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Nasir B, Vinayagam R, Massi L, Nagaraj S, Toombs M, Rae K. A Systematic Review Exploring Empirical Pharmacogenomics Research Within Global Indigenous Populations. Mol Genet Genomic Med 2024; 12:e70018. [PMID: 39435544 PMCID: PMC11494250 DOI: 10.1002/mgg3.70018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 02/19/2024] [Accepted: 09/25/2024] [Indexed: 10/23/2024] Open
Abstract
BACKGROUND This systematic review aims to highlight the scope of pharmacogenomics research within global Indigenous populations. This review also explores the barriers and facilitators of pharmacogenomics research within this population. METHODOLOGY A systematic review of literature was conducted to identify and present an understanding of current empirical evidence demonstrating the conduct of genomics or pharmacogenomics research within global Indigenous populations (PROSPERO registration: CRD42021257226). Using key search terms, relevant databases were searched for articles published between January 2010 and July 2022. Screening, data extraction, and analysis was conducted using well-defined inclusion criteria. Quality assessment and risk of bias appraisal was conducted using the mixed methods appraisal tool. Indigenous community engagement and participation in genomics research was assessed using the social-ecological framework. RESULTS From the 427 articles identified, 77 articles met inclusion criteria and underwent full-text screening. Of these, 30 articles were included in the final review, with 16 being quantitative and 14 either qualitative or mixed methods studies. Most studies were conducted with native Indigenous populations from the United States of America (36%). Content analysis revealed that studies either explored genetic variations associated with disease in Indigenous populations (23%) or markers for drug metabolism (30%) or were designed to understand perspectives of genomics research within this population (47%). Perspectives included the exploration of the role of participants in research, benefits or outcomes achieved from participation in genomics research, and levels of Indigenous engagement and participation in genomics research. CONCLUSIONS This review highlights a growing gap in Indigenous genomics research globally. It presents several important considerations from Indigenous participants, identifying how researchers can co-create culturally safe and inclusive design, implementation, analysis, and subsequent outcomes of genomics research involving Indigenous people. Indigenous governance, self-determination and leadership is essential, with researchers required to be responsive to such fundamental partnerships for research to progress.
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Affiliation(s)
- Bushra Farah Nasir
- Toowoomba Regional Clinical Unit, Medical School, Faculty of MedicineThe University of QueenslandToowoombaQueenslandAustralia
| | - Ritwika Vinayagam
- School of Public Health, Faculty of MedicineThe University of QueenslandBrisbaneQueenslandAustralia
| | - Luciana Massi
- Mater Research InstituteThe University of QueenslandBrisbaneQueenslandAustralia
| | - Shivashankar H. Nagaraj
- Centre for Genomics and Personalised Health and the School of Biomedical SciencesQueensland University of TechnologyBrisbaneQueenslandAustralia
- Translational Research InstituteQueensland University of TechnologyBrisbaneQueenslandAustralia
| | - Maree Toombs
- School of Population Health, Faculty of Medicine and HealthThe University of New South WalesSydneyNew South WalesAustralia
| | - Kym M. Rae
- Mater Research InstituteThe University of QueenslandBrisbaneQueenslandAustralia
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Hiratsuka VY, Beans JA, Byars C, Yracheta J, Spicer PG. Use of Cognitive Interviews in the Development of a Survey Assessing American Indian and Alaska Native Adult Perspectives on Genetics and Biological Specimens. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2024; 21:1144. [PMID: 39338028 PMCID: PMC11430884 DOI: 10.3390/ijerph21091144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Revised: 08/19/2024] [Accepted: 08/23/2024] [Indexed: 09/30/2024]
Abstract
The cognitive interview process is a method to validate a survey instrument's face validity and enhance confidence in item interpretation, as well as a method to engage communities in the research process. Trained American Indian and Alaska Native (AIAN) interviewers conducted retrospective cognitive interviews at three AIAN communities to assess the item quality of a 131-item survey item that measures AIAN knowledge and attitudes on genetics and biological specimens. A cognitive interview process was used to assess cultural consonance, thought processes used when considering survey instructions, items and responses, and language preference of survey items in the development of a survey to assess public knowledge and attitudes on genetics. Content analysis was used to analyze interview data. Survey instructions, items and scales generated no cognitive difficulties. The participants noted being unfamiliar with terminology used to describe genetic and biological specimens. In several cases, the participants' written response in the survey and verbal response in the interview did not align. A resultant 52-item survey for use in AIAN communities was finalized. Cognitive interviewing is resource-intensive; however, ignoring community engagement during survey development results in inappropriate interpretations about culturally diverse populations such as AIAN peoples.
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Affiliation(s)
| | | | | | | | - Paul G. Spicer
- Center for Applied Social Research, University of Oklahoma, Norman, OK 73072, USA;
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Claw KG, Dorr CR, Woodahl EL. Implementing community-engaged pharmacogenomics in Indigenous communities. Nat Commun 2024; 15:920. [PMID: 38296967 PMCID: PMC10831049 DOI: 10.1038/s41467-024-45032-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 01/11/2024] [Indexed: 02/02/2024] Open
Affiliation(s)
- Katrina G Claw
- Department of Biomedical Informatics, Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
| | - Casey R Dorr
- Hennepin Healthcare Research Institute, Minneapolis, MN, USA
- Nephrology Division, Department of Medicine, Hennepin Healthcare, University of Minnesota, Minneapolis, MN, USA
- Experimental and Clinical Pharmacology Department, College of Pharmacy, University of Minnesota, Minneapolis, MN, USA
- Clinical and Translational Sciences Institute, University of Minnesota, Minneapolis, MN, USA
| | - Erica L Woodahl
- Department of Biomedical and Pharmaceutical Sciences, University of Montana, Missoula, MT, USA
- L.S. Skaggs Institute for Health Innovation, University of Montana, Missoula, MT, USA
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Singh DK, Basit A, Rettie AE, Alade N, Thummel K, Prasad B. Characterization of Gla proteoforms and non-Gla peptides of gamma carboxylated proteins: Application to quantification of prothrombin proteoforms in human plasma. Anal Chim Acta 2023; 1284:341972. [PMID: 37996163 PMCID: PMC10789187 DOI: 10.1016/j.aca.2023.341972] [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: 07/13/2023] [Revised: 10/17/2023] [Accepted: 10/26/2023] [Indexed: 11/25/2023]
Abstract
Gamma (γ) carboxylation is an essential post-translational modification in vitamin K-dependent proteins (VKDPs), involved in maintaining critical biological homeostasis. Alterations in the abundance or activity of these proteins have pharmacological and pathological consequences. Importantly, low levels of fully γ-carboxylated clotting factors increase plasma des-γ-carboxy precursors resulting in little or no biological activity. Therefore, it is important to characterize the levels of γ-carboxylation that reflect the active state of these proteins. The conventional enzyme-linked immunosorbent assay for protein induced by vitamin K absence or antagonist II (PIVKA-II) quantification uses an antibody that is not applicable to distinguish different γ-carboxylation states. Liquid chromatography-mass spectrometry (LC-MS) approaches have been utilized to distinguish different γ-carboxylated proteoforms, however, these attempts were impeded by poor sensitivity due to spontaneous neutral loss of CO2 and simultaneous cleavage of the backbone bond in the collision cell. In this study, we utilized an alkaline mobile phase in combination with polarity switching (positive and negative ionization modes) to simultaneously identify and quantify γ-carboxylated VKDPs. The method was applied to compare Gla proteomics of prothrombin (FII) in 10 μL plasma samples of healthy control and warfarin-treated adults. We also identified surrogate non-Gla peptides for seven other VKDPs to quantify total (active plus inactive) protein levels. The total protein approach (TPA) was used to quantify absolute levels of the VKDPs in human plasma.
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Affiliation(s)
- Dilip Kumar Singh
- Department of Pharmaceutical Sciences, Washington State University, Spokane, WA, USA
| | - Abdul Basit
- Department of Pharmaceutical Sciences, Washington State University, Spokane, WA, USA
| | - Allan E Rettie
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
| | - Nathan Alade
- Department of Pharmaceutics, University of Washington, Seattle, WA, USA
| | - Kenneth Thummel
- Department of Pharmaceutics, University of Washington, Seattle, WA, USA
| | - Bhagwat Prasad
- Department of Pharmaceutical Sciences, Washington State University, Spokane, WA, USA.
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Chatron N, Boulven M, Montagut-Romans A, Ponsot F, Jacolot M, Caruel H, Benoît E, Popowycz F, Lattard V. Design of a structure-activity relationship model of vitamin K epoxide reductase (VKORC1) inhibitors combining chemical synthesis of new compounds, enzymatic assays and molecular modelling. Bioorg Med Chem 2023; 94:117453. [PMID: 37741121 DOI: 10.1016/j.bmc.2023.117453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 08/13/2023] [Accepted: 08/21/2023] [Indexed: 09/25/2023]
Abstract
Vitamin K antagonists (VKAs) anticoagulants have been used since the 1950s as medicines and rodenticides. These molecules are mainly 4-hydroxycoumarin derivatives and act by inhibiting the vitamin K epoxide reductase (VKORC1), an endoplasmic reticulum membrane resident enzyme. However, many VKORC1 mutations have been reported over the last decade, inducing VKAs resistances and thus treatments failures. Although studies have reported experimental and computational investigations of VKAs based on VKORC1 structural homology models, the development of new effective anticoagulants has been quite complex due to the lack of structural data and reliable structure-activity relationships. However, the recent publication of VKORC1 crystal structure provides new information for further studies. Based on these findings, we combined chemical synthesis, enzymatic assays and molecular modelling methods to design a structure-activity relationship (SAR) model. Our results proved that the lipophilicity, the membrane permeability of inhibitors and their affinity towards human VKORC1 enzyme are the main characteristics for potent anticoagulants. Our SAR model managed to rank compounds according to their ability to inhibit the human VKORC1. Such a tool might constitute an alternative to evaluate new molecules potency before their chemical synthesis and biological assessment and might assist the development of new VKAs.
