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Kumar R, Mahmoud MM, Tashkandi HM, Haque S, Harakeh S, Ponnusamy K, Haider S. Combinatorial Network of Transcriptional and miRNA Regulation in Colorectal Cancer. Int J Mol Sci 2023; 24:ijms24065356. [PMID: 36982429 PMCID: PMC10048903 DOI: 10.3390/ijms24065356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/02/2023] [Accepted: 03/06/2023] [Indexed: 03/16/2023] Open
Abstract
Colorectal cancer is one of the leading causes of cancer-associated mortality across the worldwide. One of the major challenges in colorectal cancer is the understanding of the regulatory mechanisms of biological molecules. In this study, we aimed to identify novel key molecules in colorectal cancer by using a computational systems biology approach. We constructed the colorectal protein–protein interaction network which followed hierarchical scale-free nature. We identified TP53, CTNBB1, AKT1, EGFR, HRAS, JUN, RHOA, and EGF as bottleneck-hubs. The HRAS showed the largest interacting strength with functional subnetworks, having strong correlation with protein phosphorylation, kinase activity, signal transduction, and apoptotic processes. Furthermore, we constructed the bottleneck-hubs’ regulatory networks with their transcriptional (transcription factor) and post-transcriptional (miRNAs) regulators, which exhibited the important key regulators. We observed miR-429, miR-622, and miR-133b and transcription factors (EZH2, HDAC1, HDAC4, AR, NFKB1, and KLF4) regulates four bottleneck-hubs (TP53, JUN, AKT1 and EGFR) at the motif level. In future, biochemical investigation of the observed key regulators could provide further understanding about their role in the pathophysiology of colorectal cancer.
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Affiliation(s)
- Rupesh Kumar
- Department of Biotechnology, Jaypee Institute of Information Technology, A-10, Sector 62, Noida 201309, India;
| | - Maged Mostafa Mahmoud
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Molecular Genetics and Enzymology Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo 12622, Egypt
| | - Hanaa M. Tashkandi
- Department of General Surgery, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan 45142, Saudi Arabia
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut 13-5053, Lebanon
- Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman P.O. Box 346, United Arab Emirates
| | - Steve Harakeh
- King Fahd Medical Research Center, and Yousef Abdullatif Jameel Chair of Prophetic Medicine Application, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Kalaiarasan Ponnusamy
- Biotechnology Division, National Centre for Disease Control, New Delhi 110054, India
- Correspondence: (K.P.); (S.H.)
| | - Shazia Haider
- Department of Biotechnology, Jaypee Institute of Information Technology, A-10, Sector 62, Noida 201309, India;
- Correspondence: (K.P.); (S.H.)
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Wang Q, Davis PB, Qi X, Chen SG, Gurney ME, Perry G, Doraiswamy PM, Xu R. Gut-microbiota-microglia-brain interactions in Alzheimer's disease: knowledge-based, multi-dimensional characterization. Alzheimers Res Ther 2021; 13:177. [PMID: 34670619 PMCID: PMC8529734 DOI: 10.1186/s13195-021-00917-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 10/10/2021] [Indexed: 12/26/2022]
Abstract
BACKGROUND Interactions between the gut microbiota, microglia, and aging may modulate Alzheimer's disease (AD) pathogenesis but the precise nature of such interactions is not known. METHODS We developed an integrated multi-dimensional, knowledge-driven, systems approach to identify interactions among microbial metabolites, microglia, and AD. Publicly available datasets were repurposed to create a multi-dimensional knowledge-driven pipeline consisting of an integrated network of microbial metabolite-gene-pathway-phenotype (MGPPN) consisting of 34,509 nodes (216 microbial metabolites, 22,982 genes, 1329 pathways, 9982 mouse phenotypes) and 1,032,942 edges. RESULTS We evaluated the network-based ranking algorithm by showing that abnormal microglia function and physiology are significantly associated with AD pathology at both genetic and phenotypic levels: AD risk genes were ranked at the top 6.4% among 22,982 genes, P < 0.001. AD phenotypes were ranked at the top 11.5% among 9982 phenotypes, P < 0.001. A total of 8094 microglia-microbial metabolite-gene-pathway-phenotype-AD interactions were identified for top-ranked AD-associated microbial metabolites. Short-chain fatty acids (SCFAs) were ranked at the top among prioritized AD-associated microbial metabolites. Through data-driven analyses, we provided evidence that SCFAs are involved in microglia-mediated gut-microbiota-brain interactions in AD at both genetic, functional, and phenotypic levels. CONCLUSION Our analysis produces a novel framework to offer insights into the mechanistic links between gut microbial metabolites, microglia, and AD, with the overall goal to facilitate disease mechanism understanding, therapeutic target identification, and designing confirmatory experimental studies.
