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Wang L, Lu Y, Li D, Zhou Y, Yu L, Mesa Eguiagaray I, Campbell H, Li X, Theodoratou E. The landscape of the methodology in drug repurposing using human genomic data: a systematic review. Brief Bioinform 2024; 25:bbad527. [PMID: 38279645 PMCID: PMC10818097 DOI: 10.1093/bib/bbad527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 11/24/2023] [Accepted: 12/19/2023] [Indexed: 01/28/2024] Open
Abstract
The process of drug development is expensive and time-consuming. In contrast, drug repurposing can be introduced to clinical practice more quickly and at a reduced cost. Over the last decade, there has been a significant expansion of large biobanks that link genomic data to electronic health record data, public availability of various databases containing biological and clinical information and rapid development of novel methodologies and algorithms in integrating different sources of data. This review aims to provide a thorough summary of different strategies that utilize genomic data to seek drug-repositioning opportunities. We searched MEDLINE and EMBASE databases to identify eligible studies up until 1 May 2023, with a total of 102 studies finally included after two-step parallel screening. We summarized commonly used strategies for drug repurposing, including Mendelian randomization, multi-omic-based and network-based studies and illustrated each strategy with examples, as well as the data sources implemented. By leveraging existing knowledge and infrastructure to expedite the drug discovery process and reduce costs, drug repurposing potentially identifies new therapeutic uses for approved drugs in a more efficient and targeted manner. However, technical challenges when integrating different types of data and biased or incomplete understanding of drug interactions are important hindrances that cannot be disregarded in the pursuit of identifying novel therapeutic applications. This review offers an overview of drug repurposing methodologies, providing valuable insights and guiding future directions for advancing drug repurposing studies.
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Affiliation(s)
- Lijuan Wang
- Centre for Global Health, Usher Institute, The University of Edinburgh, Edinburgh, UK
- School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ying Lu
- School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Doudou Li
- School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yajing Zhou
- School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Lili Yu
- School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ines Mesa Eguiagaray
- Centre for Global Health, Usher Institute, The University of Edinburgh, Edinburgh, UK
| | - Harry Campbell
- Centre for Global Health, Usher Institute, The University of Edinburgh, Edinburgh, UK
| | - Xue Li
- School of Public Health and the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Evropi Theodoratou
- Centre for Global Health, Usher Institute, The University of Edinburgh, Edinburgh, UK
- Cancer Research UK Edinburgh Centre, The University of Edinburgh MRC Institute of Genetics and Cancer, Edinburgh, UK
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Silva S, Fatumo S, Nitsch D. Mendelian randomization studies on coronary artery disease: a systematic review and meta-analysis. Syst Rev 2024; 13:29. [PMID: 38225600 PMCID: PMC10790478 DOI: 10.1186/s13643-023-02442-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 12/20/2023] [Indexed: 01/17/2024] Open
Abstract
BACKGROUND Coronary artery disease (CAD) remains one of the leading causes of mortality worldwide. We aimed to summarize what is currently known with regard to causal modifiable risk factors associated with CAD in populations of diverse ancestries through conducting a systematic review and meta-analysis of Mendelian randomization (MR) studies on CAD. METHODS The databases Embase, Medline, Cochrane Library and Web of Science were searched on the 19th and 20th of December 2022 for MR studies with CAD as a primary outcome; keywords of the search strategy included "coronary artery disease" and "mendelian randomization". Studies were included if they were published in the English language, included only human participants, employed Mendelian randomization as the primary methodology and studied CAD as the outcome of interest. The exclusion criteria resulted in the removal of studies that did not align with the predefined inclusion criteria, as well as studies which were systematic reviews themselves, and used the same exposure and outcome source as another study. An ancestry-specific meta-analysis was subsequently conducted on studies which investigated either body mass index, lipid traits, blood pressure or type 2 diabetes as an exposure variable. Assessment of publication bias and sensitivity analyses was conducted for risk of bias assessment in the included studies. RESULTS A total of 1781 studies were identified through the database searches after de-duplication was performed, with 47 studies included in the quantitative synthesis after eligibility screening. Approximately 80% of all included study participants for MR studies on CAD were of European descent irrespective of the exposure of interest, while no study included individuals of African ancestry. We found no evidence of differences in terms of direction of causation between ancestry groups; however, the strength of the respective relationships between each exposure and CAD were different, with this finding most evident when blood pressure was the exposure of interest. CONCLUSIONS Findings from this review suggest that patterns regarding the causational relationship between modifiable risk factors and CAD do not differ in terms of direction when compared across diverse ancestry populations. Differences in the observed strengths of the respective relationships however are indicative of the value of increasing representation in non-European populations, as novel genetic pathways or functional SNPs relating to CAD may be uncovered through a more global analysis. SYSTEMATIC REVIEW REGISTRATION The protocol for this systematic review was registered to the International Prospective Register of Systematic Reviews (PROSPERO) and is publicly available online (CRD42021272726).
