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Duan QQ, Wang H, Su WM, Gu XJ, Shen XF, Jiang Z, Ren YL, Cao B, Li GB, Wang Y, Chen YP. TBK1, a prioritized drug repurposing target for amyotrophic lateral sclerosis: evidence from druggable genome Mendelian randomization and pharmacological verification in vitro. BMC Med 2024; 22:96. [PMID: 38443977 PMCID: PMC10916235 DOI: 10.1186/s12916-024-03314-1] [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: 06/22/2023] [Accepted: 02/23/2024] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND There is a lack of effective therapeutic strategies for amyotrophic lateral sclerosis (ALS); therefore, drug repurposing might provide a rapid approach to meet the urgent need for treatment. METHODS To identify therapeutic targets associated with ALS, we conducted Mendelian randomization (MR) analysis and colocalization analysis using cis-eQTL of druggable gene and ALS GWAS data collections to determine annotated druggable gene targets that exhibited significant associations with ALS. By subsequent repurposing drug discovery coupled with inclusion criteria selection, we identified several drug candidates corresponding to their druggable gene targets that have been genetically validated. The pharmacological assays were then conducted to further assess the efficacy of genetics-supported repurposed drugs for potential ALS therapy in various cellular models. RESULTS Through MR analysis, we identified potential ALS druggable genes in the blood, including TBK1 [OR 1.30, 95%CI (1.19, 1.42)], TNFSF12 [OR 1.36, 95%CI (1.19, 1.56)], GPX3 [OR 1.28, 95%CI (1.15, 1.43)], TNFSF13 [OR 0.45, 95%CI (0.32, 0.64)], and CD68 [OR 0.38, 95%CI (0.24, 0.58)]. Additionally, we identified potential ALS druggable genes in the brain, including RESP18 [OR 1.11, 95%CI (1.07, 1.16)], GPX3 [OR 0.57, 95%CI (0.48, 0.68)], GDF9 [OR 0.77, 95%CI (0.67, 0.88)], and PTPRN [OR 0.17, 95%CI (0.08, 0.34)]. Among them, TBK1, TNFSF12, RESP18, and GPX3 were confirmed in further colocalization analysis. We identified five drugs with repurposing opportunities targeting TBK1, TNFSF12, and GPX3, namely fostamatinib (R788), amlexanox (AMX), BIIB-023, RG-7212, and glutathione as potential repurposing drugs. R788 and AMX were prioritized due to their genetic supports, safety profiles, and cost-effectiveness evaluation. Further pharmacological analysis revealed that R788 and AMX mitigated neuroinflammation in ALS cell models characterized by overly active cGAS/STING signaling that was induced by MSA-2 or ALS-related toxic proteins (TDP-43 and SOD1), through the inhibition of TBK1 phosphorylation. CONCLUSIONS Our MR analyses provided genetic evidence supporting TBK1, TNFSF12, RESP18, and GPX3 as druggable genes for ALS treatment. Among the drug candidates targeting the above genes with repurposing opportunities, FDA-approved drug-R788 and AMX served as effective TBK1 inhibitors. The subsequent pharmacological studies validated the potential of R788 and AMX for treating specific ALS subtypes through the inhibition of TBK1 phosphorylation.
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Affiliation(s)
- Qing-Qing Duan
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Institute of Brain Science and Brain-Inspired Technology, West China Hospital, Sichuan University, Sichuan, Chengdu,, 610041, China
- Rare Disease Center, West China Hospital, Sichuan University, Sichuan, Chengdu, 610041, China
| | - Han Wang
- Department of Pathophysiology, West China College of Basic Medical Sciences and Forensic Medicine, Sichuan University, Sichuan, Chengdu, 610041, China
| | - Wei-Ming Su
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Institute of Brain Science and Brain-Inspired Technology, West China Hospital, Sichuan University, Sichuan, Chengdu,, 610041, China
- Rare Disease Center, West China Hospital, Sichuan University, Sichuan, Chengdu, 610041, China
| | - Xiao-Jing Gu
- Mental Health Center, West China Hospital, Sichuan University, Sichuan, Chengdu, 610041, China
| | - Xiao-Fei Shen
- TCM Regulating Metabolic Diseases Key Laboratory of Sichuan Province, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, 610072, China
| | - Zheng Jiang
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Institute of Brain Science and Brain-Inspired Technology, West China Hospital, Sichuan University, Sichuan, Chengdu,, 610041, China
- Rare Disease Center, West China Hospital, Sichuan University, Sichuan, Chengdu, 610041, China
| | - Yan-Ling Ren
- Department of Pathophysiology, West China College of Basic Medical Sciences and Forensic Medicine, Sichuan University, Sichuan, Chengdu, 610041, China
| | - Bei Cao
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Institute of Brain Science and Brain-Inspired Technology, West China Hospital, Sichuan University, Sichuan, Chengdu,, 610041, China
- Rare Disease Center, West China Hospital, Sichuan University, Sichuan, Chengdu, 610041, China
| | - Guo-Bo Li
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Yi Wang
- Department of Pathophysiology, West China College of Basic Medical Sciences and Forensic Medicine, Sichuan University, Sichuan, Chengdu, 610041, China.
| | - Yong-Ping Chen
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
- Institute of Brain Science and Brain-Inspired Technology, West China Hospital, Sichuan University, Sichuan, Chengdu,, 610041, China.
- Rare Disease Center, West China Hospital, Sichuan University, Sichuan, Chengdu, 610041, China.
