1
|
Avsar O. Identification of the effects of pathogenic genetic variations of human CYP2C9 and CYP2D6: an in silico approach. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2023; 43:356-376. [PMID: 37747773 DOI: 10.1080/15257770.2023.2262519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 09/19/2023] [Indexed: 09/26/2023]
Abstract
Genetic variations in the human cytochrome P450 family 2 subfamily C member 9 (CYP2C9) and cytochrome P450 family 2 subfamily D member 6 (CYP2D6) genes may affect drug metabolism and lead to alterations in phenotypes. Genetic variations are associated with toxicity, adverse drug reactions, inefficient treatment. Various in silico tools were combined to investigate the deleterious effects of missense non-synonymous single nucleotide polymorphisms (nsSNPs) of the human CYP2C9 and CYP2D6. The structural and functional effects of the high-risk non-synonymous SNPs in the human CYP2C9 and CYP2D6 were predicted by numerous computational mutation analysis methods. Out of 24 pathogenic missense SNPs in the CYP2C9, 22 nsSNPs had a decreasing effect on protein stability and 13 SNPs were showed to be located at conserved positions. Out of 27 high-risk deleterious non-synonymous SNPs in the human CYP2D6, 21 SNPs decreased protein stability and 16 nsSNPs were predicted to be positioned at conserved regions. Our present study suggests that the identified functional SNPs may affect drug metabolism associated with CYP2C9 and CYP2D6 enzymes.
Collapse
Affiliation(s)
- Orcun Avsar
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Hitit University, Corum, Türkiye
| |
Collapse
|
2
|
Kukal S, Thakran S, Kanojia N, Yadav S, Mishra MK, Guin D, Singh P, Kukreti R. Genic-intergenic polymorphisms of CYP1A genes and their clinical impact. Gene 2023; 857:147171. [PMID: 36623673 DOI: 10.1016/j.gene.2023.147171] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 12/16/2022] [Accepted: 01/03/2023] [Indexed: 01/08/2023]
Abstract
The humancytochrome P450 1A (CYP1A) subfamily genes, CYP1A1 and CYP1A2, encoding monooxygenases are critically involved in biotransformation of key endogenous substrates (estradiol, arachidonic acid, cholesterol) and exogenous compounds (smoke constituents, carcinogens, caffeine, therapeutic drugs). This suggests their significant involvement in multiple biological pathways with a primary role of maintaining endogenous homeostasis and xenobiotic detoxification. Large interindividual variability exist in CYP1A gene expression and/or catalytic activity of the enzyme, which is primarily due to the existence of polymorphic alleles which encode them. These polymorphisms (mainly single nucleotide polymorphisms, SNPs) have been extensively studied as susceptibility factors in a spectrum of clinical phenotypes. An in-depth understanding of the effects of polymorphic CYP1A genes on the differential metabolic activity and the resulting biological pathways is needed to explain the clinical implications of CYP1A polymorphisms. The present review is intended to provide an integrated understanding of CYP1A metabolic activity with unique substrate specificity and their involvement in physiological and pathophysiological roles. The article further emphasizes on the impact of widely studied CYP1A1 and CYP1A2 SNPs and their complex interaction with non-genetic factors like smoking and caffeine intake on multiple clinical phenotypes. Finally, we attempted to discuss the alterations in metabolism/physiology concerning the polymorphic CYP1A genes, which may underlie the reported clinical associations. This knowledge may provide insights into the disease pathogenesis, risk stratification, response to therapy and potential drug targets for individuals with certain CYP1A genotypes.
