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Veiskarami P, Houshmand M, Seifi S, Ansarinejad N, Fardad F, Abbasi B. The effect of CHRNA3 rs1051730 C>T and ABCB1 rs3842 A>G polymorphisms on non-small cell lung cancer and nicotine dependence in Iranian population. Heliyon 2021; 7:e07867. [PMID: 34522797 PMCID: PMC8426517 DOI: 10.1016/j.heliyon.2021.e07867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 12/14/2020] [Accepted: 08/20/2021] [Indexed: 12/24/2022] Open
Abstract
Aims Lung cancer is still the leading cause of cancer mortality in all over the world. Nicotine and its derivatives are the most well-known carcinogens that participate in both etiology and progression of lung cancer. The objective of the current study was to investigate whether single nucleotide polymorphisms (SNPs) rs1051730C > T in CHRNA3 and rs3842A > G in ABCB1, two genes contributing in the mechanism of disposition and metabolism of nicotine and its derivatives, could modify the risk of developing lung cancer, as well as nicotine dependence in Iranian. Main methods The genotyping analysis for these two SNPs was conducted in a case-control study of 108 lung cancer cases and 120 healthy controls using ARMS-PCR and Tetra-primer ARMS-PCR techniques. The correlation between studied SNPs and lung cancer was assessed by the regression analysis. Key findings We observed a significant association between lung cancer and rs1051730C > T by using four genetic models: allele (OR:1.83; 95% CI:1.24-2.6; p = 0.002), dominant (OR: 2.19; 95% CI:1.27-3.78; p = 0.005), recessive (OR: 2.25; 95% CI: 1.02-4.95; p = 0.043) and additive (TT vs CC: OR:3.25; 95% CI:1.38-7.60; p = 0.007, CT vs CC: OR:1.96; 95% CI:1.10-3.48; p = 0.021). Furthermore, a significant association between this variant and nicotine dependence (OR: 2.27; 95% CI: 1.52-3.39; p = 0.00005) was reported. However, no association was found for rs3842A > G. Significance The results suggested that the CHRNA3 rs1051730C > T via a smoking-dependent manner could modify susceptibility to lung cancer among Iranian population.
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Affiliation(s)
- Parisa Veiskarami
- Department of Medical Genetics, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Massoud Houshmand
- Department of Medical Genetics, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.,Research Center, Knowledge University, Erbil, Kurdistan Region, Iraq
| | - Sharareh Seifi
- Chronic Respiratory Diseases Research Center, National Research Institute of Tuberculosis and Lung Diseases (NRITLD), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Nafiseh Ansarinejad
- Department of Hematology and Medical Oncology, Rasool Akram Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Farshid Fardad
- Department of Hematology and Medical Oncology, Rasool Akram Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Bahareh Abbasi
- Department of Medical Genetics, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
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2
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Hu Y, Tan C, Lin X, Lai Z, Zhang X, Lu Q, Feng N, Yang D, Weng L. Exonuclease III-Regulated Target Cyclic Amplification-Based Single Nucleotide Polymorphism Detection Using Ultrathin Ternary Chalcogenide Nanosheets. Front Chem 2020; 7:844. [PMID: 31921768 PMCID: PMC6913186 DOI: 10.3389/fchem.2019.00844] [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: 10/16/2019] [Accepted: 11/19/2019] [Indexed: 12/30/2022] Open
Abstract
Herein, we report that the ternary chalcogenide nanosheet exhibits different affinity toward oligonucleotides with different lengths and efficiently quenches the fluorescence of dye-labeled DNA probes. Based on these findings, as a proof-of-concept application, the ternary chalcogenide nanosheet is used as a target cyclic amplification biosensor, showing high specificity in discriminating single-base mismatch. This simple strategy is fast and sensitive for the single nucleotide polymorphism detection. Ultralow detection limit of unlabeled target (250 fM) and high discrimination ratio (5%) in the mixture of perfect match (mutant-type) and single-base mismatch (wild-type) target are achieved. This sensing method is extensively compatible for the single nucleotide polymorphism detection in clinical samples, making it a promising tool for the mutation-based clinical diagnostic and genomic research.