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Affiliation(s)
- Nolan Chatron
- USC 1233 RS2GP, VetAgro Sup, INRAE, University of Lyon, 69280 Marcy L'Etoile, France.
| | - Manon Boulven
- Univ Lyon, INSA Lyon, Université Lyon 1, CNRS, CPE Lyon, UMR 5246, ICBMS, 1 rue Victor Grignard, 69621 Villeurbanne Cedex, France; Liphatech, Bonnel, 47480 Pont-du-Casse, France
| | - Adrien Montagut-Romans
- Univ Lyon, INSA Lyon, Université Lyon 1, CNRS, CPE Lyon, UMR 5246, ICBMS, 1 rue Victor Grignard, 69621 Villeurbanne Cedex, France; Liphatech, Bonnel, 47480 Pont-du-Casse, France
| | - Flavien Ponsot
- Univ Lyon, INSA Lyon, Université Lyon 1, CNRS, CPE Lyon, UMR 5246, ICBMS, 1 rue Victor Grignard, 69621 Villeurbanne Cedex, France
| | - Maïwenn Jacolot
- Univ Lyon, INSA Lyon, Université Lyon 1, CNRS, CPE Lyon, UMR 5246, ICBMS, 1 rue Victor Grignard, 69621 Villeurbanne Cedex, France
| | | | - Etienne Benoît
- USC 1233 RS2GP, VetAgro Sup, INRAE, University of Lyon, 69280 Marcy L'Etoile, France
| | - Florence Popowycz
- Univ Lyon, INSA Lyon, Université Lyon 1, CNRS, CPE Lyon, UMR 5246, ICBMS, 1 rue Victor Grignard, 69621 Villeurbanne Cedex, France
| | - Virginie Lattard
- USC 1233 RS2GP, VetAgro Sup, INRAE, University of Lyon, 69280 Marcy L'Etoile, France
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Gwynne K, Jiang S, Venema R, Christie V, Boughtwood T, Ritha M, Skinner J, Ali N, Rambaldini B, Calma T. Genomics and inclusion of Indigenous peoples in high income countries. Hum Genet 2023; 142:1407-1416. [PMID: 37479894 PMCID: PMC10449672 DOI: 10.1007/s00439-023-02587-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 07/07/2023] [Indexed: 07/23/2023]
Abstract
Genomics research related to Indigenous people has been at worst exploitative and at best, retrospectively on a journey to improve effective engagement of Indigenous individuals and communities. Genomics can positively impact all stages of clinical management, and to improve genomic effectiveness researchers aggregate genomic data from diverse global sub-populations, such as shared ancestry groupings, as people within these groupings will have a greater proportion of shared DNA traits. While genomics is already being used worldwide to improve lives, its utility and effectiveness has not been maximized for individuals with Indigenous ancestry. Several large datasets of human genetic variation have been made publicly available, of which the most widely used is the Genome Aggregation Database (gnomAD), but none of these databases currently contain any population-specific data for Indigenous populations. There are many reasons why Indigenous people have been largely left out of genomics research and, because of this, miss out on the benefits offered. It is also clear that if research is to be effective, it needs to be done 'with' and not 'on' Indigenous communities. This systematic review of the literature regarding Indigenous peoples (in high income countries) and genomics aims to review the existing literature and identify areas of strength and weakness in study design and conduct, focusing on the effectiveness of Indigenous community engagement.
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Affiliation(s)
- Kylie Gwynne
- Djurali Centre for Aboriginal and Torres Strait Islander Education and Research (Formerly Known as Poche Centre for Indigenous Health), Macquarie University, Walanga Muru Building, 6 First Walk, Sydney, NSW, 2113, Australia
| | - Shirley Jiang
- University of Toronto, 27 King's College Circuit, Toronto, Canada
| | - Robertson Venema
- University of Toronto, 27 King's College Circuit, Toronto, Canada
| | - Vita Christie
- Djurali Centre for Aboriginal and Torres Strait Islander Education and Research (Formerly Known as Poche Centre for Indigenous Health), Macquarie University, Walanga Muru Building, 6 First Walk, Sydney, NSW, 2113, Australia.
| | - Tiffany Boughtwood
- Australian Genomics, 50 Flemington Rd, Parkville, VIC, 3052, Australia
- Murdoch Children's Research Institute, Royal Children's Hospital, 50 Flemington Rd, Parkville, VIC, 3052, Australia
| | - Marida Ritha
- Djurali Centre for Aboriginal and Torres Strait Islander Education and Research (Formerly Known as Poche Centre for Indigenous Health), Macquarie University, Walanga Muru Building, 6 First Walk, Sydney, NSW, 2113, Australia
| | - John Skinner
- Djurali Centre for Aboriginal and Torres Strait Islander Education and Research (Formerly Known as Poche Centre for Indigenous Health), Macquarie University, Walanga Muru Building, 6 First Walk, Sydney, NSW, 2113, Australia
| | - Nyesa Ali
- Murdoch Children's Research Institute, Royal Children's Hospital, 50 Flemington Rd, Parkville, VIC, 3052, Australia
| | - Boe Rambaldini
- Djurali Centre for Aboriginal and Torres Strait Islander Education and Research (Formerly Known as Poche Centre for Indigenous Health), Macquarie University, Walanga Muru Building, 6 First Walk, Sydney, NSW, 2113, Australia
| | - Tom Calma
- Djurali Centre for Aboriginal and Torres Strait Islander Education and Research (Formerly Known as Poche Centre for Indigenous Health), Macquarie University, Walanga Muru Building, 6 First Walk, Sydney, NSW, 2113, Australia
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Brady A, Misra S, Abdelmalek M, Kekic A, Kunze K, Lim E, Jakob N, Mour G, Keddis MT. The Value of Pharmacogenomics for White and Indigenous Americans after Kidney Transplantation. PHARMACY 2023; 11:125. [PMID: 37624080 PMCID: PMC10457738 DOI: 10.3390/pharmacy11040125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/03/2023] [Accepted: 08/05/2023] [Indexed: 08/26/2023] Open
Abstract
BACKGROUND There is a paucity of evidence to inform the value of pharmacogenomic (PGx) results in patients after kidney transplant and how these results differ between Indigenous Americans and Whites. This study aims to identify the frequency of recommended medication changes based on PGx results and compare the pharmacogenomic (PGx) results and patients' perceptions of the findings between a cohort of Indigenous American and White kidney transplant recipients. METHODS Thirty-one Indigenous Americans and fifty White kidney transplant recipients were studied prospectively. Genetic variants were identified using the OneOme RightMed PGx test of 27 genes. PGx pharmacist generated a report of the genetic variation and recommended changes. Pre- and post-qualitative patient surveys were obtained. RESULTS White and Indigenous American subjects had a similar mean number of medications at the time of PGx testing (mean 13 (SD 4.5)). In the entire cohort, 53% received beta blockers, 30% received antidepressants, 16% anticoagulation, 47% pain medication, and 25% statin therapy. Drug-gene interactions that warranted a clinical action were present in 21.5% of patients. In 12.7%, monitoring was recommended. Compared to the Whites, the Indigenous American patients had more normal CYP2C19 (p = 0.012) and CYP2D6 (p = 0.012) activities. The Indigenous American patients had more normal CYP4F2 (p = 0.004) and lower VKORC (p = 0.041) activities, phenotypes for warfarin drug dosing, and efficacy compared to the Whites. SLC6A4, which affects antidepressant metabolism, showed statistical differences between the two cohorts (p = 0.017); specifically, SLC6A4 had reduced expression in 45% of the Indigenous American patients compared to 20% of the White patients. There was no significant difference in patient perception before and after PGx. CONCLUSIONS Kidney transplant recipients had several drug-gene interactions that were clinically actionable; over one-third of patients were likely to benefit from changes in medications or drug doses based on the PGx results. The Indigenous American patients differed in the expression of drug-metabolizing enzymes and drug transporters from the White patients.
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Affiliation(s)
- Alexandra Brady
- Department of Nephrology and Hypertension, Mayo Clinic, Scottsdale, AZ 85259, USA
| | - Suman Misra
- Department of Nephrology and Hypertension, Mayo Clinic, Scottsdale, AZ 85259, USA
| | - Mina Abdelmalek
- Department of Nephrology and Hypertension, Mayo Clinic, Scottsdale, AZ 85259, USA
| | - Adrijana Kekic
- Department of Pharmacy Clinical Practice, Mayo Clinic, Scottsdale, AZ 85259, USA
| | - Katie Kunze
- Department of Statistics, Mayo Clinic, Scottsdale, AZ 85259, USA
| | - Elisabeth Lim
- Department of Statistics, Mayo Clinic, Scottsdale, AZ 85259, USA
| | - Nicholas Jakob
- Department of Nephrology and Hypertension, Mayo Clinic, Scottsdale, AZ 85259, USA
| | - Girish Mour
- Department of Nephrology and Hypertension, Mayo Clinic, Scottsdale, AZ 85259, USA
| | - Mira T. Keddis
- Department of Nephrology and Hypertension, Mayo Clinic, Scottsdale, AZ 85259, USA
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Zhao L, Zhai Z, Li P. One Rare Warfarin Resistance Case and Possible Mechanism Exploration. Pharmgenomics Pers Med 2023; 16:609-615. [PMID: 37359384 PMCID: PMC10290475 DOI: 10.2147/pgpm.s404474] [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] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 05/26/2023] [Indexed: 06/28/2023] Open
Abstract
One 59-year-old female patient with deep venous thrombosis (DVT) and pulmonary embolism (PE) was treated with 6 mg warfarin once daily as an anticoagulant. Before taking warfarin, her international normalized ratio (INR) was 0.98. Two days after warfarin treatment, her INR did not change from baseline. Due to the high severity of the PE, the patient needed to reach her target range (INR goal = 2.5, range = 2~3) rapidly, so the dose of warfarin was increased from 6 mg daily to 27 mg daily. However, the patient's INR did not improve with the dose escalation, still maintaining an INR of 0.97-0.98. We drew a blood sample half an hour before administering 27 mg warfarin and detected single nucleotide polymorphism for the following genes, which were identified to be relevant with warfarin resistance: CYP2C9 rs1799853, rs1057910, VKORC1 rs9923231, rs61742245, rs7200749, rs55894764, CYP4F2 rs2108622, and GGCX rs2592551. The trough plasma concentration of warfarin was 196.2 ng/mL after 2 days of warfarin administration with 27 mg QD, which was much lower than the therapeutic drug concentration ranges of warfarin (500-3,000 ng/mL). The genotype results demonstrate that the CYP4F2gene has rs2108622 mutation which can explain some aspect of warfarin resistance. Further investigations are necessary to fully characterize other pharmacogenomics or pharmacodynamics determinants of warfarin dose-response in Chinese.
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Affiliation(s)
- Li Zhao
- Pharmacy Department, China-Japan Friendship Hospital, Beijing, People’s Republic of China
| | - Zhenguo Zhai
- Department of Respiratory and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, People’s Republic of China
| | - Pengmei Li
- Pharmacy Department, China-Japan Friendship Hospital, Beijing, People’s Republic of China
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Holail J, Mobarak R, Al-Ghamdi B, Aljada A, Fakhoury H. Association of VKORC1 and CYP2C9 single-nucleotide polymorphisms with warfarin dose adjustment in Saudi patients. Drug Metab Pers Ther 2022; 37:353-359. [PMID: 36476275 DOI: 10.1515/dmpt-2022-0108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 02/14/2022] [Indexed: 12/13/2022]
Abstract
OBJECTIVES Despite its wide usage, warfarin therapy remains challenging due to its narrow therapeutic index, inter-individual response variability, and risk of bleeding. Previous reports have suggested that polymorphisms in VKORC1 and CYP2C9 genes could influence warfarin therapy. Herein, we investigated whether VKORC1 -1173C>T, CYP2C9*2, and CYP2C9*3 gene polymorphisms are associated with warfarin dose adjustment and related bleeding events. METHODS This cross-sectional study was conducted on Saudi adults receiving warfarin for more than 1 month. Their demographics and relevant clinical data were obtained. Genotyping for VKORC1 -1173C>T, CYP2C9*2, and CYP2C9*2 genotypes was performed. RESULTS Patients who are homozygous for the mutant T allele VKORC1 T/T required the lowest warfarin daily maintenance dose, compared to VKORC1 C/T and VKORC1 C/C. Similarly, there was a significant reduction in warfarin daily maintenance dose among CYP2C9*1/*3 and CYP2C9*1/*2 groups compared to CYP2C9*1/*1. However, we found no significant correlation between the studied polymorphisms and warfarin-associated bleeding. CONCLUSIONS Similar to other populations, the VKORC1 and CYP2C9 gene polymorphisms are significantly associated with warfarin dosage in Saudi patients. The presence of at least one copy of the mutant alleles for VKORC1 -1173C>T, CYP2C9*2, and CYP2C9*3 is associated with a significant reduction in warfarin maintenance dose.
