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Jerome RN, Zahn LA, Abner JJ, Joly MM, Shirey-Rice JK, Wallis RS, Bernard GR, Pulley JM. Repurposing N-acetylcysteine for management of non-acetaminophen induced acute liver failure: an evidence scan from a global health perspective. Transl Gastroenterol Hepatol 2024; 9:2. [PMID: 38317753 PMCID: PMC10838616 DOI: 10.21037/tgh-23-40] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 11/01/2023] [Indexed: 02/07/2024] Open
Abstract
Background The World Health Organization (WHO)'s Essential Medicines List (EML) plays an important role in advocating for access to key treatments for conditions affecting people in all geographic settings. We applied our established drug repurposing methods to one EML agent, N-acetylcysteine (NAC), to identify additional uses of relevance to the global health community beyond its existing EML indication (acetaminophen toxicity). Methods We undertook a phenome-wide association study (PheWAS) of a variant in the glutathione synthetase (GSS) gene in approximately 35,000 patients to explore novel indications for use of NAC, which targets glutathione. We then evaluated the evidence regarding biologic plausibility, efficacy, and safety of NAC use in the new phenotype candidates. Results PheWAS of GSS variant R418Q revealed increased risk of several phenotypes related to non-acetaminophen induced acute liver failure (ALF), indicating that NAC may represent a therapeutic option for treating this condition. Evidence review identified practice guidelines, systematic reviews, clinical trials, retrospective cohorts and case series, and case reports. This evidence suggesting benefit of NAC use in this subset of ALF patients. The safety profile of NAC in this literature was also concordant with existing evidence on safety of this agent in acetaminophen-induced ALF. Conclusions This body of literature indicates efficacy and safety of NAC in non-acetaminophen induced ALF. Given the presence of NAC on the EML, this medication is likely to be available across a range of resource settings; promulgating its use in this novel subset of ALF can provide healthcare professionals and patients with a valuable and safe complement to supportive care for this disease.
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Affiliation(s)
- Rebecca N. Jerome
- Vanderbilt University Medical Center, Vanderbilt Institute for Clinical and Translational Research, Nashville, TN, USA
| | - Laura A. Zahn
- Vanderbilt University Medical Center, Vanderbilt Institute for Clinical and Translational Research, Nashville, TN, USA
| | - Jessica J. Abner
- Vanderbilt University Medical Center, Vanderbilt Institute for Clinical and Translational Research, Nashville, TN, USA
| | - Meghan M. Joly
- Vanderbilt University Medical Center, Vanderbilt Institute for Clinical and Translational Research, Nashville, TN, USA
| | - Jana K. Shirey-Rice
- Vanderbilt University Medical Center, Vanderbilt Institute for Clinical and Translational Research, Nashville, TN, USA
| | | | - Gordon R. Bernard
- Vanderbilt University Medical Center, Vanderbilt Institute for Clinical and Translational Research, Nashville, TN, USA
| | - Jill M. Pulley
- Vanderbilt University Medical Center, Vanderbilt Institute for Clinical and Translational Research, Nashville, TN, USA
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2
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Harlow CE, Patel VV, Waterworth DM, Wood AR, Beaumont RN, Ruth KS, Tyrrell J, Oguro-Ando A, Chu AY, Frayling TM. Genetically proxied therapeutic prolyl-hydroxylase inhibition and cardiovascular risk. Hum Mol Genet 2023; 32:496-505. [PMID: 36048866 PMCID: PMC9851745 DOI: 10.1093/hmg/ddac215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 08/05/2022] [Accepted: 08/22/2022] [Indexed: 01/24/2023] Open
Abstract
Prolyl hydroxylase (PHD) inhibitors are in clinical development for anaemia in chronic kidney disease. Epidemiological studies have reported conflicting results regarding safety of long-term therapeutic haemoglobin (Hgb) rises through PHD inhibition on risk of cardiovascular disease. Genetic variation in genes encoding PHDs can be used as partial proxies to investigate the potential effects of long-term Hgb rises. We used Mendelian randomization to investigate the effect of long-term Hgb level rises through genetically proxied PHD inhibition on coronary artery disease (CAD: 60 801 cases; 123 504 controls), myocardial infarction (MI: 42 561 cases; 123 504 controls) or stroke (40 585 cases; 406 111 controls). To further characterize long-term effects of Hgb level rises, we performed a phenome-wide association study (PheWAS) in up to 451 099 UK Biobank individuals. Genetically proxied therapeutic PHD inhibition, equivalent to a 1.00 g/dl increase in Hgb levels, was not associated (at P < 0.05) with increased odds of CAD; odd ratio (OR) [95% confidence intervals (CI)] = 1.06 (0.84, 1.35), MI [OR (95% CI) = 1.02 (0.79, 1.33)] or stroke [OR (95% CI) = 0.91 (0.66, 1.24)]. PheWAS revealed associations with blood related phenotypes consistent with EGLN's role, relevant kidney- and liver-related biomarkers like estimated glomerular filtration rate and microalbuminuria, and non-alcoholic fatty liver disease (Bonferroni-adjusted P < 5.42E-05) but these were not clinically meaningful. These findings suggest that long-term alterations in Hgb through PHD inhibition are unlikely to substantially increase cardiovascular disease risk; using large disease genome-wide association study data, we could exclude ORs of 1.35 for cardiovascular risk with a 1.00 g/dl increase in Hgb.
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Affiliation(s)
- Charli E Harlow
- College of Medicine and Health, University of Exeter, Exeter, Devon EX2 5DW, UK
| | - Vickas V Patel
- GlaxoSmithKline, Collegeville, PA 19426, USA.,Spark Therapeutics, Inc., Philadelphia, PA 19104, USA
| | - Dawn M Waterworth
- GlaxoSmithKline, Collegeville, PA 19426, USA.,Immunology Translational Sciences, Janssen, Spring House, PA 19044, USA
| | - Andrew R Wood
- College of Medicine and Health, University of Exeter, Exeter, Devon EX2 5DW, UK
| | - Robin N Beaumont
- College of Medicine and Health, University of Exeter, Exeter, Devon EX2 5DW, UK
| | - Katherine S Ruth
- College of Medicine and Health, University of Exeter, Exeter, Devon EX2 5DW, UK
| | - Jessica Tyrrell
- College of Medicine and Health, University of Exeter, Exeter, Devon EX2 5DW, UK
| | - Asami Oguro-Ando
- College of Medicine and Health, University of Exeter, Exeter, Devon EX2 5DW, UK
| | | | - Timothy M Frayling
- College of Medicine and Health, University of Exeter, Exeter, Devon EX2 5DW, UK
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3
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Harlow CE, Gandawijaya J, Bamford RA, Martin ER, Wood AR, van der Most PJ, Tanaka T, Leonard HL, Etheridge AS, Innocenti F, Beaumont RN, Tyrrell J, Nalls MA, Simonsick EM, Garimella PS, Shiroma EJ, Verweij N, van der Meer P, Gansevoort RT, Snieder H, Gallins PJ, Jima DD, Wright F, Zhou YH, Ferrucci L, Bandinelli S, Hernandez DG, van der Harst P, Patel VV, Waterworth DM, Chu AY, Oguro-Ando A, Frayling TM. Identification and single-base gene-editing functional validation of a cis-EPO variant as a genetic predictor for EPO-increasing therapies. Am J Hum Genet 2022; 109:1638-1652. [PMID: 36055212 PMCID: PMC9502050 DOI: 10.1016/j.ajhg.2022.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 08/03/2022] [Indexed: 11/30/2022] Open
Abstract
Hypoxia-inducible factor prolyl hydroxylase inhibitors (HIF-PHIs) are currently under clinical development for treating anemia in chronic kidney disease (CKD), but it is important to monitor their cardiovascular safety. Genetic variants can be used as predictors to help inform the potential risk of adverse effects associated with drug treatments. We therefore aimed to use human genetics to help assess the risk of adverse cardiovascular events associated with therapeutically altered EPO levels to help inform clinical trials studying the safety of HIF-PHIs. By performing a genome-wide association meta-analysis of EPO (n = 6,127), we identified a cis-EPO variant (rs1617640) lying in the EPO promoter region. We validated this variant as most likely causal in controlling EPO levels by using genetic and functional approaches, including single-base gene editing. Using this variant as a partial predictor for therapeutic modulation of EPO and large genome-wide association data in Mendelian randomization tests, we found no evidence (at p < 0.05) that genetically predicted long-term rises in endogenous EPO, equivalent to a 2.2-unit increase, increased risk of coronary artery disease (CAD, OR [95% CI] = 1.01 [0.93, 1.07]), myocardial infarction (MI, OR [95% CI] = 0.99 [0.87, 1.15]), or stroke (OR [95% CI] = 0.97 [0.87, 1.07]). We could exclude increased odds of 1.15 for cardiovascular disease for a 2.2-unit EPO increase. A combination of genetic and functional studies provides a powerful approach to investigate the potential therapeutic profile of EPO-increasing therapies for treating anemia in CKD.
