1
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Zou Z, Xu C, Li Z, Yang Y, Li Y, Sun Z, Li Q, Li M, Chen Y, Jiang G, Xiao M, Guo S, Wang Y, Wang H, Xia F, Shang Y, Wu J. Significance of Gastrokine-1 Polymorphism Rs4254535 as a Prognostic Marker and its Association with Clinical Characteristics in Chinese Lung Cancer Patients. Int J Med Sci 2024; 21:474-482. [PMID: 38250608 PMCID: PMC10797674 DOI: 10.7150/ijms.90145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 12/01/2023] [Indexed: 01/23/2024] Open
Abstract
Background: The single nucleotide polymorphism (SNP) of Gastrokine-1 (GKN1) is associated with lung cancer but its association with prognosis is not clear. Methods: Genomic DNA was extracted from the blood samples of 888 patients with lung cancer. The association between GKN1 polymorphism rs4254535 and prognostic was analyzed by the Kaplan-Meier (KM) method, Log-rank test, and Cox proportional hazards model. Results: In females and patients diagnosed with late-stage lung cancer, the CC genotype (CC vs TT, adjusted odds ratio [HR] = 0.57, 95% Confidence Interval [CI]: 0.33-0.99, P = 0.045; HR = 0.66, 95% CI: 0.48-0.92, P = 0.014) and recessive CC genotype (CC vs TT + TC, HR = 0.55, 95% CI: 0.32-0.94, P = 0.028; HR = 0.64, 95% CI: 0.47-0.89, P = 0.006) of rs4254535 conferred a better prognosis, compared with the TT and TT + TC genotype. Rs4254535 dominate TC + CC genotype, recessive CC genotype, and C allele who were adenocarcinoma patients had a significantly better prognosis. The recessive CC genotype of non-smoking patients has a better prognosis, compared to the TT + TC genotype. Additionally, in the dominant TT + TC genotype and C allele, no family history patients had a significantly better prognosis, compared to the TT genotype. Conclusion: For lung cancer patients, GKN1 polymorphism rs4254535 may be a protective genetic marker and predicts the prognosis of lung cancer patients.
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Affiliation(s)
- Zixiu Zou
- School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Chang Xu
- Clinical College of Xiangnan University, Chenzhou, 423000, China
| | - Zhengxing Li
- Department of Surgery, Navy Military Medical University Affiliated to Changhai Hospital, Shanghai, China
| | - Yajun Yang
- School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yutao Li
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics & Development, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Zhenyu Sun
- School of Basic Medicine, Navy Military Medical University, Shanghai, 200433, China
| | - Qiang Li
- Department of Respiratory and Critical Care Medicine, Shanghai East Hospital, Tongji University, Shanghai, 200120, China
| | - Miao Li
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Yuxin Chen
- Nanjing Medical University, The Fourth Clinical Medical College, Nanjing, 211166, China
| | - Gengxi Jiang
- Department of Thoracic Surgery, Navy Military Medical University Affiliated Changhai Hospital, Shanghai, 200433, China
| | - Man Xiao
- Department of Biochemistry and Molecular Biology, Hainan Medical University, Haikou, 571199, China
| | - Shicheng Guo
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics & Development, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yi Wang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics & Development, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Haijian Wang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics & Development, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Fan Xia
- Department of Respiratory Disease, Navy 905 Hospital, Shanghai, 200235, China
| | - Yan Shang
- Department of Respiratory and Critical Care Medicine, Shanghai Changhai Hospital, the First Afliated Hospital of Naval Medical University, Shanghai 200433, China
- Department of General Medicine, the First Afliated Hospital of Naval Medical University, Shanghai 200433, China
| | - Junjie Wu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics & Development, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- Department of Pulmonary and Critical Care Medicine, Shanghai Geriatric Medical Center, Shanghai, 200032, China
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2
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Ahmed F, Samantasinghar A, Manzoor Soomro A, Kim S, Hyun Choi K. A systematic review of computational approaches to understand cancer biology for informed drug repurposing. J Biomed Inform 2023; 142:104373. [PMID: 37120047 DOI: 10.1016/j.jbi.2023.104373] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/25/2023] [Accepted: 04/23/2023] [Indexed: 05/01/2023]
Abstract
Cancer is the second leading cause of death globally, trailing only heart disease. In the United States alone, 1.9 million new cancer cases and 609,360 deaths were recorded for 2022. Unfortunately, the success rate for new cancer drug development remains less than 10%, making the disease particularly challenging. This low success rate is largely attributed to the complex and poorly understood nature of cancer etiology. Therefore, it is critical to find alternative approaches to understanding cancer biology and developing effective treatments. One such approach is drug repurposing, which offers a shorter drug development timeline and lower costs while increasing the likelihood of success. In this review, we provide a comprehensive analysis of computational approaches for understanding cancer biology, including systems biology, multi-omics, and pathway analysis. Additionally, we examine the use of these methods for drug repurposing in cancer, including the databases and tools that are used for cancer research. Finally, we present case studies of drug repurposing, discussing their limitations and offering recommendations for future research in this area.
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Affiliation(s)
- Faheem Ahmed
- Department of Mechatronics Engineering, Jeju National University, Republic of Korea
| | | | | | - Sejong Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea; Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea.
| | - Kyung Hyun Choi
- Department of Mechatronics Engineering, Jeju National University, Republic of Korea.
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3
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Liu L, Liu H, Luo S, Patz EF, Glass C, Su L, Lin L, Christiani DC, Wei Q. Genetic Variants of CLEC4E and BIRC3 in Damage-Associated Molecular Patterns-Related Pathway Genes Predict Non-Small Cell Lung Cancer Survival. Front Oncol 2021; 11:717109. [PMID: 34692492 PMCID: PMC8527850 DOI: 10.3389/fonc.2021.717109] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 09/13/2021] [Indexed: 11/25/2022] Open
Abstract
Accumulating evidence supports a role of various damage-associated molecular patterns (DAMPs) in progression of lung cancer, but roles of genetic variants of the DAMPs-related pathway genes in lung cancer survival remain unknown. We investigated associations of 18,588 single-nucleotide polymorphisms (SNPs) in 195 DAMPs-related pathway genes with non-small cell lung cancer (NSCLC) survival in a subset of genotyping data for 1,185 patients from the Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial and validated the findings in another independent subset of genotyping data for 984 patients from Harvard Lung Cancer Susceptibility Study. We performed multivariate Cox proportional hazards regression analysis, followed by expression quantitative trait loci (eQTL) analysis, Kaplan-Meier survival analysis and bioinformatics functional prediction. We identified that two SNPs (i.e., CLEC4E rs10841847 G>A and BIRC3 rs11225211 G>A) were independently associated with NSCLC overall survival, with adjusted allelic hazards ratios of 0.89 (95% confidence interval=0.82-0.95 and P=0.001) and 0.82 (0.73-0.91 and P=0.0003), respectively; so were their combined predictive alleles from discovery and replication datasets (Ptrend=0.0002 for overall survival). We also found that the CLEC4E rs10841847 A allele was associated with elevated mRNA expression levels in normal lymphoblastoid cells and whole blood cells, while the BIRC3 rs11225211 A allele was associated with increased mRNA expression levels in normal lung tissues. Collectively, these findings indicated that genetic variants of CLEC4E and BIRC3 in the DAMPs-related pathway genes were associated with NSCLC survival, likely by regulating the mRNA expression of the corresponding genes.