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Affiliation(s)
- Jasmine Holail
- Department of Biochemistry and Molecular Medicine, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Reem Mobarak
- Department of Biochemistry and Molecular Medicine, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Bandar Al-Ghamdi
- Heart Center, King Faisal Specialist Hospital and Research Center (KFSH&RC), Riyadh, Saudi Arabia
| | - Ahmad Aljada
- Department of Biochemistry and Molecular Medicine, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Hana Fakhoury
- Department of Biochemistry and Molecular Medicine, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
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Li J, Chen T, Jie F, Xiang H, Huang L, Jiang H, Lu F, Zhu S, Wu L, Tang Y. Impact of VKORC1, CYP2C9, CYP1A2, UGT1A1, and GGCX polymorphisms on warfarin maintenance dose: Exploring a new algorithm in South Chinese patients accept mechanical heart valve replacement. Medicine (Baltimore) 2022; 101:e29626. [PMID: 35866816 PMCID: PMC9302374 DOI: 10.1097/md.0000000000029626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Warfarin is the most recommended oral anticoagulant after artificial mechanical valve replacement therapy. However, the narrow therapeutic window and varying safety and efficacy in individuals make dose determination difficult. It may cause adverse events such as hemorrhage or thromboembolism. Therefore, advanced algorithms are urgently required for the use of warfarin. OBJECTIVE To establish a warfarin dose model for patients after prosthetic mechanical valve replacement in southern China in combination with clinical and genetic variables, and to improve the accuracy and ideal prediction percentage of the model. METHODS Clinical data of 476 patients were tracked and recorded in detail. The gene polymorphisms of VKORC1 (rs9923231, rs9934438, rs7196161, and rs7294), CYP2C9 (rs1057910), CYP1A2 (rs2069514), GGCX (rs699664), and UGT1A1 (rs887829) were determined using Sanger sequencing. Multiple linear regressions were used to analyze the gene polymorphisms and the contribution of clinical data variables; the variables that caused multicollinearity were screened stepwise and excluded to establish an algorithm model for predicting the daily maintenance dose of warfarin. The ideal predicted percentage was used to test clinical effectiveness. RESULTS A total of 395 patients were included. Univariate linear regression analysis suggested that CYP1A2 (rs2069514) and UGT1A1 (rs887829) were not associated with the daily maintenance dose of warfarin. The new algorithm model established based on multiple linear regression was as follows: Y = 1.081 - 0.011 (age) + 1.532 (body surface area)-0.807 (rs9923231 AA) + 1.788 (rs9923231 GG) + 0.530 (rs1057910 AA)-1.061 (rs1057910 AG)-0.321 (rs699664 AA). The model accounted for 61.7% of individualized medication differences, with an ideal prediction percentage of 69%. CONCLUSION GGCX (rs699664) may be a potential predictor of warfarin dose, and our newly established model is expected to guide the individualized use of warfarin in clinical practice in southern China.
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Affiliation(s)
- Jin Li
- Emergency Department of the Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Tao Chen
- School of Science, Nanchang University, Nanchang, China
| | - Fangfang Jie
- School of Science, Nanchang University, Nanchang, China
| | - Haiyan Xiang
- Department of Cardiovascular Surgery, the Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Li Huang
- Department of Cardiovascular Surgery, the Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Hongfa Jiang
- Department of Cardiothoracic Surgery, Jiangxi Chest Hospital, Nanchang, China
| | - Fei Lu
- Comprehensive Intervention Department of the Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Shuqiang Zhu
- Department of Cardiovascular Surgery, the Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Lidong Wu
- Emergency Department of the Second Affiliated Hospital of Nanchang University, Nanchang, China
- * Correspondence: Lidong Wu, Emergency Department of the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330000, China (e-mail: ); Yanhua Tang, Department of Cardiovascular Surgery, the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330000, China (e-mail: )
| | - Yanhua Tang
- Department of Cardiovascular Surgery, the Second Affiliated Hospital of Nanchang University, Nanchang, China
- * Correspondence: Lidong Wu, Emergency Department of the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330000, China (e-mail: ); Yanhua Tang, Department of Cardiovascular Surgery, the Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330000, China (e-mail: )
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Blacksher E, Trinidad SB, Woodbury RB, Hopkins SE, Woodahl EL, Boyer BB, Burke W, Hiratsuka V. Tribal Deliberations about Precision Medicine Research: Addressing Diversity and Inequity in Democratic Deliberation Design and Evaluation. J Empir Res Hum Res Ethics 2022; 17:304-316. [PMID: 35225705 PMCID: PMC9173705 DOI: 10.1177/15562646221081267] [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] [Indexed: 11/17/2022]
Abstract
Deliberative democratic engagement is used around the globe to gather informed public input on contentious collective questions. Yet, rarely has it been used to convene individuals exclusively from Indigenous communities. The relative novelty of using this approach to engage tribal communities and concerns about diversity and inequities raise important methodological questions. We describe the design and quality outcomes for a 2.5-day deliberation that elicited views of American Indian and Alaska Native (AIAN) leaders about the potential value and ethical conduct of precision medicine research (PMR), an emerging approach to research that investigates the health effects of individual genetic variation in tandem with variation in health-relevant practices, social determinants, and environmental exposures. The event met key goals, such as relationship and rapport formation, cross-site learning, equality of opportunity to participate, and respect among participants in the context of disagreement.
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Holail J, Mobarak R, Al-Ghamdi B, Aljada A, Fakhoury H. Association of VKORC1 and CYP2C9 single-nucleotide polymorphisms with warfarin dose adjustment in Saudi patients. Drug Metab Pers Ther 2022; 0:dmdi-2022-0108. [PMID: 35365981 DOI: 10.1515/dmdi-2022-0108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 02/14/2022] [Indexed: 11/15/2022]
Abstract
OBJECTIVES Despite its wide usage, warfarin therapy remains challenging due to its narrow therapeutic index, inter-individual response variability, and risk of bleeding. Previous reports have suggested that polymorphisms in VKORC1 and CYP2C9 genes could influence warfarin therapy. Herein, we investigated whether VKORC1 -1173C>T, CYP2C9*2, and CYP2C9*3 gene polymorphisms are associated with warfarin dose adjustment and related bleeding events. METHODS This cross-sectional study was conducted on Saudi adults receiving warfarin for more than 1 month. Their demographics and relevant clinical data were obtained. Genotyping for VKORC1 -1173C>T, CYP2C9*2, and CYP2C9*2 genotypes was performed. RESULTS Patients who are homozygous for the mutant T allele VKORC1 T/T required the lowest warfarin daily maintenance dose, compared to VKORC1 C/T and VKORC1 C/C. Similarly, there was a significant reduction in warfarin daily maintenance dose among CYP2C9*1/*3 and CYP2C9*1/*2 groups compared to CYP2C9*1/*1. However, we found no significant correlation between the studied polymorphisms and warfarin-associated bleeding. CONCLUSIONS Similar to other populations, the VKORC1 and CYP2C9 gene polymorphisms are significantly associated with warfarin dosage in Saudi patients. The presence of at least one copy of the mutant alleles for VKORC1 -1173C>T, CYP2C9*2, and CYP2C9*3 is associated with a significant reduction in warfarin maintenance dose.
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Affiliation(s)
- Jasmine Holail
- Department of Biochemistry and Molecular Medicine, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Reem Mobarak
- Department of Biochemistry and Molecular Medicine, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Bandar Al-Ghamdi
- Heart Center, King Faisal Specialist Hospital and Research Center (KFSH&RC), Riyadh, Saudi Arabia
| | - Ahmad Aljada
- Department of Biochemistry and Molecular Medicine, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Hana Fakhoury
- Department of Biochemistry and Molecular Medicine, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
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Fohner AE, Dalton R, Skagen K, Jackson K, Claw KG, Hopkins SE, Robinson R, Khan BA, Prasad B, Schuetz EG, Nickerson DA, Thornton TA, Dillard DA, Boyer BB, Thummel KE, Woodahl EL. Characterization of CYP3A pharmacogenetic variation in American Indian and Alaska Native communities, targeting CYP3A4*1G allele function. Clin Transl Sci 2021; 14:1292-1302. [PMID: 33503331 PMCID: PMC8301563 DOI: 10.1111/cts.12970] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 12/13/2020] [Accepted: 12/13/2020] [Indexed: 01/08/2023] Open
Abstract
The frequencies of genetic variants in the CYP3A4 and CYP3A5 genes differ greatly across global populations, leading to profound differences in the metabolic activity of these enzymes and resulting drug metabolism rates, with important consequences for therapeutic safety and efficacy. Yet, the impact of genetic variants on enzyme activity are incompletely described, particularly in American Indian and Alaska Native (AIAN) populations. To characterize genetic variation in CYP3A4 and CYP3A5 and its effect on enzyme activity, we partnered with AIAN people living in two regions of Alaska: Yup'ik Alaska Native people living in the Yukon-Kuskokwim Delta region of rural southwest Alaska and AIAN people receiving care at the Southcentral Foundation in Anchorage, Alaska. We identified low frequencies of novel and known variation in CYP3A4 and CYP3A5, including low frequencies of the CYP3A4*1G and CYP3A5*1 variants, and linkage disequilibrium patterns that differed from those we previously identified in an American Indian population in western Montana. We also identified increased activity of the CYP3A4*1G allele in vitro and in vivo. We demonstrated that the CYP3A4*1G allele confers increased protein content in human lymphoblastoid cells and both increased protein content and increased activity in human liver microsomes. We confirmed enhanced CYP3A4-mediated 4β-vitamin D hydroxylation activity in Yup'ik people with the CYP3A4*1G allele. AIAN people in Alaska and Montana who carry the CYP3A4*1G allele-coupled with low frequency of the functional CYP3A5*1 variant-may metabolize CYP3A substrates more rapidly than people with the reference CYP3A4 allele.
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Affiliation(s)
- Alison E. Fohner
- Department of EpidemiologyUniversity of WashingtonSeattleWashingtonUSA
| | - Rachel Dalton
- Department of Biomedical and Pharmaceutical SciencesUniversity of MontanaMissoulaMontanaUSA
| | - Kasse Skagen
- Department of Biomedical and Pharmaceutical SciencesUniversity of MontanaMissoulaMontanaUSA
| | - Konner Jackson
- Department of Biomedical and Pharmaceutical SciencesUniversity of MontanaMissoulaMontanaUSA
| | - Katrina G. Claw
- Division of Biomedical Informatics and Personalized MedicineUniversity of ColoradoAuroraColoradoUSA
| | - Scarlett E. Hopkins
- Department of Obstetrics and GynecologyOregon Health & Science UniversityPortlandOregonUSA
| | | | | | - Bhagwat Prasad
- Department of PharmaceuticsUniversity of WashingtonSeattleWashingtonUSA
| | - Erin G. Schuetz
- Department of Pharmaceutical SciencesSt. Jude Children’s Research HospitalMemphisTennesseeUSA
| | | | | | | | - Bert B. Boyer
- Department of Obstetrics and GynecologyOregon Health & Science UniversityPortlandOregonUSA
| | | | - Erica L. Woodahl
- Department of Biomedical and Pharmaceutical SciencesUniversity of MontanaMissoulaMontanaUSA
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Qian JC, Cai JP, Hu GX. Han Chinese specific cytochrome P450 polymorphisms and their impact on the metabolism of anti-hypertensive drugs with adrenoreceptor blocking properties. Expert Opin Drug Metab Toxicol 2021; 17:707-716. [PMID: 33910442 DOI: 10.1080/17425255.2021.1921147] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Introduction: Cytochrome P450 (CYP) is a monooxygenase superfamily mediating the elimination of anti-hypertensive drugs. Polymorphisms of CYP would lead to differential drug efficacy. Building relationships between genotype and phenotype will benefit individual medical treatment of hypertension.Areas covered: The review systematically summarizes the polymorphisms of four CYPs (CYP2C9, CYP2C19, CYP2D6, and CYP3A4) concentrated distributed in the Han Chinese population. Moreover, the activity of variants on metabolizing anti-hypertensive drugs are reviewed, especially drugs with adrenoceptor blocking properties, as well as their clinical relevancies.Expert opinion: The polymorphisms of CYP can cause stratification in drug exposure of antihypertensive drugs. Although the clinical relevance has been built partially, the translational medicine still lacks reliable data support. Furthermore, the studies have demonstrated that even the same CYP variant will exhibit different catalytic capability for different drugs, which is another obstacle to hinder its application. With the deepening of multiomics research and structural biology, nucleotide polymorphisms can be combined with transcriptome, proteome, metabolome and molecular structure analyses to study the susceptibility to hypertension and drug efficacy. A complete data chain would be further estabolished by combining studies of pharmacokinetics-pharmacodynamics, which can effectively promote the precise application of anti-hypertensive drugs.