Collapse
Affiliation(s)
- Samiksha Kukal
- Genomics and Molecular Medicine Unit, Institute of Genomics and Integrative Biology (IGIB), Council of Scientific and Industrial Research (CSIR), Delhi 110007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sarita Thakran
- Genomics and Molecular Medicine Unit, Institute of Genomics and Integrative Biology (IGIB), Council of Scientific and Industrial Research (CSIR), Delhi 110007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Neha Kanojia
- Genomics and Molecular Medicine Unit, Institute of Genomics and Integrative Biology (IGIB), Council of Scientific and Industrial Research (CSIR), Delhi 110007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Saroj Yadav
- Genomics and Molecular Medicine Unit, Institute of Genomics and Integrative Biology (IGIB), Council of Scientific and Industrial Research (CSIR), Delhi 110007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Manish Kumar Mishra
- Genomics and Molecular Medicine Unit, Institute of Genomics and Integrative Biology (IGIB), Council of Scientific and Industrial Research (CSIR), Delhi 110007, India; Department of Biotechnology, Delhi Technological University, Shahbad Daulatpur, Main Bawana Road, Delhi 110042, India
| | - Debleena Guin
- Genomics and Molecular Medicine Unit, Institute of Genomics and Integrative Biology (IGIB), Council of Scientific and Industrial Research (CSIR), Delhi 110007, India; Department of Biotechnology, Delhi Technological University, Shahbad Daulatpur, Main Bawana Road, Delhi 110042, India
| | - Pooja Singh
- Genomics and Molecular Medicine Unit, Institute of Genomics and Integrative Biology (IGIB), Council of Scientific and Industrial Research (CSIR), Delhi 110007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Ritushree Kukreti
- Genomics and Molecular Medicine Unit, Institute of Genomics and Integrative Biology (IGIB), Council of Scientific and Industrial Research (CSIR), Delhi 110007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
| |
Collapse
|
3
|
Liu Y, Kramer JR, Sandulache VC, Yu R, Li G, Chen L, Yusuf ZI, Shi Y, Pyarajan S, Tsavachidis S, Jiao L, Mierzwa ML, Chiao E, Mowery YM, Shuman A, Shete S, Sikora AG, White DL. Immunogenetic Determinants of Susceptibility to Head and Neck Cancer in the Million Veteran Program Cohort. Cancer Res 2023; 83:386-397. [PMID: 36378845 PMCID: PMC9896026 DOI: 10.1158/0008-5472.can-22-1641] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 09/02/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022]
Abstract
Increasing rates of human papillomavirus (HPV)-driven oropharyngeal cancer (OPC) have largely offset declines in tobacco-associated head and neck squamous cell carcinoma (HNSCC) at non-OPC sites. Host immunity is an important modulator of HPV infection, persistence, and clearance, and also of immune evasion in both virally- and nonvirally-driven cancers. However, the association between collective known cancer-related immune gene variants and HNSCC susceptibility has not been fully characterized. Here, we conducted a genetic association study in the multiethnic Veterans Affairs Million Veteran Program cohort, evaluating 16,050 variants in 1,576 immune genes in 4,012 HNSCC cases (OPC = 1,823; non-OPC = 2,189) and 16,048 matched controls. Significant polymorphisms were further examined in a non-Hispanic white (NHW) validation cohort (OPC = 1,206; non-OPC = 955; controls = 4,507). For overall HNSCC susceptibility in NHWs, we discovered and validated a novel 9q31.1 SMC2 association and replicated the known 6p21.32 HLA-DQ-DR association. Six loci/genes for overall HNSCC susceptibility were selectively enriched in African-Americans (6p21.32 HLA-G, 9q21.33 GAS1, 11q12.2 CD6, 11q23.2 NCAM1/CD56, 17p13.1 CD68, 18q22.2 SOCS6); all 6 genes function in antigen-presenting regulation and T-cell activation. Two additional loci (10q26 DMBT1, 15q22.2 TPM1) were uncovered for non-OPC susceptibility, and three loci (11q24 CRTAM, 16q21 CDH5, 18q12.1 CDH2) were identified for HPV-positive OPC susceptibility. This study underscores the role of immune gene variants in modulating susceptibility for both HPV-driven and non-HPV-driven HNSCC. Additional large studies, particularly in racially diverse populations, are needed to further validate the associations and to help elucidate other potential immune factors and mechanisms that may underlie HNSCC risk. SIGNIFICANCE Several inherited variations in immune system genes are significantly associated with susceptibility to head and neck cancer, which could help improve personalized cancer risk estimates.
