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Shahjahan, Dey JK, Dey SK. Translational bioinformatics approach to combat cardiovascular disease and cancers. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2024; 139:221-261. [PMID: 38448136 DOI: 10.1016/bs.apcsb.2023.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
Bioinformatics is an interconnected subject of science dealing with diverse fields including biology, chemistry, physics, statistics, mathematics, and computer science as the key fields to answer complicated physiological problems. Key intention of bioinformatics is to store, analyze, organize, and retrieve essential information about genome, proteome, transcriptome, metabolome, as well as organisms to investigate the biological system along with its dynamics, if any. The outcome of bioinformatics depends on the type, quantity, and quality of the raw data provided and the algorithm employed to analyze the same. Despite several approved medicines available, cardiovascular disorders (CVDs) and cancers comprises of the two leading causes of human deaths. Understanding the unknown facts of both these non-communicable disorders is inevitable to discover new pathways, find new drug targets, and eventually newer drugs to combat them successfully. Since, all these goals involve complex investigation and handling of various types of macro- and small- molecules of the human body, bioinformatics plays a key role in such processes. Results from such investigation has direct human application and thus we call this filed as translational bioinformatics. Current book chapter thus deals with diverse scope and applications of this translational bioinformatics to find cure, diagnosis, and understanding the mechanisms of CVDs and cancers. Developing complex yet small or long algorithms to address such problems is very common in translational bioinformatics. Structure-based drug discovery or AI-guided invention of novel antibodies that too with super-high accuracy, speed, and involvement of considerably low amount of investment are some of the astonishing features of the translational bioinformatics and its applications in the fields of CVDs and cancers.
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Affiliation(s)
- Shahjahan
- Laboratory for Structural Biology of Membrane Proteins, Dr. B.R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India
| | - Joy Kumar Dey
- Central Council for Research in Homoeopathy, Ministry of Ayush, Govt. of India, New Delhi, Delhi, India
| | - Sanjay Kumar Dey
- Laboratory for Structural Biology of Membrane Proteins, Dr. B.R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India.
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Wang Y, Huang X, Xian B, Jiang H, Zhou T, Chen S, Wen F, Pei J. Machine learning and bioinformatics-based insights into the potential targets of saponins in Paris polyphylla smith against non-small cell lung cancer. Front Genet 2022; 13:1005896. [PMID: 36386821 PMCID: PMC9649596 DOI: 10.3389/fgene.2022.1005896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/17/2022] [Indexed: 12/24/2022] Open
Abstract
Background: Lung cancer has the highest mortality rate among cancers worldwide, and non-small cell lung cancer (NSCLC) is the major lethal factor. Saponins in Paris polyphylla smith exhibit antitumor activity against non-small cell lung cancer, but their targets are not fully understood. Methods: In this study, we used differential gene analysis, lasso regression analysis and support vector machine recursive feature elimination (SVM-RFE) to screen potential key genes for NSCLC by using relevant datasets from the GEO database. The accuracy of the signature genes was verified by using ROC curves and gene expression values. Screening of potential active ingredients for the treatment of NSCLC by molecular docking of the reported active ingredients of saponins in Paris polyphylla Smith with the screened signature genes. The activity of the screened components and their effects on key genes expression were further validated by CCK-8, flow cytometry (apoptosis and cycling) and qPCR. Results: 204 differential genes and two key genes (RHEBL1, RNPC3) stood out in the bioinformatics analysis. Overall survival (OS), First-progression survival (FP) and post-progression survival (PPS) analysis revealed that low expression of RHEBL1 and high expression of RNPC3 indicated good prognosis. In addition, Polyphyllin VI(PPVI) and Protodioscin (Prot) effectively inhibited the proliferation of non-small cell lung cancer cell line with IC50 of 4.46 μM ± 0.69 μM and 8.09 μM ± 0.67μM, respectively. The number of apoptotic cells increased significantly with increasing concentrations of PPVI and Prot. Prot induces G1/G0 phase cell cycle arrest and PPVI induces G2/M phase cell cycle arrest. After PPVI and Prot acted on this cell line for 48 h, the expression of RHEBL1 and RNPC3 was found to be consistent with the results of bioinformatics analysis. Conclusion: This study identified two potential key genes (RHEBL1 and RNPC3) in NSCLC. Additionally, PPVI and Prot may act on RHEBL1 and RNPC3 to affect NSCLC. Our findings provide a reference for clinical treatment of NSCLC.
