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Leitão LPC, Souza TP, Rodrigues JCG, Fernandes MR, Santos S, Santos NPC. The Metabolization Profile of the CYP2D6 Gene in Amerindian Populations: A Review. Genes (Basel) 2020; 11:genes11030262. [PMID: 32121156 PMCID: PMC7140882 DOI: 10.3390/genes11030262] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 02/04/2020] [Accepted: 02/14/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND the CYP2D6 gene is clinically important and is known to have a number of variants. This gene has four distinct metabolization profiles that are determined by the different allelic forms present in the individual. The relative frequency of these profiles varies considerably among human populations around the world. Populations from more isolated regions, such as Native Americans, are still relatively poorly studied, however. Even so, recent advances in genotyping techniques and increasing interest in the study of these populations has led to a progressive increase in publication rates. Given this, the review presented here compiled the principal papers published on the CYP2D6 gene in Amerindian populations to determine the metabolic profile of this group. METHODS a systematic literature review was conducted in three scientific publication platforms (Google Scholar, Science Direct, and Pubmed). The search was run using the keywords "CYP2D6 Amerindians" and "CYP2D6 native Americans". RESULTS a total of 13 original papers met the inclusion criteria established for this study. All the papers presented frequencies of the different CYP2D6 alleles in Amerindian populations. Seven of the papers focused specifically on Amerindian populations from Mexico, while the others included populations from Argentina, Chile, Costa Rica, Mexico, Paraguay, Peru, and the United States. The results of the papers reviewed here showed that the extensive metabolization profile was the most prevalent in all Amerindian populations studied to date, followed by the intermediate, slow, and ultra-rapid, in that order. CONCLUSION the metabolization profiles of the Amerindian populations reviewed in the present study do not diverge in any major way from those of other populations from around the world. Given the paucity of the data available on Amerindian populations, further research is required to better characterize the metabolization profile of these populations to ensure the development of adequate therapeutic strategies.
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Affiliation(s)
- Luciana P. C. Leitão
- Oncology Research Center, Federal University of Pará, Belém, Pará 66073, Brazil; (L.P.C.L.); (T.P.S.); (J.C.G.R.); (M.R.F.); (S.S.)
| | - Tatiane P. Souza
- Oncology Research Center, Federal University of Pará, Belém, Pará 66073, Brazil; (L.P.C.L.); (T.P.S.); (J.C.G.R.); (M.R.F.); (S.S.)
| | - Juliana C. G. Rodrigues
- Oncology Research Center, Federal University of Pará, Belém, Pará 66073, Brazil; (L.P.C.L.); (T.P.S.); (J.C.G.R.); (M.R.F.); (S.S.)
| | - Marianne R. Fernandes
- Oncology Research Center, Federal University of Pará, Belém, Pará 66073, Brazil; (L.P.C.L.); (T.P.S.); (J.C.G.R.); (M.R.F.); (S.S.)
| | - Sidney Santos
- Oncology Research Center, Federal University of Pará, Belém, Pará 66073, Brazil; (L.P.C.L.); (T.P.S.); (J.C.G.R.); (M.R.F.); (S.S.)
- Laboratory of Human and Medical Genetics, Institute of Biological Science, Federal University of Pará, Belém, Pará 66077-830, Brazil
| | - Ney P. C. Santos
- Oncology Research Center, Federal University of Pará, Belém, Pará 66073, Brazil; (L.P.C.L.); (T.P.S.); (J.C.G.R.); (M.R.F.); (S.S.)
- Laboratory of Human and Medical Genetics, Institute of Biological Science, Federal University of Pará, Belém, Pará 66077-830, Brazil
- Correspondence:
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Naranjo MEG, Rodrigues-Soares F, Peñas-Lledó EM, Tarazona-Santos E, Fariñas H, Rodeiro I, Terán E, Grazina M, Moya GE, López-López M, Sarmiento AP, Calzadilla LR, Ramírez-Roa R, Ortiz-López R, Estévez-Carrizo FE, Sosa-Macías M, Barrantes R, LLerena A. Interethnic Variability in CYP2D6, CYP2C9, and CYP2C19 Genes and Predicted Drug Metabolism Phenotypes Among 6060 Ibero- and Native Americans: RIBEF-CEIBA Consortium Report on Population Pharmacogenomics. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2018; 22:575-588. [PMID: 30183544 DOI: 10.1089/omi.2018.0114] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Pharmacogenetic variation in Latin Americans is understudied, which sets a barrier for the goal of global precision medicine. The RIBEF-CEIBA Network Consortium was established to characterize interindividual and between population variations in CYP2D6, CYP2C9, and CYP2C19 drug metabolizing enzyme genotypes, which were subsequently utilized to catalog their "predicted drug metabolism phenotypes" across Native American and Ibero American populations. Importantly, we report in this study, a total of 6060 healthy individuals from Ibero-America who were classified according to their self-reported ancestry: 1395 Native Americans, 2571 Admixed Latin Americans, 96 Afro-Latin Americans, 287 white Latin Americans (from Cuba), 1537 Iberians, and 174 Argentinean Ashkenazi Jews. Moreover, Native Americans were grouped into North-, Central-, and South Amerindians (from Mexico, Costa Rica, and Peru, respectively). All subjects were studied for the most common and functional CYP2D6, CYP2C9, and CYP2C19 allelic variants, and grouped as genotype-predicted poor or ultrarapid metabolizer phenotypes (gPMs and gUMs, respectively). Native Americans showed differences from each ethnic group in at least two alleles of CYP2D6, CYP2C9, and CYP2C19. Native Americans had higher frequencies of wild-type alleles for all genes, and lower frequency of CYP2D6*41, CYP2C9*2, and CYP2C19*17 (p < 0.05). Native Americans also showed less CYP2C19 gUMs than the rest of the population sample. In addition, differences within Native Americans (mostly North vs. South) were also found. The interethnic differences described supports the need for population-specific personalized and precision medicine programs for Native Americans. To the best of our knowledge, this is the largest study carried out in Native Americans and other Ibero-American populations analyzing CYP2D6, CYP2C9, and CYP2C19 genetic polymorphisms. Population pharmacogenomics is a nascent field of global health and warrants further research and education.
