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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.
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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.
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Du Q, Zhou R, Wang H, Li Q, Yan Q, Dang W, Guo J. A metabolism-related gene signature for predicting the prognosis in thyroid carcinoma. Front Genet 2023; 13:972950. [PMID: 36685893 PMCID: PMC9846547 DOI: 10.3389/fgene.2022.972950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 11/23/2022] [Indexed: 01/06/2023] Open
Abstract
Metabolic reprogramming is one of the cancer hallmarks, important for the survival of malignant cells. We investigated the prognostic value of genes associated with metabolism in thyroid carcinoma (THCA). A prognostic risk model of metabolism-related genes (MRGs) was built and tested based on datasets in The Cancer Genome Atlas (TCGA), with univariate Cox regression analysis, LASSO, and multivariate Cox regression analysis. We used Kaplan-Meier (KM) curves, time-dependent receiver operating characteristic curves (ROC), a nomogram, concordance index (C-index) and restricted mean survival (RMS) to assess the performance of the risk model, indicating the splendid predictive performance. We established a three-gene risk model related to metabolism, consisting of PAPSS2, ITPKA, and CYP1A1. The correlation analysis in patients with different risk statuses involved immune infiltration, mutation and therapeutic reaction. We also performed pan-cancer analyses of model genes to predict the mutational value in various cancers. Our metabolism-related risk model had a powerful predictive capability in the prognosis of THCA. This research will provide the fundamental data for further development of prognostic markers and individualized therapy in THCA.
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Affiliation(s)
- Qiujing Du
- Department of General Medicine, Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, China
| | - Ruhao Zhou
- Department of Orthopedics, Shanxi Key Laboratory of Bone and Soft Tissue Injury Repair, Second Clinical Medical College, Shanxi Medical University, Taiyuan, China
| | - Heng Wang
- Department of Vascular Surgery, Second Clinical Medical College, Shanxi Medical University, Taiyuan, China
| | - Qian Li
- Basic Medical College, Shanxi Medical University, Jinzhong, China
| | - Qi Yan
- Department of Endocrinology, Second Clinical Medical College, Shanxi Medical University, Taiyuan, China
| | - Wenjiao Dang
- Department of General Medicine, Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, China
| | - Jianjin Guo
- Department of General Medicine, Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, China,*Correspondence: Jianjin Guo,
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Liu A, Li X, Hao Z, Cao J, Li H, Sun M, Zhang Z, Liang R, Zhang H. Alterations of DNA methylation and mRNA levels of CYP1A1, GSTP1, and GSTM1 in human bronchial epithelial cells induced by benzo[a]pyrene. Toxicol Ind Health 2022; 38:127-138. [PMID: 35193440 DOI: 10.1177/07482337211069233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Benzo[a]pyrene (B[a]P) is a known human carcinogen and plays a major function in the initiation of lung cancer at its first proximity. However, the underlying molecular mechanisms are less well understood. In this study, we investigated the impact of B[a]P treatment on the DNA methylation and mRNA levels of CYP1A1, GSTP1, and GSTM1 in human bronchial epithelial cells (16HBEs), and provide scientific evidence for the mechanism study on the carcinogenesis of B[a]P. We treated 16HBEs with DMSO or concentrations of B[a]P at 1, 2, and 5 mmol/L for 24 h, observed the morphological changes, determined the cell viability, DNA methylation, and mRNA levels of CYP1A1, GSTP1, and GSTM1. Compared to the DMSO controls, B[a]P treatment had significantly increased the neoplastic cell number and cell viability in 16HBEs at all three doses (1, 2, and 5 mmol/L), and had significantly reduced the CYP1A1 and GSTP1 DNA promoter methylation levels. Following B[a]P treatment, the GSTM1 promoter methylation level in 16HBEs was profoundly reduced at low dose group compared to the DMSO controls, yet it was significantly increased at both middle and high dose groups. The mRNA levels of CYP1A1, GSTP1, and GSTM1 were significantly decreased in 16HBEs following B[a]P treatment at all three doses. The findings demonstrate that B[a]P promoted cell proliferation in 16HBEs, which was possibly related to the altered DNA methylations and the inhibited mRNA levels in CYP1A1, GSTP1, and GSTM1.
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Affiliation(s)
- Aixiang Liu
- Department of Environmental Health, School of Public Health, 74648Shanxi Medical University, Taiyuan, Shanxi, China.,Department of Health Information Management, 74648Shanxi Medical University Fenyang College, Fenyang, Shanxi, China
| | - Xin Li
- Center of Disease Control and Prevention, 442190Taiyuan Iron and Steel Co Ltd, Taiyuan, Shanxi, China
| | - Zhongsuo Hao
- Department of Environmental Health, School of Public Health, 74648Shanxi Medical University, Taiyuan, Shanxi, China
| | - Jingjing Cao
- Department of Environmental Health, School of Public Health, 74648Shanxi Medical University, Taiyuan, Shanxi, China
| | - Huan Li
- Department of Environmental Health, School of Public Health, 74648Shanxi Medical University, Taiyuan, Shanxi, China
| | - Min Sun
- Department of Environmental Health, School of Public Health, 74648Shanxi Medical University, Taiyuan, Shanxi, China
| | - Zhihong Zhang
- Department of Environmental Health, School of Public Health, 74648Shanxi Medical University, Taiyuan, Shanxi, China
| | - Ruifeng Liang
- Department of Environmental Health, School of Public Health, 74648Shanxi Medical University, Taiyuan, Shanxi, China
| | - Hongmei Zhang
- Department of Environmental Health, School of Public Health, 74648Shanxi Medical University, Taiyuan, Shanxi, China
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Association of GSTP1 p.Ile105Val (rs1695, c.313A > G) Variant with the Risk of Breast Carcinoma among Egyptian Women. Biochem Genet 2021; 59:1487-1505. [PMID: 33939082 DOI: 10.1007/s10528-021-10070-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 04/19/2021] [Indexed: 01/01/2023]
Abstract
Several reports examined the association of the GSTP1 p.Ile105Val (rs1695, c.313A > G) variant with the elevated risk of multiple cancerous diseases involving breast carcinoma, but with inconclusive findings. The primary purpose of this study is to test the association of this essential variant with the risk of breast carcinoma among Egyptian females. This case-control study was conducted based on 200 participants involving 100 women diagnosed with breast carcinoma and 100 unrelated cancer-free controls from the same district. The genomic DNA for all participants was genotyped utilizing T-ARMS-PCR procedure. The frequencies of the GSTP1 p.Ile105Val (rs1695, c.313A > G) variant indicated a statistically significant with the elevated risk of breast carcinoma under various genetic models, including allelic (OR = 2.48, P-value < 0.001) and dominant (OR = 2.36, P-value = 0.003) models. In conclusion, the GSTP1 p.Ile105Val (rs1695, c.313A > G) variant was considered as an independent risk factor for breast carcinoma among Egyptian women.