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Affiliation(s)
- Jian-Chang Qian
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou Zhejiang, P.R. China
| | - Jian-Ping Cai
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou Zhejiang, P.R. China.,The MOH Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Beijing P.R. China
| | - Guo-Xin Hu
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou Zhejiang, P.R. China
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15
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Henderson LM, Hopkins SE, Boyer BB, Thornton TA, Rettie AE, Thummel KE. In Vivo Functional Effects of CYP2C9 M1L, a Novel and Common Variant in the Yup'ik Alaska Native Population. Drug Metab Dispos 2021; 49:345-352. [PMID: 33632714 PMCID: PMC8008381 DOI: 10.1124/dmd.120.000301] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/04/2021] [Indexed: 12/03/2022] Open
Abstract
Alaska Native people are under-represented in genetic research but have unique gene variation that may critically impact their response to pharmacotherapy. Full resequencing of CYP2C9 in a cross-section of this population identified CYP2C9 Met1Leu (M1L), a novel, relatively common single nucleotide polymorphism hypothesized to confer CYP2C9 poor metabolizer phenotype by disrupting the start codon. M1L is present at a minor allele frequency of 6.3% in Yup'ik Alaska Native people and thus can contribute to the risk of an adverse drug response from narrow-therapeutic-index CYP2C9 substrates such as (S)-warfarin. This study's objective was to characterize the catalytic efficiency of the Leu1 variant enzyme in vivo by evaluating the pharmacokinetic behavior of naproxen, a probe substrate for CYP2C9 activity, in genotyped Yup'ik participants. We first confirmed the selectivity of (S)-naproxen O-demethylation by CYP2C9 using activity-phenotyped human liver microsomes and selective cytochrome P450 inhibitors and then developed and validated a novel liquid chromatography mass spectrometry method for simultaneous quantification of (S)-naproxen, (S)-O-desmethylnaproxen, and naproxen acyl glucuronide in human urine. The average ratio of (S)-O-desmethylnaproxen to unchanged (S)-naproxen in urine was 18.0 ± 8.0 (n = 11) for the homozygous CYP2C9Met1 reference group and 10.3 ± 6.6 (n = 11) for the Leu1 variant carrier group (P = 0.011). The effect of M1L variation on CYP2C9 function and its potential to alter the pharmacokinetics of drugs metabolized by the enzyme has clinical implications and should be included in a variant screening panel when pharmacogenetic testing in the Alaska Native population is warranted. SIGNIFICANCE STATEMENT: The novel CYP2C9 Met1Leu variant in Alaska Native people was recently identified. This study validated (S)-naproxen as a CYP2C9 probe substrate to characterize the in vivo functional activity of the CYP2C9 Leu1 variant. The results of this pharmacogenetic-pharmacokinetic study suggest that the CYP2C9 Leu1 variant exhibits loss of enzyme activity. This finding may be important to consider when administering narrow-therapeutic-index medications metabolized by CYP2C9 and also compels further investigation to characterize novel genetic variation in understudied populations.
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Affiliation(s)
- Lindsay M Henderson
- Departments of Pharmaceutics (L.M.H., K.E.T.), Biostatistics (T.A.T.), and Medicinal Chemistry (A.E.R.), University of Washington, Seattle, Washington; and Department of Obstetrics and Gynecology (S.E.H., B.B.B.), Oregon Health & Science University, Portland, Oregon
| | - Scarlett E Hopkins
- Departments of Pharmaceutics (L.M.H., K.E.T.), Biostatistics (T.A.T.), and Medicinal Chemistry (A.E.R.), University of Washington, Seattle, Washington; and Department of Obstetrics and Gynecology (S.E.H., B.B.B.), Oregon Health & Science University, Portland, Oregon
| | - Bert B Boyer
- Departments of Pharmaceutics (L.M.H., K.E.T.), Biostatistics (T.A.T.), and Medicinal Chemistry (A.E.R.), University of Washington, Seattle, Washington; and Department of Obstetrics and Gynecology (S.E.H., B.B.B.), Oregon Health & Science University, Portland, Oregon
| | - Timothy A Thornton
- Departments of Pharmaceutics (L.M.H., K.E.T.), Biostatistics (T.A.T.), and Medicinal Chemistry (A.E.R.), University of Washington, Seattle, Washington; and Department of Obstetrics and Gynecology (S.E.H., B.B.B.), Oregon Health & Science University, Portland, Oregon
| | - Allan E Rettie
- Departments of Pharmaceutics (L.M.H., K.E.T.), Biostatistics (T.A.T.), and Medicinal Chemistry (A.E.R.), University of Washington, Seattle, Washington; and Department of Obstetrics and Gynecology (S.E.H., B.B.B.), Oregon Health & Science University, Portland, Oregon
| | - Kenneth E Thummel
- Departments of Pharmaceutics (L.M.H., K.E.T.), Biostatistics (T.A.T.), and Medicinal Chemistry (A.E.R.), University of Washington, Seattle, Washington; and Department of Obstetrics and Gynecology (S.E.H., B.B.B.), Oregon Health & Science University, Portland, Oregon
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Abstract
Genomic information is poised to play an increasing role in clinical care, extending beyond highly penetrant genetic conditions to less penetrant genotypes and common disorders. But with this shift, the question of clinical utility becomes a major challenge. A collaborative effort is necessary to determine the information needed to evaluate different uses of genomic information and then acquire that information. Another challenge must also be addressed if that process is to provide equitable benefits: the lack of diversity of genomic data. Current genomic knowledge comes primarily from populations of European descent, which poses the risk that most of the human population will be shortchanged when health benefits of genomics emerge. These two challenges have defined my career as a geneticist and have taught me that solutions must start with dialogue across disciplinary and social divides.
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Affiliation(s)
- Wylie Burke
- Department of Bioethics and Humanities, University of Washington, Seattle, Washington 98195, USA;
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17
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Lin YS, Thummel KE, Thompson BD, Totah RA, Cho CW. Sources of Interindividual Variability. Methods Mol Biol 2021; 2342:481-550. [PMID: 34272705 DOI: 10.1007/978-1-0716-1554-6_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The efficacy, safety, and tolerability of drugs are dependent on numerous factors that influence their disposition. A dose that is efficacious and safe for one individual may result in sub-therapeutic or toxic blood concentrations in others. A significant source of this variability in drug response is drug metabolism, where differences in presystemic and systemic biotransformation efficiency result in variable degrees of systemic exposure (e.g., AUC, Cmax, and/or Cmin) following administration of a fixed dose.Interindividual differences in drug biotransformation have been studied extensively. It is recognized that both intrinsic factors (e.g., genetics, age, sex, and disease states) and extrinsic factors (e.g., diet , chemical exposures from the environment, and the microbiome) play a significant role. For drug-metabolizing enzymes, genetic variation can result in the complete absence or enhanced expression of a functional enzyme. In addition, upregulation and downregulation of gene expression, in response to an altered cellular environment, can achieve the same range of metabolic function (phenotype), but often in a less predictable and time-dependent manner. Understanding the mechanistic basis for variability in drug disposition and response is essential if we are to move beyond the era of empirical, trial-and-error dose selection and into an age of personalized medicine that will improve outcomes in maintaining health and treating disease.
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Affiliation(s)
- Yvonne S Lin
- Department of Pharmaceutics, University of Washington, Seattle, WA, USA.
| | - Kenneth E Thummel
- Department of Pharmaceutics, University of Washington, Seattle, WA, USA
| | - Brice D Thompson
- Department of Pharmaceutics, University of Washington, Seattle, WA, USA
| | - Rheem A Totah
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
| | - Christi W Cho
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
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18
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Blanchard J, Hiratsuka V, Beans JA, Lund J, Saunkeah B, Yracheta J, Woodbury RB, Blacksher E, Peercy M, Ketchum S, Byars C, Spicer P. Power Sharing, Capacity Building, and Evolving Roles in ELSI: The Center for the Ethics of Indigenous Genomic Research. COLLABORATIONS (CORAL GABLES, FLA.) 2020; 3:18. [PMID: 34708212 PMCID: PMC8547310 DOI: 10.33596/coll.71] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Persistent, unresolved issues stemming from a legacy of scientific exploitation and bio-colonialism have kept many tribal nations from participating in genomic research. The Center for the Ethics of Indigenous Genomic Research (CEIGR) aims to model meaningful community engagement that moves toward more inclusive and equitable research practices related to genomics. This article reflects on key successes and challenges behind CEIGR's efforts to shape Ethical, Legal and Social Implications (ELSI) research in ways that are informed by Indigenous perspectives, to locate community partnerships at the center of genomics research, and to conduct normative and empirical research with Indigenous communities that is grounded in the concepts of reciprocity, transparency and cultural competency. The structure of CEIGR represents an important shift away from a traditional model centered on a university-based principal investigators toward a partner-centered research approach that emphasizes equity and community control by distributing power and decision-making across all CEIGR partner sites. We discuss three features of CEIGR that have contributed to this shift towards an equitable, community-driven partnership: 1) balancing local priorities with collective goals; 2) distributing power in ways that promote equitable partnerships; and 3) capacity building and co-learning across partner sites. The discussion of these three areas in this article speaks to a particular strength of our Center: the interdependence among partners and collective willingness to maintain a plasticity of leadership that creates space for all of our partners to lead, support, exchange and strengthen ELSI research.
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Beans JA, Woodbury RB, Wark KA, Hiratsuka VY, Spicer P. Perspectives on Precision Medicine in a Tribally Managed Primary Care Setting. AJOB Empir Bioeth 2020; 11:246-256. [PMID: 32940567 PMCID: PMC7606746 DOI: 10.1080/23294515.2020.1817172] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023]
Abstract
BACKGROUND Precision medicine (PM) research and clinical application is moving forward at a rapid pace. To ensure ethical inclusion of all populations in PM, in-depth understanding of diverse communities' views of PM research and PM implementation is necessary. METHODS Semi-structured interviews were conducted to explore perspectives on PM in a tribally managed healthcare organization. Thematic analysis was used to analyze data from 46 interviews. RESULTS Participants described gains in diagnostic efficiency, risk identification for preventable disease, and the advancement of population-specific biomedical research as key benefits of PM. Concerns expressed related to privacy risks associated with data-sharing, overpromising on PM, and managing patient expectations related to PM. Stakeholders encouraged PM implementation to be preceded by health education activities that leverage a range of communication strategies. CONCLUSION Perspectives described in this study may aid in and should be considered prior to implementation of PM in this and other healthcare systems, especially those serving diverse populations.