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Affiliation(s)
- Yanling Hu
- School of Electrical and Control Engineering, Nanjing Polytechnic Institute, Nanjing, China.,Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing, China
| | - Chaoliang Tan
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, Singapore
| | - Xin Lin
- School of Ophthalmology and Optometry, Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Zhuangchai Lai
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, Singapore
| | - Xiao Zhang
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, Singapore
| | - Qipeng Lu
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, Singapore
| | - Ning Feng
- Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing, China
| | - Dongliang Yang
- Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing, China.,School of Physical and Mathematical Sciences, Nanjing Tech University (NanjingTech), Nanjing, China
| | - Lixing Weng
- Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing, China
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3
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Han Z, Hua J, Xue W, Zhu F. Integrating the Ribonucleic Acid Sequencing Data From Various Studies for Exploring the Multiple Sclerosis-Related Long Noncoding Ribonucleic Acids and Their Functions. Front Genet 2019; 10:1136. [PMID: 31781177 PMCID: PMC6861379 DOI: 10.3389/fgene.2019.01136] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 10/18/2019] [Indexed: 12/19/2022] Open
Abstract
Multiple sclerosis (MS) is a chronic fatal central nervous system (CNS) disease involving in complex immunity dysfunction. Recently, long noncoding RNAs (lncRNAs) were discovered as the important regulatory factors for the pathogenesis of MS. However, these findings often cannot be repeated and confirmed by the subsequent studies. We considered that the small-scale samples or the heterogeneity among various tissues may result in the divergence of the results. Currently, RNA-seq has become a powerful approach to quantify the abundances of lncRNA transcripts. Therefore, we comprehensively collected the MS-related RNA-seq data from a variety of previous studies, and integrated these data using an expression-based meta-analysis to identify the differentially expressed lncRNA between MS patients and controls in whole samples and subgroups. Then, we performed the Jensen-Shannon (JS) divergence and cluster analysis to explore the heterogeneity and expression specificity among various tissues. Finally, we investigated the potential function of identified lncRNAs for MS using weighted gene co-expression network analysis (WGCNA) and gene set enrichment analysis (GSEA), and 5,420 MS-related lncRNAs specifically expressed in the brain tissue were identified. The subgroup analysis found a small heterogeneity of the lncRNA expression profiles between brain and blood tissues. The results of WGCNA and GSEA showed that a potential important function of lncRNAs in MS may be involved in the regulation of ribonucleoproteins and tumor necrosis factor cytokines receptors. In summary, this study provided a strategy to explore disease-related lncRNAs on genome-wide scale, and our findings will be benefit to improve the understanding of MS pathogenesis.
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Affiliation(s)
- Zhijie Han
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
- School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Jiao Hua
- School of Mathematics, Harbin Institute of Technology, Harbin, China
| | - Weiwei Xue
- School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
- School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
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4
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Hsu JHM, Chang PMH, Cheng TS, Kuo YL, Wu ATH, Tran TH, Yang YH, Chen JM, Tsai YC, Chu YS, Huang TH, Huang CYF, Lai JM. Identification of Withaferin A as a Potential Candidate for Anti-Cancer Therapy in Non-Small Cell Lung Cancer. Cancers (Basel) 2019; 11:cancers11071003. [PMID: 31319622 PMCID: PMC6678286 DOI: 10.3390/cancers11071003] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 07/15/2019] [Indexed: 12/21/2022] Open
Abstract
Low response rate and recurrence are common issues in lung cancer; thus, identifying a potential compound for these patients is essential. Utilizing an in silico screening method, we identified withaferin A (WA), a cell-permeable steroidal lactone initially extracted from Withania somnifera, as a potential anti-lung cancer and anti-lung cancer stem-like cell (CSC) agent. First, we demonstrated that WA exhibited potent cytotoxicity in several lung cancer cells, as evidenced by low IC50 values. WA concurrently induced autophagy and apoptosis and the activation of reactive oxygen species (ROS), which plays an upstream role in mediating WA-elicited effects. The increase in p62 indicated that WA may modulate the autophagy flux followed by apoptosis. In vivo research also demonstrated the anti-tumor effect of WA treatment. We subsequently demonstrated that WA could inhibit the growth of lung CSCs, decrease side population cells, and inhibit lung cancer spheroid-forming capacity, at least through downregulation of mTOR/STAT3 signaling. Furthermore, the combination of WA and chemotherapeutic drugs, including cisplatin and pemetrexed, exerted synergistic effects on the inhibition of epidermal growth factor receptor (EGFR) wild-type lung cancer cell viability. In addition, WA can further enhance the cytotoxic effect of cisplatin in lung CSCs. Therefore, WA alone or in combination with standard chemotherapy is a potential treatment option for EGFR wild-type lung cancer and may decrease the occurrence of cisplatin resistance by inhibiting lung CSCs.