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Affiliation(s)
- María-Eugenia G Naranjo
- 1 RIBEF Ibero-American Network of Pharmacogenetics and Pharmacogenomics , Badajoz, Spain .,2 Universidad de Extremadura , Badajoz, Spain
| | - Fernanda Rodrigues-Soares
- 1 RIBEF Ibero-American Network of Pharmacogenetics and Pharmacogenomics , Badajoz, Spain .,3 Universidade Federal de Minas Gerais , Belo Horizonte, Brazil .,4 Faculdade Uninassau , Manaus, Brazil
| | - Eva M Peñas-Lledó
- 1 RIBEF Ibero-American Network of Pharmacogenetics and Pharmacogenomics , Badajoz, Spain .,2 Universidad de Extremadura , Badajoz, Spain
| | - Eduardo Tarazona-Santos
- 1 RIBEF Ibero-American Network of Pharmacogenetics and Pharmacogenomics , Badajoz, Spain .,3 Universidade Federal de Minas Gerais , Belo Horizonte, Brazil .,5 PRISMA , Lima, Peru
| | - Humberto Fariñas
- 1 RIBEF Ibero-American Network of Pharmacogenetics and Pharmacogenomics , Badajoz, Spain .,2 Universidad de Extremadura , Badajoz, Spain
| | - Idania Rodeiro
- 1 RIBEF Ibero-American Network of Pharmacogenetics and Pharmacogenomics , Badajoz, Spain .,6 Instituto de Ciencias del Mar , La Habana, Cuba
| | - Enrique Terán
- 1 RIBEF Ibero-American Network of Pharmacogenetics and Pharmacogenomics , Badajoz, Spain .,7 Universidad San Francisco de Quito , Quito, Ecuador
| | - Manuela Grazina
- 1 RIBEF Ibero-American Network of Pharmacogenetics and Pharmacogenomics , Badajoz, Spain .,8 UC, CNC-Center for Neuroscience and Cell Biology, FMUC-Faculty of Medicine, University of Coimbra , Coimbra, Portugal
| | - Graciela E Moya
- 1 RIBEF Ibero-American Network of Pharmacogenetics and Pharmacogenomics , Badajoz, Spain .,9 Universidad Católica de Argentina , Buenos Aires, Argentina
| | - Marisol López-López
- 1 RIBEF Ibero-American Network of Pharmacogenetics and Pharmacogenomics , Badajoz, Spain .,10 Universidad Autónoma Metropolitana , Ciudad de México, Mexico
| | - Alba P Sarmiento
- 1 RIBEF Ibero-American Network of Pharmacogenetics and Pharmacogenomics , Badajoz, Spain .,11 Pontifica Universidad Javeriana , Bogotá, Colombia
| | - Luis R Calzadilla
- 1 RIBEF Ibero-American Network of Pharmacogenetics and Pharmacogenomics , Badajoz, Spain .,12 Centro Comunitario de SaludMental de la Habana Vieja, La Habana, Cuba
| | - Ronald Ramírez-Roa
- 1 RIBEF Ibero-American Network of Pharmacogenetics and Pharmacogenomics , Badajoz, Spain .,13 Universidad Nacional Autónoma de Nicaragua , León, Nicaragua
| | - Rocío Ortiz-López
- 1 RIBEF Ibero-American Network of Pharmacogenetics and Pharmacogenomics , Badajoz, Spain .,14 Tecnológico de Monterrey , Monterrey, Mexico
| | - Francisco E Estévez-Carrizo
- 1 RIBEF Ibero-American Network of Pharmacogenetics and Pharmacogenomics , Badajoz, Spain .,15 Universidad de Montevideo , Montevideo, Uruguay
| | - Martha Sosa-Macías
- 1 RIBEF Ibero-American Network of Pharmacogenetics and Pharmacogenomics , Badajoz, Spain .,16 Instituto Politécnico Nacional , Durango, Mexico
| | - Ramiro Barrantes
- 1 RIBEF Ibero-American Network of Pharmacogenetics and Pharmacogenomics , Badajoz, Spain .,17 Universidad de Costa Rica , San José, Costa Rica
| | - Adrián LLerena
- 1 RIBEF Ibero-American Network of Pharmacogenetics and Pharmacogenomics , Badajoz, Spain .,2 Universidad de Extremadura , Badajoz, Spain
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Weich N, Roisman A, Cerliani B, Aráoz HV, Chertkoff L, Richard SM, Slavutsky I, Larripa IB, Fundia AF. Gene polymorphism profiles of drug-metabolising enzymes GSTM1, GSTT1 and GSTP1 in an Argentinian population. Ann Hum Biol 2016; 44:379-383. [PMID: 27892694 DOI: 10.1080/03014460.2016.1259429] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
