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Takundwa MM, Thimiri Govinda Raj DB. Novel strategies for drug repurposing. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 205:9-21. [PMID: 38789188 DOI: 10.1016/bs.pmbts.2024.03.021] [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: 05/26/2024]
Abstract
Synthetic biology, precision medicine, and nanobiotechnology are the three main emerging areas that drive translational innovation toward commercialization. There are several strategies used in precision medicine and drug repurposing is one of the key approaches as it addresses the challenges in drug discovery (high cost and time). Here, we provide a perspective on various new approaches to drug repurposing for cancer precision medicine. We report here our optimized wound healing methodology that can be used to validate drug sensitivity and drug repurposing. Using HeLa as our benchmark, we demonstrated that the assay can be applied to identify drugs that limit cell proliferation. From a future perspective, this assay can be expanded to ex vivo culturing of solid tumors in 2D culture and leukemia in 3D culture.
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Affiliation(s)
- Mutsa Monica Takundwa
- Synthetic Nanobiotechnology and Biomachines, Synthetic Biology and Precision Medicine Centre, Future Production Chemicals Cluster, Council for Scientific and Industrial Research, Pretoria, South Africa
| | - Deepak B Thimiri Govinda Raj
- Synthetic Nanobiotechnology and Biomachines, Synthetic Biology and Precision Medicine Centre, Future Production Chemicals Cluster, Council for Scientific and Industrial Research, Pretoria, South Africa.
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2
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Cao Q, Du X, Jiang XY, Tian Y, Gao CH, Liu ZY, Xu T, Tao XX, Lei M, Wang XQ, Ye LL, Duan DD. Phenome-wide association study and precision medicine of cardiovascular diseases in the post-COVID-19 era. Acta Pharmacol Sin 2023; 44:2347-2357. [PMID: 37532784 PMCID: PMC10692238 DOI: 10.1038/s41401-023-01119-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 05/29/2023] [Indexed: 08/04/2023] Open
Abstract
SARS-CoV-2 infection causes injuries of not only the lungs but also the heart and endothelial cells in vasculature of multiple organs, and induces systemic inflammation and immune over-reactions, which makes COVID-19 a disease phenome that simultaneously affects multiple systems. Cardiovascular diseases (CVD) are intrinsic risk and causative factors for severe COVID-19 comorbidities and death. The wide-spread infection and reinfection of SARS-CoV-2 variants and the long-COVID may become a new common threat to human health and propose unprecedented impact on the risk factors, pathophysiology, and pharmacology of many diseases including CVD for a long time. COVID-19 has highlighted the urgent demand for precision medicine which needs new knowledge network to innovate disease taxonomy for more precise diagnosis, therapy, and prevention of disease. A deeper understanding of CVD in the setting of COVID-19 phenome requires a paradigm shift from the current phenotypic study that focuses on the virus or individual symptoms to phenomics of COVID-19 that addresses the inter-connectedness of clinical phenotypes, i.e., clinical phenome. Here, we summarize the CVD manifestations in the full clinical spectrum of COVID-19, and the phenome-wide association study of CVD interrelated to COVID-19. We discuss the underlying biology for CVD in the COVID-19 phenome and the concept of precision medicine with new phenomic taxonomy that addresses the overall pathophysiological responses of the body to the SARS-CoV-2 infection. We also briefly discuss the unique taxonomy of disease as Zheng-hou patterns in traditional Chinese medicine, and their potential implications in precision medicine of CVD in the post-COVID-19 era.
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Affiliation(s)
- Qian Cao
- Center for Phenomics of Traditional Chinese Medicine, the Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646000, China
| | - Xin Du
- Center for Phenomics of Traditional Chinese Medicine, the Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646000, China
| | - Xiao-Yan Jiang
- Center for Phenomics of Traditional Chinese Medicine, the Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646000, China
| | - Yuan Tian
- Center for Phenomics of Traditional Chinese Medicine, the Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646000, China
| | - Chen-Hao Gao
- Center for Phenomics of Traditional Chinese Medicine, the Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646000, China
| | - Zi-Yu Liu
- Center for Phenomics of Traditional Chinese Medicine, the Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646000, China
| | - Ting Xu
- Center for Phenomics of Traditional Chinese Medicine, the Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646000, China
| | - Xing-Xing Tao
- Center for Phenomics of Traditional Chinese Medicine, the Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646000, China
| | - Ming Lei
- Center for Phenomics of Traditional Chinese Medicine, the Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646000, China
| | - Xiao-Qiang Wang
- Center for Phenomics of Traditional Chinese Medicine, the Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646000, China
| | - Lingyu Linda Ye
- Center for Phenomics of Traditional Chinese Medicine, the Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646000, China.
- Institute of Integrated Chinese and Western Medicine, Southwest Medical University, Luzhou, 646000, China.
- Key Laboratory of Autoimmune Diseases and Precision Medicie, People's Hospital of Ningxia Hui Autonomous Region, Yinchuan, 750001, China.
| | - Dayue Darrel Duan
- Center for Phenomics of Traditional Chinese Medicine, the Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, 646000, China.
- Institute of Integrated Chinese and Western Medicine, Southwest Medical University, Luzhou, 646000, China.
- Key Laboratory of Autoimmune Diseases and Precision Medicie, People's Hospital of Ningxia Hui Autonomous Region, Yinchuan, 750001, China.
- The Department of Pharmacology, University of Nevada Reno School of Medicine, Reno, NV, 89557, USA.
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3
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Ying W. Phenomic Studies on Diseases: Potential and Challenges. PHENOMICS (CHAM, SWITZERLAND) 2023; 3:285-299. [PMID: 36714223 PMCID: PMC9867904 DOI: 10.1007/s43657-022-00089-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 11/21/2022] [Accepted: 11/24/2022] [Indexed: 01/23/2023]
Abstract
The rapid development of such research field as multi-omics and artificial intelligence (AI) has made it possible to acquire and analyze the multi-dimensional big data of human phenomes. Increasing evidence has indicated that phenomics can provide a revolutionary strategy and approach for discovering new risk factors, diagnostic biomarkers and precision therapies of diseases, which holds profound advantages over conventional approaches for realizing precision medicine: first, the big data of patients' phenomes can provide remarkably richer information than that of the genomes; second, phenomic studies on diseases may expose the correlations among cross-scale and multi-dimensional phenomic parameters as well as the mechanisms underlying the correlations; and third, phenomics-based studies are big data-driven studies, which can significantly enhance the possibility and efficiency for generating novel discoveries. However, phenomic studies on human diseases are still in early developmental stage, which are facing multiple major challenges and tasks: first, there is significant deficiency in analytical and modeling approaches for analyzing the multi-dimensional data of human phenomes; second, it is crucial to establish universal standards for acquirement and management of phenomic data of patients; third, new methods and devices for acquirement of phenomic data of patients under clinical settings should be developed; fourth, it is of significance to establish the regulatory and ethical guidelines for phenomic studies on diseases; and fifth, it is important to develop effective international cooperation. It is expected that phenomic studies on diseases would profoundly and comprehensively enhance our capacity in prevention, diagnosis and treatment of diseases.