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Affiliation(s)
- QuanQiu Wang
- Center for Artificial Intelligence in Drug Discovery, School of Medicine, Case Western Reserve University, 2103 Cornell Rd, Cleveland, OH, 44106, USA
| | - Pamela B Davis
- Center for Community Health Integration, Division of General Medical Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Xin Qi
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Shu G Chen
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | | | - George Perry
- College of Sciences, The University of Texas at San Antonio, San Antonio, TX, USA
| | - P Murali Doraiswamy
- Duke University School of Medicine and the Duke Institute for Brain Sciences, Durham, NC, 27710, USA
| | - Rong Xu
- Center for Artificial Intelligence in Drug Discovery, School of Medicine, Case Western Reserve University, 2103 Cornell Rd, Cleveland, OH, 44106, USA.
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An Alternative Pipeline for Glioblastoma Therapeutics: A Systematic Review of Drug Repurposing in Glioblastoma. Cancers (Basel) 2021; 13:cancers13081953. [PMID: 33919596 PMCID: PMC8073966 DOI: 10.3390/cancers13081953] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/13/2021] [Accepted: 04/16/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Glioblastoma is a devastating malignancy that has continued to prove resistant to a variety of therapeutics. No new systemic therapy has been approved for use against glioblastoma in almost two decades. This observation is particularly disturbing given the amount of money invested in identifying novel therapies for this disease. A relatively rapid and economical pipeline for identification of novel agents is drug repurposing. Here, a comprehensive review detailing the state of drug repurposing in glioblastoma is provided. We reveal details on studies that have examined agents in vitro, in animal models and in patients. While most agents have not progressed beyond the initial stages, several drugs, from a variety of classes, have demonstrated promising results in early phase clinical trials. Abstract The treatment of glioblastoma (GBM) remains a significant challenge, with outcome for most pa-tients remaining poor. Although novel therapies have been developed, several obstacles restrict the incentive of drug developers to continue these efforts including the exorbitant cost, high failure rate and relatively small patient population. Repositioning drugs that have well-characterized mechanistic and safety profiles is an attractive alternative for drug development in GBM. In ad-dition, the relative ease with which repurposed agents can be transitioned to the clinic further supports their potential for examination in patients. Here, a systematic analysis of the literature and clinical trials provides a comprehensive review of primary articles and unpublished trials that use repurposed drugs for the treatment of GBM. The findings demonstrate that numerous drug classes that have a range of initial indications have efficacy against preclinical GBM models and that certain agents have shown significant potential for clinical benefit. With examination in randomized, placebo-controlled trials and the targeting of particular GBM subgroups, it is pos-sible that repurposing can be a cost-effective approach to identify agents for use in multimodal anti-GBM strategies.
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Chelliah SS, Paul EAL, Kamarudin MNA, Parhar I. Challenges and Perspectives of Standard Therapy and Drug Development in High-Grade Gliomas. Molecules 2021; 26:1169. [PMID: 33671796 PMCID: PMC7927069 DOI: 10.3390/molecules26041169] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 02/05/2021] [Accepted: 02/06/2021] [Indexed: 12/18/2022] Open
Abstract
Despite their low incidence rate globally, high-grade gliomas (HGG) remain a fatal primary brain tumor. The recommended therapy often is incapable of resecting the tumor entirely and exclusively targeting the tumor leads to tumor recurrence and dismal prognosis. Additionally, many HGG patients are not well suited for standard therapy and instead, subjected to a palliative approach. HGG tumors are highly infiltrative and the complex tumor microenvironment as well as high tumor heterogeneity often poses the main challenges towards the standard treatment. Therefore, a one-fit-approach may not be suitable for HGG management. Thus, a multimodal approach of standard therapy with immunotherapy, nanomedicine, repurposing of older drugs, use of phytochemicals, and precision medicine may be more advantageous than a single treatment model. This multimodal approach considers the environmental and genetic factors which could affect the patient's response to therapy, thus improving their outcome. This review discusses the current views and advances in potential HGG therapeutic approaches and, aims to bridge the existing knowledge gap that will assist in overcoming challenges in HGG.