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Manavalan R, Priya S. Genetic interactions effects for cancer disease identification using computational models: a review. Med Biol Eng Comput 2021; 59:733-758. [PMID: 33839998 DOI: 10.1007/s11517-021-02343-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 03/10/2021] [Indexed: 11/29/2022]
Abstract
Genome-wide association studies (GWAS) provide clear insight into understanding genetic variations and environmental influences responsible for various human diseases. Cancer identification through genetic interactions (epistasis) is one of the significant ongoing researches in GWAS. The growth of the cancer cell emerges from multi-locus as well as complex genetic interaction. It is impractical for the physician to detect cancer via manual examination of SNPs interaction. Due to its importance, several computational approaches have been modeled to infer epistasis effects. This article includes a comprehensive and multifaceted review of all relevant genetic studies published between 2001 and 2020. In this contemporary review, various computational methods are as follows: multifactor dimensionality reduction-based approaches, statistical strategies, machine learning, and optimization-based techniques are carefully reviewed and presented with their evaluation results. Moreover, these computational approaches' strengths and limitations are described. The issues behind the computational methods for identifying the cancer disease through genetic interactions and the various evaluation parameters used by researchers have been analyzed. This review is highly beneficial for researchers and medical professionals to learn techniques adapted to discover the epistasis and aids to design novel automatic epistasis detection systems with strong robustness and maximum efficiency to address the different research problems in finding practical solutions effectively.
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Affiliation(s)
- R Manavalan
- Department of Computer Science, Arignar Anna Government Arts College, Villupuram, Tamil Nadu, 605602, India.
| | - S Priya
- Computer Science, Arignar Anna Government Arts College, Villupuram, Tamil Nadu, India
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Al-Omoush TK, Alzoubi KH, Khabour OF, Alsheyab FM, Abu-Siniyeh A, Al-Sawalha NA, Mayyas FA, Cobb CO, Eissenberg T. The CHRNA5 Polymorphism (rs16969968) and its Association with Waterpipe Smoking Addiction among Jordanians. ARAB JOURNAL OF BASIC AND APPLIED SCIENCES 2021; 27:450-455. [PMID: 33511332 DOI: 10.1080/25765299.2020.1849491] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Waterpipe smoking is a form of tobacco use that causes nicotine/tobacco dependence and has become a global health problem. In the current study, the association of rs16969968 SNP in the CHRNA5 gene with waterpipe dependence was investigated. A total of 386 men and women who used a waterpipe to smoke tobacco were recruited and divided into less dependent and more dependent smokers based on their score on the Lebanon Waterpipe Dependence Scale (LWDS). Results showed a significant difference in the distribution of GG, GA, and AA genotypes by waterpipe dependence status (P<0.001). The more dependent group showed a higher frequency of the AA genotype than the less dependent smokers' group (38% versus 23% respectively). In addition, the more dependent smokers exhibited more A allele than less dependent smokers (53% versus 37% respectively, P<0.001). In conclusion, there is an association between the rs16969968 SNP and waterpipe dependence as assessed by the LWDS.
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Affiliation(s)
- Thaka'a K Al-Omoush
- Department of Applied Biology, Faculty of Science and Arts, Jordan University of Science and Technology, Irbid, Jordan
| | - Karem H Alzoubi
- Department of Clinical Pharmacy, Jordan University of Science and Technology, Irbid, Jordan
| | - Omar F Khabour
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, Jordan University of Science and Technology, Irbid, Jordan
| | - Fawzi M Alsheyab
- Department of Applied Biology, Faculty of Science and Arts, Jordan University of Science and Technology, Irbid, Jordan
| | - Ahmed Abu-Siniyeh
- Department of Medical Laboratories, Faculty of Health Sciences, American University of Madaba, Madaba, Jordan
| | - Nour A Al-Sawalha
- Department of Clinical Pharmacy, Jordan University of Science and Technology, Irbid, Jordan
| | - Fadia A Mayyas
- Department of Clinical Pharmacy, Jordan University of Science and Technology, Irbid, Jordan
| | - Caroline O Cobb
- Department of Psychology, Virginia Commonwealth University, Richmond, VA, USA.,Center for the Study of Tobacco Products, Virginia Commonwealth University, Richmond, VA, USA
| | - Thomas Eissenberg
- Department of Psychology, Virginia Commonwealth University, Richmond, VA, USA.,Center for the Study of Tobacco Products, Virginia Commonwealth University, Richmond, VA, USA
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