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He L, Zhong C, Chang H, Inman JL, Celniker SE, Ioakeim-Ioannidou M, Liu KX, Haas-Kogan D, MacDonald SM, Threadgill DW, Kogan SC, Mao JH, Snijders AM. Genetic architecture of the acute and persistent immune cell response after radiation exposure. CELL GENOMICS 2023; 3:100422. [PMID: 38020972 PMCID: PMC10667298 DOI: 10.1016/j.xgen.2023.100422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/19/2023] [Accepted: 09/12/2023] [Indexed: 12/01/2023]
Abstract
Hematologic toxicity is a common side effect of multimodal cancer therapy. Nearly all animal studies investigating the causes of radiotherapy-induced hematologic toxicity use inbred strains with limited genetic diversity and do not reflect the diverse responses observed in humans. We used the population-based Collaborative Cross (CC) mouse resource to investigate the genetic architecture of the acute and persistent immune response after radiation exposure by measuring 22 immune parameters in 1,720 CC mice representing 35 strains. We determined relative acute and persistent radiation resistance scores at the individual strain level considering contributions from all immune parameters. Genome-wide association analysis identified quantitative trait loci associated with baseline and radiation responses. A cross-species radiation resistance score predicted recurrence-free survival in medulloblastoma patients. We present a community resource of immune parameters and genome-wide association analyses before and after radiation exposure for future investigations of the contributions of host genetics on radiosensitivity.
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Affiliation(s)
- Li He
- Department of Hematology, Zhongnan Hospital, Wuhan University, Wuhan, Hubei 430079, China
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Chenhan Zhong
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Medical Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Hang Chang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jamie L. Inman
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Susan E. Celniker
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Comparative Biochemistry Program, University of California Berkeley, Berkeley, CA 94720, USA
| | | | - Kevin X. Liu
- Department of Radiation Oncology, Brigham and Women’s Hospital, Dana-Farber Cancer Institute, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Daphne Haas-Kogan
- Department of Radiation Oncology, Brigham and Women’s Hospital, Dana-Farber Cancer Institute, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Shannon M. MacDonald
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - David W. Threadgill
- Texas A&M Institute for Genome Sciences and Society, Texas A&M University, College Station, TX 77843, USA
- Departments of Nutrition and Cell Biology and Genetics, Texas A&M University, College Station, TX 77843, USA
| | - Scott C. Kogan
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Comparative Biochemistry Program, University of California Berkeley, Berkeley, CA 94720, USA
| | - Antoine M. Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Comparative Biochemistry Program, University of California Berkeley, Berkeley, CA 94720, USA
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Jin X, Shi G. Cauchy combination methods for the detection of gene-environment interactions for rare variants related to quantitative phenotypes. Heredity (Edinb) 2023; 131:241-252. [PMID: 37481617 PMCID: PMC10539363 DOI: 10.1038/s41437-023-00640-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 07/09/2023] [Accepted: 07/12/2023] [Indexed: 07/24/2023] Open
Abstract
The characterization of gene-environment interactions (GEIs) can provide detailed insights into the biological mechanisms underlying complex diseases. Despite recent interest in GEIs for rare variants, published GEI tests are underpowered for an extremely small proportion of causal rare variants in a gene or a region. By extending the aggregated Cauchy association test (ACAT), we propose three GEI tests to address this issue: a Cauchy combination GEI test with fixed main effects (CCGEI-F), a Cauchy combination GEI test with random main effects (CCGEI-R), and an omnibus Cauchy combination GEI test (CCGEI-O). ACAT was applied to combine p values of single-variant GEI analyses to obtain CCGEI-F and CCGEI-R and p values of multiple GEI tests were combined in CCGEI-O. Through numerical simulations, for small numbers of causal variants, CCGEI-F, CCGEI-R and CCGEI-O provided approximately 5% higher power than the existing GEI tests INT-FIX and INT-RAN; however, they had slightly higher power than the existing GEI test TOW-GE. For large numbers of causal variants, although CCGEI-F and CCGEI-R exhibited comparable or slightly lower power values than the competing tests, the results were still satisfactory. Among all simulation conditions evaluated, CCGEI-O provided significantly higher power than that of competing GEI tests. We further applied our GEI tests in genome-wide analyses of systolic blood pressure or diastolic blood pressure to detect gene-body mass index (BMI) interactions, using whole-exome sequencing data from UK Biobank. At a suggestive significance level of 1.0 × 10-4, KCNC4, GAR1, FAM120AOS and NT5C3B showed interactions with BMI by our GEI tests.
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Affiliation(s)
- Xiaoqin Jin
- State Key Laboratory of Integrated Services Networks, Xidian University, 2 South Taibai Road, Xi'an, Shaanxi, 710071, China.
| | - Gang Shi
- State Key Laboratory of Integrated Services Networks, Xidian University, 2 South Taibai Road, Xi'an, Shaanxi, 710071, China
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Baker BH, Zhang S, Simon JM, McLarnan SM, Chung WK, Pearson BL. Environmental carcinogens disproportionally mutate genes implicated in neurodevelopmental disorders. Front Neurosci 2023; 17:1106573. [PMID: 37599994 PMCID: PMC10435087 DOI: 10.3389/fnins.2023.1106573] [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: 11/23/2022] [Accepted: 07/17/2023] [Indexed: 08/22/2023] Open
Abstract
Introduction De novo mutations contribute to a large proportion of sporadic psychiatric and developmental disorders, yet the potential role of environmental carcinogens as drivers of causal de novo mutations in neurodevelopmental disorders is poorly studied. Methods To explore environmental mutation vulnerability of disease-associated gene sets, we analyzed publicly available whole genome sequencing datasets of mutations in human induced pluripotent stem cell clonal lines exposed to 12 classes of environmental carcinogens, and human lung cancers from individuals living in highly polluted regions. We compared observed rates of exposure-induced mutations in disease-related gene sets with the expected rates of mutations based on control genes randomly sampled from the genome using exact binomial tests. To explore the role of sequence characteristics in mutation vulnerability, we modeled the effects of sequence length, gene expression, and percent GC content on mutation rates of entire genes and gene coding sequences using multivariate Quasi-Poisson regressions. Results We demonstrate that several mutagens, including radiation and polycyclic aromatic hydrocarbons, disproportionately mutate genes related to neurodevelopmental disorders including autism spectrum disorders, schizophrenia, and attention deficit hyperactivity disorder. Other disease genes including amyotrophic lateral sclerosis, Alzheimer's disease, congenital heart disease, orofacial clefts, and coronary artery disease were generally not mutated more than expected. Longer sequence length was more strongly associated with elevated mutations in entire genes compared with mutations in coding sequences. Increased expression was associated with decreased coding sequence mutation rate, but not with the mutability of entire genes. Increased GC content was associated with increased coding sequence mutation rates but decreased mutation rates in entire genes. Discussion Our findings support the possibility that neurodevelopmental disorder genetic etiology is partially driven by a contribution of environment-induced germ line and somatic mutations.
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Affiliation(s)
- Brennan H. Baker
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Shaoyi Zhang
- Master of Public Health Program, Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Jeremy M. Simon
- Department of Genetics and Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Sarah M. McLarnan
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Wendy K. Chung
- Department of Pediatrics and Medicine, Columbia University Irving Medical Center, New York, NY, United States
| | - Brandon L. Pearson
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, United States
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Singh S, Singh N, Baranwal M, Sharma S. Structural, functional analysis and association of MSH6 rs1800932, rs1042821 polymorphisms with clinical outcome in North Indian lung cancer patients treated with platinum-based doublet chemotherapy. Am J Med Sci 2022; 364:735-745. [PMID: 35868444 DOI: 10.1016/j.amjms.2022.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 03/03/2022] [Accepted: 07/15/2022] [Indexed: 01/25/2023]
Abstract
BACKGROUND In this study, we have done structural and functional analysis of rs1800932 rs1042821 polymorphisms and tried to estimate any association of these polymorphisms with clinical outcomes in north Indian lung cancer patients. METHODS Genotyping of 500 lung cancer patients was completed utilizing PCR-RFLP (Polymerase chain reaction- Restriction fragment length polymorphism). MedCalc statistical software was used to calculate adjusted and unadjusted odds ratios. Various computational tools like SIFT PROVEAN are used for functional analysis. Structural analysis was completed via MODELLER and CHIMERA. RESULTS In our study, patients suffering from small cell lung cancer (SCLC) and harboring heterozygous genotype (AG) for MSH6 (rs1800932) polymorphism have reported a significant increase in median survival time (MST) (20.6 vs. 7.6 months, p = 0.03). Furthermore, for MSH6 rs1042821 polymorphism, patients undergoing docetaxel and carbo/cisplatin combination chemotherapeutic regimen and carrying heterogeneous genotype (CT) reported a significant increase in MST (16.6 vs.8.36 months, p = 0.03) and a corresponding decrease in hazard ratio 0.42 (95% CI= 0.18-1.03). Structural and Functional analysis of rs1042821 polymorphism revealed that it is present in the non-coding region of MSH6 protein and is significantly associated with increased overall survival. CONCLUSIONS These results suggest that MSH6 rs1800932 rs1042821 polymorphisms are involved in increasing the overall survival of lung cancer patients, further confirmed by computational analysis.
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Affiliation(s)
- Sidhartha Singh
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, Punjab, 147004, India
| | - Navneet Singh
- Department of Pulmonary Medicine, Post Graduate Institute of Medical Education & Research (PGIMER), Chandigarh, India
| | - Manoj Baranwal
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, Punjab, 147004, India
| | - Siddharth Sharma
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, Punjab, 147004, India.
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Sharma S, Singh S, Singh N, Baranwal M. Association of MLH1-93G>A polymorphisms toward lung cancer susceptibility and its association with clinical outcome in North Indian patients treated with platinum-based chemotherapy. J Cancer Res Ther 2022; 19:S0. [PMID: 37147951 DOI: 10.4103/jcrt.jcrt_465_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Background Lung cancer is one of the most prevalent and main causes of malignancy-related deaths worldwide, especially in developed countries. Epidemiological studies have demonstrated that individuals having alterations in a particular gene may have a high risk of developing certain types of cancer. Materials and Methods In the present study, 500 Indian lung cancer patients and 500 healthy controls were enrolled. Polymerase chain reaction-restriction fragment length polymorphism method was used to identify the genotype of enrolled individuals and MedCalc statistical package was used for carrying out statistical analysis. Results In this study, we found a reduced risk of developing adenocarcinoma in patients harboring variant (P = 0.0007) and combined type genotype (P = 0.008), whereas an increased risk for small-cell lung carcinoma (SCLC) development for those subject harboring GA genotypes (P = 0.03) was also observed. Further, heterozygous type and combined type genotype of heavy smokers for MLH1 polymorphism reported a 2-fold (P = 0.001) and 1.8-fold increased risk toward lung cancer development, respectively (P = 0.007). In case of females, the subjects harboring a variant allele have a significantly reduced risk for lung cancer development (P = 0.0001). For MLH1 polymorphism, reduced risk of developing tumor to T3 or T4 stage was observed (P = 0.04). Moreover, this is the first study reporting overall survival (OS) association for north Indian lung cancer patients with platinum-based doublet chemotherapy; for docetaxel, a three-fold increase in hazard ratio and corresponding low median standard survival time (8.4 months) for mutant and combined type genotype (P = 0.04) was observed. Conclusions These results suggest that MLH1-93G>A polymorphism is involved in modulating the risk toward lung cancer. Our study also concluded a negative association of OS in patients undergoing carboplatin/cisplatin and docetaxel chemotherapy.
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Mc Auley MT. DNA methylation in genes associated with the evolution of ageing and disease: A critical review. Ageing Res Rev 2021; 72:101488. [PMID: 34662746 DOI: 10.1016/j.arr.2021.101488] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 09/30/2021] [Accepted: 10/12/2021] [Indexed: 12/28/2022]
Abstract
Ageing is characterised by a physical decline in biological functioning which results in a progressive risk of mortality with time. As a biological phenomenon, it is underpinned by the dysregulation of a myriad of complex processes. Recently, however, ever-increasing evidence has associated epigenetic mechanisms, such as DNA methylation (DNAm) with age-onset pathologies, including cancer, cardiovascular disease, and Alzheimer's disease. These diseases compromise healthspan. Consequently, there is a medical imperative to understand the link between epigenetic ageing, and healthspan. Evolutionary theory provides a unique way to gain new insights into epigenetic ageing and health. This review will: (1) provide a brief overview of the main evolutionary theories of ageing; (2) discuss recent genetic evidence which has revealed alleles that have pleiotropic effects on fitness at different ages in humans; (3) consider the effects of DNAm on pleiotropic alleles, which are associated with age related disease; (4) discuss how age related DNAm changes resonate with the mutation accumulation, disposable soma and programmed theories of ageing; (5) discuss how DNAm changes associated with caloric restriction intersect with the evolution of ageing; and (6) conclude by discussing how evolutionary theory can be used to inform investigations which quantify age-related DNAm changes which are linked to age onset pathology.
