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Langlois AWR, Chenoweth MJ, Twesigomwe D, Scantamburlo G, Whirl-Carrillo M, Sangkuhl K, Klein TE, Nofziger C, Tyndale RF, Gaedigk A. PharmVar GeneFocus: CYP2A6. Clin Pharmacol Ther 2024; 116:948-962. [PMID: 39051767 DOI: 10.1002/cpt.3387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 07/08/2024] [Indexed: 07/27/2024]
Abstract
The Pharmacogene Variation Consortium (PharmVar) provides nomenclature for the human CYP2A gene locus containing the highly polymorphic CYP2A6 gene. CYP2A6 plays a role in the metabolism of nicotine and various drugs. Thus, genetic variation can substantially contribute to the function of this enzyme and associated efficacy and safety. This GeneFocus provides an overview of the clinical significance of CYP2A6, including its genetic variation and function. We also highlight and discuss caveats in the identification and characterization of allelic variation of this complex pharmacogene, a prerequisite for accurate genotype determination and prediction of phenotype status.
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Affiliation(s)
- Alec W R Langlois
- Department of Pharmacology & Toxicology, University of Toronto, Toronto, Ontario, Canada
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Meghan J Chenoweth
- Department of Pharmacology & Toxicology, University of Toronto, Toronto, Ontario, Canada
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
| | - David Twesigomwe
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | | | | | - Katrin Sangkuhl
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
| | - Teri E Klein
- Department of Biomedical Data Science, Stanford University, Stanford, California, USA
- Departments of Medicine (BMIR) and Genetics, Stanford University, Stanford, California, USA
| | | | - Rachel F Tyndale
- Department of Pharmacology & Toxicology, University of Toronto, Toronto, Ontario, Canada
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
| | - Andrea Gaedigk
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Research Institute (CMRI), Kansas City, Missouri, USA
- School of Medicine, University of Missouri-Kansas City, Kansas City, Missouri, USA
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Langlois AWR, Pouget JG, Knight J, Chenoweth MJ, Tyndale RF. Associating CYP2A6 structural variants with ovarian and lung cancer risk in the UK Biobank: replication and extension. Eur J Hum Genet 2024; 32:357-360. [PMID: 38097766 PMCID: PMC10923790 DOI: 10.1038/s41431-023-01518-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 10/27/2023] [Accepted: 11/28/2023] [Indexed: 03/10/2024] Open
Abstract
CYP2A6 is a polymorphic enzyme that inactivates nicotine; structural variants (SVs) include gene deletions and hybrids with the neighboring pseudogene CYP2A7. Two studies found that CYP2A7 deletions were associated with ovarian cancer risk. Using their methodology, we aimed to characterize CYP2A6 SVs (which may be misidentified by prediction software as CYP2A7 SVs), then assess CYP2A6 SV-associated risk for ovarian cancer, and extend analyses to lung cancer. An updated reference panel was created to impute CYP2A6 SVs from UK Biobank array data. Logistic regression models analyzed the association between CYP2A6 SVs and cancer risk, adjusting for covariates. Software-predicted CYP2A7 deletions were concordant with known CYP2A6 SVs. Deleterious CYP2A6 SVs were not associated with ovarian cancer (OR = 1.06; 95% CI: 0.80-1.37; p = 0.7) but did reduce the risk of lung cancer (OR = 0.44; 95% CI: 0.29-0.64; p < 0.0001), and a lung cancer subtype. Replication of known lung cancer associations indicates the validity of array-based SV analyses.
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Affiliation(s)
- Alec W R Langlois
- Department of Pharmacology & Toxicology, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, 100 Stokes Street, Toronto, ON, M6J 1H4, Canada
| | - Jennie G Pouget
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, 100 Stokes Street, Toronto, ON, M6J 1H4, Canada
- Department of Psychiatry, University of Toronto, 250 College Street, Toronto, ON, M5T 1R8, Canada
| | - Jo Knight
- Data Science Institute and Medical School, Lancaster University, Lancaster, UK
| | - Meghan J Chenoweth
- Department of Pharmacology & Toxicology, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, 100 Stokes Street, Toronto, ON, M6J 1H4, Canada
- Department of Psychiatry, University of Toronto, 250 College Street, Toronto, ON, M5T 1R8, Canada
| | - Rachel F Tyndale
- Department of Pharmacology & Toxicology, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada.
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, 100 Stokes Street, Toronto, ON, M6J 1H4, Canada.
- Department of Psychiatry, University of Toronto, 250 College Street, Toronto, ON, M5T 1R8, Canada.
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Giratallah H, Chenoweth MJ, Pouget JG, El-Boraie A, Alsaafin A, Lerman C, Knight J, Tyndale RF. CYP2A6 associates with respiratory disease risk and younger age of diagnosis: a phenome-wide association Mendelian Randomization study. Hum Mol Genet 2024; 33:198-210. [PMID: 37802914 PMCID: PMC10772040 DOI: 10.1093/hmg/ddad172] [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: 02/28/2023] [Revised: 09/21/2023] [Accepted: 10/02/2023] [Indexed: 10/08/2023] Open
Abstract
CYP2A6, a genetically variable enzyme, inactivates nicotine, activates carcinogens, and metabolizes many pharmaceuticals. Variation in CYP2A6 influences smoking behaviors and tobacco-related disease risk. This phenome-wide association study examined associations between a reconstructed version of our weighted genetic risk score (wGRS) for CYP2A6 activity with diseases in the UK Biobank (N = 395 887). Causal effects of phenotypic CYP2A6 activity (measured as the nicotine metabolite ratio: 3'-hydroxycotinine/cotinine) on the phenome-wide significant (PWS) signals were then estimated in two-sample Mendelian Randomization using the wGRS as the instrument. Time-to-diagnosis age was compared between faster versus slower CYP2A6 metabolizers for the PWS signals in survival analyses. In the total sample, six PWS signals were identified: two lung cancers and four obstructive respiratory diseases PheCodes, where faster CYP2A6 activity was associated with greater disease risk (Ps < 1 × 10-6). A significant CYP2A6-by-smoking status interaction was found (Psinteraction < 0.05); in current smokers, the same six PWS signals were found as identified in the total group, whereas no PWS signals were found in former or never smokers. In the total sample and current smokers, CYP2A6 activity causal estimates on the six PWS signals were significant in Mendelian Randomization (Ps < 5 × 10-5). Additionally, faster CYP2A6 metabolizer status was associated with younger age of disease diagnosis for the six PWS signals (Ps < 5 × 10-4, in current smokers). These findings support a role for faster CYP2A6 activity as a causal risk factor for lung cancers and obstructive respiratory diseases among current smokers, and a younger onset of these diseases. This research utilized the UK Biobank Resource.
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Affiliation(s)
- Haidy Giratallah
- Department of Pharmacology and Toxicology, University of Toronto, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
- Campbell Family Mental Health Research Institute, CAMH, 250 College St, Toronto, ON M5T 1R8, Canada
| | - Meghan J Chenoweth
- Department of Pharmacology and Toxicology, University of Toronto, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
- Campbell Family Mental Health Research Institute, CAMH, 250 College St, Toronto, ON M5T 1R8, Canada
- Department of Psychiatry, University of Toronto, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
| | - Jennie G Pouget
- Campbell Family Mental Health Research Institute, CAMH, 250 College St, Toronto, ON M5T 1R8, Canada
- Department of Psychiatry, University of Toronto, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
| | - Ahmed El-Boraie
- Department of Pharmacology and Toxicology, University of Toronto, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
- Campbell Family Mental Health Research Institute, CAMH, 250 College St, Toronto, ON M5T 1R8, Canada
| | - Alaa Alsaafin
- Department of Pharmacology and Toxicology, University of Toronto, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
- Campbell Family Mental Health Research Institute, CAMH, 250 College St, Toronto, ON M5T 1R8, Canada
| | - Caryn Lerman
- Norris Comprehensive Cancer Center, University of Southern California, 1441 Eastlake Ave, Los Angeles, CA 90033, United States
| | - Jo Knight
- Department of Psychiatry, University of Toronto, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
- Data Science Institute, Lancaster University Medical School, Lancaster LA1 4YE, United Kingdom
| | - Rachel F Tyndale
- Department of Pharmacology and Toxicology, University of Toronto, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
- Campbell Family Mental Health Research Institute, CAMH, 250 College St, Toronto, ON M5T 1R8, Canada
- Department of Psychiatry, University of Toronto, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
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Langlois AWR, El-Boraie A, Pouget JG, Cox LS, Ahluwalia JS, Fukunaga K, Mushiroda T, Knight J, Chenoweth MJ, Tyndale RF. Genotyping, characterization, and imputation of known and novel CYP2A6 structural variants using SNP array data. J Hum Genet 2023:10.1038/s10038-023-01148-y. [PMID: 37059825 DOI: 10.1038/s10038-023-01148-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/23/2023] [Accepted: 03/30/2023] [Indexed: 04/16/2023]
Abstract
CYP2A6 metabolically inactivates nicotine. Faster CYP2A6 activity is associated with heavier smoking and higher lung cancer risk. The CYP2A6 gene is polymorphic, including functional structural variants (SV) such as gene deletions (CYP2A6*4), duplications (CYP2A6*1 × 2), and hybrids with the CYP2A7 pseudogene (CYP2A6*12, CYP2A6*34). SVs are challenging to genotype due to their complex genetic architecture. Our aims were to develop a reliable protocol for SV genotyping, functionally phenotype known and novel SVs, and investigate the feasibility of CYP2A6 SV imputation from SNP array data in two ancestry populations. European- (EUR; n = 935) and African- (AFR; n = 964) ancestry individuals from smoking cessation trials were genotyped for SNPs using an Illumina array and for CYP2A6 SVs using Taqman copy number (CN) assays. SV-specific PCR amplification and Sanger sequencing was used to characterize a novel SV. Individuals with SVs were phenotyped using the nicotine metabolite ratio, a biomarker of CYP2A6 activity. SV diplotype and SNP array data were integrated and phased to generate ancestry-specific SV reference panels. Leave-one-out cross-validation was used to investigate the feasibility of CYP2A6 SV imputation. A minimal protocol requiring three Taqman CN assays for CYP2A6 SV genotyping was developed and known SV associations with activity were replicated. The first domain swap CYP2A6-CYP2A7 hybrid SV, CYP2A6*53, was identified, sequenced, and associated with lower CYP2A6 activity. In both EURs and AFRs, most SV alleles were identified using imputation (>70% and >60%, respectively); importantly, false positive rates were <1%. These results confirm that CYP2A6 SV imputation can identify most SV alleles, including a novel SV.
