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Yu X, Luo X, Cai G, Xiao F. OSCAA: A two-dimensional Gaussian mixture model for copy number variation association analysis. Genet Epidemiol 2024. [PMID: 38533840 DOI: 10.1002/gepi.22558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 01/30/2024] [Accepted: 03/05/2024] [Indexed: 03/28/2024]
Abstract
Copy number variants (CNVs) are prevalent in the human genome and are found to have a profound effect on genomic organization and human diseases. Discovering disease-associated CNVs is critical for understanding the pathogenesis of diseases and aiding their diagnosis and treatment. However, traditional methods for assessing the association between CNVs and disease risks adopt a two-stage strategy conducting quantitative CNV measurements first and then testing for association, which may lead to biased association estimation and low statistical power, serving as a major barrier in routine genome-wide assessment of such variation. In this article, we developed One-Stage CNV-disease Association Analysis (OSCAA), a flexible algorithm to discover disease-associated CNVs for both quantitative and qualitative traits. OSCAA employs a two-dimensional Gaussian mixture model that is built upon the PCs from copy number intensities, accounting for technical biases in CNV detection while simultaneously testing for their effect on outcome traits. In OSCAA, CNVs are identified and their associations with disease risk are evaluated simultaneously in a single step, taking into account the uncertainty of CNV identification in the statistical model. Our simulations demonstrated that OSCAA outperformed the existing one-stage method and traditional two-stage methods by yielding a more accurate estimate of the CNV-disease association, especially for short CNVs or CNVs with weak signals. In conclusion, OSCAA is a powerful and flexible approach for CNV association testing with high sensitivity and specificity, which can be easily applied to different traits and clinical risk predictions.
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Affiliation(s)
- Xuanxuan Yu
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, South Carolina, USA
| | - Xizhi Luo
- Data and Statistical Sciences, AbbVie Inc., North Chicago, Illinois, USA
| | - Guoshuai Cai
- Department of Surgery, College of Medicine, University of Florida, Gainesville, Florida, USA
| | - Feifei Xiao
- Department of Biostatistics, College of Public Health and Health Promotion & College of Medicine, University of Florida, Gainesville, Florida, USA
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Yu X, Luo X, Cai G, Xiao F. OSCAA: A Two-Dimensional Gaussian Mixture Model for Copy Number Variation Association Analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.25.559392. [PMID: 37808739 PMCID: PMC10557568 DOI: 10.1101/2023.09.25.559392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Copy number variants (CNVs) are prevalent in the human genome which provide profound effect on genomic organization and human diseases. Discovering disease associated CNVs is critical for understanding the pathogenesis of diseases and aiding their diagnosis and treatment. However, traditional methods for assessing the association between CNVs and disease risks adopt a two-stage strategy conducting quantitative CNV measurements first and then testing for association, which may lead to biased association estimation and low statistical power, serving as a major barrier in routine genome wide assessment of such variation. In this article, we developed OSCAA, a flexible algorithm to discover disease associated CNVs for both quantitative and qualitative traits. OSCAA employs a two-dimensional Gaussian mixture model that is built upon the principal components from copy number intensities, accounting for technical biases in CNV detection while simultaneously testing for their effect on outcome traits. In OSCAA, CNVs are identified and their associations with disease risk are evaluated simultaneously in a single step, taking into account the uncertainty of CNV identification in the statistical model. Our simulations demonstrated that OSCAA outperformed the existing one-stage method and traditional two-stage methods by yielding a more accurate estimate of the CNV-disease association, especially for short CNVs or CNVs with weak signal. In conclusion, OSCAA is a powerful and flexible approach for CNV association testing with high sensitivity and specificity, which can be easily applied to different traits and clinical risk predictions.
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3
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Zhang X, Zhu Y, Kremling KAG, Romay MC, Bukowski R, Sun Q, Gao S, Buckler ES, Lu F. Genome-wide analysis of deletions in maize population reveals abundant genetic diversity and functional impact. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:273-290. [PMID: 34661697 DOI: 10.1007/s00122-021-03965-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 09/30/2021] [Indexed: 06/13/2023]
Abstract
Two read depth methods were jointly used in next-generation sequencing data to identify deletions in maize population. GWAS by deletions were analyzed for gene expression pattern and classical traits, respectively. Many studies have confirmed that structural variation (SV) is pervasive throughout the maize genome. Deletion is one type of SV that may impact gene expression and cause phenotypic changes in quantitative traits. In this study, two read count approaches were used to analyze the deletions in the whole-genome sequencing data of 270 maize inbred lines. A total of 19,754 deletion windows overlapped 12,751 genes, which were unevenly distributed across the genome. The deletions explained population structure well and correlated with genomic features. The deletion proportion of genes was determined to be negatively correlated with its expression. The detection of gene expression quantitative trait loci (eQTL) indicated that local eQTL were fewer but had larger effects than distant ones. The common associated genes were related to basic metabolic processes, whereas unique associated genes with eQTL played a role in the stress or stimulus responses in multiple tissues. Compared with the eQTL detected by SNPs derived from the same sequencing data, 89.4% of the associated genes could be detected by both markers. The effect of top eQTL detected by SNPs was usually larger than that detected by deletions for the same gene. A genome-wide association study (GWAS) on flowering time and plant height illustrated that only a few loci could be consistently captured by SNPs, suggesting that combining deletion and SNP for GWAS was an excellent strategy to dissect trait architecture. Our findings will provide insights into characteristic and biological function of genome-wide deletions in maize.
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Affiliation(s)
- Xiao Zhang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China.
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, Sichuan, China.
- Institute for Genomic Diversity, Cornell University, 175 Biotechnology Building, Ithaca, NY, USA.
| | - Yonghui Zhu
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China
| | - Karl A G Kremling
- Institute for Genomic Diversity, Cornell University, 175 Biotechnology Building, Ithaca, NY, USA
| | - M Cinta Romay
- Institute for Genomic Diversity, Cornell University, 175 Biotechnology Building, Ithaca, NY, USA
| | - Robert Bukowski
- Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, USA
| | - Qi Sun
- Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, USA
| | - Shibin Gao
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, Sichuan, China
| | - Edward S Buckler
- Institute for Genomic Diversity, Cornell University, 175 Biotechnology Building, Ithaca, NY, USA
- USDA-ARS, R. W. Holley Center, Cornell University, Ithaca, NY, USA
| | - Fei Lu
- Institute for Genomic Diversity, Cornell University, 175 Biotechnology Building, Ithaca, NY, USA.
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China.
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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4
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Lin X. Genomic Variation Prediction: A Summary From Different Views. Front Cell Dev Biol 2021; 9:795883. [PMID: 34901036 PMCID: PMC8656232 DOI: 10.3389/fcell.2021.795883] [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: 10/15/2021] [Accepted: 11/11/2021] [Indexed: 12/02/2022] Open
Abstract
Structural variations in the genome are closely related to human health and the occurrence and development of various diseases. To understand the mechanisms of diseases, find pathogenic targets, and carry out personalized precision medicine, it is critical to detect such variations. The rapid development of high-throughput sequencing technologies has accelerated the accumulation of large amounts of genomic mutation data, including synonymous mutations. Identifying pathogenic synonymous mutations that play important roles in the occurrence and development of diseases from all the available mutation data is of great importance. In this paper, machine learning theories and methods are reviewed, efficient and accurate pathogenic synonymous mutation prediction methods are developed, and a standardized three-level variant analysis framework is constructed. In addition, multiple variation tolerance prediction models are studied and integrated, and new ideas for structural variation detection based on deep information mining are explored.
