1
|
Echeverría O, Angulo-Aguado M, Vela R, Calderón-Ospina C, Parra K, Contreras N, Morel A, Cabrera R, Restrepo C, Ramírez-Santana C, Ortega-Recalde O, Rojas-Quintana ME, Murcia L, Gaviria-Sabogal CC, Valero N, Fonseca-Mendoza DJ. The polygenic implication of clopidogrel responsiveness: Insights from platelet reactivity analysis and next-generation sequencing. PLoS One 2024; 19:e0306445. [PMID: 38991024 PMCID: PMC11239111 DOI: 10.1371/journal.pone.0306445] [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: 01/15/2024] [Accepted: 06/18/2024] [Indexed: 07/13/2024] Open
Abstract
Clopidogrel is widely used worldwide as an antiplatelet therapy in patients with acute coronary disease. Genetic factors influence interindividual variability in response. Some studies have explored the polygenic contributions in the drug response, generating pharmacogenomic risk scores (PgxPRS). Importantly, these factors are less explored in underrepresented populations, such as Latin-American countries. Identifying patients at risk of high-on-treatment platelet reactivity (HTPR) is highly valuable in translational medicine. In this study we used a custom next-generation sequencing (NGS) panel composed of 91 single nucleotide polymorphisms (SNPs) and 28 genes related to clopidogrel metabolism, to analyze 70 patients with platelet reactivity values, assessed through closure time (CT). Our results demonstrated the association of SNPs with HTPR and non-HTPR, revealing the strongest associations with rs2286823 (OR: 5,0; 95% CI: 1,02-24,48; p: 0,03), rs2032582 (OR: 4,41; 95% CI: 1,20-16,12; p: 0,019), and rs1045642 (OR: 3,38; 95% CI: 0,96-11,9; p: 0,05). Bivariate regression analysis demonstrated the significant association of several SNPs with the CT value, a "surrogate" biomarker of clopidogrel response. Exploratory results from the LASSO regression model showed a high discriminatory capacity between HTPR and non-HTPR patients (AUC: 0,955), and the generated PgxPRS demonstrated a significant negative association between the risk score, CT value, and the condition of HTPR and non-HTPR. To our knowledge, our study addresses for the first time the analysis of the polygenic contribution in platelet reactivity using NGS and establishes PgxPRS derived from the LASSO model. Our results demonstrate the polygenic implication of clopidogrel response and offer insights applicable to the translational medicine of antiplatelet therapy in an understudied population.
Collapse
Affiliation(s)
- Omar Echeverría
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá D.C., Colombia
| | - Mariana Angulo-Aguado
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá D.C., Colombia
| | - Ricardo Vela
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá D.C., Colombia
| | - Carlos Calderón-Ospina
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá D.C., Colombia
| | - Katherine Parra
- Hospital Universitario Mayor—Méderi—Universidad del Rosario, Bogotá D.C., Colombia
| | - Nora Contreras
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá D.C., Colombia
| | - Adrien Morel
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá D.C., Colombia
| | - Rodrigo Cabrera
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá D.C., Colombia
| | - Carlos Restrepo
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá D.C., Colombia
| | - Carolina Ramírez-Santana
- Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad del Rosario, Bogotá D.C., Colombia
| | - Oscar Ortega-Recalde
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá D.C., Colombia
- Departamento de Morfología, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá D.C., Colombia
| | - Manuel Eduardo Rojas-Quintana
- Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad del Rosario, Bogotá D.C., Colombia
- Division of Rheumatology, Allergy and Clinical Immunology, University of California, Davis, CA, United States of America
| | - Luisa Murcia
- Hospital Universitario Mayor—Méderi—Universidad del Rosario, Bogotá D.C., Colombia
| | - Cristian Camilo Gaviria-Sabogal
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá D.C., Colombia
| | - Nattaly Valero
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá D.C., Colombia
| | - Dora Janeth Fonseca-Mendoza
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá D.C., Colombia
| |
Collapse
|
2
|
Yang G, González P, Moneró M, Carrasquillo K, Renta JY, Hernandez-Suarez DF, Botton MR, Melin K, Scott SA, Ruaño G, Roche-Lima A, Alarcon C, Ritchie MD, Perera MA, Duconge J. Discovery of Ancestry-specific Variants Associated with Clopidogrel Response among Caribbean Hispanics. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.29.23296372. [PMID: 37873439 PMCID: PMC10593031 DOI: 10.1101/2023.09.29.23296372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Background High on-treatment platelet reactivity (HTPR) with clopidogrel is predictive of ischemic events in adults with coronary artery disease. Despite strong data suggesting HTPR varies with ethnicity, including clinical and genetic variables, no genome-wide association study (GWAS) of clopidogrel response has been performed among Caribbean Hispanics. This study aimed to identify genetic predictors of HTPR in a cohort of Caribbean Hispanic cardiovascular patients from Puerto Rico. Methods Local Ancestry inference (LAI) and traditional GWASs were performed on a cohort of 511 clopidogrel-treated patients, stratified based on their P2Y12 reaction units (PRU) into responders and non-responders (HTPR). Results The LAI GWAS identified variants within the CYP2C19 region associated with HTPR, predominantly driven by individuals of European ancestry and absent in those with native ancestry. Incorporating local ancestry adjustment notably enhanced our ability to detect associations. While no loci reached traditional GWAS significance, three variants showed suggestive significance at chromosomes 3, 14 and 22 (OSBPL10 rs1376606, DERL3 rs5030613, and RGS6 rs9323567). In addition, a variant in the UNC5C gene on chromosome 4 was associated with an increased risk of HTPR. These findings were not identified in other cohorts, highlighting the unique genetic landscape of Caribbean Hispanics. Conclusion This is the first GWAS of clopidogrel response in Hispanics, confirming the relevance of the CYP2C19 cluster, particularly among those with European ancestry, and also identifying novel markers in a diverse patient population. Further studies are warranted to replicate our findings in other diverse cohorts and meta-analyses.