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Affiliation(s)
| | | | | | | | | | | | | | - Jin Pei
- *Correspondence: Feiyan Wen, ; Jin Pei,
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3
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Singh S, Singh DB, Gautam B, Singh A, Yadav N. Pharmacokinetics and pharmacodynamics analysis of drug candidates. Bioinformatics 2022. [DOI: 10.1016/b978-0-323-89775-4.00001-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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4
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Xie Q, Liu L, Chen X, Cheng Y, Li J, Zhang X, Xu N, Han Y, Liu H, Wei L, Peng J, Shen A. Identification of Cysteine Protease Inhibitor CST2 as a Potential Biomarker for Colorectal Cancer. J Cancer 2021; 12:5144-5152. [PMID: 34335931 PMCID: PMC8317524 DOI: 10.7150/jca.53983] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 05/26/2021] [Indexed: 12/14/2022] Open
Abstract
Additional biomarkers for the development and progression of colorectal cancer (CRC) remain to be identified. Hence, the current study aimed to identify potential diagnostic markers for CRC. Analyses of cysteine protease inhibitor [cystatins (CSTs)] expression in CRC samples and its correlation with cancer stage or survival in patients with CRC demonstrated that CRC tissues had greater CST1 and CST2 mRNA expression compared to noncancerous adjacent tissues, while higher CST2 mRNA expression in CRC tissues was correlated with advanced stages and disease-free survival in patients with CRC, encouraging further exploration on the role of CST2 in CRC. Through an online database search and tissue microarray (TMA), we confirmed that CRC samples had higher CST2 expression compared to noncancerous adjacent tissue or normal colorectal tissues at both the mRNA and protein levels. TMA also revealed that colorectal adenoma, CRC, and metastatic CRC tissues exhibited a significantly increased CST2 protein expression. Accordingly, survival analysis demonstrated that the increase in CST2 protein expression was correlated with shorter overall survival of patients with CRC. Moreover, our results found a significant upregulation of CST2 in multiple cancer tissues. Taken together, these findings suggest the potential role of CST2 as a diagnostic and prognostic biomarker for CRC.
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Affiliation(s)
- Qiurong Xie
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, 1 Qiuyang Road, Minhou Shangjie, Fuzhou, Fujian 350122, China.,Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, 1 Qiuyang Road, Minhou Shangjie, Fuzhou, Fujian 350122, China
| | - Liya Liu
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, 1 Qiuyang Road, Minhou Shangjie, Fuzhou, Fujian 350122, China.,Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, 1 Qiuyang Road, Minhou Shangjie, Fuzhou, Fujian 350122, China
| | - Xiaoping Chen
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, 1 Qiuyang Road, Minhou Shangjie, Fuzhou, Fujian 350122, China.,Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, 1 Qiuyang Road, Minhou Shangjie, Fuzhou, Fujian 350122, China
| | - Ying Cheng
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, 1 Qiuyang Road, Minhou Shangjie, Fuzhou, Fujian 350122, China.,Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, 1 Qiuyang Road, Minhou Shangjie, Fuzhou, Fujian 350122, China
| | - Jiapeng Li
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, 1 Qiuyang Road, Minhou Shangjie, Fuzhou, Fujian 350122, China.,Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, 1 Qiuyang Road, Minhou Shangjie, Fuzhou, Fujian 350122, China.,Department of Physical Education, Fujian University of Traditional Chinese Medicine, 1 Qiuyang Road, Minhou Shangjie, Fuzhou, Fujian 350122, China
| | - Xiuli Zhang
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, 1 Qiuyang Road, Minhou Shangjie, Fuzhou, Fujian 350122, China.,Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, 1 Qiuyang Road, Minhou Shangjie, Fuzhou, Fujian 350122, China
| | - Nanhui Xu
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, 1 Qiuyang Road, Minhou Shangjie, Fuzhou, Fujian 350122, China.,Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, 1 Qiuyang Road, Minhou Shangjie, Fuzhou, Fujian 350122, China
| | - Yuying Han