BACKGROUND Glutathione S-transferases (GSTs) are drug-metabolising enzymes involved in biotransformation of carcinogens, drugs, xenobiotics and oxygen free radicals. Polymorphisms of GST genes contribute to inter-individual and population variability in the susceptibility to environmental risk factors, cancer predisposition and pharmacotherapy responses. However, data about GST variability in Argentina are lacking. AIM The purpose was to determine the prevalence of GSTM1, GSTT1 and GSTP1 polymorphisms in the general population from a central region of Argentina and to perform inter-population comparisons. SUBJECTS AND METHODS GSTM1 and GSTT1 gene deletions and GSTP1 c.313A > G were genotyped by PCR assays in 609 healthy and unrelated Argentinians. RESULTS The frequencies of variant genotypes in Argentinians were GSTM1-null (45%), GSTT1-null (17%) and GSTP1-GG (11%). GSTM1-present genotype was significantly associated with GSTP1-AG or GSTP1-GG variants (p = 0.037; p = 0.034, respectively). Comparison with worldwide populations demonstrated that the GST distributions in Argentina are similar to those reported for Italy and Spain, whereas significant differences were observed regarding Asian and African populations (p < 0.001). CONCLUSION This study has determined, for the first time, the normative profile of three pharmacogenetically relevant polymorphisms (GSTM1, GSTT1 and GSTP1) in the largest Argentinian cohort described to date, providing the basis for further epidemiological and pharmacogenetic studies in this country.
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Affiliation(s)
- Natalia Weich
- a Hematological Genetics Laboratory , Instituto de Medicina Experimental, CONICET-Academia Nacional de Medicina , Ciudad de Buenos Aires , Argentina
| | - Alejandro Roisman
- b Laboratory of Genetics of Lymphoid Malignancies , Instituto de Medicina Experimental, CONICET-Academia Nacional de Medicina , Ciudad de Buenos Aires , Argentina
| | - Belén Cerliani
- c Laboratory of Cytogenetics and Mutagenesis , IMBICE, CCT-La Plata-CONICET , Buenos Aires , Argentina
| | - Hilda V Aráoz
- d Laboratory of Molecular Biology, Genetics Department , Hospital de Pediatría 'Prof. Juan P. Garrahan' , Ciudad de Buenos Aires , Argentina
| | - Lilien Chertkoff
- d Laboratory of Molecular Biology, Genetics Department , Hospital de Pediatría 'Prof. Juan P. Garrahan' , Ciudad de Buenos Aires , Argentina
| | - Silvina M Richard
- c Laboratory of Cytogenetics and Mutagenesis , IMBICE, CCT-La Plata-CONICET , Buenos Aires , Argentina
| | - Irma Slavutsky
- b Laboratory of Genetics of Lymphoid Malignancies , Instituto de Medicina Experimental, CONICET-Academia Nacional de Medicina , Ciudad de Buenos Aires , Argentina
| | - Irene B Larripa
- a Hematological Genetics Laboratory , Instituto de Medicina Experimental, CONICET-Academia Nacional de Medicina , Ciudad de Buenos Aires , Argentina
| | - Ariela F Fundia
- a Hematological Genetics Laboratory , Instituto de Medicina Experimental, CONICET-Academia Nacional de Medicina , Ciudad de Buenos Aires , Argentina
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Cerliani MB, Pavicic W, Gili JA, Klein G, Saba S, Richard S. Cigarette smoking, dietary habits and genetic polymorphisms in GSTT1, GSTM1 and CYP1A1 metabolic genes: A case-control study in oncohematological diseases. World J Clin Oncol 2016; 7:395-405. [PMID: 27777882 PMCID: PMC5056331 DOI: 10.5306/wjco.v7.i5.395] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 09/02/2016] [Accepted: 09/22/2016] [Indexed: 02/06/2023] Open
Abstract
AIM To analyze the association between oncohematological diseases and GSTT1/GSTM1/CYP1A1 polymorphisms, dietary habits and smoking, in an argentine hospital-based case-control study.