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Affiliation(s)
- Mark Tomás Mc Auley
- Faculty of Science and Engineering, University of Chester, Exton Park, Chester CH1 4BJ, UK.
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Walia HK, Singh N, Sharma S. MTHFR polymorphism as a predictive biomarker for gastrointestinal and hematological toxicity in North Indian adenocarcinoma patients. J Chemother 2021; 34:326-340. [PMID: 34730065 DOI: 10.1080/1120009x.2021.1997008] [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: 10/19/2022]
Abstract
In the present study, we investigated the relationship between the methylenetetrahydrofolate reductase (MTHFR) C677T and A1298C polymorphisms and overall survival, toxicity and treatment response for North Indian adenocarcinoma patients. The polymorphisms of MTHFR gene in north Indian adenocarcinoma patients were assessed by PCR-RFLP. Our data observed that patients with mutant genotype (C/C) for 1298 A>C) polymorphism showed higher trend of median survival time compared to patients bearing the wild type genotype (A/A) (MST= 13.93 vs. 7.97, p=0.12). Further, we observed patients with the heterozygous genotype for A1298C polymorphism had 12-fold risk of diarrhea (AOR =12.54, 95% CI = 1.54-101.86, p=0.018). The patients with heterozygous genotype (CT) of the C677T polymorphism had 5.34-fold increased risk of developing neutropenia (AOR=5.34, 95% CI=1.49-19.06, p=0.009). Our results suggest that MTHFR polymorphisms are associated with hematological toxicity. MTHFR polymorphism might impact the development of pemetrexed and platinum-related toxicities but not as a clinical predictor of efficiency.
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Affiliation(s)
- Harleen Kaur Walia
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, India
| | - Navneet Singh
- Department of Pulmonary Medicine, Post Graduate Institute of Medical Education & Research (PGIMER), Chandigarh, India
| | - Siddharth Sharma
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, India
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Zhou J, Li S, Zhou Y, Sheng X. A two-stage testing strategy for detecting genes×environment interactions in association studies. G3-GENES GENOMES GENETICS 2021; 11:6312559. [PMID: 34568910 PMCID: PMC8496220 DOI: 10.1093/g3journal/jkab220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 06/22/2021] [Indexed: 11/15/2022]
Abstract
Identifying gene×environment (G×E) interactions, especially when rare variants are included in genome-wide association studies, is a major challenge in statistical genetics. However, the detection of G×E interactions is very important for understanding the etiology of complex diseases. Although currently some statistical methods have been developed to detect the interactions between genes and environment, the detection of the interactions for the case of rare variants is still limited. Therefore, it is particularly important to develop a new method to detect the interactions between genes and environment for rare variants. In this study, we extend an existing method of adaptive combination of P-values (ADA) and design a novel strategy (called iSADA) for testing the effects of G×E interactions for rare variants. We propose a new two-stage test to detect the interactions between genes and environment in a certain region of a chromosome or even for the whole genome. First, the score statistic is used to test the associations between trait value and the interaction terms of genes and environment and obtain the original P-values. Then, based on the idea of the ADA method, we further construct a full test statistic via the P-values of the preliminary tests in the first stage, so that we can comprehensively test the interactions between genes and environment in the considered genome region. Simulation studies are conducted to compare our proposed method with other existing methods. The results show that the iSADA has higher power than other methods in each case. A GAW17 data set is also applied to illustrate the applicability of the new method.
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Affiliation(s)
- Jiabin Zhou
- Department of Statistics, School of Mathematical Sciences, Heilongjiang University, Harbin 150080, China
| | - Shitao Li
- Department of Basic Course, Shenyang University of Technology, Liaoyang 111000, China
| | - Ying Zhou
- Department of Statistics, School of Mathematical Sciences, Heilongjiang University, Harbin 150080, China
| | - Xiaona Sheng
- School of Information Engineering, Harbin University, Harbin 150086, China
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Matejcic M, Shaban HA, Quintana MW, Schumacher FR, Edlund CK, Naghi L, Pai RK, Haile RW, Levine AJ, Buchanan DD, Jenkins MA, Figueiredo JC, Rennert G, Gruber SB, Li L, Casey G, Conti DV, Schmit SL. Rare Variants in the DNA Repair Pathway and the Risk of Colorectal Cancer. Cancer Epidemiol Biomarkers Prev 2021; 30:895-903. [PMID: 33627384 DOI: 10.1158/1055-9965.epi-20-1457] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/14/2020] [Accepted: 02/22/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Inherited susceptibility is an important contributor to colorectal cancer risk, and rare variants in key genes or pathways could account in part for the missing proportion of colorectal cancer heritability. METHODS We conducted an exome-wide association study including 2,327 cases and 2,966 controls of European ancestry from three large epidemiologic studies. Single variant associations were tested using logistic regression models, adjusting for appropriate study-specific covariates. In addition, we examined the aggregate effects of rare coding variation at the gene and pathway levels using Bayesian model uncertainty techniques. RESULTS In an exome-wide gene-level analysis, we identified ST6GALNAC2 as the top associated gene based on the Bayesian risk index (BRI) method [summary Bayes factor (BF)BRI = 2604.23]. A rare coding variant in this gene, rs139401613, was the top associated variant (P = 1.01 × 10-6) in an exome-wide single variant analysis. Pathway-level association analyses based on the integrative BRI (iBRI) method found extreme evidence of association with the DNA repair pathway (BFiBRI = 17852.4), specifically with the nonhomologous end joining (BFiBRI = 437.95) and nucleotide excision repair (BFiBRI = 36.96) subpathways. The iBRI method also identified RPA2, PRKDC, ERCC5, and ERCC8 as the top associated DNA repair genes (summary BFiBRI ≥ 10), with rs28988897, rs8178232, rs141369732, and rs201642761 being the most likely associated variants in these genes, respectively. CONCLUSIONS We identified novel variants and genes associated with colorectal cancer risk and provided additional evidence for a role of DNA repair in colorectal cancer tumorigenesis. IMPACT This study provides new insights into the genetic predisposition to colorectal cancer, which has potential for translation into improved risk prediction.
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Affiliation(s)
- Marco Matejcic
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida
| | - Hiba A Shaban
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida
| | | | - Fredrick R Schumacher
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio.,Seidman Cancer Center, University Hospitals, Cleveland, Ohio
| | - Christopher K Edlund
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Leah Naghi
- Department of Medicine, Montefiore Medical Center, Albert Einstein College of Medicine, New York, New York
| | - Rish K Pai
- Department of Laboratory Medicine and Pathology, Mayo Clinic Arizona, Scottsdale, Arizona
| | - Robert W Haile
- Department of Medicine, Research Center for Health Equity, Cedars-Sinai Samuel Oschin Comprehensive Cancer Center, Los Angeles, California
| | - A Joan Levine
- Department of Medicine, Research Center for Health Equity, Cedars-Sinai Samuel Oschin Comprehensive Cancer Center, Los Angeles, California
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia.,Victorian Comprehensive Cancer Centre, University of Melbourne, Centre for Cancer Research, Parkville, Victoria, Australia.,Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Jane C Figueiredo
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Gad Rennert
- Clalit National Cancer Control Center, Carmel Medical Center and Technion Faculty of Medicine, Haifa, Israel
| | | | - Li Li
- Department of Family Medicine, University of Virginia, Charlottesville, Virginia
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - David V Conti
- Department of Preventive Medicine, Division of Biostatistics, University of Southern California, Los Angeles, California
| | - Stephanie L Schmit
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida. .,Department of Gastrointestinal Oncology, Moffitt Cancer Center, Tampa, Florida
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10
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The potential of long noncoding RNAs for precision medicine in human cancer. Cancer Lett 2020; 501:12-19. [PMID: 33359450 DOI: 10.1016/j.canlet.2020.11.040] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/13/2020] [Accepted: 11/26/2020] [Indexed: 12/20/2022]
Abstract
Precision medicine promises to better classify patients by individual clinical and biological biomarkers, which may provide an accurate assessment of disease risk, diagnosis, prognosis and treatment response. Cancer frequently displays substantial inter-tumor and intra-tumor heterogeneity and hence oncology is well suited for application of precision approaches. Recent studies have demonstrated that dysregulated lncRNAs play pivotal roles in tumor heterogeneity. In this review, attention is focused on the potential applications of lncRNAs as biomarker candidates for cancer risk evaluation, detection, surveillance and prognosis. LncRNAs are often stable in clinical samples and easily detected. The functional implications and therapeutic potential of targeting lncRNAs in human cancer are further discussed. Finally, existing deficiencies and future perspectives in translating fundamental lncRNA knowledge into clinical practice are highlighted.
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Røe OD. Democratic and ethical problem of lung cancer screening: exclusion of true high-risk populations. Can it be fixed? Yes. BMJ Open Respir Res 2020; 7:7/1/e000811. [PMID: 33323364 PMCID: PMC7745524 DOI: 10.1136/bmjresp-2020-000811] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 11/29/2020] [Accepted: 11/30/2020] [Indexed: 01/01/2023] Open
Abstract
Screening a population for a potentially deadly disease, the ultimate goal must be to prevent morbidity and mortality from this disease for the whole population. Unlike breast cancer or cervical cancer screening, where all women are screened after a certain age, CT screening for lung cancer has been based on selection of putative high-risk individuals based on age and smoking cut-off values. The type of selection used leaves too many high-risk individuals behind. The solution is to use only validated risk prediction models for selection.
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Affiliation(s)
- Oluf Dimitri Røe
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway .,Cancer Clinic, Levanger Hospital, Nord-Trondelag Health Trust, Levanger, Norway
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12
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Dai P, Li J, Li W, Qin X, Wu X, Di W, Zhang Y. Genetic polymorphisms and pancreatic cancer risk: A PRISMA-compliant systematic review and meta-analysis. Medicine (Baltimore) 2019; 98:e16541. [PMID: 31393355 PMCID: PMC6708677 DOI: 10.1097/md.0000000000016541] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 06/10/2019] [Accepted: 06/27/2019] [Indexed: 01/09/2023] Open
Abstract
BACKGROUNDS Previous investigations yielded inconsistent results for the associations between pancreatic cancer (PC) risk and genetic polymorphisms. The study aimed to perform a systematic review and meta-analysis of studies exploring association of some genetic polymorphisms and PC risk. METHODS We systematically searched on PubMed and Web of Science for association of genetic polymorphisms and PC risk published from 1969 to January 2019. We computed the multivariate odd ratio (OR) and 95% confidence intervals (CI), comparing different genetic types. RESULTS The present meta-analysis showed significant associations between deoxyribonucleic acid (DNA) repair gene (X-ray repair cross-complementing group 1 (XRCC1) Arg399GIn and Arg194Trp, excision repair cross complementation 1 (ERCC1) rs11615 and rs3212986, ERCC2 rs13181) polymorphisms and PC risk. CONCLUSIONS Because of the limited sample size and ethnicity enrolled in the present meta-analysis, further larger scaled studies should be performed to demonstrate the association.
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Affiliation(s)
- Peng Dai
- Department of Hepato-Biliary-Pancreatic Surgery, Shanxi Provincial People's Hospital Affiliated to Shanxi Medical University
| | - Jing Li
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Shanxi Medical University
| | - Weibin Li
- Department of General Surgery, Shanxi Academy of Medical Sciences, Shanxi Dayi Hospital, Taiyuan, Shanxi, China
| | - Xueliang Qin
- Department of Hepato-Biliary-Pancreatic Surgery, Shanxi Provincial People's Hospital Affiliated to Shanxi Medical University
| | - Xiaoyong Wu
- Department of Hepato-Biliary-Pancreatic Surgery, Shanxi Provincial People's Hospital Affiliated to Shanxi Medical University
| | - Weidong Di
- Department of Hepato-Biliary-Pancreatic Surgery, Shanxi Provincial People's Hospital Affiliated to Shanxi Medical University
| | - Yanzhong Zhang
- Department of Hepato-Biliary-Pancreatic Surgery, Shanxi Provincial People's Hospital Affiliated to Shanxi Medical University
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Kumar A, Misra BB. Challenges and Opportunities in Cancer Metabolomics. Proteomics 2019; 19:e1900042. [PMID: 30950571 DOI: 10.1002/pmic.201900042] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/22/2019] [Indexed: 12/23/2022]
Abstract
Challenges in metabolomics for a given spectrum of disease are more or less comparable, ranging from the accurate measurement of metabolite abundance, compound annotation, identification of unknown constituents, and interpretation of untargeted and analysis of high throughput targeted metabolomics data leading to the identification of biomarkers. However, metabolomics approaches in cancer studies specifically suffer from several additional challenges and require robust ways to sample the cells and tissues in order to tackle the constantly evolving cancer landscape. These constraints include, but are not limited to, discriminating the signals from given cell types and those that are cancer specific, discerning signals that are systemic and confounded, cell culture-based challenges associated with cell line identities and media standardizations, the need to look beyond Warburg effects, citrate cycle, lactate metabolism, and identifying and developing technologies to precisely and effectively sample and profile the heterogeneous tumor environment. This review article discusses some of the current and pertinent hurdles in cancer metabolomics studies. In addition, it addresses some of the most recent and exciting developments in metabolomics that may address some of these issues. The aim of this article is to update the oncometabolomics research community about the challenges and potential solutions to these issues.
