development of novel validation techniques are needed to facilitate the development of the drug repositioning field. Although there are still many challenges in drug repositioning and personalized medicine, stratification of patients based on their molecular signatures and testing of signature-targeting drugs should improve drug efficacy in clinical trials.
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Affiliation(s)
- David Vogrinc
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Slovenia
| | - Tanja Kunej
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Slovenia
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29
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Chen Y, Xu R. Context-sensitive network-based disease genetics prediction and its implications in drug discovery. Bioinformatics 2017; 33:1031-1039. [PMID: 28062449 DOI: 10.1093/bioinformatics/btw737] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 11/19/2016] [Indexed: 01/05/2023] Open
Abstract
Motivation Disease phenotype networks play an important role in computational approaches to identifying new disease-gene associations. Current disease phenotype networks often model disease relationships based on pairwise similarities, therefore ignore the specific context on how two diseases are connected. In this study, we propose a new strategy to model disease associations using context-sensitive networks (CSNs). We developed a CSN-based phenome-driven approach for disease genetics prediction, and investigated the translational potential of the predicted genes in drug discovery. Results We constructed CSNs by directly connecting diseases with associated phenotypes. Here, we constructed two CSNs using different data sources; the two networks contain 26 790 and 13 822 nodes respectively. We integrated the CSNs with a genetic functional relationship network and predicted disease genes using a network-based ranking algorithm. For comparison, we built Similarity-Based disease Networks (SBN) using the same disease phenotype data. In a de novo cross validation for 3324 diseases, the CSN-based approach significantly increased the average rank from top 12.6 to top 8.8% for all tested genes comparing with the SBN-based approach ( p<e-22 ). The area under the receiver operating characteristic curve for the CSN approach was also significantly higher than the SBN approach (0.91 versus 0.87, p<e-3 ). In addition, we predicted genes for Parkinson's disease using CSNs, and demonstrated that the top-ranked genes are highly relevant to PD pathologenesis. We pin-pointed a top-ranked drug target gene for PD, and found its association with neurodegeneration supported by literature. In summary, CSNs lead to significantly improve the disease genetics prediction comparing with SBNs and provide leads for potential drug targets. Availability and Implementation nlp.case.edu/public/data/. Contact rxx@case.edu.
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Chen B, Wei W, Ma L, Yang B, Gill RM, Chua MS, Butte AJ, So S. Computational Discovery of Niclosamide Ethanolamine, a Repurposed Drug Candidate That Reduces Growth of Hepatocellular Carcinoma Cells In Vitro and in Mice by Inhibiting Cell Division Cycle 37 Signaling. Gastroenterology 2017; 152:2022-2036. [PMID: 28284560 PMCID: PMC5447464 DOI: 10.1053/j.gastro.2017.02.039] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 02/17/2017] [Indexed: 02/08/2023]
Abstract
BACKGROUND & AIMS Drug repositioning offers a shorter approval process than new drug development. We therefore searched large public datasets of drug-induced gene expression signatures to identify agents that might be effective against hepatocellular carcinoma (HCC). METHODS We searched public databases of messenger RNA expression patterns reported from HCC specimens from patients, HCC cell lines, and cells exposed to various drugs. We identified drugs that might specifically increase expression of genes that are down-regulated in HCCs and reduce expression of genes up-regulated in HCCs using a nonparametric, rank-based pattern-matching strategy based on the Kolmogorov-Smirnov statistic. We evaluated the anti-tumor activity of niclosamide and its ethanolamine salt (NEN) in HCC cell lines (HepG2, Huh7, Hep3B, Hep40, and PLC/PRF/5), primary human hepatocytes, and 2 mouse models of HCC. In one model of HCC, liver tumor development was induced by hydrodynamic delivery of a sleeping beauty transposon expressing an activated form of Ras (v12) and truncated β-catenin (N90). In another mouse model, patient-derived xenografts were established by implanting HCC cells from patients into livers of immunocompromised mice. Tumor growth was monitored by bioluminescence imaging. Tumor-bearing mice were fed a regular chow diet or a chow diet containing niclosamide or NEN. In a separate experiment using patient-derived xenografts, tumor-bearing mice were given sorafenib (the standard of care for patients with advanced HCC), NEN, or niclosamide alone; a combination of sorafenib and NEN; or a combination sorafenib and niclosamide in their drinking water, or regular water (control), and tumor