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Affiliation(s)
- Sarah Silva
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK.
- The African Computational Genomics (TACG) Research Group, MRC/UVRI, and LSHTM, Entebbe, Uganda.
| | - Segun Fatumo
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK.
- The African Computational Genomics (TACG) Research Group, MRC/UVRI, and LSHTM, Entebbe, Uganda.
| | - Dorothea Nitsch
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
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Gogate A, Belcourt J, Shah M, Wang AZ, Frankel A, Kolmel H, Chalon M, Stephen P, Kolli A, Tawfik SM, Jin J, Bahal R, Rasmussen TP, Manautou JE, Zhong XB. Targeting the Liver with Nucleic Acid Therapeutics for the Treatment of Systemic Diseases of Liver Origin. Pharmacol Rev 2023; 76:49-89. [PMID: 37696583 PMCID: PMC10753797 DOI: 10.1124/pharmrev.123.000815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 08/25/2023] [Accepted: 09/06/2023] [Indexed: 09/13/2023] Open
Abstract
Systemic diseases of liver origin (SDLO) are complex diseases in multiple organ systems, such as cardiovascular, musculoskeletal, endocrine, renal, respiratory, and sensory organ systems, caused by irregular liver metabolism and production of functional factors. Examples of such diseases discussed in this article include primary hyperoxaluria, familial hypercholesterolemia, acute hepatic porphyria, hereditary transthyretin amyloidosis, hemophilia, atherosclerotic cardiovascular diseases, α-1 antitrypsin deficiency-associated liver disease, and complement-mediated diseases. Nucleic acid therapeutics use nucleic acids and related compounds as therapeutic agents to alter gene expression for therapeutic purposes. The two most promising, fastest-growing classes of nucleic acid therapeutics are antisense oligonucleotides (ASOs) and small interfering RNAs (siRNAs). For each listed SDLO disease, this article discusses epidemiology, symptoms, genetic causes, current treatment options, and advantages and disadvantages of nucleic acid therapeutics by either ASO or siRNA drugs approved or under development. Furthermore, challenges and future perspectives on adverse drug reactions and toxicity of ASO and siRNA drugs for the treatment of SDLO diseases are also discussed. In summary, this review article will highlight the clinical advantages of nucleic acid therapeutics in targeting the liver for the treatment of SDLO diseases. SIGNIFICANCE STATEMENT: Systemic diseases of liver origin (SDLO) contain rare and common complex diseases caused by irregular functions of the liver. Nucleic acid therapeutics have shown promising clinical advantages to treat SDLO. This article aims to provide the most updated information on targeting the liver with antisense oligonucleotides and small interfering RNA drugs. The generated knowledge may stimulate further investigations in this growing field of new therapeutic entities for the treatment of SDLO, which currently have no or limited options for treatment.