Collapse
Affiliation(s)
- Yanhong Liu
- Department of Medicine, Baylor College of Medicine, Houston, Texas.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas.,Veterans Affairs (VA) Health Services Research & Development Center of Innovations in Quality, Effectiveness, and Safety (IQuESt), Michael E. DeBakey VA Medical Center, Houston, Texas
| | - Jennifer R. Kramer
- Department of Medicine, Baylor College of Medicine, Houston, Texas.,Veterans Affairs (VA) Health Services Research & Development Center of Innovations in Quality, Effectiveness, and Safety (IQuESt), Michael E. DeBakey VA Medical Center, Houston, Texas
| | - Vlad C. Sandulache
- ENT Section, Operative Care Line, Michael E. DeBakey VA Medical Center, Houston, Texas.,Bobby R. Alford Department of Otolaryngology‐Head and Neck Surgery, Baylor College of Medicine, Houston, Texas.,Center for Translational Research in Inflammatory Disease (CTRID), Michael E. DeBakey VA Medical Center, Houston, Texas
| | - Robert Yu
- Department of Biostatistics, Division of Basic Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Guojun Li
- Department of Head and Neck Surgery, Division of Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Liang Chen
- Department of Medicine, Baylor College of Medicine, Houston, Texas.,Veterans Affairs (VA) Health Services Research & Development Center of Innovations in Quality, Effectiveness, and Safety (IQuESt), Michael E. DeBakey VA Medical Center, Houston, Texas
| | - Zenab I. Yusuf
- Department of Medicine, Baylor College of Medicine, Houston, Texas.,Veterans Affairs (VA) Health Services Research & Development Center of Innovations in Quality, Effectiveness, and Safety (IQuESt), Michael E. DeBakey VA Medical Center, Houston, Texas
| | - Yunling Shi
- Center for Data and Computational Sciences, VA Boston Healthcare System, Boston, Massachusetts
| | - Saiju Pyarajan
- Center for Data and Computational Sciences, VA Boston Healthcare System, Boston, Massachusetts
| | | | - Li Jiao
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | | | - Elizabeth Chiao
- Departments of Epidemiology and General Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Yvonne M. Mowery
- Departments of Radiation Oncology and Head and Neck Surgery & Communication Sciences, Duke University Medical Center, Durham, North Carolina
| | - Andrew Shuman
- Department of Otolaryngology, University of Michigan Medical School, Ann Arbor, Michigan.,Veterans Affairs Ann Arbor Health System, Ann Arbor, Michigan
| | - Sanjay Shete
- Department of Biostatistics, Division of Basic Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Andrew G. Sikora
- Department of Head and Neck Surgery, Division of Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Corresponding Authors: Donna L. White, Department of Medicine, Baylor College of Medicine, Houston, TX 77021. E-mail: ; and Andrew G. Sikora, Department of Head and Neck Surgery, Division of Surgery, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030. E-mail:
| | - Donna L. White
- Department of Medicine, Baylor College of Medicine, Houston, Texas.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas.,Veterans Affairs (VA) Health Services Research & Development Center of Innovations in Quality, Effectiveness, and Safety (IQuESt), Michael E. DeBakey VA Medical Center, Houston, Texas.,Center for Translational Research in Inflammatory Disease (CTRID), Michael E. DeBakey VA Medical Center, Houston, Texas.,Corresponding Authors: Donna L. White, Department of Medicine, Baylor College of Medicine, Houston, TX 77021. E-mail: ; and Andrew G. Sikora, Department of Head and Neck Surgery, Division of Surgery, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030. E-mail:
| |
Collapse
|
4
|
Ramezani M, Sadeghi M, Zavattaro E, Mozaffari HR. Association between CYP1A1 Ile462Val (m2, A2455G, rs1048943) polymorphism and head and neck cancer susceptibility: A meta-analysis, meta-regression, and trial sequential analysis. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
5
|
Rotimi SO, Rotimi OA, Salhia B. A Review of Cancer Genetics and Genomics Studies in Africa. Front Oncol 2021; 10:606400. [PMID: 33659210 PMCID: PMC7917259 DOI: 10.3389/fonc.2020.606400] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 12/14/2020] [Indexed: 12/24/2022] Open
Abstract
Cancer is the second leading cause of death globally and is projected to overtake infectious disease as the leading cause of mortality in Africa within the next two decades. Cancer is a group of genomic diseases that presents with intra- and inter-population unique phenotypes, with Black populations having the burden of morbidity and mortality for most types. At large, the prevention and treatment of cancers have been propelled by the understanding of the genetic make-up of the disease of mostly non-African populations. By the same token, there is a wide knowledge gap in understanding the underlying genetic causes of, and genomic alterations associated with, cancer among black Africans. Accordingly, we performed a review of the literature to survey existing studies on cancer genetics/genomics and curated findings pertaining to publications across multiple cancer types conducted on African populations. We used PubMed MeSH terms to retrieve the relevant publications from 1990 to December 2019. The metadata of these publications were extracted using R text mining packages: RISmed and Pubmed.mineR. The data showed that only 0.329% of cancer publications globally were on Africa, and only 0.016% were on cancer genetics/genomics from Africa. Although the most prevalent cancers in Africa are cancers of the breast, cervix, uterus, and prostate, publications representing breast, colorectal, liver, and blood cancers were the most frequent in our review. The most frequently reported cancer genes were BRCA1, BRCA2, and TP53. Next, the genes reported in the reviewed publications’ abstracts were extracted and annotated into three gene ontology classes. Genes in the cellular component class were mostly associated with cell part and organelle part, while those in biological process and molecular function classes were mainly associated with cell process, biological regulation, and binding, and catalytic activity, respectively. Overall, this review highlights the paucity of research on cancer genomics on African populations, identified gaps, and discussed the need for concerted efforts to encourage more research on cancer genomics in Africa.
