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Zhou Y, Nevosadová L, Eliasson E, Lauschke VM. Global distribution of functionally important CYP2C9 alleles and their inferred metabolic consequences. Hum Genomics 2023; 17:15. [PMID: 36855170 PMCID: PMC9976394 DOI: 10.1186/s40246-023-00461-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 02/16/2023] [Indexed: 03/02/2023] Open
Abstract
BACKGROUND Genetic variability in the cytochrome P450 CYP2C9 constitutes an important predictor for efficacy and safety of various commonly prescribed drugs, including coumarin anticoagulants, phenytoin and multiple non-steroidal anti-inflammatory drugs (NSAIDs). A global map of CYP2C9 variability and its inferred functional consequences has been lacking. RESULTS Frequencies of eight functionally relevant CYP2C9 alleles (*2, *3, *5, *6, *8, *11, *13 and *14) were analyzed. In total, 108 original articles were identified that included genotype data from a total of 81,662 unrelated individuals across 70 countries and 40 unique ethnic groups. The results revealed that CYP2C9*2 was most abundant in Europe and the Middle East, whereas CYP2C9*3 was the main reason for reduced CYP2C9 activity across South Asia. Our data show extensive variation within superpopulations with up to tenfold differences between geographically adjacent populations in Malaysia, Thailand and Vietnam. Translation of genetic CYP2C9 variability into functional consequences indicates that up to 40% of patients in Southern Europe and the Middle East might benefit from warfarin and phenytoin dose reductions, while 3% of patients in Southern Europe and Israel are recommended to reduce starting doses of NSAIDs. CONCLUSIONS This study provides a comprehensive map of the genetic and functional variability of CYP2C9 with high ethnogeographic resolution. The presented data can serve as a useful resource for CYP2C9 allele and phenotype frequencies and might guide the optimization of genotyping strategies, particularly for indigenous and founder populations with distinct genetic profiles.
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Affiliation(s)
- Yitian Zhou
- Division of Clinical Pharmacology, Department of Laboratory Medicine, Karolinska Institutet, 141 52, Huddinge, Sweden.
| | - Lenka Nevosadová
- grid.4714.60000 0004 1937 0626Department of Physiology and Pharmacology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Erik Eliasson
- grid.4714.60000 0004 1937 0626Division of Clinical Pharmacology, Department of Laboratory Medicine, Karolinska Institutet, 141 52 Huddinge, Sweden ,grid.24381.3c0000 0000 9241 5705Medical Diagnostics, Clinical Pharmacology, Karolinska University Hospital, 141 86 Stockholm, Sweden
| | - Volker M. Lauschke
- grid.4714.60000 0004 1937 0626Department of Physiology and Pharmacology, Karolinska Institutet, 171 77 Stockholm, Sweden ,grid.502798.10000 0004 0561 903XDr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany ,grid.10392.390000 0001 2190 1447University of Tübingen, Tübingen, Germany
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Zhang Q, Qi Y, Wang S, Zhao F, Zou L, Zhou Q, Geng P, Hong Y, Yang H, Luo Q, Cai J, Wu H, Wang D, Chen H, Yang J, Dai D. Identification and in vitro functional assessment of 10 CYP2C9 variants found in Chinese Han subjects. Front Endocrinol (Lausanne) 2023; 14:1139805. [PMID: 37008923 PMCID: PMC10052410 DOI: 10.3389/fendo.2023.1139805] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 02/22/2023] [Indexed: 03/17/2023] Open
Abstract
Cytochrome P450 2C9 (CYP2C9) participates in about 15% of clinical drug metabolism, and its polymorphism is associated with individual drug metabolism differences, which may lead to the adverse drug reactions (ADRs). In this study, 1163 Chinese Han individuals were recruited to investigate their distribution pattern of CYP2C9 gene and find out the variants that may affect their drug metabolic activities. We successfully developed a multiplex PCR amplicon sequencing method and used it for the genetic screening of CYP2C9 in a large scale. Besides the wild type CYP2C9*1, totally 26 allelic variants of CYP2C9 were detected, which included 16 previously reported alleles and 10 new non-synonymous variants that had not been listed on the PharmVar website. The characteristics of these newly detected CYP2C9 variants were then evaluated after co-expressing them with CYPOR in S. cerevisiae microsomes. Immunoblot analysis revealed that except for Pro163Ser, Glu326Lys, Gly431Arg and Ile488Phe, most of newly detected variants showed comparable protein expression levels to wild type in yeast cells. Two typical CYP2C9 probe drugs, losartan and glimepiride, were then used for the evaluation of metabolic activities of variants. As a result, 3 variants Thr301Met, Glu326Lys, and Gly431Arg almost lost their catalytic activities and most of other variants exhibited significantly elevated activities for drug metabolism. Our data not only enriches the knowledge of naturally occurring CYP2C9 variants in the Chinese Han population, but also provides the fundamental evidence for its potential clinical usage for personalized medicine in the clinic.
