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Relevance of CYP2D6 Gene Variants in Population Genetic Differentiation. Pharmaceutics 2022; 14:pharmaceutics14112481. [PMID: 36432672 PMCID: PMC9694252 DOI: 10.3390/pharmaceutics14112481] [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: 10/13/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 11/18/2022] Open
Abstract
A significant portion of the variability in complex features, such as drug response, is likely caused by human genetic diversity. One of the highly polymorphic pharmacogenes is CYP2D6, encoding an enzyme involved in the metabolism of about 25% of commonly prescribed drugs. In a directed search of the 1000 Genomes Phase III variation data, 86 single nucleotide polymorphisms (SNPs) in the CYP2D6 gene were extracted from the genotypes of 2504 individuals from 26 populations, and then used to reconstruct haplotypes. Analyses were performed using Haploview, Phase, and Arlequin softwares. Haplotype and nucleotide diversity were high in all populations, but highest in populations of African ancestry. Pairwise FST showed significant results for eleven SNPs, six of which were characteristic of African populations, while four SNPs were most common in East Asian populations. A principal component analysis of CYP2D6 haplotypes showed that African populations form one cluster, Asian populations form another cluster with East and South Asian populations separated, while European populations form the third cluster. Linkage disequilibrium showed that all African populations have three or more haplotype blocks within the CYP2D6 gene, while other world populations have one, except for Chinese Dai and Punjabi in Pakistan populations, which have two.
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From Croatian Roma to 1000 Genomes: The Story of the CYP2D6 Gene Promoter and Enhancer SNPs. J Pers Med 2022; 12:jpm12081353. [PMID: 36013302 PMCID: PMC9409800 DOI: 10.3390/jpm12081353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 11/24/2022] Open
Abstract
The CYP2D6 gene encodes an enzyme responsible for the metabolism of ~20% of clinically prescribed drugs. In this study, 18 SNPs from the enhancer and promoter regions of CYP2D6 in 323 Roma from Croatia were genotyped, to find out whether the demographic history of Roma affected the distribution of the studied SNPs and their linkage disequilibrium (LD) values, with the major SNPs defining the CYP2D6 star alleles. No differences were found between the three Roma groups in allele and genotype frequencies. The distribution of LD values of Roma was compared with LD values of European and Asian populations. Regulatory CYP2D6 SNPs (rs5758550, rs28624811, rs1080985 and rs1080983) showed similar distribution and the highest LDs with rs16947 from the gene-coding region in all populations. In the promoter region, a complete LD between rs1080989 and rs28588594, and between rs1080983 and rs28624811, was found in Croatian Roma and investigated populations from 1000 genomes. A high LD was also found between rs1080985 from the promoter and rs5758550 from the enhancer region. SNP rs28735595 from the gene promoter region had the highest LD, with two gene region SNPs, rs1058164 and rs1135840. To conclude, the Croatian Roma population shows an LD pattern of the CYP2D6 gene region similar to the 1000 Genomes European and Asian populations.
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Stojanović Marković A, Zajc Petranović M, Tomas Ž, Puljko B, Šetinc M, Škarić-Jurić T, Peričić Salihović M. Untangling SNP Variations within CYP2D6 Gene in Croatian Roma. J Pers Med 2022; 12:jpm12030374. [PMID: 35330374 PMCID: PMC8951754 DOI: 10.3390/jpm12030374] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/18/2022] [Accepted: 02/23/2022] [Indexed: 02/06/2023] Open
Abstract
CYP2D6 is a highly polymorphic gene whose variations affect its enzyme activity. To assess whether the specific population history of Roma, characterized by constant migrations and endogamy, influenced the distribution of alleles and thus phenotypes, the CYP2D6 gene was sequenced using NGS (Next Generation Sequencing) method-targeted sequencing in three groups of Croatian Roma (N = 323) and results were compared to European and Asian populations. Identified single nucleotide polymorphisms (SNPs) were used to reconstruct haplotypes, which were translated into the star-allele nomenclature and later into phenotypes. A total of 43 polymorphic SNPs were identified. The three Roma groups differed significantly in the frequency of alleles of polymorphisms 6769 A > G, 6089 G > A, and 5264 A > G (p < 0.01), as well as in the prevalence of the five most represented star alleles: *1, *2, *4, *10, and *41 (p < 0.0001). Croatian Roma differ from the European and Asian populations in the accumulation of globally rare SNPs (6089 G > A, 4589 C > T, 4622 G > C, 7490 T > C). Our results also show that demographic history influences SNP variations in the Roma population. The three socio-culturally different Roma groups studied differ significantly in the distribution of star alleles, which confirms the importance of a separate study of different Roma groups.