growth was monitored. RESULTS Based on gene expression signatures, we identified 3 anthelmintics that significantly altered the expression of genes that are up- or down-regulated in HCCs. Niclosamide and NEN specifically reduced the viability of HCC cells: the agents were at least 7-fold more cytotoxic to HCCs than primary hepatocytes. Oral administration of NEN to mice significantly slowed growth of genetically induced liver tumors and patient-derived xenografts, whereas niclosamide did not, coinciding with the observed greater bioavailability of NEN compared with niclosamide. The combination of NEN and sorafenib was more effective at slowing growth of patient-derived xenografts than either agent alone. In HepG2 cells and in patient-derived xenografts, administration of niclosamide or NEN increased expression of 20 genes down-regulated in HCC and reduced expression of 29 genes up-regulated in the 274-gene HCC signature. Administration of NEN to mice with patient-derived xenografts reduced expression of proteins in the Wnt-β-catenin, signal transducer and activator of transcription 3, AKT-mechanistic target of rapamycin, epidermal growth factor receptor-Ras-Raf signaling pathways. Using immunoprecipitation assays, we found NEN to bind cell division cycle 37 protein and disrupt its interaction with heat shock protein 90. CONCLUSIONS In a bioinformatics search for agents that alter the HCC-specific gene expression pattern, we identified the anthelmintic niclosamide as a potential anti-tumor agent. Its ethanolamine salt, with greater bioavailability, was more effective than niclosamide at slowing the growth of genetically induced liver tumors and patient-derived xenografts in mice. Both agents disrupted interaction between cell division cycle 37 and heat shock protein 90 in HCC cells, with concomitant inhibition of their downstream signaling pathways. NEN might be effective for treatment of patients with HCC.
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Affiliation(s)
- Bin Chen
- Institute for Computational Health Sciences and Department of Pediatrics, University of California, San Francisco, California
| | - Wei Wei
- Asian Liver Center and Department of Surgery, Stanford University School of Medicine, Stanford University, Stanford, California
| | - Li Ma
- Asian Liver Center and Department of Surgery, Stanford University School of Medicine, Stanford University, Stanford, California
| | - Bin Yang
- Department of Interventional Radiology, Beijing 302 Hospital, Beijing, China
| | - Ryan M Gill
- Department of Pathology, University of California, San Francisco, California
| | - Mei-Sze Chua
- Asian Liver Center and Department of Surgery, Stanford University School of Medicine, Stanford University, Stanford, California.
| | - Atul J Butte
- Institute for Computational Health Sciences and Department of Pediatrics, University of California, San Francisco, California.
| | - Samuel So
- Asian Liver Center and Department of Surgery, Stanford University School of Medicine, Stanford University, Stanford, California
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Cha Y, Erez T, Reynolds IJ, Kumar D, Ross J, Koytiger G, Kusko R, Zeskind B, Risso S, Kagan E, Papapetropoulos S, Grossman I, Laifenfeld D. Drug repurposing from the perspective of pharmaceutical companies. Br J Pharmacol 2017; 175:168-180. [PMID: 28369768 DOI: 10.1111/bph.13798] [Citation(s) in RCA: 221] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/06/2017] [Accepted: 03/08/2017] [Indexed: 02/01/2023] Open
Abstract
Drug repurposing holds the potential to bring medications with known safety profiles to new patient populations. Numerous examples exist for the identification of new indications for existing molecules, most stemming from serendipitous findings or focused recent efforts specifically limited to the mode of action of a specific drug. In recent years, the need for new approaches to drug research and development, combined with the advent of big data repositories and associated analytical methods, has generated interest in developing systematic approaches to drug repurposing. A variety of innovative computational methods to enable systematic repurposing screens, experimental as well as through in silico approaches, have emerged. An efficient drug repurposing pipeline requires the combination of access to molecular data, appropriate analytical expertise to enable robust insights, expertise and experimental set-up for validation and clinical development know-how. In this review, we describe some of the main approaches to systematic repurposing and discuss the various players in this field and the need for strategic collaborations to increase the likelihood of success in bringing existing molecules to new indications, as well as the current advantages, considerations and challenges in repurposing as a drug development strategy pursued by pharmaceutical companies. LINKED ARTICLES This article is part of a themed section on Inventing New Therapies Without Reinventing the Wheel: The Power of Drug Repurposing. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v175.2/issuetoc.