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Affiliation(s)
- Weihai Ying
- Med-X Research Institute and School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Huashan Road, Shanghai, 200030 China
- Collaborative Innovation Center for Genetics and Development, Shanghai, 200043 China
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4
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Statzer C, Luthria K, Sharma A, Kann MG, Ewald CY. The Human Extracellular Matrix Diseasome Reveals Genotype-Phenotype Associations with Clinical Implications for Age-Related Diseases. Biomedicines 2023; 11:biomedicines11041212. [PMID: 37189830 DOI: 10.3390/biomedicines11041212] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/07/2023] [Accepted: 04/14/2023] [Indexed: 05/17/2023] Open
Abstract
The extracellular matrix (ECM) is earning an increasingly relevant role in many disease states and aging. The analysis of these disease states is possible with the GWAS and PheWAS methodologies, and through our analysis, we aimed to explore the relationships between polymorphisms in the compendium of ECM genes (i.e., matrisome genes) in various disease states. A significant contribution on the part of ECM polymorphisms is evident in various types of disease, particularly those in the core-matrisome genes. Our results confirm previous links to connective-tissue disorders but also unearth new and underexplored relationships with neurological, psychiatric, and age-related disease states. Through our analysis of the drug indications for gene-disease relationships, we identify numerous targets that may be repurposed for age-related pathologies. The identification of ECM polymorphisms and their contributions to disease will play an integral role in future therapeutic developments, drug repurposing, precision medicine, and personalized care.
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Affiliation(s)
- Cyril Statzer
- Department of Health Sciences and Technology, Institute of Translational Medicine, Eidgenössische Technische Hochschule Zürich, Schwerzenbach, CH-8603 Zurich, Switzerland
| | - Karan Luthria
- Department of Biological Sciences, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Arastu Sharma
- Department of Health Sciences and Technology, Institute of Translational Medicine, Eidgenössische Technische Hochschule Zürich, Schwerzenbach, CH-8603 Zurich, Switzerland
| | - Maricel G Kann
- Department of Biological Sciences, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Collin Y Ewald
- Department of Health Sciences and Technology, Institute of Translational Medicine, Eidgenössische Technische Hochschule Zürich, Schwerzenbach, CH-8603 Zurich, Switzerland
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Tan GSQ, Sloan EK, Lambert P, Kirkpatrick CMJ, Ilomäki J. Drug repurposing using real-world data. Drug Discov Today 2023; 28:103422. [PMID: 36341896 DOI: 10.1016/j.drudis.2022.103422] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 06/18/2022] [Accepted: 10/25/2022] [Indexed: 02/02/2023]
Abstract
The use of real-world data in drug repurposing has emerged due to well-established advantages of drug repurposing in supplementing de novo drug discovery and incentives in incorporating real-world evidence in regulatory approvals. We conducted a scoping review to characterize repurposing studies using real-world data and discuss their potential challenges and solutions. A total of 250 studies met the inclusion criteria, of which 36 were original studies on hypothesis generation, 101 on hypothesis validation, and seven on safety assessment. Key challenges that should be addressed for future progress in using real-world data for repurposing include isolated data sources with poor clinical granularity, false-positive signals from data mining, the sensitivity of hypothesis validation to bias and confounding, and the lack of clear regulatory guidance.
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Affiliation(s)
- George S Q Tan
- Centre for Medicine Use and Safety, Monash University, Parkville, Victoria, Australia
| | - Erica K Sloan
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Pete Lambert
- Drug Delivery Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Carl M J Kirkpatrick
- Centre for Medicine Use and Safety, Monash University, Parkville, Victoria, Australia.
| | - Jenni Ilomäki
- Centre for Medicine Use and Safety, Monash University, Parkville, Victoria, Australia.
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Campbell MS, Bastarache LA, Van Driest SL, Adgent MA, Goldstein JA, Weitkamp JH, Ransom MA, Lister RL, Shelton EL, Sucre JMS. Bronchopulmonary dysplasia is associated with polyhydramnios in a scan for novel perinatal risk factors. Pediatr Res 2023; 93:154-159. [PMID: 35393523 PMCID: PMC9537351 DOI: 10.1038/s41390-022-02043-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 02/28/2022] [Accepted: 03/10/2022] [Indexed: 02/05/2023]
Abstract
BACKGROUND The pathogenesis of bronchopulmonary dysplasia (BPD) is multifactorial, and there are limited data about prenatal exposures and risk of BPD. STUDY DESIGN Our study performed parallel analyses using a logistic regression model in a cohort of 4527 infants with data from a curated registry and using a phenome wide association study (PheWAS) based on ICD9/10-based phecodes. We examined 20 prenatal exposures from a neonatal intensive care unit (NICU) curated registry database related to pregnancy and maternal health as well as 94 maternal diagnosis phecodes with a PheWAS analysis. RESULT In both the curated registry and PheWAS analyses, polyhydramnios was associated with an increased risk of BPD (OR 5.70, 95% CI 2.78-11.44, p = 1.37 × 10-6). CONCLUSION Our data suggest that polyhydramnios may be a clinical indicator of premature infants at increased risk for bronchopulmonary dysplasia. Combining curated registry data with PheWAS analysis creates a valuable tool to generate hypotheses. IMPACT Polyhydramnios was significantly associated with bronchopulmonary dysplasia in both a curated registry and by ICD coding analysis with a phenome wide association study (PheWAS). Preterm polyhydramnios may be a clinical indicator of infants at increased risk for developing bronchopulmonary dysplasia after preterm birth. Combining curated registry with PheWAS analysis creates a valuable tool to generate hypotheses about perinatal risk factors and morbidities associated with preterm birth.
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Affiliation(s)
- Meredith S Campbell
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Lisa A Bastarache
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Sara L Van Driest
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Margaret A Adgent
- Department of Health Policy, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | | | - Meaghan A Ransom
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Rolanda L Lister
- Department of Obstetrics and Gynecology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Elaine L Shelton
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jennifer M S Sucre
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA.
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN, USA.