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Affiliation(s)
- Alec W R Langlois
- Department of Pharmacology and Toxicology, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, 100 Stokes Street, Toronto, ON, M6J 1H4, Canada
| | - Ahmed El-Boraie
- Department of Pharmacology and Toxicology, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, 100 Stokes Street, Toronto, ON, M6J 1H4, Canada
| | - Jennie G Pouget
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, 100 Stokes Street, Toronto, ON, M6J 1H4, Canada
- Department of Psychiatry, University of Toronto, 250 College Street, Toronto, ON, M5T 1R8, Canada
| | - Lisa Sanderson Cox
- Department of Population Health, University of Kansas School of Medicine, Kansas City, KS, 66160, USA
| | - Jasjit S Ahluwalia
- Departments of Behavioral and Social Sciences and Medicine, Brown University School of Public Health, Providence, RI, 02912, USA
| | - Koya Fukunaga
- Center for Integrative Medical Sciences, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Taisei Mushiroda
- Center for Integrative Medical Sciences, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Jo Knight
- Data Science Institute and Medical School, Lancaster University, Lancaster, UK
| | - Meghan J Chenoweth
- Department of Pharmacology and Toxicology, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, 100 Stokes Street, Toronto, ON, M6J 1H4, Canada
- Department of Psychiatry, University of Toronto, 250 College Street, Toronto, ON, M5T 1R8, Canada
| | - Rachel F Tyndale
- Department of Pharmacology and Toxicology, University of Toronto, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada.
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, 100 Stokes Street, Toronto, ON, M6J 1H4, Canada.
- Department of Psychiatry, University of Toronto, 250 College Street, Toronto, ON, M5T 1R8, Canada.
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James BA, Williams JL, Nemesure B. A systematic review of genetic ancestry as a risk factor for incidence of non-small cell lung cancer in the US. Front Genet 2023; 14:1141058. [PMID: 37082203 PMCID: PMC10110850 DOI: 10.3389/fgene.2023.1141058] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 03/14/2023] [Indexed: 04/22/2023] Open
Abstract
Background: Non-Small Cell Lung Cancer (NSCLC), the leading cause of cancer-related death in the United States, is the most diagnosed form of lung cancer. While lung cancer incidence has steadily declined over the last decade, disparities in incidence and mortality rates persist among African American (AA), Caucasian American (CA), and Hispanic American (HA) populations. Researchers continue to explore how genetic ancestry may influence differential outcomes in lung cancer risk and development. The purpose of this evaluation is to highlight experimental research that investigates the differential impact of genetic mutations and ancestry on NSCLC incidence. Methods: This systematic review was conducted using PubMed and Google Scholar search engines. The following key search terms were used to select articles published between 2011 and 2022: "African/European/Latin American Ancestry NSCLC"; "Racial Disparities NSCLC"; "Genetic Mutations NSCLC"; "NSCLC Biomarkers"; "African Americans/Hispanic Americans/Caucasian Americans NSCLC incidence." Systematic reviews, meta-analyses, and studies outside of the US were excluded. A total of 195 articles were initially identified and after excluding 156 which did not meet eligibility criteria, 38 were included in this investigation. Results: Studies included in this analysis focused on racial/ethnic disparities in the following common genetic mutations observed in NSCLC: KRAS, EGFR, TP53, PIK3CA, ALK Translocations, ROS-1 Rearrangements, STK11, MET, and BRAF. Results across studies varied with respect to absolute differential expression. No significant differences in frequencies of specific genetic mutational profiles were noted between racial/ethnic groups. However, for HAs, lower mutational frequencies in KRAS and STK11 genes were observed. In genetic ancestry level analyses, multiple studies suggest that African ancestry is associated with a higher frequency of EGFR mutations. Conversely, Latin ancestry is associated with TP53 mutations. At the genomic level, several novel predisposing variants associated with African ancestry and increased risk of NSCLC were discovered. Family history among all racial/ethnic groups was also considered a risk factor for NSCLC. Conclusion: Results from racially and ethnically diverse studies can elucidate driving factors that may increase susceptibility and subsequent lung cancer risk across different racial/ethnic groups. Identification of biomarkers that can be used as diagnostic, prognostic, and therapeutic tools may help improve lung cancer survival among high-risk populations.
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Langlois AW, El-Boraie A, Fukunaga K, Mushiroda T, Kubo M, Lerman C, Knight J, Scherer SE, Chenoweth MJ, Tyndale RF. Accuracy and applications of sequencing and genotyping approaches for CYP2A6 and homologous genes. Pharmacogenet Genomics 2022; 32:159-172. [PMID: 35190513 PMCID: PMC9081136 DOI: 10.1097/fpc.0000000000000466] [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: 11/27/2022]
Abstract
OBJECTIVES We evaluated multiple genotyping/sequencing approaches in a homologous region of chromosome 19, and investigated associations of two common 3'-UTR CYP2A6 variants with activity in vivo. METHODS Individuals (n = 1704) of European and African ancestry were phenotyped for the nicotine metabolite ratio (NMR), an index of CYP2A6 activity, and genotyped/sequenced using deep amplicon exon sequencing, SNP array, genotype imputation and targeted capture sequencing. Amplicon exon sequencing was the gold standard to which other methods were compared within-individual for CYP2A6, CYP2A7, CYP2A13, and CYP2B6 exons to identify highly discordant positions. Linear regression models evaluated the association of CYP2A6*1B and rs8192733 genotypes (coded additively) with logNMR. RESULTS All approaches were ≤2.6% discordant with the gold standard; discordant calls were concentrated at few positions. Fifteen positions were discordant in >10% of individuals, with 12 appearing in regions of high identity between homologous genes (e.g. CYP2A6 and CYP2A7). For six, allele frequencies in our study and online databases were discrepant, suggesting errors in online sources. In the European-ancestry group (n = 935), CYP2A6*1B and rs8192733 were associated with logNMR (P < 0.001). A combined model found main effects of both variants on increasing logNMR. Similar trends were found in those of African ancestry (n = 506). CONCLUSION Multiple genotyping/sequencing approaches used in this chromosome 19 region contain genotyping/sequencing errors, as do online databases. Gene-specific primers and SNP array probes must consider gene homology; short-read sequencing of related genes in a single reaction should be avoided. Using improved sequencing approaches, we characterized two gain-of-function 3'-UTR variants, including the relatively understudied rs8192733.
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Affiliation(s)
- Alec W.R. Langlois
- Department of Pharmacology & Toxicology, University of Toronto; 1 King’s College Circle, Toronto, ON, M5S 1A8, Canada. Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health 100 Stokes Street, Toronto, ON, M6J 1H4, Canada
| | - Ahmed El-Boraie
- Department of Pharmacology & Toxicology, University of Toronto; 1 King’s College Circle, Toronto, ON, M5S 1A8, Canada. Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health 100 Stokes Street, Toronto, ON, M6J 1H4, Canada
| | - Koya Fukunaga
- Center for Integrative Medical Sciences, RIKEN; 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Taisei Mushiroda
- Center for Integrative Medical Sciences, RIKEN; 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Michiaki Kubo
- Center for Integrative Medical Sciences, RIKEN; 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Caryn Lerman
- Department of Psychiatry and USC Norris Comprehensive Cancer Center, University of Southern California, 1441 Eastlake Avenue, Cancer Center, Los Angeles, CA, 90089, United States
| | - Jo Knight
- Data Science Institute and Lancaster University Medical School, Lancaster, UK
- Department of Psychiatry, University of Toronto; 250 College Street, Toronto, ON, M5T 1R8, Canada
| | - Steven E. Scherer
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Meghan J. Chenoweth
- Department of Pharmacology & Toxicology, University of Toronto; 1 King’s College Circle, Toronto, ON, M5S 1A8, Canada. Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health 100 Stokes Street, Toronto, ON, M6J 1H4, Canada
| | - Rachel F. Tyndale
- Department of Pharmacology & Toxicology, University of Toronto; 1 King’s College Circle, Toronto, ON, M5S 1A8, Canada. Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health 100 Stokes Street, Toronto, ON, M6J 1H4, Canada
- Department of Psychiatry, University of Toronto; 250 College Street, Toronto, ON, M5T 1R8, Canada
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Integrative Modeling of Multiomics Data for Predicting Tumor Mutation Burden in Patients with Lung Cancer. BIOMED RESEARCH INTERNATIONAL 2022; 2022:2698190. [PMID: 35097114 PMCID: PMC8794677 DOI: 10.1155/2022/2698190] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 11/24/2021] [Indexed: 12/23/2022]
Abstract
Immunotherapy has been widely used in the treatment of lung cancer, and one of the most effective biomarkers for the prognosis of immunotherapy currently is tumor mutation burden (TMB). Although whole-exome sequencing (WES) could be utilized to assess TMB, several problems prevent its routine clinical application. To develop a simplified TMB prediction model, patients with lung adenocarcinoma (LUAD) in The Cancer Genome Atlas (TCGA) were randomly split into training and validation cohorts and categorized into the TMB-high (TMB-H) and TMB-low (TMB-L) groups, respectively. Based on the 610 differentially expressed genes, 50 differentially expressed miRNAs and 58 differentially methylated CpG sites between TMB-H and TMB-L patients, we constructed 4 predictive signatures and established TMB prediction model through machine learning methods that integrating the expression or methylation profiles of 7 genes, 7 miRNAs, and 6 CpG sites. The multiomics model exhibited excellent performance in predicting TMB with the area under curve (AUC) of 0.911 in the training cohort and 0.859 in the validation cohort. Besides, the significant correlation between the multiomics model score and TMB was observed. In summary, we developed a prognostic TMB prediction model by integrating multiomics data in patients with LUAD, which might facilitate the further development of quantitative real time-polymerase chain reaction- (qRT-PCR-) based TMB prediction assay.
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El-Boraie A, Tanner JA, Zhu AZX, Claw KG, Prasad B, Schuetz EG, Thummel KE, Fukunaga K, Mushiroda T, Kubo M, Benowitz NL, Lerman C, Tyndale RF. Functional characterization of novel rare CYP2A6 variants and potential implications for clinical outcomes. Clin Transl Sci 2021; 15:204-220. [PMID: 34476898 PMCID: PMC8742641 DOI: 10.1111/cts.13135] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/23/2021] [Accepted: 07/24/2021] [Indexed: 11/28/2022] Open
Abstract
CYP2A6 activity, phenotyped by the nicotine metabolite ratio (NMR), is a predictor of several smoking behaviors, including cessation and smoking‐related disease risk. The heritability of the NMR is 60–80%, yet weighted genetic risk scores (wGRSs) based on common variants explain only 30–35%. Rare variants (minor allele frequency <1%) are hypothesized to explain some of this missing heritability. We present two targeted sequencing studies where rare protein‐coding variants are functionally characterized in vivo, in silico, and in vitro to examine this hypothesis. In a smoking cessation trial, 1687 individuals were sequenced; characterization measures included the in vivo NMR, in vitro protein expression, and metabolic activity measured from recombinant proteins. In a human liver bank, 312 human liver samples were sequenced; measures included RNA expression, protein expression, and metabolic activity from extracted liver tissue. In total, 38 of 47 rare coding variants identified were novel; characterizations ranged from gain‐of‐function to loss‐of‐function. On a population level, the portion of NMR variation explained by the rare coding variants was small (~1%). However, upon incorporation, the accuracy of the wGRS was improved for individuals with rare protein‐coding variants (i.e., the residuals were reduced), and approximately one‐third of these individuals (12/39) were re‐assigned from normal to slow metabolizer status. Rare coding variants can alter an individual’s CYP2A6 activity; their integration into wGRSs through precise functional characterization is necessary to accurately assess clinical outcomes and achieve precision medicine for all. Investigation into noncoding variants is warranted to further explain the missing heritability in the NMR.