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Affiliation(s)
- Y Cha
- Immuneering Corporation, Cambridge, MA, USA
| | - T Erez
- Global Research and Development, Teva Pharmaceutical Industries, Netanya, Israel
| | - I J Reynolds
- Global Research and Development, Teva Pharmaceutical Industries, West Chester, PA, USA
| | - D Kumar
- Immuneering Corporation, Cambridge, MA, USA
| | - J Ross
- Immuneering Corporation, Cambridge, MA, USA
| | - G Koytiger
- Immuneering Corporation, Cambridge, MA, USA
| | - R Kusko
- Immuneering Corporation, Cambridge, MA, USA
| | - B Zeskind
- Immuneering Corporation, Cambridge, MA, USA
| | - S Risso
- Global Research and Development, Teva Pharmaceutical Industries, West Chester, PA, USA
| | - E Kagan
- Global Research and Development, Teva Pharmaceutical Industries, Netanya, Israel
| | - S Papapetropoulos
- Global Research and Development, Teva Pharmaceutical Industries, Frazer, PA, USA
| | - I Grossman
- Global Research and Development, Teva Pharmaceutical Industries, Netanya, Israel
| | - D Laifenfeld
- Global Research and Development, Teva Pharmaceutical Industries, Netanya, Israel
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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: 41] [Impact Index Per Article: 5.9] [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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Chen HR, Sherr DH, Hu Z, DeLisi C. A network based approach to drug repositioning identifies plausible candidates for breast cancer and prostate cancer. BMC Med Genomics 2016; 9:51. [PMID: 27475327 PMCID: PMC4967295 DOI: 10.1186/s12920-016-0212-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 07/20/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The high cost and the long time required to bring drugs into commerce is driving efforts to repurpose FDA approved drugs-to find new uses for which they weren't intended, and to thereby reduce the overall cost of commercialization, and shorten the lag between drug discovery and availability. We report on the development, testing and application of a promising new approach to repositioning. METHODS Our approach is based on mining a human functional linkage network for inversely correlated modules of drug and disease gene targets. The method takes account of multiple information sources, including gene mutation, gene expression, and functional connectivity and proximity of within module genes. RESULTS The method was used to identify candidates for treating breast and prostate cancer. We found that (i) the recall rate for FDA approved drugs for breast (prostate) cancer is 20/20 (10/11), while the rates for drugs in clinical trials were 131/154 and 82/106; (ii) the ROC/AUC performance substantially exceeds that of comparable methods; (iii) preliminary in vitro studies indicate that 5/5 candidates have therapeutic indices superior to that of Doxorubicin in MCF7 and SUM149 cancer cell lines. We briefly discuss the biological plausibility of the candidates at a molecular level in the context of the biological processes that they mediate. CONCLUSIONS Our method appears to offer promise for the identification of multi-targeted drug candidates that can correct aberrant cellular functions. In particular the computational performance exceeded that of other CMap-based methods, and in vitro experiments indicate that 5/5 candidates have therapeutic indices superior to that of Doxorubicin in MCF7 and SUM149 cancer cell lines. The approach has the potential to provide a more efficient drug discovery pipeline.
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Affiliation(s)
- Hsiao-Rong Chen
- Bioinformatics Program, College of Engineering, Boston University, Boston, MA, USA.,Graduate Program in Translational Molecular Medicine, Boston University School of Medicine, Boston, MA, USA
| | - David H Sherr
- Department of Environmental Health, Boston University School of Public Health, Boston, MA, USA
| | - Zhenjun Hu
- Bioinformatics Program, College of Engineering, Boston University, Boston, MA, USA
| | - Charles DeLisi
- Bioinformatics Program, College of Engineering, Boston University, Boston, MA, USA. .,Department of Biomedical Engineering, Boston University, Boston, MA, USA.
