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Li Z, Xin J, Chen W, Liu J, Zhu M, Zhao C, Yuan J, Jin G, Ma H, Du J, Hu Z, Wu T, Shen H, Dai J, Yu H. Genetic variants in autophagy associated genes are associated with DNA damage levels in Chinese population. Gene 2017; 626:414-419. [PMID: 28512061 DOI: 10.1016/j.gene.2017.05.017] [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: 01/04/2017] [Revised: 05/03/2017] [Accepted: 05/09/2017] [Indexed: 10/19/2022]
Abstract
Autophagy associated genes (ATGs) played an important role in the repair process of DNA damage and decreased autophagy may weaken the repair process and aggravate DNA damage. Based on this, we hypothesized that DNA damage levels might be modified by genetic variants in autophagy associated genes. In order to validate our hypothesis, 307 subjects were recruited from three different cities (Zhuhai, Wuhan and Tianjin) in China. Demographic data, individual 24-h PM2.5 exposure and peripheral blood DNA damage levels were also detected. Seven potentially functional polymorphisms in four essential autophagy associated genes (ATG5, ATG7, ATG8 and ATG13) were screened to evaluate the relationship between the polymorphisms of autophagy associated genes and DNA damage levels. This association was assessed by using multivariable linear regression model, age, sex, smoke and PM2.5 exposure levels were adjusted in each city. We found that rs12599322 in ATG8 (A>G, β=0.263, 95% CI: 0.108-0.419, P=8.98×10-4) and rs7484002 in ATG13 (A>G, β=0.396, 95% CI: 0.085-0.708, P=0.013) were significantly associated with higher DNA damage levels. Furthermore, functional annotations showed that both rs12599322 and rs7484002 located at transcription factor binding sites (TFBS), indicating that they could regulate the expression of related genes through TF regulation. Following allelic trend analysis revealed that the DNA damage levels were significantly aggravated with the increasing number of risk variants in autophagy associated genes (P for trend: 8.09×10-5). Our findings suggested that the polymorphisms in ATGs may influence DNA damage levels in one of the Chinese population.
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Affiliation(s)
- Zhihua Li
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Junyi Xin
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Weihong Chen
- Ministry of Education Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jia Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Meng Zhu
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Congwen Zhao
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jing Yuan
- Ministry of Education Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Guangfu Jin
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Hongxia Ma
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jiangbo Du
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Zhibin Hu
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Tangchun Wu
- Ministry of Education Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Hongbing Shen
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Juncheng Dai
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Hao Yu
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China.
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Etemadi A, Islami F, Phillips DH, Godschalk R, Golozar A, Kamangar F, Malekshah AFT, Pourshams A, Elahi S, Ghojaghi F, Strickland PT, Taylor PR, Boffetta P, Abnet CC, Dawsey SM, Malekzadeh R, van Schooten FJ. Variation in PAH-related DNA adduct levels among non-smokers: the role of multiple genetic polymorphisms and nucleotide excision repair phenotype. Int J Cancer 2013; 132:2738-47. [PMID: 23175176 PMCID: PMC3597757 DOI: 10.1002/ijc.27953] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 11/02/2012] [Indexed: 02/03/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) likely play a role in many cancers even in never-smokers. We tried to find a model to explain the relationship between variation in PAH-related DNA adduct levels among people with similar exposures, multiple genetic polymorphisms in genes related to metabolic and repair pathways, and nucleotide excision repair (NER) capacity. In 111 randomly selected female never-smokers from the Golestan Cohort Study in Iran, we evaluated 21 SNPs in 14 genes related to xenobiotic metabolism and 12 SNPs in eight DNA repair genes. NER capacity was evaluated by a modified comet assay, and aromatic DNA adduct levels were measured in blood by32P-postlabeling. Multivariable regression models were compared by Akaike's information criterion (AIC). Aromatic DNA adduct levels ranged between 1.7 and 18.6 per 10(8) nucleotides (mean: 5.8 ± 3.1). DNA adduct level was significantly lower in homozygotes for NAT2 slow alleles and ERCC5 non-risk-allele genotype, and was higher in the MPO homozygote risk-allele genotype. The sum of risk alleles in these genes significantly correlated with the log-adduct level (r = 0.4, p < 0.001). Compared with the environmental model, adding Phase I SNPs and NER capacity provided the best fit, and could explain 17% more of the variation in adduct levels. NER capacity was affected by polymorphisms in the MTHFR and ERCC1 genes. Female non-smokers in this population had PAH-related DNA adduct levels three to four times higher than smokers and occupationally-exposed groups in previous studies, with large inter-individual variation which could best be explained by a combination of Phase I genes and NER capacity.