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Affiliation(s)
- Lihua Liu
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.,Duke Cancer Institute, Duke University Medical Center, Durham, NC, United States.,Department of Population Health Sciences, Duke University School of Medicine, Durham, NC, United States
| | - Hongliang Liu
- Duke Cancer Institute, Duke University Medical Center, Durham, NC, United States.,Department of Population Health Sciences, Duke University School of Medicine, Durham, NC, United States
| | - Sheng Luo
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, United States
| | - Edward F Patz
- Duke Cancer Institute, Duke University Medical Center, Durham, NC, United States.,Department of Radiology, Duke University Medical Center, Durham, NC, United States.,Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, United States
| | - Carolyn Glass
- Duke Cancer Institute, Duke University Medical Center, Durham, NC, United States.,Department of Pathology, Duke University School of Medicine, Durham, NC, United States
| | - Li Su
- Departments of Environmental Health and Department of Epidemiology, Harvard School of Public Health, Boston, MA, United States
| | - Lijuan Lin
- Departments of Environmental Health and Department of Epidemiology, Harvard School of Public Health, Boston, MA, United States
| | - David C Christiani
- Departments of Environmental Health and Department of Epidemiology, Harvard School of Public Health, Boston, MA, United States.,Department of Medicine, Massachusetts General Hospital, Boston, MA, United States
| | - Qingyi Wei
- Duke Cancer Institute, Duke University Medical Center, Durham, NC, United States.,Department of Population Health Sciences, Duke University School of Medicine, Durham, NC, United States.,Department of Medicine, Duke University Medical Center, Durham, NC, United States
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4
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Jiang Y, Huang Y, Du Y, Zhao Y, Ren J, Ma S, Wu C. Identification of Prognostic Genes and Pathways in Lung Adenocarcinoma Using a Bayesian Approach. Cancer Inform 2020; 16:1176935116684825. [PMID: 33354107 PMCID: PMC7736146 DOI: 10.1177/1176935116684825] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 11/24/2016] [Indexed: 01/02/2023] Open
Abstract
Lung cancer is the leading cause of cancer-associated mortality in the United States and the world. Adenocarcinoma, the most common subtype of lung cancer, is generally diagnosed at the late stage with poor prognosis. In the past, extensive effort has been devoted to elucidating lung cancer pathogenesis and pinpointing genes associated with survival outcomes. As the progression of lung cancer is a complex process that involves coordinated actions of functionally associated genes from cancer-related pathways, there is a growing interest in simultaneous identification of both prognostic pathways and important genes within those pathways. In this study, we analyse The Cancer Genome Atlas lung adenocarcinoma data using a Bayesian approach incorporating the pathway information as well as the interconnections among genes. The top 11 pathways have been found to play significant roles in lung adenocarcinoma prognosis, including pathways in mitogen-activated protein kinase signalling, cytokine-cytokine receptor interaction, and ubiquitin-mediated proteolysis. We have also located key gene signatures such as RELB, MAP4K1, and UBE2C. These results indicate that the Bayesian approach may facilitate discovery of important genes and pathways that are tightly associated with the survival of patients with lung adenocarcinoma.
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Affiliation(s)
- Yu Jiang
- Division of Epidemiology, Biostatistics
and Environmental Health, School of Public Health, University of Memphis, Memphis,
TN, USA
- Cooperative Studies Program, VA
Connecticut Healthcare System, West Haven, CT, USA
| | - Yuan Huang
- Cooperative Studies Program, VA
Connecticut Healthcare System, West Haven, CT, USA
- Department of Biostatistics, Yale
University, New Haven, CT, USA
| | - Yinhao Du
- Department of Statistics, Kansas State
University, Manhattan, KS, USA
| | - Yinjun Zhao
- Department of Biostatistics, Yale
University, New Haven, CT, USA
| | - Jie Ren
- Department of Statistics, Kansas State
University, Manhattan, KS, USA
| | - Shuangge Ma
- Cooperative Studies Program, VA
Connecticut Healthcare System, West Haven, CT, USA
- Department of Biostatistics, Yale
University, New Haven, CT, USA
| | - Cen Wu
- Department of Statistics, Kansas State
University, Manhattan, KS, USA
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5
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Abstract
Hepatocellular carcinoma (HCC) is one of the most common cancers and a leading cause of cancer-related deaths worldwide. Early diagnosis of HCC remains a great challenge in clinic. Novel and effective biomarkers are in urgent need in early diagnosis of HCC.Serum levels of neurotrophin-receptor-interacting melanoma antigen-encoding gene homolog (NRAGE) were measured for 107 patients with HCC, 98 patients with benign liver diseases, and 89 healthy controls using quantitative real-time polymerase chain reaction. Receiver operating characteristic curve was applied to evaluate the diagnostic capacity of serum NRAGE in HCC.NRAGE expression was significantly higher in patients with HCC than in controls (all, P < .05). Moreover, its expression was tightly correlated with TNM stage (P = .004). NRAGE could distinguish patients with HCC from healthy controls with the area under the curve (AUC) of 0.874, yielding a sensitivity of 81.3% and a specificity of 78.7%. Additionally, in differentiation between benign liver diseases and HCC, the AUC value of NRAGE was 0.726, with a sensitivity of 63.6% and a specificity of 73.5%. Meanwhile, alpha-fetoprotein also could distinguish patients with HCC from benign liver disease cases, with an AUC of 0.677, a sensitivity of 64.4%, and a specificity of 60.2%.NRAGE could be a potential biomarker for HCC early diagnosis.