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Cai X, Chen Y, Gao Z, Xu R. Explore Small Molecule-induced Genome-wide Transcriptional Profiles for Novel Inflammatory Bowel Disease Drug. AMIA JOINT SUMMITS ON TRANSLATIONAL SCIENCE PROCEEDINGS. AMIA JOINT SUMMITS ON TRANSLATIONAL SCIENCE 2016; 2016:22-31. [PMID: 27570643 PMCID: PMC5001780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Inflammatory Bowel Disease (IBD) is a chronic and relapsing disorder, which affects millions people worldwide. Current drug options cannot cure the disease and may cause severe side effects. We developed a systematic framework to identify novel IBD drugs exploiting millions of genomic signatures for chemical compounds. Specifically, we searched all FDA-approved drugs for candidates that share similar genomic profiles with IBD. In the evaluation experiments, our approach ranked approved IBD drugs averagely within top 26% among 858 candidates, significantly outperforming a state-of-art genomics-based drug repositioning method (p-value < e-8). Our approach also achieved significantly higher average precision than the state-of-art approach in predicting potential IBD drugs from clinical trials (0.072 vs. 0.043, p<0.1) and off-label IBD drugs (0.198 vs. 0.138, p<0.1). Furthermore, we found evidences supporting the therapeutic potential of the top-ranked drugs, such as Naloxone, in literature and through analyzing target genes and pathways.
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Affiliation(s)
- Xiaoshu Cai
- Department of Electrical Engineering and Computer Science, School of Engineering, Case Western Reserve University, Cleveland, Ohio, USA
| | - Yang Chen
- Department of Epidemiology & Biostatistics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Zhen Gao
- Department of Epidemiology & Biostatistics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Rong Xu
- Department of Epidemiology & Biostatistics, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
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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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Large-Scale Computational Screening Identifies First in Class Multitarget Inhibitor of EGFR Kinase and BRD4. Sci Rep 2015; 5:16924. [PMID: 26596901 PMCID: PMC4657038 DOI: 10.1038/srep16924] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 10/22/2015] [Indexed: 12/18/2022] Open
Abstract
Inhibition of cancer-promoting kinases is an established therapeutic strategy for the treatment of many cancers, although resistance to kinase inhibitors is common. One way to overcome resistance is to target orthogonal cancer-promoting pathways. Bromo and Extra-Terminal (BET) domain proteins, which belong to the family of epigenetic readers, have recently emerged as promising therapeutic targets in multiple cancers. The development of multitarget drugs that inhibit kinase and BET proteins therefore may be a promising strategy to overcome tumor resistance and prolong therapeutic efficacy in the clinic. We developed a general computational screening approach to identify novel dual kinase/bromodomain inhibitors from millions of commercially available small molecules. Our method integrated machine learning using big datasets of kinase inhibitors and structure-based drug design. Here we describe the computational methodology, including validation and characterization of our models and their application and integration into a scalable virtual screening pipeline. We screened over 6 million commercially available compounds and selected 24 for testing in BRD4 and EGFR biochemical assays. We identified several novel BRD4 inhibitors, among them a first in class dual EGFR-BRD4 inhibitor. Our studies suggest that this computational screening approach may be broadly applicable for identifying dual kinase/BET inhibitors with potential for treating various cancers.
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Kaus A, Sareen D. ALS Patient Stem Cells for Unveiling Disease Signatures of Motoneuron Susceptibility: Perspectives on the Deadly Mitochondria, ER Stress and Calcium Triad. Front Cell Neurosci 2015; 9:448. [PMID: 26635528 PMCID: PMC4652136 DOI: 10.3389/fncel.2015.00448] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 11/02/2015] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a largely sporadic progressive neurodegenerative disease affecting upper and lower motoneurons (MNs) whose specific etiology is incompletely understood. Mutations in superoxide dismutase-1 (SOD1), TAR DNA-binding protein 43 (TARDBP/TDP-43) and C9orf72, have been identified in subsets of familial and sporadic patients. Key associated molecular and neuropathological features include ubiquitinated TDP-43 inclusions, stress granules, aggregated dipeptide proteins from mutant C9orf72 transcripts, altered mitochondrial ultrastructure, dysregulated calcium homeostasis, oxidative and endoplasmic reticulum (ER) stress, and an unfolded protein response (UPR). Such impairments have been documented in ALS animal models; however, whether these mechanisms are initiating factors or later consequential events leading to MN vulnerability in ALS patients is debatable. Human induced pluripotent stem cells (iPSCs) are a valuable tool that could resolve this “chicken or egg” causality dilemma. Relevant systems for probing pathophysiologically affected cells from large numbers of ALS patients and discovering phenotypic disease signatures of early MN susceptibility are described. Performing unbiased ‘OMICS and high-throughput screening in relevant neural cells from a cohort of ALS patient iPSCs, and rescuing mitochondrial and ER stress impairments, can identify targeted therapeutics for increasing MN longevity in ALS.