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Affiliation(s)
| | | | | | | | - Paul Spicer
- Department of Anthropology, University of Oklahoma, Norman, Oklahoma, USA
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20
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McDonald MG, Henderson LM, Ray S, Yeung CK, Johnson AL, Kowalski JP, Hanenberg H, Wiek C, Thummel KE, Rettie AE. Heterologous Expression and Functional Characterization of Novel CYP2C9 Variants Identified in the Alaska Native People. J Pharmacol Exp Ther 2020; 374:233-240. [PMID: 32423989 DOI: 10.1124/jpet.120.265850] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 05/12/2020] [Indexed: 01/27/2023] Open
Abstract
CYP2C9 is a major form of human liver cytochrome P450 that is responsible for the oxidative metabolism of several widely used low-therapeutic index drugs, including (S)-warfarin and phenytoin. In a cohort of Alaska Native people, ultrarare or novel CYP2C9 protein variants, M1L (rs114071557), N218I (rs780801862), and P279T (rs182132442, CYP2C9*29), are expressed with higher frequencies than the well characterized CYP2C9*2 and CYP2C9*3 alleles. We report here on their relative expression in lentivirus-infected HepG2 cells and the functional characterization of purified reconstituted enzyme variants expressed in Escherichia coli toward (S)-warfarin, phenytoin, flurbiprofen, and (S)-naproxen. In the infected HepG2 cells, robust mRNA and protein expression were obtained for wild-type, N218I, and P279T variants, but as expected, the M1L variant protein was not translated in this liver-derived cell line. His-tagged wild-type protein and the N218I and P279T variants, but not M1L, expressed well in E. coli and were highly purified after affinity chromatography. Upon reconstitution with cytochrome P450 oxidoreductase and cytochrome b5, the N218I and P279T protein variants metabolized (S)-warfarin, phenytoin, flurbiprofen, and (S)-naproxen to the expected monohydroxylated or O-demethylated metabolites. Steady-state kinetic analyses revealed that the relative catalytic efficiency ratios of (S)-warfarin metabolism by the P279T and N218I variants were 87% and 24%, respectively, of wild-type CYP2C9 protein. A similar rank ordering was observed for metabolism of phenytoin, flurbiprofen, and (S)-naproxen. We conclude that carriers of the variant N218I and, especially, the M1L alleles would be at risk of exacerbated therapeutic effects from drugs that rely on CYP2C9 for their metabolic clearance. SIGNIFICANCE STATEMENT: Novel gene variants of CYP2C9-M1L, and N218I, along with P279T (CYP2C9*29)-are expressed in Alaska Native people at relatively high frequencies. In vitro characterization of their functional effects revealed that each variant confers reduced catalytic efficiency toward several substrates, including the low-therapeutic index drugs (S)-warfarin and phenytoin. These data provide the first functional information for new, common CYP2C9 variants in this understudied population. The data may help guide dose adjustments in allele carriers, thus mitigating potential healthcare disparities.
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Affiliation(s)
- Matthew G McDonald
- Departments of Medicinal Chemistry (M.G.M., S.R., A.L.J., J.P.K., A.E.R.), Pharmaceutics (L.M.H., K.E.T.), and Pharmacy (C.K.Y.), University of Washington, Seattle, Washington; Department of Otorhinolaryngology and Head/Neck Surgery, Heinrich-Heine University, Düsseldorf, Germany (H.H., C.W.); and Department of Pediatrics III, University Children's Hospital Essen, University of Duisburg-Essen, Essen, Germany (H.H.)
| | - Lindsay M Henderson
- Departments of Medicinal Chemistry (M.G.M., S.R., A.L.J., J.P.K., A.E.R.), Pharmaceutics (L.M.H., K.E.T.), and Pharmacy (C.K.Y.), University of Washington, Seattle, Washington; Department of Otorhinolaryngology and Head/Neck Surgery, Heinrich-Heine University, Düsseldorf, Germany (H.H., C.W.); and Department of Pediatrics III, University Children's Hospital Essen, University of Duisburg-Essen, Essen, Germany (H.H.)
| | - Sutapa Ray
- Departments of Medicinal Chemistry (M.G.M., S.R., A.L.J., J.P.K., A.E.R.), Pharmaceutics (L.M.H., K.E.T.), and Pharmacy (C.K.Y.), University of Washington, Seattle, Washington; Department of Otorhinolaryngology and Head/Neck Surgery, Heinrich-Heine University, Düsseldorf, Germany (H.H., C.W.); and Department of Pediatrics III, University Children's Hospital Essen, University of Duisburg-Essen, Essen, Germany (H.H.)
| | - Catherine K Yeung
- Departments of Medicinal Chemistry (M.G.M., S.R., A.L.J., J.P.K., A.E.R.), Pharmaceutics (L.M.H., K.E.T.), and Pharmacy (C.K.Y.), University of Washington, Seattle, Washington; Department of Otorhinolaryngology and Head/Neck Surgery, Heinrich-Heine University, Düsseldorf, Germany (H.H., C.W.); and Department of Pediatrics III, University Children's Hospital Essen, University of Duisburg-Essen, Essen, Germany (H.H.)
| | - Amanda L Johnson
- Departments of Medicinal Chemistry (M.G.M., S.R., A.L.J., J.P.K., A.E.R.), Pharmaceutics (L.M.H., K.E.T.), and Pharmacy (C.K.Y.), University of Washington, Seattle, Washington; Department of Otorhinolaryngology and Head/Neck Surgery, Heinrich-Heine University, Düsseldorf, Germany (H.H., C.W.); and Department of Pediatrics III, University Children's Hospital Essen, University of Duisburg-Essen, Essen, Germany (H.H.)
| | - John P Kowalski
- Departments of Medicinal Chemistry (M.G.M., S.R., A.L.J., J.P.K., A.E.R.), Pharmaceutics (L.M.H., K.E.T.), and Pharmacy (C.K.Y.), University of Washington, Seattle, Washington; Department of Otorhinolaryngology and Head/Neck Surgery, Heinrich-Heine University, Düsseldorf, Germany (H.H., C.W.); and Department of Pediatrics III, University Children's Hospital Essen, University of Duisburg-Essen, Essen, Germany (H.H.)
| | - Helmut Hanenberg
- Departments of Medicinal Chemistry (M.G.M., S.R., A.L.J., J.P.K., A.E.R.), Pharmaceutics (L.M.H., K.E.T.), and Pharmacy (C.K.Y.), University of Washington, Seattle, Washington; Department of Otorhinolaryngology and Head/Neck Surgery, Heinrich-Heine University, Düsseldorf, Germany (H.H., C.W.); and Department of Pediatrics III, University Children's Hospital Essen, University of Duisburg-Essen, Essen, Germany (H.H.)
| | - Constanze Wiek
- Departments of Medicinal Chemistry (M.G.M., S.R., A.L.J., J.P.K., A.E.R.), Pharmaceutics (L.M.H., K.E.T.), and Pharmacy (C.K.Y.), University of Washington, Seattle, Washington; Department of Otorhinolaryngology and Head/Neck Surgery, Heinrich-Heine University, Düsseldorf, Germany (H.H., C.W.); and Department of Pediatrics III, University Children's Hospital Essen, University of Duisburg-Essen, Essen, Germany (H.H.)
| | - Kenneth E Thummel
- Departments of Medicinal Chemistry (M.G.M., S.R., A.L.J., J.P.K., A.E.R.), Pharmaceutics (L.M.H., K.E.T.), and Pharmacy (C.K.Y.), University of Washington, Seattle, Washington; Department of Otorhinolaryngology and Head/Neck Surgery, Heinrich-Heine University, Düsseldorf, Germany (H.H., C.W.); and Department of Pediatrics III, University Children's Hospital Essen, University of Duisburg-Essen, Essen, Germany (H.H.)
| | - Allan E Rettie
- Departments of Medicinal Chemistry (M.G.M., S.R., A.L.J., J.P.K., A.E.R.), Pharmaceutics (L.M.H., K.E.T.), and Pharmacy (C.K.Y.), University of Washington, Seattle, Washington; Department of Otorhinolaryngology and Head/Neck Surgery, Heinrich-Heine University, Düsseldorf, Germany (H.H., C.W.); and Department of Pediatrics III, University Children's Hospital Essen, University of Duisburg-Essen, Essen, Germany (H.H.)
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Hiratsuka VY, Beans JA, Blanchard JW, Reedy J, Blacksher E, Lund JR, Spicer PG. An Alaska Native community's views on genetic research, testing, and return of results: Results from a public deliberation. PLoS One 2020; 15:e0229540. [PMID: 32176704 PMCID: PMC7075569 DOI: 10.1371/journal.pone.0229540] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Accepted: 02/08/2020] [Indexed: 01/06/2023] Open
Abstract
As genetic testing technology advances, genetic testing will move into standard practice in the primary care setting. Genetic research, testing, and return of results are complex topics that require input from Alaska Native and American Indian (ANAI) communities as policies are developed for implementation. This study employed a day and half long public deliberation with ANAI primary care patients to elicit value-laden views of genetic research, testing, and return of results. Participants emphasized the need for a balance between the potential for genetics research, testing, and return of results to empower individuals and improve health with the potential to expose individuals and communities to privacy breaches, discrimination, and emotional harms. Public deliberation was well received by this group of participants and elicited rich discussion on the complex topic of genetic research, testing, and return of results.
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Affiliation(s)
- Vanessa Y. Hiratsuka
- Research Department, Southcentral Foundation, Anchorage, Alaska, United States of America
| | - Julie A. Beans
- Research Department, Southcentral Foundation, Anchorage, Alaska, United States of America
| | - Jessica W. Blanchard
- Center for Applied Social Research, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Justin Reedy
- Department of Communication, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Erika Blacksher
- Department of Bioethics and Humanities, University of Washington, Seattle, Washington, United States of America
| | - Justin R. Lund
- Department of Anthropology, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Paul G. Spicer
- Department of Anthropology, University of Oklahoma, Norman, Oklahoma, United States of America
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22
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Basit A, Prasad B, Estergreen JK, Sabath DE, Alade N, Veenstra DL, Rettie AE, Thummel KE. A Novel LC-MS/MS Assay for Quantification of Des-carboxy Prothrombin and Characterization of Warfarin-Induced Changes. Clin Transl Sci 2020; 13:718-726. [PMID: 32004415 PMCID: PMC7359935 DOI: 10.1111/cts.12757] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 01/08/2020] [Indexed: 11/29/2022] Open
Abstract
Warfarin is a narrow therapeutic index anticoagulant drug and its use is associated with infrequent but significant adverse bleeding events. The international normalized ratio (INR) is the most commonly used biomarker to monitor and titrate warfarin therapy. However, INR is derived from a functional assay, which determines clotting efficiency at the time of measurement and is susceptible to technical variability. Protein induced by vitamin K antagonist-II (PIVKA-II) has been suggested as a biomarker of long-term vitamin K status, providing mechanistic insights about variation in the functional assay. However, the currently available antibody-based PIVKA-II assay does not inform on the position and number of des-carboxylation sites in prothrombin. The assay presented in this paper provides simultaneous quantification of carboxy and des-carboxy prothrombin that are essential for monitoring early changes in INR and, thus, serves as the superior tool for managing warfarin therapy. Additionally, this assay permits the quantification of total prothrombin level, which is affected by warfarin treatment. Prothrombin recovery from plasma was 95% and the liquid chromatography-tandem mass spectrometry (LC-MS/MS) assay was linear (r2 = 0.98) with a dynamic range of 1-100 µg/mL. The assay interday precision was within 20%. A des-carboxy peptide of prothrombin (GNLER) was negatively correlated with active prothrombin (Pearson r = 0.99, P < 0.0001), whereas its association was positively linked with INR values (Pearson r = 0.75, P < 0.015). This novel LC-MS/MS assay for active and inactive prothrombin quantification can be applied to titrate anticoagulant therapy and to monitor the impact of diseases, such as hepatocellular carcinoma on clotting physiology.