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Pan Y, Ren H, Lan L, Li Y, Huang T. Review of Predicting Synergistic Drug Combinations. Life (Basel) 2023; 13:1878. [PMID: 37763281 PMCID: PMC10533134 DOI: 10.3390/life13091878] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 08/31/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
The prediction of drug combinations is of great clinical significance. In many diseases, such as high blood pressure, diabetes, and stomach ulcers, the simultaneous use of two or more drugs has shown clear efficacy. It has greatly reduced the progression of drug resistance. This review presents the latest applications of methods for predicting the effects of drug combinations and the bioactivity databases commonly used in drug combination prediction. These studies have played a significant role in developing precision therapy. We first describe the concept of synergy. we study various publicly available databases for drug combination prediction tasks. Next, we introduce five algorithms applied to drug combinatorial prediction, which include traditional machine learning methods, deep learning methods, mathematical methods, systems biology methods and search algorithms. In the end, we sum up the difficulties encountered in prediction models.
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Affiliation(s)
- Yichen Pan
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; (Y.P.); (H.R.)
| | - Haotian Ren
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; (Y.P.); (H.R.)
| | - Liang Lan
- Department of Interactive Media, Hong Kong Baptist University, Hong Kong, China;
| | - Yixue Li
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; (Y.P.); (H.R.)
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- Guangzhou Laboratory, Guangzhou 510005, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai 200433, China
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; (Y.P.); (H.R.)
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Sun J, Xu M, Ru J, James-Bott A, Xiong D, Wang X, Cribbs AP. Small molecule-mediated targeting of microRNAs for drug discovery: Experiments, computational techniques, and disease implications. Eur J Med Chem 2023; 257:115500. [PMID: 37262996 DOI: 10.1016/j.ejmech.2023.115500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/05/2023] [Accepted: 05/15/2023] [Indexed: 06/03/2023]
Abstract
Small molecules have been providing medical breakthroughs for human diseases for more than a century. Recently, identifying small molecule inhibitors that target microRNAs (miRNAs) has gained importance, despite the challenges posed by labour-intensive screening experiments and the significant efforts required for medicinal chemistry optimization. Numerous experimentally-verified cases have demonstrated the potential of miRNA-targeted small molecule inhibitors for disease treatment. This new approach is grounded in their posttranscriptional regulation of the expression of disease-associated genes. Reversing dysregulated gene expression using this mechanism may help control dysfunctional pathways. Furthermore, the ongoing improvement of algorithms has allowed for the integration of computational strategies built on top of laboratory-based data, facilitating a more precise and rational design and discovery of lead compounds. To complement the use of extensive pharmacogenomics data in prioritising potential drugs, our previous work introduced a computational approach based on only molecular sequences. Moreover, various computational tools for predicting molecular interactions in biological networks using similarity-based inference techniques have been accumulated in established studies. However, there are a limited number of comprehensive reviews covering both computational and experimental drug discovery processes. In this review, we outline a cohesive overview of both biological and computational applications in miRNA-targeted drug discovery, along with their disease implications and clinical significance. Finally, utilizing drug-target interaction (DTIs) data from DrugBank, we showcase the effectiveness of deep learning for obtaining the physicochemical characterization of DTIs.
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Affiliation(s)
- Jianfeng Sun
- Botnar Research Centre, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, OX3 7LD, UK.
| | - Miaoer Xu
- Department of Biology, Emory University, Atlanta, GA, 30322, USA
| | - Jinlong Ru
- Chair of Prevention of Microbial Diseases, School of Life Sciences Weihenstephan, Technical University of Munich, Freising, 85354, Germany
| | - Anna James-Bott
- Botnar Research Centre, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, OX3 7LD, UK
| | - Dapeng Xiong
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA; Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Xia Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
| | - Adam P Cribbs
- Botnar Research Centre, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, OX3 7LD, UK.
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Zhao T, Zhu G, Dubey HV, Flaherty P. Identification of significant gene expression changes in multiple perturbation experiments using knockoffs. Brief Bioinform 2023; 24:bbad084. [PMID: 36892174 PMCID: PMC10025447 DOI: 10.1093/bib/bbad084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/20/2023] [Accepted: 02/13/2023] [Indexed: 03/10/2023] Open
Abstract
Large-scale multiple perturbation experiments have the potential to reveal a more detailed understanding of the molecular pathways that respond to genetic and environmental changes. A key question in these studies is which gene expression changes are important for the response to the perturbation. This problem is challenging because (i) the functional form of the nonlinear relationship between gene expression and the perturbation is unknown and (ii) identification of the most important genes is a high-dimensional variable selection problem. To deal with these challenges, we present here a method based on the model-X knockoffs framework and Deep Neural Networks to identify significant gene expression changes in multiple perturbation experiments. This approach makes no assumptions on the functional form of the dependence between the responses and the perturbations and it enjoys finite sample false discovery rate control for the selected set of important gene expression responses. We apply this approach to the Library of Integrated Network-Based Cellular Signature data sets which is a National Institutes of Health Common Fund program that catalogs how human cells globally respond to chemical, genetic and disease perturbations. We identified important genes whose expression is directly modulated in response to perturbation with anthracycline, vorinostat, trichostatin-a, geldanamycin and sirolimus. We compare the set of important genes that respond to these small molecules to identify co-responsive pathways. Identification of which genes respond to specific perturbation stressors can provide better understanding of the underlying mechanisms of disease and advance the identification of new drug targets.