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Affiliation(s)
- Ashish Kumar
- Department of Genetics, Texas Biomedical Research Institute, 7620 NW Loop 410, San Antonio, TX, 78227, USA
| | - Biswapriya B Misra
- Center for Precision Medicine, Department of Internal Medicine, Section on Molecular Medicine, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC, 27157, USA
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14
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Lawania S, Singh N, Behera D, Sharma S. XPG polymorphisms and their association with lung cancer susceptibility, overall survival and response in North Indian patients treated with platinum-based doublet chemotherapy. Future Oncol 2018; 15:151-165. [PMID: 30522358 DOI: 10.2217/fon-2018-0408] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
AIM The study investigates association of XPG polymorphism with lung cancer susceptibility, overall survival and clinical outcomes in North Indian population. RESULTS A significant protective effect was observed for 2228959 C/A polymorphism with lung cancer and its histological subtypes. An increased hazard ratio (HR) was observed in 17655 G/C variant among small-cell lung carcinoma patients with mutant genotype (HR: 2.55; p = 0.05). Individuals treated with irinotecan-cisplatin/carboplatin regimen showed a longer survival time (HR1: 0.04; median survival time [MST]: 32.5 months). Subjects treated with pemetrexed-cisplatin/carboplain regimen were associated with higher mortality rate in lung cancer patients (HR1: 1.83; MST: 9.13 months). CONCLUSION 2228959 C/A polymorphism contributes to protective effect in lung cancer patients. 2228959 C/A polymorphism might be associated with favorable prognosis in lung cancer risk.
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Affiliation(s)
- Shweta Lawania
- Department of Biotechnology, Thapar University, Punjab 147002, India
| | - Navneet Singh
- Department of Pulmonary Medicine, Post Graduate Institute of Medical & Educational Research (PGIMER), Sector 14, Chandigarh, India
| | - Digambar Behera
- Department of Pulmonary Medicine, Post Graduate Institute of Medical & Educational Research (PGIMER), Sector 14, Chandigarh, India
| | - Siddharth Sharma
- Department of Biotechnology, Thapar University, Punjab 147002, India
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Peltier E, Sharma V, Martí Raga M, Roncoroni M, Bernard M, Jiranek V, Gibon Y, Marullo P. Dissection of the molecular bases of genotype x environment interactions: a study of phenotypic plasticity of Saccharomyces cerevisiae in grape juices. BMC Genomics 2018; 19:772. [PMID: 30409183 PMCID: PMC6225642 DOI: 10.1186/s12864-018-5145-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 10/05/2018] [Indexed: 11/17/2022] Open
Abstract
Background The ability of a genotype to produce different phenotypes according to its surrounding environment is known as phenotypic plasticity. Within different individuals of the same species, phenotypic plasticity can vary greatly. This contrasting response is caused by gene-by-environment interactions (GxE). Understanding GxE interactions is particularly important in agronomy, since selected breeds and varieties may have divergent phenotypes according to their growing environment. Industrial microbes such as Saccharomyces cerevisiae are also faced with a large range of fermentation conditions that affect their technological properties. Finding the molecular determinism of such variations is a critical task for better understanding the genetic bases of phenotypic plasticity and can also be helpful in order to improve breeding methods. Results In this study we implemented a QTL mapping program using two independent cross (~ 100 progeny) in order to investigate the molecular basis of yeast phenotypic response in a wine fermentation context. Thanks to whole genome sequencing approaches, both crosses were genotyped, providing saturated genetic maps of thousands of markers. Linkage analyses allowed the detection of 78 QTLs including 21 with significant interaction with the environmental conditions. Molecular dissection of a major QTL demonstrated that the sulfite pump Ssu1p has a pleiotropic effect and impacts the phenotypic plasticity of several traits. Conclusions The detection of QTLs and their interactions with environment emphasizes the complexity of yeast industrial traits. The validation of the interaction of SSU1 allelic variants with the nature of the fermented juice increases knowledge about the impact of the sulfite pump during fermentation. All together these results pave the way for exploiting and deciphering the genetic determinism of phenotypic plasticity. Electronic supplementary material The online version of this article (10.1186/s12864-018-5145-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Emilien Peltier
- Univ. Bordeaux, ISVV, Unité de recherche OEnologie EA 4577, USC 1366 INRA, Bordeaux INP, Villenave d'Ornon, France. .,Biolaffort, Bordeaux, France.
| | - Vikas Sharma
- Univ. Bordeaux, ISVV, Unité de recherche OEnologie EA 4577, USC 1366 INRA, Bordeaux INP, Villenave d'Ornon, France
| | - Maria Martí Raga
- Univ. Bordeaux, ISVV, Unité de recherche OEnologie EA 4577, USC 1366 INRA, Bordeaux INP, Villenave d'Ornon, France.,Departament de Bioquímica i Biotecnologia, Facultat d'Enologia de Tarragona, Tarragona, Spain
| | - Miguel Roncoroni
- Wine Science Programme, University of Auckland, Private Bag, Auckland, 92019, New Zealand
| | - Margaux Bernard
- Univ. Bordeaux, ISVV, Unité de recherche OEnologie EA 4577, USC 1366 INRA, Bordeaux INP, Villenave d'Ornon, France.,Biolaffort, Bordeaux, France
| | - Vladimir Jiranek
- Department of Wine and Food Science, University of Adelaide, Urrbrae, South Australia, 5064, Australia
| | - Yves Gibon
- INRA, University of Bordeaux, UMR 1332 Fruit Biology and Pathology, F-33883, Villenave d'Ornon, France
| | - Philippe Marullo
- Univ. Bordeaux, ISVV, Unité de recherche OEnologie EA 4577, USC 1366 INRA, Bordeaux INP, Villenave d'Ornon, France.,Biolaffort, Bordeaux, France
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Association of Casp3 microRNA Target Site (1049216) SNP With the Risk and Progress of Cervical Squamous Cell Carcinoma. Int J Gynecol Cancer 2018; 27:206-213. [PMID: 28114230 DOI: 10.1097/igc.0000000000000881] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
OBJECTIVE In the present study, we investigated the relationship between the single-nucleotide polymorphism (SNP) of caspase-3 rs1049216 (C > T), a miRNA target site, and the risk and progression of cervical cancer. MATERIALS AND METHODS Using polymerase chain reaction-restriction fragment length polymorphism, we evaluated the genotype and distribution of caspase-3 rs1049216 in 515 patients with cervical squamous cell cancer and 415 controls. In additional experiments, we transfected luciferase reporter plasmids carrying T or C allele and/or miRNA mimics into the human cervical cell lines (HeLa and C-33A) to analyze its roles in the regulation of caspase-3 expression. By immunohistochemistry, the protein level of caspase-3 expression was examined in tumor tissues from 515 patients with cervical squamous cell cancer. RESULTS We found that the TT genotype of caspase-3 rs1049216 conferred a significantly decreased risk of cervical cancer (adjusted odds ratio, 0.35; 95% confidence interval, 0.154-0.581) and may be associated with the progression of this cancer. Although the expression of caspase-3 in the TT genotype was higher than that in CC/CT genotype in peripheral blood mononuclear cells and tumor tissues. Additional luciferase analysis showed that the rs1049216 variant T allele was associated with significantly higher luciferase activity, compared with the C allele in the transfected cells, and when cotransfected with miRNAs, miRNA-181a could downregulate the luciferase activity in the cells that transfected the construct containing C allele, compared with T allele, which had not happened in the presence of other miRNAs selected. CONCLUSIONS These data indicate that through upregulating the expression of caspase-3, the TT genotype of caspase-3 rs1049216 can be associated with not only the risk of cervical cancer but also the progression of this cancer.
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Yan Z, Tong X, Ma Y, Liu S, Yang L, Yang X, Yang X, Bai M, Fan H. Association between ATM gene polymorphisms, lung cancer susceptibility and radiation-induced pneumonitis: a meta-analysis. BMC Pulm Med 2017; 17:205. [PMID: 29246212 PMCID: PMC5731205 DOI: 10.1186/s12890-017-0555-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 12/07/2017] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Previous studies have suggested that DNA double-strand break (DSB) repair is an important protective pathway after damage. The ataxia telangiectasia mutated (ATM) gene plays an important role in the DNA DSB repair pathway. DNA damage is a major cytotoxic effect that can be caused by radiation, and the ability to repair DNA after damage varies among different tissues. Impaired DNA repair pathways are associated with high sensitivity to radiation exposure. Hence, ATM gene polymorphisms are thought to influence the risk of cancer and radiation-induced pneumonitis (RP) risk in cancer patients treated with radiotherapy. However, the results of previous studies are inconsistent. We therefore conducted this comprehensive meta-analysis. METHODS A systematic literature search was performed in the PubMed, Embase, China National Knowledge Internet (CNKI) and Wanfang databases to identify studies that investigated the association between the ATM gene polymorphisms and both lung cancer and RP radiotherapy-treated lung cancer (the last search was conducted on Dec.10, 2015). The odds ratio (OR) and 95% confidence interval (CI) were used to investigate the strength of these relationships. Funnel plots and Begg's and Egger's tests were conducted to assess the publication bias. All analyses were performed in STATA 13.0 software. RESULTS Ten eligible case-control studies (4731 cases and 5142 controls) on lung cancer susceptibility and four (192 cases and 772 controls) on RP risk were included. The results of the overall and subgroup analyses indicated that in the ATM gene, the rs189037 (-111G > A, -4519G > A), rs664677 (44831C > T, 49238C > T) and rs664143 (131,717 T > G) polymorphisms were significantly associated with lung cancer susceptibility (OR = 1.21, 95% CI = 1.04-1.39, P = 0.01; OR = 1.26, 95% CI = 1.06-1.49, P = 0.01; OR = 1.43, 95% CI = 1.15-1.78, P < 0.01). Additionally, the rs189037 variant was significantly associated with RP risk (OR = 1.74, 95% CI = 1.02-2.97, P = 0.04). No publication bias was found in the funnel plots, Begg's tests or Egger's tests. CONCLUSIONS The results indicate that the ATM rs189037, rs664677 and rs664143 gene polymorphisms are risk factors for lung cancer, while the ATM rs189037 variant was significantly associated with RP risk.
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Affiliation(s)
- Zhipeng Yan
- Department of Respiratory Medicine and Critical Care Medicine, West China Hospital/West China School of Medicine, Sichuan University, Guoxuexiang 37, Chengdu, 610041, China
| | - Xiang Tong
- Department of Respiratory Medicine and Critical Care Medicine, West China Hospital/West China School of Medicine, Sichuan University, Guoxuexiang 37, Chengdu, 610041, China
| | - Yao Ma
- Department of Respiratory Medicine and Critical Care Medicine, West China Hospital/West China School of Medicine, Sichuan University, Guoxuexiang 37, Chengdu, 610041, China.,Department of Internal Medicine, No.4 West China Teaching Hospital, Sichuan University, Renming South Road 3rd Section 18, Chengdu, 610041, China
| | - Sitong Liu
- Department of Respiratory Medicine and Critical Care Medicine, West China Hospital/West China School of Medicine, Sichuan University, Guoxuexiang 37, Chengdu, 610041, China
| | - Lingjing Yang
- Department of Respiratory Medicine and Critical Care Medicine, West China Hospital/West China School of Medicine, Sichuan University, Guoxuexiang 37, Chengdu, 610041, China.,Department of Respiration, East Branch, Sichuan Provincial People's Hospital, Sichuan Academy of Medical Science, No. 585 Honghe North Road, Chengdu, 610110, China
| | - Xin Yang
- Department of Respiratory Medicine and Critical Care Medicine, West China Hospital/West China School of Medicine, Sichuan University, Guoxuexiang 37, Chengdu, 610041, China
| | - Xue Yang
- Department of Respiratory Medicine and Critical Care Medicine, West China Hospital/West China School of Medicine, Sichuan University, Guoxuexiang 37, Chengdu, 610041, China
| | - Min Bai
- Department of Respiratory Medicine and Critical Care Medicine, West China Hospital/West China School of Medicine, Sichuan University, Guoxuexiang 37, Chengdu, 610041, China
| | - Hong Fan
- Department of Respiratory Medicine and Critical Care Medicine, West China Hospital/West China School of Medicine, Sichuan University, Guoxuexiang 37, Chengdu, 610041, China.