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6
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Bossé Y, Amos CI. A Decade of GWAS Results in Lung Cancer. Cancer Epidemiol Biomarkers Prev 2018; 27:363-379. [PMID: 28615365 PMCID: PMC6464125 DOI: 10.1158/1055-9965.epi-16-0794] [Citation(s) in RCA: 143] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 12/06/2016] [Accepted: 04/20/2017] [Indexed: 01/03/2023] Open
Abstract
Genome-wide association studies (GWAS) were successful to identify genetic factors robustly associated with lung cancer. This review aims to synthesize the literature in this field and accelerate the translation of GWAS discoveries into results that are closer to clinical applications. A chronologic presentation of published GWAS on lung cancer susceptibility, survival, and response to treatment is presented. The most important results are tabulated to provide a concise overview in one read. GWAS have reported 45 lung cancer susceptibility loci with varying strength of evidence and highlighted suspected causal genes at each locus. Some genetic risk loci have been refined to more homogeneous subgroups of lung cancer patients in terms of histologic subtypes, smoking status, gender, and ethnicity. Overall, these discoveries are an important step for future development of new therapeutic targets and biomarkers to personalize and improve the quality of care for patients. GWAS results are on the edge of offering new tools for targeted screening in high-risk individuals, but more research is needed if GWAS are to pay off the investment. Complementary genomic datasets and functional studies are needed to refine the underlying molecular mechanisms of lung cancer preliminarily revealed by GWAS and reach results that are medically actionable. Cancer Epidemiol Biomarkers Prev; 27(4); 363-79. ©2018 AACRSee all articles in this CEBP Focus section, "Genome-Wide Association Studies in Cancer."
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Affiliation(s)
- Yohan Bossé
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Quebec, Canada.
- Department of Molecular Medicine, Laval University, Quebec, Canada
| | - Christopher I Amos
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
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7
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Tan J, Fu L, Chen H, Guan J, Chen Y, Fang J. Association study of genetic variation in the autophagy lysosome pathway genes and risk of eight kinds of cancers. Int J Cancer 2018; 143:80-87. [PMID: 29388190 DOI: 10.1002/ijc.31288] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 12/20/2017] [Accepted: 01/11/2018] [Indexed: 12/20/2022]
Abstract
The autophagy lysosome pathway is essential to maintain cell viability and homeostasis in response to many stressful environments, which is reported to play a vital role in cancer development and therapy. However, the association of genetic alterations of this pathway with risk of cancer remains unclear. Based on genome-wide association study data of eight kinds of cancers, we used an adaptive rank truncated product approach to perform a pathway-level and gene-level analysis, and used a logistic model to calculate SNP-level associations to examine whether an altered autophagy lysosome pathway contributes to cancer susceptibility. Among eight kinds of cancers, four of them showed significant statistics in the pathway-level analysis, including breast cancer (p = 0.00705), gastric cancer (p = 0.00880), lung cancer (p = 0.000100) and renal cell carcinoma (p = 0.00190). We also found that some autophagy lysosome genes had signals of association with cancer risk. Our results demonstrated that inherited genetic variants in the overall autophagy lysosome pathway and certain associated genes might contribute to cancer susceptibility, which warrant further evaluation in other independent datasets.
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Affiliation(s)
- Juan Tan
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai 200001, China
| | - Linna Fu
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai 200001, China
| | - Haoyan Chen
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai 200001, China
| | - Jian Guan
- Department of Otolaryngology Head and Neck Surgery & Center of Sleep Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Otolaryngological Institute of Shanghai Jiao Tong University, Shanghai, China
| | - Yingxuan Chen
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai 200001, China
| | - Jingyuan Fang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai 200001, China
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8
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Kiser JN, Neupane M, White SN, Neibergs HL. Identification of genes associated with susceptibility to Mycobacterium avium ssp. paratuberculosis (Map) tissue infection in Holstein cattle using gene set enrichment analysis-SNP. Mamm Genome 2017; 29:539-549. [PMID: 29185027 DOI: 10.1007/s00335-017-9725-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 11/18/2017] [Indexed: 02/07/2023]
Abstract
Multiple genome-wide association analyses have investigated susceptibility to bovine paratuberculosis, but few loci have been identified across independent cattle populations. A SNP-based gene set enrichment analysis (GSEA-SNP) allows expanded identification of genes with moderate effects on a trait through the enrichment of gene sets instead of identifying only few loci with large effects. Therefore, the objective of this study was to identify genes that were moderately associated with Mycobacterium avium ssp. paratuberculosis (Map) tissue infection using GSEA-SNP in Holstein cattle from the Pacific Northwest (PNW; n = 205) and from the PNW and Northeast (PNW+NE; n = 245) which were previously genotyped with the Illumina BovineSNP50 BeadChip. The GSEA-SNP utilized 4389 gene sets from five databases. For each annotated gene in the UMD3.1 assembly (n = 19,723), the most significant SNP within each gene and its surrounding region (10 kb up- and downstream) was selected as a proxy for that gene. Any gene set with a normalized enrichment score > 2.5 was considered enriched. Thirteen gene sets (8 PNW GSEA-SNP; 5 PNW+NE) were enriched in these analyses and all have functions that relate to nuclear factor kappa beta. Nuclear factor kappa beta is critical to gut immune responses, implicated in host immune responses to other mycobacterial diseases, and has established roles in inflammation as well as cancer. Gene sets and genes moderately associated with Map infection could be used in genomic selection to allow producers to select for less susceptible cattle, lower the prevalence of the disease, and reduce economic losses.
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Affiliation(s)
- J N Kiser
- Department of Animal Sciences, Washington State University, Pullman, WA, 99164, USA.
| | - M Neupane
- Department of Animal Sciences, Washington State University, Pullman, WA, 99164, USA
| | - S N White
- USDA-ARS Animal Disease Research Unit, Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, 99164, USA
| | - H L Neibergs
- Department of Animal Sciences, Washington State University, Pullman, WA, 99164, USA
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9
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Identification of additional loci associated with antibody response to Mycobacterium avium ssp. Paratuberculosis in cattle by GSEA-SNP analysis. Mamm Genome 2017; 28:520-527. [PMID: 28864882 DOI: 10.1007/s00335-017-9714-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Accepted: 08/27/2017] [Indexed: 10/18/2022]
Abstract
Mycobacterium avium subsp. paratuberculosis: (MAP) causes a contagious chronic infection results in Johne's disease in a wide range of animal species, including cattle. Several genome-wide association studies (GWAS) have been carried out to identify loci putatively associated with MAP susceptibility by testing each marker separately and identifying SNPs that show a significant association with the phenotype, while SNP with modest effects are usually ignored. The objective of this study was to identify modest-effect genes associated with MAP susceptibility using a pathway-based approach. The Illumina BovineSNP50 BeadChip was used to genotype 966 Holstein cows, 483 positive and 483 negative for antibody response to MAP, data were then analyzed using novel SNP-based Gene Set Enrichment Analysis (GSEA-SNP) and validated with Adaptive Rank Truncated Product methodology. An allele-based test was carried out to estimate the statistical association for each marker with the phenotype, subsequently SNPs were mapped to the closest genes, considering for each gene the single variant with the highest value within a window of 50 kb, then pathway-statistics were tested using the GSEA-SNP method. The GO biological process "embryogenesis and morphogenesis" was most highly associated with antibody response to MAP. Within this pathway, five genes code for proteins which play a role in the immune defense relevant to response to bacterial infection. The immune response genes identified would not have been considered using a standard GWAS, thus demonstrating that the pathway approach can extend the interpretation of genome-wide association analyses and identify additional candidate genes for target traits.