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Affiliation(s)
- Anagha Gogate
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut
| | - Jordyn Belcourt
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut
| | - Milan Shah
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut
| | - Alicia Zongxun Wang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut
| | - Alexis Frankel
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut
| | - Holly Kolmel
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut
| | - Matthew Chalon
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut
| | - Prajith Stephen
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut
| | - Aarush Kolli
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut
| | - Sherouk M Tawfik
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut
| | - Jing Jin
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut
| | - Raman Bahal
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut
| | - Theodore P Rasmussen
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut
| | - José E Manautou
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut
| | - Xiao-Bo Zhong
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut
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Common and Rare PCSK9 Variants Associated with Low-Density Lipoprotein Cholesterol Levels and the Risk of Diabetes Mellitus: A Mendelian Randomization Study. Int J Mol Sci 2022; 23:ijms231810418. [PMID: 36142332 PMCID: PMC9499600 DOI: 10.3390/ijms231810418] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/01/2022] [Accepted: 09/05/2022] [Indexed: 11/29/2022] Open
Abstract
PCSK9 is a candidate locus for low-density lipoprotein cholesterol (LDL-C) levels. The cause–effect relationship between LDL-C levels and diabetes mellitus (DM) has been suggested to be mechanism-specific. To identify the role of PCSK9 and genome-wide association study (GWAS)-significant variants in LDL-C levels and the risk of DM by using Mendelian randomization (MR) analysis, a total of 75,441 Taiwan Biobank (TWB) participants was enrolled for a GWAS to determine common and rare PCSK9 variants and their associations with LDL-C levels. MR studies were also conducted to determine the association of PCSK9 variants and LDL-C GWAS-associated variants with DM. A regional plot association study with conditional analysis of the PCSK9 locus revealed that PCSK9 rs10788994, rs557211, rs565436, and rs505151 exhibited genome-wide significant associations with serum LDL-C levels. Imputation data revealed that three rare nonsynonymous mutations—namely, rs151193009, rs768846693, and rs757143429—exhibited genome-wide significant association with LDL-C levels. A stepwise regression analysis indicated that seven variants exhibited independent associations with LDL-C levels. On the basis of two-stage least squares regression (2SLS), MR analyses conducted using weighted genetic risk scores (WGRSs) of seven PCSK9 variants or WGRSs of 41 LDL-C GWAS-significant variants revealed significant association with prevalent DM (p = 0.0098 and 5.02 × 10−7, respectively), which became nonsignificant after adjustment for LDL-C levels. A sensitivity analysis indicated no violation of the exclusion restriction assumption regarding the influence of LDL-C-level-determining genotypes on the risk of DM. Common and rare PCSK9 variants are independently associated with LDL-C levels in the Taiwanese population. The results of MR analyses executed using genetic instruments based on WGRSs derived from PCSK9 variants or LDL-C GWAS-associated variants demonstrate an inverse association between LDL-C levels and DM.
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Peng K, Huang YN, Sarwal V, Alachkar H, Wong‐Beringer A, Mangul S. Integrating big data computational skills in education to facilitate reproducibility and transparency in pharmaceutical sciences. JOURNAL OF THE AMERICAN COLLEGE OF CLINICAL PHARMACY 2021. [DOI: 10.1002/jac5.1519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Kerui Peng
- Department of Clinical Pharmacy School of Pharmacy, University of Southern California Los Angeles California 90089 USA
| | - Yu Ning Huang
- Department of Clinical Pharmacy School of Pharmacy, University of Southern California Los Angeles California 90089 USA
| | - Varuni Sarwal
- Department of Computer Science University of California Los Angeles California 90095 USA
| | - Houda Alachkar
- Department of Clinical Pharmacy School of Pharmacy, University of Southern California Los Angeles California 90089 USA
| | - Annie Wong‐Beringer
- Department of Clinical Pharmacy School of Pharmacy, University of Southern California Los Angeles California 90089 USA
| | - Serghei Mangul
- Department of Clinical Pharmacy School of Pharmacy, University of Southern California Los Angeles California 90089 USA
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Abstract
Diabetes mellitus is a major risk factor for coronary heart disease (CHD). The major form of diabetes mellitus is type 2 diabetes mellitus (T2D), which is thus largely responsible for the CHD association in the general population. Recent years have seen major advances in the genetics of T2D, principally through ever-increasing large-scale genome-wide association studies. This article addresses the question of whether this expanding knowledge of the genomics of T2D provides insight into the etiologic relationship between T2D and CHD. We will investigate this relationship by reviewing the evidence for shared genetic loci between T2D and CHD; by examining the formal testing of this interaction (Mendelian randomization studies assessing whether T2D is causal for CHD); and then turn to the implications of this genetic relationship for therapies for CHD, for therapies for T2D, and for therapies that affect both. In conclusion, the growing knowledge of the genetic relationship between T2D and CHD is beginning to provide the promise for improved prevention and treatment of both disorders.