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Affiliation(s)
- Ahmed El-Boraie
- Department of Pharmacology & Toxicology, University of Toronto, Toronto, ON, Canada.,Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health and Division of Brain and Therapeutics, Toronto, ON, Canada
| | | | - Andy Z X Zhu
- Department of Quantitative Translational Sciences, Takeda Pharmaceuticals, Cambridge, Massachusetts, USA
| | - Katrina G Claw
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Aurora, Colorado, USA
| | - Bhagwat Prasad
- Department of Pharmaceutical Sciences, Washington State University, Spokane, Washington, USA
| | - Erin G Schuetz
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Kenneth E Thummel
- Department of Pharmaceutics, University of Washington, Seattle, Washington, USA
| | - Koya Fukunaga
- Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | | | - Michiaki Kubo
- Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Neal L Benowitz
- Clinical Pharmacology Research Program, Division of Cardiology, Department of Medicine and Center for Tobacco Control Research and Education, University of California San Francisco, San Francisco, California, USA
| | - Caryn Lerman
- Department of Psychiatry, USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, USA
| | - Rachel F Tyndale
- Department of Pharmacology & Toxicology, University of Toronto, Toronto, ON, Canada.,Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health and Division of Brain and Therapeutics, Toronto, ON, Canada.,Department of Psychiatry, University of Toronto, Toronto, ON, Canada
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9
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Murphy SE. Biochemistry of nicotine metabolism and its relevance to lung cancer. J Biol Chem 2021; 296:100722. [PMID: 33932402 PMCID: PMC8167289 DOI: 10.1016/j.jbc.2021.100722] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 12/27/2022] Open
Abstract
Nicotine is the key addictive constituent of tobacco. It is not a carcinogen, but it drives smoking and the continued exposure to the many carcinogens present in tobacco. The investigation into nicotine biotransformation has been ongoing for more than 60 years. The dominant pathway of nicotine metabolism in humans is the formation of cotinine, which occurs in two steps. The first step is cytochrome P450 (P450, CYP) 2A6–catalyzed 5′-oxidation to an iminium ion, and the second step is oxidation of the iminium ion to cotinine. The half-life of nicotine is longer in individuals with low P450 2A6 activity, and smokers with low activity often decrease either the intensity of their smoking or the number of cigarettes they use compared with those with “normal” activity. The effect of P450 2A6 activity on smoking may influence one's tobacco-related disease risk. This review provides an overview of nicotine metabolism and a summary of the use of nicotine metabolite biomarkers to define smoking dose. Some more recent findings, for example, the identification of uridine 5′-diphosphoglucuronosyltransferase 2B10 as the catalyst of nicotine N-glucuronidation, are discussed. We also describe epidemiology studies that establish the contribution of nicotine metabolism and CYP2A6 genotype to lung cancer risk, particularly with respect to specific racial/ethnic groups, such as those with Japanese, African, or European ancestry. We conclude that a model of nicotine metabolism and smoking dose could be combined with other lung cancer risk variables to more accurately identify former smokers at the highest risk of lung cancer and to intervene accordingly.
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Affiliation(s)
- Sharon E Murphy
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA.
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10
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Jeon CY, Feldman R, Pendergast FJ, AlKaade S, Brand RE, Guda N, Sandhu BS, Singh VK, Wilcox CM, Slivka A, Whitcomb DC, Yadav D. Divergent trends in lifetime drinking and smoking between Black and White Americans diagnosed with chronic pancreatitis. Pancreatology 2020; 20:1667-1672. [PMID: 33132046 PMCID: PMC7737506 DOI: 10.1016/j.pan.2020.10.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 09/08/2020] [Accepted: 10/08/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND/OBJECTIVES Black Americans are at increased risk of chronic pancreatitis (CP) compared to their White counterparts. We aimed to describe the race-specific smoking history and lifetime drinking in patients diagnosed with CP. METHODS We analyzed data on 334 Black and White CP participants of the North American Pancreatitis Study 2 Continuation and Validation Study and Ancillary Study. Lifetime drinking history and lifetime smoking history were collected through in-person interviews. Intensity, frequency, duration and current status of drinking and smoking were compared between Black and White CP participants, stratified by physician-defined alcohol etiology. In addition, drinking levels at each successive decades in life (20s, 30s, 40s) were compared by race and graphically portrayed as heat diagrams. RESULTS Among patients with alcoholic CP, current smoking levels were not different by race (67-70%), but a smaller proportion of Black patients reported having smoked 1 or more packs per day in the past (32%) as compared to White patients (58%, p < 0.0001). Black patients were more likely to report current consumption of alcohol (31%), as opposed to White patients (17%, p = 0.016). Black patients also reported more intense drinking at age 35 and 45 years as compared to White patients, while age at CP onset were similar between the two groups. CONCLUSION We found more intense drinking but less intense smoking history in Black CP patients as compared to White CP patients. Effective alcohol abstinence and smoking cessation program with sustained impact are needed in CP patients.
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Affiliation(s)
- Christie Y. Jeon
- Cedars Sinai Cancer, Cedars-Sinai Medical Center, Los Angeles, CA,Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA
| | - Robert Feldman
- Center for Research on Healthcare Data Center, University of Pittsburgh, Pittsburgh, PA
| | | | | | - Randall E. Brand
- Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Nalini Guda
- Aurora St. Luke's Medical Center, Milwaukee, WI
| | | | - Vikesh K. Singh
- Pancreatitis Center, Division of Gastroenterology, Johns Hopkins Medical Institutions, Baltimore, MD
| | - C. Mel Wilcox
- Division of Gastroenterology and Hepatology, University of Alabama Birmingham, AL
| | - Adam Slivka
- Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - David C. Whitcomb
- Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Dhiraj Yadav
- Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh School of Medicine, Pittsburgh, PA
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11
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Gao Y, Miksys S, Palmour RM, Tyndale RF. The Influence of Tobacco Smoke/Nicotine on CYP2A Expression in Human and African Green Monkey Lungs. Mol Pharmacol 2020; 98:658-668. [PMID: 33055223 DOI: 10.1124/molpharm.120.000100] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 09/17/2020] [Indexed: 11/22/2022] Open
Abstract
CYP2A enzymes metabolically inactivate nicotine and activate tobacco-derived procarcinogens [e.g., 4-[methylnitrosamino]-1-(3-pyridyl)-1-butanone]. Smoking decreases nicotine clearance, and chronic nicotine reduces hepatic CYP2A activity. However, little is known about the impact of smoking or nicotine on the expression of CYP2A in the lung. We investigated 1) the levels of human lung CYP2A mRNA in smokers versus nonsmokers and 2) the impact of daily nicotine treatment on lung CYP2A protein levels in African green monkeys (AGMs). Lung CYP2A13, CYP2A6, and CYP2A7 (and CYP1A2) mRNA levels in smokers and nonsmokers were assessed in Gene Expression Omnibus data sets (GSE30063, GSE108134, and GSE11784). The impact of chronic, twice-daily, subcutaneous nicotine at two doses (0.3 and 0.5 mg/kg) versus vehicle on lung CYP2A protein levels was assessed. The impact of ethanol self-administration was also investigated, with and without nicotine treatment. Smokers versus nonsmokers (from GSE30063 and GSE108134) had lower (1.04- to 1.12-fold) levels of lung CYP2A13, CYP2A6, and CYP2A7 (and higher CYP1A2) mRNA. Both doses of nicotine tested decreased AGM lung CYP2A protein (3- to 7-fold). Ethanol self-administration had no effect on AGM lung CYP2A protein, and there was no interaction between ethanol and nicotine. Our results suggest that smoking was associated with a reduction in human lung CYP2A13, CYP2A6, and CYP2A7 mRNA, consistent with the role of nicotine treatment in reducing AGM lung CYP2A protein. This regulation by smoking/nicotine will increase interindividual variation in lung CYP2A levels, which may impact the localized metabolism of inhaled drugs and tobacco smoke procarcinogens. SIGNIFICANCE STATEMENT: CYP2A13 and CYP2A6 are expressed in the lung and may contribute to local procarcinogen activation. Smokers had lower lung CYP2A mRNA levels compared with nonsmokers. Lung CYP2A protein expression was decreased by systemic treatment with nicotine. Decreased lung CYP2A expression may alter smoking-related lung cancer risk and tissue damage from other inhaled toxins. This novel regulatory impact of nicotine, including nicotine found in smoking-cessation nicotine-replacement therapies, may have potential benefits on smoking-related lung cancer risk.
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Affiliation(s)
- Yuan Gao
- Department of Pharmacology and Toxicology, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health (CAMH) (Y.G., S.M., R.F.T.) and Department of Psychiatry (R.F.T.), University of Toronto, Toronto, Ontario, Canada and Department of Psychiatry and Human Genetics, McGill University, Montreal, Quebec, Canada (R.M.P.)
| | - Sharon Miksys
- Department of Pharmacology and Toxicology, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health (CAMH) (Y.G., S.M., R.F.T.) and Department of Psychiatry (R.F.T.), University of Toronto, Toronto, Ontario, Canada and Department of Psychiatry and Human Genetics, McGill University, Montreal, Quebec, Canada (R.M.P.)
| | - Roberta M Palmour
- Department of Pharmacology and Toxicology, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health (CAMH) (Y.G., S.M., R.F.T.) and Department of Psychiatry (R.F.T.), University of Toronto, Toronto, Ontario, Canada and Department of Psychiatry and Human Genetics, McGill University, Montreal, Quebec, Canada (R.M.P.)
| | - Rachel F Tyndale
- Department of Pharmacology and Toxicology, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health (CAMH) (Y.G., S.M., R.F.T.) and Department of Psychiatry (R.F.T.), University of Toronto, Toronto, Ontario, Canada and Department of Psychiatry and Human Genetics, McGill University, Montreal, Quebec, Canada (R.M.P.)