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18
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Fang Z, Wu Y, Zhang N. Association between CYP2E1 genetic polymorphisms and urinary cancer risk: a meta-analysis. Oncotarget 2017; 8:86853-86864. [PMID: 29156840 PMCID: PMC5689730 DOI: 10.18632/oncotarget.20993] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 08/29/2017] [Indexed: 12/19/2022] Open
Abstract
Objective Studies investigating the contribution of Cytochrome P4502E1 (CYP2E1) polymorphisms to the etiology of urinary cancer draw inconsistent conclusions. Thus, we performed a meta-analysis to evaluate the association between CYP2E1 Rsa I/Pst I and Dra I polymorphisms and urinary cancer susceptibility. Materials and Methods Meta-analysis based on the eligible case-control studies that assess the association of CYP2E1 Rsa I/Pst I and Dra I polymorphisms with urinary cancer was conducted. Subgroup analyses based on ethnicity and cancer type were also carried out. Odds ratios (OR) and 95% confidence intervals (95% CI) were calculated to evaluate the strength of the associations between the two polymorphisms. Funnel plot and Begg’s test were used for publication bias diagnosis. Results We found decreased urinary cancer risk among subjects carrying CYP2E1 RsaI/PstI c1c2 + c2c2 genotype and c2 allele (OR = 0.73, 95% CI = 0.68–0.79 and OR = 0.79, 95% CI = 0.74–0.85, respectively), with 3,301 cases and 3,786 controls from 14 studies. We also observed a significant difference in c1c2 + c2c2 vs. c1c1 and c2 vs. c1 among Asians (OR = 0.68, 95% CI = 0.60–0.78 and OR = 0.75, 95% CI = 0.66–0.85, respectively). However, the meta-analysis based on 5 eligible studies showed no significant association between CYP2E1 Dra I polymorphism and urinary cancer susceptibility in either dominant model or the allele model. Conclusions Our meta-analysis concluded that CYP2E1 Rsa I/Pst I polymorphism correlates with urinary cancers risk in Asian population; while CYP2E1 Dra I polymorphism might be not significantly associated with the urinary cancer risks. Large and well-designed studies are needed to confirm these results.
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Affiliation(s)
- Zhiqing Fang
- Department of Urology, Qilu Hospital, Shandong University, Jinan, Shandong, China
| | - Yun Wu
- Department of Breast Surgery, Qilu Hospital, Shandong University, Jinan, Shandong, China
| | - Ning Zhang
- Department of Breast Surgery, Qilu Hospital, Shandong University, Jinan, Shandong, China
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19
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Single-nucleotide polymorphisms and haplotypes of vascular endothelial growth factor. GENE REPORTS 2017. [DOI: 10.1016/j.genrep.2017.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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20
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Wu Y, Lu ZP, Zhang JJ, Liu DF, Shi GD, Zhang C, Qin ZQ, Zhang JZ, He Y, Wu PF, Miao Y, Jiang KR. Association between ERCC2 Lys751Gln polymorphism and the risk of pancreatic cancer, especially among Asians: evidence from a meta-analysis. Oncotarget 2017; 8:50124-50132. [PMID: 28223548 PMCID: PMC5564835 DOI: 10.18632/oncotarget.15394] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 01/29/2017] [Indexed: 12/21/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) of Excision repair cross-complementing group 2 (ERCC2) gene are suspected to affect the risk of pancreatic cancer. Many studies have reported the association between ERCC2 Lys751Gln polymorphism (rs13181) and the susceptibility to pancreatic cancer, but the outcomes remained controversial. To comprehensively determine this association, we conducted a meta-analysis based on a total of eight studies. Evidence for this association was obtained from the PubMed, EMBASE, Web of Science and Chinese National Knowledge Infrastructure (CNKI) databases. In general, a significant association was found between ERCC2 rs13181 polymorphism and the susceptibility to pancreatic cancer in four genetic models [CC vs. AA: OR = 1.56, (95% CI: 1.28-1.90), P = 0.470; AC/CC vs. AA: OR=1.20, (95% CI: 1.06-1.36), P = 0.396; CC vs. AC/CC OR = 1.50; (95% CI: 1.24-1.81), P = 0.530; C vs. A: OR=1.22, (95%CI:1.11-1.34), P = 0.159]. Furthermore, stratified analyses by ethnicity indicated a significant association only in the Asian population. Our results indicate that the ERCC2 Lys751Gln polymorphism might be important in stimulating the development of pancreatic cancer, especially for Asians.
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Affiliation(s)
- Yang Wu
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Pancreas Institute, Nanjing Medical University, Nanjing, China
| | - Zi-Peng Lu
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Pancreas Institute, Nanjing Medical University, Nanjing, China
| | - Jing-Jing Zhang
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Pancreas Institute, Nanjing Medical University, Nanjing, China
| | - Dong-Fang Liu
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Pancreas Institute, Nanjing Medical University, Nanjing, China
| | - Guo-Dong Shi
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Pancreas Institute, Nanjing Medical University, Nanjing, China
| | - Chun Zhang
- Department of Digestive Diseases, Songjiang Branch Hospital of Shanghai First People's Hospital, Nanjing Medical University, Shanghai, China
| | - Zhi-Qiang Qin
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jian-Zhong Zhang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yuan He
- Pancreas Institute, Nanjing Medical University, Nanjing, China.,Department of Gastrointestinal Surgery, Huai'an Affiliated to Xuzhou Medical University and Huai'an Second People's Hospital, Huai'an, China
| | - Peng-Fei Wu
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Pancreas Institute, Nanjing Medical University, Nanjing, China
| | - Yi Miao
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Pancreas Institute, Nanjing Medical University, Nanjing, China
| | - Kui-Rong Jiang
- Pancreas Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Pancreas Institute, Nanjing Medical University, Nanjing, China
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Genetic Variants in the Promoter Region of miR-10b and the Risk of Breast Cancer. BIOMED RESEARCH INTERNATIONAL 2017; 2017:2352874. [PMID: 28691018 PMCID: PMC5485289 DOI: 10.1155/2017/2352874] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 05/14/2017] [Indexed: 01/05/2023]
Abstract
Variants in microRNA genes may affect their expression by interfering with the microRNA maturation process and may substantially contribute to the risk of breast cancer. Recent studies have identified miR-10b as an interesting candidate because of its close association with the metastatic behavior of breast cancer. However, the roles of miR-10b-related single nucleotide polymorphisms in breast cancer susceptibility remain unclear. This case-control study evaluated the associations between variants in the upstream transcription regulation region of miR-10b and the risk of breast cancer among Chinese women. Seven potentially functional SNPs were investigated using genotyping assays. The potential biological functions of the identified positive SNPs were further evaluated using in silico databases. We found that rs4078756, which was located at the promoter region of miR-10b, was significantly associated with breast cancer risk (rs4078756 AG/GG versus AA, adjusted odds ratio: 1.17, 95% confidence interval: 1.02-1.35). The other six single nucleotide polymorphisms exhibited negative associations. Based on the in silico prediction, rs4078756 potentially regulated miR-10b expression through promoter activation or repression. These findings indicate that a potentially functional SNP (rs4078756) in the promoter region of miR-10b may contribute to breast cancer susceptibility among Chinese women.
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Lawania S, Singh N, Behera D, Sharma S. XPC Polymorphism and Risk for Lung Cancer in North Indian Patients Treated with Platinum Based Chemotherapy and Its Association with Clinical Outcomes. Pathol Oncol Res 2017; 24:353-366. [PMID: 28540485 DOI: 10.1007/s12253-017-0252-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 05/08/2017] [Indexed: 10/19/2022]
Abstract
Xeroderma pigmentosum complementation group C plays an important role in the human repair system. As reported in previous studies its polymorphism are associated with lung cancer susceptibility. The purpose of this study is to investigate the association of XPC gene with lung cancer susceptibility, overall response and clinical outcomes amongst North Indians. A hospital based study of 370 lung cancer cases and 370 healthy controls was conducted and genotypes were determined using PCR-RFLP assay. Results were assessed using logistic linear regression adjusted for age, sex and smoking status. Survival analysis was conducted using Kaplan-Meier survival analysis and Cox regression analysis. The treatment outcomes of 167 lung cancer patients treated with platinum based chemotherapy were evaluated.The mutant genotypic variant of XPC Lys939Gln has been associated with elevated risk of lung cancer(OR:2.30;95%CI:1.41-3.73;p=0.0007) whereas XPC Ala499Val showed a highly protective effect (OR:0.25;95%CI:0.10-0.63;p=0.003). The mutant genotype of XPC Lys939Gln presented a higher risk of developing lung cancer in heavy smokers (OR: 3.71; 95%CI:1.46-9.45; p=0.005). The survival analysis presented that heterozygous genotype showed least survival in comparison with mutant genotype in XPC Ala499Val genetic variant whereas no significant association was observed in XPC Lys939Gln. In conclusion, XPC Lys939Gln is associated with significant risk towards the lung cancer whereas on contrary XPC Ala499Val shows a protective effect.
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Affiliation(s)
- Shweta Lawania
- Department of Biotechnology, Thapar University, Punjab, 147002, India
| | - Navneet Singh
- Department of Pulmonary Medicine, Post Graduate Institute of Medical Education & Research (PGIMER), Sector 14, Chandigarh, India
| | - Digamber Behera
- Department of Pulmonary Medicine, Post Graduate Institute of Medical Education & Research (PGIMER), Sector 14, Chandigarh, India
| | - Siddharth Sharma
- Department of Biotechnology, Thapar University, Punjab, 147002, India.
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Hallit S, Salameh P. Exposure to toxics during pregnancy and childhood and asthma in children: A pilot study. J Epidemiol Glob Health 2017; 7:147-154. [PMID: 28756822 PMCID: PMC7320455 DOI: 10.1016/j.jegh.2017.04.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 04/21/2017] [Indexed: 11/24/2022] Open
Abstract
Environmental factors, pesticides, alcohol and smoking are linked to asthma in children. The association of toxic substances exposure with asthma has not been evaluated. Our objective is to assess such associations among children aged less than 16 years old. This is a cross-sectional study, conducted between January and May 2015, using a sample of Lebanese students from private schools in Beirut and Mount Lebanon. Out of 700 distributed questionnaires, 527 (75.2%) were returned to us. Verbal informed consent was also obtained from all parents prior to participating in the study. A significant association was found between waterpipe smoking and diagnosed asthma (p = 0.003; ORa = 13.25; 95% CI 2.472–71.026). Alcohol during pregnancy, waterpipe smoking during pregnancy and parents respiratory problems significantly increased the risk of respiratory problems by approximately 5 times, 6 times and 2 times respectively (p = 0.016; ORa = 4.889; 95% CI 1.339–17.844, p = 0.021; ORa = 6.083; 95% CI 1.314–28.172, p = 0.004; ORa = 1.748; 95% CI 1.197–2.554 respectively). Waterpipe smoking, alcohol during pregnancy, recurrent otitis and humidity at home seem to be significantly correlated with asthma in children. Spreading awareness by health care professionals is needed to permit a reduction of the prevalence of these allergic diseases, especially asthma, in children.