Collapse
Affiliation(s)
- Solomon O Rotimi
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States.,Department of Biochemistry, Covenant University, Ota, Nigeria
| | - Oluwakemi A Rotimi
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States.,Department of Biochemistry, Covenant University, Ota, Nigeria
| | - Bodour Salhia
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States.,Norris Comprehensive Cancer Centre, University of Southern California, Los Angeles, CA, United States
| |
Collapse
|
6
|
Okoturo E, Osasuyi A, Opaleye T. Genetic Polymorphism of Head and Neck Cancers in African Populations: A Systematic Review. OTO Open 2020; 4:2473974X20942202. [PMID: 32743234 PMCID: PMC7375724 DOI: 10.1177/2473974x20942202] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 06/19/2020] [Indexed: 11/29/2022] Open
Abstract
Objective Head and neck cancers are mostly composed of head and neck squamous cell carcinoma (HNSCC). The incidence and mortality of HNSCC are higher in countries with emerging health care systems, particularly Africa. Given that they are more genetically diverse, characterization of polymorphism in African HNSCC may result in the identification of distinct molecular targets as compared with the known HNSCC candidate genes. This study objective is to review the current evidence of genetic data on HNSCC among African populations as well as to demonstrate any distinctions as compared with known candidate genes and to appraise any research gaps. Data Sources Publications that interrogated susceptible gene polymorphisms to African-based populations with cancer were reviewed for this study. Review Methods Our search methodology was modeled after the Cochrane systematic review protocol, which included MeSH terms and keywords related to cancer, polymorphisms, and African countries. Results Seven articles studying 2 HNSCC cancer types in 3 of 54 African countries met the inclusion criteria. Thirteen polymorphisms from 10 genes were screened (NOS3, CYP1A1, CYP2D6, NAT1, NAT2, NQO1, IL-10, IL-12, IL-8, COX2). All articles were screened for polymorphisms based on a polymerase chain reaction–based technique. All polymorphs suggested association to HNSCC, with 10 of 13 polymorphs demonstrating a statistically significant association. Conclusion Studies on known HNSCC candidate genes should be undertaken in Africa, particularly among sub-Saharan Africans. Importantly, these studies should be large scale with multiple HNC sites and with use of high-throughput methods.