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12
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Zhao Z, He B, Cai Q, Zhang P, Peng X, Zhang Y, Xie H, Wang X. A model of twenty-three metabolic-related genes predicting overall survival for lung adenocarcinoma. PeerJ 2020; 8:e10008. [PMID: 33024640 PMCID: PMC7520091 DOI: 10.7717/peerj.10008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 08/31/2020] [Indexed: 01/27/2023] Open
Abstract
Background The highest rate of cancer-related deaths worldwide is from lung adenocarcinoma (LUAD) annually. Metabolism was associated with tumorigenesis and cancer development. Metabolic-related genes may be important biomarkers and metabolic therapeutic targets for LUAD. Materials and Methods In this study, the gleaned cohort included LUAD RNA-SEQ data from the Cancer Genome Atlas (TCGA) and corresponding clinical data (n = 445). The training cohort was utilized to model construction, and data from the Gene Expression Omnibus (GEO, GSE30219 cohort, n = 83; GEO, GSE72094, n = 393) were regarded as a testing cohort and utilized for validation. First, we used a lasso-penalized Cox regression analysis to build a new metabolic-related signature for predicting the prognosis of LUAD patients. Next, we verified the metabolic gene model by survival analysis, C-index, receiver operating characteristic (ROC) analysis. Univariate and multivariate Cox regression analyses were utilized to verify the gene signature as an independent prognostic factor. Finally, we constructed a nomogram and performed gene set enrichment analysis to facilitate subsequent clinical applications and molecular mechanism analysis. Result Patients with higher risk scores showed significantly associated with poorer survival. We also verified the signature can work as an independent prognostic factor for LUAD survival. The nomogram showed better clinical application performance for LUAD patient prognostic prediction. Finally, KEGG and GO pathways enrichment analyses suggested several especially enriched pathways, which may be helpful for us investigative the underlying mechanisms.
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Affiliation(s)
- Zhenyu Zhao
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Central South University, Changsha, Hunan, China
| | - Boxue He
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Central South University, Changsha, Hunan, China
| | - Qidong Cai
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Central South University, Changsha, Hunan, China
| | - Pengfei Zhang
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Central South University, Changsha, Hunan, China
| | - Xiong Peng
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Central South University, Changsha, Hunan, China
| | - Yuqian Zhang
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Central South University, Changsha, Hunan, China
| | - Hui Xie
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Central South University, Changsha, Hunan, China
| | - Xiang Wang
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Central South University, Changsha, Hunan, China
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13
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Borrego-Soto G, Perez-Paramo YX, Chen G, Santuario-Facio SK, Santos-Guzman J, Posadas-Valay R, Alvarado-Monroy FM, Balderas-Renteria I, Medina-Gonzalez R, Ortiz-Lopez R, Lazarus P, Rojas-Martinez A. Genetic variants in CYP2A6 and UGT1A9 genes associated with urinary nicotine metabolites in young Mexican smokers. THE PHARMACOGENOMICS JOURNAL 2020; 20:586-594. [PMID: 31959879 PMCID: PMC7375952 DOI: 10.1038/s41397-020-0147-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 12/19/2019] [Accepted: 01/07/2020] [Indexed: 12/24/2022]
Abstract
Nicotine is the major pharmacologically active substance in tobacco. Several studies have examined genotypes related to nicotine metabolism, but few studies have been performed in the Mexican population. The objective was to identify associations between gene variants in metabolizing enzymes and the urinary levels of nicotine metabolites among Mexican smokers. The levels of nicotine and its metabolites were determined in the urine of 88 young smokers from Mexico, and 167 variants in 24 genes associated with nicotine metabolism were genotyped by next-generation sequencing (NGS). Trans-3'-hydroxy-cotinine (3HC) and 4-hydroxy-4-(3-pyridyl)-butanoic acid were the most abundant metabolites (35 and 17%, respectively). CYP2A6*12 was associated with 3HC (p = 0.014). The rs145014075 was associated with creatinine-adjusted levels of nicotine (p = 0.035), while the rs12471326 (UGT1A9) was associated to cotinine-N-glucuronide (p = 0.030). CYP2A6 and UGT1A9 variants are associated to nicotine metabolism. 4HPBA metabolite was an abundant urinary metabolite in young Mexican smokers.
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Affiliation(s)
- Gissela Borrego-Soto
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico
| | - Yadira X Perez-Paramo
- Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, WA, USA
| | - Gang Chen
- Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, WA, USA
| | | | - Jesus Santos-Guzman
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico
| | - Rodolfo Posadas-Valay
- Facultad de Medicina, Centro Universitario de Salud, Universidad Autonoma de Nuevo Leon, Monterrey, Mexico
| | | | | | - Ramses Medina-Gonzalez
- Centro de Investigación y Desarrollo en Ciencias de la Salud, Universidad Autonoma de Nuevo Leon, Monterrey, Mexico
| | - Rocio Ortiz-Lopez
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico
| | - Philip Lazarus
- Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, WA, USA
| | - Augusto Rojas-Martinez
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, Mexico.
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14
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Bagby SP, Martin D, Chung ST, Rajapakse N. From the Outside In: Biological Mechanisms Linking Social and Environmental Exposures to Chronic Disease and to Health Disparities. Am J Public Health 2020; 109:S56-S63. [PMID: 30699032 DOI: 10.2105/ajph.2018.304864] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The ongoing epidemic of chronic diseases involves a spectrum of clinical entities now understood to represent late manifestations of progressive metabolic dysfunction initiated in early life. These diseases disproportionately affect disadvantaged populations, exacerbating health disparities that persist despite public health efforts. Excessive exposure to stressful psychosocial and environmental forces is 1 factor known to contribute to population-level disparities in at-risk settings. Yet increasing evidence reveals that even a single adverse environmental exposure-especially during very early developmental years-can become literally biologically embedded, inducing long-lasting disease-promoting pathways that amplify responses (e.g., cortisol, immune, inflammatory) to all future adverse stressors, thus enhancing their disease-promoting impacts. The same pathways may also interact with ancestrally linked genetic variants to modify chronic disease risk. We address how, in at-risk populations, environmentally activated disease-promoting pathways can contribute to a biologically based disease-susceptible phenotype; this is likely to be uniquely damaging in populations with multiple adverse exposures and is capable of cross-generational transmission. Intended to complement existing models, this biological perspective highlights key research opportunities and life-stage priorities with potential to enhance the reduction of health disparities.
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Affiliation(s)
- Susan P Bagby
- Susan P. Bagby is with the Bob and Charlee Moore Institute for Nutrition and Wellness and the Department of Medicine, Oregon Health & Science University, Portland. Damali Martin is with the National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD. Stephanie T. Chung is with the National Institute of Diabetes and Digestive and Kidney Diseases, NIH. Nishadi Rajapakse is with the National Institute on Minority Health and Health Disparities, NIH
| | - Damali Martin
- Susan P. Bagby is with the Bob and Charlee Moore Institute for Nutrition and Wellness and the Department of Medicine, Oregon Health & Science University, Portland. Damali Martin is with the National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD. Stephanie T. Chung is with the National Institute of Diabetes and Digestive and Kidney Diseases, NIH. Nishadi Rajapakse is with the National Institute on Minority Health and Health Disparities, NIH
| | - Stephanie T Chung
- Susan P. Bagby is with the Bob and Charlee Moore Institute for Nutrition and Wellness and the Department of Medicine, Oregon Health & Science University, Portland. Damali Martin is with the National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD. Stephanie T. Chung is with the National Institute of Diabetes and Digestive and Kidney Diseases, NIH. Nishadi Rajapakse is with the National Institute on Minority Health and Health Disparities, NIH
| | - Nishadi Rajapakse
- Susan P. Bagby is with the Bob and Charlee Moore Institute for Nutrition and Wellness and the Department of Medicine, Oregon Health & Science University, Portland. Damali Martin is with the National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD. Stephanie T. Chung is with the National Institute of Diabetes and Digestive and Kidney Diseases, NIH. Nishadi Rajapakse is with the National Institute on Minority Health and Health Disparities, NIH
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15
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Abudushataer M, Sato N, Mieno M, Sawabe M, Muramatsu M, Arai T. Association of CYP2A6 gene deletion with cancers in Japanese elderly: an autopsy study. BMC Cancer 2020; 20:186. [PMID: 32131765 PMCID: PMC7057549 DOI: 10.1186/s12885-020-6663-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 02/20/2020] [Indexed: 11/26/2022] Open
Abstract
Background CYP2A6 is an enzyme involved in oxidation of a number of environmental chemicals, including nicotine, pro-carcinogenic nitrosamines and polycyclic aromatic hydrocarbons (PAHs). The whole gene deletion of CYP2A6 (CYP2A6*4) is prevalent in East Asian population. Whether or not CYP2A6*4 associates with cancer is still controversial. Methods We undertook an association study to determine whether deletion of CYP2A6 gene associates with total cancer and major cancer types employing data of consecutive autopsy cases registered in the Japanese single-nucleotide polymorphisms for geriatric research (JG-SNP) database. The presence of cancer were inspected at the time of autopsy and pathologically confirmed. Genotyping for CYP2A6 wild type (W) and deletion (D) was done by allele specific RT-PCR method. Results Among 1373 subjects, 826 subjects (60.2%) were cancer positive and 547 subjects (39.8%) were cancer negative. The genotype frequency in the whole study group for WW, WD and DD were 65.0, 30.6 and 4.4%, respectively, which obeyed the Hardy-Weinberg equilibrium (p = 0.20). Total cancer presence, as well as major cancers including gastric, lung, colorectal, and blood cancers did not show any positive association with CYP2A6 deletion. When male and female were separately analyzed, CYP2A6 deletion associated with decreased gastric cancer risk in female (OR = 0.49, 95%CI: 0.25–0.95, p = 0.021, after adjustment for age, smoking and drinking). When smoker and non-smoker were separately analyzed, CYP2A6 deletion associated with decreased total cancer in female nonsmokers (OR = 0.67, 95%CI: 0.45–0.99, p = 0.041 after adjustment). On the other hand, CYP2A6 deletion associated increase blood cancers in smokers (OR = 2.05, 95%CI: 1.19–3.53, p = 0.01 after adjustment). Conclusion The CYP2A6 deletion may not grossly affect total cancer. It may associate with individual cancers in sex and smoking dependent manner. Further studies with larger sample size are warranted to confirm our results.