METHODS This hospital-based case-control study involved 125 patients with oncohematological diseases and 310 control subjects. A questionnaire was used to obtain sociodemographic data and information about habits. Blood samples were collected, and DNA was extracted using salting out methods. Deletions in GSTT1 and GSTM1 (null genotypes) were addressed by PCR. CYP1A1 MspI polymorphism was detected by PCR-RFLP. Odds ratio (OR) and 95%CI were calculated to estimate the association between each variable studied and oncohematological disease.
RESULTS Women showed lower risk of disease compared to men (OR 0.52, 95%CI: 0.34-0.82, P = 0.003). Higher levels of education (> 12 years) were significantly associated with an increased risk, compared to complete primary school or less (OR 3.68, 95%CI: 1.82-7.40, P < 0.001 adjusted for age and sex). With respect to tobacco, none of the smoking categories showed association with oncohematological diseases. Regarding dietary habits, consumption of grilled/barbecued meat 3 or more times per month showed significant association with an increased risk of disease (OR 1.72, 95%CI: 1.08-2.75, P = 0.02). Daily consumption of coffee also was associated with an increased risk (OR 1.77, 95%CI: 1.03-3.03, P = 0.03). Results for GSTT1, GSTM1 and CYP1A1 polymorphisms showed no significant association with oncohematological diseases. When analyzing the interaction between polymorphisms and tobacco smoking or dietary habits, no statistically significant associations that modify disease risk were found.
CONCLUSION We reported an increased risk of oncohematological diseases associated with meat and coffee intake. We did not find significant associations between genetic polymorphisms and blood cancer.
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Riffel AK, Dehghani M, Hartshorne T, Floyd KC, Leeder JS, Rosenblatt KP, Gaedigk A. CYP2D7 Sequence Variation Interferes with TaqMan CYP2D6 (*) 15 and (*) 35 Genotyping. Front Pharmacol 2016; 6:312. [PMID: 26793106 PMCID: PMC4709848 DOI: 10.3389/fphar.2015.00312] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 12/17/2015] [Indexed: 12/14/2022] Open
Abstract
TaqMan™ genotyping assays are widely used to genotype CYP2D6, which encodes a major drug metabolizing enzyme. Assay design for CYP2D6 can be challenging owing to the presence of two pseudogenes, CYP2D7 and CYP2D8, structural and copy number variation and numerous single nucleotide polymorphisms (SNPs) some of which reflect the wild-type sequence of the CYP2D7 pseudogene. The aim of this study was to identify the mechanism causing false-positive CYP2D6*15 calls and remediate those by redesigning and validating alternative TaqMan genotype assays. Among 13,866 DNA samples genotyped by the CompanionDx® lab on the OpenArray platform, 70 samples were identified as heterozygotes for 137Tins, the key SNP of CYP2D6*15. However, only 15 samples were confirmed when tested with the Luminex xTAG CYP2D6 Kit and sequencing of CYP2D6-specific long range (XL)-PCR products. Genotype and gene resequencing of CYP2D6 and CYP2D7-specific XL-PCR products revealed a CC>GT dinucleotide SNP in exon 1 of CYP2D7 that reverts the sequence to CYP2D6 and allows a TaqMan assay PCR primer to bind. Because CYP2D7 also carries a Tins, a false-positive mutation signal is generated. This CYP2D7 SNP was also responsible for generating false-positive signals for rs769258 (CYP2D6*35) which is also located in exon 1. Although alternative CYP2D6*15 and *35 assays resolved the issue, we discovered a novel CYP2D6*15 subvariant in one sample that carries additional SNPs preventing detection with the alternate assay. The frequency of CYP2D6*15 was 0.1% in this ethnically diverse U.S. population sample. In addition, we also discovered linkage between the CYP2D7 CC>GT dinucleotide SNP and the 77G>A (rs28371696) SNP of CYP2D6*43. The frequency of this tentatively functional allele was 0.2%. Taken together, these findings emphasize that regardless of how careful genotyping assays are designed and evaluated before being commercially marketed, rare or unknown SNPs underneath primer and/or probe regions can impact the performance of PCR-based genotype assays, including TaqMan. Regardless of the test platform used, it is prudent to confirm rare allele calls by an independent method.