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Affiliation(s)
- Anita Stojanović Marković
- Institute for Anthropological Research, 10000 Zagreb, Croatia; (A.S.M.); (M.Z.P.); (M.Š.); (T.Š.-J.)
| | - Matea Zajc Petranović
- Institute for Anthropological Research, 10000 Zagreb, Croatia; (A.S.M.); (M.Z.P.); (M.Š.); (T.Š.-J.)
| | - Željka Tomas
- Department for Translational Medicine, Srebrnjak Children’s Hospital, 10000 Zagreb, Croatia;
| | - Borna Puljko
- Croatian Institute for Brain Research, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia;
- Department for Chemistry and Biochemistry, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
| | - Maja Šetinc
- Institute for Anthropological Research, 10000 Zagreb, Croatia; (A.S.M.); (M.Z.P.); (M.Š.); (T.Š.-J.)
| | - Tatjana Škarić-Jurić
- Institute for Anthropological Research, 10000 Zagreb, Croatia; (A.S.M.); (M.Z.P.); (M.Š.); (T.Š.-J.)
| | - Marijana Peričić Salihović
- Institute for Anthropological Research, 10000 Zagreb, Croatia; (A.S.M.); (M.Z.P.); (M.Š.); (T.Š.-J.)
- Correspondence:
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He C, Peng L, Xing S, Li D, Wang L, Jin T. Population Genetic Difference of Pharmacogenomic VIP Variants in the Tibetan Population. Pharmgenomics Pers Med 2021; 14:1027-1040. [PMID: 34429635 PMCID: PMC8379641 DOI: 10.2147/pgpm.s316711] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 07/19/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Genetic variation influences drug reaction or adverse prognosis. The purpose of this research was to genotype very important pharmacogenetic (VIP) variants in the Tibetan population. METHODS AND MATERIALS Blood samples from 200 Tibetans were randomly collected and 59 VIP variants were genotyped, and then compared our data to 26 other populations in the 1000 project to further analyze and identify significant difference. RESULTS The results showed that on comparing with most of the 26 populations from the 1000 project, rs4291 (ACE), rs1051296 (SLC19A1) and rs1065852 (CYP2D6) significantly differed in the Tibetan population. Furthermore, three significant loci were related to drug response. In addition, the allele frequency of Tibetans least differed from that of East Asian populations, and most differed from that of Americans. CONCLUSION Three significant loci of variation ACE rs4291, SLC19A1 rs1051296 and CYP2D6 rs1065852 were associated with drug response. This result will contribute to improving the information of the Tibetan in the pharmacogenomics database, and providing a theoretical basis for clinical individualised drug use in Tibetans.
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Affiliation(s)
- Chunjuan He
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, 712082, People’s Republic of China
| | - Linna Peng
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, 712082, People’s Republic of China
| | - Shishi Xing
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, 712082, People’s Republic of China
| | - Dandan Li
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, 712082, People’s Republic of China
| | - Li Wang
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, 712082, People’s Republic of China
| | - Tianbo Jin
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang, Shaanxi, 712082, People’s Republic of China
- Key Laboratory for Basic Life Science Research of Tibet Autonomous Region, Xizang Minzu University, Xianyang, Shaanxi, 712082, People's Republic of China
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Hubáček JA, Šedová L, Olišarová V, Adámková V, Tóthová V. Increased prevalence of the CVD-associated ANRIL allele in the Roma/Gypsy population in comparison with the majority Czech population. Genet Mol Biol 2021; 44:e20200405. [PMID: 33949622 PMCID: PMC8097515 DOI: 10.1590/1678-4685-gmb-2020-0405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 02/21/2021] [Indexed: 11/22/2022] Open
Abstract
Cardiovascular disease (CVD) is a major cause of death around the world, with highest prevalence reported in minority Roma/Gypsy populations living in developed countries. Whether these differences are caused by unhealthy lifestyles or genetic factors remain unknown. The aim of our study was to examine the genotype frequencies of the rs10757274 polymorphism in the 9p.21 locus within ANRIL (antisense non-coding RNA in the INK4 locus), a long non-coding RNA located in the vicinity of the CDKN2A/2B inhibitors loci. ANRIL is understood to be the strongest genetic determinant of CVD in Caucasians. Using PCR-RFLP, we analysed the ANRIL rs10757274 polymorphism in 298 non-Roma (50% male) and 302 Roma/Gypsy (50% male) adult (39.5 ± 15.1 years and 39.2 ± 12.8 years, respectively) subjects. We found that frequencies of the ANRIL GG, GA and AA genotypes were 20.1%, 52.4% and 27.5% in the majority population and 32.9%, 47.9% and 19.2% in Roma/Gypsy subjects, respectively. The distribution of genotypes was deemed significantly different at P < 0.001. Within the Roma/Gypsy population, we detected increased prevalence of the CVD-associated GG genotype. Increased prevalence of CVD among Roma/Gypsies subjects may be significantly linked to genetic background.