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7
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Portelli MA, Rakkar K, Hu S, Guo Y, Adcock IM, Sayers I. Translational Analysis of Moderate to Severe Asthma GWAS Signals Into Candidate Causal Genes and Their Functional, Tissue-Dependent and Disease-Related Associations. FRONTIERS IN ALLERGY 2022; 2:738741. [PMID: 35386986 PMCID: PMC8974692 DOI: 10.3389/falgy.2021.738741] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 09/06/2021] [Indexed: 12/23/2022] Open
Abstract
Asthma affects more than 300 million people globally and is both under diagnosed and under treated. The most recent and largest genome-wide association study investigating moderate to severe asthma to date was carried out in 2019 and identified 25 independent signals. However, as new and in-depth downstream databases become available, the translational analysis of these signals into target genes and pathways is timely. In this study, unique (U-BIOPRED) and publicly available datasets (HaploReg, Open Target Genetics and GTEx) were investigated for the 25 GWAS signals to identify 37 candidate causal genes. Additional traits associated with these signals were identified through PheWAS using the UK Biobank resource, with asthma and eosinophilic traits amongst the strongest associated. Gene expression omnibus dataset examination identified 13 candidate genes with altered expression profiles in the airways and blood of asthmatic subjects, including MUC5AC and STAT6. Gene expression analysis through publicly available datasets highlighted lung tissue cell specific expression, with both MUC5AC and SLC22A4 genes showing enriched expression in ciliated cells. Gene enrichment pathway and interaction analysis highlighted the dominance of the HLA-DQA1/A2/B1/B2 gene cluster across many immunological diseases including asthma, type I diabetes, and rheumatoid arthritis. Interaction and prediction analyses found IL33 and IL18R1 to be key co-localization partners for other genes, predicted that CD274 forms co-expression relationships with 13 other genes, including the HLA-DQA1/A2/B1/B2 gene cluster and that MUC5AC and IL37 are co-expressed. Drug interaction analysis revealed that 11 of the candidate genes have an interaction with available therapeutics. This study provides significant insight into these GWAS signals in the context of cell expression, function, and disease relationship with the view of informing future research and drug development efforts for moderate-severe asthma.
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Affiliation(s)
- Michael A Portelli
- Centre for Respiratory Research, Translational Medical Sciences, School of Medicine, National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham University Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Kamini Rakkar
- Centre for Respiratory Research, Translational Medical Sciences, School of Medicine, National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham University Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Sile Hu
- Data Science Institute, Imperial College London, London, United Kingdom
| | - Yike Guo
- Data Science Institute, Imperial College London, London, United Kingdom
| | - Ian M Adcock
- The National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Ian Sayers
- Centre for Respiratory Research, Translational Medical Sciences, School of Medicine, National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham University Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
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8
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Choe EK, Shivakumar M, Verma A, Verma SS, Choi SH, Kim JS, Kim D. Leveraging deep phenotyping from health check-up cohort with 10,000 Korean individuals for phenome-wide association study of 136 traits. Sci Rep 2022; 12:1930. [PMID: 35121771 PMCID: PMC8817039 DOI: 10.1038/s41598-021-04580-2] [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: 08/16/2021] [Accepted: 12/17/2021] [Indexed: 11/09/2022] Open
Abstract
The expanding use of the phenome-wide association study (PheWAS) faces challenges in the context of using International Classification of Diseases billing codes for phenotype definition, imbalanced study population ethnicity, and constrained application of the results in research. We performed a PheWAS utilizing 136 deep phenotypes corroborated by comprehensive health check-ups in a Korean population, along with trans-ethnic comparisons through using the UK Biobank and Biobank Japan Project. Meta-analysis with Korean and Japanese population was done. The PheWAS associated 65 phenotypes with 14,101 significant variants (P < 4.92 × 10-10). Network analysis, visualization of cross-phenotype mapping, and causal inference mapping with Mendelian randomization were conducted. Among phenotype pairs from the genotype-driven cross-phenotype associations, we evaluated penetrance in correlation analysis using a clinical database. We focused on the application of PheWAS in order to make it robust and to aid the derivation of biological meaning post-PheWAS. This comprehensive analysis of PheWAS results based on a health check-up database will provide researchers and clinicians with a panoramic overview of the networks among multiple phenotypes and genetic variants, laying groundwork for the practical application of precision medicine.
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Affiliation(s)
- Eun Kyung Choe
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, B304 Richards Building, 3700 Hamilton Walk, Philadelphia, PA, 19104-6116, USA.,Department of Surgery, Seoul National University Hospital Healthcare System Gangnam Center, Seoul, 06236, South Korea
| | - Manu Shivakumar
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, B304 Richards Building, 3700 Hamilton Walk, Philadelphia, PA, 19104-6116, USA
| | - Anurag Verma
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Shefali Setia Verma
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Seung Ho Choi
- Department of Internal Medicine, Seoul National University Hospital Healthcare System Gangnam Center, Seoul, 06236, South Korea
| | - Joo Sung Kim
- Department of Internal Medicine, Seoul National University Hospital Healthcare System Gangnam Center, Seoul, 06236, South Korea. .,Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul, 03080, South Korea.
| | - Dokyoon Kim
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, B304 Richards Building, 3700 Hamilton Walk, Philadelphia, PA, 19104-6116, USA. .,Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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9
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Abstract
Electronic health records (EHRs) are a rich source of data for researchers, but extracting meaningful information out of this highly complex data source is challenging. Phecodes represent one strategy for defining phenotypes for research using EHR data. They are a high-throughput phenotyping tool based on ICD (International Classification of Diseases) codes that can be used to rapidly define the case/control status of thousands of clinically meaningful diseases and conditions. Phecodes were originally developed to conduct phenome-wide association studies to scan for phenotypic associations with common genetic variants. Since then, phecodes have been used to support a wide range of EHR-based phenotyping methods, including the phenotype risk score. This review aims to comprehensively describe the development, validation, and applications of phecodes and suggest some future directions for phecodes and high-throughput phenotyping.
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Affiliation(s)
- Lisa Bastarache
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA;
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10
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Martucci VL, Richmond B, Davis LK, Blackwell TS, Cox NJ, Samuels D, Velez Edwards D, Aldrich MC. Fate or coincidence: do COPD and major depression share genetic risk factors? Hum Mol Genet 2021; 30:619-628. [PMID: 33704461 PMCID: PMC8120137 DOI: 10.1093/hmg/ddab068] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 02/24/2021] [Accepted: 02/27/2021] [Indexed: 01/12/2023] Open
Abstract
Major depressive disorder (MDD) is a common comorbidity in chronic obstructive pulmonary disease (COPD), affecting up to 57% of patients with COPD. Although the comorbidity of COPD and MDD is well established, the causal relationship between these two diseases is unclear. A large-scale electronic health record clinical biobank and genome-wide association study summary statistics for MDD and lung function traits were used to investigate potential shared underlying genetic susceptibility between COPD and MDD. Linkage disequilibrium score regression was used to estimate genetic correlation between phenotypes. Polygenic risk scores (PRS) for MDD and lung function traits were developed and used to perform a phenome-wide association study (PheWAS). Multi-trait-based conditional and joint analysis identified single-nucleotide polymorphisms (SNPs) influencing both lung function and MDD. We found genetic correlations between MDD and all lung function traits were small and not statistically significant. A PRS-MDD was significantly associated with an increased risk of COPD in a PheWAS [odds ratio (OR) = 1.12, 95% confidence interval (CI): 1.09-1.16] when adjusting for age, sex and genetic ancestry, but this relationship became attenuated when controlling for smoking history (OR = 1.08, 95% CI: 1.04-1.13). No significant associations were found between the lung function PRS and MDD. Multi-trait-based conditional and joint analysis identified three SNPs that may contribute to both traits, two of which were previously associated with mood disorders and COPD. Our findings suggest that the observed relationship between COPD and MDD may not be driven by a strong shared genetic architecture.