Collapse
Affiliation(s)
- Guang Yang
- Department of Pharmacology, Center for Pharmacogenomics, Feinberg School of Medicine, Northwestern University, Chicago IL 60611, United States
| | - Pablo González
- Department of Pharmacology, School of Medicine, University of Puerto Rico - Medical Sciences Campus, San Juan, Puerto Rico, 00936, United States
| | - Mariangeli Moneró
- Department of Pharmacology, School of Medicine, University of Puerto Rico - Medical Sciences Campus, San Juan, Puerto Rico, 00936, United States
| | - Kelvin Carrasquillo
- Research Centers in Minority Institutions (RCMI) Program, Center for Collaborative Research in Health Disparities (CCRHD), Academic Affairs Deanship, University of Puerto Rico - Medical Sciences Campus, San Juan, Puerto Rico, 00936, United States
| | - Jessicca Y. Renta
- Research Centers in Minority Institutions (RCMI) Program, Center for Collaborative Research in Health Disparities (CCRHD), Academic Affairs Deanship, University of Puerto Rico - Medical Sciences Campus, San Juan, Puerto Rico, 00936, United States
| | - Dagmar F. Hernandez-Suarez
- Department of Translational Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, United States
| | - Mariana R. Botton
- Transplant Immunology and Personalized Medicine Unit, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Kyle Melin
- Department of Pharmacy Practice, School of Pharmacy, University of Puerto Rico - Medical Sciences Campus, San Juan, Puerto Rico, 00936, United States
| | - Stuart A. Scott
- Department of Pathology, Stanford University, Palo Alto, CA 94304, United States
| | - Gualberto Ruaño
- Institute of Living at Hartford Hospital, Hartford, CT 06102, United States
| | - Abiel Roche-Lima
- Research Centers in Minority Institutions (RCMI) Program, Center for Collaborative Research in Health Disparities (CCRHD), Academic Affairs Deanship, University of Puerto Rico - Medical Sciences Campus, San Juan, Puerto Rico, 00936, United States
| | - Cristina Alarcon
- Department of Pharmacology, Center for Pharmacogenomics, Feinberg School of Medicine, Northwestern University, Chicago IL 60611, United States
| | - Marylyn D. Ritchie
- Department of Genetics and Institute for Biomedical Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, United States
| | - Minoli A. Perera
- Department of Pharmacology, Center for Pharmacogenomics, Feinberg School of Medicine, Northwestern University, Chicago IL 60611, United States
| | - Jorge Duconge
- Research Centers in Minority Institutions (RCMI) Program, Center for Collaborative Research in Health Disparities (CCRHD), Academic Affairs Deanship, University of Puerto Rico - Medical Sciences Campus, San Juan, Puerto Rico, 00936, United States
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Puerto Rico - Medical Sciences Campus, San Juan, Puerto Rico, 00936, United States
| |
Collapse
|
3
|
Khan H, Ghulam T, Ahmed N, Rafai Babar M, Calaminus SDJ, Zuhair Yusuf M. Should aspirin be replaced with ADP blockers and anti-GPVI to manage thrombosis? VASCULAR BIOLOGY (BRISTOL, ENGLAND) 2023; 5:e220010. [PMID: 37931411 PMCID: PMC9986383 DOI: 10.1530/vb-22-0010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 10/31/2022] [Indexed: 11/08/2023]
Abstract
Platelets have a pivotal role in maintaining cardiovascular homeostasis. They are kept docile by endothelial-derived mediators. Aberration in haemostatic balance predisposes an individual to an elevated risk of a prothrombotic environment. Anti-platelet therapy has been a key component to reduce this risk. However, understanding how these medications affect the balance between the activation and inhibition of platelets is critical. There is no evidence that a key anti-platelet therapy - aspirin, may not be the most efficacious medicine of choice, as it can compromise both platelet inhibition and activation pathways. In this review, the rationale of aspirin as an anti-thrombotic drug has been critically discussed. This review looks at how recently published trials are raising key questions about the efficacy and safety of aspirin in countering cardiovascular diseases. There is an increasing portfolio of evidence that identifies that although aspirin is a very cheap and accessible drug, it may be used in a manner that is not always beneficial to a patient, and a more nuanced and targeted use of aspirin may increase its clinical benefit and maximize patient response. The questions about the use of aspirin raise the potential for changes in its clinical use for dual anti-platelet therapy. This highlights the need to ensure that treatment is targeted in the most effective manner and that other anti-platelet therapies may well be more efficacious and beneficial for CVD patients in their standard and personalized approaches.