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Affiliation(s)
- Jaroslav A Hubáček
- Institute for Clinical and Experimental Medicine, Experimental Medicine Centre, Prague, Czech Republic.,Charles University, 1st Faculty of Medicine, 3rd Department of Internal Medicine, Prague, Czech Republic
| | - Lenka Šedová
- University of South Bohemia, Faculty of Health and Social Sciences, České Budějovice, Czech Republic
| | - Věra Olišarová
- University of South Bohemia, Faculty of Health and Social Sciences, České Budějovice, Czech Republic
| | - Věra Adámková
- Institute for Clinical and Experimental Medicine, Department of Preventive Cardiology, Prague, Czech Republic
| | - Valérie Tóthová
- University of South Bohemia, Faculty of Health and Social Sciences, České Budějovice, Czech Republic
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Faustova M, Nikolskaya E, Sokol M, Fomicheva M, Petrov R, Yabbarov N. Metalloporphyrins in Medicine: From History to Recent Trends. ACS APPLIED BIO MATERIALS 2020; 3:8146-8171. [PMID: 35019597 DOI: 10.1021/acsabm.0c00941] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The history of metalloporphyrins dates back more than 200 years ago. Metalloporphyrins are excellent catalysts, capable of forming supramolecular systems, participate in oxygen photosynthesis, transport, and used as contrast agents or superoxide dismutase mimetics. Today, metalloporphyrins represent complexes of conjugated π-electron system and metals from the entire periodic system. However, the effect of these compounds on living systems has not been fully understood, and researchers are exploring the properties of metalloporphyrins thereby extending their further application. This review provides an overview of the variety of metalloporphyrins that are currently used in different medicine fields and how metalloporphyrins became the subject of scientists' interest. Currently, metalloporphyrins utilization has expanded significantly, which gave us an opprotunuty to summarize recent progress in metalloporphyrins derivatives and prospects of their application in the treatment and diagnosis of different diseases.
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Affiliation(s)
- Mariia Faustova
- MIREA-Russian Technological University, Lomonosov Institute of Fine Chemical Technologies, 119454 Moscow, Russia.,N. M. Emanuel Institute of Biochemical Physics of Russian Academy of Sciences, 119991 Moscow, Russia
| | - Elena Nikolskaya
- N. M. Emanuel Institute of Biochemical Physics of Russian Academy of Sciences, 119991 Moscow, Russia
| | - Maria Sokol
- N. M. Emanuel Institute of Biochemical Physics of Russian Academy of Sciences, 119991 Moscow, Russia.,JSC Russian Research Center for Molecular Diagnostics and Therapy, 117149 Moscow Russia
| | - Margarita Fomicheva
- N. M. Emanuel Institute of Biochemical Physics of Russian Academy of Sciences, 119991 Moscow, Russia.,JSC Russian Research Center for Molecular Diagnostics and Therapy, 117149 Moscow Russia
| | - Rem Petrov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Nikita Yabbarov
- N. M. Emanuel Institute of Biochemical Physics of Russian Academy of Sciences, 119991 Moscow, Russia.,JSC Russian Research Center for Molecular Diagnostics and Therapy, 117149 Moscow Russia
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Hubáček JA, Šedová L, Olišarová V, Adámková V, Tóthová V. Different prevalence of T2DM risk alleles in Roma population in comparison with the majority Czech population. Mol Genet Genomic Med 2020; 8:e1361. [PMID: 32578971 PMCID: PMC7507457 DOI: 10.1002/mgg3.1361] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 05/11/2020] [Accepted: 05/19/2020] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The Czech governmental study suggests up to a 25% higher prevalence of type 2 diabetes mellitus (T2DM) in the Roma population than within the majority population. It is not known whether and to what extent these differences have a genetic background. METHODS To analyze whether the frequencies of the alleles/genotypes of the FTO, TCF7L2, CDKN2A/2B, MAEA, TLE4, IGF2BP2, ARAP1, and KCNJ11 genes differ between the two major ethnic groups in the Czech Republic, we examined them in DNA samples from 302 Roma individuals and 298 Czech individuals. RESULTS Compared to the majority population, Roma are more likely to carry risk alleles in the FTO (26% vs. 16% GG homozygotes, p < .01), IGF2BP2 (22% vs. 10% TT homozygotes, p < .0001), ARAP1 (98% vs. 95% of A allele carriers, p < .005), and CDKN2A/2B (81% vs. 66% of TT homozygotes, p < .001) genes; however, less frequently they are carriers of the TCF7L2 risk allele (34% vs. 48% of the T allele p < .0005). Finally, we found significant accumulation of T2DM-associated alleles between the Roma population in comparison with the majority population (25.4% vs. 15.2% of the carriers of at least 12 risk alleles; p < .0001). CONCLUSION The increased prevalence of T2DM in the Roma population may have a background in different frequencies of the risk alleles of genes associated with T2DM development.
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Affiliation(s)
- Jaroslav A. Hubáček
- Centre for Experimental MedicineInstitute for Clinical and Experimental MedicinePragueCzech Republic
| | - Lenka Šedová
- Faculty of Health and Social SciencesUniversity of South BohemiaČeské BudějoviceCzech Republic
| | - Věra Olišarová
- Faculty of Health and Social SciencesUniversity of South BohemiaČeské BudějoviceCzech Republic
| | - Věra Adámková
- Department of Preventive CardiologyInstitute for Clinical and Experimental MedicinePragueCzech Republic
| | - Valérie Tóthová
- Faculty of Health and Social SciencesUniversity of South BohemiaČeské BudějoviceCzech Republic
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