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Affiliation(s)
- Victoria L Martucci
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Bradley Richmond
- Department of Veterans Affairs Medical Center, Nashville, TN 37212, USA
- Division of Allergy, Pulmonary, and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Lea K Davis
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Psychiatry and Behavioral Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Timothy S Blackwell
- Department of Veterans Affairs Medical Center, Nashville, TN 37212, USA
- Division of Allergy, Pulmonary, and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Nancy J Cox
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - David Samuels
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Digna Velez Edwards
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Division of Quantitative Sciences, Department of Obstetrics and Gynecology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Melinda C Aldrich
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Division of Epidemiology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
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11
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Yoshimura K, Morita Y, Konomi K, Ishida S, Fujiwara D, Kobayashi K, Tanaka M. A web-based survey on various symptoms of computer vision syndrome and the genetic understanding based on a multi-trait genome-wide association study. Sci Rep 2021; 11:9446. [PMID: 33941792 PMCID: PMC8093242 DOI: 10.1038/s41598-021-88827-y] [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: 12/03/2020] [Accepted: 04/16/2021] [Indexed: 11/12/2022] Open
Abstract
A variety of eye-related symptoms due to the overuse of digital devices is collectively referred to as computer vision syndrome (CVS). In this study, a web-based survey about mind and body functions, including eye strain, was conducted on 1998 Japanese volunteers. To investigate the biological mechanisms behind CVS, a multi-trait genome-wide association study (GWAS), a multivariate analysis on individual-level multivariate data, was performed based on the structural equation modeling methodology assuming a causal pathway for a genetic variant to influence each symptom via a single common latent variable. Twelve loci containing lead variants with a suggestive level of significance were identified. Two loci showed relatively strong signals and were associated with TRABD2B relative to the Wnt signaling pathway and SDK1 having neuronal adhesion and immune functions, respectively. By utilizing publicly available eQTL data, colocalization between GWAS and eQTL signals for four loci was detected, and a locus on 2p25.3 showed a strong colocalization (PPH4 > 0.9) on retinal MYT1L, known to play an important role in neuronal differentiation. This study suggested that the use of multivariate questionnaire data and multi-trait GWAS can lead to biologically reasonable findings and enhance our genetic understanding of complex relationships among symptoms related to CVS.
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Affiliation(s)
| | - Yuji Morita
- Kirin Central Research Institute, Kirin Holdings Company, Limited, Yokohama, Japan.
| | - Kenji Konomi
- Clinical and Translational Research Center, Keio University Hospital, Tokyo, Japan
| | | | - Daisuke Fujiwara
- Health Science Department, Kirin Holdings Company, Limited, Tokyo, Japan
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12
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Erdmann J. What can we learn from common variants associated with unexpected phenotypes in rare genetic diseases? Orphanet J Rare Dis 2021; 16:41. [PMID: 33478553 PMCID: PMC7818908 DOI: 10.1186/s13023-021-01684-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 01/06/2021] [Indexed: 11/30/2022] Open
Abstract
The purpose of this article is to stimulate discussion about whether a phenome-wide association study is a suitable tool for uncovering late-onset risks in patients with monogenic disorders that are not yet fully recognized because the life expectancy of people with such conditions has only recently extended, and they now reach older ages when they may develop additional complications.
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Affiliation(s)
- Jeanette Erdmann
- Institute for Cardiogenetics, University of Lübeck, Ratzeburger Allee 160, Building 67, 23562, Lübeck, Germany.
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13
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Langlois PH, Schraw JM, Hoyt AT, Lupo PJ. Leveraging a phenome-wide approach to identify novel exposure-birth defect associations: A proof of concept using maternal smoking and a spectrum of birth defects. Birth Defects Res 2020; 113:439-445. [PMID: 33275842 DOI: 10.1002/bdr2.1851] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 11/07/2020] [Accepted: 11/08/2020] [Indexed: 11/06/2022]
Abstract
BACKGROUND There are often questions about the impact of exposures on a range of birth defects, but there are few rigorous approaches for evaluating these associations. Using maternal smoking as an example we applied a phenome-wide association study (PheWAS) approach to evaluate the impact of this exposure on a comprehensive range of birth defects. METHODS Cases were obtained from the Texas Birth Defects Registry for the period 1999-2015. A total of 127 birth defects were examined. Maternal smoking at any time during the pregnancy was ascertained from the vital record. Data were randomly divided into discovery (60%) and replication (40%) partitions. Poisson regression models were run in the discovery partition, using a Bonferroni threshold of p < 3.9×10-4 . Birth defects passing that threshold in adjusted models were evaluated in the replication partition using p < 0.05 to determine statistical significance. RESULTS Four birth defects were positively and significantly associated with maternal smoking in both partitions: cleft palate, anomalies of the pulmonary artery, other specified anomalies of the mouth and pharynx, and congenital hypertrophic pyloric stenosis. Obstructive defects of the renal pelvis and ureter showed consistent negative associations. All five defects exhibited significant dose-response relationships. CONCLUSIONS We demonstrated that a statistically rigorous approach can be applied to birth defects registry data to examine the association between specified exposures and a range of birth defects. While we confirmed previously reported associations, others were not validated, likely due to misclassification in exposure based on vital records.