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Affiliation(s)
- Souheil Hallit
- Lebanese University, School of Pharmacy, Hadath, Lebanon; Universite Saint Joseph, Faculty of Pharmacy, Beirut, Lebanon; Universite Saint-Esprit Kaslik, Faculty of Medicine, Kaslik, Lebanon; Psychiatric Hospital of the Cross, P.O. Box 60096, Jal Eddib, Lebanon; Occupational Health Environment Research Team, U1219 BPH Bordeaux Population Health Research Center Inserm - Université de Bordeaux, France.
| | - Pascale Salameh
- Lebanese University, School of Pharmacy, Hadath, Lebanon; Lebanese University, Faculty of Medicine, Hadath, Lebanon
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Lin J, Zhang Y, Wang H, Chang J, Wei L, Cao L, Zhang Z, Zhang X. Genetic Polymorphisms in the Apoptosis-Associated Gene CASP3 and the Risk of Lung Cancer in Chinese Population. PLoS One 2016; 11:e0164358. [PMID: 27723786 PMCID: PMC5056705 DOI: 10.1371/journal.pone.0164358] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 09/24/2016] [Indexed: 11/30/2022] Open
Abstract
Caspase-3 (CASP3) plays a central role in executing cell apoptosis and thus in carcinogenesis. We previously investigated the relationship between functional polymorphisms in CAPS3 829 A>C and 20541 C>T and risk of esophageal squamous cell carcinoma. However little is known about the role of CASP3 variants in susceptibility to lung cancer. To figure out the contribution of CASP3 polymorphisms to lung cancer risk, genotypes of 1000 lung cancer patients and 1000 controls were conducted by RFLP-PCR (restriction fragment length polymorphism PCR). The transcriptional activity of CASP3 829 A>C was examined by dual luciferase reporter assay. Logistic regression was applied to calculate Odds ratios (OR) and 95% confidence intervals (95%CI). Compared with CASP3 829 AA genotype, AC and CC genotype had significantly increased risk of lung cancer with OR (95% CI) of 1.33 (1.09–1.63) and 1.55 (1.19–2.01), respectively. To further explore the possible impact of 829 A>C SNP on CASP3 transcriptional activity, we detected the dual luciferase activity of PGL3-promoter vectors containing 829A or 829C alleles in lung cancer cell lines and found that report gene expressions driven by 829A containing CASP3 promoter were 1.64-fold, 1.94-fold greater than those driven by CASP3 829C containing counterparts in A549 and NCI-H1975 cells (P<0.001). When stratified by sex, the significantly increased risk associated with CASP3 829 AC or CC genotype was obviousl in males with OR (95% CI) of 1.42 (1.11–1.81) and 1.51 (1.11–2.05), but not in females. When stratified by age, we found that CASP3 829 AC or CC genotype contributed to the risk of lung cancer in youngers with OR (95% CI) of 2.73 (1.71–4.34) and 4.02 (2.20–7.32), but not in elder group. We also found that 829AC or 829CC genotype increased adenocarcinoma risk compared with the AA genotype with OR (95%CI) of 1.33 (1.04–1.70) and 1.51(1.09–2.07). CASP3 polymorphism and smoking interaction was demonstrated related with higher risk of lung cancer. We achieved that the CASP3 829AC or 829CC genotypes was associated with increased risk of lung cancer in both non-smoker and smoker group, with OR (95%CI) of 1.48 (1.08–2.02) and OR (95%CI) of 1.64 (1.09–2.48) among non-smokers and OR (95%CI) of 2.68 (1.89–3.81) and OR (95%CI) of 3.23 (2.21–4.92) among smokers, respectively. Among carriers with 20541CT genotype, the ORs (95%CI) of risk with lung cancer for smoking <16, 16–28, or > 28 pack-years were 1.16(0.65–2.07), 1.66(0.98–2.82) and 5.01(3.31–7.58) compared with the 20541CC carriers. And among carriers with 20541CT genotype, the ORs (95%CI) were 0.86(0.33–2.20), 2.12(0.83–5.41) and 5.71(2.68–12.16). These results highlight apoptosis-related CASP3 as an important gene in human carcinogenesis and further support the CASP3 polymorphisms confer to the lung cancer susceptibility.
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Affiliation(s)
- Jia Lin
- Department of Molecular Genetics, College of Life Science, North China University of Science and Technology, Tangshan, China
| | - Yanyan Zhang
- Department of Molecular Genetics, College of Life Science, North China University of Science and Technology, Tangshan, China
- Department of Epidemiology, School of Public Health, North China University of Science and Technology, Tangshan, China
| | - Hongge Wang
- Department of Molecular Genetics, College of Life Science, North China University of Science and Technology, Tangshan, China
| | - Jiang Chang
- Department of Epidemiology and Biostatistics, and State Key Laboratory of Environment Health (Incubation), MOE (Ministry of Education) Key Laboratory of Environment & Health, Ministry of Environmental Protection Key Laboratory of Environment and Health (Wuhan), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lixuan Wei
- Department of Etiology and Carcinogenesis, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lei Cao
- Department of Molecular Genetics, College of Life Science, North China University of Science and Technology, Tangshan, China
| | - Zhi Zhang
- Department of Chemotherapy and Radiotherapy, Tangshan Gongren Hospital, Tangshan, China
| | - Xuemei Zhang
- Department of Molecular Genetics, College of Life Science, North China University of Science and Technology, Tangshan, China
- * E-mail:
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Potential role of gene-environment interactions in ion transport mechanisms in the etiology of renal cell cancer. Sci Rep 2016; 6:34262. [PMID: 27686058 PMCID: PMC5043233 DOI: 10.1038/srep34262] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 09/07/2016] [Indexed: 01/20/2023] Open
Abstract
We investigated the ion transport mechanism (ITM) in renal cell cancer (RCC) etiology using gene-environment interactions between candidate single nucleotide polymorphisms (SNPs) and associated environmental factors, including dietary intakes of sodium, potassium and fluid, hypertension and diuretic medication. A literature-based selection of 13 SNPs in ten ITM genes were successfully genotyped in toenail DNA of 3,048 subcohort members and 419 RCC cases from the Netherlands Cohort Study. Diet and lifestyle were measured with baseline questionnaires. Cox regression analyses were conducted for main effects and gene-environment interactions. ADD1_rs4961 was significantly associated with RCC risk, showing a Hazard Ratio (HR) of 1.24 (95% confidence intervals (CI): 1.01–1.53) for the GT + TT (versus GG) genotype. Four of 65 tested gene-environment interactions were statistically significant. Three of these interactions clustered in SLC9A3_rs4957061, including the ones with fluid and potassium intake, and diuretic medication. For fluid intake, the RCC risk was significantly lower for high versus low intake in participants with the CC genotype (HR(95% CI): 0.47(0.26–0.86)), but not for the CT + TT genotype (P-interaction = 0.002). None of the main genetic effects and gene-environment interactions remained significant after adjustment for multiple testing. Data do not support the general hypothesis that the ITM is a disease mechanism in RCC etiology.
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Zeng Y, Wei L, Wang YJ, Liu C. Genetic Association between ERCC5 rs17655 Polymorphism and Colorectal Cancer Risk: Evidence Based on a Meta-analysis. Asian Pac J Cancer Prev 2016. [PMID: 26225711 DOI: 10.7314/apjcp.2015.16.13.5565] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Previous studies evaluating the association between the excision repair cross complementing group 5 (ERCC5) gene rs17655 polymorphism and colorectal cancer susceptibility generated controversial results. To generate large-scale evidence on whether the ERCC5 rs17655 polymorphism might indeed be associated with colorectal cancer susceptibility, the present meta-analysis was performed. MATERIALS AND METHODS Data were collected from PubMed, Embase and Web of Science, with the last report up to Apr 03, 2015. Odds ratios (ORs) with 95% confidence intervals (CIs) were used to assess the strength of any association. RESULTS A total of nine studies including 5,102 cases and 6,326 controls based on the search criteria were included and significant associations were found between ERCC5 rs17655 polymorphism CG vs GG overall (OR=1.29, 95% CI=1.18~1.40) and in the dominant model (OR=1.23, 95% CI=1.13~1.33). On subgroup analysis by ethnicity and source of controls, the ERCC5 rs17655 polymorphism was found to correlate with the pathogenesis of colorectal cancer among Asians and Caucasians and with hospital-based populations. CONCLUSIONS This meta-analysis suggests that the ERCC5 rs17655 polymorphism might contribute to genetic susceptibility to colorectal cancer.
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Affiliation(s)
- Yong Zeng
- Department of Cardiothoracic Surgery, Shaoxing People's Hospital, Shaoxing Hospital of Zhejiang University, Shaoxing, Zhejiang Province, China E-mail : ,
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Orenstein L, Chetrit A, Dankner R. Healthy Lifestyle Pattern is Protective Against 30-Yr Cancer Incidence in Men and Women: A Cohort Study. Nutr Cancer 2016; 68:410-9. [PMID: 27007270 DOI: 10.1080/01635581.2016.1153673] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
OBJECTIVES Investigate associations of healthier behaviors with 30-yr cancer incidence. SUBJECTS/METHODS In 1982, 632 healthy men and women (ages 40-70) were interviewed for nutritional habits using a Food Frequency Questionnaire and a 24-h physical activity questionnaire. Blood pressure, weight, and height were measured, and blood was drawn for biochemical profiles. Thirteen and four subjects were excluded due to cancer diagnosis ≤1 yr from recruitment and extreme values of reported total daily calorie intake, respectively. RESULTS During a mean follow-up of 24.2 yr, 146 cancer incident patients (23.7%) were documented. Total cancer risk was 38% lower in the medium vegetable intake tertile [adjusted hazards ratio (HR) = 0.62, 95%confidence interval (CI): 0.40-0.95], and 66% higher in the medium fruit intake tertile (adjusted HR = 1.66, 95%CI: 1.08-2.55) compared to the lowest tertile. The risk of gastrointestinal cancers was 3 times greater for the highest, compared to the lowest, dairy consumption tertile (HR = 3.06, 95%CI: 1.01-9.23). "Healthy lifestyle" (normal BMI, never smoked, consuming high levels of dietary fiber and vegetables, and more physically active) reduced overall cancer risk (adjusted HR = 0.63, 95%CI: 0.44-0.91) as compared to the rest of the cohort. CONCLUSIONS Our findings reinforce the importance of lifestyle-related factors, which are relatively low-cost and may contribute to reduction in the burden of malignant diseases.
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Affiliation(s)
- Liat Orenstein
- a Sackler Faculty of Medicine, School of Public Health , Department of Epidemiology and Preventive Medicine , Tel Aviv University , Ramat Aviv , Tel Aviv , Israel
| | - Angela Chetrit
- b The Gertner Institute for Epidemiology and Health Policy Research, Sheba Medical Center , Israel
| | - Rachel Dankner
- a Sackler Faculty of Medicine, School of Public Health , Department of Epidemiology and Preventive Medicine , Tel Aviv University , Ramat Aviv , Tel Aviv , Israel.,b The Gertner Institute for Epidemiology and Health Policy Research, Sheba Medical Center , Israel
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Hussein AA, Tran ND, Smith JF. Fertility preservation for boys and adolescents facing sterilizing medical therapy. Transl Androl Urol 2016; 3:382-90. [PMID: 26816794 PMCID: PMC4708141 DOI: 10.3978/j.issn.2223-4683.2014.11.06] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Improvements in childhood cancer survival have allowed boys and their families to increasingly focus on quality of life after therapy, particularly their future ability to father children. Treatments should maintain comprehensive cancer care goals and consider the long-term quality of life of these children. While semen cryopreservation is a well-established method of fertility preservation for post-pubertal children, the use of cryopreserved pre-treatment testicular tissue represents a promising, yet experimental method of fertility preservation for prepubertal males facing sterilizing therapy. Healthcare providers should counsel families about the fertility risks of therapy, discuss or refer patients for standard fertility preservation options, and consider experimental approaches to fertility preservation while being mindful of the ethical questions these treatments raise.
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Affiliation(s)
- Ahmed A Hussein
- 1 Department of Urology, University of California, San Francisco, CA, USA ; 2 Department of Urology, Cairo University, Egypt ; 3 Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, CA, USA ; 4 Philip R. Lee Institute for Health Policy Studies, San Francisco, CA, USA
| | - Nam D Tran
- 1 Department of Urology, University of California, San Francisco, CA, USA ; 2 Department of Urology, Cairo University, Egypt ; 3 Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, CA, USA ; 4 Philip R. Lee Institute for Health Policy Studies, San Francisco, CA, USA
| | - James F Smith
- 1 Department of Urology, University of California, San Francisco, CA, USA ; 2 Department of Urology, Cairo University, Egypt ; 3 Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, CA, USA ; 4 Philip R. Lee Institute for Health Policy Studies, San Francisco, CA, USA
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Huang Z, Yuan L, Jiang Z, Wang D. Associations of polymorphisms in NAT2 gene with risk and metastasis of osteosarcoma in young Chinese population. Onco Targets Ther 2015; 8:2675-80. [PMID: 26445549 PMCID: PMC4590633 DOI: 10.2147/ott.s92275] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Osteosarcoma is the most common primary malignancy of bone in young individuals. Genetic factors may play an important role in the tumorigenesis of osteosarcoma. Here we carried out a case-control study to investigate seven NAT2 single-nucleotide polymorphisms (rs1799929, rs120, rs1041983, rs1801280, rs1799930, rs1799931, and rs1801279) on the risk and prognosis of osteosarcoma. This study included 260 young osteosarcoma cases and 286 controls. The TaqMan method was used to determine genotypes. We found that rs1799931 G>A polymorphisms were associated with a decreased risk of osteosarcoma in young Chinese population, and rs1041983 CT genotype seemed to play a protective role in the risk of osteosarcoma. However, further analysis showed that rs1041983 polymorphisms were associated with an elevated risk of tumor metastasis, predicting poor prognosis. This study provided the first evidence for the associations between NAT2 polymorphisms and osteosarcoma risk and metastasis in Chinese population.