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Affiliation(s)
- Amanda K Riffel
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City Kansas City, MO, USA
| | - Mehdi Dehghani
- CompanionDx® Reference LabHouston, TX, USA; Division of Oncology, Department of Internal Medicine, University of Texas Health Science Center at HoustonHouston, TX, USA
| | - Toinette Hartshorne
- Genetic Analysis, Genetic Sciences Division, Thermo Fisher Scientific South San Francisco, CA, USA
| | | | - J Steven Leeder
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas CityKansas City, MO, USA; School of Medicine, University of Missouri-Kansas CityKansas City, MO, USA
| | - Kevin P Rosenblatt
- CompanionDx® Reference LabHouston, TX, USA; Division of Oncology, Department of Internal Medicine, University of Texas Health Science Center at HoustonHouston, TX, USA
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas CityKansas City, MO, USA; School of Medicine, University of Missouri-Kansas CityKansas City, MO, USA
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Lazalde-Ramos BP, Martínez-Fierro MDLL, Galaviz-Hernández C, Garza-Veloz I, Naranjo MEG, Sosa-Macías M, Llerena A. CYP2D6 gene polymorphisms and predicted phenotypes in eight indigenous groups from northwestern Mexico. Pharmacogenomics 2014; 15:339-48. [PMID: 24533713 DOI: 10.2217/pgs.13.203] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM Polymorphisms in CYP2D6 impact the interindividual and interethnic variability of drug efficiency; therefore, we determined the CYP2D6 allele distribution in eight Amerindian groups from northwestern Mexico and compared them with the frequencies in Mexican Mestizos. MATERIALS & METHODS A total of 508 Amerindians were studied. Genotyping of CYP2D6*5 and multiplication alleles was performed by long-range PCR, while CYP2D6*2, *3, *4, *6, *10, *17, *29, *35, *41 and copy number were evaluated by real-time PCR. RESULTS The most frequent alleles were CYP2D6*2 (0.05-0.28), CYP2D6*4 (0.003-0.21) and multiplications (0.043-0.107). CYP2D6*5, *6, * 10 and *41 were not observed in the majority of Amerindians, and CYP2D6*3, *17, *35 and *29 were not detected. The poor metabolizer genotype ( *4/*5) was lower (0.2%) in Amerindians than in Mestizos (5%); conversely, the ultrarapid metabolizer genotype was higher (12.6%) in indigenous groups than in Mestizos (7%). CONCLUSION Our data show a lower frequency of CYP2D6 inactive alleles and a higher frequency of duplication/multiplication of CYP2D6 active alleles in indigenous populations that in Mestizos. Original submitted 14 August 2013; Revision submitted 7 October 2013.
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Affiliation(s)
- Blanca Patricia Lazalde-Ramos
- Laboratorio de Medicina Molecular, Unidad Académica de Ciencias Químicas, Universidad Autónoma de Zacatecas, Zacatecas, México
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LLerena A, Naranjo MEG, Rodrigues-Soares F, Penas-LLedó EM, Fariñas H, Tarazona-Santos E. Interethnic variability ofCYP2D6alleles and of predicted and measured metabolic phenotypes across world populations. Expert Opin Drug Metab Toxicol 2014; 10:1569-83. [DOI: 10.1517/17425255.2014.964204] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Pharmacogenetics in American Indian populations: analysis of CYP2D6, CYP3A4, CYP3A5, and CYP2C9 in the Confederated Salish and Kootenai Tribes. Pharmacogenet Genomics 2014; 23:403-14. [PMID: 23778323 DOI: 10.1097/fpc.0b013e3283629ce9] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
OBJECTIVES Cytochrome P450 enzymes play a dominant role in drug elimination and variation in these genes is a major source of interindividual differences in drug response. Little is known, however, about pharmacogenetic variation in American Indian and Alaska Native (AI/AN) populations. We have developed a partnership with the Confederated Salish and Kootenai Tribes (CSKT) in northwestern Montana to address this knowledge gap. METHODS We resequenced CYP2D6 in 187 CSKT individuals and CYP3A4, CYP3A5, and CYP2C9 in 94 CSKT individuals. RESULTS We identified 67 variants in CYP2D6, 15 in CYP3A4, 10 in CYP3A5, and 41 in CYP2C9. The most common CYP2D6 alleles were CYP2D6*4 and *41 (20.86 and 11.23%, respectively). CYP2D6*3, *5, *6, *9, *10, *17, *28, *33, *35, *49, *1xN, *2xN, and *4xN frequencies were less than 2%. CYP3A5*3, CYP3A4*1G, and *1B were detected with frequencies of 92.47, 26.81, and 2.20%, respectively. Allelic variation in CYP2C9 was low: CYP2C9*2 (5.17%) and *3 (2.69%). In general, allele frequencies in CYP2D6, CYP2C9, and CYP3A5 were similar to those observed in European Americans. There was, however, a marked divergence in CYP3A4 for the CYP3A4*1G allele. We also observed low levels of linkage between CYP3A4*1G and CYP3A5*1 in the CSKT. The combination of nonfunctional CYP3A5*3 and putative reduced function CYP3A4*1G alleles may predict diminished clearance of CYP3A substrates. CONCLUSION These results highlight the importance of carrying out pharmacogenomic research in AI/AN populations and show that extrapolation from other populations is not appropriate. This information could help optimize drug therapy for the CSKT population.