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Affiliation(s)
- Xiuchun Lin
- College of Information and Electrical Engineering, China Agricultural University, Beijing, China
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Ma S, Ba Y, Ji H, Wang F, Du J, Hu S. Recognition of Tumor-Associated Antigens and Immune Subtypes in Glioma for mRNA Vaccine Development. Front Immunol 2021; 12:738435. [PMID: 34603319 PMCID: PMC8484904 DOI: 10.3389/fimmu.2021.738435] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 09/02/2021] [Indexed: 12/30/2022] Open
Abstract
Background Although mRNA vaccines have been efficient for combating a variety of tumors, their effectiveness against glioma remains unclear. There is growing evidence that immunophenotyping can reflect the comprehensive immune status and microenvironment of the tumor, which correlates closely with treatment response and vaccination potency. The purpose of this research was to screen for effective antigens in glioma that could be used for developing mRNA vaccines and to further differentiate the immune subtypes of glioma to create an selection criteria for suitable patients for vaccination. Methods Gene expression profiles and clinical data of 698 glioma samples were extracted from The Cancer Genome Atlas, and RNA_seq data of 1018 glioma samples was gathered from Chinese Glioma Genome Atlas. Gene Expression Profiling Interactive Analysis was used to determine differential expression genes and prognostic markers, cBioPortal software was used to verify gene alterations, and Tumor Immune Estimation Resource was used to investigate the relationships among genes and immune infiltrating cells. Consistency clustering was applied for consistent matrix construction and data aggregation, Gene oncology enrichment was performed for functional annotation, and a graph learning-based dimensionality reduction method was applied to describe the subtypes of immunity. Results Four overexpressed and mutated tumor antigens associated with poor prognosis and infiltration of antigen presenting cells were identified in glioma, including TP53, IDH1, C3, and TCF12. Besides, four immune subtypes of glioma (IS1-IS4) and 10 immune gene modules were identified consistently in the TCGA data. The immune subtypes had diverse molecular, cellular, and clinical features. IS1 and IS4 displayed an immune-activating phenotype and were associated with worse survival than the other two subtypes, while IS2 and IS3 had lower levels of tumor immune infiltration. Immunogenic cell death regulators and immune checkpoints were also diversely expressed in the four immune subtypes. Conclusion TP53, IDH1, C3, and TCF12 are effective antigens for the development of anti-glioma mRNA vaccines. We found four stable and repeatable immune subtypes of human glioma, the classification of the immune subtypes of glioma may play a crucial role in the predicting mRNA vaccine outcome.
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Affiliation(s)
- Shuai Ma
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Yixu Ba
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Hang Ji
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Fang Wang
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jianyang Du
- Department of Neurosurgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Shaoshan Hu
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China.,Department of Neurosurgery, Emergency Medicine Center, Zhejiang Provincial People's Hospital Affiliated to Hangzhou Medical College, Hangzhou, China
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Yang X, Jin X, Xu R, Yu Z, An N. ER expression associates with poor prognosis in male lung squamous carcinoma after radical resection. BMC Cancer 2021; 21:1043. [PMID: 34548052 PMCID: PMC8456567 DOI: 10.1186/s12885-021-08777-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 09/08/2021] [Indexed: 11/30/2022] Open
Abstract
Background Clinical options for lung squamous carcinoma (LUSC) are still quite limited. Carcinogenesis is an exceedingly complicated process involving multi-level dysregulations. Therefore, only looking into one layer of genomic dysregulation is far from sufficient. Methods We identified differentially expressed genes with consistent upstream genetic or epigenetic dysregulations in LUSC. Random walk was adopted to identify genes significantly affected by upstream abnormalities. Expression differentiation and survival analysis were conducted for these significant genes, respectively. Prognostic power of selected gene was also tested in 102 male LUSC samples through immunohistochemistry assay. Results Twelve genes were successfully retrieved from biological network, including ERα (ESRS1), EGFR, AR, ATXN1, MAPK3, PRKACA, PRKCA, SMAD4, TP53, TRAF2, UBQLN4 and YWHAG, which were closely related to sex hormone signaling pathway. Survival analysis in public datasets indicated ERα was significantly associated with a poor overall survival (OS) in male LUSC. The result of our immunohistochemistry assay also demonstrated this correlation using R0 resected tumors (n = 102, HR: 2.152, 95% CI: 1.089–4.255, p = 0.024). Although disease-free survival (DFS) difference was non-significant (n = 102, p = 0.12), the tendency of distinction was straight-forward. Cox analysis indicated ERα was the only independent prognostic factor for male patients’ OS after R0 resection (HR = 2.152, p = 0.037). Conclusion ERα was significantly related to a poor prognosis in LUSC, especially for male patients after radical surgery, confirmed by our immunohistochemistry data. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-08777-6.
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Affiliation(s)
- Xue Yang
- Department of Medical Oncology, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, China
| | - Xiangfeng Jin
- Department of Thoracic Surgery, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, China
| | - Rongjian Xu
- Department of Thoracic Surgery, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, China
| | - Zhuang Yu
- Department of Medical Oncology, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, China
| | - Ning An
- Department of Radiation Oncology, The Affiliated Hospital of Qingdao University, Qingdao, 266003, Shandong, China.
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Molecular Biology of the WWOX Gene That Spans Chromosomal Fragile Site FRA16D. Cells 2021; 10:cells10071637. [PMID: 34210081 PMCID: PMC8305172 DOI: 10.3390/cells10071637] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 06/17/2021] [Accepted: 06/25/2021] [Indexed: 12/11/2022] Open
Abstract
It is now more than 20 years since the FRA16D common chromosomal fragile site was characterised and the WWOX gene spanning this site was identified. In this time, much information has been discovered about its contribution to disease; however, the normal biological role of WWOX is not yet clear. Experiments leading to the identification of the WWOX gene are recounted, revealing enigmatic relationships between the fragile site, its gene and the encoded protein. We also highlight research mainly using the genetically tractable model organism Drosophila melanogaster that has shed light on the integral role of WWOX in metabolism. In addition to this role, there are some particularly outstanding questions that remain regarding WWOX, its gene and its chromosomal location. This review, therefore, also aims to highlight two unanswered questions. Firstly, what is the biological relationship between the WWOX gene and the FRA16D common chromosomal fragile site that is located within one of its very large introns? Secondly, what is the actual substrate and product of the WWOX enzyme activity? It is likely that understanding the normal role of WWOX and its relationship to chromosomal fragility are necessary in order to understand how the perturbation of these normal roles results in disease.
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8
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Chen S, Lu L, Xian J, Shi C, Chen J, Rao B, Qiu F, Lu J, Yang L. Prognostic Value of Germline Copy Number Variants and Environmental Exposures in Non-small Cell Lung Cancer. Front Genet 2021; 12:681857. [PMID: 34178039 PMCID: PMC8226327 DOI: 10.3389/fgene.2021.681857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 05/18/2021] [Indexed: 11/13/2022] Open
Abstract
Germline copy number variant (gCNV) has been studied as a genetic determinant for prognosis of several types of cancer, but little is known about how it affects non-small cell lung cancer (NSCLC) prognosis. We aimed to develop a prognostic nomogram for NSCLC based on gCNVs. Promising gCNVs that are associated with overall survival (OS) of NSCLC were sorted by analyzing the TCGA data and were validated in a small Chinese population. Then the successfully verified gCNVs were determined in a training cohort (n = 570) to develop a prognostic nomogram, and in a validation cohort (n = 465) to validate the nomogram. Thirty-five OS-related gCNVs were sorted and were reduced to 15 predictors by the Lasso regression analysis. Of them, only CNVR395.1 and CNVR2239.1 were confirmed to be associated with OS of NSCLC in the Chinese population. High polygenic risk score (PRS), which was calculated by the hazard effects of CNVR395.1 and CNVR2239.1, exerted a significantly higher death rate in the training cohort (HR = 1.41, 95%CI: 1.16-1.74) and validation cohort (HR = 1.42, 95%CI: 1.13-1.77) than low PRS. The nomogram incorporating PRS and surrounding factors, achieved admissible concordance indexes of 0.678 (95%CI: 0.664-0.693) and 0.686 (95%CI: 0.670-0.702) in predicting OS in the training and validation cohorts, respectively, and had well-fitted calibration curves. Moreover, an interaction between PRS and asbestos exposure was observed on affecting OS (P interaction = 0.042). Our analysis developed a nomogram that achieved an admissible prediction of NSCLC survival, which would be beneficial to the personalized intervention of NSCLC.