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Affiliation(s)
- Shalini Sundramurthi Chelliah
- Brain Research Institute Monash Sunway, Jeffrey Cheah School of Medicine and Health Science, Monash University Malaysia, Bandar Sunway 47500, Malaysia; (S.S.C.); (E.A.L.P.); (M.N.A.K.)
- School of Science, Monash University Malaysia, Bandar Sunway 47500, Malaysia
| | - Ervin Ashley Lourdes Paul
- Brain Research Institute Monash Sunway, Jeffrey Cheah School of Medicine and Health Science, Monash University Malaysia, Bandar Sunway 47500, Malaysia; (S.S.C.); (E.A.L.P.); (M.N.A.K.)
| | - Muhamad Noor Alfarizal Kamarudin
- Brain Research Institute Monash Sunway, Jeffrey Cheah School of Medicine and Health Science, Monash University Malaysia, Bandar Sunway 47500, Malaysia; (S.S.C.); (E.A.L.P.); (M.N.A.K.)
| | - Ishwar Parhar
- Brain Research Institute Monash Sunway, Jeffrey Cheah School of Medicine and Health Science, Monash University Malaysia, Bandar Sunway 47500, Malaysia; (S.S.C.); (E.A.L.P.); (M.N.A.K.)
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Toroghi MK, Cluett WR, Mahadevan R. A Personalized Multiscale Modeling Framework for Dose Selection in Precision Medicine. Ind Eng Chem Res 2020. [DOI: 10.1021/acs.iecr.0c01070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Masood Khaksar Toroghi
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada, M5S 3E5
| | - William R. Cluett
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada, M5S 3E5
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada, M5S 3E5
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada, M5S 3E5
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Wang Q, Xu R. Data-driven multiple-level analysis of gut-microbiome-immune-joint interactions in rheumatoid arthritis. BMC Genomics 2019; 20:124. [PMID: 30744546 PMCID: PMC6371598 DOI: 10.1186/s12864-019-5510-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 02/05/2019] [Indexed: 12/13/2022] Open
Abstract
Background Rheumatoid arthritis (RA) is the most common autoimmune disease and affects about 1% of the population. The cause of RA remains largely unknown and could result from a complex interaction between genes and environment factors. Recent studies suggested that gut microbiota and their collective metabolic outputs exert profound effects on the host immune system and are implicated in RA. However, which and how gut microbial metabolites interact with host genetics in contributing to RA pathogenesis remains unknown. In this study, we present a data-driven study to understand how gut microbial metabolites contribute to RA at the genetic, functional and phenotypic levels. Results We used publicly available disease genetics, chemical genetics, human metabolome, genetic signaling pathways, mouse genome-wide mutation phenotypes, and mouse phenotype ontology data. We identified RA-associated microbial metabolites and prioritized them based on their genetic, functional and phenotypic relevance to RA. We evaluated the prioritization methods using short-chain fatty acids (SCFAs), which were previously shown to be involved in RA etiology. We validate the algorithms by showing that SCFAs are highly associated with RA at genetic, functional and phenotypic levels: SCFAs ranked at top 3.52% based on shared genes with RA, top 5.69% based on shared genetic pathways, and top 16.94% based on shared phenotypes. Based on the genetic-level analysis, human gut microbial metabolites directly interact with many RA-associated genes (as many as 18.1% of all 166 RA genes). Based on the functional-level analysis, human gut microbial metabolites participate in many RA-associated genetic pathways (as many as 71.4% of 311 genetic pathways significantly enriched for RA), including immune system pathways. Based on the phenotypic-level analysis, gut microbial metabolites affect many RA-related phenotypes (as many as 51.3% of 978 phenotypes significantly enriched for RA), including many immune system phenotypes. Conclusions Our study demonstrates strong gut-microbiome-immune-joint interactions in RA, which converged on both genetic, functional and phenotypic levels.