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Affiliation(s)
- Charli E Harlow
- University of Exeter Medical School, University of Exeter, Royal Devon and Exeter NHS Trust, Exeter EX2 5DW, UK
| | - Josan Gandawijaya
- University of Exeter Medical School, University of Exeter, Royal Devon and Exeter NHS Trust, Exeter EX2 5DW, UK
| | - Rosemary A Bamford
- University of Exeter Medical School, University of Exeter, Royal Devon and Exeter NHS Trust, Exeter EX2 5DW, UK
| | - Emily-Rose Martin
- University of Exeter Medical School, University of Exeter, Royal Devon and Exeter NHS Trust, Exeter EX2 5DW, UK
| | - Andrew R Wood
- University of Exeter Medical School, University of Exeter, Royal Devon and Exeter NHS Trust, Exeter EX2 5DW, UK
| | - Peter J van der Most
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen 9713, the Netherlands
| | - Toshiko Tanaka
- Longitudinal Studies Section, Translation Gerontology Branch, National Institute on Aging, Baltimore, MD 21224, USA
| | - Hampton L Leonard
- Laboratory of Neurogenetics, National Institute on Aging, NIH, Bethesda, MD 20892, USA; Data Tecnica International, Glen Echo, MD 20812, USA; Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amy S Etheridge
- Eshelman School of Pharmacy and Center for Pharmacogenomics and Individualized Therapy, University of North Carolina at Chapel Hill, 120 Mason Farm Road, Chapel Hill, NC 27599, USA
| | | | - Robin N Beaumont
- University of Exeter Medical School, University of Exeter, Royal Devon and Exeter NHS Trust, Exeter EX2 5DW, UK
| | - Jessica Tyrrell
- University of Exeter Medical School, University of Exeter, Royal Devon and Exeter NHS Trust, Exeter EX2 5DW, UK
| | - Mike A Nalls
- Laboratory of Neurogenetics, National Institute on Aging, NIH, Bethesda, MD 20892, USA; Data Tecnica International, Glen Echo, MD 20812, USA; Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eleanor M Simonsick
- Longitudinal Studies Section, Translation Gerontology Branch, National Institute on Aging, Baltimore, MD 21224, USA
| | - Pranav S Garimella
- Division of Nephrology-Hypertension, University of California San Diego, San Diego, CA, USA
| | - Eric J Shiroma
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, Bethesda, MD 20892, USA
| | - Niek Verweij
- University of Groningen, University Medical Center Groningen, Department of Cardiology, Groningen 9713, the Netherlands
| | - Peter van der Meer
- University of Groningen, University Medical Center Groningen, Department of Cardiology, Groningen 9713, the Netherlands
| | - Ron T Gansevoort
- University of Groningen, University Medical Center Groningen, Department of Nephrology, Groningen 9713, the Netherlands
| | - Harold Snieder
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen 9713, the Netherlands
| | - Paul J Gallins
- Bioinformatics Research Center, North Carolina State University, 1 Lampe Drive, Raleigh, NC 27695, USA
| | - Dereje D Jima
- Bioinformatics Research Center, North Carolina State University, 1 Lampe Drive, Raleigh, NC 27695, USA; Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27606, USA
| | - Fred Wright
- Bioinformatics Research Center, North Carolina State University, 1 Lampe Drive, Raleigh, NC 27695, USA
| | - Yi-Hui Zhou
- Bioinformatics Research Center, North Carolina State University, 1 Lampe Drive, Raleigh, NC 27695, USA
| | - Luigi Ferrucci
- Longitudinal Studies Section, Translation Gerontology Branch, National Institute on Aging, Baltimore, MD 21224, USA
| | | | - Dena G Hernandez
- Laboratory of Neurogenetics, National Institute on Aging, NIH, Bethesda, MD 20892, USA
| | - Pim van der Harst
- Department of Cardiology, University Medical Center Utrecht, Utrecht 3584, the Netherlands
| | | | | | | | - Asami Oguro-Ando
- University of Exeter Medical School, University of Exeter, Royal Devon and Exeter NHS Trust, Exeter EX2 5DW, UK.
| | - Timothy M Frayling
- University of Exeter Medical School, University of Exeter, Royal Devon and Exeter NHS Trust, Exeter EX2 5DW, UK.
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Krishnamurthy N, Grimshaw AA, Axson SA, Choe SH, Miller JE. Drug repurposing: a systematic review on root causes, barriers and facilitators. BMC Health Serv Res 2022; 22:970. [PMID: 35906687 PMCID: PMC9336118 DOI: 10.1186/s12913-022-08272-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 06/29/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Repurposing is a drug development strategy receiving heightened attention after the Food and Drug Administration granted emergency use authorization of several repurposed drugs to treat Covid-19. There remain knowledge gaps on the root causes, facilitators and barriers for repurposing. METHOD This systematic review used controlled vocabulary and free text terms to search ABI/Informa, Academic Search Premier, Business Source Complete, Cochrane Library, EconLit, Google Scholar, Ovid Embase, Ovid Medline, Pubmed, Scopus, and Web of Science Core Collection databases for the characteristics, reasons and example of companies deprioritizing development of promising drugs and barriers, facilitators and examples of successful re-purposing. RESULTS We identified 11,814 articles, screened 5,976 for relevance, found 437 eligible for full text review, 115 of which were included in full analysis. Most articles (66%, 76/115) discussed why promising drugs are abandoned, with lack of efficacy or superiority to other therapies (n = 59), strategic business reasons (n = 35), safety problems (n = 28), research design decisions (n = 12), the complex nature of a studied disease or drug (n = 7) and regulatory bodies requiring more information (n = 2) among top reasons. Key barriers to repurposing include inadequate resources (n = 42), trial data access and transparency around abandoned compounds (n = 20) and expertise (n = 11). Additional barriers include uncertainty about the value of repurposing (n = 13), liability risks (n = 5) and intellectual property (IP) challenges (n = 26). Facilitators include the ability to form multi-partner collaborations (n = 38), access to compound databases and database screening tools (n = 32), regulatory modifications (n = 5) and tax incentives (n = 2). CONCLUSION Promising drugs are commonly shelved due to insufficient efficacy or superiority to alternate therapies, poor market prospects, and industry consolidation. Inadequate resources and data access and challenges negotiating IP are key barriers to repurposing reaching its full potential as a core approach in drug development. Multi-partner collaborations and the availability and use of compound databases and tax incentives are key facilitators for repurposing. More research is needed on the current value of repurposing in drug development and how to better facilitate resources to support it, where valuable, especially financial, staffing for out-licensing shelved products, and legal expertise to negotiate IP agreements in multi-partner collaborations. TRIAL REGISTRATION The protocol was registered on Open Science Framework ( https://osf.io/f634k/ ) as it was not eligible for registration on PROSPERO as the review did not focus on a health-related outcome.