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Affiliation(s)
- Tingting Zhao
- Department of Information Systems and Analytics, College of Business, Bryant University, Smithfield, 02917, RI, USA
- Center for Health and Behavioral Sciences, Bryant University, Smithfield, 02917, RI, USA
| | - Guangyu Zhu
- Department of Computer Science and Statistics, University of Rhode Island, Kingston, 02881, RI, USA
| | - Harsh Vardhan Dubey
- Department of Mathematics & Statistics, University of Massachusetts Amherst, Amherst, 01003, MA, USA
| | - Patrick Flaherty
- Department of Mathematics & Statistics, University of Massachusetts Amherst, Amherst, 01003, MA, USA
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5
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Chen Y, Wang ZZ, Hao GF, Song BA. Web support for the more efficient discovery of kinase inhibitors. Drug Discov Today 2022; 27:2216-2225. [DOI: 10.1016/j.drudis.2022.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 02/16/2022] [Accepted: 04/01/2022] [Indexed: 11/24/2022]
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Islam S, Wang S, Bowden N, Martin J, Head R. Repurposing existing therapeutics, its importance in oncology drug development: Kinases as a potential target. Br J Clin Pharmacol 2021; 88:64-74. [PMID: 34192364 PMCID: PMC9292808 DOI: 10.1111/bcp.14964] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 05/04/2021] [Accepted: 06/19/2021] [Indexed: 12/13/2022] Open
Abstract
Repurposing the large arsenal of existing non‐cancer drugs is an attractive proposition to expand the clinical pipelines for cancer therapeutics. The earlier successes in repurposing resulted primarily from serendipitous findings, but more recently, drug or target‐centric systematic identification of repurposing opportunities continues to rise. Kinases are one of the most sought‐after anti‐cancer drug targets over the last three decades. There are many non‐cancer approved drugs that can inhibit kinases as “off‐targets” as well as many existing kinase inhibitors that can target new additional kinases in cancer. Identifying cancer‐associated kinase inhibitors through mining commercial drug databases or new kinase targets for existing inhibitors through comprehensive kinome profiling can offer more effective trial‐ready options to rapidly advance drugs for clinical validation. In this review, we argue that drug repurposing is an important approach in modern drug development for cancer therapeutics. We have summarized the advantages of repurposing, the rationale behind this approach together with key barriers and opportunities in cancer drug development. We have also included examples of non‐cancer drugs that inhibit kinases or are associated with kinase signalling as a basis for their anti‐cancer action.
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Affiliation(s)
- Saiful Islam
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA, 500, Australia
| | - Shudong Wang
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA, 500, Australia
| | - Nikola Bowden
- Centre for Human Drug Repurposing and Medicines Research, University of Newcastle, NSW, 2305, Australia
| | - Jennifer Martin
- Centre for Human Drug Repurposing and Medicines Research, University of Newcastle, NSW, 2305, Australia
| | - Richard Head
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, SA, 500, Australia
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Savage SR, Zhang B. Using phosphoproteomics data to understand cellular signaling: a comprehensive guide to bioinformatics resources. Clin Proteomics 2020; 17:27. [PMID: 32676006 PMCID: PMC7353784 DOI: 10.1186/s12014-020-09290-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 07/04/2020] [Indexed: 12/19/2022] Open
Abstract
Mass spectrometry-based phosphoproteomics is becoming an essential methodology for the study of global cellular signaling. Numerous bioinformatics resources are available to facilitate the translation of phosphopeptide identification and quantification results into novel biological and clinical insights, a critical step in phosphoproteomics data analysis. These resources include knowledge bases of kinases and phosphatases, phosphorylation sites, kinase inhibitors, and sequence variants affecting kinase function, and bioinformatics tools that can predict phosphorylation sites in addition to the kinase that phosphorylates them, infer kinase activity, and predict the effect of mutations on kinase signaling. However, these resources exist in silos and it is challenging to select among multiple resources with similar functions. Therefore, we put together a comprehensive collection of resources related to phosphoproteomics data interpretation, compared the use of tools with similar functions, and assessed the usability from the standpoint of typical biologists or clinicians. Overall, tools could be improved by standardization of enzyme names, flexibility of data input and output format, consistent maintenance, and detailed manuals.
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Affiliation(s)
- Sara R. Savage
- Department of Biomedical Informatics, Vanderbilt University, Nashville, TN USA
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX USA
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
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Kern JA, Kim J, Foster DG, Mishra R, Gardner EE, Poirier JT, Rivard C, Yu H, Finigan JH, Dowlati A, Rudin CM, Tan AC. Role of mTOR As an Essential Kinase in SCLC. J Thorac Oncol 2020; 15:1522-1534. [PMID: 32599072 DOI: 10.1016/j.jtho.2020.05.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 02/17/2020] [Accepted: 05/18/2020] [Indexed: 12/14/2022]
Abstract
OBJECTIVES SCLC represents 15% of all lung cancer diagnoses in the United States and has a particularly poor prognosis. We hypothesized that kinases regulating SCLC survival pathways represent therapeutically targetable vulnerabilities whose inhibition may improve SCLC outcome. METHODS A short-hairpin RNA (shRNA) library targeting all human kinases was introduced in seven chemonaive patient-derived xenografts (PDX) and the cells were cultured in vitro and in vivo. On harvest, lost or depleted shRNAs were considered as regulating-cell survival pathways and deemed essential kinases. RESULTS Unsupervised hierarchical cluster analysis of recovered shRNAs separated the PDXs into two clusters, suggesting kinase-based heterogeneity among the SCLC PDXs. A total of 23 kinases were identified as essential in two or more PDXs, with mechanistic Target of Rapamycin (mTOR) a candidate essential kinase in four. mTOR phosphorylation status correlated with PDX sensitivity to mTOR kinase inhibition, and mTOR inhibition sensitized the PDX to cisplatin and etoposide. In the PDX in which mTOR was defined as essential, mTOR inhibition caused a 43% decrease in tumor volume at 21 days (p < 0.01). Combining mTOR inhibition with cisplatin and etoposide decreased PDX tumor volume 96% compared with cisplatin and etoposide alone at 70 days (p < 0.002). Chemoresistance did not develop with the combination of mTOR inhibition and cisplatin and etoposide in mTOR-essential PDX over 105 days. The prevalence of phospho-mTOR-Ser-2448 in a tissue microarray of chemonaive SCLC was 27%, thus, identifying an important SCLC subtype that might benefit from the addition of mTOR inhibition to standard chemotherapy. CONCLUSIONS These studies reveal that kinases can define SCLC subgroups, can identify therapeutic vulnerabilities, and can potentially be used to optimize therapeutic approaches. Significance We used functional genomics to identify kinases regulating SCLC survival. mTOR was identified as essential in a subset of PDXs. mTOR inhibition decreased PDX growth, sensitized PDX to cisplatin and etoposide, and prevented chemoresistance.