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Affiliation(s)
- Shizhen Chen
- The State Key Laboratory of Respiratory Disease, Institute of Public Health, Guangzhou Medical University, Guangzhou, China
| | - Liming Lu
- The State Key Laboratory of Respiratory Disease, Institute of Public Health, Guangzhou Medical University, Guangzhou, China
| | - Jianfeng Xian
- The State Key Laboratory of Respiratory Disease, Institute of Public Health, Guangzhou Medical University, Guangzhou, China
| | - Changhong Shi
- The State Key Laboratory of Respiratory Disease, Institute of Public Health, Guangzhou Medical University, Guangzhou, China
| | - Jinbin Chen
- The State Key Laboratory of Respiratory Disease, Institute of Public Health, Guangzhou Medical University, Guangzhou, China
| | - Boqi Rao
- The State Key Laboratory of Respiratory Disease, Institute of Public Health, Guangzhou Medical University, Guangzhou, China
| | - Fuman Qiu
- The State Key Laboratory of Respiratory Disease, Institute of Public Health, Guangzhou Medical University, Guangzhou, China
| | - Jiachun Lu
- The State Key Laboratory of Respiratory Disease, Institute of Public Health, Guangzhou Medical University, Guangzhou, China
- The State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Diseases, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Lei Yang
- The State Key Laboratory of Respiratory Disease, Institute of Public Health, Guangzhou Medical University, Guangzhou, China
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9
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Luo X, Qin F, Cai G, Xiao F. Integrating genomic correlation structure improves copy number variations detection. Bioinformatics 2021; 37:312-317. [PMID: 32805016 DOI: 10.1093/bioinformatics/btaa737] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/23/2020] [Accepted: 08/12/2020] [Indexed: 12/16/2022] Open
Abstract
MOTIVATION Copy number variation plays important roles in human complex diseases. The detection of copy number variants (CNVs) is identifying mean shift in genetic intensities to locate chromosomal breakpoints, the step of which is referred to as chromosomal segmentation. Many segmentation algorithms have been developed with a strong assumption of independent observations in the genetic loci, and they assume each locus has an equal chance to be a breakpoint (i.e. boundary of CNVs). However, this assumption is violated in the genetics perspective due to the existence of correlation among genomic positions, such as linkage disequilibrium (LD). Our study showed that the LD structure is related to the location distribution of CNVs, which indeed presents a non-random pattern on the genome. To generate more accurate CNVs, we proposed a novel algorithm, LDcnv, that models the CNV data with its biological characteristics relating to genetic dependence structure (i.e. LD). RESULTS We theoretically demonstrated the correlation structure of CNV data in SNP array, which further supports the necessity of integrating biological structure in statistical methods for CNV detection. Therefore, we developed the LDcnv that integrated the genomic correlation structure with a local search strategy into statistical modeling of the CNV intensities. To evaluate the performance of LDcnv, we conducted extensive simulations and analyzed large-scale HapMap datasets. We showed that LDcnv presented high accuracy, stability and robustness in CNV detection and higher precision in detecting short CNVs compared to existing methods. This new segmentation algorithm has a wide scope of potential application with data from various high-throughput technology platforms. AVAILABILITY AND IMPLEMENTATION https://github.com/FeifeiXiaoUSC/LDcnv. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Xizhi Luo
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC 29208, USA
| | - Fei Qin
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC 29208, USA
| | - Guoshuai Cai
- Department of Environmental Health Science, Arnold School of Public Health, University of South Carolina, Columbia, SC 29208, USA
| | - Feifei Xiao
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC 29208, USA
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Hussain T, Liu B, Shrock MS, Williams T, Aldaz CM. WWOX, the FRA16D gene: A target of and a contributor to genomic instability. Genes Chromosomes Cancer 2018; 58:324-338. [PMID: 30350478 DOI: 10.1002/gcc.22693] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 10/10/2018] [Indexed: 12/20/2022] Open
Abstract
WWOX is one of the largest human genes spanning over 1.11 Mbp in length at chr16q23.1-q23.2 and containing FRA16D, the second most common chromosomal fragile site. FRA16D is a hot spot of genomic instability, prone to breakage and for causing germline and somatic copy number variations (CNVs). Consequentially WWOX is frequent target for deletions in cancer. Esophageal, stomach, colon, bladder, ovarian, and uterine cancers are those most commonly affected by WWOX deep focal deletions. WWOX deletions significantly correlate with various clinicopathological features in esophageal carcinoma. WWOX is also a common target for translocations in multiple myeloma. By mapping R-loop (RNA:DNA hybrid) forming sequences (RFLS) we observe this to be a consistent feature aligning with germline and somatic CNV break points at the edges and core of FRA16D spanning from introns 5 to 8 of WWOX. Germline CNV polymorphisms affecting WWOX are extremely common in humans across different ethnic groups. Importantly, structural variants datasets allowed us to identify a specific hot spot for germline duplications and deletions within intron 5 of WWOX coinciding with the 5' edge of the FRA16D core and various RFLS. Recently, multiple pathogenic CNVs spanning WWOX have been identified associated with neurological conditions such as autism spectrum disorder, infantile epileptic encephalopathies, and other developmental anomalies. Loss of WWOX function has recently been associated with DNA damage repair abnormalities, increased genomic instability, and resistance to chemoradiotherapy. The described observations place WWOX both as a target of and a contributor to genomic instability. Both of these aspects will be discussed in this review.
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Affiliation(s)
- Tabish Hussain
- Department of Epigenetics and Molecular Carcinogenesis, Science Park, The University of Texas MD Anderson Cancer Center, Smithville, Texas
| | - Bin Liu
- Department of Epigenetics and Molecular Carcinogenesis, Science Park, The University of Texas MD Anderson Cancer Center, Smithville, Texas
| | - Morgan S Shrock
- Department of Radiation Oncology, The Ohio State University Wexner Medical Center, Columbus, Ohio
| | - Terence Williams
- Department of Radiation Oncology, The Ohio State University Wexner Medical Center, Columbus, Ohio
| | - C Marcelo Aldaz
- Department of Epigenetics and Molecular Carcinogenesis, Science Park, The University of Texas MD Anderson Cancer Center, Smithville, Texas
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11
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Palumbo E, Russo A. Common fragile site instability in normal cells: Lessons and perspectives. Genes Chromosomes Cancer 2018; 58:260-269. [PMID: 30387295 DOI: 10.1002/gcc.22705] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 09/25/2018] [Accepted: 10/01/2018] [Indexed: 12/26/2022] Open
Abstract
Mechanisms and events related to common fragile site (CFS) instability are well known in cancer cells. Here, we argue that normal cells remain an important experimental model to address questions related to CFS instability in the absence of alterations in cell cycle and DNA damage repair pathways, which are common features acquired in cancer. Furthermore, a major gap of knowledge concerns the stability of CFSs during gametogenesis. CFS instability in meiotic or postmeiotic stages of the germ cell line could generate chromosome deletions or large rearrangements. This in turn can lead to the functional loss of the several CFS-associated genes with tumor suppressor function. Our hypothesis is that such mutations can potentially result in genetic predisposition to develop cancer. Indirect evidence for CFS instability in human germ cells has been provided by genomic investigations in family pedigrees associated with genetic disease. The issue of CFS instability in the germ cell line should represent one of the future efforts, and may take advantage of the existence of sequence and functional conservation of CFSs between rodents and humans.
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Affiliation(s)
- Elisa Palumbo
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Antonella Russo
- Department of Molecular Medicine, University of Padova, Padova, Italy
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12
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The phenotypic spectrum of WWOX-related disorders: 20 additional cases of WOREE syndrome and review of the literature. Genet Med 2018; 21:1308-1318. [PMID: 30356099 PMCID: PMC6752669 DOI: 10.1038/s41436-018-0339-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 10/03/2018] [Indexed: 11/18/2022] Open
Abstract
Purpose Germline WWOX pathogenic variants
have been associated with disorder of sex differentiation (DSD), spinocerebellar
ataxia (SCA), and WWOX-related epileptic
encephalopathy (WOREE syndrome). We review clinical and molecular data on
WWOX-related disorders, further
describing WOREE syndrome and phenotype/genotype correlations. Methods We report clinical and molecular findings in 20 additional patients
from 18 unrelated families with WOREE syndrome and biallelic pathogenic variants
in the WWOX gene. Different molecular
screening approaches were used (quantitative polymerase chain reaction/multiplex
ligation-dependent probe amplification [qPCR/MLPA], array comparative genomic
hybridization [array-CGH], Sanger sequencing, epilepsy gene panel, exome
sequencing), genome sequencing. Results Two copy-number variations (CNVs) or two single-nucleotide
variations (SNVs) were found respectively in four and nine families, with
compound heterozygosity for one SNV and one CNV in five families. Eight novel
missense pathogenic variants have been described. By aggregating our patients
with all cases reported in the literature, 37 patients from 27 families with
WOREE syndrome are known. This review suggests WOREE syndrome is a very severe
epileptic encephalopathy characterized by absence of language development and
acquisition of walking, early-onset drug-resistant seizures, ophthalmological
involvement, and a high likelihood of premature death. The most severe clinical
presentation seems to be associated with null genotypes. Conclusion Germline pathogenic variants in WWOX are clearly associated with a severe early-onset epileptic
encephalopathy. We report here the largest cohort of individuals with WOREE
syndrome.