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Affiliation(s)
- Nithya Krishnamurthy
- Internal Medicine Department, Yale University School of Medicine, 367 Cedar Street, 4th Floor, New Haven, CT, 06520, USA
| | - Alyssa A Grimshaw
- Cushing/Whitney Medical Library, Yale University, 333 Cedar Street, Box 208014, New Haven, CT, 06520, USA
| | - Sydney A Axson
- Internal Medicine Department, Yale University School of Medicine, 367 Cedar Street, 4th Floor, New Haven, CT, 06520, USA
| | - Sung Hee Choe
- Milken Institute Center for Faster Cures, 730 15th Street NW, Washington, DC, 20005, USA
| | - Jennifer E Miller
- Internal Medicine Department, Yale University School of Medicine, 367 Cedar Street, 4th Floor, New Haven, CT, 06520, USA.
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5
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Hong CC. The grand challenge of discovering new cardiovascular drugs. FRONTIERS IN DRUG DISCOVERY 2022; 2:1027401. [PMID: 37123434 PMCID: PMC10134778 DOI: 10.3389/fddsv.2022.1027401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
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6
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Challa AP, Zaleski NM, Jerome RN, Lavieri RR, Shirey-Rice JK, Barnado A, Lindsell CJ, Aronoff DM, Crofford LJ, Harris RC, Alp Ikizler T, Mayer IA, Holroyd KJ, Pulley JM. Human and Machine Intelligence Together Drive Drug Repurposing in Rare Diseases. Front Genet 2021; 12:707836. [PMID: 34394194 PMCID: PMC8355705 DOI: 10.3389/fgene.2021.707836] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 07/06/2021] [Indexed: 01/31/2023] Open
Abstract
Repurposing is an increasingly attractive method within the field of drug development for its efficiency at identifying new therapeutic opportunities among approved drugs at greatly reduced cost and time of more traditional methods. Repurposing has generated significant interest in the realm of rare disease treatment as an innovative strategy for finding ways to manage these complex conditions. The selection of which agents should be tested in which conditions is currently informed by both human and machine discovery, yet the appropriate balance between these approaches, including the role of artificial intelligence (AI), remains a significant topic of discussion in drug discovery for rare diseases and other conditions. Our drug repurposing team at Vanderbilt University Medical Center synergizes machine learning techniques like phenome-wide association study-a powerful regression method for generating hypotheses about new indications for an approved drug-with the knowledge and creativity of scientific, legal, and clinical domain experts. While our computational approaches generate drug repurposing hits with a high probability of success in a clinical trial, human knowledge remains essential for the hypothesis creation, interpretation, "go-no go" decisions with which machines continue to struggle. Here, we reflect on our experience synergizing AI and human knowledge toward realizable patient outcomes, providing case studies from our portfolio that inform how we balance human knowledge and machine intelligence for drug repurposing in rare disease.
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Affiliation(s)
- Anup P. Challa
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN, United States
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, United States
| | - Nicole M. Zaleski
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Rebecca N. Jerome
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Robert R. Lavieri
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Jana K. Shirey-Rice
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN, United States
| | - April Barnado
- Division of Rheumatology and Immunology, Department of Medicine, Vanderbilt Medical Center, Nashville, TN, United States
| | - Christopher J. Lindsell
- Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - David M. Aronoff
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
- Department of Obstetrics and Gynecology, Vanderbilt University Medical Center, Nashville, TN, United States
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Leslie J. Crofford
- Division of Rheumatology and Immunology, Department of Medicine, Vanderbilt Medical Center, Nashville, TN, United States
| | - Raymond C. Harris
- Division of Nephrology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - T. Alp Ikizler
- Division of Nephrology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Ingrid A. Mayer
- Division of Hematology/Oncology, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Kenneth J. Holroyd
- Center for Technology Transfer and Commercialization, Vanderbilt University, Nashville, TN, United States
| | - Jill M. Pulley
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN, United States
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7
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Johnson KB, Wei W, Weeraratne D, Frisse ME, Misulis K, Rhee K, Zhao J, Snowdon JL. Precision Medicine, AI, and the Future of Personalized Health Care. Clin Transl Sci 2020; 14:86-93. [PMID: 32961010 PMCID: PMC7877825 DOI: 10.1111/cts.12884] [Citation(s) in RCA: 267] [Impact Index Per Article: 66.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 08/11/2020] [Indexed: 12/16/2022] Open
Abstract
The convergence of artificial intelligence (AI) and precision medicine promises to revolutionize health care. Precision medicine methods identify phenotypes of patients with less‐common responses to treatment or unique healthcare needs. AI leverages sophisticated computation and inference to generate insights, enables the system to reason and learn, and empowers clinician decision making through augmented intelligence. Recent literature suggests that translational research exploring this convergence will help solve the most difficult challenges facing precision medicine, especially those in which nongenomic and genomic determinants, combined with information from patient symptoms, clinical history, and lifestyles, will facilitate personalized diagnosis and prognostication.
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Affiliation(s)
- Kevin B. Johnson
- Department of Biomedical InformaticsVanderbilt University Medical CenterNashvilleTennesseeUSA
- Department of PediatricsVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Wei‐Qi Wei
- Department of Biomedical InformaticsVanderbilt University Medical CenterNashvilleTennesseeUSA
| | | | - Mark E. Frisse
- Department of Biomedical InformaticsVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Karl Misulis
- Department of Biomedical InformaticsVanderbilt University Medical CenterNashvilleTennesseeUSA
- Department of Clinical NeurologyVanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Kyu Rhee
- IBM Watson HealthCambridgeMassachusettsUSA
| | - Juan Zhao
- Department of Biomedical InformaticsVanderbilt University Medical CenterNashvilleTennesseeUSA
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8
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Werfel TA, Hicks DJ, Rahman B, Bendeman WE, Duvernay MT, Maeng JG, Hamm H, Lavieri RR, Joly MM, Pulley JM, Elion DL, Brantley-Sieders DM, Cook RS. Repurposing of a Thromboxane Receptor Inhibitor Based on a Novel Role in Metastasis Identified by Phenome-Wide Association Study. Mol Cancer Ther 2020; 19:2454-2464. [PMID: 33033174 DOI: 10.1158/1535-7163.mct-19-1106] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 03/03/2020] [Accepted: 09/15/2020] [Indexed: 11/16/2022]
Abstract
Although new drug discoveries are revolutionizing cancer treatments, repurposing existing drugs would accelerate the timeline and lower the cost for bringing treatments to cancer patients. Our goal was to repurpose CPI211, a potent and selective antagonist of the thromboxane A2-prostanoid receptor (TPr), a G-protein-coupled receptor that regulates coagulation, blood pressure, and cardiovascular homeostasis. To identify potential new clinical indications for CPI211, we performed a phenome-wide association study (PheWAS) of the gene encoding TPr, TBXA2R, using robust deidentified health records and matched genomic data from more than 29,000 patients. Specifically, PheWAS was used to identify clinical manifestations correlating with a TBXA2R single-nucleotide polymorphism (rs200445019), which generates a T399A substitution within TPr that enhances TPr signaling. Previous studies have correlated 200445019 with chronic venous hypertension, which was recapitulated by this PheWAS analysis. Unexpectedly, PheWAS uncovered an rs200445019 correlation with cancer metastasis across several cancer types. When tested in several mouse models of metastasis, TPr inhibition using CPI211 potently blocked spontaneous metastasis from primary tumors, without affecting tumor cell proliferation, motility, or tumor growth. Further, metastasis following intravenous tumor cell delivery was blocked in mice treated with CPI211. Interestingly, TPr signaling in vascular endothelial cells induced VE-cadherin internalization, diminished endothelial barrier function, and enhanced transendothelial migration by tumor cells, phenotypes that were decreased by CPI211. These studies provide evidence that TPr signaling promotes cancer metastasis, supporting the study of TPr inhibitors as antimetastatic agents and highlighting the use of PheWAS as an approach to accelerate drug repurposing.