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10
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Zhou Y, Huang N, Wu J, Zhen N, Li N, Li Y, Li YX. Silencing of NRAGE induces autophagy via AMPK/Ulk1/Atg13 signaling pathway in NSCLC cells. Tumour Biol 2017. [PMID: 28639909 DOI: 10.1177/1010428317709676] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Affiliation(s)
- Yiyang Zhou
- Department of Oncology, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Nan Huang
- Department of Clinical Laboratory Medicine, Shanghai Tenth People’s Hospital of Tongji University, Shanghai, China
| | - Jianchun Wu
- Department of Oncology, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Ni Zhen
- Department of Clinical Laboratory Medicine, Shanghai Tenth People’s Hospital of Tongji University, Shanghai, China
| | - Ning Li
- Central Laboratory, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yan Li
- Department of Oncology, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yong-Xin Li
- Department of Oncology, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Central Laboratory, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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11
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Jia M, Zhu M, Zhou F, Wang M, Sun M, Yang Y, Wang X, Wang J, Jin L, Xiang J, Zhang Y, Chang J, Wei Q. Genetic variants of JNK and p38α pathways and risk of non-small cell lung cancer in an Eastern Chinese population. Int J Cancer 2016; 140:807-817. [DOI: 10.1002/ijc.30508] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 10/19/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Ming Jia
- Cancer Institute, Collaborative Innovation Center for Cancer Medicine, Fudan University Shanghai Cancer Center; Shanghai China
- Department of Oncology; Shanghai Medical College, Fudan University; Shanghai China
| | - Meiling Zhu
- Department of Oncology; Xinhua Hospital affiliated to Shanghai Jiaotong University, School of Medicine; Shanghai China
| | - Fei Zhou
- Cancer Institute, Collaborative Innovation Center for Cancer Medicine, Fudan University Shanghai Cancer Center; Shanghai China
- Department of Oncology; Shanghai Medical College, Fudan University; Shanghai China
| | - Mengyun Wang
- Cancer Institute, Collaborative Innovation Center for Cancer Medicine, Fudan University Shanghai Cancer Center; Shanghai China
- Department of Oncology; Shanghai Medical College, Fudan University; Shanghai China
| | - Menghong Sun
- Department of Oncology; Shanghai Medical College, Fudan University; Shanghai China
- Department of Pathology; Fudan University Shanghai Cancer Center; Xuhui, Shanghai China
| | - Yajun Yang
- Ministry of Education Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, School of Life Sciences; Fudan University; Shanghai China
- Fudan-Taizhou Institute of Health Sciences; Taizhou Jiangsu China
| | - Xiaofeng Wang
- Ministry of Education Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, School of Life Sciences; Fudan University; Shanghai China
- Fudan-Taizhou Institute of Health Sciences; Taizhou Jiangsu China
| | - Jiucun Wang
- Ministry of Education Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, School of Life Sciences; Fudan University; Shanghai China
- Fudan-Taizhou Institute of Health Sciences; Taizhou Jiangsu China
| | - Li Jin
- Ministry of Education Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, School of Life Sciences; Fudan University; Shanghai China
- Fudan-Taizhou Institute of Health Sciences; Taizhou Jiangsu China
| | - Jiaqing Xiang
- Department of Oncology; Shanghai Medical College, Fudan University; Shanghai China
- Department of Thoracic Surgery; Fudan University Shanghai Cancer Center; Xuhui, Shanghai China
| | - Yawei Zhang
- Department of Oncology; Shanghai Medical College, Fudan University; Shanghai China
- Department of Thoracic Surgery; Fudan University Shanghai Cancer Center; Xuhui, Shanghai China
| | - Jianhua Chang
- Department of Oncology; Shanghai Medical College, Fudan University; Shanghai China
- Department of Medical Oncology; Fudan University Shanghai Cancer Center; Xuhui, Shanghai China
| | - Qingyi Wei
- Cancer Institute, Collaborative Innovation Center for Cancer Medicine, Fudan University Shanghai Cancer Center; Shanghai China
- Department of Oncology; Shanghai Medical College, Fudan University; Shanghai China
- Duke Cancer Institute, Duke University Medical Center, and Department of Medicine; Duke University School of Medicine; Durham NC
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12
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Wang M, Liu H, Liu Z, Yi X, Bickeboller H, Hung RJ, Brennan P, Landi MT, Caporaso N, Christiani DC, Doherty JA, Amos CI, Wei Q. Genetic variant in DNA repair gene GTF2H4 is associated with lung cancer risk: a large-scale analysis of six published GWAS datasets in the TRICL consortium. Carcinogenesis 2016; 37:888-896. [PMID: 27288692 PMCID: PMC5008248 DOI: 10.1093/carcin/bgw070] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 05/27/2016] [Accepted: 06/07/2016] [Indexed: 12/15/2022] Open
Abstract
DNA repair pathways maintain genomic integrity and stability, and dysfunction of DNA repair leads to cancer. We hypothesize that functional genetic variants in DNA repair genes are associated with risk of lung cancer. We performed a large-scale meta-analysis of 123,371 single nucleotide polymorphisms (SNPs) in 169 DNA repair genes obtained from six previously published genome-wide association studies (GWASs) of 12160 lung cancer cases and 16838 controls. We calculated odds ratios (ORs) with 95% confidence intervals (CIs) using the logistic regression model and used the false discovery rate (FDR) method for correction of multiple testing. As a result, 14 SNPs had a significant odds ratio (OR) for lung cancer risk with P FDR < 0.05, of which rs3115672 in MSH5 (OR = 1.20, 95% CI = 1.14-1.27) and rs114596632 in GTF2H4 (OR = 1.19, 95% CI = 1.12-1.25) at 6q21.33 were the most statistically significant (P combined = 3.99×10(-11) and P combined = 5.40×10(-10), respectively). The MSH5 rs3115672, but not GTF2H4 rs114596632, was strongly correlated with MSH5 rs3131379 in that region (r (2) = 1.000 and r (2) = 0.539, respectively) as reported in a previous GWAS. Importantly, however, the GTF2H4 rs114596632 T, but not MSH5 rs3115672 T, allele was significantly associated with both decreased DNA repair capacity phenotype and decreased mRNA expression levels. These provided evidence that functional genetic variants of GTF2H4 confer susceptibility to lung cancer.