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Affiliation(s)
- Zhengxiang Huang
- Department of Orthopedics, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Li Yuan
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai, People's Republic of China
| | - Zhenghui Jiang
- Department of Orthopedics, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, People's Republic of China ; Department of Orthopedics, The First People's Hospital of Wenling, Wenling, People's Republic of China
| | - Dongliang Wang
- Department of Orthopedics, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
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Geng P, Ou J, Li J, Liao Y, Wang N, Xie G, Sa R, Liu C, Xiang L, Liang H. A Comprehensive Analysis of Influence ERCC Polymorphisms Confer on the Development of Brain Tumors. Mol Neurobiol 2015; 53:2705-14. [PMID: 26264164 DOI: 10.1007/s12035-015-9371-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 07/21/2015] [Indexed: 12/21/2022]
Abstract
Within DNA repair genes, there lie a number of single nucleotide polymorphisms that may impair protein function and attenuate DNA repair capability, resulting in genomic instability and individual predisposition to malignancies. The purpose of this study was to assess the previously reported inconsistent association of polymorphisms in ERCC1 (rs11615, rs3212986), ERCC2 (rs13181, rs1799793, rs238406), and ERCC5 (rs17655) with the development of brain tumors. In the present work, we carried out a comprehensive meta-analysis of results from all published data (5 data sets for rs11615, 7 for rs3212986, 11 for rs13181, 5 for rs1799793, 3 for rs238406, and 4 for rs17655) to evaluate risk of brain tumors contributed by the polymorphisms being investigated. Either the analytic method described by Mantel and Haenszel or that proposed by DerSimonian and Laird was properly used to summarize the risk estimates (OR and 95% CI). Data analyses were done with Stata version 12.0. Meta-analyses were performed for all polymorphisms, and only rs3212986 in the ERCC1 gene showed a significant association with glioma incidence. In the homozygote comparison, we found 1.26-fold elevated risk of glioma in relation to presence of the AA genotype (OR = 1.26, 95% CI = 1.05-1.52, P OR = 0.013, P heterogeneity = 0.849, I(2) = 0.0%). We also noted that individuals with the rs3212986-AA as compared to those with rs3212986-CC/CA had a 28% higher risk to develop glioma (OR = 1.28, 95% CI = 1.06-1.53, P OR = 0.008, Pheterogeneity = 0.808, I(2) = 0.0%). No major effects were observed for Caucasians or Asians in subgroup analysis by ethnicity. ERCC1 rs3212986 is a common single nucleotide polymorphism and may contribute toward individual susceptibility for glioma. Further research in this filed is required to verify the association obtained based on a relatively small number.
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Affiliation(s)
- Peiliang Geng
- Department of Oncology and Southwest Cancer Center, Southwest Hospital Third Military Medical University, 29 Gaotanyan Main Street, Chongqing, 400038, China
| | - Juanjuan Ou
- Department of Oncology and Southwest Cancer Center, Southwest Hospital Third Military Medical University, 29 Gaotanyan Main Street, Chongqing, 400038, China
| | - Jianjun Li
- Department of Oncology and Southwest Cancer Center, Southwest Hospital Third Military Medical University, 29 Gaotanyan Main Street, Chongqing, 400038, China
| | - Yunmei Liao
- Department of Oncology and Southwest Cancer Center, Southwest Hospital Third Military Medical University, 29 Gaotanyan Main Street, Chongqing, 400038, China
| | - Ning Wang
- Department of Oncology and Southwest Cancer Center, Southwest Hospital Third Military Medical University, 29 Gaotanyan Main Street, Chongqing, 400038, China
| | - Ganfeng Xie
- Department of Oncology and Southwest Cancer Center, Southwest Hospital Third Military Medical University, 29 Gaotanyan Main Street, Chongqing, 400038, China
| | - Rina Sa
- Department of Oncology and Southwest Cancer Center, Southwest Hospital Third Military Medical University, 29 Gaotanyan Main Street, Chongqing, 400038, China
| | - Chen Liu
- Department of Oncology and Southwest Cancer Center, Southwest Hospital Third Military Medical University, 29 Gaotanyan Main Street, Chongqing, 400038, China
| | - Lisha Xiang
- Department of Oncology and Southwest Cancer Center, Southwest Hospital Third Military Medical University, 29 Gaotanyan Main Street, Chongqing, 400038, China
| | - Houjie Liang
- Department of Oncology and Southwest Cancer Center, Southwest Hospital Third Military Medical University, 29 Gaotanyan Main Street, Chongqing, 400038, China.
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Abstract
The knowledge of molecular mechanism that underlies the genetic predisposition to lung cancer is yet limited. Results from previous studies addressing the association of AGPHD1 variant rs8034191 with lung carcinogenesis remain inconclusive. Herein, we combined these data and re-examined the association. We performed a meta-analysis of Asian studies identified through various ways. Using the data collected from each eligible study, we combined the effect estimates (ORs and its 95 % CIs) with the fixed effects model (Mantel-Haenszel method). Statistical analyses were done using STATA software. Data from nine studies (29,290 subjects) carried out in Asian populations were analyzed in this work. There was no overall association between variant rs8034191 and lung cancer risk under the allele frequency model (OR = 1.03, 95 % CI = 0.93-1.13, P heterogeneity = 0.522). We observed the same associations under other genetic models and in the subgroup analyses by ethnicity and smoking status. Our results indicate that variant rs8034191 in the AGPHD1 gene may not modify the genetic risk of lung cancer in Asian populations.
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Affiliation(s)
- Hong Wang
- Department of Lung Cancer, Affiliated Hospital of Academy of Military Medical Sciences (307 Hospital of PLA), No. 8 DongDa Road, FengTai Area, Beijing, People's Republic of China,
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Ahmad D, Bakairy AK, Katheri AM, Tamimi W. MDM2 (RS769412) G>A Polymorphism in Cigarette Smokers: a Clue for the Susceptibility to Smoking and Lung Cancer Risk. Asian Pac J Cancer Prev 2015; 16:4057-60. [PMID: 25987086 DOI: 10.7314/apjcp.2015.16.9.4057] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Cigarette smoke contains oxidants and free radicals which are carcinogens that can induce mutations in humans. Single nucleotide polymorphisms (SNPs) are the most frequent genetic alterations found in the human genome. In the present study, we have examined the ability of the murine double minute 2 (Mdm2) (rs769412) A>G polymorphism in cigarette smokers to predict risk of cancers. Our results showed that of smokers, 87% were found with AA genotype, 10% with heterozygous AG genotype, and 3% with GG genotype. The heterozygous AG genotype was observed in a lower percentage of smokers (10%) as compared to non-smokers (18%), whereas, homozygous AA genotype was observed in lower percentage of non-smokers (81%) as compared to the smokers (87%). The results from present study support the association with an allele and AG genotype in non-smokers. However, further studies are required to establish the role of Mdm2 (rs769412) C>T in cigarettes smokers and diseases.
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Affiliation(s)
- Dilshad Ahmad
- College of Pharmacy, King Saud University for Health Sciences, Riyadh, Saudi Arabia E-mail :
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Wang YD, Yang HY, Liu J, Wang HY. Updated meta-analysis of the association between CYP2E1 RsaI/PstI polymorphisms and lung cancer risk in Chinese population. Asian Pac J Cancer Prev 2015; 15:5411-6. [PMID: 25040958 DOI: 10.7314/apjcp.2014.15.13.5411] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND A number of studies have reported relationships of CYP2E1 RsaI/PstI polymorphisms with susceptibility to lung cancer in Chinese population. However, the epidemiologic results have been conflictive rather than conclusive. The purpose of this study was to address the associations of CYP2E1 RsaI/PstI polymorphisms with lung cancer risk in Chinese population comprehensively. MATERIALS AND METHODS Systematic searches were conducted in the PubMed, Science Direct, Elsevier, CNKI and Chinese Biomedical Literature Databases. Pooled odds ratios (ORs) with 95% confidence intervals (CIs) were calculated to estimate the strength of association. RESULTS Overall, we observed a decreased lung cancer risk among subjects carrying CYP2E1 RsaI/PstI c1/ c2 and c1/c2+c2/c2 genotypes (OR=0.76, 95%CI: 0.64-0.90 and OR=0.78, 95%CI: 0.66-0.93, respectively), as compared with subjects carrying the c1/c1 genotype. In subgroup analysis, we observed a decreased lung cancer risk among c1/c2 carriers in hospital-based studies (OR=0.81, 95%CI: 0.68-0.98) and among carriers with c1/ c2 and c1/c2+c2/c2 genotypes in population-based studies(OR=0.57, 95%CI: 0.42-0.79 and OR=0.58, 95%CI: 0.43-0.79, respectively), as compared with subjects carrying the c1/c1 genotype. Limiting the analysis to studies with controls in Hardy-Weinberg equilibrium (HWE), we similarly observed a decreased lung cancer risk among c1/c2 and c1/c2+c2/c2 carriers (OR=0.73, 95%CI: 0.60-0.88 and OR=0.73, 95%CI: 0.60-0.88, respectively), as compared with c1/c1. CONCLUSIONS Our results suggested that CYP2E1 RsaI/PstI c1/c2 and c1/c2+c2/c2 variants might be a protective factor for developing lung cancer in Chinese population. Further well-designed studies with larger sample size are required to verify our findings.
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Affiliation(s)
- Ya-Dong Wang
- Department of Toxicology, Henan Center for Disease Control and Prevention, Zhengzhou, China E-mail :
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Kamel AM, Ebid GTA, Moussa HS. N-Acetyltransferase 2 (NAT2) polymorphism as a risk modifier of susceptibility to pediatric acute lymphoblastic leukemia. Tumour Biol 2015; 36:6341-8. [PMID: 25804798 DOI: 10.1007/s13277-015-3320-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 03/12/2015] [Indexed: 12/18/2022] Open
Abstract
N-Acetyltransferases (NAT) have been known to modify the risk to a variety of solid tumors. However, the role of NAT2 polymorphism in risk susceptibility to childhood acute lymphoblastic leukemia (ALL) is still not well known. We performed a case-control study to determine if the common NAT2 polymorphisms play a role in altering susceptibility to pediatric ALL. DNA of 92 pediatric ALL patients and 312 healthy controls was analyzed for the NAT2 polymorphisms using the PCR-RFLP method. The wild-type NAT2*4 was encountered in 8.6 % of patients versus 11.8 % of controls (P = 0.23). The rapid acetylators NAT2*12 803A>G, AG, GG, and AG/GG were overrepresented in controls (P = 0.0001; odds ratio (OR) 0.22, 0.19, and 0.21 respectively). NAT2*5D 341T>C and NAT2*11A 481C>T were of comparable frequencies. For their combination, NAT2*5A, a slow acetylator, both TCTT and CCCT were overrepresented in patients (P < 0.001; OR 15.8 and 17.9 respectively). NAT2*5B (803A>G, 341T>C, 481C>T) was overrepresented in controls (P < 0.001; OR 0.12). Apparently, 803A>G ameliorated the combined effect of 341T>C and 481C>T. A similar effect was obtained with NAT2*5C (341T>A, 803A>G) (P < 0.0001; OR 0.11). For slow acetylator NAT2*7A 857G>A, GA and GA/AA were overrepresented in patients (P = 0.009 and 0.01; OR 2.74 and 2.72 respectively). NAT2*13 282C>T, NAT2*6B 590G>A, and NAT2*14A 191G>A were of comparable frequencies. NAT2 282C>A in combination with NAT2 857G>A (NAT2*7B) showed a synergistic effect in patients versus controls (P < 0.0001; OR 3.51). In conclusion, NAT2 gene polymorphism(s) with slow acetylator phenotype is generally associated with the risk of development of ALL in children.