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Affiliation(s)
- Jeffrey A Kern
- Department of Medicine, Oncology Division, National Jewish Health, Denver, Colorado.
| | - Jihye Kim
- Department of Medicine, University of Colorado, Denver, Colorado
| | - Daniel G Foster
- Department of Medicine, Oncology Division, National Jewish Health, Denver, Colorado
| | - Rangnath Mishra
- Department of Medicine, Oncology Division, National Jewish Health, Denver, Colorado
| | - Eric E Gardner
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - John T Poirier
- Perlmutter Cancer Center, New York University Langone Health, New York, New York
| | | | - Hui Yu
- Department of Medicine, University of Colorado, Denver, Colorado
| | - James H Finigan
- Department of Medicine, Oncology Division, National Jewish Health, Denver, Colorado
| | - Afshin Dowlati
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio
| | | | - Aik-Choon Tan
- Department of Medicine, University of Colorado, Denver, Colorado; Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, Florida
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Long S, Yuan C, Wang Y, Zhang J, Li G. Network Pharmacology Analysis of Damnacanthus indicus C.F.Gaertn in Gene-Phenotype. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2019; 2019:1368371. [PMID: 30906409 PMCID: PMC6398045 DOI: 10.1155/2019/1368371] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 01/21/2019] [Accepted: 02/03/2019] [Indexed: 12/11/2022]
Abstract
Damnacanthus indicus C.F.Gaertn is known as Huci in traditional Chinese medicine. It contains a component having anthraquinone-like structure which is a part of the many used anticancer drugs. This study was to collect the evidence of disease-modulatory activities of Huci by analyzing the published literature on the chemicals and drugs. A list of its compounds and direct protein targets is predicted by using Bioinformatics Analysis Tool for Molecular Mechanism of TCM. A protein-protein interaction network using links between its directed targets and the other known targets was constructed. The DPT-associated genes in net were scrutinized by WebGestalt. Exploring the cancer genomics data related to Huci through cBio Portal. Survival analysis for the overlap genes is done by using UALCAN. We got 16 compounds and it predicts 62 direct protein targets and 100 DPTs and they were identified for these compounds. DPT-associated genes were analyzed by WebGestalt. Through the enrichment analysis, we got top 10 identified KEGG pathways. Refined analysis of KEGG pathways showed that one of these ten pathways is linked to Rap1 signaling pathway and another one is related to breast cancer. The survival analysis for the overlap genes shows the significant negative effect of these genes on the breast cancer patients. Through the research results of Damnacanthus indicus C.F.Gaertn, it is shown that medicine network pharmacology may be regarded as a new paradigm for guiding the future studies of the traditional Chinese medicine in different fields.
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Affiliation(s)
- Shengrong Long
- Department of Neurosurgery, The First Affiliated Hospital of China Medical University, NanJing Bei Road, Heping District, Shenyang, 110001, LiaoNing Province, China
| | - Caihong Yuan
- Department of Chinese Medicine, The First Affiliated Hospital of China Medical University, NanJing Bei Road, Heping District, Shenyang, 110001, LiaoNing Province, China
| | - Yue Wang
- Department of Neurosurgery, The First Affiliated Hospital of China Medical University, NanJing Bei Road, Heping District, Shenyang, 110001, LiaoNing Province, China
| | - Jie Zhang
- Department of Chinese Medicine, The First Affiliated Hospital of China Medical University, NanJing Bei Road, Heping District, Shenyang, 110001, LiaoNing Province, China
| | - Guangyu Li
- Department of Neurosurgery, The First Affiliated Hospital of China Medical University, NanJing Bei Road, Heping District, Shenyang, 110001, LiaoNing Province, China
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Harrison PT, Huang PH. Exploiting vulnerabilities in cancer signalling networks to combat targeted therapy resistance. Essays Biochem 2018; 62:583-593. [PMID: 30072489 PMCID: PMC6204552 DOI: 10.1042/ebc20180016] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 06/29/2018] [Accepted: 07/10/2018] [Indexed: 12/13/2022]
Abstract
Drug resistance remains one of the greatest challenges facing precision oncology today. Despite the vast array of resistance mechanisms that cancer cells employ to subvert the effects of targeted therapy, a deep understanding of cancer signalling networks has led to the development of novel strategies to tackle resistance both in the first-line and salvage therapy settings. In this review, we provide a brief overview of the major classes of resistance mechanisms to targeted therapy, including signalling reprogramming and tumour evolution; our discussion also focuses on the use of different forms of polytherapies (such as inhibitor combinations, multi-target kinase inhibitors and HSP90 inhibitors) as a means of combating resistance. The promise and challenges facing each of these polytherapies are elaborated with a perspective on how to effectively deploy such therapies in patients. We highlight efforts to harness computational approaches to predict effective polytherapies and the emerging view that exceptional responders may hold the key to better understanding drug resistance. This review underscores the importance of polytherapies as an effective means of targeting resistance signalling networks and achieving durable clinical responses in the era of personalised cancer medicine.
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Affiliation(s)
- Peter T Harrison
- Division of Molecular Pathology, The Institute of Cancer Research, London, U.K
| | - Paul H Huang
- Division of Molecular Pathology, The Institute of Cancer Research, London, U.K.