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Affiliation(s)
- Arash Etemadi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20852, USA.
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Arita A, Muñoz A, Chervona Y, Niu J, Qu Q, Zhao N, Ruan Y, Kiok K, Kluz T, Sun H, Clancy HA, Shamy M, Costa M. Gene expression profiles in peripheral blood mononuclear cells of Chinese nickel refinery workers with high exposures to nickel and control subjects. Cancer Epidemiol Biomarkers Prev 2013; 22:261-9. [PMID: 23195993 PMCID: PMC3565097 DOI: 10.1158/1055-9965.epi-12-1011] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Occupational exposure to nickel (Ni) is associated with an increased risk of lung and nasal cancers. Ni compounds exhibit weak mutagenic activity, alter the cell's epigenetic homeostasis, and activate signaling pathways. However, changes in gene expression associated with Ni exposure have only been investigated in vitro. This study was conducted in a Chinese population to determine whether occupational exposure to Ni was associated with differential gene expression profiles in the peripheral blood mononuclear cells (PBMC) of Ni-refinery workers when compared with referents. METHODS Eight Ni-refinery workers and ten referents were selected. PBMC RNA was extracted and gene expression profiling was conducted using Affymetrix exon arrays. Differentially expressed genes (DEG) between both groups were identified in a global analysis. RESULTS There were a total of 2,756 DEGs in the Ni-refinery workers relative to the referents [false discovery rate (FDR) adjusted P < 0.05] with 770 upregulated genes and 1,986 downregulated genes. DNA repair and epigenetic genes were significantly overrepresented (P < 0.0002) among the DEGs. Of 31 DNA repair genes, 29 were repressed in the Ni-refinery workers and 2 were overexpressed. Of the 16 epigenetic genes, 12 were repressed in the Ni-refinery workers and 4 were overexpressed. CONCLUSIONS The results of this study indicate that occupational exposure to Ni is associated with alterations in gene expression profiles in PBMCs of subjects. IMPACT Gene expression may be useful in identifying patterns of deregulation that precede clinical identification of Ni-induced cancers.
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Affiliation(s)
- Adriana Arita
- New York University School of Medicine, Nelson Institute of Environmental Medicine, 57 Old Forge Road, NY 10987
| | - Alexandra Muñoz
- New York University School of Medicine, Nelson Institute of Environmental Medicine, 57 Old Forge Road, NY 10987
| | - Yana Chervona
- New York University School of Medicine, Nelson Institute of Environmental Medicine, 57 Old Forge Road, NY 10987
| | - Jingping Niu
- Lanzhou University School of Public Health, Lanzhou, China
| | - Qingshan Qu
- New York University School of Medicine, Nelson Institute of Environmental Medicine, 57 Old Forge Road, NY 10987
| | - Najuan Zhao
- Lanzhou University School of Public Health, Lanzhou, China
| | - Ye Ruan
- Lanzhou University School of Public Health, Lanzhou, China
| | - Kathrin Kiok
- New York University School of Medicine, Nelson Institute of Environmental Medicine, 57 Old Forge Road, NY 10987
| | - Thomas Kluz
- New York University School of Medicine, Nelson Institute of Environmental Medicine, 57 Old Forge Road, NY 10987
| | - Hong Sun
- New York University School of Medicine, Nelson Institute of Environmental Medicine, 57 Old Forge Road, NY 10987
| | - Hailey A. Clancy
- New York University School of Medicine, Nelson Institute of Environmental Medicine, 57 Old Forge Road, NY 10987
| | - Magdy Shamy
- King Abdulaziz University, Department of Environmental Sciences, Faculty of Meteorology, Environment and Arid Land Agriculture, Jeddah, Saudi Arabia
| | - Max Costa
- New York University School of Medicine, Nelson Institute of Environmental Medicine, 57 Old Forge Road, NY 10987