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Affiliation(s)
- Anjoscha Kaus
- Board of Governors-Regenerative Medicine Institute, Cedars-Sinai Medical Center Los Angeles, CA, USA ; Department of Biomedical Sciences, Cedars-Sinai Medical Center Los Angeles, CA, USA
| | - Dhruv Sareen
- Board of Governors-Regenerative Medicine Institute, Cedars-Sinai Medical Center Los Angeles, CA, USA ; Department of Biomedical Sciences, Cedars-Sinai Medical Center Los Angeles, CA, USA ; iPSC Core, The David and Janet Polak Stem Cell Laboratory, Cedars-Sinai Medical Center Los Angeles, CA, USA
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Chen B, Greenside P, Paik H, Sirota M, Hadley D, Butte AJ. Relating Chemical Structure to Cellular Response: An Integrative Analysis of Gene Expression, Bioactivity, and Structural Data Across 11,000 Compounds. CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY 2015; 4:576-84. [PMID: 26535158 PMCID: PMC4625862 DOI: 10.1002/psp4.12009] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 07/01/2015] [Indexed: 02/06/2023]
Abstract
A central premise in systems pharmacology is that structurally similar compounds have similar cellular responses; however, this principle often does not hold. One of the most widely used measures of cellular response is gene expression. By integrating gene expression data from Library of Integrated Network-based Cellular Signatures (LINCS) with chemical structure and bioactivity data from PubChem, we performed a large-scale correlation analysis of chemical structures and gene expression profiles of over 11,000 compounds taking into account confounding factors such as biological conditions (e.g., cell line, dose) and bioactivities. We found that structurally similar compounds do indeed yield similar gene expression profiles. There is an ∼20% chance that two structurally similar compounds (Tanimoto Coefficient ≥ 0.85) share significantly similar gene expression profiles. Regardless of structural similarity, two compounds tend to share similar gene expression profiles in a cell line when they are administrated at a higher dose or when the cell line is sensitive to both compounds.
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Affiliation(s)
- B Chen
- Institute for Computational Health Sciences, University of California San Francisco, San Francisco, California, USA
| | - P Greenside
- Biomedical Informatics Training Program, Stanford University School of Medicine Stanford, California, USA
| | - H Paik
- Institute for Computational Health Sciences, University of California San Francisco, San Francisco, California, USA
| | - M Sirota
- Institute for Computational Health Sciences, University of California San Francisco, San Francisco, California, USA
| | - D Hadley
- 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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Li J, Zheng S, Chen B, Butte AJ, Swamidass SJ, Lu Z. A survey of current trends in computational drug repositioning. Brief Bioinform 2015; 17:2-12. [PMID: 25832646 DOI: 10.1093/bib/bbv020] [Citation(s) in RCA: 338] [Impact Index Per Article: 37.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Indexed: 12/26/2022] Open
Abstract
Computational drug repositioning or repurposing is a promising and efficient tool for discovering new uses from existing drugs and holds the great potential for precision medicine in the age of big data. The explosive growth of large-scale genomic and phenotypic data, as well as data of small molecular compounds with granted regulatory approval, is enabling new developments for computational repositioning. To achieve the shortest path toward new drug indications, advanced data processing and analysis strategies are critical for making sense of these heterogeneous molecular measurements. In this review, we show recent advancements in the critical areas of computational drug repositioning from multiple aspects. First, we summarize available data sources and the corresponding computational repositioning strategies. Second, we characterize the commonly used computational techniques. Third, we discuss validation strategies for repositioning studies, including both computational and experimental methods. Finally, we highlight potential opportunities and use-cases, including a few target areas such as cancers. We conclude with a brief discussion of the remaining challenges in computational drug repositioning.
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