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Chiurillo MA, Griman P, Santiago L, Torres K, Moran Y, Borjas L. Distribution of GSTM1, GSTT1, GSTP1 and TP53 disease-associated gene variants in native and urban Venezuelan populations. Gene 2013; 531:106-11. [PMID: 23994684 DOI: 10.1016/j.gene.2013.08.055] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 08/14/2013] [Accepted: 08/14/2013] [Indexed: 02/06/2023]
Abstract
The contemporary Venezuelan population is the product of major admixture process across various historical events, which has provided it a particular genetic background. The aim of this study concerns the analysis of glutathione S-transferase (GST) GSTM1, GSTP1 and GSTT1 genetic variants and five polymorphisms at the TP53 gene, which are related to cancer susceptibility, in an urban/admixed population and five Amerindian tribes (Bari, Panare, Pemon, Warao and Wayuu) from Venezuela. Genotyping was carried out in 120 individuals from an urban sample and 188 Amerindians. The analysis performed on TP53 haplotype and GST allele distribution showed a close correlation for Pemon and Warao populations, while Bari group appears isolated from the other populations. GSTT1 null variant frequency in our admixed (11%) and native samples (0.0-11.4%) was lower when compared with Caucasians, Africans and Asians. Frequency of the GSTP1*Val cancer-associated allele found in Bari (88.6%) and Panare (63.0%) is of the highest so far reported. Fourteen TP53 haplotypes were observed in the admixed populations, whereas only 3 to 5 in Amerindians. To our knowledge this is the first report of GST polymorphisms and TP53 haplotype distribution in Venezuelans. The distribution of most of analyzed polymorphisms in the urban sample is consistent with the admixed origin of the present-day population of Venezuela. While, the inter-ethnic variations in genetic polymorphisms found in Native American tribes seem to be the result of the influence of demographic factors. These results provide additional data for undertaking ethnographic and disease association studies in Venezuela.
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Affiliation(s)
- Miguel Angel Chiurillo
- Laboratorio de Genetica Molecular, Decanato de Ciencias de la Salud, Universidad Centroccidental Lisandro Alvarado, Barquisimeto, Venezuela.
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Chamorro JG, Castagnino JP, Musella RM, Nogueras M, Aranda FM, Frías A, Visca M, Aidar O, Perés S, de Larrañaga GF. Sex, ethnicity, and slow acetylator profile are the major causes of hepatotoxicity induced by antituberculosis drugs. J Gastroenterol Hepatol 2013. [PMID: 23190413 DOI: 10.1111/jgh.12069] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND AND AIM Treatment with antituberculosis (TB) drugs produces liver damage in a large proportion of patients. Isoniazid, an antibacterial drug, is primarily responsible for this hepatotoxicity. Several polymorphisms of the N-acetyltransferase 2 (NAT-2) and cytochrome P450 2E1 enzymes, which are involved in the metabolism of isoniazid, may be directly associated with the development of hepatotoxicity. This study was designed to analyze the association between the NAT-2 and CYP2E1 polymorphisms with the development of anti-TB drug-induced hepatotoxicity (ATDH). METHODS One hundred and seventy-five TB patients who had been treated with anti-TB drugs were studied. The allelic and genotypic frequency distributions of the NAT-2 and CYP2E1 enzymes were studied using polymerase chain reaction-restriction fragment length polymorphisms methodology. A binary logistic regression analysis was used to compare the results between TB patients with and without the development of hepatotoxicity. RESULTS Having a slow acetylator status (odds ratio [OR] = 2.615; confidence interval [CI] = 1.264-5.411; P = 0.01), being female (OR = 2.734; CI = 1.325-5.639, P = 0.006), and having Bolivian ethnicity (OR = 2.711; CI = 1.307-6.625, P = 0.007) were found to be independent predictor variables for ATDH. CONCLUSIONS This study showed that a patient's NAT-2 acetylator status, gender, and ethnic origin may be regarded as important risk factors for developing hepatotoxicity. Contrary to expectations, the CYP2E1 c1/c2 polymorphism did not show a significant association with hepatotoxicity in this study. Given the increases in TB cases and ATDH incidence levels, as well as the associated hospitalization costs, it may also be helpful to know patients' acetylator status prior to or at the beginning of the TB treatment regimen.
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Affiliation(s)
- Julián G Chamorro
- Hemostasis and Thrombosis Laboratory, Hospital of Infectious Diseases Dr. F. J. Muñiz, Buenos Aires, Argentina
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11
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Griman P, Moran Y, Valero G, Loreto M, Borjas L, Chiurillo MA. CYP2D6 gene variants in urban/admixed and Amerindian populations of Venezuela: pharmacogenetics and anthropological implications. Ann Hum Biol 2012; 39:137-42. [PMID: 22324840 DOI: 10.3109/03014460.2012.656703] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND Differences in genes encoding enzymes involved in the biotransformation of a large number of compounds, such as CYP2D6, are related to inter-individual and inter-ethnic variability in the metabolism of many drugs, which have also been linked to susceptibility to cancer and other health outcomes. Therefore, populations are likely to benefit from inclusion in pharmacogenetic research studies. AIM To determine the frequency of functionally important allele variants of CYP2D6 gene in a sample of an Urban/admixed and five Amerindian Venezuelan populations. SUBJECTS AND METHODS DNA of 328 unrelated volunteers was analysed for the presence of CYP2D6 *2, *3, *4, *5, *6 and *10 variants. RESULTS The frequency in the Urban/admixed population for *2, *3, *4, *5, *6 and *10 alleles was 37.9%, 0%, 13.4%, 2.0%, 1.2% and 4.0%, respectively. In the Bari population, the prevalence of *4 allele associated with decreased enzyme activity was observed in 42.5%, whereas the poor metabolizer genotype *4/*4 was found in 25%. In the Panare, Pemon, Warao and Wayuu populations the *4 allele was found in 5.4%, 2.5%, 1.7% and 4.2%, respectively. The *10 allele frequency found in Amerindians (0.0-6.3%) was lower than reported for Asians. CONCLUSION The results are consistent with the known genetic admixture origin of most Venezuela populations. Nevertheless, the observed significant differences among Amerindians highlight the need for pharmacogenetic studies taking into account biogeographical and anthropological considerations.