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Affiliation(s)
- Peter H Langlois
- Division of Epidemiology, Human Genetics, and Environmental Sciences, University of Texas School of Public Health - Austin Regional Campus, Austin, Texas, USA
| | - Jeremy M Schraw
- Center for Epidemiology and Population Health, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA.,Section of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA.,Texas Children's Cancer and Hematology Centers, Texas Children's Hospital, Houston, Texas, USA
| | - Adrienne T Hoyt
- University of Texas School of Public Health - Austin Regional Campus, Austin, Texas, USA
| | - Philip J Lupo
- Center for Epidemiology and Population Health, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA.,Section of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA.,Texas Children's Cancer and Hematology Centers, Texas Children's Hospital, Houston, Texas, USA
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14
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Statzer C, Ewald CY. The extracellular matrix phenome across species. Matrix Biol Plus 2020; 8:100039. [PMID: 33543035 PMCID: PMC7852310 DOI: 10.1016/j.mbplus.2020.100039] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/11/2020] [Accepted: 05/26/2020] [Indexed: 12/12/2022] Open
Abstract
Extracellular matrices are essential for cellular and organismal function. Recent genome-wide and phenome-wide association studies started to reveal a broad spectrum of phenotypes associated with genetic variants. However, the phenome or spectrum of all phenotypes associated with genetic variants in extracellular matrix genes is unknown. Here, we analyzed over two million recorded genotype-to-phenotype relationships across multiple species to define their extracellular matrix phenomes. By using the previously defined matrisomes of humans, mice, zebrafish, Drosophila, and C. elegans, we found that the extracellular matrix phenome comprises of 3-10% of the entire phenome. Collagens (COL1A1, COL2A1) and fibrillin (FBN1) are each associated with >150 distinct phenotypes in humans, whereas collagen COL4A1, Wnt- and sonic hedgehog (shh) signaling are predominantly associated in other species. We determined the phenotypic fingerprints of matrisome genes and found that MSTN, CTSD, LAMB2, HSPG2, and COL11A2 and their corresponding orthologues have the most phenotypes across species. Out of the 42,551 unique matrisome genotype-to-phenotype relationships across the five species with defined matrisomes, we have constructed interaction networks to identify the underlying molecular components connecting with orthologues phenotypes and with novel phenotypes. Thus, our networks provide a framework to predict unassessed phenotypes and their potential underlying molecular interactions. These frameworks inform on matrisome genotype-to-phenotype relationships and potentially provide a sophisticated choice of biological model system to study human phenotypes and diseases.
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Affiliation(s)
- Cyril Statzer
- Eidgenössische Technische Hochschule Zürich, Department of Health Sciences and Technology, Institute of Translational Medicine, Schwerzenbach, Zürich CH-8603, Switzerland
| | - Collin Y. Ewald
- Eidgenössische Technische Hochschule Zürich, Department of Health Sciences and Technology, Institute of Translational Medicine, Schwerzenbach, Zürich CH-8603, Switzerland
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15
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A Comprehensive Assessment of the Associations Between Season of Conception and Birth Defects, Texas, 1999-2015. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17197120. [PMID: 33003294 PMCID: PMC7579376 DOI: 10.3390/ijerph17197120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 09/25/2020] [Accepted: 09/26/2020] [Indexed: 12/23/2022]
Abstract
Birth defects prevalence may vary seasonally, but previous studies have focused on a few commonly occurring phenotypes. We performed a phenome-wide association study (PheWAS) in order to evaluate the associations between season of conception and a broad range of birth defects. Date of conception was estimated for all livebirths and birth defect cases in Texas from 1999-2015 using data from vital records, provided by the Texas Department of State Health Services Center for Health Statistics. Birth defects diagnoses were obtained from the Texas Birth Defects Registry, a statewide, active surveillance system. We estimated prevalence ratios (PRs) for phenotypes with ≥50 cases according to conception in spring (March-May), summer (June-August) or fall (September-November) relative to winter (December-February), using Poisson regression. Season of conception was associated with 5% of birth defects studied in models adjusted for maternal age, education, race/ethnicity, and number of previous livebirths. Specifically, summer conception was associated with any monitored birth defect (PR 1.03, 95% CI 1.02-1.04) and five specific phenotypes, most notably Hirschsprung disease (PR 1.46, 95% CI 1.22-1.75). These findings suggest that seasonally variable exposures influence the development of several birth defects and may assist in identifying novel environmental risk factors.
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16
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Comprehensive assessment of the associations between maternal diabetes and structural birth defects in offspring: a phenome-wide association study. Ann Epidemiol 2020; 53:14-20.e8. [PMID: 32920098 DOI: 10.1016/j.annepidem.2020.08.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 08/07/2020] [Accepted: 08/10/2020] [Indexed: 12/16/2022]
Abstract
PURPOSE Our objective was to comprehensively evaluate the risk of a broad range of birth defects among offspring of women with diabetes, overall and stratified by pregestational versus gestational diagnosis, using the phenome-wide association (PheWAS) methodology. METHODS We performed a registry linkage study of all live births (>6,500,000) and birth defects cases (>290,000) in Texas, 1999-2015. We ascertained diabetes from birth and fetal death certificates. We calculated prevalence rate ratios (PRR) for phenotypes with ≥10 cases among exposed offspring (n = 130). RESULTS Diabetes was associated with the prevalence of any defect (PRR 1.40, 95% confidence interval [CI] 1.38-1.42), multiple defects (PRR 1.86, 95% CI 1.81-1.91), and 60 specific phenotypes, including novel (hypospadias, mitral stenosis) and previously reported phenotypes (renal a-/dysgenesis, spinal anomalies). Pregestational diabetes was a stronger risk factor for any defect (PRR 2.00, 95% CI 1.93-2.07), multiple defects (PRR 3.27, 95% CI 3.11-3.44), and the 60 specific phenotypes evaluated. Gestational diabetes was associated with any defect (PRR 1.21, 95% CI 1.19-1.23) and 47 specific birth defects phenotypes, although associations were weaker than for pregestational diabetes. CONCLUSIONS The PheWAS is an efficient way to identify risk factors for disease using population-based registry data. Pregestational diabetes is associated with a broader range of phenotypes than previously reported. Because diabetes is diagnosed in 1% of women prior to pregnancy and 6%-9% during pregnancy, our results highlight a significant public health concern.