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Affiliation(s)
- Maidina Abudushataer
- Department of Molecular Epidemiology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Noriko Sato
- Department of Molecular Epidemiology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Makiko Mieno
- Center for Information, Jichi Medical University, Tochigi, Japan
| | - Motoji Sawabe
- Department of Molecular Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Masaaki Muramatsu
- Department of Molecular Epidemiology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.
| | - Tomio Arai
- Department of Pathology, Tokyo Metropolitan Geriatric Hospital, Tokyo, Japan
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16
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Tindle HA, Stevenson Duncan M, Greevy RA, Vasan RS, Kundu S, Massion PP, Freiberg MS. Lifetime Smoking History and Risk of Lung Cancer: Results From the Framingham Heart Study. J Natl Cancer Inst 2019; 110:1201-1207. [PMID: 29788259 DOI: 10.1093/jnci/djy041] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 02/16/2018] [Indexed: 12/16/2022] Open
Abstract
Background The relative risk of lung cancer decreases with years since quitting (YSQ) smoking, but risk beyond 25 YSQ remains unclear. Current lung cancer screening guidelines, which exclude smokers with more than 15 YSQ, may not detect lung cancers in this population. Methods We analyzed data from Framingham Heart Study Original (n = 3905) and Offspring cohort (n = 5002) participants for lifetime smoking and lung cancer incidence from 1954 to 1958 (Exam 4) and 1971 to 1975 (Exam 1), respectively, through 2013. We used multivariable-adjusted Cox proportional hazards regression models to compare current, former, and never smokers and lung cancer risk. Smoking status and covariates were time-updated every two years (Original) or four years (Offspring). Primary analyses were restricted to heavy ever smokers with more than 21.3 pack-years; additional analyses included all ever smokers. Results On follow-up (median = 28.7 years), 284 lung cancers were detected: incidence rates/1000 person-years in current, former, and never smokers were 1.97 (95% confidence interval [CI] = 1.66 to 2.33), 1.61 (95% CI = 1.34 to 1.93), and 0.26 (95% CI = 0.17 to 0.39), respectively. Heavy former (vs never) smokers had elevated lung cancer risk at all YSQ (<5: hazard ratio [HR] = 12.12, 95% CI = 6.94 to 21.17; 5-9: HR = 11.77, 95% CI = 6.78 to 20.45; 10-14: HR = 7.81, 95% CI = 3.98 to 15.33; 15-24: HR = 5.88, 95% CI = 3.19-10.83; ≥25: HR = 3.85, 95% CI = 1.80 to 8.26). Heavy former (vs current) smokers had 39.1% lower lung cancer risk within five YSQ. Among all former smokers, 40.8% of lung cancers occurred after more than 15 YSQ. Conclusions Among heavy former smokers, lung cancer risk drops within five YSQ relative to continuing smokers, yet it remains more than threefold higher than never smokers after 25 YSQ. Four of ten lung cancers occurred in former smokers with more 15 YSQ, beyond the screening window of the current guideline.
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Affiliation(s)
- Hilary A Tindle
- Vanderbilt University Medical Center, Nashville, TN.,Geriatric Research Education and Clinical Centers, Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN
| | - Meredith Stevenson Duncan
- Vanderbilt University Medical Center, Nashville, TN.,Framingham Heart Study, Framingham and Boston University Schools of Medicine and Public Health, Boston, MA
| | - Robert A Greevy
- Vanderbilt University Medical Center, Nashville, TN.,Geriatric Research Education and Clinical Centers, Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN
| | - Ramachandran S Vasan
- Framingham Heart Study, Framingham and Boston University Schools of Medicine and Public Health, Boston, MA
| | - Suman Kundu
- Vanderbilt University Medical Center, Nashville, TN
| | - Pierre P Massion
- Vanderbilt University Medical Center, Nashville, TN.,the Medical Service, Section of Pulmonary and Critical Care Medicine, Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN
| | - Matthew S Freiberg
- Vanderbilt University Medical Center, Nashville, TN.,Geriatric Research Education and Clinical Centers, Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN
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17
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Yazdani A, Yazdani A, Elsea SH, Schaid DJ, Kosorok MR, Dangol G, Samiei A. Genome analysis and pleiotropy assessment using causal networks with loss of function mutation and metabolomics. BMC Genomics 2019; 20:395. [PMID: 31113383 PMCID: PMC6528192 DOI: 10.1186/s12864-019-5772-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 05/03/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Many genome-wide association studies have detected genomic regions associated with traits, yet understanding the functional causes of association often remains elusive. Utilizing systems approaches and focusing on intermediate molecular phenotypes might facilitate biologic understanding. RESULTS The availability of exome sequencing of two populations of African-Americans and European-Americans from the Atherosclerosis Risk in Communities study allowed us to investigate the effects of annotated loss-of-function (LoF) mutations on 122 serum metabolites. To assess the findings, we built metabolomic causal networks for each population separately and utilized structural equation modeling. We then validated our findings with a set of independent samples. By use of methods based on concepts of Mendelian randomization of genetic variants, we showed that some of the affected metabolites are risk predictors in the causal pathway of disease. For example, LoF mutations in the gene KIAA1755 were identified to elevate the levels of eicosapentaenoate (p-value = 5E-14), an essential fatty acid clinically identified to increase essential hypertension. We showed that this gene is in the pathway to triglycerides, where both triglycerides and essential hypertension are risk factors of metabolomic disorder and heart attack. We also identified that the gene CLDN17, harboring loss-of-function mutations, had pleiotropic actions on metabolites from amino acid and lipid pathways. CONCLUSION Using systems biology approaches for the analysis of metabolomics and genetic data, we integrated several biological processes, which lead to findings that may functionally connect genetic variants with complex diseases.
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Affiliation(s)
| | - Akram Yazdani
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, 10029 USA
| | - Sarah H. Elsea
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Daniel J. Schaid
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55905 USA
| | - Michael R. Kosorok
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 USA
| | - Gita Dangol
- Health Science Center, The University of Texas MD Anderson Cancer Center, Austin, TX 77030 USA
| | - Ahmad Samiei
- Hasso Plattner Institute, 14482 Potsdam, Germany
- Climax Data Pattern, Boston, MA USA
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18
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Bloom AJ, Wang P, Kharasch ED. Nicotine oxidation by genetic variants of CYP2B6 and in human brain microsomes. Pharmacol Res Perspect 2019; 7:e00468. [PMID: 30906561 PMCID: PMC6411694 DOI: 10.1002/prp2.468] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 01/20/2019] [Indexed: 11/16/2022] Open
Abstract
Common variation in the CYP2B6 gene, encoding the cytochrome P450 2B6 enzyme, is associated with substrate-specific altered clearance of multiple drugs. CYP2B6 is a minor contributor to hepatic nicotine metabolism, but the enzyme has been proposed as relevant to nicotine-related behaviors because of reported CYP2B6 mRNA expression in human brain tissue. Therefore, we hypothesized that CYP2B6 variants would be associated with altered nicotine oxidation, and that nicotine metabolism by CYP2B6 would be detected in human brain microsomes. We generated recombinant enzymes in insect cells corresponding to nine common CYP2B6 haplotypes and demonstrate genetically determined differences in nicotine oxidation to nicotine iminium ion and nornicotine for both (S) and (R)-nicotine. Notably, the CYP2B6.6 and CYP2B6.9 variants demonstrated lower intrinsic clearance relative to the reference enzyme, CYP2B6.1. In the presence of human brain microsomes, along with nicotine-N-oxidation, we also detect nicotine oxidation to nicotine iminium ion. However, unlike N-oxidation, this activity is NADPH independent, does not follow Michaelis-Menten kinetics, and is not inhibited by NADP or carbon monoxide. Furthermore, metabolism of common CYP2B6 probe substrates, methadone and ketamine, is not detected in the presence of brain microsomes. We conclude that CYP2B6 metabolizes nicotine stereoselectively and common CYP2B6 variants differ in nicotine metabolism activity, but did not find evidence of CYP2B6 activity in human brain.
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Affiliation(s)
- Adam Joseph Bloom
- Department of Psychiatry and AnesthesiologyWashington UniversitySt. LouisMissouri
| | - Pan‐Fen Wang
- Department of AnesthesiologyDuke University School of MedicineDurhamNorth Carolina
| | - Evan D. Kharasch
- Department of AnesthesiologyDuke University School of MedicineDurhamNorth Carolina
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19
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Stancil SL, Pearce RE, Tyndale RF, Kearns GL, Vyhlidal CA, Leeder JS, Abdel-Rahman S. Evaluating metronidazole as a novel, safe CYP2A6 phenotyping probe in healthy adults. Br J Clin Pharmacol 2019; 85:960-969. [PMID: 30706508 DOI: 10.1111/bcp.13884] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 01/21/2019] [Accepted: 01/23/2019] [Indexed: 01/18/2023] Open
Abstract
AIMS CYP2A6 is a genetically polymorphic enzyme resulting in differential substrate metabolism and health behaviours. Current phenotyping probes for CYP2A6 exhibit limitations related to procurement (deuterated cotinine), toxicity (coumarin), specificity (caffeine) and age-appropriate administration (nicotine, NIC). In vitro, CYP2A6 selectively forms 2-hydroxymetronidazole (2HM) from metronidazole (MTZ). The purpose of this study was to evaluate MTZ as a CYP2A6 phenotyping probe drug in healthy adults against the well-established method of measuring trans-3-hydroxycotinine (3HC)/cotinine (COT). METHODS A randomized, cross-over, pharmacokinetic study was completed in 16 healthy, nonsmoking adults. Separated by a washout period of at least 2 weeks, MTZ 500 mg and NIC gum 2 mg were administered and plasma was sampled over 48 hours and 8 hours, respectively. Correlations of plasma metabolite/parent ratios (2HM/MTZ; 3HC/COT) were assessed by Pearson coefficient. CYP2A6 genotyping was conducted and incorporated as a variable of plasma ratio response. RESULTS Correlations between the plasma ratio 2HM/MTZ and 3HC/COT were ≥ 0.9 at multiple time points (P < 0.001), demonstrating a wide window during which 2HM/MTZ can be queried post-MTZ dose. CYP2A6 genotype had significant impacts on both MTZ and NIC phenotyping ratios with decreased activity predicted phenotypes demonstrating 2HM/MTZ ratios ≤58% and 3HC/COT ratios ≤56% compared with extensive activity predicted phenotypes at all time points examined in the study (P < 0.05). No adverse events were reported in the MTZ arm while 38% (n = 6) of participants reported mild adverse events in the NIC arm. CONCLUSIONS Metronidazole via 2HM/MTZ performed well as a novel, safe phenotyping probe for CYP2A6 in healthy adults.
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Affiliation(s)
- Stephani L Stancil
- Division of Adolescent Medicine, Children's Mercy Kansas City, MO, USA.,Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, MO, USA.,Division of Pharmacology & Toxicology, University of Missouri-Kansas City School of Pharmacy, Kansas City, MO, USA
| | - Robin E Pearce
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, MO, USA.,Department of Pediatrics, University of Missouri-Kansas City School of Medicine, MO, USA
| | - Rachel F Tyndale
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Departments of Pharmacology & Toxicology, and Psychiatry, University of Toronto, Toronto, Ontario, Canada
| | - Gregory L Kearns
- Arkansas Children's Research Institute and the Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Carrie A Vyhlidal
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, MO, USA.,Department of Pediatrics, University of Missouri-Kansas City School of Medicine, MO, USA
| | - J Steven Leeder
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, MO, USA.,Department of Pediatrics, University of Missouri-Kansas City School of Medicine, MO, USA
| | - Susan Abdel-Rahman
- Division of Clinical Pharmacology, Toxicology and Therapeutic Innovation, Children's Mercy Kansas City, MO, USA.,Department of Pediatrics, University of Missouri-Kansas City School of Medicine, MO, USA
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20
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Ryan BM. Lung cancer health disparities. Carcinogenesis 2019; 39:741-751. [PMID: 29547922 DOI: 10.1093/carcin/bgy047] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 03/13/2018] [Indexed: 12/16/2022] Open
Abstract
Compared with all other racial and ethnic groups in the United States, African Americans are disproportionally affected by lung cancer, both in terms of incidence and survival. It is likely that smoking, as the main etiological factor associated with lung cancer, contributes to these disparities, but the precise mechanism is still unclear. This paper seeks to explore the history of lung cancer disparities and review to the literature regarding the various factors that contribute to them.