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Affiliation(s)
- Meilin Wang
- Duke Cancer Institute, Duke University Medical Center, 905 Lasalle Street, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 21116, China
| | - Hongliang Liu
- Duke Cancer Institute, Duke University Medical Center, 905 Lasalle Street, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Zhensheng Liu
- Duke Cancer Institute, Duke University Medical Center, 905 Lasalle Street, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Xiaohua Yi
- Duke Cancer Institute, Duke University Medical Center, 905 Lasalle Street, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Heike Bickeboller
- Department of Genetic Epidemiology, University Medical Center, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | - Rayjean J. Hung
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai hospital, Toronto, Ontario, Canada
| | - Paul Brennan
- Genetic Epidemiology Group, International Agency for Research on Cancer, 69372 Lyon, France
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Neil Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
| | - David C. Christiani
- Department of Environmental Health and
- Department of Epidemiology, Harvard University School of Public Health, Boston, MA 02115, USA and
| | - Jennifer Anne Doherty
- Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH 03756, USA
| | - The TRICL Research Team
- Duke Cancer Institute, Duke University Medical Center, 905 Lasalle Street, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 21116, China
- Department of Genetic Epidemiology, University Medical Center, Georg-August-University Göttingen, 37073 Göttingen, Germany
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai hospital, Toronto, Ontario, Canada
- Genetic Epidemiology Group, International Agency for Research on Cancer, 69372 Lyon, France
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA
- Department of Environmental Health and
- Department of Epidemiology, Harvard University School of Public Health, Boston, MA 02115, USA and
- Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH 03756, USA
| | - Christopher I. Amos
- Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH 03756, USA
| | - Qingyi Wei
- Duke Cancer Institute, Duke University Medical Center, 905 Lasalle Street, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
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13
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Kanda M, Shimizu D, Fujii T, Tanaka H, Tanaka Y, Ezaka K, Shibata M, Takami H, Hashimoto R, Sueoka S, Iwata N, Kobayashi D, Tanaka C, Yamada S, Nakayama G, Sugimoto H, Koike M, Fujiwara M, Kodera Y. Neurotrophin Receptor-Interacting Melanoma Antigen-Encoding Gene Homolog is Associated with Malignant Phenotype of Gastric Cancer. Ann Surg Oncol 2016; 23:532-539. [PMID: 27364510 DOI: 10.1245/s10434-016-5375-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Indexed: 01/04/2023]
Abstract
BACKGROUND Identification of novel molecules implicated in the malignancy of gastric cancer (GC) is key to the development of personalized treatments and the improvement of patient outcome. Neurotrophin receptor-interacting melanoma antigen-encoding protein (NRAGE) regulates apoptosis and metastasis via interactions with various genes. This study aimed to evaluate the function and clinical significance of NRAGE in GC. METHODS The expression of NRAGE and its putative interacting genes apoptosis antagonizing transcription factor (AATF), p75 neurotrophin receptor (p75NTR), and proliferating cell nuclear antigen (PCNA) were determined in GC cell lines using reverse transcription-polymerase chain reaction (RT-PCR). The effect of NRAGE knockdown by small interfering RNA (siRNA) on GC cell behavior also was evaluated. In addition, NRAGE expression was determined in 179 pairs of resected gastric tissues. RESULTS Expression of NRAGE mRNA positively correlated with that of AATF, and NRAGE knockdown significantly decreased the proliferation, migration, and invasion of GC cells. The mean level of NRAGE mRNA expression was significantly higher in GC tissues than in corresponding adjacent normal tissues. The expression patterns of NRAGE mRNA and protein were closely correlated. A stepwise elevation in NRAGE mRNA expression in GC tissues was observed with increasing Union for International Cancer Control (UICC) stage. High NRAGE expression in GCs was associated with shortened recurrence-free survival and identified as an independent prognostic factor (hazard ratio, 1.83; 95 % CI, 1.12-3.02, p = 0.017). CONCLUSIONS The results indicate that NRAGE represents a putative oncogene associated with a malignant phenotype of GC. In GC, NRAGE may serve as a predictive biomarker and a target of molecular therapy.
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Affiliation(s)
- Mitsuro Kanda
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Japan.
| | - Dai Shimizu
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tsutomu Fujii
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Haruyoshi Tanaka
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuri Tanaka
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kazuhiro Ezaka
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Masahiro Shibata
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hideki Takami
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Ryoji Hashimoto
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Satoshi Sueoka
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Naoki Iwata
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Daisuke Kobayashi
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Chie Tanaka
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Suguru Yamada
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Goro Nakayama
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hiroyuki Sugimoto
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Masahiko Koike
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Michitaka Fujiwara
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yasuhiro Kodera
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Japan
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14
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Zhang G, Zhou H, Xue X. Complex roles of NRAGE on tumor. Tumour Biol 2016; 37:11535-11540. [PMID: 27209410 DOI: 10.1007/s13277-016-5084-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 05/15/2016] [Indexed: 10/21/2022] Open
Abstract
NRAGE, also known as Dlxin-1or MAGE-D1, is a member of type II melanoma-associated antigen (MAGE) and plays an essential role in life activities, including differentiation, apoptosis, and cell cycle. Studies increasingly found that NRAGE is closely related to the tumor events, such as tumor occurrence, invasion, and metastasis. However, complex and contradictory functions of NRAGE in different circumstances are observed, suggesting that NRAGE is unique from other MAGE gene family members. This review summarizes recent findings concerning the structure and biological functions of NRAGE, which may provide a basis for a more comprehensive understanding of and further research on NRAGE.
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Affiliation(s)
- Ge Zhang
- Department of Radiotherapy, the Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Huandi Zhou
- Department of Radiotherapy, the Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Xiaoying Xue
- Department of Radiotherapy, the Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China.