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Liu L, Qiu F, Chen J, Wu D, Nong Q, Zhou Y, Lu J. Functional Polymorphism in the MSI1 Gene Promoter Confers a Decreased Risk of Lung Cancer in Chinese by Reducing MSI1 Expression. Curr Genomics 2018; 19:375-383. [PMID: 30065613 PMCID: PMC6030856 DOI: 10.2174/1389202919666171128151544] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 12/12/2016] [Accepted: 01/29/2017] [Indexed: 12/15/2022] Open
Abstract
Background: Musashi1 (MSI1) is a characteristic stem cell marker that regulates the balance between cell self-renewal and differentiation. Evidence has identified MSI1 as a pivotal oncogenic regulator in diverse malignancies. However, little evidence uncovers the role of genetic variations of MSI1 gene in cancer etiology. Objective: The aim of this study was to investigate the association between genetic variants in the MSI1 gene and lung cancer risk. Methods: Based on a two-stage retrospective study with a total of 1559 patients with lung cancer and 1667 healthy controls, we evaluated the relevance between three putative functional SNPs in the MSI1 promoter (i.e., -2696T>C[rs7959801], -2297T>C[rs3742038] and -1081C>T[rs34570155]) and lung cancer risk. Results: We found that the SNP rs7959801T>C was significantly associated with lung cancer susceptibility. Compared to those with rs7959801TT wild-genotype, individuals with CT/CC variant genotypes exerted consistently beneficial roles in lung cancer risk in the discovery set (adjusted odd ratios [OR] = 0.67; 95% confidence interval [CI] = 0.57-0.80), and in the validation set (OR=0.69; 95%CI=0.54-0.88). Functional assays indicated that the allele transformation from T to C in rs7959801 of MSI1 gene arrestingly decreased its transcription activity in vitro. Furthermore, the expression levels of MSI1 were significantly lower in the patients with CT/CC variants than in those who were with TT genotype. Conclusion: Our findings suggested that the rs7959801T>C polymorphism in the MSI1 promoter conferred a decreased risk to lung cancer by reducing the expression of MSI1 and it may be a promising indicator for lung cancer predisposition.
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Affiliation(s)
- Lin Liu
- The State Key Laboratory of Respiratory Disease, The First Affiliated Hospital, Guangzhou Medical University, 151 Yanjiangxi Road, Guangzhou, 510120, China.,The School of Public Health, The Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, 195 Dongfengxi Road, Guangzhou, 510182, China
| | - Fuman Qiu
- The State Key Laboratory of Respiratory Disease, The First Affiliated Hospital, Guangzhou Medical University, 151 Yanjiangxi Road, Guangzhou, 510120, China.,The School of Public Health, The Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, 195 Dongfengxi Road, Guangzhou, 510182, China
| | - Jiansong Chen
- The State Key Laboratory of Respiratory Disease, The First Affiliated Hospital, Guangzhou Medical University, 151 Yanjiangxi Road, Guangzhou, 510120, China.,The School of Public Health, The Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, 195 Dongfengxi Road, Guangzhou, 510182, China
| | - Di Wu
- The State Key Laboratory of Respiratory Disease, The First Affiliated Hospital, Guangzhou Medical University, 151 Yanjiangxi Road, Guangzhou, 510120, China.,The School of Public Health, The Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, 195 Dongfengxi Road, Guangzhou, 510182, China
| | - Qingqing Nong
- Department of Environmental Health, Guangxi Medical University, 22 Shuangyong road, Nanning530021, China
| | - Yifeng Zhou
- Department of Genetics, Medical College of Soochow University, 199 Renai road, Suzhou215123, China
| | - Jiachun Lu
- The State Key Laboratory of Respiratory Disease, The First Affiliated Hospital, Guangzhou Medical University, 151 Yanjiangxi Road, Guangzhou, 510120, China.,The School of Public Health, The Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, 195 Dongfengxi Road, Guangzhou, 510182, China
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14
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High Vimentin Expression Predicts a Poor Prognosis and Progression in Colorectal Cancer: A Study with Meta-Analysis and TCGA Database. BIOMED RESEARCH INTERNATIONAL 2018; 2018:6387810. [PMID: 29955607 PMCID: PMC6000861 DOI: 10.1155/2018/6387810] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 04/10/2018] [Accepted: 04/29/2018] [Indexed: 12/17/2022]
Abstract
The aim of this study was to evaluate the role of vimentin expression in the prognosis and progression of CRC. Meta-analysis was conducted to investigate the correlations between vimentin and prognosis and clinicopathological features in CRC. Literatures were searched by PubMed, Embase, ClinicalKey, CNKI, VIP, and WanFang databases. The Cancer Genome Atlas (TCGA) database was used to assess the association of vimentin expression with survival rate in CRC. Eleven reports with 1969 cases were included in the meta-analysis. The results showed that positive vimentin expression predicted a poor overall survival (OS) in the univariate analysis (HR: 2.087, 95%CI: 1.660-2.625) and multivariate analysis (HR: 1.633, 95%CI: 1.223-2.181). Vimentin overexpression also conferred worse disease-free survival (DFS) in the univariate analysis (HR: 2.069, 95%CI: 1.024-4.179) and multivariate analysis (HR: 2.802, 95%CI: 1.421-5.527). Moreover, upregulated vimentin is related to lymph node metastasis (OR: 2.288, 95%CI: 1.159-4.517), TNM stages (OR: 1.957, 95%CI: 1.333-2.873), and N stage (OR: 2.316, 95%CI: 1.482-3.620). Analysis of TCGA database indicated that elevated vimentin predicated a shorter OS (p=0.033). Our findings reveal that upregulated vimentin contributes to the progression and poor prognosis of CRC. Vimentin may be a prognostic biomarker and therapeutic target in patients with CRC.
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15
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Du L, Lei L, Zhao X, He H, Chen E, Dong J, Zeng Y, Yang J. The Interaction of Smoking with Gene Polymorphisms on Four Digestive Cancers: A Systematic Review and Meta-Analysis. J Cancer 2018; 9:1506-1517. [PMID: 29721061 PMCID: PMC5929096 DOI: 10.7150/jca.22797] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 01/22/2018] [Indexed: 12/15/2022] Open
Abstract
The main purpose of this study was to perform a meta-analysis to assess the interaction between smoking and nine genes (GSTM1, GSTT1, GSTP1, CYP1A1, NAT2, SULT1A1, hOGG1, XRCC1 and p53) on colorectal cancer, gastric cancer, liver cancer and oesophageal cancer. Published articles from the PubMed, ISI and EMBASE databases were retrieved. A total of 67 case-control studies or nested case-control studies were identified for the analysis. The pooled jodds ratio (OR) with 95% confidence interval (CI) was calculated using the random effect model. The overall study showed that the GSTM1 polymorphism was associated with the risk of the four digestive cancers among Asian population (OR 1.284, 95% CI: 1.122-1.470, p: 0). Subgroup analyses by cancer site showed that GSTM1 null genotype increased the gastric cancer risk in total population (OR 1.335, 95% CI: 1.145-1.556, p: 0). However, the association of GSTM1 null genotype with the oesophageal cancer risk was found in smokers (OR 1.382, 95% CI: 1.009-1.894, p:0.044), but not in non-smokers (OR 1.250, 95% CI: 0.826-1.891, p:0.290). Moreover, smokers with the CYP1A1 IIe462Val polymorphism were at an increased cancer risk in Asian population (OR=1.585, 95% CI 1.029-2.442, p: 0.037). None of the other gene-smoking interactions was observed in the above cancers. This meta-analysis reveals two potential gene-smoking interactions, one is between smoking and GSTM1 on oesophageal cancer, and the other is between smoking and CYP1A1 IIe462Val on the four cancers in Asian population. Future studies need to be conducted to verify the conclusions.
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Affiliation(s)
- Le Du
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi'an 710069, China.,Institute of Preventive Genomic Medicine, Xi'an 710069, China
| | - Lei Lei
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi'an 710069, China.,Institute of Preventive Genomic Medicine, Xi'an 710069, China
| | - Xiaojuan Zhao
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi'an 710069, China.,Institute of Preventive Genomic Medicine, Xi'an 710069, China
| | - Hongjuan He
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi'an 710069, China.,Institute of Preventive Genomic Medicine, Xi'an 710069, China
| | - Erfei Chen
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi'an 710069, China.,Institute of Preventive Genomic Medicine, Xi'an 710069, China
| | - Jing Dong
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi'an 710069, China.,Institute of Preventive Genomic Medicine, Xi'an 710069, China
| | - Yuan Zeng
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi'an 710069, China.,Institute of Preventive Genomic Medicine, Xi'an 710069, China
| | - Jin Yang
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Science, Northwest University, Xi'an 710069, China.,Institute of Preventive Genomic Medicine, Xi'an 710069, China
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16
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Cheng HL, Liu YF, Su CW, Su SC, Chen MK, Yang SF, Lin CW. Functional genetic variant in the Kozak sequence of WW domain-containing oxidoreductase (WWOX) gene is associated with oral cancer risk. Oncotarget 2018; 7:69384-69396. [PMID: 27655721 PMCID: PMC5342485 DOI: 10.18632/oncotarget.12082] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 09/10/2016] [Indexed: 12/11/2022] Open
Abstract
In Taiwan, oral cancer is the fourth leading cancer in males and is associated with exposure to environmental carcinogens. WW domain-containing oxidoreductase (WWOX), a tumor suppressor gene, is associated with the development of various cancers. We hypothesized that genetic variants of WWOX influence the susceptibility to oral cancer. Five polymorphisms of WWOX gene from 761 male patients with oral cancer and 1199 male cancer-free individuals were genotyped. We observed that individuals carrying the polymorphic allele of WWOX rs11545028 are more susceptible to oral cancer. Furthermore, patients with advanced-stage oral cancer were associated with a higher frequency of WWOX rs11545028 polymorphisms with the variant genotype TT than did patients with the wild-type gene. An additional integrated in silico analysis confirmed that rs11545028 affects WWOX expression, which significantly correlates with tumor expression and subsequently with tumor development and aggressiveness. In conclusion, genetic variants of WWOX contribute to the occurrence of oral cancer, and the findings regarding these biomarkers provided a prediction model for risk assessment.