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Affiliation(s)
- Bríd M Ryan
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
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21
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Ezzeldin N, El-Lebedy D, Darwish A, El Bastawisy A, Abd Elaziz SH, Hassan MM, Saad-Hussein A. Association of genetic polymorphisms CYP2A6*2 rs1801272 and CYP2A6*9 rs28399433 with tobacco-induced lung Cancer: case-control study in an Egyptian population. BMC Cancer 2018; 18:525. [PMID: 29724170 PMCID: PMC5934827 DOI: 10.1186/s12885-018-4342-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 04/08/2018] [Indexed: 11/10/2022] Open
Abstract
Background Several studies have reported the role of CYP2A6 genetic polymorphisms in smoking and lung cancer risk with some contradictory results in different populations. The purpose of the current study is to assess the contribution of the CYP2A6*2 rs1801272 and CYP2A6*9 rs28399433 gene polymorphisms and tobacco smoking in the risk of lung cancer in an Egyptian population. Methods A case-control study was conducted on 150 lung cancer cases and 150 controls. All subjects were subjected to blood sampling for Extraction of genomic DNA and Genotyping of the CYP2A6 gene SNPs (CYP2A6*2 (1799 T > A) rs1801272 and CYP2A6*9 (− 48 T > G) rs28399433 by Real time PCR. Results AC and CC genotypes were detected in CYP2A6*9; and AT genotype in CYP2A6*2. The frequency of CYP2A6*2 and CYP2A6*9 were 0.7% and 3.7% respectively in the studied Egyptian population. All cancer cases with slow metabolizer variants were NSCLC. Non-smokers represented 71.4% of the CYP2A6 variants. There was no statistical significant association between risk of lung cancer, smoking habits, heaviness of smoking and the different polymorphisms of CYP2A6 genotypes. Conclusion The frequency of slow metabolizers CYP2A6*2 and CYP2A6*9 are poor in the studied Egyptian population. Our findings did not suggest any association between CYP2A6 genotypes and risk of lung cancer.
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Affiliation(s)
- Nada Ezzeldin
- Chest Diseases, National Research Center, Cairo, Egypt
| | | | - Amira Darwish
- Medical Oncology, National Cancer Institute, Cairo University, Cairo, Egypt. .,National Cancer Institute (NCI), Fom-Elkhalig Square, P.O.Box: 11796, Cairo, Egypt.
| | - Ahmed El Bastawisy
- Medical Oncology, National Cancer Institute, Cairo University, Cairo, Egypt
| | | | | | - Amal Saad-Hussein
- Environmental Health & Preventive Medicine, National Research Center, Cairo, Egypt
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22
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Chen LS, Horton A, Bierut L. Pathways to precision medicine in smoking cessation treatments. Neurosci Lett 2018; 669:83-92. [PMID: 27208830 PMCID: PMC5115988 DOI: 10.1016/j.neulet.2016.05.033] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 05/12/2016] [Accepted: 05/17/2016] [Indexed: 02/06/2023]
Abstract
Cigarette smoking is highly addictive and modern genetic research has identified robust genetic influences on nicotine dependence. An important step in translating these genetic findings to clinical practice is identifying the genetic factors affecting smoking cessation in order to enhance current smoking cessation treatments. We reviewed the significant genetic variants that predict nicotine dependence, smoking cessation, and response to cessation pharmacotherapy. These data suggest that genetic risks can predict smoking cessation outcomes and moderate the effect of pharmacological treatments. Some pharmacogenetic findings have been replicated in meta-analyses or in multiple smoking cessation trials. The variation in efficacy between smokers with different genetic markers supports the notion that personalized smoking cessation intervention based upon genotype could maximize the efficiency of such treatment while minimizing side effects, thus influencing the number needed to treat (NNT) and the number needed to harm. In summary, as precision medicine is revolutionizing healthcare, smoking cessation may be one of the first areas where genetic variants may identify individuals at increased risk. Current evidence strongly suggests that genetic variants predict cessation failure and that cessation pharmacotherapy effectiveness is modulated by biomarkers such as nicotinic cholinergic receptor α5 subunit (CHRNA5) genotypes or nicotine metabolism ratio (NMR). These findings strengthen the case for the development and rigorous testing of treatments that target patients with different biological risk profiles.
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Affiliation(s)
- Li-Shiun Chen
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, United States.
| | - Amy Horton
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, United States
| | - Laura Bierut
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, United States
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23
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Tanner JA, Tyndale RF. Variation in CYP2A6 Activity and Personalized Medicine. J Pers Med 2017; 7:jpm7040018. [PMID: 29194389 PMCID: PMC5748630 DOI: 10.3390/jpm7040018] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Revised: 11/17/2017] [Accepted: 11/27/2017] [Indexed: 12/16/2022] Open
Abstract
The cytochrome P450 2A6 (CYP2A6) enzyme metabolizes several clinically relevant substrates, including nicotine-the primary psychoactive component in cigarette smoke. The gene that encodes the CYP2A6 enzyme is highly polymorphic, resulting in extensive interindividual variation in CYP2A6 enzyme activity and the rate of metabolism of nicotine and other CYP2A6 substrates including cotinine, tegafur, letrozole, efavirenz, valproic acid, pilocarpine, artemisinin, artesunate, SM-12502, caffeine, and tyrosol. CYP2A6 expression and activity are also impacted by non-genetic factors, including induction or inhibition by pharmacological, endogenous, and dietary substances, as well as age-related changes, or interactions with other hepatic enzymes, co-enzymes, and co-factors. As variation in CYP2A6 activity is associated with smoking behavior, smoking cessation, tobacco-related lung cancer risk, and with altered metabolism and resulting clinical responses for several therapeutics, CYP2A6 expression and enzyme activity is an important clinical consideration. This review will discuss sources of variation in CYP2A6 enzyme activity, with a focus on the impact of CYP2A6 genetic variation on metabolism of the CYP2A6 substrates.
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Affiliation(s)
- Julie-Anne Tanner
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health (CAMH), Toronto, ON M5T 1R8, Canada.
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5S 1A8, Canada.
| | - Rachel F Tyndale
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health (CAMH), Toronto, ON M5T 1R8, Canada.
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5S 1A8, Canada.
- Department of Psychiatry, University of Toronto, Toronto, ON M5T 1R8, Canada.
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24
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Park SL, Murphy SE, Wilkens LR, Stram DO, Hecht SS, Le Marchand L. Association of CYP2A6 activity with lung cancer incidence in smokers: The multiethnic cohort study. PLoS One 2017; 12:e0178435. [PMID: 28542511 PMCID: PMC5444837 DOI: 10.1371/journal.pone.0178435] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 05/12/2017] [Indexed: 12/21/2022] Open
Abstract
While smoking is the primary cause of lung cancer, only 11-24% of smokers develop the malignancy over their lifetime. The primary addictive agent in tobacco smoke is nicotine and variation in nicotine metabolism may influence the smoking levels of an individual. Therefore, inter-individual variation in lung cancer risk among smokers may be due in part to differences in the activity of enzymes involved in nicotine metabolism. In most smokers, cytochrome P450 2A6 (CYP2A6)-catalyzed C-oxidation accounts for >75% of nicotine metabolism, and the activity of this enzyme has been shown to correlate with the amount of nicotine and carcinogens drawn from cigarettes. We prospectively evaluated the association of urinary biomarkers of nicotine uptake (total nicotine equivalents [TNE]) and CYP2A6 activity (ratio of urinary total trans-3'-hydroxycotinine to cotinine) with lung cancer risk among 2,309 Multiethnic Cohort Study participants who were current smokers at time of urine collection; 92 cases were diagnosed during a mean follow-up of 9.5 years. We found that higher CYP2A6 activity and TNE was associated with increased lung cancer risk after adjusting for age, sex, race/ethnicity, body mass index, smoking duration, and urinary creatinine (p's = 0.002). The association for CYP2A6 activity remained even after adjusting for self-reported cigarettes per day (CPD) (Hazard Ratio [HR] per unit increase in log-CYP2A6 activity = 1.52; p = 0.005) and after adjusting for TNE (HR = 1.46; p = 0.01). In contrast, the association between TNE and lung cancer risk was of borderline statistical significance when adjusted for CPD (HR = 1.53; p = 0.06) and not statistically significant when further adjusted for CYP2A6 activity (HR = 1.30; p = 0.22). These findings suggest that CYP2A6 activity provides information on lung cancer risk that is not captured by smoking history or a (short-term) biomarker of dose. CYP2A6 activity should be further studied as a risk biomarker for smoking-related lung cancer.
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Affiliation(s)
- Sungshim L. Park
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Sharon E. Murphy
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Lynne R. Wilkens
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii, United States of America
| | - Daniel O. Stram
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Stephen S. Hecht
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Loïc Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii, United States of America
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25
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Tanner JA, Henderson JA, Buchwald D, Howard BV, Henderson PN, Tyndale RF. Variation in CYP2A6 and nicotine metabolism among two American Indian tribal groups differing in smoking patterns and risk for tobacco-related cancer. Pharmacogenet Genomics 2017; 27:169-178. [PMID: 28181923 PMCID: PMC5382092 DOI: 10.1097/fpc.0000000000000271] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE The Northern Plains (NP) and Southwest (SW) American Indian populations differ in their smoking patterns and lung cancer incidence. We aimed to compare CYP2A6 genetic variation and CYP2A6 enzyme activity (representative of the rate of nicotine metabolism) between the two tribal populations as these have previously been associated with differences in smoking, quitting, and lung cancer risk. PARTICIPANTS AND METHODS American Indians (N=636) were recruited from two different tribal populations (NP in South Dakota, SW in Arizona) as part of a study carried out as part of the Collaborative to Improve Native Cancer Outcomes P50 Project. A questionnaire assessed smoking-related traits and demographics. Participants were genotyped for CYP2A6 genetic variants *1B, *2, *4, *7, *9, *12, *17, and *35. Plasma and/or saliva samples were used to measure nicotine's metabolites cotinine and 3'-hydroxycotinine and determine CYP2A6 activity (3'-hydroxycotinine/cotinine, i.e. the nicotine metabolite ratio, NMR). RESULTS The overall frequency of genetically reduced nicotine metabolizers, those with CYP2A6 decrease-of-function or loss-of-function alleles, was lower in the NP compared with the SW (P=0.0006). The CYP2A6 genotype was associated with NMR in both tribal groups (NP, P<0.0001; SW, P=0.04). Notably, the rate of nicotine metabolism was higher in NP compared with SW smokers (P=0.03), and in comparison with other ethnic groups in the USA. Of the variables studied, the CYP2A6 genotype was the only variable to significantly independently influence NMR among smokers in both tribal populations (NP, P<0.001; SW, P=0.05). CONCLUSION Unique CYP2A6 allelic patterns and rates of nicotine metabolism among these American Indian populations suggest different risks for smoking, and tobacco-related disease.