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, 1 Qiuyang Road, Minhou Shangjie, Fuzhou, Fujian 350122, China.,Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, 1 Qiuyang Road, Minhou Shangjie, Fuzhou, Fujian 350122, China
| | - Huixin Liu
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, 1 Qiuyang Road, Minhou Shangjie, Fuzhou, Fujian 350122, China.,Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, 1 Qiuyang Road, Minhou Shangjie, Fuzhou, Fujian 350122, China
| | - Lihui Wei
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, 1 Qiuyang Road, Minhou Shangjie, Fuzhou, Fujian 350122, China.,Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, 1 Qiuyang Road, Minhou Shangjie, Fuzhou, Fujian 350122, China
| | - Jun Peng
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, 1 Qiuyang Road, Minhou Shangjie, Fuzhou, Fujian 350122, China.,Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, 1 Qiuyang Road, Minhou Shangjie, Fuzhou, Fujian 350122, China
| | - Aling Shen
- Academy of Integrative Medicine, Fujian University of Traditional Chinese Medicine, 1 Qiuyang Road, Minhou Shangjie, Fuzhou, Fujian 350122, China.,Fujian Key Laboratory of Integrative Medicine on Geriatrics, Fujian University of Traditional Chinese Medicine, 1 Qiuyang Road, Minhou Shangjie, Fuzhou, Fujian 350122, China
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Birer-Williams C, Gufford BT, Chou E, Alilio M, VanAlstine S, Morley RE, McCune JS, Paine MF, Boyce RD. A New Data Repository for Pharmacokinetic Natural Product-Drug Interactions: From Chemical Characterization to Clinical Studies. Drug Metab Dispos 2020; 48:1104-1112. [PMID: 32601103 PMCID: PMC7543481 DOI: 10.1124/dmd.120.000054] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/01/2020] [Indexed: 12/11/2022] Open
Abstract
There are many gaps in scientific knowledge about the clinical significance of pharmacokinetic natural product–drug interactions (NPDIs) in which the natural product (NP) is the precipitant and a conventional drug is the object. The National Center for Complimentary and Integrative Health created the Center of Excellence for NPDI Research (NaPDI Center) (www.napdi.org) to provide leadership and guidance on the study of pharmacokinetic NPDIs. A key contribution of the Center is the first user-friendly online repository that stores and links pharmacokinetic NPDI data across chemical characterization, metabolomics analyses, and pharmacokinetic in vitro and clinical experiments (repo.napdi.org). The design is expected to help researchers more easily arrive at a complete understanding of pharmacokinetic NPDI research on a particular NP. The repository will also facilitate multidisciplinary collaborations, as the repository links all of the experimental data for a given NP across the study types. The current work describes the design of the repository, standard operating procedures used to enter data, and pharmacokinetic NPDI data that have been entered to date. To illustrate the usefulness of the NaPDI Center repository, more details on two high-priority NPs, cannabis and kratom, are provided as case studies.
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Affiliation(s)
- Caroline Birer-Williams
- Department of Biomedical Informatics (C.B.-W., E.C., R.D.B.) and School of Pharmacy (M.A.), University of Pittsburgh, School of Medicine, Pittsburgh, Pennsylvania; School of Pharmacy, University of Utah, Salt Lake City, Utah (S.V., R.E.M.); Covance Inc., Clinical Pharmacology, Madison, Wisconsin (B.T.G.); Department of Population Sciences and Department of Hematology & HCT, City of Hope Comprehensive Cancer Center, Duarte, California (J.S.M.); Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington (M.F.P.); and Center of Excellence for Natural Product Drug Interaction Research, Spokane, Washington (J.S.M., M.F.P., R.D.B.)
| | - Brandon T Gufford
- Department of Biomedical Informatics (C.B.-W., E.C., R.D.B.) and School of Pharmacy (M.A.), University of Pittsburgh, School of Medicine, Pittsburgh, Pennsylvania; School of Pharmacy, University of Utah, Salt Lake City, Utah (S.V., R.E.M.); Covance Inc., Clinical Pharmacology, Madison, Wisconsin (B.T.G.); Department of Population Sciences and Department of Hematology & HCT, City of Hope Comprehensive Cancer Center, Duarte, California (J.S.M.); Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington (M.F.P.); and Center of Excellence for Natural Product Drug Interaction Research, Spokane, Washington (J.S.M., M.F.P., R.D.B.)