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Affiliation(s)
- Hsin-Lin Cheng
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Yu-Fan Liu
- Department of Biomedical Sciences, Chung Shan Medical University, Taichung, Taiwan
| | - Chun-Wen Su
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Shih-Chi Su
- Whole-Genome Research Core Laboratory of Human Diseases, Chang Gung Memorial Hospital, Keelung, Taiwan
| | - Mu-Kuan Chen
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan.,Department of Otorhinolaryngology-Head and Neck Surgery, Changhua Christian Hospital, Changhua, Taiwan
| | - Shun-Fa Yang
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan.,Department of Medical Research, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Chiao-Wen Lin
- Institute of Oral Sciences, Chung Shan Medical University, Taichung, Taiwan.,Department of Dentistry, Chung Shan Medical University Hospital, Taichung, Taiwan
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17
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Clinical significance of germline copy number variation in susceptibility of human diseases. J Genet Genomics 2018; 45:3-12. [PMID: 29396143 DOI: 10.1016/j.jgg.2018.01.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 12/27/2017] [Accepted: 01/02/2018] [Indexed: 02/06/2023]
Abstract
Germline copy number variation (CNV) is considered to be an important form of human genetic polymorphisms. Previous studies have identified amounts of CNVs in human genome by advanced technologies, such as comparative genomic hybridization, single nucleotide genotyping, and high-throughput sequencing. CNV is speculated to be derived from multiple mechanisms, such as nonallelic homologous recombination (NAHR) and nonhomologous end-joining (NHEJ). CNVs cover a much larger genome scale than single nucleotide polymorphisms (SNPs), and may alter gene expression levels by means of gene dosage, gene fusion, gene disruption, and long-range regulation effects, thus affecting individual phenotypes and playing crucial roles in human pathogenesis. The number of studies linking CNVs with common complex diseases has increased dramatically in recent years. Here, we provide a comprehensive review of the current understanding of germline CNVs, and summarize the association of germline CNVs with the susceptibility to a wide variety of human diseases that were identified in recent years. We also propose potential issues that should be addressed in future studies.
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18
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Lin YH, Hsiao YH, Wu WJ, Yang SF, Hsu CF, Kang YT, Wang PH. Relationship of genetic variant distributions of WW domain-containing oxidoreductase gene with uterine cervical cancer. Int J Med Sci 2018; 15:1005-1013. [PMID: 30013442 PMCID: PMC6036151 DOI: 10.7150/ijms.25553] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 05/31/2018] [Indexed: 12/11/2022] Open
Abstract
To our knowledge, no study investigates the association of genetic variant distributions of WW domain-containing oxidoreductase (WWOX) gene with development of invasive cancer, clinicopathologic variables and patient survival in uterine cervical cancer for Taiwanese women. We therefore conducted this study to explore the clinical involvements of WWOX single nucleotide polymorphisms (SNPs) in cervical cancer. One hundred and thirty-one patients with cervical invasive cancer and 93 patients with precancerous lesions as well as 316 control women were consecutively enrolled. The genotypic frequencies of WWOX genetic variants rs73569323, rs383362, rs11545028, rs3764340 and rs12918952 were determined by real-time polymerase chain reaction. The results revealed that only WWOX SNP rs3764340 was associated between patients with cervical invasive cancer and normal controls among 5 WWOX genetic variants. Cervical cancer patients with genotypes GA/AA in WWOX SNP rs12918952 were associated with parametrium invasion and pelvic lymph node metastasis. Univariate analysis found that WWOX SNPs rs73569323 and rs11545028 were associated with patient survival, whereas multivariate analysis revealed CT/TT in rs11545028 was the only genetic variant, which could predict better overall survival, among 5 WWOX SNPs in Taiwan. In conclusion, Taiwanese women with CG/GG in WWOX SNP rs3764340 are susceptible to cervical invasive cancer. Cervical cancer patients with GA/AA in rs12918952 tend to have more risk to develop parametrium invasion and pelvic lymph node metastasis. Among 5 WWOX SNPs, rs11545028 is the only genetic variant associated with patient survival, in which CT/TT could predict better overall survival in Taiwanese women.
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Affiliation(s)
- Yu-Hsiang Lin
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Yi-Hsuan Hsiao
- School of Medicine, Chung Shan Medical University, Taichung, Taiwan.,Department of Obstetrics and Gynecology, Changhua Christian Hospital, Changhua, Taiwan
| | - Wen-Jun Wu
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan.,Department of Medical Research, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Shun-Fa Yang
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan.,Department of Medical Research, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Chun-Fang Hsu
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Yu-Ting Kang
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Po-Hui Wang
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan.,School of Medicine, Chung Shan Medical University, Taichung, Taiwan.,Department of Obstetrics and Gynecology, Chung Shan Medical University Hospital, Taichung, Taiwan
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19
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Yang L, Wu D, Chen J, Chen J, Qiu F, Li Y, Liu L, Cao Y, Yang B, Zhou Y, Lu J. A functional CNVR_3425.1 damping lincRNA FENDRR increases lifetime risk of lung cancer and COPD in Chinese. Carcinogenesis 2017; 39:347-359. [DOI: 10.1093/carcin/bgx149] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 12/19/2017] [Indexed: 11/13/2022] Open
Affiliation(s)
- Lei Yang
- The State Key Lab of Respiratory Disease, The institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou, China
- The State Key Lab of Respiratory Disease, Guangzhou Institute of Respiratory Diseases, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Di Wu
- The State Key Lab of Respiratory Disease, The institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou, China
| | - Jinbin Chen
- The State Key Lab of Respiratory Disease, The institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou, China
| | - Jiansong Chen
- The State Key Lab of Respiratory Disease, The institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou, China
| | - Fuman Qiu
- The State Key Lab of Respiratory Disease, The institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou, China
| | - Yinyan Li
- The State Key Lab of Respiratory Disease, The institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou, China
| | - Li Liu
- The State Key Lab of Respiratory Disease, The institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou, China
| | - Yi Cao
- The State Key Lab of Respiratory Disease, The institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou, China
| | - Binyao Yang
- The State Key Lab of Respiratory Disease, The institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou, China
| | - Yifeng Zhou
- Department of Genetics, Medical College of Soochow University, Suzhou, China
| | - Jiachun Lu
- The State Key Lab of Respiratory Disease, The institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou, China
- The State Key Lab of Respiratory Disease, Guangzhou Institute of Respiratory Diseases, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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20
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Fan J, Sun W, Lin M, Yu K, Wang J, Duan D, Zheng B, Yang Z, Wang Q. Genetic association study identifies a functional CNV in the WWOX gene contributes to the risk of intracranial aneurysms. Oncotarget 2017; 7:16104-11. [PMID: 26910372 PMCID: PMC4941300 DOI: 10.18632/oncotarget.7546] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 01/31/2016] [Indexed: 01/19/2023] Open
Abstract
Intracranial aneurysms (IAs) accounts for 85% of hemorrhagic stroke. Genetic factors have been known to play an important role in the development of IAs. A functional CNV (CNV-67048) of human WW domain-containing oxidoreductase (WWOX), which has been identified as a tumor suppressor gene in multiple cancers, was identified to be associated with gliomas risk previously. Here, we hypothesized that the CNV-67048 could also affect susceptibility of IAs. Based on a two-stage, case− control study with a total of 976 patients of IAs and 1,200 matched healthy controls, we found the effect size for per copy deletion was 1.35 (95% CI = 1.16–1.57; Ptrend = 1.18 × 10−4). Compared with the individuals having no deletion, significantly higher risk of IAs was detected for both subjects carrying 1 copy deletion (OR = 1.24, 95% CI = 1.02–1.52) and subjects carrying 2 copy deletion (OR = 1.77, 95% CI = 1.24–2.53). Real-time PCR was used to confirm the abnormal expression of WWOX in tissues of IA patients and influence of genotypes of CNV-67048. The expression level of WWOX in IA tissues was significantly lower than that in corresponding normal tissues (P = 0.004), and the deletion genotypes of CNV-67048 have lower WWOX mRNA levels in both tumor tissues and border tissues (P < 0.01). Our data suggests that the deletion genotypes of CNV-67048 in WWOX predispose their carriers to IAs, which might be a genetic biomarker to predict risk of IAs in Chinese.