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17
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Yang J, Wang Z, Liu S, Wang W, Zhang H, Gui C. Functional Characterization Reveals the Significance of Rare Coding Variations in Human Organic Anion Transporting Polypeptide 2B1 (SLCO2B1). Mol Pharm 2020; 17:3966-3978. [DOI: 10.1021/acs.molpharmaceut.0c00747] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Jingjie Yang
- College of Pharmaceutical Sciences, Soochow University, 199 Renai Road, Suzhou Industrial Park, Suzhou 215123, China
| | - Zhongmin Wang
- College of Pharmaceutical Sciences, Soochow University, 199 Renai Road, Suzhou Industrial Park, Suzhou 215123, China
| | - Shuai Liu
- College of Pharmaceutical Sciences, Soochow University, 199 Renai Road, Suzhou Industrial Park, Suzhou 215123, China
| | - Weipeng Wang
- College of Pharmaceutical Sciences, Soochow University, 199 Renai Road, Suzhou Industrial Park, Suzhou 215123, China
| | - Hongjian Zhang
- College of Pharmaceutical Sciences, Soochow University, 199 Renai Road, Suzhou Industrial Park, Suzhou 215123, China
| | - Chunshan Gui
- College of Pharmaceutical Sciences, Soochow University, 199 Renai Road, Suzhou Industrial Park, Suzhou 215123, China
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18
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King C, Mulugeta A, Nabi F, Walton R, Zhou A, Hyppönen E. Mendelian randomization case-control PheWAS in UK Biobank shows evidence of causality for smoking intensity in 28 distinct clinical conditions. EClinicalMedicine 2020; 26:100488. [PMID: 33089118 PMCID: PMC7564324 DOI: 10.1016/j.eclinm.2020.100488] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/14/2020] [Accepted: 07/15/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Smoking is one of the greatest threats to public health worldwide. We integrated phenome-wide association study (PheWAS) and Mendelian randomization (MR) approaches to explore causal effects of genetically predicted smoking intensity across the human disease spectrum. METHODS We conducted PheWAS case-control analyses in 152,483 ever smokers of White-British ancestry, aged 39-73 years. Disease diagnoses were based on hospital inpatient and mortality registrations. Smoking intensity was instrumented by four genetic variants, and disease risks estimated for one cigarette per day heavier intakes. Associations passing the FDR threshold (p<0•0025) were assessed for causality using several complementary MR approaches. FINDINGS Genetically instrumented smoking intensity was associated with 48 conditions, with MR supporting a possible causal effect for 28 distinct outcomes. Each cigarette smoked per day elevated the odds of respiratory diseases by 5% to 33% (nine distinct diseases, including pneumonia, emphysema, obstructive chronic bronchitis, pleurisy, pulmonary collapse, respiratory failure) and the odds of circulatory disease by 5% to 23% (seven diseases, including atherosclerosis, myocardial infarction, congestive heart failure, arterial embolisms). Further effects were seen for cancer within the respiratory system and other neoplasms, renal failure, septicaemia, and retinal disorders. No associations were observed in sensitivity analyses on 185,002 never smokers. INTERPRETATION These genetic data demonstrate the substantial adverse health impacts by smoking intensity and suggest notable increases in the risks of several diseases. Public health initiatives should highlight the damage caused by smoking intensity and the potential benefits of reducing or ideally quitting smoking.
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Affiliation(s)
- Catherine King
- Australian Centre for Precision Health, University of South Australia Cancer Research Institute, Adelaide, SA 5001, Australia
- South Australian Health and Medical Research Institute, Adelaide, Australia
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
| | - Anwar Mulugeta
- Australian Centre for Precision Health, University of South Australia Cancer Research Institute, Adelaide, SA 5001, Australia
- South Australian Health and Medical Research Institute, Adelaide, Australia
- Department of Pharmacology and Clinical Sciences, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Farhana Nabi
- Australian Centre for Precision Health, University of South Australia Cancer Research Institute, Adelaide, SA 5001, Australia
| | - Robert Walton
- Asthma UK Centre for Applied Research, Barts Institute of Population Health Sciences, Queen Mary University of London, London, United Kingdom
| | - Ang Zhou
- Australian Centre for Precision Health, University of South Australia Cancer Research Institute, Adelaide, SA 5001, Australia
- South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Elina Hyppönen
- Australian Centre for Precision Health, University of South Australia Cancer Research Institute, Adelaide, SA 5001, Australia
- South Australian Health and Medical Research Institute, Adelaide, Australia
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, SA, Australia
- Corresponding author.
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19
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Unlu G, Qi X, Gamazon ER, Melville DB, Patel N, Rushing AR, Hashem M, Al-Faifi A, Chen R, Li B, Cox NJ, Alkuraya FS, Knapik EW. Phenome-based approach identifies RIC1-linked Mendelian syndrome through zebrafish models, biobank associations and clinical studies. Nat Med 2020; 26:98-109. [PMID: 31932796 PMCID: PMC7147997 DOI: 10.1038/s41591-019-0705-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 11/15/2019] [Indexed: 12/17/2022]
Abstract
Discovery of genotype-phenotype relationships remains a major challenge in clinical medicine. Here, we combined three sources of phenotypic data to uncover a novel mechanism for rare and common diseases resulting from collagen secretion deficits. Using zebrafish genetic screen, we identified the ric1 gene to be essential for skeletal biology. Using a gene-based phenome-wide association study (PheWAS) in the EHR-linked BioVU biobank, we show that reduced genetically determined expression of RIC1 is associated with musculoskeletal and dental conditions. Whole exome sequencing (WES) identified individuals homozygous-by-descent for a rare variant in RIC1, and, through a guided clinical re-evaluation, they were discovered to share signs with the BioVU-associated phenome. We named this novel Mendelian syndrome CATIFA (Cleft lip, cAtaract, Tooth abnormality, Intellectual disability, Facial dysmorphism, ADHD), and revealed further disease mechanisms. This gene-based PheWAS-guided approach can accelerate the discovery of clinically relevant disease phenome and associated biological mechanisms.
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Affiliation(s)
- Gokhan Unlu
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA.,Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Xinzi Qi
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Eric R Gamazon
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA.,Clare Hall, University of Cambridge, Cambridge, UK
| | - David B Melville
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Molecular and Cellular Biology, Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | - Nisha Patel
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Amy R Rushing
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mais Hashem
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Abdullah Al-Faifi
- Department of Pediatrics, Security Forces Hospital, Riyadh, Saudi Arabia
| | - Rui Chen
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Bingshan Li
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Nancy J Cox
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.,Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ela W Knapik
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA. .,Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA. .,Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA.
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20
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Abdellaoui A, Sanchez-Roige S, Sealock J, Treur JL, Dennis J, Fontanillas P, Elson S, Nivard MG, Ip HF, van der Zee M, Baselmans BML, Hottenga JJ, Willemsen G, Mosing M, Lu Y, Pedersen NL, Denys D, Amin N, M van Duijn C, Szilagyi I, Tiemeier H, Neumann A, Verweij KJH, Cacioppo S, Cacioppo JT, Davis LK, Palmer AA, Boomsma DI. Phenome-wide investigation of health outcomes associated with genetic predisposition to loneliness. Hum Mol Genet 2019; 28:3853-3865. [PMID: 31518406 PMCID: PMC6935385 DOI: 10.1093/hmg/ddz219] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 07/24/2019] [Accepted: 08/21/2019] [Indexed: 12/31/2022] Open
Abstract
Humans are social animals that experience intense suffering when they perceive a lack of social connection. Modern societies are experiencing an epidemic of loneliness. Although the experience of loneliness is universally human, some people report experiencing greater loneliness than others. Loneliness is more strongly associated with mortality than obesity, emphasizing the need to understand the nature of the relationship between loneliness and health. Although it is intuitive that circumstantial factors such as marital status and age influence loneliness, there is also compelling evidence of a genetic predisposition toward loneliness. To better understand the genetic architecture of loneliness and its relationship with associated outcomes, we extended the genome-wide association study meta-analysis of loneliness to 511 280 subjects, and detect 19 significant genetic variants from 16 loci, including four novel loci, as well as 58 significantly associated genes. We investigated the genetic overlap with a wide range of physical and mental health traits by computing genetic correlations and by building loneliness polygenic scores in an independent sample of 18 498 individuals with EHR data to conduct a PheWAS with. A genetic predisposition toward loneliness was associated with cardiovascular, psychiatric, and metabolic disorders and triglycerides and high-density lipoproteins. Mendelian randomization analyses showed evidence of a causal, increasing, the effect of both BMI and body fat on loneliness. Our results provide a framework for future studies of the genetic basis of loneliness and its relationship to mental and physical health.