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Affiliation(s)
- QuanQiu Wang
- Department of Population and Quantitative Health Science, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Rong Xu
- Department of Population and Quantitative Health Science, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA.
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7
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Wang Q, Xu R. Disease comorbidity-guided drug repositioning: a case study in schizophrenia. AMIA ... ANNUAL SYMPOSIUM PROCEEDINGS. AMIA SYMPOSIUM 2018; 2018:1300-1309. [PMID: 30815174 PMCID: PMC6371343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The key to any computational drug repositioning is the availability of relevant data in machine-understandable format. While large amount of genetic, genomic and chemical data are publicly available, large-scale higher-level disease and drug phenotypic data are limited. We recently constructed a large-scale disease-comorbidity relationship knowledge base (dCombKB) and a comprehensive drug-treatment relationship knowledge base (TreatKB) from 21 million biomedical research articles and other resources. In this study, we demonstrated the potential of dCombKB and TreatKB in drug repositioning for schizophrenia, one of the top ten illnesses contributing to the global burden of disease. dCombKB contains 121,359 unique disease-disease comorbidity pairs for 23,041 diseases. TreatKB contains 208,330 unique drug-disease treatment pairs for 2,484 drugs and 24,511 diseases. We constructed a phenotypic comorbidity disease network (PDN) of 14,645 disease nodes and 101,275 edges based on dCombKB. We applied standard network-based ranking algorithm to find diseases that are phenotypically related to SCZ. We developed a drug prioritization system, PhenoPredict-CDN, to systematically reposition drugs for SCZ from diseases phenotypically related to SCZ. PhenoPredict-CDN found all 18 FDA-approved SCZ drugs and ranked them highly as tested in a de-novo validation setting (recall: 1.0, mean ranking: top 6.05%, median ranking: top 1.65%). When compared to PREDICT, a comprehensive drug repositioning system, for novel predictions, Pheno-Predict-CDN outperformed PREDICT in Precision-Recall (PR) curves across three different evaluation datasets. Compared to PREDICT, PhenoPredict-CDN showed a significant 110.0-230.0% improvements in mean average precision. In summary, large-scale higher-level disease-comorbidity relationships data extracted from biomedical literature has potential in drug discovery for SCZ, a complex disease with unknown pathophysiological mechanisms. All the data are publicly available: dCombKB at http://nlp. CASE edu/public/data/dCombKB, TreatKB at http://nlp. CASE edu/public/data/treatKB/, and predictions for SCZ at http://nlp. CASE edu/public/data/SCZ_CDN/.
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Affiliation(s)
- QuanQiu Wang
- Department of Population and Quantitative Health Sciences, School of Medicine, Case Western Reserve University, Cleveland OH 44106
| | - Rong Xu
- Department of Population and Quantitative Health Sciences, School of Medicine, Case Western Reserve University, Cleveland OH 44106
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Wang Q, Li L, Xu R. A systems biology approach to predict and characterize human gut microbial metabolites in colorectal cancer. Sci Rep 2018; 8:6225. [PMID: 29670137 PMCID: PMC5906656 DOI: 10.1038/s41598-018-24315-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 03/26/2018] [Indexed: 12/16/2022] Open
Abstract
Colorectal cancer (CRC) is the second leading cause of cancer-related deaths. It is estimated that about half the cases of CRC occurring today are preventable. Recent studies showed that human gut microbiota and their collective metabolic outputs play important roles in CRC. However, the mechanisms by which human gut microbial metabolites interact with host genetics in contributing CRC remain largely unknown. We hypothesize that computational approaches that integrate and analyze vast amounts of publicly available biomedical data have great potential in better understanding how human gut microbial metabolites are mechanistically involved in CRC. Leveraging vast amount of publicly available data, we developed a computational algorithm to predict human gut microbial metabolites for CRC. We validated the prediction algorithm by showing that previously known CRC-associated gut microbial metabolites ranked highly (mean ranking: top 10.52%; median ranking: 6.29%; p-value: 3.85E-16). Moreover, we identified new gut microbial metabolites likely associated with CRC. Through computational analysis, we propose potential roles for tartaric acid, the top one ranked metabolite, in CRC etiology. In summary, our data-driven computation-based study generated a large amount of associations that could serve as a starting point for further experiments to refute or validate these microbial metabolite associations in CRC cancer.