Collapse
Affiliation(s)
- Hafsa Khan
- International Centre for Chemical and Biological Sciences (ICCBS), Pakistan
| | | | - Naseer Ahmed
- Institute of Basic Medical Sciences, Khyber Medical University, Pakistan
| | | | | | | |
Collapse
|
4
|
Silgado-Guzmán DF, Angulo-Aguado M, Morel A, Niño-Orrego MJ, Ruiz-Torres DA, Contreras Bravo NC, Restrepo CM, Ortega-Recalde O, Fonseca-Mendoza DJ. Characterization of ADME Gene Variation in Colombian Population by Exome Sequencing. Front Pharmacol 2022; 13:931531. [PMID: 35846994 PMCID: PMC9280300 DOI: 10.3389/fphar.2022.931531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/08/2022] [Indexed: 11/18/2022] Open
Abstract
In genes related to drug pharmacokinetics, molecular variations determine interindividual variability in the therapeutic efficacy and adverse drug reactions. The assessment of single-nucleotide variants (SNVs) is used with growing frequency in pharmacogenetic practice, and recently, high-throughput genomic analyses obtained through next-generation sequencing (NGS) have been recognized as powerful tools to identify common, rare and novel variants. These genetic profiles remain underexplored in Latin-American populations, including Colombia. In this study, we investigated the variability of 35 genes included in the ADME core panel (absorption, distribution, metabolism, and excretion) by whole-exome sequencing (WES) of 509 unrelated Colombian individuals with no previous reports of adverse drug reactions. Rare variants were filtered according to the minor allele frequencies (MAF) <1% and potential deleterious consequences. The functional impact of novel and rare missense variants was assessed using an optimized framework for pharmacogenetic variants. Bioinformatic analyses included the identification of clinically validated variants described in PharmGKB and ClinVar databases. Ancestry from WES data was inferred using the R package EthSEQ v2.1.4. Allelic frequencies were compared to other populations reported in the public gnomAD database. Our analysis revealed that rare missense pharmacogenetic variants were 2.1 times more frequent than common variants with 121 variants predicted as potentially deleterious. Rare loss of function (LoF) variants were identified in 65.7% of evaluated genes. Regarding variants with clinical pharmacogenetic effect, our study revealed 89 sequence variations in 28 genes represented by missense (62%), synonymous (22.5%), splice site (11.2%), and indels (3.4%). In this group, ABCB1, ABCC2, CY2B6, CYP2D6, DPYD, NAT2, SLC22A1, and UGTB2B7, are the most polymorphic genes. NAT2, CYP2B6 and DPYD metabolizer phenotypes demonstrated the highest variability. Ancestry analysis indicated admixture in 73% of the population. Allelic frequencies exhibit significant differences with other Latin-American populations, highlighting the importance of pharmacogenomic studies in populations of different ethnicities. Altogether, our data revealed that rare variants are an important source of variability in pharmacogenes involved in the pharmacokinetics of drugs and likely account for the unexplained interindividual variability in drug response. These findings provide evidence of the utility of WES for pharmacogenomic testing and into clinical practice.