Collapse
Affiliation(s)
- Eyituoyo Okoturo
- Head and Neck Cancer Division, Oral and Maxillofacial Surgery Department, Lagos State University Teaching Hospital, Lagos, Nigeria.,Molecular Oncology Program, Medical Research Centre, Lagos State University College of Medicine, Lagos, Nigeria
| | - Anslem Osasuyi
- Oral and Maxillofacial Surgery Department, Nigerian Airforce Hospital, Ikeja, Nigeria
| | - Taofiq Opaleye
- Oral and Maxillofacial Surgery Department, Lagos State University Teaching Hospital, Lagos, Nigeria
| |
Collapse
|
7
|
Genetic variants association with cancers in African-based populations: A systematic review. Cancer Epidemiol 2020; 67:101739. [PMID: 32554299 DOI: 10.1016/j.canep.2020.101739] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 04/21/2020] [Accepted: 04/25/2020] [Indexed: 12/24/2022]
Abstract
BACKGROUND Cancer is the single leading cause of human deaths worldwide. The highest incidence and mortality are recorded from Africa. The last two decades have witnessed extensive research which has led to emerging prognosis and new gene therapy technologies. Cancer therapy in Africa is derived with little input from African population data. While a number of cancer studies on African populations have suggested varied susceptible variant, no comprehensive review of these studies has been undertaken to assess their coverage across Africa. METHODS This study aimed to undertake a review of all molecular genetic studies that interrogated the genetic variants of cancers in African-based populations. Our search methodology was modelled after the Cochrane systematic review protocol, which included MeSH terms and related keywords. RESULTS Ninety-seven articles studying 13 cancer types, were reviewed. 91 articles screened for polymorphisms using PCR-based techniques while three used SNP array, two used whole exome sequencing and one used pyrosequencing. North African (NA) countries undertook 51/97 (53 %) studies on 12/13 (92 %) cancer types while the Sub Saharan Africa (SSA) countries undertook 46/97 (47 %) studies on 7/13 (54 %) cancer types. Twelve out of these thirteen cancer type studies suggested susceptibility to their target polymorphism (p > 0.05). No study replicated or validated variants detected. CONCLUSION Research on genetic determinants in African-based population cancer offers translational benefits. We recommended large scale, multi-national genome association studies using high throughput techniques. SSA needs to receive more attention due to the shortage of this type of study and data in the region.
Collapse
|
8
|
Manoharan A, Shewade DG, Ravindranath PA, Rajkumar RP, Ramprasad VL, Adithan S, Damodaran SE. Resequencing CYP2D6 gene in Indian population: CYP2D6*41 identified as the major reduced function allele. Pharmacogenomics 2019; 20:719-729. [PMID: 31368850 DOI: 10.2217/pgs-2019-0049] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Aim: The CYP2D6 gene is highly polymorphic and harbors population specific alleles that define its predominant metabolizer phenotype. This study aimed to identify polymorphisms in Indian population owing to scarcity of CYP2D6 data in this population. Materials & methods: The CYP2D6 gene was resequenced in 105 south Indians using next generation sequencing technology and haplotypes were reconstructed. Results & conclusion: Four novel missense variants have been designated as CYP2D6*110, *111, *112 and *113. The most common alleles were CYP2D6*1 (42%), *2 (32%), and *41 (12.3%) and diplotypes were CYP2D6*1/*2 (26%), *1/*1 (11%), *2/*41 (10%) and *1/*41 (7%) accounting for high incidence of extensive metabolizers in Indians.
Collapse
Affiliation(s)
- Aarthi Manoharan
- Department of Pharmacology, Jawaharlal Institute of Postgraduate Medical Education & Research, Puducherry 605006, India
| | - Deepak Gopal Shewade
- Department of Pharmacology, Jawaharlal Institute of Postgraduate Medical Education & Research, Puducherry 605006, India
| | | | - Ravi Philip Rajkumar
- Department of Psychiatry, Jawaharlal Institute of Postgraduate Medical Education & Research, Puducherry 605006, India
| | | | - Surendiran Adithan
- Department of Pharmacology, Jawaharlal Institute of Postgraduate Medical Education & Research, Puducherry 605006, India
| | - Solai Elango Damodaran
- Department of Pharmacology, Jawaharlal Institute of Postgraduate Medical Education & Research, Puducherry 605006, India
| |
Collapse
|
9
|
Abstract
In first part of this study, a systematic review was designed to explore the involvement of CYP1A1 and GSTP1 genes in breast cancerogenesis. Based on systematic review, we designed a study to screen CYP1A1 and GSTP1 genes for mutation and their possible association with breast carcinogenesis. A total of 400 individuals were collected and analyzed by PCR-SSCP. After sequence analysis of coding region of CYP1A1 we identified eleven mutations in different exons of respective gene. Among these eleven mutations, ~3 folds increased breast cancer risk was found associated with Asp82Glu mutation (OR 2.99; 95% CI 1.26-7.09), with Ser83Thr mutation (OR 2.99; 95% CI 1.26-7.09) and with Glu86Ala mutation (OR 3.18; 95% CI 1.27-7.93) in cancer patients compared to controls. Furthermore, ~4 folds increase in breast cancer risk was found associated with Asp347Glu, Phe398Tyr and 5178delT mutations (OR 3.92; 95% CI 1.35-11.3) in patients compared to controls. The sequence analysis of GSTP1 resulted in identification of total five mutations. Among these five mutations, ~3 folds increase in breast cancer risk was observed associated with 1860G>A mutation, with 1861-1876delCAGCCCTCTGGAGTGG mutation (OR 2.70; 95% CI 1.10-6.62) and with 1861C>A mutation (OR 2.97; 95% CI 1.01-8.45) in cancer patients compared to controls. Furthermore, ~5 folds increase in breast cancer risk was associated with 1883G>T mutation (OR 4.75; 95% CI 1.46-15.3) and ~6 folds increase in breast cancer risk was found associated with Iso105Val mutation (OR 6.43; 95% CI 1.41-29.3) in cancer patients compared to controls. Our finding, based on systematic review and experimental data suggest that the polymorphic CYP1A1 and GSTP1 genes may contribute to risk of developing breast cancer.