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Affiliation(s)
| | - Li Li
- Department of Family Medicine and Community Health, Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Rong Xu
- Department of Population and Quantitative Health Sciences, School of Medicine, Case Western Reserve University, 2103 Cornell Road, Cleveland, Ohio, 44106, USA.
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Wang Q, McCormick TS, Ward NL, Cooper KD, Conic R, Xu R. Combining mechanism-based prediction with patient-based profiling for psoriasis metabolomics biomarker discovery. AMIA ... ANNUAL SYMPOSIUM PROCEEDINGS. AMIA SYMPOSIUM 2018; 2017:1734-1743. [PMID: 29854244 PMCID: PMC5977692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
UNLABELLED Psoriasis is a chronic, debilitating skin condition that affects approximately 125 million individuals worldwide. The cause of psoriasis appears multifactorial, and no unified mitigating signal or single antigenic target has been identified to date. Metabolomic studies hold great potential for explaining disease mechanism, facilitating early diagnosis, and identifying potential therapeutic areas. Here, we present an integrated disease metabolomic biomarker discovery strategy that combines mechanism-based biomarker discovery with clinical sample-based metabolomic profiling. We applied this strategy in identifying and understanding metabolite biomarkers for psoriasis. The key innovation of our strategy is a novel mechanism-based metabolite prediction system, mmPredict, which assimilates vast amounts of existing knowledge of diseases and metabolites. mmPredict first constructed a psoriasis-specific mouse mutational phenotype profile. It then constructed phenotype profiles for a total of 259,170 chemicals/metabolites using known chemical genetics and human metabolomic data. Metabolites were then prioritized based on the phenotypic similarities between disease- and metabolites. We evaluated mmPredict using 150 metabolites identified using our in-house metabolome profiling study of psoriasis patient samples. mmPredict found 96 of the 150 metabolites and ranked them highly (recall: 0.64, mean ranking: 8.73%, median ranking: 2.33%, p-value: 4.75E-44). These results show that mmPredict is consistent with, as well as a complement to, traditional human metabolomic profiling studies. We then developed a strategy to combine outputs from both systems and found that the oxidative product of linoleic acid, 13(S)-hydroxy-9Z,11E-octadecadienoic acid (13- HODE), ranked highly by both mmPredict and our in-house experiments. Our integrated analysis indicates that 13- HODE may be a mechanistic link between psoriasis and cardiovascular comorbidities associated with psoriasis. In summary, we developed an integrated metabolomic prediction system that combines both human metabolomic studies and mechanism-based prediction and demonstrated its application in the skin disease psoriasis. Our system is highly general and can be applied to other diseases when patient-based metabolomic profiling data becomes more increasingly available. Data is publicly available at: http://nlp. CASE edu/public/data/mmPredict_PSO.