| | - Eric Chou
- Department of Biomedical Informatics (C.B.-W., E.C., R.D.B.) and School of Pharmacy (M.A.), University of Pittsburgh, School of Medicine, Pittsburgh, Pennsylvania; School of Pharmacy, University of Utah, Salt Lake City, Utah (S.V., R.E.M.); Covance Inc., Clinical Pharmacology, Madison, Wisconsin (B.T.G.); Department of Population Sciences and Department of Hematology & HCT, City of Hope Comprehensive Cancer Center, Duarte, California (J.S.M.); Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington (M.F.P.); and Center of Excellence for Natural Product Drug Interaction Research, Spokane, Washington (J.S.M., M.F.P., R.D.B.)
| | - Marijanel Alilio
- Department of Biomedical Informatics (C.B.-W., E.C., R.D.B.) and School of Pharmacy (M.A.), University of Pittsburgh, School of Medicine, Pittsburgh, Pennsylvania; School of Pharmacy, University of Utah, Salt Lake City, Utah (S.V., R.E.M.); Covance Inc., Clinical Pharmacology, Madison, Wisconsin (B.T.G.); Department of Population Sciences and Department of Hematology & HCT, City of Hope Comprehensive Cancer Center, Duarte, California (J.S.M.); Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington (M.F.P.); and Center of Excellence for Natural Product Drug Interaction Research, Spokane, Washington (J.S.M., M.F.P., R.D.B.)
| | - Sidney VanAlstine
- Department of Biomedical Informatics (C.B.-W., E.C., R.D.B.) and School of Pharmacy (M.A.), University of Pittsburgh, School of Medicine, Pittsburgh, Pennsylvania; School of Pharmacy, University of Utah, Salt Lake City, Utah (S.V., R.E.M.); Covance Inc., Clinical Pharmacology, Madison, Wisconsin (B.T.G.); Department of Population Sciences and Department of Hematology & HCT, City of Hope Comprehensive Cancer Center, Duarte, California (J.S.M.); Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington (M.F.P.); and Center of Excellence for Natural Product Drug Interaction Research, Spokane, Washington (J.S.M., M.F.P., R.D.B.)
| | - Rachael E Morley
- Department of Biomedical Informatics (C.B.-W., E.C., R.D.B.) and School of Pharmacy (M.A.), University of Pittsburgh, School of Medicine, Pittsburgh, Pennsylvania; School of Pharmacy, University of Utah, Salt Lake City, Utah (S.V., R.E.M.); Covance Inc., Clinical Pharmacology, Madison, Wisconsin (B.T.G.); Department of Population Sciences and Department of Hematology & HCT, City of Hope Comprehensive Cancer Center, Duarte, California (J.S.M.); Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington (M.F.P.); and Center of Excellence for Natural Product Drug Interaction Research, Spokane, Washington (J.S.M., M.F.P., R.D.B.)
| | - Jeannine S McCune
- Department of Biomedical Informatics (C.B.-W., E.C., R.D.B.) and School of Pharmacy (M.A.), University of Pittsburgh, School of Medicine, Pittsburgh, Pennsylvania; School of Pharmacy, University of Utah, Salt Lake City, Utah (S.V., R.E.M.); Covance Inc., Clinical Pharmacology, Madison, Wisconsin (B.T.G.); Department of Population Sciences and Department of Hematology & HCT, City of Hope Comprehensive Cancer Center, Duarte, California (J.S.M.); Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington (M.F.P.); and Center of Excellence for Natural Product Drug Interaction Research, Spokane, Washington (J.S.M., M.F.P., R.D.B.)
| | - Mary F Paine
- Department of Biomedical Informatics (C.B.-W., E.C., R.D.B.) and School of Pharmacy (M.A.), University of Pittsburgh, School of Medicine, Pittsburgh, Pennsylvania; School of Pharmacy, University of Utah, Salt Lake City, Utah (S.V., R.E.M.); Covance Inc., Clinical Pharmacology, Madison, Wisconsin (B.T.G.); Department of Population Sciences and Department of Hematology & HCT, City of Hope Comprehensive Cancer Center, Duarte, California (J.S.M.); Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington (M.F.P.); and Center of Excellence for Natural Product Drug Interaction Research, Spokane, Washington (J.S.M., M.F.P., R.D.B.)