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Affiliation(s)
- Jin Fan
- Department of Neurology, Chengdu Military General Hospital, Chengdu, China
| | - Wen Sun
- Department of Neurology, Jinling Hospital of Nanjing University, Nanjing, China
| | - Min Lin
- Department of Neurology, Fuzhou General Hospital of Nanjing Command, PLA and Clinical Medical College of Fujian Medical University, Fuzhou, China
| | - Ke Yu
- Department of Neurology, Chengdu Military General Hospital, Chengdu, China
| | - Jian Wang
- Department of Neurology, Chengdu Military General Hospital, Chengdu, China
| | - Dan Duan
- Department of Neurology, Chengdu Military General Hospital, Chengdu, China
| | - Bo Zheng
- Department of Neurology, Chengdu Military General Hospital, Chengdu, China
| | - Zhenghui Yang
- Department of Neurology, Chengdu Military General Hospital, Chengdu, China
| | - Qingsong Wang
- Department of Neurology, Chengdu Military General Hospital, Chengdu, China
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21
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Ma D, Yang J, Wang Y, Huang X, Du G, Zhou L. Whole exome sequencing identified genetic variations in Chinese hemangioblastoma patients. Am J Med Genet A 2017; 173:2605-2613. [PMID: 28742274 DOI: 10.1002/ajmg.a.38350] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 06/05/2017] [Accepted: 06/09/2017] [Indexed: 02/04/2023]
Abstract
Hemangioblastomas (HBs) are uncommon tumors characterized by the presence of inactivating alterations in the von Hippel-Lindau (VHL) gene in inherited cases and by infrequent somatic mutation in sporadic entities. We performed whole exome sequencing on 11 HB patients to further elucidate the genetics of HBs. A total of 270 somatic variations in 219 genes, of which there were 86 mutations in 67 genes, were found in sporadic HBs, and 184 mutations were found in 154 genes in familial HBs. C: G>T: A and T: A>C: G mutations are relatively common in most HB patients. Genes harboring the most significant mutations include PCDH9, KLHL12, DCAF4L1, and VHL in sporadic HBs, and ZNF814, DLG2, RIMS1, PNN, and MUC7 in familial HBs. The frequency of CNV varied considerably within sporadic HBs but was relatively similar within familial HBs. Five genes, including OTOGL, PLCB4, SCEL, THSD4, and WWOX, have CNVs in the six patients with sporadic HBs, and three genes, including ABCA6, CWC27, and LAMA2, have CNVs in the five patients with familial HBs. We found new genetic mutations and CNVs that might be involved in HBs; these findings highlight the complexity of the tumorigenesis of HBs and pinpoint potential therapeutic targets for the treatment of HBs.
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Affiliation(s)
- Dexuan Ma
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Jingyun Yang
- School of Economics, Shanghai University, Shanghai, China.,Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois.,Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois
| | - Ying Wang
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Xiang Huang
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Guhong Du
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Liangfu Zhou
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
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22
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Functions and Epigenetic Regulation of Wwox in Bone Metastasis from Breast Carcinoma: Comparison with Primary Tumors. Int J Mol Sci 2017; 18:ijms18010075. [PMID: 28045433 PMCID: PMC5297710 DOI: 10.3390/ijms18010075] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 10/26/2016] [Accepted: 11/24/2016] [Indexed: 02/07/2023] Open
Abstract
Epigenetic mechanisms influence molecular patterns important for the bone-metastatic process, and here we highlight the role of WW-domain containing oxidoreductase (Wwox). The tumor-suppressor Wwox lacks in almost all cancer types; the variable expression in osteosarcomas is related to lung-metastasis formation, and exogenous Wwox destabilizes HIF-1α (subunit of Hypoxia inducible Factor-1, HIF-1) affecting aerobic glycolysis. Our recent studies show critical functions of Wwox present in 1833-osteotropic clone, in the corresponding xenograft model, and in human bone metastasis from breast carcinoma. In hypoxic-bone metastatic cells, Wwox enhances HIF-1α stabilization, phosphorylation, and nuclear translocation. Consistently, in bone-metastasis specimens Wwox localizes in cytosolic/perinuclear area, while TAZ (transcriptional co-activator with PDZ-binding motif) and HIF-1α co-localize in nuclei, playing specific regulatory mechanisms: TAZ is a co-factor of HIF-1, and Wwox regulates HIF-1 activity by controlling HIF-1α. In vitro, DNA methylation affects Wwox-protein synthesis; hypoxia decreases Wwox-protein level; hepatocyte growth factor (HGF) phosphorylates Wwox driving its nuclear shuttle, and counteracting a Twist program important for the epithelial phenotype and metastasis colonization. In agreement, in 1833-xenograft mice under DNA-methyltransferase blockade with decitabine, Wwox increases in nuclei/cytosol counteracting bone metastasis with prolongation of the survival. However, Wwox seems relevant for the autophagic process which sustains metastasis, enhancing more Beclin-1 than p62 protein levels, and p62 accumulates under decitabine consistent with adaptability of metastasis to therapy. In conclusion, Wwox methylation as a bone-metastasis therapeutic target would depend on autophagy conditions, and epigenetic mechanisms regulating Wwox may influence the phenotype of bone metastasis.
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23
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WWOX inhibits the invasion of lung cancer cells by downregulating RUNX2. Cancer Gene Ther 2016; 23:433-438. [PMID: 27834355 DOI: 10.1038/cgt.2016.59] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 10/05/2016] [Accepted: 10/07/2016] [Indexed: 02/06/2023]
Abstract
The WW domain-containing oxidoreductase (WWOX) is a tumor suppressor that is lost or decreased in most human tumors. The role of WWOX in human lung carcinoma invasion is still not clear. This study aimed to elucidate the potential role of WWOX in lung cancer cell invasion. WWOX mRNA levels in human lung cancers and lung cancer cell lines were assayed by quantitative real-time PCR. WWOX in lung cancer cell lines was manipulated by transfection of expression vector or small interfering RNA. Cell migration and invasion were assessed by wound healing and/or transwell migration and invasion assays. The protein levels of WWOX, E-cadherin and RUNX2 were analyzed by western blot or immunofluorescence. WWOX expression is inversely correlated to invasiveness of lung cancer. WWOX overexpression in highly invasive H1299 cells reduced cell motility and invasiveness, and inhibited the expression of RUNX2 and its target gene matrix metalloproteinase-9 (MMP-9). Silencing WWOX in less invasive NL9980 cells resulted in opposite effects. Overexpressing RUNX2 in H1299 or silencing RUNX2 in NL9980 cells reversed the effects of WWOX. These results suggested that WWOX inhibited the invasive phenotype of lung cancer through downregulating the expression of RUNX2.
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He H, Lei L, Chen E, Dong J, Zhang K, Yang J. The c.553G>T Genetic Variant of the APOA5 Gene and Altered Triglyceride Levels in the Asian Population: A Meta-Analysis of Case-Control Studies. Genet Test Mol Biomarkers 2016; 20:758-765. [PMID: 27813673 DOI: 10.1089/gtmb.2016.0047] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
AIM To explore the association of the APOA5 gene c.553G>T polymorphism with hypertriglyceridemia (HTG) susceptibility and altered triglyceride levels. METHODS We searched the PubMed, Google Scholar, and CNKI databases for published studies relating to analyses of these associations. Case-control and comparative studies of the association between the APOA5 c.553G>T variant and altered triglyceride levels were included. In total, the meta-analysis involved 10 studies on HTG, which provided 2219 cases and 3401 controls. To measure the correlation between the c.553G>T polymorphism and HTG susceptibility, odds ratios (ORs) and 95% confidence intervals (CIs) were calculated. The overall OR was calculated using a random-effects model. RESULTS Compared with APOA5 c.553 GG carriers, c.553T carriers displayed an increased risk of HTG in the Asian population, with an overall random effects OR of 3.55 (95% CI: 2.46-5.13) in the dominant model. There was significant heterogeneity among the studies (Pheterogeneity: Chi2 = 45.80, I2 = 75.98%), which may be largely explained by certain patient types. Both the sensitivity analysis and publication bias suggested that the overall result was acceptable. Subgroup analysis showed a large difference in serum triglyceride levels based on the c.553 G > T polymorphism in healthy individuals and HTG patients. APOA5 c.553T carriers exhibit higher triglyceride levels than GG carriers. CONCLUSION Our results suggest that APOA5 c. 553T is an independent risk factor for HTG and increased triglyceride levels in the Asian population. APOA5 c. 553T could be employed as a genetic risk marker for HTG and increased triglyceride levels.