Collapse
|
10
|
Singh SA, Choudhury JH, Kapfo W, Kundu S, Dhar B, Laskar S, Das R, Kumar M, Ghosh SK. Influence of the CYP1A1 T3801C Polymorphism on Tobacco and Alcohol-Associated Head and Neck Cancer Susceptibility in Northeast India. Asian Pac J Cancer Prev 2016; 16:6953-61. [PMID: 26514474 DOI: 10.7314/apjcp.2015.16.16.6953] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tobacco and alcohol contain or may generate carcinogenic compounds related to cancers. CYP1A1 enzymes act upon these carcinogens before elimination from the body. The aim of this study was to investigate whether CYP1A1 T3801C polymorphism modulates the relationship between tobacco and alcohol- associated head and neck cancer (HNC) susceptibility among the northeast Indian population. MATERIALS AND METHODS One hundred and seventy histologically confirmed HNC cases and 230 controls were included within the study. The CYP1A1 T3801C polymorphism was determined using PCR-RFLP, and the results were confirmed by DNA sequencing. Logistic regression (LR) and multifactor dimensionality reduction (MDR) approaches were applied for statistical analysis. RESULTS The CYP1A1 CC genotype was significantly associated with HNC risk (P=0.045). A significantly increased risk of HNC (OR=6.09; P<0.0001) was observed in individuals with combined habits of smoking, alcohol drinking and tobacco-betel quid chewing. Further, gene-environment interactions revealed enhanced risks of HNC among smokers, alcohol drinkers and tobacco-betel quid chewers carrying CYP1A1 TC or CC genotypes. The highest risk of HNC was observed among smokers (OR=7.55; P=0.009) and chewers (OR=10.8; P<0.0001) carrying the CYP1A1 CC genotype. In MDR analysis, the best model for HNC risk was the three-factor model combination of smoking, tobacco-betel quid chewing and the CYP1A1 variant genotype (CVC=99/100; TBA=0.605; P<0.0001); whereas interaction entropy graphs showed synergistic interaction between tobacco habits and CYP1A1. CONCLUSIONS Our results confirm that the CYP1A1 T3801C polymorphism modifies the risk of HNC and further demonstrated importance of gene-environment interaction.
Collapse
Affiliation(s)
- Seram Anil Singh
- Molecular Medicine Laboratory, Department of Biotechnology, Assam University, Silchar, Assam, India E-mail :
| | | | | | | | | | | | | | | | | |
Collapse
|
11
|
He ZX, Chen XW, Zhou ZW, Zhou SF. Impact of physiological, pathological and environmental factors on the expression and activity of human cytochrome P450 2D6 and implications in precision medicine. Drug Metab Rev 2015; 47:470-519. [PMID: 26574146 DOI: 10.3109/03602532.2015.1101131] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
With only 1.3-4.3% in total hepatic CYP content, human CYP2D6 can metabolize more than 160 drugs. It is a highly polymorphic enzyme and subject to marked inhibition by a number of drugs, causing a large interindividual variability in drug clearance and drug response and drug-drug interactions. The expression and activity of CYP2D6 are regulated by a number of physiological, pathological and environmental factors at transcriptional, post-transcriptional, translational and epigenetic levels. DNA hypermethylation and histone modifications can repress the expression of CYP2D6. Hepatocyte nuclear factor-4α binds to a directly repeated element in the promoter of CYP2D6 and thus regulates the expression of CYP2D6. Small heterodimer partner represses hepatocyte nuclear factor-4α-mediated transactivation of CYP2D6. GW4064, a farnesoid X receptor agonist, decreases hepatic CYP2D6 expression and activity while increasing small heterodimer partner expression and its recruitment to the CYP2D6 promoter. The genotypes are key determinants of interindividual variability in CYP2D6 expression and activity. Recent genome-wide association studies have identified a large number of genes that can regulate CYP2D6. Pregnancy induces CYP2D6 via unknown mechanisms. Renal or liver diseases, smoking and alcohol use have minor to moderate effects only on CYP2D6 activity. Unlike CYP1 and 3 and other CYP2 members, CYP2D6 is resistant to typical inducers such as rifampin, phenobarbital and dexamethasone. Post-translational modifications such as phosphorylation of CYP2D6 Ser135 have been observed, but the functional impact is unknown. Further functional and validation studies are needed to clarify the role of nuclear receptors, epigenetic factors and other factors in the regulation of CYP2D6.