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Affiliation(s)
- Thomas A Werfel
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee.,Department of Chemical Engineering, University of Mississippi, Oxford, Mississippi
| | - Donna J Hicks
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Bushra Rahman
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Wendy E Bendeman
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Matthew T Duvernay
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jae G Maeng
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Heidi Hamm
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Robert R Lavieri
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Meghan M Joly
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jill M Pulley
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee
| | - David L Elion
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Dana M Brantley-Sieders
- Breast Cancer Research Program, Vanderbilt Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee.,Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Rebecca S Cook
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee. .,Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee.,Breast Cancer Research Program, Vanderbilt Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee.,Department of Biomedical Engineering, Vanderbilt University School of Engineering, Nashville, Tennessee
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9
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Campion TR, Craven CK, Dorr DA, Knosp BM. Understanding enterprise data warehouses to support clinical and translational research. J Am Med Inform Assoc 2020; 27:1352-1358. [PMID: 32679585 PMCID: PMC7647350 DOI: 10.1093/jamia/ocaa089] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 04/24/2020] [Accepted: 05/12/2020] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVE Among National Institutes of Health Clinical and Translational Science Award (CTSA) hubs, adoption of electronic data warehouses for research (EDW4R) containing data from electronic health record systems is nearly ubiquitous. Although benefits of EDW4R include more effective, efficient support of scientists, little is known about how CTSA hubs have implemented EDW4R services. The goal of this qualitative study was to understand the ways in which CTSA hubs have operationalized EDW4R to support clinical and translational researchers. MATERIALS AND METHODS After conducting semistructured interviews with informatics leaders from 20 CTSA hubs, we performed a directed content analysis of interview notes informed by naturalistic inquiry. RESULTS We identified 12 themes: organization and data; oversight and governance; data access request process; data access modalities; data access for users with different skill sets; engagement, communication, and literacy; service management coordinated with enterprise information technology; service management coordinated within a CTSA hub; service management coordinated between informatics and biostatistics; funding approaches; performance metrics; and future trends and current technology challenges. DISCUSSION This study is a step in developing an improved understanding and creating a common vocabulary about EDW4R operations across institutions. Findings indicate an opportunity for establishing best practices for EDW4R operations in academic medicine. Such guidance could reduce the costs associated with developing an EDW4R by establishing a clear roadmap and maturity path for institutions to follow. CONCLUSIONS CTSA hubs described varying approaches to EDW4R operations that may assist other institutions in better serving investigators with electronic patient data.
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Affiliation(s)
- Thomas R Campion
- Department of Population Health Sciences, Weill Cornell Medicine, New York, New York, USA
| | - Catherine K Craven
- Institute for Health Care Delivery Science, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - David A Dorr
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, Oregon, USA
| | - Boyd M Knosp
- Institute for Clinical and Translational Science, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
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10
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Jerome RN, Joly MM, Kennedy N, Shirey-Rice JK, Roden DM, Bernard GR, Holroyd KJ, Denny JC, Pulley JM. Leveraging Human Genetics to Identify Safety Signals Prior to Drug Marketing Approval and Clinical Use. Drug Saf 2020; 43:567-582. [PMID: 32112228 PMCID: PMC7398579 DOI: 10.1007/s40264-020-00915-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
INTRODUCTION When a new drug or biologic product enters the market, its full spectrum of side effects is not yet fully understood, as use in the real world often uncovers nuances not suggested within the relatively narrow confines of preapproval preclinical and trial work. OBJECTIVE We describe a new, phenome-wide association study (PheWAS)- and evidence-based approach for detection of potential adverse drug effects. METHODS We leveraged our established platform, which integrates human genetic data with associated phenotypes in electronic health records from 29,722 patients of European ancestry, to identify gene-phenotype associations that may represent known safety issues. We examined PheWAS data and the published literature for 16 genes, each of which encodes a protein targeted by at least one drug or biologic product. RESULTS Initial data demonstrated that our novel approach (safety ascertainment using PheWAS [SA-PheWAS]) can replicate published safety information across multiple drug classes, with validated findings for 13 of 16 gene-drug class pairs. CONCLUSIONS By connecting and integrating in vivo and in silico data, SA-PheWAS offers an opportunity to supplement current methods for predicting or confirming safety signals associated with therapeutic agents.
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Affiliation(s)
- Rebecca N Jerome
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Meghan Morrison Joly
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Nan Kennedy
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jana K Shirey-Rice
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dan M Roden
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, USA
| | - Gordon R Bernard
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kenneth J Holroyd
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN, USA
- Center for Technology Transfer and Commercialization, Vanderbilt University, Nashville, TN, USA
| | - Joshua C Denny
- Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, USA
| | - Jill M Pulley
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN, USA
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11
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Challa AP, Lavieri RR, Lewis JT, Zaleski NM, Shirey-Rice JK, Harris PA, Aronoff DM, Pulley JM. Systematically Prioritizing Candidates in Genome-Based Drug Repurposing. Assay Drug Dev Technol 2019; 17:352-363. [PMID: 31769998 PMCID: PMC6921094 DOI: 10.1089/adt.2019.950] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Drug repurposing is the application of approved drugs to treat diseases separate and distinct from their original indications. Herein, we define the scope of all practical precision drug repurposing using DrugBank, a publicly available database of pharmacological agents, and BioVU, a large, de-identified DNA repository linked to longitudinal electronic health records at Vanderbilt University Medical Center. We present a method of repurposing candidate prioritization through integration of pharmacodynamic and marketing variables from DrugBank with quality control thresholds for genomic data derived from the DNA samples within BioVU. Through the synergy of delineated "target-action pairs," along with target genomics, we identify ∼230 "pairs" that represent all practical opportunities for genomic drug repurposing. From this analysis, we present a pipeline of 14 repurposing candidates across 7 disease areas that link to our repurposability platform and present high potential for randomized controlled trial startup in upcoming months.
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Affiliation(s)
- Anup P. Challa
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Robert R. Lavieri
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Judith T. Lewis
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Nicole M. Zaleski
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jana K. Shirey-Rice
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Paul A. Harris
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - David M. Aronoff
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Jill M. Pulley
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee
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12
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Abstract
Metastatic cancers impose significant burdens on patients, affecting quality of life, morbidity, and mortality. Even during remission, microscopic metastases can lurk, but few therapies directly target tumor cell metastasis. Agents that interfere with this process would represent a new paradigm in cancer management, changing the 'waiting game' into a time of active prevention. These therapies could take multiple forms based on the pathways involved in the metastatic process. For example, a phenome-wide association study showed that a single nucleotide polymorphism in the gene TBXA2R is associated with increased metastasis in multiple primary cancers (P = 0.003), suggesting clinical applicability of TBXA2R antagonists. Emerging data related to the role of platelets in metastasis are concordant with our sense that these pathways present significant opportunities for therapeutic development. However, before real progress can be made toward clinical targeting of the metastatic process, foundational work is needed to define informative measures of critical elements such as circulating tumor cells and tumor DNA, and circulatory vs. lymphatic spread. These challenges require an expansion of team science and composition to obtain competitive funding. At our academic medical center, we have implemented a Cancer Metastasis Inhibition (CMI) program investigating this approach across multiple cancers.