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Affiliation(s)
- Jade H-M Hsu
- Department of Biotechnology and Laboratory Science in Medicine, National Yang-Ming University, Taipei 112, Taiwan
| | - Peter M-H Chang
- Division of Medical Oncology, Department of Oncology, Taipei Veterans General Hospital, Taipei 112, Taiwan
- Faculty of Medicine, National Yang-Ming University, Taipei 112, Taiwan
| | - Tai-Shan Cheng
- Institute of Biopharmaceutical Sciences, National Yang-Ming University, Taipei 112, Taiwan
| | - Yu-Lun Kuo
- Department of Computer Science and Information Engineering, National Taiwan University, Taipei 106, Taiwan
| | - Alexander T-H Wu
- The PhD Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan
| | - Thu-Ha Tran
- Institute of Biopharmaceutical Sciences, National Yang-Ming University, Taipei 112, Taiwan
- Taiwan International Graduate Program in Molecular Medicine, National Yang-Ming University and Academia Sinica, Taipei 112, Taiwan
| | - Yun-Hsuan Yang
- The Ph.D. Program in Pharmaceutical Biotechnology, College of Medicine, Fu Jen Catholic University, New Taipei City 242, Taiwan
| | - Jing-Ming Chen
- Graduate Institute of Applied Science and Engineering, College of Science and Engineering, Fu Jen Catholic University, New Taipei City 242, Taiwan
| | - Yu-Chen Tsai
- Department of Biotechnology and Laboratory Science in Medicine, National Yang-Ming University, Taipei 112, Taiwan
| | - Yeh-Shiu Chu
- Brain Research Center, National Yang-Ming University, Taipei 112, Taiwan
| | - Tse-Hung Huang
- Graduate Institute of Traditional Chinese Medicine, School of Traditional Chinese Medicine, Chang Gung University, Taoyuan 333, Taiwan.
- School of Nursing, National Taipei University of Nursing and Health Sciences, Taipei 110, Taiwan.
- Department of Traditional Chinese Medicine, Chang Gung Memorial Hospital, Keelung 204, Taiwan.
- Graduate Institute of Health Industry Technology, Chang Gung University of Science and Technology, Taoyuan 333, Taiwan.
| | - Chi-Ying F Huang
- Department of Biotechnology and Laboratory Science in Medicine, National Yang-Ming University, Taipei 112, Taiwan.
- Institute of Biopharmaceutical Sciences, National Yang-Ming University, Taipei 112, Taiwan.
| | - Jin-Mei Lai
- The Ph.D. Program in Pharmaceutical Biotechnology, College of Medicine, Fu Jen Catholic University, New Taipei City 242, Taiwan.
- Graduate Institute of Applied Science and Engineering, College of Science and Engineering, Fu Jen Catholic University, New Taipei City 242, Taiwan.
- Department of Life Science, College of Science and Engineering, Fu Jen Catholic University, New Taipei City 242, Taiwan.
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5
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Han Z, Xue W, Tao L, Zhu F. Identification of Key Long Non-Coding RNAs in the Pathology of Alzheimer’s Disease and their Functions Based on Genome-Wide Associations Study, Microarray, and RNA-seq Data. J Alzheimers Dis 2019; 68:339-355. [DOI: 10.3233/jad-181051] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Zhijie Han
- Innovative Drug Research and Bioinformatics Group, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
- School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing, China
| | - Weiwei Xue
- School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing, China
| | - Lin Tao
- Key Laboratory of Elemene Class Anti-cancer Chinese Medicine of Zhejiang Province, School of Medicine, Hangzhou Normal University, Hangzhou, P. R. China
| | - Feng Zhu
- Innovative Drug Research and Bioinformatics Group, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
- School of Pharmaceutical Sciences and Collaborative Innovation Center for Brain Science, Chongqing University, Chongqing, China
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6
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Identifying genetic markers associated with susceptibility to cardiovascular diseases. Future Sci OA 2018; 5:FSO350. [PMID: 30652019 PMCID: PMC6331704 DOI: 10.4155/fsoa-2018-0031] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 09/18/2018] [Indexed: 12/25/2022] Open
Abstract
The development of cardiovascular diseases (CVDs) is due to a complex interaction between the genome and the environment. Understanding how genetic differences in individuals contribute to their susceptibility to CVDs can help guide practitioners to give the best advice to achieve a favorable outcome for the patient. As genome technologies evolve, genotyping of individuals could be available to all patients using a simple saliva test. Large-scale genome-wide association studies and meta analyses have provided powerful insights into polymorphisms that may be predictive of disease and an individual's response to certain nutrients, but moving forward it is imperative that these insights can be applied in the medical setting to reduce the incidence and mortality of CVDs. Cardiovascular diseases (CVDs) are the leading cause of death worldwide, and while most CVDs can be prevented by adopting a healthy lifestyle, this is only half the story. Evidence suggests changes in an individual's genes or DNA can cause some form of CVDs, highlighting a complex relationship between genes and the environment. Genotyping, a process used to determine genetic differences within an individual's DNA, can provide doctors with relevant information to identify individuals who are at high risk of developing CVDs. This would allow treatment to begin early and encourage individuals to adopt a healthy lifestyle to reduce their risk.