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15
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Moorthy B, Chu C, Carlin DJ. Polycyclic aromatic hydrocarbons: from metabolism to lung cancer. Toxicol Sci 2016; 145:5-15. [PMID: 25911656 DOI: 10.1093/toxsci/kfv040] [Citation(s) in RCA: 434] [Impact Index Per Article: 54.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Excessive exposure to polycyclic aromatic hydrocarbons (PAHs) often results in lung cancer, a disease with the highest cancer mortality in the United States. After entry into the lung, PAHs induce phase I metabolic enzymes such as cytochrome P450 (CYP) monooxygenases, i.e. CYP1A1/2 and 1B1, and phase II enzymes such as glutathione S-transferases, UDP glucuronyl transferases, NADPH quinone oxidoreductases (NQOs), aldo-keto reductases (AKRs), and epoxide hydrolases (EHs), via the aryl hydrocarbon receptor (AhR)-dependent and independent pathways. Humans can also be exposed to PAHs through diet, via consumption of charcoal broiled foods. Metabolism of PAHs through the CYP1A1/1B1/EH pathway, CYP peroxidase pathway, and AKR pathway leads to the formation of the active carcinogens diol-epoxides, radical cations, and o-quinones. These reactive metabolites produce DNA adducts, resulting in DNA mutations, alteration of gene expression profiles, and tumorigenesis. Mutations in xenobiotic metabolic enzymes, as well as polymorphisms of tumor suppressor genes (e.g. p53) and/or genes involved in gene expression (e.g. X-ray repair cross-complementing proteins), are associated with lung cancer susceptibility in human populations from different ethnicities, gender, and age groups. Although various metabolic activation/inactivation pathways, AhR signaling, and genetic susceptibilities contribute to lung cancer, the precise points at which PAHs induce tumor initiation remain unknown. The goal of this review is to provide a current state-of-the-science of the mechanisms of human lung carcinogenesis mediated by PAHs, the experimental approaches used to study this complex class of compounds, and future directions for research of these compounds.
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Affiliation(s)
- Bhagavatula Moorthy
- *Department of Pediatrics, Baylor College of Medicine, Houston, Texas and Division of Extramural Research and Training, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709
| | - Chun Chu
- *Department of Pediatrics, Baylor College of Medicine, Houston, Texas and Division of Extramural Research and Training, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709
| | - Danielle J Carlin
- *Department of Pediatrics, Baylor College of Medicine, Houston, Texas and Division of Extramural Research and Training, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709
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16
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Hyland PL, Zhang H, Yang Q, Yang HH, Hu N, Lin SW, Su H, Wang L, Wang C, Ding T, Fan JH, Qiao YL, Sung H, Wheeler W, Giffen C, Burdett L, Wang Z, Lee MP, Chanock SJ, Dawsey SM, Freedman ND, Abnet CC, Goldstein AM, Yu K, Taylor PR. Pathway, in silico and tissue-specific expression quantitative analyses of oesophageal squamous cell carcinoma genome-wide association studies data. Int J Epidemiol 2016; 45:206-20. [PMID: 26635288 PMCID: PMC4881832 DOI: 10.1093/ije/dyv294] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/05/2015] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Oesophageal cancer is the fourth leading cause of cancer death in China where essentially all cases are histologically oesophageal squamous cell carcinoma (ESCC). Agnostic pathway-based analyses of genome-wide association study (GWAS) data combined with tissue-specific expression quantitative trait loci (eQTL) analysis and publicly available functional data can identify biological pathways and/or genes enriched with functionally-relevant disease-associated variants. METHOD We used the adaptive multilocus joint test to analyse 1827 pathways containing 6060 genes using GWAS data from 1942 ESCC cases and 2111 controls with Chinese ancestry. We examined the function of risk alleles using in silico and eQTL analyses in oesophageal tissues. RESULTS Associations with ESCC risk were observed for 36 pathways predominantly involved in apoptosis, cell cycle regulation and DNA repair and containing known GWAS-associated genes. After excluding genes with previous GWAS signals, candidate pathways (and genes) for ESCC risk included taste transduction (KEGG_hsa04742; TAS2R13, TAS2R42, TAS2R14, TAS2R46,TAS2R50), long-patch base excision repair (Reactome_pid; POLD2) and the metabolics pathway (KEGG_hsa01100; MTAP, GAPDH, DCTD, POLD2, AMDHD1). We identified and validated CASP8 rs13016963 and IDH2 rs11630814 as eQTLs, and CASP8 rs3769823 and IDH2 rs4561444 as the potential functional variants in high-linkage disequilibrium with these single nucleotide polymorphisms (SNPs), respectively. Further, IDH2 mRNA levels were down-regulated in ESCC (tumour:normal-fold change = 0.69, P = .75E-14). CONCLUSION Agnostic pathway-based analyses and integration of multiple types of functional data provide new evidence for the contribution of genes in taste transduction and metabolism to ESCC susceptibility, and for the functionality of both established and new ESCC risk-related SNPs.
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Affiliation(s)
| | - Han Zhang
- Division of Cancer Epidemiology and Genetics, and
| | - Qi Yang
- Division of Cancer Epidemiology and Genetics, and
| | | | - Nan Hu
- Division of Cancer Epidemiology and Genetics, and
| | - Shih-Wen Lin
- Division of Cancer Epidemiology and Genetics, and
| | - Hua Su
- Division of Cancer Epidemiology and Genetics, and
| | - Lemin Wang
- Division of Cancer Epidemiology and Genetics, and
| | - Chaoyu Wang
- Division of Cancer Epidemiology and Genetics, and
| | - Ti Ding
- Division of Cancer Epidemiology and Genetics, and
| | - Jin-Hu Fan
- Division of Cancer Epidemiology and Genetics, and
| | - You-Lin Qiao
- Division of Cancer Epidemiology and Genetics, and
| | - Hyuna Sung
- Division of Cancer Epidemiology and Genetics, and
| | | | - Carol Giffen
- Division of Cancer Epidemiology and Genetics, and
| | | | - Zhaoming Wang
- Division of Cancer Epidemiology and Genetics, and Division of Cancer Epidemiology and Genetics, and
| | | | | | | | | | | | | | - Kai Yu
- Division of Cancer Epidemiology and Genetics, and
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17
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Shimizu D, Kanda M, Sugimoto H, Sueoka S, Takami H, Ezaka K, Tanaka Y, Hashimoto R, Okamura Y, Iwata N, Tanaka C, Yamada S, Fujii T, Nakayama G, Koike M, Nomoto S, Fujiwara M, Kodera Y. NRAGE promotes the malignant phenotype of hepatocellular carcinoma. Oncol Lett 2016; 11:1847-1854. [PMID: 26998088 DOI: 10.3892/ol.2016.4120] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 01/05/2016] [Indexed: 12/16/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is a fatal disease, primarily due to the limited effective therapies available for patients with advanced or recurrent stages of the disease. Therefore, in order to improve patient prognosis, it is important to identify an informative biomarker for HCC progression, as well as a molecular target for therapy. Neurotrophin receptor-interacting melanoma antigen-encoding protein (NRAGE), a member of the type II melanoma-associated antigen family, mediates apoptosis and cell death through interactions with a wide range of proteins, and is implicated as a tumor suppressor or oncoprotein depending on cell type. However, the role of NRAGE in HCC is currently unknown, therefore, the present study aimed to identify the underlying function of NRAGE in HCC tumorigenesis. Resected tumor and non-cancerous liver tissues from 151 patients with HCC, alongside HCC cell lines, were analyzed by polymerase chain reaction and immunohistochemical techniques to determine NRAGE expression levels, as well as the expression levels of potential genes encoding interacting proteins. It was demonstrated that the expression levels of NRAGE mRNA correlated significantly with those of apoptosis-antagonizing transcription factor (AATF), and were not affected by cirrhosis in non-cancerous liver tissues when compared to elevated levels in HCC tissues. The expression patterns of NRAGE protein and mRNA were consistent among 30 representative specimen pairs. Furthermore, increased NRAGE expression in patients with HCC correlated significantly with a shorter disease-specific survival time, and was identified as an independent prognostic factor via multivariate analysis (hazard ratio, 2.23; 95% confidence interval, 1.06-3.83; P=0.020). Therefore, the results of the present study indicated that increased NRAGE expression affects HCC progression via its interaction with AATF, and may represent a novel biomarker and molecular target for the treatment of HCC.