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Affiliation(s)
- Julie-Anne Tanner
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health (CAMH), Toronto, Ontario, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| | | | - Dedra Buchwald
- Elson S. Floyd College of Medicine, Initiative for Research and Education to Advance Community Health (IREACH), Washington State University, Seattle, Washington
| | - Barbara V. Howard
- MedStar Health Research Institute, Hyattsville, Maryland; the Georgetown-Howard Universities Center for Clinical and Translational Sciences, Washington, District of Columbia
| | | | - Rachel F. Tyndale
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health (CAMH), Toronto, Ontario, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
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26
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Yuan JM, Nelson HH, Carmella SG, Wang R, Kuriger-Laber J, Jin A, Adams-Haduch J, Hecht SS, Koh WP, Murphy SE. CYP2A6 genetic polymorphisms and biomarkers of tobacco smoke constituents in relation to risk of lung cancer in the Singapore Chinese Health Study. Carcinogenesis 2017; 38:411-418. [PMID: 28182203 PMCID: PMC6248819 DOI: 10.1093/carcin/bgx012] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 01/16/2017] [Accepted: 01/24/2017] [Indexed: 01/01/2023] Open
Abstract
Cytochrome P450 2A6 (CYP2A6) catalyzes the metabolism of nicotine and the tobacco-specific lung carcinogen, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK). Genetic variation in CYP2A6 may affect smoking behavior and contribute to lung cancer risk. A nested case-control study of 197 lung cancer cases and 197 matched controls was conducted within a prospective cohort of 63 257 Chinese men and women in Singapore. Quantified were five genetic variants of CYP2A6 (*1A, *4, *7, *9 and *12) and urinary metabolites of nicotine [total nicotine, total cotinine, total trans-3'-hydroxycotinine (3HC)] and NNK (total NNAL, free NNAL, NNAL-glucuronide, NNAL-N-glucuronide, and NNAL-O-glucuronide). Higher urinary metabolites of nicotine and NNK were significantly associated with a 2- to 3-fold increased risk of lung cancer after adjustment for smoking intensity and duration. Lower CYP2A6-determined nicotine metabolizer status was significantly associated with a lower ratio of total 3HC over total cotinine, lower total nicotine equivalent and reduced risk of developing lung cancer (all Ptrend < 0.001). Compared with normal metabolizers, odds ratios (95% confidence intervals) of developing lung cancer for intermediate, slow and poor metabolizers determined by CYP2A6 genotypes were 0.85 (0.41-1.77), 0.55 (0.28-1.08) and 0.32 (0.15-0.70), respectively, after adjustment for smoking intensity and duration and urinary total nicotine equivalents. Thus the reduced risk of lung cancer in smokers with lower CYP2A6 activity may be explained by lower consumption of cigarettes, less intense smoking and reduced CYP2A6-catalyzed activation of the tobacco-specific lung carcinogen NNK.
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Affiliation(s)
- Jian-Min Yuan
- Division of Cancer Control and Population Sciences, University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Heather H Nelson
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Steven G Carmella
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Renwei Wang
- Division of Cancer Control and Population Sciences, University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
| | | | - Aizhen Jin
- National Registry of Diseases Office, Health Promotion Board, Singapore, Singapore
| | - Jennifer Adams-Haduch
- Division of Cancer Control and Population Sciences, University of Pittsburgh Cancer Institute, Pittsburgh, PA, USA
| | - Stephen S Hecht
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Woon-Puay Koh
- Duke-NUS Medical School Singapore, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore and
| | - Sharon E Murphy
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Department of Biochemistry, Molecular Biology and BioPhysics, University of Minnesota, MN, USA
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27
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López-Flores LA, Pérez-Rubio G, Falfán-Valencia R. Distribution of polymorphic variants of CYP2A6 and their involvement in nicotine addiction. EXCLI JOURNAL 2017; 16:174-196. [PMID: 28507465 PMCID: PMC5427481 DOI: 10.17179/excli2016-847] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 02/13/2017] [Indexed: 01/08/2023]
Abstract
Tobacco consumption has become a major public health issue, which has motivated studies to identify and understand the biological processes involved in the smoking behavior for prevention and smoking cessation treatments. CYP2A6 has been identified as the main gene that codifies the enzyme that metabolizes nicotine. Many alleles have been identified after the discovery of CYP2A6, suggesting a wide interethnic variability and a diverse smoking behavior of the allele carrying individuals. The main purpose of this review is to update and highlight the effects of the CYP2A6 gene variability related to tobacco consumption reported from diverse human populations. The review further aims to consider CYP2A6 in future studies as a possible genetic marker for the prevention and treatment of nicotine addiction. Therefore, we analyzed several population studies and their importance at addressing and characterizing a population using specific parameters. Our efforts may contribute to a personalized system for detecting, preventing and treating populations at a higher risk of smoking to avoid diseases related to tobacco consumption.
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Abstract
Nicotine is the primary addictive agent in tobacco, and P450 2A6 (gene name: CYP2A6) is the primary catalyst of nicotine metabolism. It was proposed more than 20 years ago that individuals who metabolize nicotine poorly would smoke less, either fewer cigarettes per day or less intensely per cigarette, compared to smokers who metabolize nicotine more efficiently. These poor metabolizers would then be less likely to develop lung cancer due to their lower exposure to the many carcinogens delivered with nicotine in each puff of smoke. Numerous studies have reported that smokers who carry reduced activity or null CYP2A6 alleles do smoke less. Yet only in Asian populations, both Japanese and Chinese, which have a high prevalence of genetic variants, has a link between CYP2A6, smoking dose, and lung cancer been established. In other ethnic groups, it has been challenging to confirm a direct link between P450 2A6-mediated nicotine metabolism and the risk of lung cancer. This challenge is due in part to the difficulty in accurately quantifying smoking dose and accurately predicting or measuring P450 2A6-mediated nicotine metabolism. Biomarkers of nicotine metabolism and smoking exposure, including the ratio of trans-3-hydroxycotine to cotinine, a measure of P450 2A6 activity and plasma cotinine, or urinary total nicotine equivalents (the sum of nicotine and six metabolites) as measures of exposure are useful for addressing this challenge. However, to take full advantage of these biomarkers in the study of ethnic/racial differences in the risk of lung cancer requires the complete characterization of nicotine metabolism across ethnic/racial groups. Variation in metabolism pathways, other than those catalyzed by P450 2A6, can impact biomarkers of both nicotine metabolism and dose. This is clearly important for smokers with low levels of UGT2B10-catalyzed nicotine and cotinine glucuronidation because the UGT2B10 genotype influences plasma cotinine levels. Cotinine is not glucuronidated in 15% of African American smokers (compared to 1% of Whites) due to the prevalence of a UGT2B10 splice variant. This variant contributes significantly to the higher plasma cotinine levels per cigarette in this group and may also influence the accuracy of the 3HCOT to cotinine ratio as a measure of P450 2A6 activity.
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Affiliation(s)
- Sharon E. Murphy
- Department of Biochemistry Molecular Biology and Biophysics and Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455
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29
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Application of a pharmacokinetic/pharmacogenetic approach to assess the nicotine metabolic profile of smokers in the real-life setting. J Pharm Biomed Anal 2016; 131:208-213. [PMID: 27599351 DOI: 10.1016/j.jpba.2016.08.041] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 08/29/2016] [Accepted: 08/30/2016] [Indexed: 11/22/2022]
Abstract
The nicotine metabolite ratio, i.e., the ratio 3-hydroxycotinine/cotinine, is used to assess the nicotine metabolic status and has been proven to predict the response to smoking cessation treatments in randomized clinical trials. In the current study, a pharmacokinetic-pharmacogenetic integrated approach is described, based on the development of a liquid chromatography-tandem mass spectrometry (LC/MS/MS) method for nicotine metabolite ratio assay in plasma and a real-time PCR analysis for fast genotyping of CYP2A6. The pharmacokinetic-pharmacogenetic approach was validated in 66 subjects with different smoking status. The LC/MS/MS assay was rapid and sensitive enough to detect plasma cotinine levels also in second-hand exposed abstainers. In the cohort of patients of the present study the following results were obtained: (i) the frequencies of CYP2A6 genetic variants were comparable with those from clinical trials carried out in Caucasian populations; (ii) all the subjects carrying the CYP2A6 deficient allele also had a slow metabolizer phenotype; (iii) slow metabolizers had mean nicotine metabolite ratio approximately 50% of that of the normal/fast metabolizers; (iv) women had higher nicotine metabolite ratio than men; and (v) salivary nicotine metabolite ratio measures were comparable to plasma levels. Overall, the findings of the current study demonstrate that the simultaneous assessment of nicotine metabolite ratio and CYP2A6 genotype from human blood samples is feasible and accurate and could be used in a smoking cessation program to optimize treatments and identify those smokers who inherit metabolically deficient CYP2A6 alleles.
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30
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Sugimura H. Susceptibility to human cancer: From the perspective of a pathologist. Pathol Int 2016; 66:359-68. [PMID: 27216305 DOI: 10.1111/pin.12418] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Revised: 03/10/2016] [Accepted: 04/13/2016] [Indexed: 12/29/2022]
Abstract
The etiologies of human cancer can only be discerned when the genetic clustering of cancer occurs within a family or when cancer occurs endemically in a particular environment. The possible approaches to solving the nature/nurture problem, especially for human carcinogenesis, posit a fascinating challenge for pathologists. This perspective review presents some examples of how clues to human cancer etiologies and/or susceptibilities reside in the realm of pathology practice. These examples using various omics techniques including adductomics, which I would like to highlight in this article, show that the currently available concepts and methods in human pathology can open a path toward the brave new world of a post-genomic era of medicine for young pathologists, whether their original intention was toward the pursuit of diagnostic or investigative knowledge.