| | - Richard D Boyce
- Department of Biomedical Informatics (C.B.-W., E.C., R.D.B.) and School of Pharmacy (M.A.), University of Pittsburgh, School of Medicine, Pittsburgh, Pennsylvania; School of Pharmacy, University of Utah, Salt Lake City, Utah (S.V., R.E.M.); Covance Inc., Clinical Pharmacology, Madison, Wisconsin (B.T.G.); Department of Population Sciences and Department of Hematology & HCT, City of Hope Comprehensive Cancer Center, Duarte, California (J.S.M.); Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington (M.F.P.); and Center of Excellence for Natural Product Drug Interaction Research, Spokane, Washington (J.S.M., M.F.P., R.D.B.)
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6
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Swindell WR, Bojanowski K, Kindy MS, Chau RMW, Ko D. GM604 regulates developmental neurogenesis pathways and the expression of genes associated with amyotrophic lateral sclerosis. Transl Neurodegener 2018; 7:30. [PMID: 30524706 PMCID: PMC6276193 DOI: 10.1186/s40035-018-0135-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 10/21/2018] [Indexed: 12/11/2022] Open
Abstract
Background Amyotrophic lateral sclerosis (ALS) is currently an incurable disease without highly effective pharmacological treatments. The peptide drug GM604 (GM6 or Alirinetide) was developed as a candidate ALS therapy, which has demonstrated safety and good drug-like properties with a favorable pharmacokinetic profile. GM6 is hypothesized to bolster neuron survival through the multi-target regulation of developmental pathways, but mechanisms of action are not fully understood. Methods This study used RNA-seq to evaluate transcriptome responses in SH-SY5Y neuroblastoma cells following GM6 treatment (6, 24 and 48 h). Results We identified 2867 protein-coding genes with expression significantly altered by GM6 (FDR < 0.10). Early (6 h) responses included up-regulation of Notch and hedgehog signaling components, with increased expression of developmental genes mediating neurogenesis and axon growth. Prolonged GM6 treatment (24 and 48 h) altered the expression of genes contributing to cell adhesion and the extracellular matrix. GM6 further down-regulated the expression of genes associated with mitochondria, inflammatory responses, mRNA processing and chromatin organization. GM6-increased genes were located near GC-rich motifs interacting with C2H2 zinc finger transcription factors, whereas GM6-decreased genes were located near AT-rich motifs associated with helix-turn-helix homeodomain factors. Such motifs interacted with a diverse network of transcription factors encoded by GM6-regulated genes (STAT3, HOXD11, HES7, GLI1). We identified 77 ALS-associated genes with expression significantly altered by GM6 treatment (FDR < 0.10), which were known to function in neurogenesis, axon guidance and the intrinsic apoptosis pathway. Conclusions Our findings support the hypothesis that GM6 acts through developmental-stage pathways to influence neuron survival. Gene expression responses were consistent with neurotrophic effects, ECM modulation, and activation of the Notch and hedgehog neurodevelopmental pathways. This multifaceted mechanism of action is unique among existing ALS drug candidates and may be applicable to multiple neurodegenerative diseases. Electronic supplementary material The online version of this article (10.1186/s40035-018-0135-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- William R Swindell
- 1Heritage College of Osteopathic Medicine, Ohio University, Athens, OH USA
| | | | - Mark S Kindy
- 3Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, Tampa, FL USA.,4James A. Haley VAMC, Tampa, FL USA
| | | | - Dorothy Ko
- Genervon Biopharmaceuticals LLC, Pasadena, CA USA
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7
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Held F, Le Couteur DG, Blyth FM, Hirani V, Naganathan V, Waite LM, Seibel MJ, Handelsman DJ, Cumming RG, Allore HG, Gnjidic D. Polypharmacy in older adults: Association Rule and Frequent-Set Analysis to evaluate concomitant medication use. Pharmacol Res 2016; 116:39-44. [PMID: 27988385 DOI: 10.1016/j.phrs.2016.12.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 12/13/2016] [Indexed: 12/01/2022]
Abstract
The aim of this study was to apply Association Rule and Frequent-Set analysis, and novel means of data visualisation to ascertain patterns of medication use and medication combinations contributing to medication group clusters according to geriatric syndrome status in older adults. Participants were community-dwelling men (aged ≥70 years, n=1686), Sydney, Australia. Medication exposure was categorised at medication class level and data were analysed according to geriatric syndrome status (presence of at least one syndrome including frailty, falls, cognitive impairment and urinary incontinence). Association Rule and Frequent-Set analysis were performed to identify "interesting" patterns of medication combinations that occur together. This analysis involves advanced computer algorithms that investigated all possible combinations of medications in the dataset in order to identify those which are observed more or much less frequently than expected. Frequent-Set Analysis demonstrated one unexpected medication combination, antiulcer and antidiabetic medications (3.5% of participants) in the overall population (n=1687). Frequency of medication combinations was similar in participants with (n=666) and without (n=1020) geriatric syndromes. Among participants with geriatric syndromes, the most frequent combinations included antigout with lipid-lowering agents (5.7%) followed by angiotensin II and diuretics combination (22%). This novel methodology can be used to detect common medication combinations overall by data visualisation, and against specific adverse drug reactions such as geriatric syndromes. This methodology may be a valuable pharmacovigilance approach to monitor large databases for the safety of medications.