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Affiliation(s)
- Dai Shimizu
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Mitsuro Kanda
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Hiroyuki Sugimoto
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Satoshi Sueoka
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Hideki Takami
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Kazuhiro Ezaka
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Yuri Tanaka
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Ryoji Hashimoto
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Yukiyasu Okamura
- Department of Hepatobiliary-Pancreatic Surgery, Shizuoka Cancer Center, Shizuoka 411-8777, Japan
| | - Naoki Iwata
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Chie Tanaka
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Suguru Yamada
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Tsutomu Fujii
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Goro Nakayama
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Masahiko Koike
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Shuji Nomoto
- Department of Surgery, Aichi-Gakuin University School of Dentistry, Nagoya, Aichi 464-8651, Japan
| | - Michitaka Fujiwara
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Yasuhiro Kodera
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
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18
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Qian DC, Byun J, Han Y, Greene CS, Field JK, Hung RJ, Brhane Y, Mclaughlin JR, Fehringer G, Landi MT, Rosenberger A, Bickeböller H, Malhotra J, Risch A, Heinrich J, Hunter DJ, Henderson BE, Haiman CA, Schumacher FR, Eeles RA, Easton DF, Seminara D, Amos CI. Identification of shared and unique susceptibility pathways among cancers of the lung, breast, and prostate from genome-wide association studies and tissue-specific protein interactions. Hum Mol Genet 2015; 24:7406-20. [PMID: 26483192 PMCID: PMC4664175 DOI: 10.1093/hmg/ddv440] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 09/11/2015] [Accepted: 10/12/2015] [Indexed: 12/18/2022] Open
Abstract
Results from genome-wide association studies (GWAS) have indicated that strong single-gene effects are the exception, not the rule, for most diseases. We assessed the joint effects of germline genetic variations through a pathway-based approach that considers the tissue-specific contexts of GWAS findings. From GWAS meta-analyses of lung cancer (12 160 cases/16 838 controls), breast cancer (15 748 cases/18 084 controls) and prostate cancer (14 160 cases/12 724 controls) in individuals of European ancestry, we determined the tissue-specific interaction networks of proteins expressed from genes that are likely to be affected by disease-associated variants. Reactome pathways exhibiting enrichment of proteins from each network were compared across the cancers. Our results show that pathways associated with all three cancers tend to be broad cellular processes required for growth and survival. Significant examples include the nerve growth factor (P = 7.86 × 10(-33)), epidermal growth factor (P = 1.18 × 10(-31)) and fibroblast growth factor (P = 2.47 × 10(-31)) signaling pathways. However, within these shared pathways, the genes that influence risk largely differ by cancer. Pathways found to be unique for a single cancer focus on more specific cellular functions, such as interleukin signaling in lung cancer (P = 1.69 × 10(-15)), apoptosis initiation by Bad in breast cancer (P = 3.14 × 10(-9)) and cellular responses to hypoxia in prostate cancer (P = 2.14 × 10(-9)). We present the largest comparative cross-cancer pathway analysis of GWAS to date. Our approach can also be applied to the study of inherited mechanisms underlying risk across multiple diseases in general.
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Affiliation(s)
- David C Qian
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Jinyoung Byun
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Younghun Han
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Casey S Greene
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - John K Field
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool Cancer Research Centre, Liverpool L69 3GA, UK
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Yonathan Brhane
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - John R Mclaughlin
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7, Canada
| | - Gordon Fehringer
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Maria Teresa Landi
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Albert Rosenberger
- Department of Genetic Epidemiology, University Medical Centre Göttingen, 37099 Göttingen, Germany
| | - Heike Bickeböller
- Department of Genetic Epidemiology, University Medical Centre Göttingen, 37099 Göttingen, Germany
| | - Jyoti Malhotra
- Division of Hematology and Oncology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Angela Risch
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Joachim Heinrich
- Institute of Epidemiology I, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - David J Hunter
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Brian E Henderson
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Fredrick R Schumacher
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Rosalind A Eeles
- Department of Cancer Genetics, Institute of Cancer Research, London SW7 3RP, UK and
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Daniela Seminara
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Christopher I Amos
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA,
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19
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Jiao H, Wang K, Yang F, Grant SFA, Hakonarson H, Price RA, Li WD. Pathway-Based Genome-Wide Association Studies for Plasma Triglycerides in Obese Females and Normal-Weight Controls. PLoS One 2015; 10:e0134923. [PMID: 26308950 PMCID: PMC4550433 DOI: 10.1371/journal.pone.0134923] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 07/15/2015] [Indexed: 12/27/2022] Open
Abstract
Pathway-based analysis as an alternative approach can provide complementary information to single-marker genome-wide association studies (GWASs), which always ignore the epistasis and does not have sufficient power to find rare variants. In this study, using genotypes from a genome-wide association study (GWAS), pathway-based association studies were carried out by a modified Gene Set Enrichment Algorithm (GSEA) method (GenGen) for triglyceride in 1028 unrelated European-American extremely obese females (BMI≥35kg/m2) and normal-weight controls (BMI<25kg/m2), and another pathway association analysis (ICSNPathway) was also used to verify the GenGen result in the same data. The GO0009110 pathway (vitamin anabolism) was among the strongest associations with triglyceride (empirical P<0.001); the result remained significant after FDR correction (P = 0.022). MMAB, an obesity-related locus, included in this pathway. The ABCG1 and BCL6 gene was found in several triglyceride-related pathways (empirical P<0.05), which were also replicated by ICSNPathway (empirical P<0.05, FDR<0.05). We also performed single-marked GWAS using PLINK for TG levels (log-transformed). Significant associations were found between ASTN2 gene SNPs and plasma triglyceride levels (rs7035794, P = 2.24×10−10). Our study suggested that vitamin anabolism pathway, BCL6 gene pathways and ASTN2 gene may contribute to the genetic variation of plasma triglyceride concentrations.