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13
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Adhesion G protein-coupled receptors: opportunities for drug discovery. Nat Rev Drug Discov 2019; 18:869-884. [PMID: 31462748 DOI: 10.1038/s41573-019-0039-y] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/18/2019] [Indexed: 12/24/2022]
Abstract
Adhesion G protein-coupled receptors (aGPCRs) - one of the five main families in the GPCR superfamily - have several atypical characteristics, including large, multi-domain N termini and a highly conserved region that can be autoproteolytically cleaved. Although GPCRs overall have well-established pharmacological tractability, currently no therapies that target any of the 33 members of the aGPCR family are either approved or in clinical trials. However, human genetics and preclinical research have strengthened the links between aGPCRs and disease in recent years. This, together with a greater understanding of their functional complexity, has led to growing interest in aGPCRs as drug targets. A framework for prioritizing aGPCR targets and supporting approaches to develop aGPCR modulators could therefore be valuable in harnessing the untapped therapeutic potential of this family. With this in mind, here we discuss the unique opportunities and challenges for drug discovery in modulating aGPCR functions, including target identification, target validation, assay development and safety considerations, using ADGRG1 as an illustrative example.
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14
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Roden DM, McLeod HL, Relling MV, Williams MS, Mensah GA, Peterson JF, Van Driest SL. Pharmacogenomics. Lancet 2019; 394:521-532. [PMID: 31395440 PMCID: PMC6707519 DOI: 10.1016/s0140-6736(19)31276-0] [Citation(s) in RCA: 211] [Impact Index Per Article: 42.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 04/04/2019] [Accepted: 05/16/2019] [Indexed: 02/08/2023]
Abstract
Genomic medicine, which uses DNA variation to individualise and improve human health, is the subject of this Series of papers. The idea that genetic variation can be used to individualise drug therapy-the topic addressed here-is often viewed as within reach for genomic medicine. We have reviewed general mechanisms underlying variability in drug action, the role of genetic variation in mediating beneficial and adverse effects through variable drug concentrations (pharmacokinetics) and drug actions (pharmacodynamics), available data from clinical trials, and ongoing efforts to implement pharmacogenetics in clinical practice.
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Affiliation(s)
- Dan M Roden
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Howard L McLeod
- DeBartolo Family Personalized Medicine Institute, Moffitt Cancer Center, Tampa, FL, USA
| | - Mary V Relling
- Pharmaceutical Department, St Jude Children's Research Hospital, Memphis, TN, USA
| | | | - George A Mensah
- Center for Translation Research and Implementation Science, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Josh F Peterson
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Sara L Van Driest
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
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15
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Pulley JM, Rhoads JP, Jerome RN, Challa AP, Erreger KB, Joly MM, Lavieri RR, Perry KE, Zaleski NM, Shirey-Rice JK, Aronoff DM. Using What We Already Have: Uncovering New Drug Repurposing Strategies in Existing Omics Data. Annu Rev Pharmacol Toxicol 2019; 60:333-352. [PMID: 31337270 DOI: 10.1146/annurev-pharmtox-010919-023537] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The promise of drug repurposing is to accelerate the translation of knowledge to treatment of human disease, bypassing common challenges associated with drug development to be more time- and cost-efficient. Repurposing has an increased chance of success due to the previous validation of drug safety and allows for the incorporation of omics. Hypothesis-generating omics processes inform drug repurposing decision-making methods on drug efficacy and toxicity. This review summarizes drug repurposing strategies and methodologies in the context of the following omics fields: genomics, epigenomics, transcriptomics, proteomics, metabolomics, microbiomics, phenomics, pregomics, and personomics. While each omics field has specific strengths and limitations, incorporating omics into the drug repurposing landscape is integral to its success.
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Affiliation(s)
- Jill M Pulley
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee 37203, USA
| | - Jillian P Rhoads
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee 37203, USA
| | - Rebecca N Jerome
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee 37203, USA
| | - Anup P Challa
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee 37203, USA
| | - Kevin B Erreger
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee 37203, USA
| | - Meghan M Joly
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee 37203, USA
| | - Robert R Lavieri
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee 37203, USA
| | - Kelly E Perry
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee 37203, USA
| | - Nicole M Zaleski
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee 37203, USA
| | - Jana K Shirey-Rice
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee 37203, USA
| | - David M Aronoff
- Department of Medicine, Division of Infectious Diseases, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA.,Departments of Obstetrics and Gynecology, and Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA;
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16
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Eslam M, George J. Genetic Insights for Drug Development in NAFLD. Trends Pharmacol Sci 2019; 40:506-516. [PMID: 31160124 DOI: 10.1016/j.tips.2019.05.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 04/10/2019] [Accepted: 05/06/2019] [Indexed: 12/21/2022]
Abstract
Drug development is a costly, time-consuming, and challenging endeavour, with only a few agents reaching the threshold of approval for clinical use. Therefore, approaches to more efficiently identify targets that are likely to translate to clinical benefit are required. Interrogation of the human genome in large patient cohorts has rapidly advanced our knowledge of the genetic architecture and underlying mechanisms of many diseases, including nonalcoholic fatty liver disease (NAFLD). There are no approved pharmacotherapies for NAFLD currently. Genetic insights provide a powerful and new approach to infer and prioritise candidate drugs, with such selection avoiding myriad pitfalls, while defining likely benefits. In this review, we discuss the prospects and challenges for the optimal utilisation of genetic findings for improving and accelerating the NAFLD drug discovery pipeline.
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Affiliation(s)
- Mohammed Eslam
- Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital and University of Sydney, Westmead, NSW, Australia.
| | - Jacob George
- Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital and University of Sydney, Westmead, NSW, Australia.
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17
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A Phenome-Wide Association Study Uncovers a Pathological Role of Coagulation Factor X during Acinetobacter baumannii Infection. Infect Immun 2019; 87:IAI.00031-19. [PMID: 30782860 DOI: 10.1128/iai.00031-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 02/14/2019] [Indexed: 01/30/2023] Open
Abstract
Coagulation and inflammation are interconnected, suggesting that coagulation plays a key role in the inflammatory response to pathogens. A phenome-wide association study (PheWAS) was used to identify clinical phenotypes of patients with a polymorphism in coagulation factor X. Patients with this single nucleotide polymorphism (SNP) were more likely to be hospitalized with hemostatic and infection-related disorders, suggesting that factor X contributes to the immune response to infection. To investigate this, we modeled infections by human pathogens in a mouse model of factor X deficiency. Factor X-deficient mice were protected from systemic Acinetobacter baumannii infection, suggesting that factor X plays a role in the immune response to A. baumannii Factor X deficiency was associated with reduced cytokine and chemokine production and alterations in immune cell population during infection: factor X-deficient mice demonstrated increased abundance of neutrophils, macrophages, and effector T cells. Together, these results suggest that factor X activity is associated with an inefficient immune response and contributes to the pathology of A. baumannii infection.