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Affiliation(s)
- Abdul Basit
- Department of Pharmaceutics, University of Washington, Seattle, Washington, USA
| | - Bhagwat Prasad
- Department of Pharmaceutics, University of Washington, Seattle, Washington, USA
| | - Joanne K Estergreen
- Departments of Laboratory Medicine and Medicine, University of Washington, Seattle, Washington, USA
| | - Daniel E Sabath
- Departments of Laboratory Medicine and Medicine, University of Washington, Seattle, Washington, USA
| | - Nathan Alade
- Department of Pharmaceutics, University of Washington, Seattle, Washington, USA
| | - David L Veenstra
- Department of Pharmacy, University of Washington, Seattle, Washington, USA
| | - Allan E Rettie
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA
| | - Kenneth E Thummel
- Department of Pharmaceutics, University of Washington, Seattle, Washington, USA
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23
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Alshogran OY. Warfarin Dosing and Outcomes in Chronic Kidney Disease: A Closer Look at Warfarin Disposition. Curr Drug Metab 2019; 20:633-645. [PMID: 31267868 DOI: 10.2174/1389200220666190701095807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/02/2019] [Accepted: 06/12/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Chronic Kidney Disease (CKD) is a prevalent worldwide health problem. Patients with CKD are more prone to developing cardiovascular complications such as atrial fibrillation and stroke. This warrants the use of oral anticoagulants, such as warfarin, in this population. While the efficacy and safety of warfarin in this setting remain controversial, a growing body of evidence emphasizes that warfarin use in CKD can be problematic. This review discusses 1) warfarin use, dosing and outcomes in CKD patients; and 2) possible pharmacokinetic mechanisms for altered warfarin dosing and response in CKD. METHODS Structured search and review of literature articles evaluating warfarin dosing and outcomes in CKD. Data and information about warfarin metabolism, transport, and pharmacokinetics in CKD were also analyzed and summarized. RESULTS The literature data suggest that changes in warfarin pharmacokinetics such as protein binding, nonrenal clearance, the disposition of warfarin metabolites may partially contribute to altered warfarin dosing and response in CKD. CONCLUSION Although the evidence to support warfarin use in advanced CKD is still unclear, this synthesis of previous findings may help in improving optimized warfarin therapy in CKD settings.
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Affiliation(s)
- Osama Y Alshogran
- Department of Clinical Pharmacy, Faculty of Pharmacy, Jordan University of Science and Technology, Irbid, Jordan
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24
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León-Moreno LC, Saldaña-Cruz AM, Sánchez-Corona J, Mendoza-Carrera F, García-Zapién AG, Revilla-Monsalve C, Islas-Andrade S, Brito-Zurita O, Pérez-Vargas A, Flores-Martínez SE. Distribution of potential risk alleles and haplotypes of the CYP2C9 and CYP2C19 genes in Mexican native populations: A comparative study among Amerindian populations. Meta Gene 2019. [DOI: 10.1016/j.mgene.2019.100565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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25
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Henderson LM, Robinson RF, Ray L, Khan BA, Li T, Dillard DA, Schilling BD, Mosley M, Janssen PL, Fohner AE, Rettie AE, Thummel KE, Thornton TA, Veenstra DL. VKORC1 and Novel CYP2C9 Variation Predict Warfarin Response in Alaska Native and American Indian People. Clin Transl Sci 2019; 12:312-320. [PMID: 30821933 PMCID: PMC6510382 DOI: 10.1111/cts.12611] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 12/05/2018] [Indexed: 12/21/2022] Open
Abstract
Alaska Native and American Indian (AN/AI) people have unique pharmacogene variation that may affect warfarin disposition and therapeutic response. We performed targeted genotyping for cytochrome P450 (CYP)2C9, vitamin K epoxide oxidase reductase complex subunit 1 (VKORC1), CYP4F2, CYP4F11, and gamma-glutamyl carboxylase (GGCX) variants in AN/AI people receiving warfarin. The primary outcome was stable warfarin dose, defined as one dose, and associated international normalized ratio within the target range, at least 6 months after starting therapy, with two matching doses at least 2 weeks apart. Genotype-phenotype relationships were assessed by multivariate regression analysis, adjusted for self-reported heritage, age, gender, and concurrent statin use. VKORC1 genotype explained 34% of dose variability, with VKORC1 -1639G>A and 1173C>T associated with a 1.7 mg/day (P = 1.4e-05) dose reduction. Additionally, CYP2C9 N218I was suggestively significant (P = 0.077), with heterozygotes requiring 1.1 mg/day less than reference individuals. Self-reported heritage was significantly associated with dose, largely driven by differences in the diagnostic VKORC1 allele frequencies among AN/AI people.
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Affiliation(s)
| | | | - Lily Ray
- Southcentral FoundationAnchorageAlaskaUSA
| | | | - Tianran Li
- Department of BiostatisticsUniversity of WashingtonSeattleWashingtonUSA
| | | | | | | | - Patricia L. Janssen
- Department of Environmental Health SciencesUniversity of WashingtonSeattleWashingtonUSA
| | - Alison E. Fohner
- Department of EpidemiologyUniversity of WashingtonSeattleWashingtonUSA
| | - Allan E. Rettie
- Department of Medicinal ChemistryUniversity of WashingtonSeattleWashingtonUSA
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26
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Hull SC. Changing the Conversation about The Ethics of Genomics and Health Disparities Research with American Indian and Alaska Native Communities: A Report from the Field. J Health Care Poor Underserved 2019; 30:21-26. [PMID: 31735714 PMCID: PMC7593832 DOI: 10.1353/hpu.2019.0111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
"Changing the conversation" around genomic research with U.S. tribal communities may lead to new pathways to address persistent health disparities. Restoring trustworthiness between researchers and communities entails a willingness to listen to Indigenous voices, being flexible, and refining existing policies and frameworks to adapt to communities' needs.
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James RD, West KM, Claw KG, EchoHawk A, Dodge L, Dominguez A, Taualii M, Forquera R, Thummel K, Burke W. Responsible Research With Urban American Indians and Alaska Natives. Am J Public Health 2018; 108:1613-1616. [PMID: 30359103 PMCID: PMC6236730 DOI: 10.2105/ajph.2018.304708] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2018] [Indexed: 11/04/2022]
Abstract
American Indian and Alaska Native (AI/AN) communities harbor understandable mistrust of research. Outside researchers have historically controlled processes, promulgating conclusions and recommended policies with virtually no input from the communities studied. Reservation-based communities can apply sovereignty rights conferred by the federal government to change this research trajectory. Many tribes now require review and approval before allowing research activities to occur, in part through the development of regulatory codes and oversight measures. Tribal oversight ensures that research is directed toward questions of importance to the community and that results are returned in ways that optimize problem solving. Unfortunately, tribal governance protections do not always extend to AI/ANs residing in urban environments. Although they represent the majority of AI/ANs, urban Indians face an ongoing struggle for visibility and access to health care. It is against this backdrop that urban Indians suffer disproportionate health problems. Improved efforts to ensure responsible research with urban Indian populations requires attention to community engagement, research oversight, and capacity building. We consider strategies to offset these limitations and develop a foundation for responsible research with urban Indians.
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Affiliation(s)
- Rosalina D James
- Rosalina D. James, Abigail EchoHawk, Adrian Dominguez, Leah Dodge, and Ralph Forquera are with the Urban Indian Health Institute, Seattle Indian Health Board, Seattle, WA. Kathleen M. West, Maile Taualii, and Wylie Burke are with the Department of Bioethics and Humanities, University of Washington, Seattle. Katrina G. Claw and Kenneth Thummel are with the Department of Pharmaceutics, University of Washington, Seattle
| | - Kathleen M West
- Rosalina D. James, Abigail EchoHawk, Adrian Dominguez, Leah Dodge, and Ralph Forquera are with the Urban Indian Health Institute, Seattle Indian Health Board, Seattle, WA. Kathleen M. West, Maile Taualii, and Wylie Burke are with the Department of Bioethics and Humanities, University of Washington, Seattle. Katrina G. Claw and Kenneth Thummel are with the Department of Pharmaceutics, University of Washington, Seattle
| | - Katrina G Claw
- Rosalina D. James, Abigail EchoHawk, Adrian Dominguez, Leah Dodge, and Ralph Forquera are with the Urban Indian Health Institute, Seattle Indian Health Board, Seattle, WA. Kathleen M. West, Maile Taualii, and Wylie Burke are with the Department of Bioethics and Humanities, University of Washington, Seattle. Katrina G. Claw and Kenneth Thummel are with the Department of Pharmaceutics, University of Washington, Seattle
| | - Abigail EchoHawk
- Rosalina D. James, Abigail EchoHawk, Adrian Dominguez, Leah Dodge, and Ralph Forquera are with the Urban Indian Health Institute, Seattle Indian Health Board, Seattle, WA. Kathleen M. West, Maile Taualii, and Wylie Burke are with the Department of Bioethics and Humanities, University of Washington, Seattle. Katrina G. Claw and Kenneth Thummel are with the Department of Pharmaceutics, University of Washington, Seattle
| | - Leah Dodge
- Rosalina D. James, Abigail EchoHawk, Adrian Dominguez, Leah Dodge, and Ralph Forquera are with the Urban Indian Health Institute, Seattle Indian Health Board, Seattle, WA. Kathleen M. West, Maile Taualii, and Wylie Burke are with the Department of Bioethics and Humanities, University of Washington, Seattle. Katrina G. Claw and Kenneth Thummel are with the Department of Pharmaceutics, University of Washington, Seattle
| | - Adrian Dominguez
- Rosalina D. James, Abigail EchoHawk, Adrian Dominguez, Leah Dodge, and Ralph Forquera are with the Urban Indian Health Institute, Seattle Indian Health Board, Seattle, WA. Kathleen M. West, Maile Taualii, and Wylie Burke are with the Department of Bioethics and Humanities, University of Washington, Seattle. Katrina G. Claw and Kenneth Thummel are with the Department of Pharmaceutics, University of Washington, Seattle
| | - Maile Taualii
- Rosalina D. James, Abigail EchoHawk, Adrian Dominguez, Leah Dodge, and Ralph Forquera are with the Urban Indian Health Institute, Seattle Indian Health Board, Seattle, WA. Kathleen M. West, Maile Taualii, and Wylie Burke are with the Department of Bioethics and Humanities, University of Washington, Seattle. Katrina G. Claw and Kenneth Thummel are with the Department of Pharmaceutics, University of Washington, Seattle
| | - Ralph Forquera
- Rosalina D. James, Abigail EchoHawk, Adrian Dominguez, Leah Dodge, and Ralph Forquera are with the Urban Indian Health Institute, Seattle Indian Health Board, Seattle, WA. Kathleen M. West, Maile Taualii, and Wylie Burke are with the Department of Bioethics and Humanities, University of Washington, Seattle. Katrina G. Claw and Kenneth Thummel are with the Department of Pharmaceutics, University of Washington, Seattle
| | - Kenneth Thummel
- Rosalina D. James, Abigail EchoHawk, Adrian Dominguez, Leah Dodge, and Ralph Forquera are with the Urban Indian Health Institute, Seattle Indian Health Board, Seattle, WA. Kathleen M. West, Maile Taualii, and Wylie Burke are with the Department of Bioethics and Humanities, University of Washington, Seattle. Katrina G. Claw and Kenneth Thummel are with the Department of Pharmaceutics, University of Washington, Seattle
| | - Wylie Burke
- Rosalina D. James, Abigail EchoHawk, Adrian Dominguez, Leah Dodge, and Ralph Forquera are with the Urban Indian Health Institute, Seattle Indian Health Board, Seattle, WA. Kathleen M. West, Maile Taualii, and Wylie Burke are with the Department of Bioethics and Humanities, University of Washington, Seattle. Katrina G. Claw and Kenneth Thummel are with the Department of Pharmaceutics, University of Washington, Seattle
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28
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Khan BA, Robinson R, Fohner AE, Muzquiz LI, Schilling BD, Beans JA, Olnes MJ, Trawicki L, Frydenlund H, Laukes C, Beatty P, Phillips B, Nickerson D, Howlett K, Dillard DA, Thornton TA, Thummel KE, Woodahl EL. Cytochrome P450 Genetic Variation Associated with Tamoxifen Biotransformation in American Indian and Alaska Native People. Clin Transl Sci 2018; 11:312-321. [PMID: 29436156 PMCID: PMC5944577 DOI: 10.1111/cts.12542] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 12/12/2017] [Accepted: 01/15/2017] [Indexed: 01/24/2023] Open
Abstract
Despite evidence that pharmacogenetics can improve tamoxifen pharmacotherapy, there are few studies with American Indian and Alaska Native (AIAN) people. We examined variation in cytochrome P450 (CYP) genes (CYP2D6, CYP3A4, CYP3A5, and CYP2C9) and tamoxifen biotransformation in AIAN patients with breast cancer (n = 42) from the Southcentral Foundation in Alaska and the Confederated Salish and Kootenai Tribes in Montana. We tested for associations between CYP diplotypes and plasma concentrations of tamoxifen and metabolites. Only the CYP2D6 variation was significantly associated with concentrations of endoxifen (P = 0.0008) and 4-hydroxytamoxifen (P = 0.0074), tamoxifen's principal active metabolites, as well as key metabolic ratios. The CYP2D6 was also the most significant predictor of active metabolites and metabolic ratios in a multivariate regression model, including all four genes as predictors, with minor roles for other CYP genes. In AIAN populations, CYP2D6 is the largest contributor to tamoxifen bioactivation, illustrating the importance of validating pharmacogenetic testing for therapy optimization in an understudied population.