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Affiliation(s)
- Mark O. Goodarzi
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jerome I. Rotter
- Institute for Translational Genomics and Population Sciences and Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
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Newman CB, Preiss D, Tobert JA, Jacobson TA, Page RL, Goldstein LB, Chin C, Tannock LR, Miller M, Raghuveer G, Duell PB, Brinton EA, Pollak A, Braun LT, Welty FK. Statin Safety and Associated Adverse Events: A Scientific Statement From the American Heart Association. Arterioscler Thromb Vasc Biol 2019; 39:e38-e81. [PMID: 30580575 DOI: 10.1161/atv.0000000000000073] [Citation(s) in RCA: 375] [Impact Index Per Article: 75.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
One in 4 Americans >40 years of age takes a statin to reduce the risk of myocardial infarction, ischemic stroke, and other complications of atherosclerotic disease. The most effective statins produce a mean reduction in low-density lipoprotein cholesterol of 55% to 60% at the maximum dosage, and 6 of the 7 marketed statins are available in generic form, which makes them affordable for most patients. Primarily using data from randomized controlled trials, supplemented with observational data where necessary, this scientific statement provides a comprehensive review of statin safety and tolerability. The review covers the general patient population, as well as demographic subgroups, including the elderly, children, pregnant women, East Asians, and patients with specific conditions such as chronic disease of the kidney and liver, human immunodeficiency viral infection, and organ transplants. The risk of statin-induced serious muscle injury, including rhabdomyolysis, is <0.1%, and the risk of serious hepatotoxicity is ≈0.001%. The risk of statin-induced newly diagnosed diabetes mellitus is ≈0.2% per year of treatment, depending on the underlying risk of diabetes mellitus in the population studied. In patients with cerebrovascular disease, statins possibly increase the risk of hemorrhagic stroke; however, they clearly produce a greater reduction in the risk of atherothrombotic stroke and thus total stroke, as well as other cardiovascular events. There is no convincing evidence for a causal relationship between statins and cancer, cataracts, cognitive dysfunction, peripheral neuropathy, erectile dysfunction, or tendonitis. In US clinical practices, roughly 10% of patients stop taking a statin because of subjective complaints, most commonly muscle symptoms without raised creatine kinase. In contrast, in randomized clinical trials, the difference in the incidence of muscle symptoms without significantly raised creatinine kinase in statin-treated compared with placebo-treated participants is <1%, and it is even smaller (0.1%) for patients who discontinued treatment because of such muscle symptoms. This suggests that muscle symptoms are usually not caused by pharmacological effects of the statin. Restarting statin therapy in these patients can be challenging, but it is important, especially in patients at high risk of cardiovascular events, for whom prevention of these events is a priority. Overall, in patients for whom statin treatment is recommended by current guidelines, the benefits greatly outweigh the risks.
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Tragante V, Hemerich D, Alshabeeb M, Brænne I, Lempiäinen H, Patel RS, den Ruijter HM, Barnes MR, Moore JH, Schunkert H, Erdmann J, Asselbergs FW. Druggability of Coronary Artery Disease Risk Loci. CIRCULATION-GENOMIC AND PRECISION MEDICINE 2019; 11:e001977. [PMID: 30354342 DOI: 10.1161/circgen.117.001977] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
BACKGROUND Genome-wide association studies have identified multiple loci associated with coronary artery disease and myocardial infarction, but only a few of these loci are current targets for on-market medications. To identify drugs suitable for repurposing and their targets, we created 2 unique pipelines integrating public data on 49 coronary artery disease/myocardial infarction-genome-wide association studies loci, drug-gene interactions, side effects, and chemical interactions. METHODS We first used publicly available genome-wide association studies results on all phenotypes to predict relevant side effects, identified drug-gene interactions, and prioritized candidates for repurposing among existing drugs. Second, we prioritized gene product targets by calculating a druggability score to estimate how accessible pockets of coronary artery disease/myocardial infarction-associated gene products are, then used again the genome-wide association studies results to predict side effects, excluded loci with widespread cross-tissue expression to avoid housekeeping and genes involved in vital processes and accordingly ranked the remaining gene products. RESULTS These pipelines ultimately led to 3 suggestions for drug repurposing: pentolinium, adenosine triphosphate, and riociguat (to target CHRNB4, ACSS2, and GUCY1A3, respectively); and 3 proteins for drug development: LMOD1 (leiomodin 1), HIP1 (huntingtin-interacting protein 1), and PPP2R3A (protein phosphatase 2, regulatory subunit b-double prime, α). Most current therapies for coronary artery disease/myocardial infarction treatment were also rediscovered. CONCLUSIONS Integration of genomic and pharmacological data may prove beneficial for drug repurposing and development, as evidence from our pipelines suggests.