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Affiliation(s)
- Hongjuan He
- College of Life Science, Institute of Preventive Genomic Medicine, Northwest University , Xi'an, China
| | - Lei Lei
- College of Life Science, Institute of Preventive Genomic Medicine, Northwest University , Xi'an, China
| | - Erfei Chen
- College of Life Science, Institute of Preventive Genomic Medicine, Northwest University , Xi'an, China
| | - Jing Dong
- College of Life Science, Institute of Preventive Genomic Medicine, Northwest University , Xi'an, China
| | - Kejin Zhang
- College of Life Science, Institute of Preventive Genomic Medicine, Northwest University , Xi'an, China
| | - Jin Yang
- College of Life Science, Institute of Preventive Genomic Medicine, Northwest University , Xi'an, China
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25
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Jenkins GM, Goddard ME, Black MA, Brauning R, Auvray B, Dodds KG, Kijas JW, Cockett N, McEwan JC. Copy number variants in the sheep genome detected using multiple approaches. BMC Genomics 2016; 17:441. [PMID: 27277319 PMCID: PMC4898393 DOI: 10.1186/s12864-016-2754-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Accepted: 05/19/2016] [Indexed: 02/07/2023] Open
Abstract
Background Copy number variants (CNVs) are a type of polymorphism found to underlie phenotypic variation, both in humans and livestock. Most surveys of CNV in livestock have been conducted in the cattle genome, and often utilise only a single approach for the detection of copy number differences. Here we performed a study of CNV in sheep, using multiple methods to identify and characterise copy number changes. Comprehensive information from small pedigrees (trios) was collected using multiple platforms (array CGH, SNP chip and whole genome sequence data), with these data then analysed via multiple approaches to identify and verify CNVs. Results In total, 3,488 autosomal CNV regions (CNVRs) were identified in this study, which substantially builds on an initial survey of the sheep genome that identified 135 CNVRs. The average length of the identified CNVRs was 19 kb (range of 1 kb to 3.6 Mb), with shorter CNVRs being more frequent than longer CNVRs. The total length of all CNVRs was 67.6Mbps, which equates to 2.7 % of the sheep autosomes. For individuals this value ranged from 0.24 to 0.55 %, and the majority of CNVRs were identified in single animals. Rather than being uniformly distributed throughout the genome, CNVRs tended to be clustered. Application of three independent approaches for CNVR detection facilitated a comparison of validation rates. CNVs identified on the Roche-NimbleGen 2.1M CGH array generally had low validation rates with lower density arrays, while whole genome sequence data had the highest validation rate (>60 %). Conclusions This study represents the first comprehensive survey of the distribution, prevalence and characteristics of CNVR in sheep. Multiple approaches were used to detect CNV regions and it appears that the best method for verifying CNVR on a large scale involves using a combination of detection methodologies. The characteristics of the 3,488 autosomal CNV regions identified in this study are comparable to other CNV regions reported in the literature and provide a valuable and sizeable addition to the small subset of published sheep CNVs. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2754-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gemma M Jenkins
- AbacusBio Limited, 442 Moray Place, PO Box 5585, Dunedin, 9058, New Zealand.
| | - Michael E Goddard
- Victorian Department of Economic Development, Jobs, Transport and Resources, Bundoora, VIC, 3083, Australia
| | - Michael A Black
- Department of Biochemistry, University of Otago, 710 Cumberland St, Dunedin, 9054, New Zealand
| | - Rudiger Brauning
- AgResearch, Invermay Agricultural Centre, PB 50034, Mosgiel, 9053, New Zealand
| | - Benoit Auvray
- Department of Biochemistry, University of Otago, 710 Cumberland St, Dunedin, 9054, New Zealand
| | - Ken G Dodds
- AgResearch, Invermay Agricultural Centre, PB 50034, Mosgiel, 9053, New Zealand
| | - James W Kijas
- CSIRO Animal, Food and Health Sciences, Queensland Bioscience Precinct, 306 Carmody Road, St Lucia, QLD 4067, Australia
| | - Noelle Cockett
- Utah State University, 1435 Old Main Hill, Logan, UT, 84322-1435-1435, USA
| | - John C McEwan
- AgResearch, Invermay Agricultural Centre, PB 50034, Mosgiel, 9053, New Zealand
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Shi Y, Du M, Fang Y, Tong N, Zhai X, Sheng X, Li Z, Xue Y, Li J, Chu H, Chen J, Song Z, Shen J, Ji J, Li X, Hu Z, Shen H, Xu J, Wang M, Zhang Z. Identification of a novel susceptibility locus at 16q23.1 associated with childhood acute lymphoblastic leukemia in Han Chinese. Hum Mol Genet 2016; 25:2873-2880. [PMID: 27094129 DOI: 10.1093/hmg/ddw112] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 03/13/2016] [Accepted: 04/11/2016] [Indexed: 12/11/2022] Open
Abstract
Recently, genome-wide association studies (GWAS) have identified several susceptibility loci for childhood acute lymphoblastic leukemia (ALL) in populations of European descent; only a few loci could be confirmed in Asian populations because of those populations' genetic heterogeneity. To identify genetic factors associated with childhood ALL risk in the Chinese population, we performed a three-stage GWAS of 1184 childhood ALL cases and 3219 non-ALL controls. The combined analysis identified a new locus (rs1121404 in WWOX) at 16q23.1 associated with childhood ALL susceptibility (odds ratio (OR) = 1.38, P = 5.29 × 10-10), especially in the subtype of B-ALL (OR = 1.39, P = 2.47 × 10-9). The functional studies subsequently revealed that the expression of WWOX in ALL bone marrow was significantly lower than that in normal bone marrow. The G allele of rs1121404 displayed significantly decreased levels of mRNA expression of WWOX These results suggest that WWOX plays an important role in the development of childhood ALL and provide new insights into the etiology of childhood ALL.
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Affiliation(s)
- Yongyong Shi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200030, China .,The Affiliated Hospital of Qingdao University, Qingdao 266003, China.,Institute of Social Cognitive and Behavioral Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Mulong Du
- Department of Genetic Toxicology, the Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China.,Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Yongjun Fang
- Department of Hematology and Oncology, Nanjing Children's Hospital Affiliated with Nanjing Medical University, Nanjing 210000, China
| | - Na Tong
- Department of Genetic Toxicology, the Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China.,Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Xiaowen Zhai
- Department of Hematology and Oncology, Children's hospital of Fudan University, Shanghai 200032, China
| | - Xiaojing Sheng
- Department of Children's healthcare, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210000, China
| | - Zhiqiang Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200030, China.,Institute of Social Cognitive and Behavioral Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yao Xue
- Department of Hematology and Oncology, Nanjing Children's Hospital Affiliated with Nanjing Medical University, Nanjing 210000, China
| | - Jie Li
- Department of Hematology and Oncology, The Affiliated Children's Hospital of Soochow University, Suzhou 215025, China
| | - Haiyan Chu
- Department of Genetic Toxicology, the Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China.,Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Jianhua Chen
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200030, China.,Institute of Social Cognitive and Behavioral Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhijian Song
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200030, China.,Institute of Social Cognitive and Behavioral Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jiawei Shen
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200030, China.,Institute of Social Cognitive and Behavioral Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jue Ji
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Xingwang Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Zhibin Hu
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Hongbing Shen
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Jianfeng Xu
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, Illinois 60201, USA
| | - Meilin Wang
- Department of Genetic Toxicology, the Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China .,Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Zhengdong Zhang
- Department of Genetic Toxicology, the Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 211166, China .,Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
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27
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WWOX CNV-67048 Functions as a Risk Factor for Epithelial Ovarian Cancer in Chinese Women by Negatively Interacting with Oral Contraceptive Use. BIOMED RESEARCH INTERNATIONAL 2016; 2016:6594039. [PMID: 27190995 PMCID: PMC4842385 DOI: 10.1155/2016/6594039] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 03/22/2016] [Indexed: 12/22/2022]
Abstract
Copy number variations (CNVs) have attracted increasing evidences to represent their roles as cancer susceptibility regulators. However, little is known about the role of CNV in epithelia ovarian cancer (EOC). Recently, the CNV-67048 of WW domain-containing oxidoreductase (WWOX) was reported to alter cancer risks. Considering that WWOX also plays a role in EOC, we hypothesized that the CNV-67048 was associated with EOC risk. In a case-control study of 549 EOC patients and 571 age (±5 years) matched cancer-free controls, we found that the low copy number of CNV-67048 (1-copy and 0-copy) conferred a significantly increased risk of EOC (OR = 1.346, 95% CI = 1.037–1.747) and it determined the risk by means of copy number-dependent dosage effect (P = 0.009). Data from TCGA also confirmed the abovementioned association as the frequency of low copies in EOC group was 3.68 times more than that in healthy group (P = 0.023). The CNV also negatively interacted with oral contraceptive use on EOC risk (P = 0.042). Functional analyses further showed a lower mRNA level of WWOX in tissues with the 0-copy or 1-copy than that in those with the 2-copy (P = 0.045). Our data suggested the CNV-67048 to be a risk factor of EOC in Chinese women.