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Affiliation(s)
- Burhan A. Khan
- Department of Biomedical and Pharmaceutical SciencesUniversity of MontanaMissoulaMontanaUSA
- Southcentral FoundationAnchorageAlaskaUSA
| | | | - Alison E. Fohner
- Institute for Public Health GeneticsUniversity of WashingtonSeattleWashingtonUSA
| | - LeeAnna I. Muzquiz
- Tribal Health DepartmentConfederated Salish and Kootenai TribesMontanaUSA
| | | | | | | | - Laura Trawicki
- Alaska Native Tribal Health ConsortiumAnchorageAlaskaUSA
| | | | - Cindi Laukes
- Department of Biomedical and Pharmaceutical SciencesUniversity of MontanaMissoulaMontanaUSA
- Montana Cancer Institute FoundationMissoulaMontanaUSA
| | - Patrick Beatty
- Montana Cancer Institute FoundationMissoulaMontanaUSA
- Montana Cancer SpecialistsMissoulaMontanaUSA
| | - Brian Phillips
- Department of PharmaceuticsUniversity of WashingtonSeattleWashingtonUSA
| | - Deborah Nickerson
- Department of Genome SciencesUniversity of WashingtonSeattleWashingtonUSA
| | - Kevin Howlett
- Tribal Health DepartmentConfederated Salish and Kootenai TribesMontanaUSA
| | | | | | | | - Erica L. Woodahl
- Department of Biomedical and Pharmaceutical SciencesUniversity of MontanaMissoulaMontanaUSA
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29
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Au NT, Ryman T, Rettie AE, Hopkins SE, Boyer BB, Black J, Philip J, Yracheta J, Fohner AE, Reyes M, Thornton TA, Austin MA, Thummel KE. Dietary Vitamin K and Association with Hepatic Vitamin K Status in a Yup'ik Study Population from Southwestern Alaska. Mol Nutr Food Res 2018; 62:10.1002/mnfr.201700746. [PMID: 29094808 PMCID: PMC5803412 DOI: 10.1002/mnfr.201700746] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 10/10/2017] [Indexed: 01/15/2023]
Abstract
SCOPE The relationship between dietary vitamin K and plasma PIVKA-II concentration, a biomarker of hepatic vitamin K status, in a Yup'ik study population in southwestern Alaska is investigated. METHODS AND RESULTS A total of 659 male and female, self-reported Yup'ik people, ≥14 years of age, were enrolled. Blood is collected for genotyping and plasma PIVKA-II biomarker analysis. A Yup'ik-specific dietary food frequency questionnaire is used to assess vitamin K intake. Among the participants, 22% report not consuming foods rich in vitamin K during the past year and 36% have a PIVKA-II concentration ≥ 2 ng mL-1 , indicating vitamin K insufficiency. The odds of an elevated PIVKA-II concentration are 33% lower in individuals reporting any versus no consumption of vitamin-K-rich foods. The association is significant after adjusting for CYP4F2*3 genotype. Tundra greens are high in vitamin K1 content, but an exploratory analysis suggests that subsistence meat sources have a greater effect on vitamin K status. CONCLUSIONS A substantial proportion of the Yup'ik population exhibits vitamin K insufficiency, which is associated with low consumption of vitamin K rich foods and which might affect an individual's response to anticoagulant drugs such as warfarin that target the vitamin K cycle.
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Affiliation(s)
- Nicholas T Au
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
| | - Tove Ryman
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Allan E Rettie
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
| | - Scarlett E Hopkins
- Center for Alaska Native Health Research, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Bert B Boyer
- Center for Alaska Native Health Research, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Jynene Black
- Center for Alaska Native Health Research, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Jacques Philip
- Center for Alaska Native Health Research, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Joseph Yracheta
- Department of Pharmaceutics, University of Washington, Seattle, WA, USA
| | - Alison E Fohner
- Institute for Public Health Genetics, University of Washington, Seattle, WA, USA
| | - Morayma Reyes
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | | | - Melissa A Austin
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Kenneth E Thummel
- Department of Pharmaceutics, University of Washington, Seattle, WA, USA
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30
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Henderson LM, Claw KG, Woodahl EL, Robinson RF, Boyer BB, Burke W, Thummel KE. P450 Pharmacogenetics in Indigenous North American Populations. J Pers Med 2018; 8:jpm8010009. [PMID: 29389890 PMCID: PMC5872083 DOI: 10.3390/jpm8010009] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 01/19/2018] [Accepted: 01/22/2018] [Indexed: 12/14/2022] Open
Abstract
Indigenous North American populations, including American Indian and Alaska Native peoples in the United States, the First Nations, Métis and Inuit peoples in Canada and Amerindians in Mexico, are historically under-represented in biomedical research, including genomic research on drug disposition and response. Without adequate representation in pharmacogenetic studies establishing genotype-phenotype relationships, Indigenous populations may not benefit fully from new innovations in precision medicine testing to tailor and improve the safety and efficacy of drug treatment, resulting in health care disparities. The purpose of this review is to summarize and evaluate what is currently known about cytochrome P450 genetic variation in Indigenous populations in North America and to highlight the importance of including these groups in future pharmacogenetic studies for implementation of personalized drug therapy.
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Affiliation(s)
- Lindsay M Henderson
- Departments of Pharmaceutics, University of Washington, Seattle, WA 98195, USA.
| | - Katrina G Claw
- Departments of Pharmaceutics, University of Washington, Seattle, WA 98195, USA.
| | - Erica L Woodahl
- Department of Biomedical and Pharmaceutical Sciences, University of Montana, Missoula, MT 59812, USA.
| | - Renee F Robinson
- Southcentral Foundation, Anchorage, AK 99508, USA.
- United States Public Health Service, Department of Human Services, Washington, DC 20201, USA.
| | - Bert B Boyer
- Center for Alaska Native Health Research, University of Alaska Fairbanks, Fairbanks, AK 99775, USA.
| | - Wylie Burke
- Bioethics & Humanities, University of Washington, Seattle, WA 98195, USA.
| | - Kenneth E Thummel
- Departments of Pharmaceutics, University of Washington, Seattle, WA 98195, USA.
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31
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Beans JA, Hiratsuka VY, Apok CR, Caindec K, Dillard DA, Robinson RF. Community Dissemination in a Tribal Health Setting: A Pharmacogenetics Case Study. AMERICAN INDIAN AND ALASKA NATIVE MENTAL HEALTH RESEARCH 2018; 25:80-94. [PMID: 29671859 PMCID: PMC6367726 DOI: 10.5820/aian.2501.2018.80] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Alaska Native and American Indian (AN/AI) people experience a disproportionate burden of health disparities in the United States. Including AN/AI people in pharmacogenetic research offers an avenue to address these health disparities, however the dissemination of pharmacogenetic research results in the community context can be a challenging task. In this paper, we describe a case-study that explores the preferences of AN/AI community members regarding pharmacogenetic research results dissemination. Results were presented as a PowerPoint presentation at the 2016 Alaska Native Health Research Forum (Forum). An audience response system and discussion groups were used to gather feedback from participants. Descriptive statistics were used to assess attendee understanding of the presentation content. Thematic analysis was used to analyze discussion group data. Forum attendees needed time to work through the concept of pharmacogenetics and looked for ways pharmacogenetics could apply to their daily life. Attendees found pharmacogenetics interesting, but wanted a simple description of pharmacogenetics. Community members were optimistic about the potential benefit pharmacogenetic medicine could have in the delivery of health care and expressed excitement this research was taking place. Researchers were urged to communicate throughout the study, not just end research results, to the community. Furthermore, attendees insisted their providers stay informed of research results that may have an impact on health care delivery. Conversational forms of dissemination are recommended when disseminating pharmacogenetic research results at the community level.
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32
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Daly AK, Rettie AE, Fowler DM, Miners JO. Pharmacogenomics of CYP2C9: Functional and Clinical Considerations. J Pers Med 2017; 8:E1. [PMID: 29283396 PMCID: PMC5872075 DOI: 10.3390/jpm8010001] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/18/2017] [Accepted: 12/20/2017] [Indexed: 02/07/2023] Open
Abstract
CYP2C9 is the most abundant CYP2C subfamily enzyme in human liver and the most important contributor from this subfamily to drug metabolism. Polymorphisms resulting in decreased enzyme activity are common in the CYP2C9 gene and this, combined with narrow therapeutic indices for several key drug substrates, results in some important issues relating to drug safety and efficacy. CYP2C9 substrate selectivity is detailed and, based on crystal structures for the enzyme, we describe how CYP2C9 catalyzes these reactions. Factors relevant to clinical response to CYP2C9 substrates including inhibition, induction and genetic polymorphism are discussed in detail. In particular, we consider the issue of ethnic variation in pattern and frequency of genetic polymorphisms and clinical implications. Warfarin is the most well studied CYP2C9 substrate; recent work on use of dosing algorithms that include CYP2C9 genotype to improve patient safety during initiation of warfarin dosing are reviewed and prospects for their clinical implementation considered. Finally, we discuss a novel approach to cataloging the functional capabilities of rare 'variants of uncertain significance', which are increasingly detected as more exome and genome sequencing of diverse populations is conducted.