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Affiliation(s)
- Hongxiao Jiao
- Research Center of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Kai Wang
- Zilkha Neurogenetic Institute and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, 90089, United States of America
| | - Fuhua Yang
- Research Center of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Struan F. A. Grant
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, United States of America
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, United States of America
| | - Hakon Hakonarson
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, United States of America
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, United States of America
| | - R. Arlen Price
- Center for Neurobiology and Behavior, Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, United States of America
- * E-mail: (WDL); (RAP)
| | - Wei-Dong Li
- Research Center of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
- Center for Neurobiology and Behavior, Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, United States of America
- * E-mail: (WDL); (RAP)
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Tan J, Yu CY, Wang ZH, Chen HY, Guan J, Chen YX, Fang JY. Genetic variants in the inositol phosphate metabolism pathway and risk of different types of cancer. Sci Rep 2015; 5:8473. [PMID: 25683757 PMCID: PMC4329558 DOI: 10.1038/srep08473] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 01/21/2015] [Indexed: 12/23/2022] Open
Abstract
Members of the inositol phosphate metabolism pathway regulate cell proliferation, migration and phosphatidylinositol-3-kinase (PI3K)/Akt signaling, and are frequently dysregulated in cancer. Whether germline genetic variants in inositol phosphate metabolism pathway are associated with cancer risk remains to be clarified. We examined the association between inositol phosphate metabolism pathway genes and risk of eight types of cancer using data from genome-wide association studies. Logistic regression models were applied to evaluate SNP-level associations. Gene- and pathway-based associations were tested using the permutation-based adaptive rank-truncated product method. The overall inositol phosphate metabolism pathway was significantly associated with risk of lung cancer (P = 2.00 × 10−4), esophageal squamous cell carcinoma (P = 5.70 × 10−3), gastric cancer (P = 3.03 × 10−2) and renal cell carcinoma (P = 1.26 × 10−2), but not with pancreatic cancer (P = 1.40 × 10−1), breast cancer (P = 3.03 × 10−1), prostate cancer (P = 4.51 × 10−1), and bladder cancer (P = 6.30 × 10−1). Our results provide a link between inherited variation in the overall inositol phosphate metabolism pathway and several individual genes and cancer. Further studies will be needed to validate these positive findings, and to explore its mechanisms.
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Affiliation(s)
- Juan Tan
- State Key Laboratory of Oncogene and Related Genes, Key Laboratory of Gastroenterology &Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, Shanghai Institution of Digestive Disease, 145 Middle Shandong Rd, Shanghai 200001, China
| | - Chen-Yang Yu
- State Key Laboratory of Oncogene and Related Genes, Key Laboratory of Gastroenterology &Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, Shanghai Institution of Digestive Disease, 145 Middle Shandong Rd, Shanghai 200001, China
| | - Zhen-Hua Wang
- State Key Laboratory of Oncogene and Related Genes, Key Laboratory of Gastroenterology &Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, Shanghai Institution of Digestive Disease, 145 Middle Shandong Rd, Shanghai 200001, China
| | - Hao-Yan Chen
- State Key Laboratory of Oncogene and Related Genes, Key Laboratory of Gastroenterology &Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, Shanghai Institution of Digestive Disease, 145 Middle Shandong Rd, Shanghai 200001, China
| | - Jian Guan
- Department of Otolaryngology, The Affiliated Sixth People's Hospital, Otolaryngology Institute of Shanghai Jiao Tong University, Shanghai 200233, China
| | - Ying-Xuan Chen
- State Key Laboratory of Oncogene and Related Genes, Key Laboratory of Gastroenterology &Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, Shanghai Institution of Digestive Disease, 145 Middle Shandong Rd, Shanghai 200001, China
| | - Jing-Yuan Fang
- State Key Laboratory of Oncogene and Related Genes, Key Laboratory of Gastroenterology &Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, Shanghai Institution of Digestive Disease, 145 Middle Shandong Rd, Shanghai 200001, China
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Zhu K, Jiang B, Hu R, Yang Y, Miao M, Li Y, Liu Z. The CXCL12 G801A polymorphism is associated with cancer risk: a meta-analysis. PLoS One 2014; 9:e108953. [PMID: 25268356 PMCID: PMC4182572 DOI: 10.1371/journal.pone.0108953] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 08/27/2014] [Indexed: 12/12/2022] Open
Abstract
Background CXCL12 is a small chemotactic cytokine belonging to the CXC chemokine family expressed in various organs. It contributes to the migration, invasion and angiogenesis of cancer cells. Recently, the CXCL12 G801A polymorphism was shown to be associated with an increased risk of various kinds of cancers, but the results were too inconsistent to be conclusive. Methods To solve the problem of inadequate statistical power and conflicting results, a meta-analysis of published case-control studies was performed, including 4,435 cancer cases and 6,898 controls. Odds ratios (ORs) and their 95% confidence intervals (CIs) were used to determine the strength of association between CXCL12 G801A polymorphism and cancer risk. Results A significant association between CXCL12 G801A polymorphism and cancer risk was found under all genetic models. Further, subgroup analysis stratified by ethnicity suggested a significant association between CXCL12 G801A polymorphism and cancer risk in the Asian subgroup under all genetic models. However, in the Caucasian subgroup, a significant association was only found under an additive genetic model and a dominant genetic model. The analysis stratified by cancer type found that CXCL12 G801A polymorphism may increase the risk of breast cancer, lung cancer, and “other” cancers. Based on subgroup stratified by source of controls, a significant association was observed in hospital-based studies under all genetic models. Conclusions The CXCL12 G801A polymorphism is associated with an increased risk of cancer based on current published data. In the future, large-scale well-designed studies with more information are needed to better estimate possible gene-gene or gene-environment interactions.
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Affiliation(s)
- Ke Zhu
- Department of Hematology, Affiliated Shengjing Hospital, China Medical University, Shenyang, Liaoning, China
| | - Benchun Jiang
- Department of General Surgery, Affiliated Shengjing Hospital, China Medical University, Shenyang, Liaoning, China
| | - Rong Hu
- Department of Hematology, Affiliated Shengjing Hospital, China Medical University, Shenyang, Liaoning, China
| | - Ying Yang
- Department of Hematology, Affiliated Shengjing Hospital, China Medical University, Shenyang, Liaoning, China
| | - Miao Miao
- Department of Hematology, Affiliated Shengjing Hospital, China Medical University, Shenyang, Liaoning, China
| | - Yingchun Li
- Department of Hematology, Affiliated Shengjing Hospital, China Medical University, Shenyang, Liaoning, China
| | - Zhuogang Liu
- Department of Hematology, Affiliated Shengjing Hospital, China Medical University, Shenyang, Liaoning, China
- * E-mail:
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