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Affiliation(s)
| | - Thomas S McCormick
- Department of Dermatology, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Nicole L Ward
- Department of Dermatology, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Kevin D Cooper
- Department of Dermatology, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Ruzica Conic
- ThinTek, LLC, Palo Alto, CA, USA
- Department of Dermatology, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Department of Epidemiology and Biostatistics, Institute of Computational Biology, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Rong Xu
- Department of Epidemiology and Biostatistics, Institute of Computational Biology, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
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Using a novel computational drug-repositioning approach (DrugPredict) to rapidly identify potent drug candidates for cancer treatment. Oncogene 2017; 37:403-414. [PMID: 28967908 PMCID: PMC5799769 DOI: 10.1038/onc.2017.328] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 06/28/2017] [Accepted: 07/03/2017] [Indexed: 12/25/2022]
Abstract
Computation-based drug-repurposing/repositioning approaches can greatly speed up the traditional drug discovery process. To date, systematic and comprehensive computation-based approaches to identify and validate drug-repositioning candidates for epithelial ovarian cancer (EOC) have not been undertaken. Here, we present a novel drug discovery strategy that combines a computational drug-repositioning system (DrugPredict) with biological testing in cell lines in order to rapidly identify novel drug candidates for EOC. DrugPredict exploited unique repositioning opportunities rendered by a vast amount of disease genomics, phenomics, drug treatment, and genetic pathway and uniquely revealed that non-steroidal anti-inflammatories (NSAIDs) rank just as high as currently used ovarian cancer drugs. As epidemiological studies have reported decreased incidence of ovarian cancer associated with regular intake of NSAIDs, we assessed whether NSAIDs could have chemoadjuvant applications in EOC and found that (i) NSAID Indomethacin induces robust cell death in primary patient-derived platinum-sensitive and platinum- resistant ovarian cancer cells and ovarian cancer stem cells and (ii) downregulation of β-catenin is partially driving effects of Indomethacin in cisplatin-resistant cells. In summary, we demonstrate that DrugPredict represents an innovative computational drug- discovery strategy to uncover drugs that are routinely used for other indications that could be effective in treating various cancers, thus introducing a potentially rapid and cost-effective translational opportunity. As NSAIDs are already in routine use in gynecological treatment regimens and have acceptable safety profile, our results will provide with a rationale for testing NSAIDs as potential chemoadjuvants in EOC patient trials.
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Ran D, Mao J, Zhan C, Xie C, Ruan H, Ying M, Zhou J, Lu WL, Lu W. d-Retroenantiomer of Quorum-Sensing Peptide-Modified Polymeric Micelles for Brain Tumor-Targeted Drug Delivery. ACS APPLIED MATERIALS & INTERFACES 2017; 9:25672-25682. [PMID: 28548480 DOI: 10.1021/acsami.7b03518] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Compared to that of other tumors, various barriers, such as the blood-brain barrier (BBB), enzymatic barriers, and the blood-brain tumor barrier, severely impede the successful treatment of gliomas. Peptide ligands were frequently used as targeting moieties to mediate brain tumor-targeted drug delivery. LWSW (SYPGWSW) is a recently reported quorum-sensing (QS) peptide that is able to efficiently cross the BBB. Even though linear LWSW traverses the BBB in vitro, its in vivo targeting ability has been greatly impaired due to proteolysis. Here, we developed a stable peptide, DWSW (DWDSDWDGDPDYDS), using the retro-inverso isomerization technique to achieve an enhanced antiglioma effect. In vitro studies have demonstrated that both the LWSW and DWSW peptides possessed excellent tumor-homing properties and barrier-penetration abilities, whereas DWSW exhibited exceptional stability in serum and maintained its targeting ability after serum preincubation. In vivo, DWSW-modified probes and micelles accumulated more efficiently in the glioma region in comparison with LWSW-modified probes and micelles because of full resistance to proteolysis in blood circulation. As expected, DWSW-modified paclitaxel (PTX)-loaded micelles (DWSW Micelle/PTX) exhibited the longest median survival time among glioma-bearing nude mice. Our results suggested that the QS peptide appears to be a promising targeting moiety, with potential applications in glioma-targeted drug delivery.