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18
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Fox CS. Using Human Genetics to Drive Drug Discovery: A Perspective. Am J Kidney Dis 2019; 74:111-119. [PMID: 30898364 DOI: 10.1053/j.ajkd.2018.12.045] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Accepted: 12/24/2018] [Indexed: 12/11/2022]
Abstract
The probability of success of developing medicines to treat human disease can be improved by leveraging human genetics. Different types of genetic data and techniques, including genome-wide association, whole-exome sequencing, and whole-genome sequencing, can be used to gain insight into human disease. Layering different types of genetic evidence from Mendelian disease, coding variants, and common variation can bolster support for a genetic target. Human knockouts offer the potential to perform reverse genetic screens in humans to identify physiologically relevant targets. Other components of a good genetic target include protective loss-of-function mutations, some degree of known biology, tractability, and a clean on-target safety profile. In addition to using human genetics to inspire new drug programs, phenome-wide association studies can be used to identify alternative indications or repurposing opportunities. This information can be combined into a 5-step approach for selecting a genetic target for validation, which is presented in detail in this review. Finally, current challenges in leveraging human genetics are highlighted, including the difficulties translating certain types of genetic data, relatively small number of bona fide disease-associated coding rare variants, and current sample sizes of large well-curated biobanks linked to comprehensive genetic information.
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19
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Shrine N, Guyatt AL, Erzurumluoglu AM, Jackson VE, Hobbs BD, Melbourne CA, Batini C, Fawcett KA, Song K, Sakornsakolpat P, Li X, Boxall R, Reeve NF, Obeidat M, Zhao JH, Wielscher M, Weiss S, Kentistou KA, Cook JP, Sun BB, Zhou J, Hui J, Karrasch S, Imboden M, Harris SE, Marten J, Enroth S, Kerr SM, Surakka I, Vitart V, Lehtimäki T, Allen RJ, Bakke PS, Beaty TH, Bleecker ER, Bossé Y, Brandsma CA, Chen Z, Crapo JD, Danesh J, DeMeo DL, Dudbridge F, Ewert R, Gieger C, Gulsvik A, Hansell AL, Hao K, Hoffman JD, Hokanson JE, Homuth G, Joshi PK, Joubert P, Langenberg C, Li X, Li L, Lin K, Lind L, Locantore N, Luan J, Mahajan A, Maranville JC, Murray A, Nickle DC, Packer R, Parker MM, Paynton ML, Porteous DJ, Prokopenko D, Qiao D, Rawal R, Runz H, Sayers I, Sin DD, Smith BH, Soler Artigas M, Sparrow D, Tal-Singer R, Timmers PRHJ, Van den Berge M, Whittaker JC, Woodruff PG, Yerges-Armstrong LM, Troyanskaya OG, Raitakari OT, Kähönen M, Polašek O, Gyllensten U, Rudan I, Deary IJ, Probst-Hensch NM, Schulz H, James AL, Wilson JF, Stubbe B, Zeggini E, Jarvelin MR, Wareham N, Silverman EK, Hayward C, Morris AP, Butterworth AS, Scott RA, Walters RG, Meyers DA, Cho MH, Strachan DP, Hall IP, Tobin MD, Wain LV. New genetic signals for lung function highlight pathways and chronic obstructive pulmonary disease associations across multiple ancestries. Nat Genet 2019; 51:481-493. [PMID: 30804560 PMCID: PMC6397078 DOI: 10.1038/s41588-018-0321-7] [Citation(s) in RCA: 283] [Impact Index Per Article: 56.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 11/27/2018] [Indexed: 02/02/2023]
Abstract
Reduced lung function predicts mortality and is key to the diagnosis of chronic obstructive pulmonary disease (COPD). In a genome-wide association study in 400,102 individuals of European ancestry, we define 279 lung function signals, 139 of which are new. In combination, these variants strongly predict COPD in independent populations. Furthermore, the combined effect of these variants showed generalizability across smokers and never smokers, and across ancestral groups. We highlight biological pathways, known and potential drug targets for COPD and, in phenome-wide association studies, autoimmune-related and other pleiotropic effects of lung function-associated variants. This new genetic evidence has potential to improve future preventive and therapeutic strategies for COPD.
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Affiliation(s)
- Nick Shrine
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Anna L Guyatt
- Department of Health Sciences, University of Leicester, Leicester, UK
| | | | - Victoria E Jackson
- Department of Health Sciences, University of Leicester, Leicester, UK
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Brian D Hobbs
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Carl A Melbourne
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Chiara Batini
- Department of Health Sciences, University of Leicester, Leicester, UK
| | | | - Kijoung Song
- Target Sciences, GlaxoSmithKline, Collegeville, PA, USA
| | - Phuwanat Sakornsakolpat
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Xingnan Li
- Division of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona, Tucson, AZ, USA
| | - Ruth Boxall
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Medical Research Council Population Health Research Unit, University of Oxford, Oxford, UK
| | - Nicola F Reeve
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Ma'en Obeidat
- The University of British Columbia Centre for Heart Lung Innovation, St Paul's Hospital, Vancouver, British Columbia, Canada
| | - Jing Hua Zhao
- Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Matthias Wielscher
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, UK
| | - Stefan Weiss
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Katherine A Kentistou
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
- Centre for Cardiovascular Sciences, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - James P Cook
- Department of Biostatistics, University of Liverpool, Liverpool, UK
| | - Benjamin B Sun
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Jian Zhou
- Flatiron Institute, Simons Foundation, New York, NY, USA
| | - Jennie Hui
- Busselton Population Medical Research Institute, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
- School of Population Health, The University of Western Australia, Crawley, Western Australia, Australia
- PathWest Laboratory Medicine of WA, Sir Charles Gairdner Hospital, Crawley, Western Australia, Australia
- School of Pathology and Laboratory Medicine, The University of Western Australia, Crawley, Western Australia, Australia
| | - Stefan Karrasch
- Institute of Epidemiology, Helmholtz Zentrum Muenchen-German Research Center for Environmental Health, Neuherberg, Germany
- Institute and Outpatient Clinic for Occupational, Social and Environmental Medicine, Ludwig-Maximilians-Universität, Munich, Germany
- Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Medea Imboden
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Sarah E Harris
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Centre for Genomic and Experimental Medicine, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Jonathan Marten
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Stefan Enroth
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala Universitet, Uppsala, Sweden
| | - Shona M Kerr
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Ida Surakka
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- The National Institute for Health and Welfare (THL), Helsinki, Finland
| | - Veronique Vitart
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, and Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Richard J Allen
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Per S Bakke
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Terri H Beaty
- Department of Epidemiology, Johns Hopkins University School of Public Health, Baltimore, MD, USA
| | - Eugene R Bleecker
- Division of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona, Tucson, AZ, USA
| | - Yohan Bossé
- Department of Molecular Medicine, Laval University, Québec, Canada
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Laval University, Québec, Canada
| | - Corry-Anke Brandsma
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, GRIAC Research Institute, University of Groningen, Groningen, The Netherlands
| | - Zhengming Chen
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - James D Crapo
- National Jewish Health, Denver, CO, USA
- Division of Pulmonary, Critical Care and Sleep Medicine, National Jewish Health, Denver, CO, USA
| | - John Danesh
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Cambridge Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Cambridge, UK
- Department of Human Genetics, Wellcome Trust Sanger Institute, Cambridge, UK
- NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Frank Dudbridge
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Ralf Ewert
- Department of Internal Medicine B - Cardiology, Intensive Care, Pulmonary Medicine and Infectious Diseases, University Medicine Greifswald, Greifswald, Germany
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum Muenchen - German Research Center for Environmental Health, Neuherberg, Germany
| | - Amund Gulsvik
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Anna L Hansell
- Centre for Environmental Health & Sustainability, University of Leicester, Leicester, UK
- UK Small Area Health Statistics Unit, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
- Imperial College Healthcare NHS Trust, St Mary's Hospital, London, UK
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - John E Hokanson
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Georg Homuth
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Peter K Joshi
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Philippe Joubert
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Laval University, Québec, Canada
- Department of Molecular Biology, Medical Biochemistry, and Pathology, Laval University, Québec, Canada
| | - Claudia Langenberg
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Xuan Li
- The University of British Columbia Centre for Heart Lung Innovation, St Paul's Hospital, Vancouver, British Columbia, Canada
| | - Liming Li
- Department of Epidemiology & Biostatistics, Peking University Health Science Center, Beijing, China
| | - Kuang Lin
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Lars Lind
- Department of Medical Sciences, Cardiovascular Epidemiology, Uppsala University, Uppsala, Sweden
| | | | - Jian'an Luan