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Affiliation(s)
- Azza M Kamel
- Clinical Pathology Department, NCI, Cairo University, Fom El-Khalig square, Kasr El-Aini St, Cairo, 11796, Egypt,
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Shi TY, He J, Wang MY, Zhu ML, Yu KD, Shao ZM, Sun MH, Wu X, Cheng X, Wei Q. CASP7 variants modify susceptibility to cervical cancer in Chinese women. Sci Rep 2015; 5:9225. [PMID: 25784056 PMCID: PMC4363885 DOI: 10.1038/srep09225] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 02/05/2015] [Indexed: 02/07/2023] Open
Abstract
Polymorphisms in Caspase-7 (CASP7) may modulate the programmed cell death and thus contribute to cervical cancer risk. In this case-control study of 1,486 cervical cancer cases and 1,301 controls, we investigated associations between four potentially functional polymorphisms in CASP7 and cervical cancer risk and evaluated their locus-locus interaction effects on the risk. The genotype-phenotype correlation was performed by a generalized linear regression model. We found that the rs4353229 polymorphism was associated with cervical cancer risk (under a recessive model: crude OR = 1.20, 95% CI = 1.02-1.40). Compared with the TT genotype, the rs10787498GT genotype was associated with an increased cervical cancer risk (adjusted OR = 1.19, 95% CI = 1.00-1.41). Combination analysis showed that subjects with four putative risk genotypes had a 1.54-fold increased cancer risk, compared with those who carried three or less putative risk genotypes. We also observed significant locus-locus joint effects on the risk, which may be mediated by the polymorphisms regulating CASP7 mRNA expression. Subsequent multifactor dimensionality reduction and classification and regression tree analyses indicated that the CASP7 genotypes might have a locus-locus interaction effect that modulated cervical cancer risk. Out data suggest that CASP7 polymorphisms may interact to modify cervical cancer risk by a possible mechanism of regulating CASP7 mRNA expression.
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Affiliation(s)
- Ting-Yan Shi
- Cancer Institute, Fudan University Shanghai Cancer
Center, Shanghai 200032, China
- Department of Obstetrics and Gynecology, Zhongshan
Hospital Fudan University, Shanghai 200032, China
| | - Jing He
- Cancer Institute, Fudan University Shanghai Cancer
Center, Shanghai 200032, China
- State Key Laboratory of Oncology in South China, Department
of Experimental Research, Collaborative Innovation Center for Cancer Medicine,
Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong
510060, China
| | - Meng-Yun Wang
- Cancer Institute, Fudan University Shanghai Cancer
Center, Shanghai 200032, China
| | - Mei-Ling Zhu
- Cancer Institute, Fudan University Shanghai Cancer
Center, Shanghai 200032, China
| | - Ke-Da Yu
- Department of Breast Surgery, Fudan University Shanghai
Cancer Center, Shanghai 200032, China
| | - Zhi-Ming Shao
- Department of Breast Surgery, Fudan University Shanghai
Cancer Center, Shanghai 200032, China
| | - Meng-Hong Sun
- Department of Pathology, Fudan University Shanghai
Cancer Center, Shanghai 200032, China
| | - Xiaohua Wu
- Department of Gynecologic Oncology, Fudan University
Shanghai Cancer Center, Shanghai 200032, China
| | - Xi Cheng
- Department of Gynecologic Oncology, Fudan University
Shanghai Cancer Center, Shanghai 200032, China
| | - Qingyi Wei
- Cancer Institute, Fudan University Shanghai Cancer
Center, Shanghai 200032, China
- Duke Cancer Institute, Duke University Medical Center, Durham,
NC 27710, USA
- ;
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X-ray repair cross-complementing group 1 (XRCC1) Arg399Gln polymorphism significantly associated with prostate cancer. Int J Biol Markers 2015; 30:e12-21. [PMID: 25262700 DOI: 10.5301/jbm.5000111] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2014] [Indexed: 12/20/2022]
Abstract
Prostate cancer (Pca) is one of the noncutaneous cancers occurring worldwide. Its high morbidity and mortality make it a concern. X-ray repair cross-complementing group 1 (XRCC1) Arg399Gln polymorphism (rs25487) has been reported to be related to Pca. However, the conclusions are controversial. In this study, PubMed, HuGENet and Chinese National Knowledge Infrastructure (CNKI) databases were combined with a comprehensive literature search. Four models including dominant (AA + AG vs. GG), recessive (AA vs. AG+GG), codominant (AA vs. AG, AA vs. GG) and per-allele analysis (A vs. G) were applied. Finally, 15 studies with 18 sets of data were included. A positive association was discovered in pooled results for recessive (odds ratio [OR]=1.202, 95% confidence interval [95% CI], 1.060-1.363, I2=46.20%), codominant (AA vs. AG; OR=1.258, 95% CI, 1.099-1.439, I2=38.50%; AA vs. GG; OR=1.283, 95% CI, 1.027-1.602, I2=51.70%) and allele analysis (OR=1.116, 95% CI, 1.001-1.244, I2=58.00%). In ethnicity subgroup analysis, these 4 models were also significant in the Asian subgroup. However, for whites, only 2 models seemed to be significant (AA vs. AG+GG: OR=1.525, 95% CI, 1.111-2.093, I2=52.60%; AA vs. AG: OR=1.678, 95% CI, 1.185-2.375, I2=30.70%). In further analysis, we regrouped the data based on race, in which pooled results and Asian subgroup were again shown to be positive. In the next analysis, expression quantitative trait loci (eQTL), linkage disequilibrium (LD), TagSNP and functional analysis were used. The results showed that the SNP was a tag and functional SNP with LD block in both Asians and whites. In summary, we suggest that XRCC1 Arg399Gln might be significantly associated with development of Pca.
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Evaluating the association of polymorphisms in the HAP1 gene with lung cancer risk: a meta-analysis. Tumour Biol 2014; 35:10825-31. [DOI: 10.1007/s13277-014-2236-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 06/12/2014] [Indexed: 01/25/2023] Open
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Chang Z, Zhou H, Liu Y. Promoter methylation and polymorphism of E-cadherin gene may confer a risk to prostate cancer: a meta-analysis based on 22 studies. Tumour Biol 2014; 35:10503-13. [PMID: 25056535 DOI: 10.1007/s13277-014-2323-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 07/07/2014] [Indexed: 01/06/2023] Open
Abstract
Emerging evidence has suggested that -160C/A polymorphism and promoter methylation of E-cadherin gene may contribute to the risk of prostate cancer. However, the results are still conflicting. We aim to systematically evaluate the potential of promoter methylation and polymorphism in E-cadherin gene to confer a risk to prostate cancer through meta-analysis. PubMed, Embase, Web of Science, Cochrane Library, and Chinese National Knowledge Infrastructure (CNKI) databases were searched to identify eligible studies published before April 1, 2014. Pooled odds ratios (ORs) with their 95 % confidence intervals (95 % CIs) were calculated by using the random-effect model or the fixed-effect model, according to heterogeneity test. Subgroup analyses were also performed to explore the potential sources of heterogeneity. Sensitivity and publication bias analyses were used to test the robustness of our results. We performed a meta-analysis of 22 included studies, with 11 on -160C/A polymorphism and another 11 on promoter methylation of E-cadherin gene. Our meta-analysis results suggested that E-cadherin -160C/A polymorphism may be a potential risk factor for prostate cancer. Furthermore, we observed that the frequencies of promoter methylation of E-cadherin gene in the prostate cancer tissues were significantly higher than those of normal tissues, indicating that promoter methylation of E-cadherin gene may play an important role in prostate carcinogenesis. In conclusion, the present meta-analysis provides further evidence that promoter methylation and -160C/A polymorphism of E-cadherin gene may confer a risk to prostate cancer. Identifying these risk factors for prostate cancer will improve early detection, allow for selective chemoprevention, and provide further insights into its disease mechanisms.
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Affiliation(s)
- Zheng Chang
- Department of Urology, General Hospital of Jinan Military Command, 25 Shifan Road, Jinan, 250031, People's Republic of China
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Wang HM, Zhang XY, Jin B. TERT genetic polymorphism rs2736100 was associated with lung cancer: a meta-analysis based on 14,492 subjects. Genet Test Mol Biomarkers 2014; 17:937-41. [PMID: 24283584 DOI: 10.1089/gtmb.2013.0322] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Previous studies focused on the association of the telomerase reverse transcriptase (TERT) gene polymorphism rs2736100 with lung cancer did not reach the same conclusion. In the present study, we performed a meta-analysis to systematically summarize the possible association between TERT polymorphism rs2736100 and the risk for lung cancer. METHOD We conducted a search of case-control studies on the association of TERT with susceptibility to lung cancer in PubMed, EMBASE, ISI Web of Science, Wanfang database in China, and Chinese National Knowledge Infrastructure (CNKI) databases. Data from eligible studies were extracted for meta-analysis. Lung cancer risk associated with rs2736100 was estimated by pooled odds ratios (ORs) and 95% confidence intervals (95% CIs). RESULTS Six independent case-control studies on rs2736100 were included in our meta-analysis. Our results showed that rs2736100 was associated with the risk of lung cancer not only in an additive model (OR=1.19, 95% CI: 1.04-1.35; p=0.01), but also in a dominant model (OR=1.14, 95% CI: 1.01-1.28; p=0.03). CONCLUSIONS This meta-analysis suggests that rs2736100 is associated with the risk of lung cancer.
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Affiliation(s)
- Hui-Min Wang
- Department of Respiratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University , Shanghai, People's Republic of China
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Association of XPC polymorphisms and lung cancer risk: a meta-analysis. PLoS One 2014; 9:e93937. [PMID: 24736739 PMCID: PMC3988015 DOI: 10.1371/journal.pone.0093937] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 03/10/2014] [Indexed: 12/05/2022] Open
Abstract
Background Xeroderma pigmentosum complementation group C gene (XPC) is a key member of nucleotide excision repair pathway and plays an important role in human DNA repair system. It is reported that several common polymorphisms of XPC are associated with susceptibility to lung cancer. However, the conclusion is still elusive. Method This meta-analysis was performed to determine the relationship between XPC polymorphisms (Lys939Gln, Ala499Val, and PAT) and lung cancer risk. Published literatures were identified by searching online databases and reference lists of relevant studies. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated to estimate the association strength. Publication bias were detected by Egger’s and Begg’s test. Result After strict screening, we identified 14 eligible studies in this meta-analysis, including 5647 lung cancer cases and 6908 controls. By pooling all eligible studies, we found that the homozygote Gln939Gln genotype was associated with a significantly increased risk of lung cancer in Asian population (GlnGln vs LysLys, OR = 1.229, 95% CI: 1.000–1.510; GlnGln vs LysLys/LysGln, OR = 1.257, 95% CI: 1.038–1.522). As for the PAT polymorphism, in Caucasian population, we found carriers of the −/− genotype were associated significantly reduced risk of lung cancer in homozygote comparison model (−/− vs +/+, OR = 0.735, 95% CI: 0.567–0.952). Conclusion In this meta-analysis we found that Gln939Gln genotype was associated with significantly increased risk of lung cancer in Asian population; the PAT −/− genotype significantly reduced susceptibility to lung cancer in Caucasian population; while the XPC Ala499Val polymorphism was not associated with lung cancer risk.
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Genetic polymorphism of APE1 rs1130409 can contribute to the risk of lung cancer. Tumour Biol 2014; 35:6665-71. [DOI: 10.1007/s13277-014-1829-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 03/05/2014] [Indexed: 10/25/2022] Open
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Yang J, Jiao S. Increased lung cancer risk associated with the TERT rs2736100 polymorphism: an updated meta-analysis. Tumour Biol 2014; 35:5763-9. [PMID: 24590268 DOI: 10.1007/s13277-014-1765-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2013] [Accepted: 02/17/2014] [Indexed: 10/25/2022] Open
Abstract
The rs2736100 polymorphism in the telomerase reverse transcriptase (TERT) gene has been implicated in lung cancer risk in multiple populations, but the existing evidence lacks statistical power to draw a convincing conclusion. Therefore, the present study was devised to derive a more precise estimation of the association between rs2736100 and lung cancer risk. The PubMed, Embase, and Web of Science databases were comprehensively searched for papers concerning lung cancer risk in relation to rs2736100. Pooled odds ratios (ORs) and the 95 % confidence intervals (CIs) were appropriately calculated using the fixed or random effects model. Meta-analysis of 20 independent studies involving 39,715 cancer cases and 61,462 control subjects showed statistical evidence for an association between rs2736100 and increased risk of lung cancer. Subgroup analysis by ethnicity demonstrated a significant association among both Asian and Caucasian populations. We additionally found an increased risk of non-small cell lung cancer and lung adenocarcinoma strongly associated with rs2736100. These data provide further evidence supporting a role for genetic susceptibility of TERT rs2736100 in the development of lung cancer.