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Affiliation(s)
- Vinicius Tragante
- Division of Heart and Lungs, Department of Cardiology (V.T., D.H., F.W.A.)
| | - Daiane Hemerich
- Division of Heart and Lungs, Department of Cardiology (V.T., D.H., F.W.A.).,University Medical Center Utrecht, Utrecht University, The Netherlands. CAPES Foundation, Ministry of Education of Brazil, Brasília (D.H.)
| | - Mohammad Alshabeeb
- Developmental Medicine Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Kingdom of Saudi Arabia (M.A.)
| | - Ingrid Brænne
- Institute for Cardiogenetics, University of Lübeck, Germany (I.B., J.E.)
| | | | - Riyaz S Patel
- Institute of Cardiovascular Science, University College London, United Kingdom (R.P., F.W.A.). Bart's Heart Centre, St Bartholomew's Hospital, London, United Kingdom (R.P.).,William Harvey Research Institute, Centre for Translational Bioinformatics, Barts and The London School of Medicine and Dentistry, Charterhouse Square, United Kingdom (M.R.B.)
| | | | - Michael R Barnes
- William Harvey Research Institute, Centre for Translational Bioinformatics, Barts and The London School of Medicine and Dentistry, Charterhouse Square, United Kingdom (M.R.B.)
| | - Jason H Moore
- Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia (J.H.M.)
| | - Heribert Schunkert
- Deutsches Herzzentrum München, Technische Universität München, Germany (H.S.).,DZHK (German Center for Cardiovascular Research), partner site Munich Heart Alliance, Germany (H.S.)
| | - Jeanette Erdmann
- Institute for Cardiogenetics, University of Lübeck, Germany (I.B., J.E.).,DZHK (German Research Center for Cardiovascular Research), partner site Hamburg/Lübeck/Kiel, Munich, Germany (J.E.).,University Heart Center Lübeck, Germany (J.E.)
| | - Folkert W Asselbergs
- Division of Heart and Lungs, Department of Cardiology (V.T., D.H., F.W.A.).,Institute of Cardiovascular Science, University College London, United Kingdom (R.P., F.W.A.). Bart's Heart Centre, St Bartholomew's Hospital, London, United Kingdom (R.P.).,Durrer Center for Cardiovascular Research, Netherlands Heart Institute, Utrecht (F.W.A.).,Institute of Cardiovascular Science, Faculty of Population Health Sciences, University College London, United Kingdom (F.W.A.)
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Karami F, Salahshourifar I, Houshmand M. The Study of rs693 and rs515135 in APOB in People with Familial Hypercholestrolemia. CELL JOURNAL 2018; 21:86-91. [PMID: 30507093 PMCID: PMC6275425 DOI: 10.22074/cellj.2019.5692] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 06/03/2018] [Indexed: 11/04/2022]
Abstract
Objective APOB-related familial hypercholesterolemia (FH) is the most common hereditary hyperchlosterolemia with
an autosomal dominant pattern. A number of APOB variants are the most important risk factors for hyperchlosterolemia.
APOB is a large glycoprotein that plays an important role in the metabolism of lipoproteins in the human body. Small
changes in the structure and function of APOB can cause major problems in lipid metabolism. Two forms of APOB are
produced by an editing process of gene replication. APOB48 is required for the production of chylomicrons in the small
intestine and APOB100 is essential in liver for the production of very low density lipoprotein (VLDL) and is also a ligand
for LDL receptor (LDLR) that mediates LDL endocytosis.
Materials and Methods In this case-control study, rs693 (in exon 26 of APOB) and rs515135 (5 'end of APOB) single
nucleotide polymorphisms (SNPs) were analyzed in 120 cases of familial hypercholesterolemia and 120 controls. Both
SNPs were genotyped by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) where
PCR products were digested with specific restriction enzymes recognising each single nucleotide polymorphism.
Results This study was analyzed by odds-ratio (OR) and its 95% confidence interval (CI) to examine the association of
the two SNPs with familial hypercholostermia susceptibility. Statistical analysis showed that both SNPs were in Hardy-
Weinberg equilibrium.
Conclusion We found no significant relationship between rs515135 and familiar hypercholesterolemia. However,
there was a significant association between the C allele of rs693 and high familial cholesterol levels. Furthermore, it
seems the dominant model of T allele occurrence has a protective role in emergence of disease.