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Affiliation(s)
- Pedro Griman
- Laboratorio de Genética Molecular Dr Jorge Yunis-Turbay, Decanato de Ciencias de la Salud, Universidad Centroccidental Lisandro Alvarado, Barquisimeto 3001, Venezuela
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12
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Zanrosso CW, Emerenciano M, Faro A, de Aguiar Gonçalves BA, Mansur MB, Pombo-de-Oliveira MS. Genetic variability inN-acetyltransferase 2gene determines susceptibility to childhood lymphoid or myeloid leukemia in Brazil. Leuk Lymphoma 2011; 53:323-7. [DOI: 10.3109/10428194.2011.619605] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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13
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Contreras AV, Monge-Cazares T, Alfaro-Ruiz L, Hernandez-Morales S, Miranda-Ortiz H, Carrillo-Sanchez K, Jimenez-Sanchez G, Silva-Zolezzi I. Resequencing, haplotype construction and identification of novel variants of CYP2D6 in Mexican Mestizos. Pharmacogenomics 2011; 12:745-56. [PMID: 21391885 DOI: 10.2217/pgs.11.8] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
AIM The CYP2D6 enzyme participates in the metabolism of commonly prescribed drugs: antidepressants, antipsychotics and antihypertensives. The CYP2D6 gene shows a high degree of interindividual and interethnic variability that influences its expression and function. Mexican Mestizos are a recently admixed population resulting from the combination of Amerindian, European and, to a lesser extent, African populations. This study aimed to comprehensively characterize the CYP2D6 gene in Mexican Mestizos. MATERIALS & METHODS We performed linkage disequilibrium and network analyses in resequencing data of 96 individuals from two regions within Mexico with a different history of admixture and particular population dynamics, the Northwestern state of Sonora and the Central-Pacific state of Guerrero. RESULTS & CONCLUSION We identified 64 polymorphisms, including 14 novel variants: 13 SNPs and a CYP2D7 exon 2 conversion, that was assigned CYP2D6*82 by the Human Cytochrome P450 (CYP) Allele Nomenclature Committee. Three novel SNPs were predicted to have functional effects. For CYP2D6*82 we hypothesize an Amerindian origin that is supported by its identification in three Mexican Amerindian groups (Mayas, Tepehuanos and Mixtecos). Frequencies of CYP2D6*1, *2, *4, *5, *10, *29, *53, *82 and its duplications were 50.0, 25.5, 14.1, 2.0, 2.6, 1.0, 0.5, 2.1 and 3.6%, respectively. We found significant frequency differences in CYP2D6*1 and *2 between Mexican Mestizos and in CYP2D6*1, *2, *4, *5, *10 and *29 between Mexicans and at least one other population. We observed strong linkage disequilibrium and phylogenetic relationships between haplotypes. To our knowledge, this study is the first comprehensive resequencing analysis of CYP2D6 in Mexicans or any other Latin American population, providing information about genetic diversity relevant in the development of pharmacogenomics in this region.
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Affiliation(s)
- Alejandra V Contreras
- National Institute of Genomic Medicine (MEXICO), Periférico Sur 4124 Torre Zafiro II Piso 6, Col. Ex-Rancho de Anzaldo, Mexico DF 01900, Mexico
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14
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CORDERO KARINA, ESPINOZA IRIS, CACERES DANTE, ROCO ANGELA, MIRANDA CARLA, SQUICCIARINI VALENTINA, SANTANDER PAULA, LEE KUEN, SAAVEDRA IVÁN, QUIÑONES LUIS. Oral cancer susceptibility associated with the CYP1A1 and GSTM1 genotypes in Chilean individuals. Oncol Lett 2010; 1:549-553. [PMID: 22966341 PMCID: PMC3436421 DOI: 10.3892/ol_00000097] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Accepted: 03/03/2010] [Indexed: 11/06/2022] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) contained in tobacco smoke acquire carcinogenicity following their activation by xenobiotic-metabolizing enzymes to highly reactive metabolites. The cytochrome P4501A1 (CYP1A1) enzyme is central to the metabolic activation of these PAHs, and GSTM1 is the main enzyme responsible for its detoxification. CYP1A1 and GSTM1 polymorphisms were evaluated in 124 Chilean healthy controls and 48 oral cancer patients through PCR-based restriction fragment length polymorphism. In the healthy controls, frequencies of the CYP1A1 variant alleles for m1 (CYP1A1(*)2A) and the GSTM1null genotype were found to be 0.25 and 0.19, respectively. In the oral cancer patients, these frequencies were 0.33 and 0.50, respectively. Thus, the GSTM1 and m1 rare alleles were significantly more frequent in the oral cancer patients compared to the controls. The estimated relative risk for oral cancer associated with the single genotype CYP1A1 or GSTM1 was 2.08 for wt/m1, 1.04 for m1/m1 and 4.16 for the GSTM1null genotype. For smokers, the estimated relative risk (adjusted by age and gender) was higher in the individuals carrying the m1 allele of CYP1A1 [wt/m1: odds ratio (OR)=5.68, P=0.0080; m1/m1: OR=7.77, P=0.0420] or GSTM1null genotype (OR=20.81, P<0.0001). Combined genotypes CYP1A1 and GSTM1 increased the risk significantly (wt/m1/GSTM1null: OR=19.14, P=0.0030; m1/m1/GSTM1null: OR=21.39, P=0.0130). Taken together, these findings suggest that Chilean individuals carrying single or combined GSTM1 and CYP1A1 polymorphisms may be more susceptible to oral cancer induced by environmental tobacco smoking.