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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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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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Vyse S, Howitt A, Huang PH. Exploiting Synthetic Lethality and Network Biology to Overcome EGFR Inhibitor Resistance in Lung Cancer. J Mol Biol 2017; 429:1767-1786. [PMID: 28478283 PMCID: PMC6175049 DOI: 10.1016/j.jmb.2017.04.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 04/25/2017] [Accepted: 04/27/2017] [Indexed: 12/16/2022]
Abstract
Despite the recent approval of third-generation therapies, overcoming resistance to epidermal growth factor receptor (EGFR) inhibitors remains a major challenge in non-small cell lung cancer. Conceptually, synthetic lethality holds the promise of identifying non-intuitive targets for tackling both acquired and intrinsic resistance in this setting. However, translating these laboratory findings into effective clinical strategies continues to be elusive. Here, we provide an overview of the synthetic lethal approaches that have been employed to study EGFR inhibitor resistance and review the oncogene and non-oncogene signalling mechanisms that have thus far been unveiled by synthetic lethality screens. We highlight the potential challenges associated with progressing these discoveries into the clinic including context dependency, signalling plasticity, and tumour heterogeneity, and we offer a perspective on emerging network biology and computational solutions to exploit these phenomena for cancer therapy and biomarker discovery. We conclude by presenting a number of tangible steps to bolster our understanding of fundamental synthetic lethality mechanisms and advance these findings beyond the confines of the laboratory.
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Affiliation(s)
- Simon Vyse
- Division of Cancer Biology, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Annie Howitt
- Division of Cancer Biology, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Paul H Huang
- Division of Cancer Biology, The Institute of Cancer Research, London, SW3 6JB, UK.
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Abstract
Background The advance in targeted therapy has greatly increased the effectiveness of clinical cancer therapy and reduced the cytotoxicity of treatments to normal cells. However, patients still suffer from cancer relapse due to the occurrence of drug resistance. It is of great need to explore potential combinatorial drug therapy since individual drug alone may not be sufficient to inhibit continuous activation of cancer-addicted genes or pathways. The DREAM challenge has confirmed the potentiality of computational methods for predicting synergistic drug combinations, while the prediction accuracy can be further improved. Methods Based on previous reports, we hypothesized the similarity in biological functions or genes perturbed by two drugs can determine their synergistic effects. To test the feasibility of the hypothesis, we proposed three scoring systems: co-gene score, co-GS score, and co-gene/GS score, measuring the similarities in genes with significant expressional changes, enriched gene sets, and significantly changed genes within an enriched gene sets between a pair of drugs, respectively. Performances of these scoring systems were evaluated by the probabilistic c-index (PC-index) devised by the DREAM consortium. We also applied the proposed method to the Connectivity Map dataset to explore more potential synergistic drug combinations. Results Using a gold standard derived by the DREAM consortium, we confirmed the prediction power of the three scoring systems (all P-values < 0.05). The co-gene/GS score achieved the best prediction of drug synergy (PC-index = 0.663, P-value < 0.0001), outperforming all methods proposed during DREAM challenge. Furthermore, a binary classification test showed that co-gene/GS scoring was highly accurate and specific. Since our method is constructed on a gene set-based analysis, in addition to synergy prediction, it provides insights into the functional relevance of drug combinations and the underlying mechanisms by which drugs achieve synergy. Conclusions Here we proposed a novel and simple method to predict and investigate drug synergy, and validated its efficacy to accurately predict synergistic drug combinations and to comprehensively explore their underlying mechanisms. The method is widely applicable to expression profiles of other drug treatments and is expected to accelerate the realization of precision cancer treatment. Electronic supplementary material The online version of this article (doi:10.1186/s12918-016-0310-3) contains supplementary material, which is available to authorized users.
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Tan AC, Ryall KA, Huang PH. Expanding the computational toolbox for interrogating cancer kinomes. Pharmacogenomics 2015; 17:95-7. [PMID: 26666839 DOI: 10.2217/pgs.15.154] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Affiliation(s)
- Aik Choon Tan
- Translational Bioinformatics & Cancer Systems Biology Laboratory, Department of Medicine, Division of Medical Oncology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Karen A Ryall
- Translational Bioinformatics & Cancer Systems Biology Laboratory, Department of Medicine, Division of Medical Oncology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Paul H Huang
- Protein Networks Team, Division of Cancer Biology, The Institute of Cancer Research, London, SW3 6JB, UK
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Ryall KA, Kim J, Klauck PJ, Shin J, Yoo M, Ionkina A, Pitts TM, Tentler JJ, Diamond JR, Eckhardt SG, Heasley LE, Kang J, Tan AC. An integrated bioinformatics analysis to dissect kinase dependency in triple negative breast cancer. BMC Genomics 2015; 16 Suppl 12:S2. [PMID: 26681397 PMCID: PMC4682411 DOI: 10.1186/1471-2164-16-s12-s2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Triple-Negative Breast Cancer (TNBC) is an aggressive disease with a poor prognosis. Clinically, TNBC patients have limited treatment options besides chemotherapy. The goal of this study was to determine the kinase dependency in TNBC cell lines and to predict compounds that could inhibit these kinases using integrative bioinformatics analysis. RESULTS We integrated publicly available gene expression data, high-throughput pharmacological profiling data, and quantitative in vitro kinase binding data to determine the kinase dependency in 12 TNBC cell lines. We employed Kinase Addiction Ranker (KAR), a novel bioinformatics approach, which integrated these data sources to dissect kinase dependency in TNBC cell lines. We then used the kinase dependency predicted by KAR for each TNBC cell line to query K-Map for compounds targeting these kinases. We validated our predictions using published and new experimental data. CONCLUSIONS In summary, we implemented an integrative bioinformatics analysis that determines kinase dependency in TNBC. Our analysis revealed candidate kinases as potential targets in TNBC for further pharmacological and biological studies.