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Affiliation(s)
- Fatemeh Karami
- Department of Biology, Science Faculty, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Iman Salahshourifar
- Department of Biology, Science Faculty, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Masoud Houshmand
- Department of Medical Genetics, National Institute for Genetic Engineering and Biotechnology, Tehran, Iran. Electronic Address:
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Blood CSF1 and CXCL12 as Causal Mediators of Coronary Artery Disease. J Am Coll Cardiol 2018; 72:300-310. [DOI: 10.1016/j.jacc.2018.04.067] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 03/26/2018] [Accepted: 04/16/2018] [Indexed: 11/21/2022]
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Filippatos TD, Panagiotopoulou T, Tzavella E, Elisaf MS. Hypolipidemic Drugs and Diabetes Mellitus-Mechanisms and Data From Genetic Trials. J Cardiovasc Pharmacol Ther 2018; 23:187-191. [PMID: 29409336 DOI: 10.1177/1074248418757011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Clinical trials and meta-analyses have shown that statins can dose dependently increase the incidence of new-onset diabetes mellitus (DM) especially in patients with underlying abnormalities of carbohydrate homeostasis. Mendelian randomization studies support these findings since genetic variants in the gene encoding the target of statins, the enzyme 3-hydroxy-3-methylglutaryl coenzyme A reductase, are associated with increased incidence of new-onset DM, suggesting that the so-called diabetogenic effect of statins is an "on-target effect" possibly related to their main mechanism of action, that is the increased low-density lipoprotein (LDL) receptor expression. Additionally, Mendelian randomization studies have shown that genetic variants as proxies of other drugs that increase LDL receptor expression (ezetimibe and proprotein convertase subtilisin/kexin type 9 [PCSK9] inhibitors) also increase the risk of new-onset DM. This concept is supported by the fact of decreased DM prevalence in patients with familial hypercholesterolemia who have decreased LDL receptor expression. In contrast, hypolipidemic drugs, such as the cholesteryl ester transfer protein inhibitors, that decrease LDL cholesterol without directly interfering with the LDL receptor expression do not seem to detrimentally affect carbohydrate homeostasis. However, the clinical trials of ezetimibe and PCSK9 inhibitors have not shown an increased DM risk, possibly suggesting that other potential non-well-defined "off-target effects" of hypolipidemic drugs may affect carbohydrate homeostasis. Thus, the long-term effect of hypolipidemic drugs on DM risk depends not only on their final mechanism of hypolipidemic action but also on other "on-target" and "off-target" effects of these drugs.
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Affiliation(s)
- Theodosios D Filippatos
- 1 Department of Internal Medicine, School of Medicine, University of Ioannina, Ioannina, Greece
| | - Thalia Panagiotopoulou
- 1 Department of Internal Medicine, School of Medicine, University of Ioannina, Ioannina, Greece
| | - Eleftheria Tzavella
- 1 Department of Internal Medicine, School of Medicine, University of Ioannina, Ioannina, Greece
| | - Moses S Elisaf
- 1 Department of Internal Medicine, School of Medicine, University of Ioannina, Ioannina, Greece
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Tragante V, Gho JMIH, Felix JF, Vasan RS, Smith NL, Voight BF, Palmer C, van der Harst P, Moore JH, Asselbergs FW. Gene Set Enrichment Analyses: lessons learned from the heart failure phenotype. BioData Min 2017; 10:18. [PMID: 28559929 PMCID: PMC5446754 DOI: 10.1186/s13040-017-0137-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 05/09/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genetic studies for complex diseases have predominantly discovered main effects at individual loci, but have not focused on genomic and environmental contexts important for a phenotype. Gene Set Enrichment Analysis (GSEA) aims to address this by identifying sets of genes or biological pathways contributing to a phenotype, through gene-gene interactions or other mechanisms, which are not the focus of conventional association methods. RESULTS Approaches that utilize GSEA can now take input from array chips, either gene-centric or genome-wide, but are highly sensitive to study design, SNP selection and pruning strategies, SNP-to-gene mapping, and pathway definitions. Here, we present lessons learned from our experience with GSEA of heart failure, a particularly challenging phenotype due to its underlying heterogeneous etiology. CONCLUSIONS This case study shows that proper data handling is essential to avoid false-positive results. Well-defined pipelines for quality control are needed to avoid reporting spurious results using GSEA.