Collapse
Affiliation(s)
| | - Mariana Angulo-Aguado
- Center for Research in Genetics and Genomics—CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, Colombia
| | - Adrien Morel
- Center for Research in Genetics and Genomics—CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, Colombia
| | - María José Niño-Orrego
- Center for Research in Genetics and Genomics—CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, Colombia
| | - Daniel-Armando Ruiz-Torres
- Center for Research in Genetics and Genomics—CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, Colombia
| | - Nora Constanza Contreras Bravo
- Center for Research in Genetics and Genomics—CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, Colombia
| | - Carlos Martin Restrepo
- Center for Research in Genetics and Genomics—CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, Colombia
| | - Oscar Ortega-Recalde
- Center for Research in Genetics and Genomics—CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, Colombia
- *Correspondence: Oscar Ortega-Recalde, ; Dora Janeth Fonseca-Mendoza,
| | - Dora Janeth Fonseca-Mendoza
- Center for Research in Genetics and Genomics—CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, Colombia
- *Correspondence: Oscar Ortega-Recalde, ; Dora Janeth Fonseca-Mendoza,
| |
Collapse
|
5
|
Pharmacogenetics to Avoid Adverse Drug Reactions. J Pers Med 2022; 12:jpm12020159. [PMID: 35207648 PMCID: PMC8879652 DOI: 10.3390/jpm12020159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 01/11/2022] [Indexed: 01/27/2023] Open
|
6
|
Corredor-Orlandelli D, Sambracos-Parrado S, Mantilla-García S, Tovar-Tirado J, Vega-Ramírez V, Mendoza-Ayús SD, Peña LC, Leal MF, Rodríguez-Carrillo J, León-Torres J, Pardo-Oviedo JM, Parra Abaunza K, Contreras Bravo NC, Ortega-Recalde O, Fonseca Mendoza DJ. Association between Paraoxonase-1 p.Q192R Polymorphism and Coronary Artery Disease susceptibility in the Colombian Population. Vasc Health Risk Manag 2021; 17:689-699. [PMID: 34764653 PMCID: PMC8573264 DOI: 10.2147/vhrm.s330766] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 09/11/2021] [Indexed: 12/24/2022] Open
Abstract
Background Paraoxonase-1 (PON1), a glycoprotein associated with serum high-density lipoprotein (HDL), has a central role in metabolizing lipid peroxides, exhibiting antiatherogenic properties. The polymorphism p.Q192R has been previously associated with coronary artery disease (CAD) susceptibility and clopidogrel response. Purpose We aimed at investigating the association of PON1 p.Q192R with CAD and clopidogrel response in Colombian population. Patients and Methods The study was conducted among 163 patients diagnosed with CAD and treated with clopidogrel. The allele frequencies for the PON1 192Q and 192R alleles were determined in cases and Latin-American controls obtained from the public database gnomAD (n = 17,711). Response to clopidogrel was determined by assessing the platelet function using the INNOVANCE PFA-200 System. We determined the association between PON1 p.Q192R polymorphism, increased susceptibility to CAD and high on-treatment platelet reactivity (HPR) by using odds ratio (OR) and 95% confidence interval (CI) on four genetic models. Results The allele frequencies for the PON1 192Q and 192R alleles were 0.60 and 0.40, respectively. The allele distribution was found to be statistically different from the control group and other ethnic groups. The allele 192R was positively associated with decreased susceptibility to CAD under a dominant model (OR, 0.58; 95% CI, 0.42–0.8; P < 0.01). We found no association between the polymorphism and HPR. Conclusion We propose that PON1 p.Q192R is a potentially useful marker for CAD susceptibility in the Colombian population and lacks association with HPR under clopidogrel treatment.
Collapse
Affiliation(s)
- David Corredor-Orlandelli
- Center for Research in Genetics and Genomics - CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, Colombia
| | - Santiago Sambracos-Parrado
- Center for Research in Genetics and Genomics - CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, Colombia
| | - Santiago Mantilla-García
- Center for Research in Genetics and Genomics - CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, Colombia
| | - Josué Tovar-Tirado
- Center for Research in Genetics and Genomics - CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, Colombia
| | - Valentina Vega-Ramírez
- Center for Research in Genetics and Genomics - CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, Colombia
| | - Santiago David Mendoza-Ayús
- Center for Research in Genetics and Genomics - CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, Colombia
| | - Laura Catalina Peña
- Center for Research in Genetics and Genomics - CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, Colombia
| | - María Fernanda Leal
- Center for Research in Genetics and Genomics - CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, Colombia
| | - Juliana Rodríguez-Carrillo
- Center for Research in Genetics and Genomics - CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, Colombia
| | - Juanita León-Torres
- Center for Research in Genetics and Genomics - CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, Colombia
| | | | | | - Nora Contreras Contreras Bravo
- Center for Research in Genetics and Genomics - CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, Colombia
| | - Oscar Ortega-Recalde
- Center for Research in Genetics and Genomics - CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, Colombia
| | - Dora Janeth Fonseca Mendoza
- Center for Research in Genetics and Genomics - CIGGUR, GENIUROS Research Group, School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, Colombia
| |
Collapse
|