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Affiliation(s)
- KARINA CORDERO
- Center of Pharmacological and Toxicological Research (IFT), Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Chile
| | - IRIS ESPINOZA
- Department of Oral Pathology, Faculty of Odontology, University of Chile, Chile
| | - DANTE CACERES
- Center of Pharmacological and Toxicological Research (IFT), Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Chile
- Epidemiology Division, School of Public Health, Faculty of Medicine, University of Chile, Chile
| | - ANGELA ROCO
- Center of Pharmacological and Toxicological Research (IFT), Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Chile
- San Juan de Dios Hospital, Santiago, Chile
| | - CARLA MIRANDA
- Center of Pharmacological and Toxicological Research (IFT), Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Chile
- San Juan de Dios Hospital, Santiago, Chile
| | - VALENTINA SQUICCIARINI
- Center of Pharmacological and Toxicological Research (IFT), Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Chile
| | - PAULA SANTANDER
- Center of Pharmacological and Toxicological Research (IFT), Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Chile
| | - KUEN LEE
- Center of Pharmacological and Toxicological Research (IFT), Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Chile
| | - IVÁN SAAVEDRA
- Center of Pharmacological and Toxicological Research (IFT), Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Chile
| | - LUIS QUIÑONES
- Center of Pharmacological and Toxicological Research (IFT), Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Chile
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Possuelo LG, Castelan JA, de Brito TC, Ribeiro AW, Cafrune PI, Picon PD, Santos AR, Teixeira RLF, Gregianini TS, Hutz MH, Rossetti MLR, Zaha A. Association of slow N-acetyltransferase 2 profile and anti-TB drug-induced hepatotoxicity in patients from Southern Brazil. Eur J Clin Pharmacol 2008; 64:673-81. [PMID: 18421452 DOI: 10.1007/s00228-008-0484-8] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2007] [Accepted: 03/03/2008] [Indexed: 01/01/2023]
Abstract
PURPOSE To determine the frequency of N-acetyltransferase 2 (NAT2) polymorphisms, the NAT2 acetylation profile and its relation to the incidence of gastrointestinal adverse drug reactions (ADRs), anti-tuberculosis (TB) drug-induced hepatotoxicity, and the clinical risk factors for hepatotoxicity in a population from Brazil. METHODS Two hundred and fifty-four Brazilian TB patients using isoniazid (INH), rifampicin (RMP), and pirazinamide (PZA) were tested in a prospective cohort study. NAT2 genotyping was performed by direct PCR sequencing. The association between gastrointestinal ADRs/hepatotoxicity and the NAT2 profile genotype was evaluated by univariate analysis and multiple logistic regression. RESULTS Of the 254 patients analyzed, 69 (27.2%) were slow acetylators and 185 (72.8%) were fast acetylators. Sixty-five (25.6%) patients were human immunodeficiency virus (HIV)-positive. Thirty-three (13%) and 14 (5.5%) patients developed gastrointestinal ADR and hepatotoxicity, respectively. Of the 14 hepatotoxicity patients, nine (64.3%) were slow acetylators and five (35.7%) were fast acetylators. Sex, age, presence of hepatitis C virus, alcohol abuse, and baseline aminotransferases were not found to be risk factors for hepatotoxicity. However, logistic regression analysis revealed that slow acetylator status and the presence of HIV (p < 0.05) were independent risk factors for hepatotoxicity. CONCLUSIONS Our findings show that HIV-positive patients that have the slow acetylation profile are significantly associated with a higher risk of developing hepatotoxicity due to anti-TB drugs.
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Affiliation(s)
- L G Possuelo
- Centro de Desenvolvimento Científico e Tecnológico da Fundação Estadual de Produção e Pesquisa em Saúde, 5400 Avenida Ipiranga, Porto Alegre, RS 90610-000, Brazil
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