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Affiliation(s)
- Vinicius Tragante
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Johannes M. I. H. Gho
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Janine F. Felix
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Ramachandran S. Vasan
- Departments of Medicine and Preventive Medicine, Boston University School of Medicine, Boston, MA USA
| | - Nicholas L. Smith
- Department of Epidemiology, University of Washington, Seattle, WA USA
| | - Benjamin F. Voight
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - CHARGE Heart Failure Working Group
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Departments of Medicine and Preventive Medicine, Boston University School of Medicine, Boston, MA USA
- Department of Epidemiology, University of Washington, Seattle, WA USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
- Population Pharmacogenetics Group, University of Dundee, Dundee, UK
- Department of Cardiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department of Biostatistics and Epidemiology, Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
- Durrer Center for Cardiovascular Research, ICIN-Netherlands Heart Institute, Utrecht, The Netherlands
- Institute of Cardiovascular Science, Faculty of Population Health Sciences, University College London, London, UK
- Farr Institute of Health Informatics Research and Institute of Health Informatics, University College London, London, UK
| | - Colin Palmer
- Population Pharmacogenetics Group, University of Dundee, Dundee, UK
| | - Pim van der Harst
- Department of Cardiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Jason H. Moore
- Department of Biostatistics and Epidemiology, Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - Folkert W. Asselbergs
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
- Durrer Center for Cardiovascular Research, ICIN-Netherlands Heart Institute, Utrecht, The Netherlands
- Institute of Cardiovascular Science, Faculty of Population Health Sciences, University College London, London, UK
- Farr Institute of Health Informatics Research and Institute of Health Informatics, University College London, London, UK
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13
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Effect on Fasting Serum Glucose Levels of Adding Ezetimibe to Statins in Patients With Nondiabetic Hypercholesterolemia. Am J Cardiol 2016; 118:1812-1820. [PMID: 27756478 DOI: 10.1016/j.amjcard.2016.08.071] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 08/23/2016] [Accepted: 08/23/2016] [Indexed: 11/21/2022]
Abstract
Statin therapy is associated with a slightly increased risk of developing diabetes mellitus and insulin resistance in patients without diabetes. Ezetimibe combined with statins may be considered for high-risk patients who do not achieve optimal low-density lipoprotein cholesterol lowering on statin monotherapy or who are statin intolerant. Changes in fasting serum glucose (FSG) levels during ezetimibe, ezetimibe/statin, and statin treatments were assessed using data pooled from clinical trials in hypercholesterolemic and heterozygous familial hypercholesterolemic patients, who were or were not receiving statin therapy. Study types included first-line trials in statin-naive/wash-out patients and second-line add-on and uptitration studies in patients on stable statin therapy. Similar analyses of FSG changes were performed separately for each study type in patients who were nondiabetic at baseline. Across all study types and treatments, mean FSG increases from baseline were small (0.5 to 3.7 mg/dl with ezetimibe/statin; 0.2 to 4.6 mg/dl with statins) and decreased over time; between-treatment differences (0.3 to 1.4 mg/dl) were nonsignificant for all comparisons. Proportions of patients with elevated FSG ≥126 mg/dl during therapy were low and similar for all treatments in the overall cohort (1.2% to 4.3%). Elevations were highest (3.3% to 25.7%) among patients with baseline factors characteristic of metabolic syndrome and prediabetes, including higher FSG, body mass index, and triglyceride levels, and numerically lower baseline high-density lipoprotein cholesterol; however, these factors were not related to FSG increases. Changes in low-density lipoprotein cholesterol, body mass index, high-density lipoprotein cholesterol, triglycerides, and apolipoprotein B were not significantly correlated with FSG increases. In conclusion, statin therapy was associated with small FSG increases, and the addition of ezetimibe did not further increase FSG levels beyond those of statins when given to patients who are statin naive or those on statin therapy.