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Affiliation(s)
- Abdel Abdellaoui
- Department of Psychiatry, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Department of Biological Psychology, Vrije Universiteit, Amsterdam, The Netherlands
| | | | - Julia Sealock
- Vanderbilt Genetics Institute, Division of Genetic Medicine, Department of Medicine, Vanderbilt University, Nashville, TN, USA
| | - Jorien L Treur
- Department of Psychiatry, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- School of Experimental Psychology, University of Bristol, Bristol, UK
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Jessica Dennis
- Vanderbilt Genetics Institute, Division of Genetic Medicine, Department of Medicine, Vanderbilt University, Nashville, TN, USA
| | | | | | | | - Michel G Nivard
- Department of Biological Psychology, Vrije Universiteit, Amsterdam, The Netherlands
| | - Hill Fung Ip
- Department of Biological Psychology, Vrije Universiteit, Amsterdam, The Netherlands
| | - Matthijs van der Zee
- Department of Biological Psychology, Vrije Universiteit, Amsterdam, The Netherlands
| | - Bart M L Baselmans
- Department of Biological Psychology, Vrije Universiteit, Amsterdam, The Netherlands
| | - Jouke Jan Hottenga
- Department of Biological Psychology, Vrije Universiteit, Amsterdam, The Netherlands
| | - Gonneke Willemsen
- Department of Biological Psychology, Vrije Universiteit, Amsterdam, The Netherlands
| | - Miriam Mosing
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Yi Lu
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Nancy L Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Damiaan Denys
- Department of Psychiatry, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Najaf Amin
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Cornelia M van Duijn
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Translational Epidemiology, Faculty Science, Leiden University, Leiden, The Netherlands
| | - Ingrid Szilagyi
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Henning Tiemeier
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Psychiatry, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Alexander Neumann
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Karin J H Verweij
- Department of Psychiatry, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Stephanie Cacioppo
- Center for Cognitive and Social Neuroscience, Department of Psychology, The University of Chicago, Chicago, Illinois, USA
| | - John T Cacioppo
- Center for Cognitive and Social Neuroscience, Department of Psychology, The University of Chicago, Chicago, Illinois, USA
| | - Lea K Davis
- Vanderbilt Genetics Institute, Division of Genetic Medicine, Department of Medicine, Vanderbilt University, Nashville, TN, USA
| | - Abraham A Palmer
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit, Amsterdam, The Netherlands
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21
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Gu HF. Genetic and Epigenetic Studies in Diabetic Kidney Disease. Front Genet 2019; 10:507. [PMID: 31231424 PMCID: PMC6566106 DOI: 10.3389/fgene.2019.00507] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 05/08/2019] [Indexed: 01/19/2023] Open
Abstract
Chronic kidney disease is a worldwide health crisis, while diabetic kidney disease (DKD) has become the leading cause of end-stage renal disease (ESRD). DKD is a microvascular complication and occurs in 30–40% of diabetes patients. Epidemiological investigations and clinical observations on the familial clustering and heritability in DKD have highlighted an underlying genetic susceptibility. Furthermore, DKD is a progressive and long-term diabetic complication, in which epigenetic effects and environmental factors interact with an individual’s genetic background. In recent years, researchers have undertaken genetic and epigenetic studies of DKD in order to better understand its molecular mechanisms. In this review, clinical material, research approaches and experimental designs that have been used for genetic and epigenetic studies of DKD are described. Current information from genetic and epigenetic studies of DKD and ESRD in patients with diabetes, including the approaches of genome-wide association study (GWAS) or epigenome-wide association study (EWAS) and candidate gene association analyses, are summarized. Further investigation of molecular defects in DKD with new approaches such as next generation sequencing analysis and phenome-wide association study (PheWAS) is also discussed.
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Affiliation(s)
- Harvest F Gu
- Center for Pathophysiology, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, China
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22
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Genomic and Phenomic Research in the 21st Century. Trends Genet 2018; 35:29-41. [PMID: 30342790 DOI: 10.1016/j.tig.2018.09.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 09/24/2018] [Accepted: 09/25/2018] [Indexed: 02/06/2023]
Abstract
The field of human genomics has changed dramatically over time. Initial genomic studies were predominantly restricted to rare disorders in small families. Over the past decade, researchers changed course from family-based studies and instead focused on common diseases and traits in populations of unrelated individuals. With further advancements in biobanking, computer science, electronic health record (EHR) data, and more affordable high-throughput genomics, we are experiencing a new paradigm in human genomic research. Rapidly changing technologies and resources now make it possible to study thousands of diseases simultaneously at the genomic level. This review will focus on these advancements as scientists begin to incorporate phenome-wide strategies in human genomic research to understand the etiology of human diseases and develop new drugs to treat them.
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23
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Phenome-wide association studies across large population cohorts support drug target validation. Nat Commun 2018; 9:4285. [PMID: 30327483 PMCID: PMC6191429 DOI: 10.1038/s41467-018-06540-3] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 09/05/2018] [Indexed: 12/12/2022] Open
Abstract
Phenome-wide association studies (PheWAS) have been proposed as a possible aid in drug development through elucidating mechanisms of action, identifying alternative indications, or predicting adverse drug events (ADEs). Here, we select 25 single nucleotide polymorphisms (SNPs) linked through genome-wide association studies (GWAS) to 19 candidate drug targets for common disease indications. We interrogate these SNPs by PheWAS in four large cohorts with extensive health information (23andMe, UK Biobank, FINRISK, CHOP) for association with 1683 binary endpoints in up to 697,815 individuals and conduct meta-analyses for 145 mapped disease endpoints. Our analyses replicate 75% of known GWAS associations (P < 0.05) and identify nine study-wide significant novel associations (of 71 with FDR < 0.1). We describe associations that may predict ADEs, e.g., acne, high cholesterol, gout, and gallstones with rs738409 (p.I148M) in PNPLA3 and asthma with rs1990760 (p.T946A) in IFIH1. Our results demonstrate PheWAS as a powerful addition to the toolkit for drug discovery. Testing the association between genetic variants and a range of phenotypes can assist drug development. Here, in a phenome-wide association study in up to 697,815 individuals, Diogo et al. identify genotype–phenotype associations predicting efficacy, alternative indications or adverse drug effects.