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Affiliation(s)
- Danni Ran
- Department of Pharmaceutics, School of Pharmacy, Fudan University & Key Laboratory of Smart Drug Delivery (Fudan University), Ministry of Education , Shanghai 201203, China
| | - Jiani Mao
- Department of Pharmaceutics, School of Pharmacy, Fudan University & Key Laboratory of Smart Drug Delivery (Fudan University), Ministry of Education , Shanghai 201203, China
| | - Changyou Zhan
- Department of Pharmaceutics, School of Pharmacy, Fudan University & Key Laboratory of Smart Drug Delivery (Fudan University), Ministry of Education , Shanghai 201203, China
- Department of Pharmacology, School of Basic Medical Sciences, Fudan University , Shanghai 200032, China
- State Key Laboratory of Molecular Engineering of Polymers, Fudan University , Shanghai 200433, China
| | - Cao Xie
- Department of Pharmaceutics, School of Pharmacy, Fudan University & Key Laboratory of Smart Drug Delivery (Fudan University), Ministry of Education , Shanghai 201203, China
| | - Huitong Ruan
- Department of Pharmaceutics, School of Pharmacy, Fudan University & Key Laboratory of Smart Drug Delivery (Fudan University), Ministry of Education , Shanghai 201203, China
| | - Man Ying
- Department of Pharmaceutics, School of Pharmacy, Fudan University & Key Laboratory of Smart Drug Delivery (Fudan University), Ministry of Education , Shanghai 201203, China
| | - Jianfen Zhou
- Department of Pharmaceutics, School of Pharmacy, Fudan University & Key Laboratory of Smart Drug Delivery (Fudan University), Ministry of Education , Shanghai 201203, China
| | - Wan-Liang Lu
- State Kay Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Science, Peking University , Beijing 100191, China
| | - Weiyue Lu
- Department of Pharmaceutics, School of Pharmacy, Fudan University & Key Laboratory of Smart Drug Delivery (Fudan University), Ministry of Education , Shanghai 201203, China
- State Key Laboratory of Molecular Engineering of Polymers, Fudan University , Shanghai 200433, China
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Cai X, Chen Y, Zheng C, Xu R. Interrogating Patient-level Genomics and Mouse Phenomics towards Understanding Cytokines in Colorectal Cancer Metastasis. AMIA JOINT SUMMITS ON TRANSLATIONAL SCIENCE PROCEEDINGS. AMIA JOINT SUMMITS ON TRANSLATIONAL SCIENCE 2017; 2017:227-236. [PMID: 28815134 PMCID: PMC5543389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Background: Colorectal cancer is the second leading cancer-related death worldwide and a majority of patients die from metastasis. Chronic intestinal inflammation plays an important role in tumor progression of colorectal cancer. However, few study works on systematically predicting colorectal cancer metastasis using inflammatory cytokine genes. Results: We developed a supervised machine learning approach to predict colorectal cancer tumor progression using patient level genomic features. To better understand the role of cytokines, we integrated the metastatic-related genes from mouse phenotypic data. In addition, pathway analysis and network visualization were also applied to top significant genes ranked by feature weights of the final prediction model. The combined model of cytokines and mouse phenotypes achieved a predictive accuracy of 75.54%, higher than the model based on mouse phenotypes independently (70.42%, p-value<0.05). In additional, the combined model outperformed the model based on the existing metastatic-related epithelial-to-mesenchymal transition (EMT) genes (75.54% vs. 71.61%, p-value<0.05). We also observed that the most important cytokine gene features of the our model interact with the cancer driver genes and are highly associated with the colorectal cancer metastasis signaling pathway. Conclusion: We developed a combined model using both cytokine and mouse phenotype information to predict colorectal cancer metastasis. The results suggested that the inflammatory cytokines increase the power of predicting metastasis. We also systematically demonstrated the critical role of cytokines in progression of colorectal tumor.