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14
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White J, Swerdlow DI, Preiss D, Fairhurst-Hunter Z, Keating BJ, Asselbergs FW, Sattar N, Humphries SE, Hingorani AD, Holmes MV. Association of Lipid Fractions With Risks for Coronary Artery Disease and Diabetes. JAMA Cardiol 2016; 1:692-9. [PMID: 27487401 PMCID: PMC5642865 DOI: 10.1001/jamacardio.2016.1884] [Citation(s) in RCA: 209] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
IMPORTANCE Low-density lipoprotein cholesterol (LDL-C) is causally related to coronary artery disease (CAD), but the relevance of high-density lipoprotein cholesterol (HDL-C) and triglycerides (TGs) is uncertain. Lowering of LDL-C levels by statin therapy modestly increases the risk of type 2 diabetes, but it is unknown whether this effect is specific to statins. OBJECTIVE To investigate the associations of 3 routinely measured lipid fractions with CAD and diabetes through mendelian randomization (MR) using conventional MR and making use of newer approaches, such as multivariate MR and MR-Egger, that address the pleiotropy of genetic instruments where relevant. DESIGN, SETTING, AND PARTICIPANTS Published data from genome-wide association studies were used to construct genetic instruments and then applied to investigate associations between lipid fractions and the risk of CAD and diabetes using MR approaches that took into account pleiotropy of genetic instruments. The study was conducted from March 12 to December 31, 2015. MAIN OUTCOMES AND MEASURES Coronary artery disease and diabetes. RESULTS Genetic instruments composed of 130 single-nucleotide polymorphisms (SNPs) were used for LDL-C (explaining 7.9% of its variance), 140 SNPs for HDL-C (6.6% of variance), and 140 SNPs for TGs (5.9% of variance). A 1-SD genetically instrumented elevation in LDL-C levels (equivalent to 38 mg/dL) and TG levels (equivalent to 89 mg/dL) was associated with higher CAD risk; odds ratios (ORs) were 1.68 (95% CI, 1.51-1.87) for LDL-C and 1.28 (95% CI, 1.13-1.45) for TGs. The corresponding OR for HDL-C (equivalent to a 16-mg/dL increase) was 0.95 (95% CI, 0.85-1.06). All 3 lipid traits were associated with a lower risk of type 2 diabetes. The ORs were 0.79 (95% CI, 0.71-0.88) for LDL-C and 0.83 (95% CI, 0.76-0.90) for HDL-C per 1-SD elevation. For TG, the MR estimates for diabetes were inconsistent, with MR-Egger giving an OR of 0.83 (95%CI, 0.72-0.95) per 1-SD elevation. CONCLUSIONS AND RELEVANCE Routinely measured lipid fractions exhibit contrasting associations with the risk of CAD and diabetes. Increased LDL-C, HDL-C, and possibly TG levels are associated with a lower risk of diabetes. This information will be relevant to the design of clinical trials of lipid-modifying agents, which should carefully monitor participants for dysglycemia and the incidence of diabetes.
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Affiliation(s)
- Jon White
- UCL Genetics Institute, University College London, Gower Street,
London WC1E 6BT
| | - Daniel I Swerdlow
- Farr Institute at University College London, Gower Street, London
WC1E 6BT
- Department of Medicine, Imperial College London, London W12
0HS
| | - David Preiss
- Clinical Trial Service Unit & Epidemiological Studies Unit
(CTSU), Nuffield Department of Population Health, University of Oxford, Richard Doll
Building, Old Road Campus, Roosevelt Drive, Oxford OX3 7LF
| | - Zammy Fairhurst-Hunter
- The Wellcome Trust Centre for Human Genetics, Roosevelt Drive,
University of Oxford, Oxford, OX3 7BN
| | - Brendan J Keating
- Children’s Hospital of Philadelphia, Philadelphia, PA 19104,
USA
- Department of Surgery, University of Pennsylvania, 3400 Spruce
Street, Philadelphia, PA 19104, ISA
| | - Folkert W Asselbergs
- Department of Cardiology, Division Heart & Lungs, UMC
Utrecht, the Netherlands
- Durrer Center for Cardiogenetic Research, ICIN-Netherlands Heart
Institute, Utrecht, the Netherlands
- Institute of Cardiovascular Science, University College London,
Gower Street, London, United Kingdom
| | - Naveed Sattar
- Institute of Cardiovascular and Medical Science, University of
Glasgow, Glasgow
| | - Steve E Humphries
- Cardiovascular Genetics, BHF Laboratories, Institute Cardiovascular
Science, University College London, Gower Street, London WC1E 6BT
| | - Aroon D Hingorani
- Farr Institute at University College London, Gower Street, London
WC1E 6BT
- Institute of Cardiovascular Science, University College London,
Gower Street, London, United Kingdom
| | - Michael V Holmes
- Clinical Trial Service Unit & Epidemiological Studies Unit
(CTSU), Nuffield Department of Population Health, University of Oxford, Richard Doll
Building, Old Road Campus, Roosevelt Drive, Oxford OX3 7LF
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