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Anubha Mahajan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Alison Murray
- The Institute of Medical Sciences, Aberdeen Biomedical Imaging Centre, University of Aberdeen, Aberdeen, UK
| | - David C Nickle
- MRL, Merck & Co., Inc, Kenilworth, NJ, USA
- Gossamer Bio, San Diego, CA, USA
| | - Richard Packer
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Margaret M Parker
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Megan L Paynton
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - David J Porteous
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Centre for Genomic and Experimental Medicine, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Dmitry Prokopenko
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Dandi Qiao
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Rajesh Rawal
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum Muenchen - German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology and Social Medicine, University of Münster, Münster, Germany
| | - Heiko Runz
- MRL, Merck & Co., Inc, Kenilworth, NJ, USA
| | - Ian Sayers
- Division of Respiratory Medicine and NIHR-Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | - Don D Sin
- The University of British Columbia Centre for Heart Lung Innovation, St Paul's Hospital, Vancouver, British Columbia, Canada
- Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Blair H Smith
- Division of Population Health and Genomics, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - María Soler Artigas
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
- Department of Psychiatry, Hospital Universitari Vall d'Hebron, Barcelona, Spain
- Biomedical Network Research Centre on Mental Health (CIBERSAM), Instituto de Salud Carlos III, Barcelona, Spain
| | - David Sparrow
- VA Boston Healthcare System, Boston, MA, USA
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | | | - Paul R H J Timmers
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Maarten Van den Berge
- University of Groningen, University Medical Center Groningen, Department of Pulmonology, GRIAC Research Institute, University of Groningen, Groningen, The Netherlands
| | - John C Whittaker
- Target Sciences - R&D, GSK Medicines Research Centre, Stevenage, UK
| | - Prescott G Woodruff
- UCSF Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA, USA
| | | | - Olga G Troyanskaya
- Department of Computer Science, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Olli T Raitakari
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, and Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Ozren Polašek
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
- University of Split School of Medicine, Split, Croatia
| | - Ulf Gyllensten
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala Universitet, Uppsala, Sweden
| | - Igor Rudan
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Nicole M Probst-Hensch
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Holger Schulz
- Institute of Epidemiology, Helmholtz Zentrum Muenchen-German Research Center for Environmental Health, Neuherberg, Germany
- Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Alan L James
- Busselton Population Medical Research Institute, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
- Department of Pulmonary Physiology and Sleep Medicine, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
- School of Medicine and Pharmacology, The University of Western Australia, Crawley, Western Australia, Australia
| | - James F Wilson
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Beate Stubbe
- Department of Internal Medicine B - Cardiology, Intensive Care, Pulmonary Medicine and Infectious Diseases, University Medicine Greifswald, Greifswald, Germany
| | - Eleftheria Zeggini
- Wellcome Sanger Institute, Hinxton, UK
- Institute of Translational Genomics, Helmholtz Zentrum Muenchen - German Research Center for Environmental Health, Neuherberg, Germany
| | - Marjo-Riitta Jarvelin
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, UK
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Unit of Primary Health Care, Oulu University Hospital, Oulu, Finland
- Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, UK
| | - Nick Wareham
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Andrew P Morris
- Department of Biostatistics, University of Liverpool, Liverpool, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Adam S Butterworth
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Robert A Scott
- Target Sciences - R&D, GSK Medicines Research Centre, Stevenage, UK
| | - Robin G Walters
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Deborah A Meyers
- Division of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona, Tucson, AZ, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - David P Strachan
- Population Health Research Institute, St George's, University of London, London, UK
| | - Ian P Hall
- Division of Respiratory Medicine and NIHR-Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | - Martin D Tobin
- Department of Health Sciences, University of Leicester, Leicester, UK.
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK.
| | - Louise V Wain
- Department of Health Sciences, University of Leicester, Leicester, UK.
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK.
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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: 107] [Impact Index Per Article: 17.8] [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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Jerome RN, Pulley JM, Roden DM, Shirey-Rice JK, Bastarache LA, R Bernard G, B Ekstrom L, Lancaster WJ, Denny JC. Using Human 'Experiments of Nature' to Predict Drug Safety Issues: An Example with PCSK9 Inhibitors. Drug Saf 2018; 41:303-311. [PMID: 29185237 DOI: 10.1007/s40264-017-0616-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
INTRODUCTION When a new drug enters the market, its full array of side effects remains to be defined. Current surveillance approaches targeting these effects remain largely reactive. There is a need for development of methods to predict specific safety events that should be sought for a given new drug during development and postmarketing activities. OBJECTIVE We present here a safety signal identification approach applied to a new set of drug entities, inhibitors of the serine protease proprotein convertase subtilisin/kexin type 9 (PCSK9). METHODS Using phenome-wide association study (PheWAS) methods, we analyzed available genotype and clinical data from 29,722 patients, leveraging the known effects of changes in PCSK9 to identify novel phenotypes in which this protein and its inhibitors may have impact. RESULTS PheWAS revealed a significantly reduced risk of hypercholesterolemia (odds ratio [OR] 0.68, p = 7.6 × 10-4) in association with a known loss-of-function variant in PCSK9, R46L. Similarly, laboratory data indicated significantly reduced beta mean low-density lipoprotein cholesterol (- 14.47 mg/dL, p = 2.58 × 10-23) in individuals carrying the R46L variant. The R46L variant was also associated with an increased risk of spina bifida (OR 5.90, p = 2.7 × 10-4), suggesting that further investigation of potential connections between inhibition of PCSK9 and neural tube defects may be warranted. CONCLUSION This novel methodology provides an opportunity to put in place new mechanisms to assess the safety and long-term tolerability of PCSK9 inhibitors specifically, and other new agents in general, as they move into human testing and expanded clinical use.
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Affiliation(s)
- Rebecca N Jerome
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Jill M Pulley
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dan M Roden
- Office of Research, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jana K Shirey-Rice
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Lisa A Bastarache
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Gordon R Bernard
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN, USA
- Office of Research, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Leeland B Ekstrom
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN, USA
- Nashville Biosciences, Nashville, TN, USA
| | - William J Lancaster
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Joshua C Denny
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA
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23
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Ozsoy MG, Özyer T, Polat F, Alhajj R. Realizing drug repositioning by adapting a recommendation system to handle the process. BMC Bioinformatics 2018; 19:136. [PMID: 29649971 PMCID: PMC5898022 DOI: 10.1186/s12859-018-2142-1] [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: 09/14/2017] [Accepted: 03/27/2018] [Indexed: 12/26/2022] Open
Abstract
Background Drug repositioning is the process of identifying new targets for known drugs. It can be used to overcome problems associated with traditional drug discovery by adapting existing drugs to treat new discovered diseases. Thus, it may reduce associated risk, cost and time required to identify and verify new drugs. Nowadays, drug repositioning has received more attention from industry and academia. To tackle this problem, researchers have applied many different computational methods and have used various features of drugs and diseases. Results In this study, we contribute to the ongoing research efforts by combining multiple features, namely chemical structures, protein interactions and side-effects to predict new indications of target drugs. To achieve our target, we realize drug repositioning as a recommendation process and this leads to a new perspective in tackling the problem. The utilized recommendation method is based on Pareto dominance and collaborative filtering. It can also integrate multiple data-sources and multiple features. For the computation part, we applied several settings and we compared their performance. Evaluation results show that the proposed method can achieve more concentrated predictions with high precision, where nearly half of the predictions are true. Conclusions Compared to other state of the art methods described in the literature, the proposed method is better at making right predictions by having higher precision. The reported results demonstrate the applicability and effectiveness of recommendation methods for drug repositioning.