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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
| | - Chunlei Zheng
- 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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13
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Gao Z, Chen Y, Cai X, Xu R. Predict drug permeability to blood-brain-barrier from clinical phenotypes: drug side effects and drug indications. Bioinformatics 2017; 33:901-908. [PMID: 27993785 PMCID: PMC5860495 DOI: 10.1093/bioinformatics/btw713] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 10/16/2016] [Accepted: 11/19/2016] [Indexed: 12/25/2022] Open
Abstract
Motivation Blood-Brain-Barrier (BBB) is a rigorous permeability barrier for maintaining homeostasis of Central Nervous System (CNS). Determination of compound's permeability to BBB is prerequisite in CNS drug discovery. Existing computational methods usually predict drug BBB permeability from chemical structure and they generally apply to small compounds passing BBB through passive diffusion. As abundant information on drug side effects and indications has been recorded over time through extensive clinical usage, we aim to explore BBB permeability prediction from a new angle and introduce a novel approach to predict BBB permeability from drug clinical phenotypes (drug side effects and drug indications). This method can apply to both small compounds and macro-molecules penetrating BBB through various mechanisms besides passive diffusion. Results We composed a training dataset of 213 drugs with known brain and blood steady-state concentrations ratio and extracted their side effects and indications as features. Next, we trained SVM models with polynomial kernel and obtained accuracy of 76.0%, AUC 0.739, and F 1 score (macro weighted) 0.760 with Monte Carlo cross validation. The independent test accuracy was 68.3%, AUC 0.692, F 1 score 0.676. When both chemical features and clinical phenotypes were available, combining the two types of features achieved significantly better performance than chemical feature based approach (accuracy 85.5% versus 72.9%, AUC 0.854 versus 0.733, F 1 score 0.854 versus 0.725; P < e -90 ). We also conducted de novo prediction and identified 110 drugs in SIDER database having the potential to penetrate BBB, which could serve as start point for CNS drug repositioning research. Availability and Implementation https://github.com/bioinformatics-gao/CASE-BBB-prediction-Data. Contact rxx@case.edu. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Zhen Gao
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA
| | - Yang Chen
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA
| | - Xiaoshu Cai
- Department of Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, OH, USA
| | - Rong Xu
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH, USA
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14
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Chen Y, Xu R. Drug repurposing for glioblastoma based on molecular subtypes. J Biomed Inform 2016; 64:131-138. [PMID: 27697594 PMCID: PMC6146394 DOI: 10.1016/j.jbi.2016.09.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 08/23/2016] [Accepted: 09/27/2016] [Indexed: 01/12/2023]
Abstract
A recent multi-platform analysis by The Cancer Genome Atlas identified four distinct molecular subtypes for glioblastoma (GBM) and demonstrated that the subtypes correlate with clinical phenotypes and treatment responses. In this study, we developed a computational drug repurposing approach to predict GBM drugs based on the molecular subtypes. Our approach leverages the genomic signature for each GBM subtype, and integrates the human cancer genomics with mouse phenotype data to identify the opportunity of reusing the FDA-approved agents to treat specific GBM subtypes. Specifically, we first constructed the phenotype profile for each GBM subtype using their genomic signatures. For each approved drug, we also constructed a phenotype profile using the drug target genes. Then we developed an algorithm to match and prioritize drugs based on their phenotypic similarities to the GBM subtypes. Our approach is highly generalizable for other disorders if provided with a list of disorder-specific genes. We first evaluated the approach in predicting drugs for the whole GBM. For a combined set of approved, potential and off-label GBM drugs, we achieved a median rank of 9.3%, which is significantly higher (p
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Affiliation(s)
- Yang Chen
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH 44106, United States
| | - Rong Xu
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH 44106, United States.
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15
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Huang K, Liu Y, Huang Y, Li L, Cooper L, Ruan J, Zhao Z. Intelligent biology and medicine in 2015: advancing interdisciplinary education, collaboration, and data science. BMC Genomics 2016; 17 Suppl 7:524. [PMID: 27556295 PMCID: PMC5001210 DOI: 10.1186/s12864-016-2893-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
We summarize the 2015 International Conference on Intelligent Biology and Medicine (ICIBM 2015) and the editorial report of the supplement to BMC Genomics. The supplement includes 20 research articles selected from the manuscripts submitted to ICIBM 2015. The conference was held on November 13-15, 2015 at Indianapolis, Indiana, USA. It included eight scientific sessions, three tutorials, four keynote presentations, three highlight talks, and a poster session that covered current research in bioinformatics, systems biology, computational biology, biotechnologies, and computational medicine.
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Affiliation(s)
- Kun Huang
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210 USA
| | - Yunlong Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202 USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202 USA
| | - Yufei Huang
- Department of Electrical and Computer Engineering, The University of Texas at San Antonio, San Antonio, TX 78249 USA
| | - Lang Li
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202 USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202 USA
| | - Lee Cooper
- Department of Biomedical Informatics, Emory University, Atlanta, GA 30322 USA
- Department of Biomedical Engineering, Emory University / Georgia Institute of Technology, Atlanta, GA 30322 USA
| | - Jianhua Ruan
- Department of Computer Science, The University of Texas at San Antonio, San Antonio, TX 78249 USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030 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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