Collapse
Affiliation(s)
- Zhi-Xu He
- a Guizhou Provincial Key Laboratory for Regenerative Medicine, Stem Cell and Tissue Engineering Research Center & Sino-US Joint Laboratory for Medical Sciences, Guizhou Medical University , Guiyang , Guizhou , China
| | - Xiao-Wu Chen
- b Department of General Surgery , The First People's Hospital of Shunde, Southern Medical University , Shunde , Foshan , Guangdong , China , and
| | - Zhi-Wei Zhou
- c Department of Pharmaceutical Science , College of Pharmacy, University of South Florida , Tampa , FL , USA
| | - Shu-Feng Zhou
- a Guizhou Provincial Key Laboratory for Regenerative Medicine, Stem Cell and Tissue Engineering Research Center & Sino-US Joint Laboratory for Medical Sciences, Guizhou Medical University , Guiyang , Guizhou , China .,c Department of Pharmaceutical Science , College of Pharmacy, University of South Florida , Tampa , FL , USA
| |
Collapse
|
12
|
Khlifi R, Ben Salah G, Chakroun A, Hamza-Chaffai A, Rebai A. Inter-ethnic differences in genetic polymorphisms of xenobiotic-metabolizing enzymes (CYP1A1, CYP2D6, NAT1 and NAT2) in healthy populations: correlation with the functional in silico prediction. Mol Biol Rep 2014; 41:5735-43. [PMID: 24934312 DOI: 10.1007/s11033-014-3445-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 06/03/2014] [Indexed: 10/25/2022]
Abstract
Several studies have shown that many polymorphisms of the xenobiotic-metabolizing enzymes (XME) affect either enzymatic functions or are associated with various aspects of human health. Owing to the presence of these single nucleotide variants (SNVs), differences in detoxification capacity have been observed between many ethnicities. The aim of this investigation was to study the prevalence of four polymorphisms in XME among various ethnic groups. Attention was focused on polymorphisms of CYP2D6 (rs1058172, G>A, p.Arg365His), CYP1A1 (rs4646421, c.-26-728C>T), NAT1 (rs4921880, c.-85-1014T>A) and NAT2 (rs1208, A>G, p.Arg268Lys). These polymorphisms were analyzed in 261 healthy Tunisians individuals in comparison with different ethnic backgrounds from hapmap database. In addition, in silico functional prediction was also performed to determine the loss of function variants. Our results demonstrated that population's origins widely affect the genetic variability of XME enzymes and Tunisians show a characteristic pattern. In silico predictions showed a deleterious effect for p.Arg268Lys substitution on CYP2D6 function, findings confirmed its key role played in cancer susceptibility. These data show that detoxification genes structures depend on the studied population. This suggests that ethnic differences impact on disease risk or response to drugs and therefore should be taken into consideration in genetic association studies focusing on XME enzymes. Our results provide the first report on these SNV in Tunisian population and could be useful for further epidemiological investigations including targeted therapy.
Collapse
Affiliation(s)
- Rim Khlifi
- Unit of Marine and Environmental Toxicology, UR 09-03, IPEIS, Sfax University, BP 1172, 3018, Sfax, Tunisia,
| | | | | | | | | |
Collapse
|