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Affiliation(s)
- Makbule Gulcin Ozsoy
- Department of Computer Engineering, Middle East Technical University, Ankara, Turkey
| | - Tansel Özyer
- Department of Computer Engineering, TOBB University, Ankara, Turkey
| | - Faruk Polat
- Department of Computer Engineering, Middle East Technical University, Ankara, Turkey
| | - Reda Alhajj
- Department of Computer Science, University of Calgary, Calgary, AB, Canada.
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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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25
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Ratan ZA, Son YJ, Haidere MF, Uddin BMM, Yusuf MA, Zaman SB, Kim JH, Banu LA, Cho JY. CRISPR-Cas9: a promising genetic engineering approach in cancer research. Ther Adv Med Oncol 2018; 10:1758834018755089. [PMID: 29434679 PMCID: PMC5802696 DOI: 10.1177/1758834018755089] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 12/22/2017] [Indexed: 12/26/2022] Open
Abstract
Bacteria and archaea possess adaptive immunity against foreign genetic materials through clustered regularly interspaced short palindromic repeat (CRISPR) systems. The discovery of this intriguing bacterial system heralded a revolutionary change in the field of medical science. The CRISPR and CRISPR-associated protein 9 (Cas9) based molecular mechanism has been applied to genome editing. This CRISPR-Cas9 technique is now able to mediate precise genetic corrections or disruptions in in vitro and in vivo environments. The accuracy and versatility of CRISPR-Cas have been capitalized upon in biological and medical research and bring new hope to cancer research. Cancer involves complex alterations and multiple mutations, translocations and chromosomal losses and gains. The ability to identify and correct such mutations is an important goal in cancer treatment. In the context of this complex cancer genomic landscape, there is a need for a simple and flexible genetic tool that can easily identify functional cancer driver genes within a comparatively short time. The CRISPR-Cas system shows promising potential for modeling, repairing and correcting genetic events in different types of cancer. This article reviews the concept of CRISPR-Cas, its application and related advantages in oncology.
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Affiliation(s)
- Zubair Ahmed Ratan
- Department of Biomedical Engineering, Khulna University of Engineering and Technology, Khulna, Bangladesh
| | - Young-Jin Son
- Department of Pharmacy, Sunchon National University, Suncheon, Korea
| | | | | | - Md Abdullah Yusuf
- Department of Microbiology, National Institute of Neurosciences & Hospital, Dhaka, Bangladesh
| | - Sojib Bin Zaman
- International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Jong-Hoon Kim
- Department of Physiology, College of Veterinary Medicine, Chonbuk National University, Iksan 54596, Korea
| | - Laila Anjuman Banu
- Department of Anatomy, Bangabandhu Sheikh Mujib Medical University (BSMMU), Shahbag, Dhaka 1000, Bangladesh
| | - Jae Youl Cho
- Department of Genetic Engineering, Sungkyunkwan University, 2066 Seobu-ro, Suwon 16419, Korea
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Pulley JM, Jerome RN, Zaleski NM, Shirey-Rice JK, Pruijssers AJ, Lavieri RR, Chettiar SN, Naylor HM, Aronoff DM, Edwards DA, Niswender CM, Dugan LL, Crofford LJ, Bernard GR, Holroyd KJ. When Enough Is Enough: Decision Criteria for Moving a Known Drug into Clinical Testing for a New Indication in the Absence of Preclinical Efficacy Data. Assay Drug Dev Technol 2017; 15:354-361. [PMID: 29193979 DOI: 10.1089/adt.2017.821] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Many animal models of disease are suboptimal in their representation of human diseases and lack of predictive power in the success of pivotal human trials. In the context of repurposing drugs with known human safety, it is sometimes appropriate to conduct the "last experiment first," that is, progressing directly to human investigations. However, there are not accepted criteria for when to proceed straight to humans to test a new indication. We propose a specific set of criteria to guide the decision-making around when to initiate human proof of principle without preclinical efficacy studies in animal models. This approach could accelerate the transition of novel therapeutic approaches to human applications.
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Affiliation(s)
- Jill M Pulley
- 1 Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center , Nashville, Tennessee
| | - Rebecca N Jerome
- 1 Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center , Nashville, Tennessee
| | - Nicole M Zaleski
- 1 Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center , Nashville, Tennessee
| | - Jana K Shirey-Rice
- 1 Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center , Nashville, Tennessee
| | - Andrea J Pruijssers
- 1 Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center , Nashville, Tennessee
| | - Robert R Lavieri
- 1 Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center , Nashville, Tennessee
| | - Somsundaram N Chettiar
- 1 Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center , Nashville, Tennessee
| | - Helen M Naylor
- 2 Center for Knowledge Management, Vanderbilt University Medical Center , Nashville, Tennessee
| | - David M Aronoff
- 3 Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine , Nashville, Tennessee
| | - David A Edwards
- 4 Division of Pain Medicine, Department of Anesthesiology, Vanderbilt University School of Medicine , Nashville, Tennessee
| | - Colleen M Niswender
- 5 Department of Pharmacology, Vanderbilt Center for Neuroscience Drug Discovery, Vanderbilt University Medical Center , Nashville, Tennessee.,6 Vanderbilt Kennedy Center for Research on Human Development , Nashville Tennessee
| | - Laura L Dugan
- 7 Division of Geriatric Medicine, Department of Medicine, Vanderbilt University School of Medicine , Nashville, Tennessee
| | - Leslie J Crofford
- 8 Division of Rheumatology and Immunology, Department of Medicine, Vanderbilt University School of Medicine , Nashville, Tennessee
| | - Gordon R Bernard
- 1 Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center , Nashville, Tennessee
| | - Kenneth J Holroyd
- 1 Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center , Nashville, Tennessee.,9 Center for Technology Transfer and Commercialization, Vanderbilt University , Nashville, Tennessee
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Gyawali B, Parsad S, Feinberg BA, Nabhan C. Real-World Evidence and Randomized Studies in the Precision Oncology Era: The Right Balance. JCO Precis Oncol 2017; 1:1-5. [DOI: 10.1200/po.17.00132] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Bishal Gyawali
- Bishal Gyawali, Institute of Cancer Policy, London, United Kingdom; Sandeep Parsad, University of Chicago, Chicago, IL; and Bruce A. Feinberg and Chadi Nabhan, Cardinal Health, Dublin, OH
| | - Sandeep Parsad
- Bishal Gyawali, Institute of Cancer Policy, London, United Kingdom; Sandeep Parsad, University of Chicago, Chicago, IL; and Bruce A. Feinberg and Chadi Nabhan, Cardinal Health, Dublin, OH
| | - Bruce A. Feinberg
- Bishal Gyawali, Institute of Cancer Policy, London, United Kingdom; Sandeep Parsad, University of Chicago, Chicago, IL; and Bruce A. Feinberg and Chadi Nabhan, Cardinal Health, Dublin, OH
| | - Chadi Nabhan
- Bishal Gyawali, Institute of Cancer Policy, London, United Kingdom; Sandeep Parsad, University of Chicago, Chicago, IL; and Bruce A. Feinberg and Chadi Nabhan, Cardinal Health, Dublin, OH
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28
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Computational biology: future challenges for the patenting of repurposed drugs. Pharm Pat Anal 2017; 6:201-203. [PMID: 28818005 DOI: 10.4155/ppa-2017-0018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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