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Affiliation(s)
- Qing Zhang
- Department of Cardiovascular, Beijing Hospital, National Center of Gerontology, Beijing, China
- Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Yuying Qi
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, China
- Beijing Institute of Geriatrics, Peking University Fifth School of Clinical Medicine, Beijing, China
| | - Shuanghu Wang
- Laboratory of Clinical Pharmacy, The Sixth Affiliated Hospital of Wenzhou Medical University, The People’s Hospital of Lishui, Lishui, China
| | - Fangling Zhao
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, China
- Beijing Institute of Geriatrics, Peking University Fifth School of Clinical Medicine, Beijing, China
| | - Lili Zou
- Department of Cardiovascular, Beijing Hospital, National Center of Gerontology, Beijing, China
- Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, China
| | - Quan Zhou
- Laboratory of Clinical Pharmacy, The Sixth Affiliated Hospital of Wenzhou Medical University, The People’s Hospital of Lishui, Lishui, China
| | - Peiwu Geng
- Laboratory of Clinical Pharmacy, The Sixth Affiliated Hospital of Wenzhou Medical University, The People’s Hospital of Lishui, Lishui, China
| | - Yun Hong
- Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Department of Gastroenterology, Beijing Hospital, National Center of Gerontology, Beijing, China
| | - Hang Yang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, China
- Beijing Institute of Geriatrics, Peking University Fifth School of Clinical Medicine, Beijing, China
| | - Qingfeng Luo
- Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Department of Gastroenterology, Beijing Hospital, National Center of Gerontology, Beijing, China
| | - Jianping Cai
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, China
| | - Hualan Wu
- Department of Cardiovascular, Beijing Hospital, National Center of Gerontology, Beijing, China
- Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Dongxu Wang
- Department of Cardiovascular, Beijing Hospital, National Center of Gerontology, Beijing, China
- Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Hao Chen
- Department of Cardiovascular, Beijing Hospital, National Center of Gerontology, Beijing, China
- Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- *Correspondence: Dapeng Dai, ; Jiefu Yang, ; Hao Chen,
| | - Jiefu Yang
- Department of Cardiovascular, Beijing Hospital, National Center of Gerontology, Beijing, China
- Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
- *Correspondence: Dapeng Dai, ; Jiefu Yang, ; Hao Chen,
| | - Dapeng Dai
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, China
- *Correspondence: Dapeng Dai, ; Jiefu Yang, ; Hao Chen,
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Zhao FL, Zhang Q, Wang SH, Hong Y, Zhou S, Zhou Q, Geng PW, Luo QF, Yang JF, Chen H, Cai JP, Dai DP. Identification and drug metabolic characterization of four new CYP2C9 variants CYP2C9*72- *75 in the Chinese Han population. Front Pharmacol 2022; 13:1007268. [PMID: 36582532 PMCID: PMC9792615 DOI: 10.3389/fphar.2022.1007268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 12/01/2022] [Indexed: 12/15/2022] Open
Abstract
Cytochrome 2C9 (CYP2C9), one of the most important drug metabolic enzymes in the human hepatic P450 superfamily, is required for the metabolism of 15% of clinical drugs. Similar to other CYP2C family members, CYP2C9 gene has a high genetic polymorphism which can cause significant racial and inter-individual differences in drug metabolic activity. To better understand the genetic distribution pattern of CYP2C9 in the Chinese Han population, 931 individuals were recruited and used for the genotyping in this study. As a result, seven synonymous and 14 non-synonymous variations were identified, of which 4 missense variants were designated as new alleles CYP2C9*72, *73, *74 and *75, resulting in the amino acid substitutions of A149V, R150C, Q214H and N418T, respectively. When expressed in insect cell microsomes, all four variants exhibited comparable protein expression levels to that of the wild-type CYP2C9 enzyme. However, drug metabolic activity analysis revealed that these variants exhibited significantly decreased catalytic activities toward three CYP2C9 specific probe drugs, as compared with that of the wild-type enzyme. These data indicate that the amino acid substitution in newly designated variants can cause reduced function of the enzyme and its clinical significance still needs further investigation in the future.