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Affiliation(s)
- Fabian Held
- Charles Perkins Centre, University of Sydney, Sydney NSW, Australia
| | - David G Le Couteur
- Charles Perkins Centre, University of Sydney, Sydney NSW, Australia; Centre for Education and Research on Ageing, the Ageing and Alzheimers Institute, Concord Hospital and University of Sydney, Sydney NSW, Australia; ANZAC Research Institute, University of Sydney, New South Wales, Australia
| | - Fiona M Blyth
- Centre for Education and Research on Ageing, the Ageing and Alzheimers Institute, Concord Hospital and University of Sydney, Sydney NSW, Australia; School of Public Health, University of Sydney, Sydney NSW, Australia
| | - Vasant Hirani
- Centre for Education and Research on Ageing, the Ageing and Alzheimers Institute, Concord Hospital and University of Sydney, Sydney NSW, Australia
| | - Vasi Naganathan
- Centre for Education and Research on Ageing, the Ageing and Alzheimers Institute, Concord Hospital and University of Sydney, Sydney NSW, Australia
| | - Louise M Waite
- Centre for Education and Research on Ageing, the Ageing and Alzheimers Institute, Concord Hospital and University of Sydney, Sydney NSW, Australia
| | - Markus J Seibel
- ANZAC Research Institute, University of Sydney, New South Wales, Australia
| | - David J Handelsman
- ANZAC Research Institute, University of Sydney, New South Wales, Australia
| | - Robert G Cumming
- Centre for Education and Research on Ageing, the Ageing and Alzheimers Institute, Concord Hospital and University of Sydney, Sydney NSW, Australia; School of Public Health, University of Sydney, Sydney NSW, Australia
| | - Heather G Allore
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Danijela Gnjidic
- Charles Perkins Centre, University of Sydney, Sydney NSW, Australia; Faculty of Pharmacy, University of Sydney, Sydney NSW, Australia.
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8
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Rieder M, Ferro A. Adverse drug reactions. Br J Clin Pharmacol 2015; 80:613-4. [PMID: 26388499 DOI: 10.1111/bcp.12695] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 06/05/2015] [Indexed: 12/13/2022] Open
Affiliation(s)
- Michael Rieder
- Department of Paediatrics, University of Western Ontario, Canada
| | - Albert Ferro
- Department of Clinical Pharmacology, King's College London, UK
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9
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Li L, van der Graaf PH. Database: A New Article Type in CPT: Pharmacometrics & Systems Pharmacology. CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY 2015; 4:443-4. [PMID: 26380152 PMCID: PMC4562159 DOI: 10.1002/psp4.12004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 06/02/2015] [Indexed: 11/28/2022]
Affiliation(s)
- L Li
- Associate Editor, Center for Computational Biology and Bioinformatics, Department of Medical and Molecular Genetics, School of Medicine, Indiana University Indianapolis, USA
| | - P H van der Graaf
- Editor-in-Chief, Leiden Academic Centre for Drug Research (LACDR), Systems Pharmacology Leiden, The Netherlands
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