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Affiliation(s)
- Ann K Daly
- Institute of Cellular Medicine, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK.
| | - Allan E Rettie
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA.
| | - Douglas M Fowler
- Department of Genome Sciences and Department of Bioengineering, University of Washington, Seattle, WA 98195, USA.
| | - John O Miners
- Department of Clinical Pharmacology, Flinders University School of Medicine, Adelaide 5042, Australia.
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Kaye JB, Schultz LE, Steiner HE, Kittles RA, Cavallari LH, Karnes JH. Warfarin Pharmacogenomics in Diverse Populations. Pharmacotherapy 2017; 37:1150-1163. [PMID: 28672100 DOI: 10.1002/phar.1982] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Genotype-guided warfarin dosing algorithms are a rational approach to optimize warfarin dosing and potentially reduce adverse drug events. Diverse populations, such as African Americans and Latinos, have greater variability in warfarin dose requirements and are at greater risk for experiencing warfarin-related adverse events compared with individuals of European ancestry. Although these data suggest that patients of diverse populations may benefit from improved warfarin dose estimation, the vast majority of literature on genotype-guided warfarin dosing, including data from prospective randomized trials, is in populations of European ancestry. Despite differing frequencies of variants by race/ethnicity, most evidence in diverse populations evaluates variants that are most common in populations of European ancestry. Algorithms that do not include variants important across race/ethnic groups are unlikely to benefit diverse populations. In some race/ethnic groups, development of race-specific or admixture-based algorithms may facilitate improved genotype-guided warfarin dosing algorithms above and beyond that seen in individuals of European ancestry. These observations should be considered in the interpretation of literature evaluating the clinical utility of genotype-guided warfarin dosing. Careful consideration of race/ethnicity and additional evidence focused on improving warfarin dosing algorithms across race/ethnic groups will be necessary for successful clinical implementation of warfarin pharmacogenomics. The evidence for warfarin pharmacogenomics has a broad significance for pharmacogenomic testing, emphasizing the consideration of race/ethnicity in discovery of gene-drug pairs and development of clinical recommendations for pharmacogenetic testing.
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Affiliation(s)
- Justin B Kaye
- Department of Pharmacy Practice and Science, University of Arizona College of Pharmacy, Tucson, Arizona
| | - Lauren E Schultz
- Department of Pharmacology and Toxicology, University of Arizona College of Pharmacy, Tucson, Arizona
| | - Heidi E Steiner
- Department of Pharmacy Practice and Science, University of Arizona College of Pharmacy, Tucson, Arizona
| | - Rick A Kittles
- Department of Public Health, University of Arizona College of Medicine, Tucson, Arizona.,Department of Surgery, University of Arizona College of Medicine, Tucson, Arizona.,Center for Applied Genetics and Genomic Medicine, University of Arizona College of Medicine, Tucson, Arizona
| | - Larisa H Cavallari
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics, University of Florida, Gainesville, Florida
| | - Jason H Karnes
- Department of Pharmacy Practice and Science, University of Arizona College of Pharmacy, Tucson, Arizona.,Center for Applied Genetics and Genomic Medicine, University of Arizona College of Medicine, Tucson, Arizona.,Sarver Heart Center, University of Arizona College of Medicine, Tucson, Arizona
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Au NT, Reyes M, Boyer BB, Hopkins SE, Black J, O’Brien D, Fohner AE, Yracheta J, Thornton T, Austin MA, Burke W, Thummel KE, Rettie AE. Dietary and genetic influences on hemostasis in a Yup'ik Alaska Native population. PLoS One 2017; 12:e0173616. [PMID: 28376131 PMCID: PMC5380313 DOI: 10.1371/journal.pone.0173616] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 02/23/2017] [Indexed: 11/23/2022] Open
Abstract
Fish and marine animals are important components of the subsistence diet of Alaska Native people, resulting in a high ω3 PUFA intake. The historical record for circumpolar populations highlights a tendency for facile bleeding, possibly related to ω3 PUFA effects on platelet activation and/or vitamin K-dependent clotting factors. To evaluate these two scenarios in Yup'ik people of southwestern Alaska, we examined the association between dietary ω3 PUFA intake and activities of clotting factor II, V, fibrinogen, PT, INR, PTT, and sP-selectin in 733 study participants, using the nitrogen isotope ratio of red blood cells as a biomarker of ω3 PUFA consumption. sP-selectin alone correlated strongly and inversely with ω3 PUFA consumption. Approximately 36% of study participants exhibited PIVKA-II values above the threshold of 2 ng/ml, indicative of low vitamin K status. To assess genetic influences on vitamin K status, study participants were genotyped for common vitamin K cycle polymorphisms in VKORC1, GGCX and CYP4F2. Only CYP4F2*3 associated significantly with vitamin K status, for both acute (plasma vitamin K) and long-term (PIVKA-II) measures. These findings suggest: (i) a primary association of ω3 PUFAs on platelet activation, as opposed to vitamin K-dependent clotting factor activity, (ii) that reduced CYP4F2 enzyme activity associates with vitamin K status. We conclude that high ω3 PUFA intake promotes an anti-platelet effect and speculate that the high frequency of the CYP4F2*3 allele in Yup'ik people (~45%) evolved in response to a need to conserve body stores of vitamin K due to environmental limitations on its availability.
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Affiliation(s)
- Nicholas T. Au
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, United States of America
| | - Morayma Reyes
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
| | - Bert B. Boyer
- Center for Alaska Native Health Research, University of Alaska Fairbanks, Fairbanks, Alaska, United States of America
| | - Scarlett E. Hopkins
- Center for Alaska Native Health Research, University of Alaska Fairbanks, Fairbanks, Alaska, United States of America
| | - Jynene Black
- Center for Alaska Native Health Research, University of Alaska Fairbanks, Fairbanks, Alaska, United States of America
| | - Diane O’Brien
- Center for Alaska Native Health Research, University of Alaska Fairbanks, Fairbanks, Alaska, United States of America
| | - Alison E. Fohner
- Public Health Genetics, University of Washington, Seattle, Washington, United States of America
| | - Joe Yracheta
- Department of Pharmaceutics, University of Washington, Seattle, Washington, United States of America
| | - Timothy Thornton
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Melissa A. Austin
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
| | - Wylie Burke
- Department of Medical Ethics, University of Washington, Seattle, Washington, United States of America
| | - Kenneth E. Thummel
- Department of Pharmaceutics, University of Washington, Seattle, Washington, United States of America
| | - Allan E. Rettie
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, United States of America
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Yi M, Cho SA, Min J, Kim DH, Shin JG, Lee SJ. Functional characterization of a common CYP4F11 genetic variant and identification of functionally defective CYP4F11 variants in erythromycin metabolism and 20-HETE synthesis. Arch Biochem Biophys 2017; 620:43-51. [DOI: 10.1016/j.abb.2017.03.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 03/08/2017] [Accepted: 03/19/2017] [Indexed: 12/31/2022]
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Fujikura K. Data on single-step purification method for dye-labeled DNA sequencing. Data Brief 2016; 7:873-6. [PMID: 27077088 PMCID: PMC4816862 DOI: 10.1016/j.dib.2016.02.050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Revised: 02/01/2016] [Accepted: 02/19/2016] [Indexed: 11/28/2022] Open
Abstract
Dye-labelled DNA sequencing is one of the most common and robust technique required for molecular biology since 1977 (Sanger, 1977) [1]. I have recently provided the single-step purification method for dye-labeled sequencing products, which is based on the removal of the washing step in EDTA/ethanol precipitation (Fujikura, 2015) [2]. Here I assess and report the accumulated data of the modified method on the larger scale in practice.
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Fohner AE, Wang Z, Yracheta J, O’Brien DM, Hopkins SE, Black J, Philip J, Wiener HW, Tiwari HK, Stapleton PL, Tsai JM, Thornton TA, Boyer BB, Thummel KE. Genetics, Diet, and Season Are Associated with Serum 25-Hydroxycholecalciferol Concentration in a Yup'ik Study Population from Southwestern Alaska. J Nutr 2016; 146:318-25. [PMID: 26661839 PMCID: PMC4725435 DOI: 10.3945/jn.115.223388] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 11/09/2015] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Low blood vitamin D concentration is a concern for people living in circumpolar regions, where sunlight is insufficient for vitamin D synthesis in winter months and the consumption of traditional dietary sources of vitamin D is decreasing. OBJECTIVE The objective was to characterize the effects of diet, genetic variation, and season on serum 25-hydroxycholecalciferol [25(OH)D3] concentrations in Yup'ik Alaska Native people living in rural southwest Alaska. METHODS This study was a cross-sectional design that assessed the associations of traditional diet (via a biomarker, the RBC δ(15)N value), age, gender, body mass index (BMI), community location, and genotype of select single nucleotide polymorphisms (SNPs) in cytochrome P450 family 2, subfamily R, peptide 1 (CYP2R1), 7-dehydrocholesterol reductase (DHCR7), and vitamin D binding protein (GC) with serum 25(OH)D3 concentrations in 743 Yup'ik male and female participants, aged 14-93 y, recruited between September 2009 and December 2013. RESULTS Yup'ik participants, on average, had adequate concentrations of serum 25(OH)D3 (31.1 ± 1.0 ng/mL). Variations in diet, BMI, age, gender, season of sample collection, and inland or coastal community geography were all significantly associated with serum 25(OH)D3 concentration. In models not adjusting for other covariates, age, diet, and seasonal effects explained 33.7%, 20.7%, and 9.8%, respectively, of variability in serum 25(OH)D3 concentrations. Of the 8 SNPs interrogated in CYP2R1 and DHCR7, only rs11023374 in CYP2R1 was significantly associated with serum 25(OH)D3, explaining 1.5% of variability. The GC haplotype explained an additional 2.8% of variability. Together, age, diet, gender, season of sample collection, BMI, geography of the community, and genotype at rs11023374 explained 52.5% of the variability in serum 25(OH)D3 concentrations. CONCLUSIONS Lower consumption of the traditional diet was associated with lower serum concentrations of 25(OH)D3. Younger adults and youth in this community may be at increased risk of adverse outcomes associated with vitamin D insufficiency compared with older members of the community, especially during seasons of low sunlight exposure, because of lower consumption of dietary sources of vitamin D.
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Affiliation(s)
| | | | | | - Diane M O’Brien
- Center for Alaska Native Health Research, University of Alaska Fairbanks, Fairbanks, AK; and
| | - Scarlett E Hopkins
- Center for Alaska Native Health Research, University of Alaska Fairbanks, Fairbanks, AK; and
| | - Jynene Black
- Center for Alaska Native Health Research, University of Alaska Fairbanks, Fairbanks, AK; and
| | - Jacques Philip
- Center for Alaska Native Health Research, University of Alaska Fairbanks, Fairbanks, AK; and
| | - Howard W Wiener
- School of Public Health, University of Alabama at Birmingham, Birmingham, AL
| | - Hemant K Tiwari
- School of Public Health, University of Alabama at Birmingham, Birmingham, AL
| | | | | | | | - Bert B Boyer
- Center for Alaska Native Health Research, University of Alaska Fairbanks, Fairbanks, AK; and
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