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Affiliation(s)
- Fang-Ling Zhao
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, China,Peking University Fifth School of Clinical Medicine, Beijing, China
| | - Qing Zhang
- Department of Cardiovascular, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Shuang-Hu Wang
- Laboratory of Clinical Pharmacy, The Sixth Affiliated Hospital of Wenzhou Medical University, The People’s Hospital of Lishui, Lishui, China
| | - Yun Hong
- Department of Gastroenterology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Shan Zhou
- Peking University Fifth School of Clinical Medicine, Beijing, China
| | - Quan Zhou
- Laboratory of Clinical Pharmacy, The Sixth Affiliated Hospital of Wenzhou Medical University, The People’s Hospital of Lishui, Lishui, China
| | - Pei-Wu Geng
- Laboratory of Clinical Pharmacy, The Sixth Affiliated Hospital of Wenzhou Medical University, The People’s Hospital of Lishui, Lishui, China
| | - Qing-Feng Luo
- Department of Gastroenterology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Jie-Fu Yang
- Department of Cardiovascular, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Hao Chen
- Department of Cardiovascular, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China,*Correspondence: Da-Peng Dai, ; Jian-Ping Cai, ; Hao Chen,
| | - Jian-Ping Cai
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, China,*Correspondence: Da-Peng Dai, ; Jian-Ping Cai, ; Hao Chen,
| | - Da-Peng Dai
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, China,Peking University Fifth School of Clinical Medicine, Beijing, China,*Correspondence: Da-Peng Dai, ; Jian-Ping Cai, ; Hao Chen,
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Liu Z, Qi Y, Wang H, Zhang Q, Wu Z, Wu W. Risk model of hepatocellular carcinoma based on cuproptosis-related genes. Front Genet 2022; 13:1000652. [PMID: 36186455 PMCID: PMC9521278 DOI: 10.3389/fgene.2022.1000652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 08/31/2022] [Indexed: 11/23/2022] Open
Abstract
Background: Owing to the heterogeneity displayed by hepatocellular carcinoma (HCC) and the complexity of tumor microenvironment (TME), it is noted that the long-term effectiveness of the cancer therapy poses a severe clinical challenge. Hence, it is essential to categorize and alter the treatment intervention decisions for these tumors. Materials and methods: "ConsensusClusterPlus" tool was used for developing a secure molecular classification system that was based on the cuproptosis-linked gene expression. Furthermore, all clinical properties, pathway characteristics, genomic changes, and immune characteristics of different cell types involved in the immune pathways were also assessed. Univariate Cox regression and the least absolute shrinkage and selection operator (Lasso) analyses were used for designing the prognostic risk model associated with cuproptosis. Results: Three cuproptosis-linked subtypes (clust1, clust2, and clust3) were detected. Out of these, Clust3 showed the worst prognosis, followed by clust2, while Clust1 showed the best prognosis. Three subtypes had significantly different enrichment in pathways related to Tricarboxylic Acid (TCA) cycle, cell cycle, and cell senescence (p < 0.01). The clust3 subtype with poor prognosis had a low "ImmuneScore" and low immune cell infiltration, and the three subtypes had significant differences in the antigen processing and presentation pathway of the macrophages. Clust1 had a low TIDE score and was sensitive to immunotherapy. Then, according to the prognosis-related genes of cuproptosis, a prognosis risk model related to cuproptosis was constructed, containing seven genes (KIF2C, PTTG1, CENPM, CDC20, CYP2C9, SFN, and CFHR3). "High" group had a higher TIDE score compared to the TIDE score value shown by the "Low" group, which benefited less from immunotherapy, whereas the "High" group patients were more sensitive to the conventional drugs. Finally, the prognosis risk model related to cuproptosis was combined with clinical pathological characteristics to further improve the prognostic model and survival prediction. Conclusion: Three new molecular subgroups based on cuproptosis-linked genes were revealed, and a cuproptosis-related prognostic risk model comprising seven genes was established in this study, which could assist in predicting the prognosis and identifying the patients benefit from immunotherapy.