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Affiliation(s)
- Karen A Ryall
- Division of Medical Oncology, Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora CO 80045 USA
| | - Jihye Kim
- Division of Medical Oncology, Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora CO 80045 USA
| | - Peter J Klauck
- Division of Medical Oncology, Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora CO 80045 USA
| | - Jimin Shin
- Division of Medical Oncology, Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora CO 80045 USA
| | - Minjae Yoo
- Division of Medical Oncology, Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora CO 80045 USA
| | - Anastasia Ionkina
- Division of Medical Oncology, Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora CO 80045 USA
| | - Todd M Pitts
- Division of Medical Oncology, Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora CO 80045 USA
| | - John J Tentler
- Division of Medical Oncology, Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora CO 80045 USA
| | - Jennifer R Diamond
- Division of Medical Oncology, Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora CO 80045 USA
| | - S Gail Eckhardt
- Division of Medical Oncology, Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora CO 80045 USA
| | - Lynn E Heasley
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora CO 80045 USA
| | - Jaewoo Kang
- Department of Computer Science, Korea University, Seoul, Korea
| | - Aik Choon Tan
- Division of Medical Oncology, Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora CO 80045 USA
- Department of Computer Science, Korea University, Seoul, Korea
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora CO 80045 USA
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López Villar E, Madero L, A López-Pascual J, C Cho W. Study of phosphorylation events for cancer diagnoses and treatment. Clin Transl Med 2015; 4:59. [PMID: 26055493 PMCID: PMC4460185 DOI: 10.1186/s40169-015-0059-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 05/19/2015] [Indexed: 02/07/2023] Open
Abstract
The activation of signaling cascades in response to extracellular and intracellular stimuli to control cell growth, proliferation and survival, is orchestrated by protein kinases via phosphorylation. A critical issue is the study of the mechanisms of cancer cells for the development of more effective drugs. With the application of the new proteomic technologies, together with the advancement in the sequencing of the human proteome, patients will therefore be benefited by the discovery of novel therapeutic and/or diagnostic protein targets. Furthermore, the advances in proteomic approaches and the Human Proteome Organization (HUPO) have opened a new door which is helpful in the identification of patients at risk and towards improving current therapies. Modification of the signaling-networks via mutations or abnormal protein expression underlies the cause or consequence of many diseases including cancer. Resulting data is used to reveal connections between genes proteins and compounds and the related molecular pathways for underlining disease states. As a delegate of HUPO, for human proteome on children assays and studies, we, at Hospital Universitario Niño Jesús, are seeking to support the human proteome in this context. Clinical goals have to be clearly established and proteomics experts have to set up the appropriate proteomic strategy, which coupled to bioinformatics will make it possible to achieve new therapies for patients with poor prognosis. We envision to combine our up-coming data to the HUPO organization in order to support international efforts to advance the cure of cancer disease.
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Affiliation(s)
- Elena López Villar
- Oncohematology of Children Department, Hospital Universitario Infantil Niño Jesús, Av. Menéndez Pelayo 65, Madrid, Spain,
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Ryall KA, Tan AC. Systems biology approaches for advancing the discovery of effective drug combinations. J Cheminform 2015; 7:7. [PMID: 25741385 PMCID: PMC4348553 DOI: 10.1186/s13321-015-0055-9] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Accepted: 02/02/2015] [Indexed: 01/23/2023] Open
Abstract
Complex diseases like cancer are regulated by large, interconnected networks with many pathways affecting cell proliferation, invasion, and drug resistance. However, current cancer therapy predominantly relies on the reductionist approach of one gene-one disease. Combinations of drugs may overcome drug resistance by limiting mutations and induction of escape pathways, but given the enormous number of possible drug combinations, strategies to reduce the search space and prioritize experiments are needed. In this review, we focus on the use of computational modeling, bioinformatics and high-throughput experimental methods for discovery of drug combinations. We highlight cutting-edge systems approaches, including large-scale modeling of cell signaling networks, network motif analysis, statistical association-based models, identifying correlations in gene signatures, functional genomics, and high-throughput combination screens. We also present a list of publicly available data and resources to aid in discovery of drug combinations. Integration of these systems approaches will enable faster discovery and translation of clinically relevant drug combinations. Spectrum of Systems Biology Approaches for Drug Combinations. ![]()
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Affiliation(s)
- Karen A Ryall
- Translational Bioinformatics and Cancer Systems Biology Laboratory, Division of Medical Oncology, Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, 12801 E.17th Ave., L18-8116, Aurora, CO 80045 USA
| | - Aik Choon Tan
- Translational Bioinformatics and Cancer Systems Biology Laboratory, Division of Medical Oncology, Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, 12801 E.17th Ave., L18-8116, Aurora, CO 80045 USA ; Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO USA ; Department of Computer Science and Engineering, Korea University, Seoul, South Korea
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Ferrè F, Palmeri A, Helmer-Citterich M. Computational methods for analysis and inference of kinase/inhibitor relationships. Front Genet 2014; 5:196. [PMID: 25071826 PMCID: PMC4075008 DOI: 10.3389/fgene.2014.00196] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 06/13/2014] [Indexed: 12/21/2022] Open
Abstract
The central role of kinases in virtually all signal transduction networks is the driving motivation for the development of compounds modulating their activity. ATP-mimetic inhibitors are essential tools for elucidating signaling pathways and are emerging as promising therapeutic agents. However, off-target ligand binding and complex and sometimes unexpected kinase/inhibitor relationships can occur for seemingly unrelated kinases, stressing that computational approaches are needed for learning the interaction determinants and for the inference of the effect of small compounds on a given kinase. Recently published high-throughput profiling studies assessed the effects of thousands of small compound inhibitors, covering a substantial portion of the kinome. This wealth of data paved the road for computational resources and methods that can offer a major contribution in understanding the reasons of the inhibition, helping in the rational design of more specific molecules, in the in silico prediction of inhibition for those neglected kinases for which no systematic analysis has been carried yet, in the selection of novel inhibitors with desired selectivity, and offering novel avenues of personalized therapies.