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7
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Han Z, Qu J, Zhao J, Zou X. Analyzing 74,248 Samples Confirms the Association Between CLU rs11136000 Polymorphism and Alzheimer's Disease in Caucasian But Not Chinese population. Sci Rep 2018; 8:11062. [PMID: 30038359 PMCID: PMC6056482 DOI: 10.1038/s41598-018-29450-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 07/11/2018] [Indexed: 01/09/2023] Open
Abstract
Clusterin (CLU) is considered one of the most important roles for pathogenesis of Alzheimer's Disease (AD). The early genome-wide association studies (GWAS) identified the CLU rs11136000 polymorphism is significantly associated with AD in Caucasian. However, the subsequent studies are unable to replicate these findings in different populations. Although two independent meta-analyses show evidence to support significant association in Asian and Caucasian populations by integrating the data from 18 and 25 related GWAS studies, respectively, many of the following 18 studies also reported the inconsistent results. Moreover, there are six missed and a misclassified GWAS studies in the two meta-analyses. Therefore, we suspected that the small-scale and incompletion or heterogeneity of the samples maybe lead to different results of these studies. In this study, large-scale samples from 50 related GWAS studies (28,464 AD cases and 45,784 controls) were selected afresh from seven authoritative sources to reevaluate the effect of rs11136000 polymorphism to AD risk. Similarly, we identified that the minor allele variant of rs11136000 significantly decrease AD risk in Caucasian ethnicity using the allele, dominant and recessive model. Different from the results of the previous studies, however, the results showed a negligible or no association in Asian and Chinese populations. Collectively, our analysis suggests that, for Asian and Chinese populations, the variant of rs11136000 may be irrelevant to AD risk. We believe that these findings can help to improve the understanding of the AD's pathogenesis.
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Affiliation(s)
- Zhijie Han
- Innovative Drug Research and Bioinformatics Group, School of Pharmaceutical Sciences, Chongqing University, Chongqing, 401331, China
| | - Jiaojiao Qu
- Institute of Fungus Resources, College of Life Sciences, Guizhou University, Guiyang, 550025, China
| | - Jiehong Zhao
- College of Pharmacy, Guiyang University of Chinese Medicine, Guian new area, 550025, China
| | - Xiao Zou
- Institute of Fungus Resources, College of Life Sciences, Guizhou University, Guiyang, 550025, China.
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8
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Ding W, Xu L, Zhang L, Han Z, Jiang Q, Wang Z, Jin S. Meta-analysis of association between TCF7L2 polymorphism rs7903146 and type 2 diabetes mellitus. BMC MEDICAL GENETICS 2018. [PMID: 29514658 PMCID: PMC5842570 DOI: 10.1186/s12881-018-0553-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
BACKGROUND Large scale association studies have found a significant association between type 2 diabetes mellitus (T2DM) and transcription factor 7-like 2 (TCF7L2) polymorphism rs7903146. However, the quality of data varies greatly, as the studies report inconsistent results in different populations. Hence, we perform this meta-analysis to give a more convincing result. METHODS The articles, published from January 1st, 2000 to April 1st, 2017, were identified by searching in PubMed and Google Scholar. A total of 56628 participants (34232 cases and 22396 controls) were included in the meta-analysis. A total of 28 studies were divided into 4 subgroups: Caucasian (10 studies), East Asian (5 studies), South Asian (5 studies) and Others (8 studies). All the data analyses were analyzed by the R package meta. RESULTS The significant association was observed by using the dominant model (OR = 1.41, CI = 1.36 - 1.47, p < 0.0001), recessive model (OR = 1.58, CI = 1.48 - 1.69, p < 0.0001), additive model(CT vs CC) (OR = 1.34, CI = 1.28-1.39, p < 0.0001), additive model(TT vs CC) (OR = 1.81, CI = 1.69-1.94, p < 0.0001)and allele model (OR = 1.35, CI = 1.31-1.39, p < 0.0001). CONCLUSION The meta-analysis suggested that rs7903146 was significantly associated with T2DM in Caucasian, East Asian, South Asian and other ethnicities.