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25
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Ng FL, Warren HR, Caulfield MJ. Hypertension genomics and cardiovascular prevention. ANNALS OF TRANSLATIONAL MEDICINE 2018; 6:291. [PMID: 30211179 DOI: 10.21037/atm.2018.06.34] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Hypertension continues to be a major risk factor for global mortality, and recent genome-wide association studies (GWAS) have expanded in size, leading to the identification of further genetic loci influencing blood pressure. In light of the new knowledge from the largest cardiovascular GWAS to date, we review the potential impact of genomics on discovering potential drug targets, risk stratification with genetic risk scores, drug selection with pharmacogenetics, and exploring insights provided by gene-environment interactions.
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Affiliation(s)
- Fu Liang Ng
- William Harvey Research Institute, The NIHR Biomedical Research Centre at Barts, Queen Mary University London, London, UK.,Barts BP Centre of Excellence, Barts Heart Centre, The NIHR Biomedical Research Centre at Barts, St Bartholomew's Hospital, W Smithfield, London, UK
| | - Helen R Warren
- William Harvey Research Institute, The NIHR Biomedical Research Centre at Barts, Queen Mary University London, London, UK
| | - Mark J Caulfield
- William Harvey Research Institute, The NIHR Biomedical Research Centre at Barts, Queen Mary University London, London, UK.,Barts BP Centre of Excellence, Barts Heart Centre, The NIHR Biomedical Research Centre at Barts, St Bartholomew's Hospital, W Smithfield, London, UK
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26
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Robinson JR, Denny JC, Roden DM, Van Driest SL. Genome-wide and Phenome-wide Approaches to Understand Variable Drug Actions in Electronic Health Records. Clin Transl Sci 2018; 11:112-122. [PMID: 29148204 PMCID: PMC5866959 DOI: 10.1111/cts.12522] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 10/14/2017] [Indexed: 12/24/2022] Open
Affiliation(s)
- Jamie R. Robinson
- Department of Biomedical InformaticsVanderbilt University Medical CenterNashvilleTennesseeUSA
- Department of SurgeryVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Joshua C. Denny
- Department of Biomedical InformaticsVanderbilt University Medical CenterNashvilleTennesseeUSA
- Department of MedicineVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Dan M. Roden
- Department of Biomedical InformaticsVanderbilt University Medical CenterNashvilleTennesseeUSA
- Department of MedicineVanderbilt University Medical CenterNashvilleTennesseeUSA
- Department of PharmacologyVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Sara L. Van Driest
- Department of MedicineVanderbilt University Medical CenterNashvilleTennesseeUSA
- Department of PediatricsVanderbilt University Medical CenterNashvilleTennesseeUSA
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27
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Abstract
PURPOSE OF REVIEW Over many decades, researchers have been designing studies to investigate the relationship between genotypes and phenotypes to gain an understanding about the effect of genetics on disease. Recently, a high-throughput approach called phenome-wide associations studies (PheWAS) have been extensively used to identify associations between genetic variants and many diseases and traits simultaneously. In this review, we describe the value of PheWAS along with methodological issues and challenges in interpretation for current applications of PheWAS. RECENT FINDINGS PheWAS have uncovered a paradigm to identify new associations for genetic loci across many diseases. The application of PheWAS have been effective with phenotype data from electronic health records, epidemiological studies, and clinical trials data. SUMMARY The key strength of a PheWAS is to identify the association of one or more genetic variants with multiple phenotypes, which can showcase interconnections among the phenotypes due to shared genetic associations. While the PheWAS approach appears promising, there are a number of challenges that need to be addressed to provide additional robustness to PheWAS findings.
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Affiliation(s)
- Anurag Verma
- Biomedical and Translational Informatics Institute, Geisinger Health System, Danville, PA
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA
| | - Marylyn D Ritchie
- Biomedical and Translational Informatics Institute, Geisinger Health System, Danville, PA
- The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA
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28
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Prom-Wormley EC, Ebejer J, Dick DM, Bowers MS. The genetic epidemiology of substance use disorder: A review. Drug Alcohol Depend 2017; 180:241-259. [PMID: 28938182 PMCID: PMC5911369 DOI: 10.1016/j.drugalcdep.2017.06.040] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 06/20/2017] [Accepted: 06/23/2017] [Indexed: 12/15/2022]
Abstract
BACKGROUND Substance use disorder (SUD) remains a significant public health issue. A greater understanding of how genes and environment interact to regulate phenotypes comprising SUD will facilitate directed treatments and prevention. METHODS The literature studying the neurobiological correlates of SUD with a focus on the genetic and environmental influences underlying these mechanisms was reviewed. Results from twin/family, human genetic association, gene-environment interaction, epigenetic literature, phenome-wide association studies are summarized for alcohol, nicotine, cannabinoids, cocaine, and opioids. RESULTS There are substantial genetic influences on SUD that are expected to influence multiple neurotransmission pathways, and these influences are particularly important within the dopaminergic system. Genetic influences involved in other aspects of SUD etiology including drug processing and metabolism are also identified. Studies of gene-environment interaction emphasize the importance of environmental context in SUD. Epigenetic studies indicate drug-specific changes in gene expression as well as differences in gene expression related to the use of multiple substances. Further, gene expression is expected to differ by stage of SUD such as substance initiation versus chronic substance use. While a substantial literature has developed for alcohol and nicotine use disorders, there is comparatively less information for other commonly abused substances. CONCLUSIONS A better understanding of genetically-mediated mechanisms involved in the neurobiology of SUD provides increased opportunity to develop behavioral and biologically based treatment and prevention of SUD.
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Affiliation(s)
- Elizabeth C Prom-Wormley
- Dvision of Epidemiology, Department of Family Medicine and Population Health, Virginia Commonwealth University, PO Box 980212, Richmond, VA 23298-0212, USA.
| | - Jane Ebejer
- School of Cognitive Behavioural and Social Sciences, University of New England, Armidale, NSW 2350, Australia
| | - Danielle M Dick
- Department of Psychology, Virginia Commonwealth University, PO Box 842509, Richmond, VA 23284-2509, USA
| | - M Scott Bowers
- Faulk Center for Molecular Therapeutics, Biomedical Engeneering, Northwestern University, Evanston, IL 60201, USA
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29
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Knollmann BC. Cardiac regulatory mechanisms: new concepts and challenges. J Physiol 2017. [DOI: 10.1113/jp274290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Björn C. Knollmann
- Vanderbilt University Medical Center, 1265 MRB4; Vanderbilt University Medical Center; Nashville TN 37232-0575 USA
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