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Vuskovic M, Barbuti AM, Goldsmith-Rooney E, Glassman L, Bovin N, Pass H, Tchou-Wong KM, Chen M, Yan B, Niu J, Qu Q, Costa M, Huflejt M. Plasma Anti-Glycan Antibody Profiles Associated with Nickel level in Urine. ACTA ACUST UNITED AC 2013; 6:302-312. [PMID: 24737927 PMCID: PMC3984841 DOI: 10.4172/jpb.1000295] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Nickel (Ni) compounds are widely used in industrial and commercial products including household and cooking utensils, jewelry, dental appliances and implants. Occupational exposure to nickel is associated with an increased risk for lung and nasal cancers, is the most common cause of contact dermatitis and has an extensive effect on the immune system. The purpose of this study was two-fold: (i) to evaluate immune response to the occupational exposure to nickel measured by the presence of anti-glycan antibodies (AGA) using a new biomarker-discovery platform based on printed glycan arrays (PGA), and (ii) to evaluate and compile a sequence of bioinformatics and statistical methods which are specifically relevant to PGA-derived information and to identification of putative "Ni toxicity signature". The PGAs are similar to DNA microarrays, but contain deposits of various carbohydrates (glycans) instead of spotted DNAs. The study uses data derived from a set of 89 plasma specimens and their corresponding demographic information. The study population includes three subgroups: subjects directly exposed to Nickel that work in a refinery, subjects environmentally exposed to Nickel that live in a city where the refinery is located and subjects that live in a remote location. The paper describes the following sequence of nine data processing and analysis steps: (1) Analysis of inter-array reproducibility based on benchmark sera; (2) Analysis of intra-array reproducibility; (3) Screening of data - rejecting glycans which result in low intra-class correlation coefficient (ICC), high coefficient of variation and low fluorescent intensity; (4) Analysis of inter-slide bias and choice of data normalization technique; (5) Determination of discriminatory subsamples based on multiple bootstrap tests; (6) Determination of the optimal signature size (cardinality of selected feature set) based on multiple cross-validation tests; (7) Identification of the top discriminatory glycans and their individual performance based on nonparametric univariate feature selection; (8) Determination of multivariate performance of combined glycans; (9) Establishing the statistical significance of multivariate performance of combined glycan signature. The above analysis steps have delivered the following results: inter-array reproducibility ρ=0.920 ± 0.030; intra-array reproducibility ρ=0.929 ± 0.025; 249 out of 380 glycans passed the screening at ICC>80%, glycans in selected signature have ICC ≥ 88.7%; optimal signature size (after quantile normalization)=3; individual significance for the signature glycans p=0.00015 to 0.00164, individual AUC values 0.870 to 0.815; observed combined performance for three glycans AUC=0.966, p=0.005, CI=[0.757, 0947]; specifity=94.4%, sensitivity=88.9%; predictive (cross-validated) AUC value 0.836.
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Affiliation(s)
- Marko Vuskovic
- Department of Computer Science, San Diego State University, San Diego, 92182 CA, USA
| | - Anna-Maria Barbuti
- Department of Cardiothoracic Surgery, NYU School of Medicine, New York, 10016 NY, USA
| | - Emma Goldsmith-Rooney
- Department of Cardiothoracic Surgery, NYU School of Medicine, New York, 10016 NY, USA
| | - Laura Glassman
- Department of Cardiothoracic Surgery, NYU School of Medicine, New York, 10016 NY, USA
| | - Nicolai Bovin
- Shemyakin Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Harvey Pass
- Department of Cardiothoracic Surgery, NYU School of Medicine, New York, 10016 NY, USA
| | - Kam-Meng Tchou-Wong
- Department of Environmental Medicine, NYU School of Medicine, New York, 10016 NY, USA
| | - Meichi Chen
- Lanzhou University School of Public Health, Lanzhou, Gansu 730000, China
| | - Bing Yan
- Lanzhou University School of Public Health, Lanzhou, Gansu 730000, China
| | - Jingping Niu
- Lanzhou University School of Public Health, Lanzhou, Gansu 730000, China
| | - Qingshan Qu
- Department of Environmental Medicine, NYU School of Medicine, New York, 10016 NY, USA
| | - Max Costa
- Department of Environmental Medicine, NYU School of Medicine, New York, 10016 NY, USA
| | - Margaret Huflejt
- Department of Cardiothoracic Surgery, NYU School of Medicine, New York, 10016 NY, USA
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Arita A, Niu J, Qu Q, Zhao N, Ruan Y, Nadas A, Chervona Y, Wu F, Sun H, Hayes RB, Costa M. Global levels of histone modifications in peripheral blood mononuclear cells of subjects with exposure to nickel. ENVIRONMENTAL HEALTH PERSPECTIVES 2012; 120:198-203. [PMID: 22024396 PMCID: PMC3279455 DOI: 10.1289/ehp.1104140] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Accepted: 10/24/2011] [Indexed: 05/03/2023]