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Affiliation(s)
- Haruhiko Sugimura
- Department of Tumor Pathology, Hamamatsu University School of Medicine, Higashi-ku, Hamamatsu, Japan
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31
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Yuan JM, Nelson HH, Butler LM, Carmella SG, Wang R, Kuriger-Laber JK, Adams-Haduch J, Hecht SS, Gao YT, Murphy SE. Genetic determinants of cytochrome P450 2A6 activity and biomarkers of tobacco smoke exposure in relation to risk of lung cancer development in the Shanghai cohort study. Int J Cancer 2016; 138:2161-71. [PMID: 26662855 PMCID: PMC5155585 DOI: 10.1002/ijc.29963] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 11/30/2015] [Indexed: 11/06/2022]
Abstract
Cytochrome P450 2A6 (CYP2A6) catalyzes nicotine metabolism and contributes to the metabolism of the tobacco-specific lung carcinogen, NNK. Genetic variation in CYP2A6 may affect smoking behavior and contribute to lung cancer risk. A nested case-control study of 325 lung cancer cases and 356 controls was conducted within a prospective cohort of 18,244 Chinese men in Shanghai, China. Quantified were 4 allelic variants of CYP2A6 [*1(+51A), *4, *7, and *9] and urinary total nicotine, total cotinine, total trans-3'-hydroxycotinine (3HC) and total NNAL (an NNK metabolite). Calculated were total nicotine equivalents (TNE), the sum of total nicotine, total cotinine and total 3HC and the total 3HC:total cotinine ratio as a measure of CYP2A6 activity. The nicotine metabolizer status (normal, intermediate, slow and poor) was determined by CYP2A6 genotypes. The smoking-adjusted odds ratios (95% confidence intervals) of lung cancer for the highest vs lowest quartile of total nicotine, total cotinine, total 3HC, TNE and total NNAL were 3.03 (1.80-5.10), 4.70 (2.61-8.46), 4.26 (2.37-7.68), 4.71 (2.61-8.52), and 3.15 (1.86-5.33) (all Ptrend < 0.001), respectively. Among controls CYP2A6 poor metabolizers had a 78% lower total 3HC:total cotinine ratio and 72% higher total nicotine (Ptrend ≤ 0.002). Poor metabolizers had an odds ratio of 0.64 (95% confidence interval = 0.43-0.97) for lung cancer, which was statistically nonsignificant (odds ratio = 0.74, 95% confidence interval = 0.48-1.15) after adjustment for urinary TNE and smoking intensity and duration. The lower lung cancer risk observed in CYP2A6 poor metabolizers is partially explained by the strong influence of CYP2A6 genetic polymorphisms on nicotine uptake and metabolism.
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Affiliation(s)
- Jian-Min Yuan
- Division of Cancer Control and Population Sciences, University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania, USA
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Heather H. Nelson
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, USA
| | - Lesley M. Butler
- Division of Cancer Control and Population Sciences, University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania, USA
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Steven G. Carmella
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Renwei Wang
- Division of Cancer Control and Population Sciences, University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania, USA
| | | | - Jennifer Adams-Haduch
- Division of Cancer Control and Population Sciences, University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania, USA
| | - Stephen S. Hecht
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
| | - Yu-Tang Gao
- Department of Epidemiology, Shanghai Cancer Institute, Shanghai Jiaotong University, Shanghai, China
| | - Sharon E. Murphy
- Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA
- Department of Biochemistry, Molecular Biology and BioPhysics, University of Minnesota, Minneapolis, USA
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Park SL, Tiirikainen MI, Patel YM, Wilkens LR, Stram DO, Le Marchand L, Murphy SE. Genetic determinants of CYP2A6 activity across racial/ethnic groups with different risks of lung cancer and effect on their smoking intensity. Carcinogenesis 2016; 37:269-279. [PMID: 26818358 DOI: 10.1093/carcin/bgw012] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 01/19/2016] [Indexed: 01/22/2023] Open
Abstract
Genetic variation in cytochrome P450 2A6 (CYP2A6) gene is the primary contributor to the intraindividual and interindividual differences in nicotine metabolism and has been found to influence smoking intensity. However, no study has evaluated the relationship between CYP2A6 genetic variants and the CYP2A6 activity ratio (total 3-hydroxycotinine/cotinine) and their influence on smoking intensity [total nicotine equivalents (TNE)], across five racial/ethnic groups found to have disparate rates of lung cancer. This study genotyped 10 known functional CYP2A6 genetic or copy number variants in 2115 current smokers from the multiethnic cohort study [African Americans (AA) = 350, Native Hawaiians (NH) = 288, Whites = 413, Latinos (LA) = 437 and Japanese Americans (JA) = 627] to conduct such an investigation. Here, we found that LA had the highest CYP2A6 activity followed by Whites, AA, NH and JA, who had the lowest levels. Adjusting for age, sex, race/ethnicity and body mass index, we found that CYP2A6 diplotypes were predictive of TNE levels, particularly in AA and JA (P trend < 0.0001). However, only in JA did the association remain after accounting for cigarettes per day. Also, it is only in this population that the lower activity ratio supports lower TNE levels, carcinogen exposure and thereby lower risk of lung cancer. Despite the association between nicotine metabolism (CYP2A6 activity phenotype and diplotypes) and smoking intensity (TNE), CYP2A6 levels did not correlate with the higher TNE levels found in AA nor the lower TNE levels found in LA, suggesting that other factors may influence smoking dose in these populations. Therefore, further study in these populations is recommended.
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Affiliation(s)
| | - Maarit I Tiirikainen
- Epidemiology Program, University of Hawaii Cancer Center , Honolulu, HI 96813 , USA and
| | | | - Lynne R Wilkens
- Epidemiology Program, University of Hawaii Cancer Center , Honolulu, HI 96813 , USA and
| | | | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center , Honolulu, HI 96813 , USA and
| | - Sharon E Murphy
- Department of Biochemistry, Molecular Biology and Biophysics, Masonic Cancer Center, University of Minnesota , 2231 6th Street SE, 2-127 CCRB, Minneapolis, MN 55455 , USA
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Wassenaar CA, Zhou Q, Tyndale RF. CYP2A6 genotyping methods and strategies using real-time and end point PCR platforms. Pharmacogenomics 2015; 17:147-62. [PMID: 26670214 DOI: 10.2217/pgs.15.156] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
CYP2A6 genotyping is of clinical importance--CYP2A6 gene variants influence nicotine metabolism and are associated with nicotine dependence, cigarettes per day, smoking cessation and the risk for tobacco-associated cancers. CYP2A6 gene variants also influence the metabolism of therapeutic drugs, such as the anticancer agents, tegafur and letrozole. Over the years, CYP2A6 genotyping methods have evolved to incorporate novel gene variants and to circumvent genotyping errors resulting from the high degree of homology between CYP2A6 and neighboring CYP2A genes. Herein, CYP2A6 genotyping strategies are described for commonly genotyped functionally significant alleles including SNPs, small insertions/deletions and more complex structural variants. The methods presented utilize higher throughput SYBR green real-time PCR technology in addition to standard thermocycling.
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Affiliation(s)
- Catherine A Wassenaar
- Department of Pharmacology & Toxicology, University of Toronto, 1 King's College Circle, Toronto, M5S 1A8 ON, Canada
| | - Qian Zhou
- Department of Pharmacology & Toxicology, University of Toronto, 1 King's College Circle, Toronto, M5S 1A8 ON, Canada
| | - Rachel F Tyndale
- Campbell Family Mental Health Research Institute, Centre for Addiction & Mental Health (CAMH), Departments of Pharmacology & Toxicology & Psychiatry, University of Toronto, 1 King's College Circle, Toronto, M5S 1A8 ON, Canada
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Hosono H, Kumondai M, Arai T, Sugimura H, Sasaki T, Hirasawa N, Hiratsuka M. CYP2A6 genetic polymorphism is associated with decreased susceptibility to squamous cell lung cancer in Japanese smokers. Drug Metab Pharmacokinet 2015; 30:263-8. [DOI: 10.1016/j.dmpk.2015.04.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Revised: 04/06/2015] [Accepted: 04/08/2015] [Indexed: 11/30/2022]
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Daly AK. Polymorphic Variants of Cytochrome P450. CYTOCHROME P450 FUNCTION AND PHARMACOLOGICAL ROLES IN INFLAMMATION AND CANCER 2015; 74:85-111. [DOI: 10.1016/bs.apha.2015.03.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Wassenaar CA, Conti DV, Das S, Chen P, Cook EH, Ratain MJ, Benowitz NL, Tyndale RF. UGT1A and UGT2B genetic variation alters nicotine and nitrosamine glucuronidation in european and african american smokers. Cancer Epidemiol Biomarkers Prev 2014; 24:94-104. [PMID: 25277794 DOI: 10.1158/1055-9965.epi-14-0804] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Identifying sources of variation in the nicotine and nitrosamine metabolic inactivation pathways is important to understanding the relationship between smoking and cancer risk. Numerous UGT1A and UGT2B enzymes are implicated in nicotine and nitrosamine metabolism in vitro; however, little is known about their roles in vivo. METHODS Within UGT1A1, UGT1A4, UGT1A9, UGT2B7, UGT2B10, and UGT2B17, 47 variants were genotyped, including UGT2B10*2 and UGT2B17*2. The association between variation in these UGTs and glucuronidation activity within European and African American current smokers (n = 128), quantified as urinary ratios of the glucuronide over unconjugated compound for nicotine, cotinine, trans-3'-hydroxycotinine, and 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol (NNAL), was investigated in regression models assuming a dominant effect of variant alleles. RESULTS Correcting for multiple testing, three UGT2B10 variants were associated with cotinine glucuronidation, rs2331559 and rs11726322 in European Americans and rs835309 in African Americans (P ≤ 0.0002). Additional variants predominantly in UGT2B10 were nominally associated with nicotine (P = 0.008-0.04) and cotinine (P = <0.001-0.02) glucuronidation in both ethnicities in addition to UGT2B10*2 in European Americans (P = 0.01, P < 0.001). UGT2B17*2 (P = 0.03) in European Americans and UGT2B7 variants (P = 0.02-0.04) in African Americans were nominally associated with 3HC glucuronidation. UGT1A (P = 0.007-0.01), UGT2B10 (P = 0.02), and UGT2B7 (P = 0.02-0.03) variants in African Americans were nominally associated with NNAL glucuronidation. CONCLUSIONS Findings from this initial in vivo study support a role for multiple UGTs in the glucuronidation of tobacco-related compounds in vivo, in particular UGT2B10 and cotinine glucuronidation. IMPACT Findings also provide insight into ethnic differences in glucuronidation activity, which could be contributing to ethnic disparities in the risk for smoking-related cancers. Cancer Epidemiol Biomarkers Prev; 24(1); 94-104. ©2014 AACR.
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Affiliation(s)
- Catherine A Wassenaar
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - David V Conti
- Department of Preventive Medicine, University of Southern California, Los Angeles, California
| | - Soma Das
- Department of Human Genetics, University of Chicago, Chicago, Illinois
| | - Peixian Chen
- Department of Human Genetics, University of Chicago, Chicago, Illinois
| | - Edwin H Cook
- Department of Psychiatry, University of Illinois at Chicago, Chicago, Illinois
| | - Mark J Ratain
- Department of Medicine, Committee on Clinical Pharmacology and Pharmacogenomics, Cancer Research Center, University of Chicago, Chicago, Illinois
| | - Neal L Benowitz
- Division of Clinical Pharmacology and Experimental Therapeutics, Department of Medicine, University of California San Francisco, San Francisco, California. Department of Bioengineering and Therapeutic Science, University of California San Francisco, San Francisco, California
| | - Rachel F Tyndale
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada. Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, University of Toronto, Toronto, Ontario, Canada. Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada.
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