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Affiliation(s)
- Weiyue Ding
- College of Computer Science and Technology, Harbin Engineering University, No.145 Nantong Street, Nangang District, Harbin, 150001, China
| | - Li Xu
- College of Computer Science and Technology, Harbin Engineering University, No.145 Nantong Street, Nangang District, Harbin, 150001, China.
| | - Lejun Zhang
- School of Information Engineering, Yangzhou University, No.196, Huayang West Road, Yangzhou, 225127, China
| | - Zhijie Han
- School of Life Science and Technology, Harbin Institute of Technology, No.92 Xidazhi Street, Nangang District, Harbin, 150001, China
| | - Qinghua Jiang
- School of Life Science and Technology, Harbin Institute of Technology, No.92 Xidazhi Street, Nangang District, Harbin, 150001, China
| | - Zhe Wang
- Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, No.2699, Qianjin Avenue, Qianweinan District, Changchun, 130012, China
| | - Shuilin Jin
- Department of Mathematics, Harbin Institute of Technology, No.92, Xidazhi Street, Nangang District, Harbin, 150001, China.
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Lang BM, Biedermann L, van Haaften WT, de Vallière C, Schuurmans M, Begré S, Zeitz J, Scharl M, Turina M, Greuter T, Schreiner P, Heinrich H, Kuntzen T, Vavricka SR, Rogler G, Beerenwinkel N, Misselwitz B. Genetic polymorphisms associated with smoking behaviour predict the risk of surgery in patients with Crohn's disease. Aliment Pharmacol Ther 2018; 47:55-66. [PMID: 29052254 DOI: 10.1111/apt.14378] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 08/04/2017] [Accepted: 09/22/2017] [Indexed: 12/11/2022]
Abstract
BACKGROUND Smoking is a strong environmental factor leading to adverse outcomes in Crohn's disease, but a more benign course in ulcerative colitis. Several single nucleotide polymorphisms (SNPs) are associated with smoking quantity and behaviour. AIM To assess whether smoking-associated SNPs interact with smoking to influence the clinical course of inflammatory bowel diseases. METHODS Genetic and prospectively obtained clinical data from 1434 Swiss inflammatory bowel disease cohort patients (821 Crohn's disease and 613 ulcerative colitis) were analysed. Six SNPs associated with smoking quantity and behaviour (rs588765, rs1051730, rs1329650, rs4105144, rs6474412 and rs3733829) were combined to form a risk score (range: 0-12) by adding the number of risk alleles. We calculated multivariate models for smoking, risk of surgery, fistula, Crohn's disease location and ulcerative colitis disease extent. RESULTS In Crohn's disease patients who smoke, the number of surgeries was associated with the genetic risk score. This translates to a predicted 3.5-fold (95% confidence interval: 2.4- to 5.7-fold, P<.0001) higher number of surgical procedures in smokers with 12 risk alleles than individuals with the lowest risk. Patients with a risk score >7 had a significantly shorter time to first intestinal surgery. The genetic risk score did not predict surgery in ulcerative colitis or occurrence of fistulae in Crohn's disease. SNP rs6265 was associated with ileal disease in Crohn's disease (P<.05) and proctitis in ulcerative colitis (P<.05). CONCLUSIONS SNPs associated with smoking quantity is associated with an increased risk for surgery in Crohn's disease patients who smoke. Our data provide an example of genetics interacting with the environment to influence the disease course of inflammatory bowel disease.