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Affiliation(s)
- Fabrizio Ferrè
- Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata Rome, Italy
| | - Antonio Palmeri
- Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata Rome, Italy
| | - Manuela Helmer-Citterich
- Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata Rome, Italy
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20
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Chen YA, Eschrich SA. Computational methods and opportunities for phosphorylation network medicine. Transl Cancer Res 2014; 3:266-278. [PMID: 25530950 PMCID: PMC4271781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Protein phosphorylation, one of the most ubiquitous post-translational modifications (PTM) of proteins, is known to play an essential role in cell signaling and regulation. With the increasing understanding of the complexity and redundancy of cell signaling, there is a growing recognition that targeting the entire network or system could be a necessary and advantageous strategy for treating cancer. Protein kinases, the proteins that add a phosphate group to the substrate proteins during phosphorylation events, have become one of the largest groups of 'druggable' targets in cancer therapeutics in recent years. Kinase inhibitors are being regularly used in clinics for cancer treatment. This therapeutic paradigm shift in cancer research is partly due to the generation and availability of high-dimensional proteomics data. Generation of this data, in turn, is enabled by increased use of mass-spectrometry (MS)-based or other high-throughput proteomics platforms as well as companion public databases and computational tools. This review briefly summarizes the current state and progress on phosphoproteomics identification, quantification, and platform related characteristics. We review existing database resources, computational tools, methods for phosphorylation network inference, and ultimately demonstrate the connection to therapeutics. Finally, many research opportunities exist for bioinformaticians or biostatisticians based on developments and limitations of the current and emerging technologies.
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Affiliation(s)
- Yian Ann Chen
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, 12902 Magnolia Drive Tampa, FL 33612, USA
| | - Steven A Eschrich
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, 12902 Magnolia Drive Tampa, FL 33612, USA
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21
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Kim J, Vasu VT, Mishra R, Singleton KR, Yoo M, Leach SM, Farias-Hesson E, Mason RJ, Kang J, Ramamoorthy P, Kern JA, Heasley LE, Finigan JH, Tan AC. Bioinformatics-driven discovery of rational combination for overcoming EGFR-mutant lung cancer resistance to EGFR therapy. Bioinformatics 2014; 30:2393-8. [PMID: 24812339 DOI: 10.1093/bioinformatics/btu323] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
MOTIVATION Non-small-cell lung cancer (NSCLC) is the leading cause of cancer death in the United States. Targeted tyrosine kinase inhibitors (TKIs) directed against the epidermal growth factor receptor (EGFR) have been widely and successfully used in treating NSCLC patients with activating EGFR mutations. Unfortunately, the duration of response is short-lived, and all patients eventually relapse by acquiring resistance mechanisms. RESULT We performed an integrative systems biology approach to determine essential kinases that drive EGFR-TKI resistance in cancer cell lines. We used a series of bioinformatics methods to analyze and integrate the functional genetics screen and RNA-seq data to identify a set of kinases that are critical in survival and proliferation in these TKI-resistant lines. By connecting the essential kinases to compounds using a novel kinase connectivity map (K-Map), we identified and validated bosutinib as an effective compound that could inhibit proliferation and induce apoptosis in TKI-resistant lines. A rational combination of bosutinib and gefitinib showed additive and synergistic effects in cancer cell lines resistant to EGFR TKI alone. CONCLUSIONS We have demonstrated a bioinformatics-driven discovery roadmap for drug repurposing and development in overcoming resistance in EGFR-mutant NSCLC, which could be generalized to other cancer types in the era of personalized medicine. AVAILABILITY AND IMPLEMENTATION K-Map can be accessible at: http://tanlab.ucdenver.edu/kMap. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jihye Kim
- Division of Medical Oncology, Department of Medicine, Translational Bioinformatics and Cancer Systems Biology Laboratory, University of Colorado Anschutz Medical Campus, 80045 Aurora, Department of Medicine, National Jewish Health, 80206 Denver, Department of Craniofacial Biology, School of Dental Medicine, Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, 80045 Aurora, CO, USA and Department of Computer Science and Engineering, Korea University, Seoul 136-713, Korea
| | - Vihas T Vasu
- Division of Medical Oncology, Department of Medicine, Translational Bioinformatics and Cancer Systems Biology Laboratory, University of Colorado Anschutz Medical Campus, 80045 Aurora, Department of Medicine, National Jewish Health, 80206 Denver, Department of Craniofacial Biology, School of Dental Medicine, Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, 80045 Aurora, CO, USA and Department of Computer Science and Engineering, Korea University, Seoul 136-713, Korea
| | - Rangnath Mishra
- Division of Medical Oncology, Department of Medicine, Translational Bioinformatics and Cancer Systems Biology Laboratory, University of Colorado Anschutz Medical Campus, 80045 Aurora, Department of Medicine, National Jewish Health, 80206 Denver, Department of Craniofacial Biology, School of Dental Medicine, Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, 80045 Aurora, CO, USA and Department of Computer Science and Engineering, Korea University, Seoul 136-713, Korea
| | - Katherine R Singleton
- Division of Medical Oncology, Department of Medicine, Translational Bioinformatics and Cancer Systems Biology Laboratory, University of Colorado Anschutz Medical Campus, 80045 Aurora, Department of Medicine, National Jewish Health, 80206 Denver, Department of Craniofacial Biology, School of Dental Medicine, Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, 80045 Aurora, CO, USA and Department of Computer Science and Engineering, Korea University, Seoul 136-713, Korea
| | - Minjae Yoo