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Affiliation(s)
- Jihua Yang
- Department of Oncology, Chinese PLA General Hospital, 28# Fuxing Road, Haidian District, Beijing, 100853, People's Republic of China
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Hu J, Liu C, Yin Q, Ying M, Li J, Li L, Zhou CX, Wang Y. Association between the CYP1A2-164 A/C polymorphism and colorectal cancer susceptibility: a meta-analysis. Mol Genet Genomics 2014; 289:271-7. [PMID: 24514875 DOI: 10.1007/s00438-013-0806-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2013] [Accepted: 12/18/2013] [Indexed: 01/11/2023]
Abstract
To date, epidemiological studies have assessed the association between CYP1A2-164 A/C polymorphism and colorectal cancer susceptibility. However, the results of these studies remained controversial. We aimed to examine the associations by conducting a meta-analysis of case-control studies. A total of 11 studies including 5,093 cases and 5,941 controls evaluated the association between the CYP1A2-164 A/C polymorphism and colorectal cancer susceptibility. No significantly associations were found in all genetic models (CC vs. AA: OR = 1.14, 95 % CI = 0.93-1.40; AC vs. AA: OR = 1.05, 95 % CI = 0.91-1.20; dominant model: OR = 1.08, 95 % CI = 0.95-1.24; recessive model: OR = 1.10, 95 % CI = 0.95-1.28). In the subgroup analysis by ethnicity or source of controls, there were still no significant associations detected in all genetic models. This meta-analysis suggested the CYP1A2-164 A/C polymorphism was not a risk factor for increasing colorectal cancer, further large and well-designed studies are needed to confirm these conclusions.
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Affiliation(s)
- Jianbing Hu
- Department of Oncology, The First People's Hospital of Yueyang, Yueyang, People's Republic of China,
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Association between NQO1 C609T polymorphism and acute lymphoblastic leukemia risk: evidence from an updated meta-analysis based on 17 case-control studies. J Cancer Res Clin Oncol 2014; 140:873-81. [PMID: 24488035 DOI: 10.1007/s00432-014-1595-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 01/20/2014] [Indexed: 10/25/2022]
Abstract
PURPOSE Quinone oxidoreductase (NQO1) C609T polymorphisms have been implicated in acute lymphoblastic leukemia (ALL) risk, but previously published studies were inconsistent and recent meta-analyses were not adequate. The aim of this study was to determine more precise estimations for the relationship between the NQO1 C609T polymorphism and the risk of ALL. METHODS Electronic searches for all publications were conducted on association between this variant and ALL in several databases updated in May 2013. The quality of studies was evaluated using the Newcastle-Ottawa Scale. Crude odds ratios (ORs) with 95 % confidence intervals (CIs) were used to assess the strength of the association. Seventeen studies were identified, including 2,264 ALL patients and 3,798 controls. RESULTS Overall, significantly elevated ALL risk was associated with NQO1 C609T variant genotypes when all of the studies were pooled into the meta-analysis (TT vs. CC: OR 1.46, 95 % CI 1.18-1.79; dominant model: OR 1.45, 95 % CI 1.19-1.77). In the subgroup analysis by ethnicity, significantly increased risks were found for non-Asians (T/T vs. C/C: OR 1.74, 95 % CI 1.29-2.36; dominant model: T/T + C/T vs. C/C: OR 1.7, 95 % CI 1.27-2.29). When stratified by adult or children studies, statistically significantly elevated risks were found among adult studies (codominant model: C/T vs. C/C: OR 1.38, 95 % CI 1.02-1.87; dominant model: T/T + C/T vs. C/C: OR 1.52, 95 % CI 1.18-1.97) and children studies (recessive model: T/T vs. C/T + C/C: OR 1.34, 95 % CI 1.05-1.7). CONCLUSIONS Our results indicate that the C609T polymorphism of the NQO1 gene is an important genetic risk factor in ALL.
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Shi J, Tong JH, Cai S. GH1 T1663A polymorphism and cancer risk: a meta-analysis of case–control studies. Tumour Biol 2014; 35:4529-38. [DOI: 10.1007/s13277-013-1596-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 12/23/2013] [Indexed: 01/01/2023] Open
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Liu C, Yin Q, Ying M, Lin J, Li L, Jiao G, Wang M, Wang Y. XPC Lys939Gln and Ala499Val polymorphisms in colorectal cancer susceptibility: a meta-analysis of case-control studies. Mol Biol Rep 2014; 41:1171-8. [PMID: 24385304 DOI: 10.1007/s11033-013-2964-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Accepted: 12/22/2013] [Indexed: 01/27/2023]
Abstract
The XPC Lys939Gln and Ala499Val polymorphisms were likely to be involved with the development of colorectal cancer. However, there had been inconsistent reports of association. This meta-analysis of literatures was performed to draw a more precise estimation of the relationship. We systematically searched PubMed, Embase and Web of Science for relevant articles with a time limit of December 2012. The strength of association between the XPC Lys939Gln and Ala499Val polymorphisms and colorectal cancer susceptibility were assessed by odds ratio (OR) with the corresponding 95 % confidence interval (95 % CI). This meta-analysis including six case-control studies evaluated the associations between the two XPC polymorphisms (Lys939Gln, Ala499Val) and colorectal cancer susceptibility. For XPC Lys939Gln, no obvious associations were found for all genetic models [CC vs AA: OR (95 % CI) = 1.12 (0.94-1.32); CA vs AA: OR (95 % CI) = 1.08 (0.94-1.24); the dominant model: OR (95 % CI) = 1.09 (0.97-1.23); the recessive model: OR (95 % CI) = 1.07 (0.92-1.25)]. For XPC Ala499Val, no obvious associations were also not found for all genetic models [TT vs CC: OR (95 % CI) = 0.84 (0.65-1.10); CT vs CC: OR (95 % CI) = 1.00 (0.86-1.15); the dominant model: OR (95 % CI) = 0.98 (0.85-1.12); the recessive model: OR (95 % CI) = 0.87 (0.67-1.12)]. This meta-analysis suggested that both the XPC Lys939Gln and Ala499Val polymorphisms were not risk factors for increasing colorectal cancer.
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Affiliation(s)
- Chuan Liu
- Department of Oncology, Changhai Hospital, Second Military Medical University, 168 Changhai Road, Shanghai, 200433, People's Republic of China,
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Ning B, Su Z, Mei N, Hong H, Deng H, Shi L, Fuscoe JC, Tolleson WH. Toxicogenomics and cancer susceptibility: advances with next-generation sequencing. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART C, ENVIRONMENTAL CARCINOGENESIS & ECOTOXICOLOGY REVIEWS 2014; 32:121-58. [PMID: 24875441 PMCID: PMC5712441 DOI: 10.1080/10590501.2014.907460] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The aim of this review is to comprehensively summarize the recent achievements in the field of toxicogenomics and cancer research regarding genetic-environmental interactions in carcinogenesis and detection of genetic aberrations in cancer genomes by next-generation sequencing technology. Cancer is primarily a genetic disease in which genetic factors and environmental stimuli interact to cause genetic and epigenetic aberrations in human cells. Mutations in the germline act as either high-penetrance alleles that strongly increase the risk of cancer development, or as low-penetrance alleles that mildly change an individual's susceptibility to cancer. Somatic mutations, resulting from either DNA damage induced by exposure to environmental mutagens or from spontaneous errors in DNA replication or repair are involved in the development or progression of the cancer. Induced or spontaneous changes in the epigenome may also drive carcinogenesis. Advances in next-generation sequencing technology provide us opportunities to accurately, economically, and rapidly identify genetic variants, somatic mutations, gene expression profiles, and epigenetic alterations with single-base resolution. Whole genome sequencing, whole exome sequencing, and RNA sequencing of paired cancer and adjacent normal tissue present a comprehensive picture of the cancer genome. These new findings should benefit public health by providing insights in understanding cancer biology, and in improving cancer diagnosis and therapy.
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Affiliation(s)
- Baitang Ning
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas, USA
| | - Zhenqiang Su
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas, USA
| | - Nan Mei
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas, USA
| | - Huixiao Hong
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas, USA
| | - Helen Deng
- Arkansas Department of Health and Human Service, Little Rock, Arkansas, USA
| | - Leming Shi
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas, USA
- Center for Pharmacogenomics, School of Pharmacy, Fudan University, Pudong District, Shanghai, China
| | - James C. Fuscoe
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas, USA
| | - William H. Tolleson
- National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas, USA
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Zhu ML, Hua RX, Zheng L. Associations between polymorphisms of the XPC gene and lung cancer susceptibility: a meta-analysis. Tumour Biol 2013; 35:2931-9. [PMID: 24375193 DOI: 10.1007/s13277-013-1377-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 10/30/2013] [Indexed: 11/24/2022] Open
Abstract
Xeroderma pigmentosum complementation group C (XPC) gene plays a critical role in DNA damage recognition, and its functional single nucleotide polymorphisms (SNPs) may alter DNA repair capacity and cancer susceptibility. Numerous epidemiological studies have investigated the associations between XPC Lys939Gln and Ala499Val polymorphisms and lung cancer susceptibility, but the conclusions are inconclusive. We searched three electronic databases (MEDLINE, EMBASE and EBSCO) for eligible publications and performed a meta-analysis assessing the associations between XPC Lys939Gln and Ala499Val polymorphisms and lung cancer risk. We also analysed the genotype-mRNA expression correlation using the data of HapMap phase II release 23 with 270 individuals from 4 ethnicities for exploring biological plausibility of our findings. We included ten published studies of 3,882 cases and 5,219 controls for Lys939Gln, and five studies with 2,605 cases and 3,329 controls for Ala499Val. When all studies were pooled, we found a significantly increased overall lung cancer risk for Lys939Gln polymorphism (recessive model: OR = 1.14, 95 % CI = 1.01-1.29, P = 0.218 for heterogeneity). Stratification analysis also showed a higher lung cancer risk in Asian populations (recessive model: OR = 1.26, 95% CI = 1.04-1.52, P = 0.263 for heterogeneity). Interestingly, we found significant correlation between Lys939Gln genotypes and XPC mRNA expression for Asian populations as well. However, we did not observe any association between Ala499Val polymorphism and overall lung cancer risk, nor in further stratification analysis. This meta-analysis suggests that XPC Lys939Gln polymorphism may contribute to lung cancer risk, which needs further validation in single larger studies.
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Affiliation(s)
- Mei-Ling Zhu
- Department of Oncology, Xin Hua Hospital affiliated to Shanghai Jiaotong University School of Medicine, No. 1665, Kong Jiang Road, Shanghai, 200092, China
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Li SX, Dai QS, Chen SX, Zhang SD, Liao XY, Deng X, Chi HB, Li FJ, Zhu JH, Jiang YY. Xeroderma pigmentosum complementation group D (XPD) gene polymorphisms contribute to bladder cancer risk: a meta-analysis. Tumour Biol 2013; 35:3905-15. [PMID: 24347488 DOI: 10.1007/s13277-013-1519-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 12/04/2013] [Indexed: 11/24/2022] Open
Abstract
Numerous epidemiological studies have been conducted to investigate the association between Xeroderma pigmentosum complementation group D (XPD) Asp312Asn (rs1799793 G > A) and Lys751Gln (rs13181 A > C) polymorphisms and bladder cancer risk; however, the conclusions remain controversial. With this in mind, we performed this meta-analysis with 11 studies including 3,797 cases and 5,094 controls for Asp312Asn and 21 studies including 6,360 cases and 7,894 controls for Lys751Gln polymorphism. We searched available literatures from PubMed, Embase, and CBM databases. Crude odds ratios (ORs) and 95% confidence intervals (CIs) were calculated to assess the strength of the associations. Moreover, to validate biological plausibility of our findings, the effects of these two polymorphisms on XPD gene expression within three ethnicities was determine by gene expression analysis based on imputed genotypes from HapMap. Overall, the variant allele of Asp312Asn polymorphism was associated with an increased risk of bladder cancer (Asn/Asn vs. Asp/Asp: OR = 1.51, 95% CI = 1.19-1.91; Asp/Asn vs. Asp/Asp: OR = 1.23, 95% CI = 1.12-1.35; recessive model: OR = 1.33, 95% CI = 1.10-1.61; dominant model: OR = 1.32, 95% CI = 1.14-1.52; and allele comparing: OR = 1.26, 95% CI = 1.11-1.42). We found the Lys751Gln was associated with increased bladder cancer risk only under the recessive model (OR = 1.14, 95% CI = 1.01-1.29). Stratification analyses demonstrated an increased risk for Asians and hospital-based studies under all genetic models while only under the dominant model for Caucasians as to the Asp312Asn polymorphism and for Caucasians under the recessive model as to the Lys751Gln polymorphism. We also found the Asp312Asn polymorphism can significantly influence mRNA expression levels among Asians and Caucasians, and the Lys751Gln polymorphism has a similar effect for Caucasians. Despite some limitations, this meta-analysis suggests that polymorphisms in XPD gene may contribute to bladder cancer susceptibility. These findings need further validation by large well-designed prospective studies.
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Affiliation(s)
- Su-Xia Li
- Department of Tumor Rehabilitation, First Hospital, Wenzhou Medical University, No.2 Fuxue Lane, Wenzhou, Zhejiang, 325000, China
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