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Affiliation(s)
- Zhiqiang Liu
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yong Qi
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Haibo Wang
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Qikun Zhang
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Zhengsheng Wu
- Department of Pathology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Wenyong Wu
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
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Bharti N, Banerjee R, Achalere A, Kasibhatla SM, Joshi R. Genetic diversity of 'Very Important Pharmacogenes' in two South-Asian populations. PeerJ 2021; 9:e12294. [PMID: 34824904 PMCID: PMC8590392 DOI: 10.7717/peerj.12294] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 09/21/2021] [Indexed: 01/09/2023] Open
Abstract
OBJECTIVES Reliable identification of population-specific variants is important for building the single nucleotide polymorphism (SNP) profile. In this study, genomic variation using allele frequency differences of pharmacologically important genes for Gujarati Indians in Houston (GIH) and Indian Telugu in the U.K. (ITU) from the 1000 Genomes Project vis-à-vis global population data was studied to understand its role in drug response. METHODS Joint genotyping approach was used to derive variants of GIH and ITU independently. SNPs of both these populations with significant allele frequency variation (minor allele frequency ≥ 0.05) with super-populations from the 1000 Genomes Project and gnomAD based on Chi-square distribution with p-value of ≤ 0.05 and Bonferroni's multiple adjustment tests were identified. Population stratification and fixation index analysis was carried out to understand genetic differentiation. Functional annotation of variants was carried out using SnpEff, VEP and CADD score. RESULTS Population stratification of VIP genes revealed four clusters viz., single cluster of GIH and ITU, one cluster each of East Asian, European, African populations and Admixed American was found to be admixed. A total of 13 SNPs belonging to ten pharmacogenes were identified to have significant allele frequency variation in both GIH and ITU populations as compared to one or more super-populations. These SNPs belong to VKORC1 (rs17708472, rs2359612, rs8050894) involved in Vitamin K cycle, cytochrome P450 isoforms CYP2C9 (rs1057910), CYP2B6 (rs3211371), CYP2A2 (rs4646425) and CYP2A4 (rs4646440); ATP-binding cassette (ABC) transporter ABCB1 (rs12720067), DPYD1 (rs12119882, rs56160474) involved in pyrimidine metabolism, methyltransferase COMT (rs9332377) and transcriptional factor NR1I2 (rs6785049). SNPs rs1544410 (VDR), rs2725264 (ABCG2), rs5215 and rs5219 (KCNJ11) share high fixation index (≥ 0.5) with either EAS/AFR populations. Missense variants rs1057910 (CYP2C9), rs1801028 (DRD2) and rs1138272 (GSTP1), rs116855232 (NUDT15); intronic variants rs1131341 (NQO1) and rs115349832 (DPYD) are identified to be 'deleterious'. CONCLUSIONS Analysis of SNPs pertaining to pharmacogenes in GIH and ITU populations using population structure, fixation index and allele frequency variation provides a premise for understanding the role of genetic diversity in drug response in Asian Indians.
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Affiliation(s)
- Neeraj Bharti
- High Performance Computing: Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing, Pune, Maharashtra, India
| | - Ruma Banerjee
- High Performance Computing: Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing, Pune, Maharashtra, India
| | - Archana Achalere
- High Performance Computing: Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing, Pune, Maharashtra, India
| | - Sunitha Manjari Kasibhatla
- High Performance Computing: Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing, Pune, Maharashtra, India
| | - Rajendra Joshi
- High Performance Computing: Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing, Pune, Maharashtra, India
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