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Affiliation(s)
- B M Lang
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - L Biedermann
- Division of Gastroenterology, University Hospital Zurich (USZ) and Zurich University, Zurich, Switzerland
| | - W T van Haaften
- Division of Gastroenterology, University Hospital Zurich (USZ) and Zurich University, Zurich, Switzerland.,Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen, The Netherlands
| | - C de Vallière
- Division of Gastroenterology, University Hospital Zurich (USZ) and Zurich University, Zurich, Switzerland
| | - M Schuurmans
- Division of Pneumology, University Hospital Zurich (USZ) and Zurich University, Zurich, Switzerland
| | - S Begré
- Hohenegg Hospital, Meilen, Switzerland
| | - J Zeitz
- Division of Gastroenterology, University Hospital Zurich (USZ) and Zurich University, Zurich, Switzerland
| | - M Scharl
- Division of Gastroenterology, University Hospital Zurich (USZ) and Zurich University, Zurich, Switzerland
| | - M Turina
- Division of Visceral Surgery, University Hospital Zurich (USZ), Zurich, Switzerland
| | - T Greuter
- Division of Gastroenterology, University Hospital Zurich (USZ) and Zurich University, Zurich, Switzerland
| | - P Schreiner
- Division of Gastroenterology, University Hospital Zurich (USZ) and Zurich University, Zurich, Switzerland
| | - H Heinrich
- Division of Gastroenterology, University Hospital Zurich (USZ) and Zurich University, Zurich, Switzerland
| | - T Kuntzen
- Division of Gastroenterology, University Hospital Zurich (USZ) and Zurich University, Zurich, Switzerland
| | - S R Vavricka
- Division of Gastroenterology, Triemli Hospital Zurich, Zürich, Switzerland
| | - G Rogler
- Division of Gastroenterology, University Hospital Zurich (USZ) and Zurich University, Zurich, Switzerland
| | - N Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - B Misselwitz
- Division of Gastroenterology, University Hospital Zurich (USZ) and Zurich University, Zurich, Switzerland
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Liu C, Cui H, Gu D, Zhang M, Fang Y, Chen S, Tang M, Zhang B, Chen H. Genetic polymorphisms and lung cancer risk: Evidence from meta-analyses and genome-wide association studies. Lung Cancer 2017; 113:18-29. [PMID: 29110844 DOI: 10.1016/j.lungcan.2017.08.026] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 08/18/2017] [Accepted: 08/25/2017] [Indexed: 01/30/2023]
Abstract
A growing number of studies investigating the association between Single Nucleotide Polymorphisms (SNPs) and lung cancer risk have been published since over a decade ago. An updated integrative assessment on the credibility and strength of the associations is required. We searched PubMed, Medline, and Web of Science on or before August 29th, 2016. A total of 198 articles were deemed eligible for inclusion, which addressed the associations between 108 variants and lung cancer. Among the 108 variants, 63 were reported to be significantly associated with lung cancer while the remaining 45 were reported non-significant. Further evaluation integrating the Venice Criteria and false-positive report probability (FPRP) was performed to determine the strength of cumulative epidemiological evidence for the 63 significant associations. As a result, 15 SNPs on or near 12 genes and one miRNA with strong evidence of association with lung cancer risk were identified, including TERT (rs2736098), CHRNA3 (rs1051730), AGPHD1 (rs8034191), CLPTM1L (rs401681 and rs402710), BAT3 (rs3117582), TRNAA (rs4324798), ERCC2 (Lys751Gln), miR-146a2 (rs2910164), CYP1B1 (Arg48Gly), GSTM1 (null/present), SOD2 (C47T), IL-10 (-592C/A and -819C/T), and TP53 (intron 6). 19 SNPs were given moderate rating and 17 SNPs were rated as having weak evidence. In addition, all of the 29 SNPs identified in 12 genome-wide association studies (GWAS) were proved to be noteworthy based on FPRP value. This review summarizes and evaluates the cumulative evidence of genetic polymorphisms and lung cancer risk, which can serve as a general and useful reference for further genetic studies.
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Affiliation(s)
- Caiyang Liu
- Department of Cardiothoracic Surgery, First Affiliated Hospital of Chongqing Medical University, No.1, Youyi Road, Yuzhong District, Chongqing 400010, China
| | - Huijie Cui
- Division of Noncommunicable Disease Epidemiology, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing 400038, China
| | - Dongqing Gu
- Division of Noncommunicable Disease Epidemiology, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing 400038, China
| | - Min Zhang
- Division of Noncommunicable Disease Epidemiology, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing 400038, China
| | - Yanfei Fang
- Division of Noncommunicable Disease Epidemiology, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing 400038, China
| | - Siyu Chen
- Division of Noncommunicable Disease Epidemiology, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing 400038, China
| | - Mingshuang Tang
- Division of Noncommunicable Disease Epidemiology, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing 400038, China
| | - Ben Zhang
- Division of Noncommunicable Disease Epidemiology, First Affiliated Hospital and Southwest School of Medicine, Third Military Medical University, Chongqing 400038, China
| | - Huanwen Chen
- Department of Cardiothoracic Surgery, First Affiliated Hospital of Chongqing Medical University, No.1, Youyi Road, Yuzhong District, Chongqing 400010, China.
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