Abstract
BACKGROUND Occupational exposure to nickel (Ni) is associated with an increased risk for lung and nasal cancers. Ni compounds exhibit weak mutagenic activity, cause gene amplification, and disrupt cellular epigenetic homeostasis. However, the Ni-induced changes in global histone modification levels have only been tested in vitro. OBJECTIVE This study was conducted in a Chinese population to determine whether occupational exposure to Ni is associated with alterations of global histone modification levels and to evaluate the inter- and intraindividual variance of global histone modification levels. METHOD Forty-five subjects with occupational exposure to Ni and 75 referents were recruited. Urinary Ni and global H3K4 trimethylation, H3K9 acetylation, and H3K9 dimethylation levels were measured in peripheral blood mononuclear cells (PBMCs) of subjects. RESULTS H3K4me3 was elevated in Ni-exposed subjects (0.25% ± 0.11%) compared with referents (0.15% ± 0.04%; p = 0.0004), and H3K9me2 was decreased (Ni-exposed subjects, 0.11% ± 0.05%; referents, 0.15% ± 0.04%; p = 0.003). H3K4me3 was positively (r = 0.4, p = 0.0008) and H3K9ac was negatively (r = 0.1, p = 0.01) associated with urinary Ni. Interindividual variances of H3K4me3, H3K9ac, and H3K9me2 were larger compared with intraindividual variance in both exposure test groups, resulting in reliability coefficients (an estimate of consistency of a set of measurements) of 0.60, 0.67, and 0.79 for H3K4me3, H3K9ac, and H3K9me2, respectively, for Ni-exposed subjects and of 0.75, 0.74, and 0.97, respectively, for referent subjects. CONCLUSION The results of this study indicate that occupational exposure to Ni is associated with alterations of global histone modification levels and that measurements of global levels of histone modifications are relatively stable over time in human PBMCs.
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Affiliation(s)
- Adriana Arita
- Department of Environmental Medicine, New York University School of Medicine, New York, New York, USA
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McCarty KM, Santella RM, Steck SE, Cleveland RJ, Ahn J, Ambrosone CB, North K, Sagiv SK, Eng SM, Teitelbaum SL, Neugut AI, Gammon MD. PAH-DNA adducts, cigarette smoking, GST polymorphisms, and breast cancer risk. ENVIRONMENTAL HEALTH PERSPECTIVES 2009; 117:552-8. [PMID: 19440493 PMCID: PMC2679598 DOI: 10.1289/ehp.0800119] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2008] [Accepted: 12/08/2008] [Indexed: 05/21/2023]
Abstract
BACKGROUND Polycyclic aromatic hydrocarbons (PAHs) may increase breast cancer risk, and the association may be modified by inherited differences in deactivation of PAH intermediates by glutathione S-transferases (GSTs). Few breast cancer studies have investigated the joint effects of multiple GSTs and a PAH biomarker. OBJECTIVE We estimated the breast cancer risk associated with multiple polymorphisms in the GST gene (GSTA1, GSTM1, GSTP1, and GSTT1) and the interaction with PAH-DNA adducts and cigarette smoking. METHODS We conducted unconditional logistic regression using data from a population-based sample of women (cases/controls, respectively): GST polymorphisms were genotyped using polymerase chain reaction and matrix-assisted laser desorption/ionization time-of-flight assays (n = 926 of 916), PAH-DNA adduct blood levels were measured by competitive enzyme-linked immunosorbent assay (n = 873 of 941), and smoking status was assessed by in-person questionnaires (n = 943 of 973). RESULTS Odds ratios for joint effects on breast cancer risk among women with at least three variant alleles were 1.56 [95% confidence interval (CI), 1.13-2.16] for detectable PAH-DNA adducts and 0.93 (95% CI, 0.56-1.56) for no detectable adducts; corresponding odds ratios for three or more variants were 1.18 (95% CI, 0.82-1.69) for ever smokers and 1.44 (95% CI, 0.97-2.14) for never smokers. Neither interaction was statistically significant (p = 0.43 and 0.62, respectively). CONCLUSION We found little statistical evidence that PAHs interacted with GSTT1, GSTM1, GSTP1, and GSTA1 polymorphisms to further increase breast cancer risk.
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Affiliation(s)
- Kathleen M McCarty
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
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