- Division of Medical Oncology, Department of Medicine, Translational Bioinformatics and Cancer Systems Biology Laboratory, University of Colorado Anschutz Medical Campus, 80045 Aurora, Department of Medicine, National Jewish Health, 80206 Denver, Department of Craniofacial Biology, School of Dental Medicine, Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, 80045 Aurora, CO, USA and Department of Computer Science and Engineering, Korea University, Seoul 136-713, Korea
| | - Sonia M Leach
- Division of Medical Oncology, Department of Medicine, Translational Bioinformatics and Cancer Systems Biology Laboratory, University of Colorado Anschutz Medical Campus, 80045 Aurora, Department of Medicine, National Jewish Health, 80206 Denver, Department of Craniofacial Biology, School of Dental Medicine, Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, 80045 Aurora, CO, USA and Department of Computer Science and Engineering, Korea University, Seoul 136-713, Korea
| | - Eveline Farias-Hesson
- Division of Medical Oncology, Department of Medicine, Translational Bioinformatics and Cancer Systems Biology Laboratory, University of Colorado Anschutz Medical Campus, 80045 Aurora, Department of Medicine, National Jewish Health, 80206 Denver, Department of Craniofacial Biology, School of Dental Medicine, Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, 80045 Aurora, CO, USA and Department of Computer Science and Engineering, Korea University, Seoul 136-713, Korea
| | - Robert J Mason
- Division of Medical Oncology, Department of Medicine, Translational Bioinformatics and Cancer Systems Biology Laboratory, University of Colorado Anschutz Medical Campus, 80045 Aurora, Department of Medicine, National Jewish Health, 80206 Denver, Department of Craniofacial Biology, School of Dental Medicine, Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, 80045 Aurora, CO, USA and Department of Computer Science and Engineering, Korea University, Seoul 136-713, Korea Division of Medical Oncology, Department of Medicine, Translational Bioinformatics and Cancer Systems Biology Laboratory, University of Colorado Anschutz Medical Campus, 80045 Aurora, Department of Medicine, National Jewish Health, 80206 Denver, Department of Craniofacial Biology, School of Dental Medicine, Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, 80045 Aurora, CO, USA and Department of Computer Science and Engineering, Korea University, Seoul 136-713, Korea
| | - Jaewoo Kang
- Division of Medical Oncology, Department of Medicine, Translational Bioinformatics and Cancer Systems Biology Laboratory, University of Colorado Anschutz Medical Campus, 80045 Aurora, Department of Medicine, National Jewish Health, 80206 Denver, Department of Craniofacial Biology, School of Dental Medicine, Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, 80045 Aurora, CO, USA and Department of Computer Science and Engineering, Korea University, Seoul 136-713, Korea
| | - Preveen Ramamoorthy
- Division of Medical Oncology, Department of Medicine, Translational Bioinformatics and Cancer Systems Biology Laboratory, University of Colorado Anschutz Medical Campus, 80045 Aurora, Department of Medicine, National Jewish Health, 80206 Denver, Department of Craniofacial Biology, School of Dental Medicine, Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, 80045 Aurora, CO, USA and Department of Computer Science and Engineering, Korea University, Seoul 136-713, Korea
| | - Jeffrey A Kern
- Division of Medical Oncology, Department of Medicine, Translational Bioinformatics and Cancer Systems Biology Laboratory, University of Colorado Anschutz Medical Campus, 80045 Aurora, Department of Medicine, National Jewish Health, 80206 Denver, Department of Craniofacial Biology, School of Dental Medicine, Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, 80045 Aurora, CO, USA and Department of Computer Science and Engineering, Korea University, Seoul 136-713, Korea Division of Medical Oncology, Department of Medicine, Translational Bioinformatics and Cancer Systems Biology Laboratory, University of Colorado Anschutz Medical Campus, 80045 Aurora, Department of Medicine, National Jewish Health, 80206 Denver, Department of Craniofacial Biology, School of Dental Medicine, Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, 80045 Aurora, CO, USA and Department of Computer Science and Engineering, Korea University, Seoul 136-713, Korea
| | - Lynn E Heasley
- Division of Medical Oncology, Department of Medicine, Translational Bioinformatics and Cancer Systems Biology Laboratory, University of Colorado Anschutz Medical Campus, 80045 Aurora, Department of Medicine, National Jewish Health, 80206 Denver, Department of Craniofacial Biology, School of Dental Medicine, Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, 80045 Aurora, CO, USA and Department of Computer Science and Engineering, Korea University, Seoul 136-713, Korea
| | - James H Finigan
- Division of Medical Oncology, Department of Medicine, Translational Bioinformatics and Cancer Systems Biology Laboratory, University of Colorado Anschutz Medical Campus, 80045 Aurora, Department of Medicine, National Jewish Health, 80206 Denver, Department of Craniofacial Biology, School of Dental Medicine, Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, 80045 Aurora, CO, USA and Department of Computer Science and Engineering, Korea University, Seoul 136-713, Korea Division of Medical Oncology, Department of Medicine, Translational Bioinformatics and Cancer Systems Biology Laboratory, University of Colorado Anschutz Medical Campus, 80045 Aurora, Department of Medicine, National Jewish Health, 80206 Denver, Department of Craniofacial Biology, School of Dental Medicine, Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, 80045 Aurora, CO, USA and Department of Computer Science and Engineering, Korea University, Seoul 136-713, Korea
| | - Aik Choon Tan
- Division of Medical Oncology, Department of Medicine, Translational Bioinformatics and Cancer Systems Biology Laboratory, University of Colorado Anschutz Medical Campus, 80045 Aurora, Department of Medicine, National Jewish Health, 80206 Denver, Department of Craniofacial Biology, School of Dental Medicine, Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, 80045 Aurora, CO, USA and Department of Computer Science and Engineering, Korea University, Seoul 136-713, Korea Division of Medical Oncology, Department of Medicine, Translational Bioinformatics and Cancer Systems Biology Laboratory, University of Colorado Anschutz Medical Campus, 80045 Aurora, Department of Medicine, National Jewish Health, 80206 Denver, Department of Craniofacial Biology, School of Dental Medicine, Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado Anschutz Medical Campus, 80045 Aurora, CO, USA and Department of Computer Science and Engineering, Korea University, Seoul 136-713, Korea
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