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28
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Zhou Y, Shou F, Zhang H, You Q. Adenovirus-delivered wwox inhibited lung cancer growth in vivo in a mouse model. Cancer Gene Ther 2015; 23:1-6. [DOI: 10.1038/cgt.2015.56] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 09/01/2015] [Accepted: 09/02/2015] [Indexed: 01/17/2023]
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29
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Abu-Remaileh M, Joy-Dodson E, Schueler-Furman O, Aqeilan RI. Pleiotropic Functions of Tumor Suppressor WWOX in Normal and Cancer Cells. J Biol Chem 2015; 290:30728-35. [PMID: 26499798 DOI: 10.1074/jbc.r115.676346] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
WW domain-containing oxidoreductase (WWOX), originally marked as a likely tumor suppressor gene, has over the years become recognized for its role in a much wider range of cellular activities. Phenotypic effects displayed in animal studies, along with resolution of WWOX's architecture, fold, and binding partners, point to the protein's multifaceted biological functions. Results from a series of complementary experiments seem to indicate WWOX's involvement in metabolic regulation. More recently, clinical studies involving cases of severe encephalopathy suggest that WWOX also plays a part in controlling CNS development, further expanding our understanding of the breadth and complexity of WWOX behavior. Here we present a short overview of the various approaches taken to study this dynamic gene, emphasizing the most recent findings regarding WWOX's metabolic- and CNS-associated functions and their underlying molecular basis.
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Affiliation(s)
| | - Emma Joy-Dodson
- Microbiology & Molecular Genetics, Institute for Medical Research Israel-Canada (IMRIC), Hebrew University-Hadassah Medical School, Jerusalem, Israel 91120
| | - Ora Schueler-Furman
- Microbiology & Molecular Genetics, Institute for Medical Research Israel-Canada (IMRIC), Hebrew University-Hadassah Medical School, Jerusalem, Israel 91120
| | - Rami I Aqeilan
- From the Departments of Immunology & Cancer Research and
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30
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Hazan I, Aqeilan RI. Current questions and controversies in chromosome fragile site research: does WWOX, the gene product of common fragile site FRA16D, have a passive or active role in cancer? Cell Death Discov 2015; 1:15040. [PMID: 27551470 PMCID: PMC4979517 DOI: 10.1038/cddiscovery.2015.40] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- I Hazan
- Lautenberg Center for Immunology and Cancer Research, IMRIC, Hebrew University-Hadassah Medical School , Jerusalem, Israel
| | - R I Aqeilan
- Lautenberg Center for Immunology and Cancer Research, IMRIC, Hebrew University-Hadassah Medical School , Jerusalem, Israel
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31
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Choo A, O'Keefe LV, Lee CS, Gregory SL, Shaukat Z, Colella A, Lee K, Denton D, Richards RI. Tumor suppressor WWOX moderates the mitochondrial respiratory complex. Genes Chromosomes Cancer 2015; 54:745-61. [PMID: 26390919 DOI: 10.1002/gcc.22286] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 06/26/2015] [Indexed: 01/11/2023] Open
Abstract
Fragile site FRA16D exhibits DNA instability in cancer, resulting in diminished levels of protein from the WWOX gene that spans it. WWOX suppresses tumor growth by an undefined mechanism. WWOX participates in pathways involving aerobic metabolism and reactive oxygen species. WWOX comprises two WW domains as well as a short-chain dehydrogenase/reductase enzyme. Herein is described an in vivo genetic analysis in Drosophila melanogaster to identify functional interactions between WWOX and metabolic pathways. Altered WWOX levels modulate variable cellular outgrowths caused by genetic deficiencies of components of the mitochondrial respiratory complexes. This modulation requires the enzyme active site of WWOX, and the defective respiratory complex-induced cellular outgrowths are mediated by reactive oxygen species, dependent upon the Akt pathway and sensitive to levels of autophagy and hypoxia-inducible factor. WWOX is known to contribute to homeostasis by regulating the balance between oxidative phosphorylation and glycolysis. Reduction of WWOX levels results in diminished ability to respond to metabolic perturbation of normal cell growth. Thus, the ability of WWOX to facilitate escape from mitochondrial damage-induced glycolysis (Warburg effect) is, therefore, a plausible mechanism for its tumor suppressor activity.
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Affiliation(s)
- Amanda Choo
- Department of Genetics and Evolution and Centre for Molecular Pathology, School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Louise V O'Keefe
- Department of Genetics and Evolution and Centre for Molecular Pathology, School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Cheng Shoou Lee
- Department of Genetics and Evolution and Centre for Molecular Pathology, School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Stephen L Gregory
- Department of Genetics and Evolution and Centre for Molecular Pathology, School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Zeeshan Shaukat
- Department of Genetics and Evolution and Centre for Molecular Pathology, School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Alexander Colella
- Department of Genetics and Evolution and Centre for Molecular Pathology, School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Kristie Lee
- Department of Genetics and Evolution and Centre for Molecular Pathology, School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Donna Denton
- Department of Genetics and Evolution and Centre for Molecular Pathology, School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Robert I Richards
- Department of Genetics and Evolution and Centre for Molecular Pathology, School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
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O’Keefe LV, Lee CS, Choo A, Richards RI. Tumor Suppressor WWOX Contributes to the Elimination of Tumorigenic Cells in Drosophila melanogaster. PLoS One 2015; 10:e0136356. [PMID: 26302329 PMCID: PMC4547717 DOI: 10.1371/journal.pone.0136356] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 07/31/2015] [Indexed: 01/27/2023] Open
Abstract
WWOX is a >1Mb gene spanning FRA16D Common Chromosomal Fragile Site, a region of DNA instability in cancer. Consequently, altered WWOX levels have been observed in a wide variety of cancers. In vitro studies have identified a large number and variety of potential roles for WWOX. Although its normal role in vivo and functional contribution to cancer have not been fully defined, WWOX does have an integral role in metabolism and can suppress tumor growth. Using Drosophila melanogaster as an in vivo model system, we find that WWOX is a modulator of TNFα/Egr-mediated cell death. We found that altered levels of WWOX can modify phenotypes generated by low level ectopic expression of TNFα/Egr and this corresponds to altered levels of Caspase 3 activity. These results demonstrate an in vivo role for WWOX in promoting cell death. This form of cell death is accompanied by an increase in levels of reactive oxygen species, the regulation of which we have previously shown can also be modified by altered WWOX activity. We now hypothesise that, through regulation of reactive oxygen species, WWOX constitutes a link between alterations in cellular metabolism observed in cancer cells and their ability to evade normal cell death pathways. We have further shown that WWOX activity is required for the efficient removal of tumorigenic cells from a developing epithelial tissue. Together these results provide a molecular basis for the tumor suppressor functions of WWOX and the better prognosis observed in cancer patients with higher levels of WWOX activity. Understanding the conserved cellular pathways to which WWOX contributes provides novel possibilities for the development of therapeutic approaches to restore WWOX function in cancer.
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Affiliation(s)
- Louise V. O’Keefe
- Department of Genetics and Evolution, Centre for Molecular Pathology, School of Biological Sciences, The University of Adelaide, Adelaide, Australia
| | - Cheng Shoou Lee
- Department of Genetics and Evolution, Centre for Molecular Pathology, School of Biological Sciences, The University of Adelaide, Adelaide, Australia
| | - Amanda Choo
- Department of Genetics and Evolution, Centre for Molecular Pathology, School of Biological Sciences, The University of Adelaide, Adelaide, Australia
| | - Robert I. Richards
- Department of Genetics and Evolution, Centre for Molecular Pathology, School of Biological Sciences, The University of Adelaide, Adelaide, Australia
- * E-mail:
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33
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Del Mare S, Aqeilan RI. Tumor Suppressor WWOX inhibits osteosarcoma metastasis by modulating RUNX2 function. Sci Rep 2015; 5:12959. [PMID: 26256646 PMCID: PMC4542681 DOI: 10.1038/srep12959] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 07/15/2015] [Indexed: 12/19/2022] Open
Abstract
Osteosarcoma (OS) is among the most frequently occurring primary bone tumors, primarily affecting adolescents and young adults. This malignant osteoid forming tumor is characterized by its metastatic potential, mainly to lungs. We recently demonstrated that WW domain-containing oxidoreductase (WWOX) is frequently inactivated in human OS and that WWOX restoration in WWOX-negative OS cells suppresses tumorigenicity. Of note, WWOX levels are reduced in paired OS samples of post-treatment metastastectomies as compared to pre-treatment biopsies suggesting that decreased WWOX levels are associated with a more aggressive phenotype at the metastatic site. Nevertheless, little is known about WWOX function in OS metastasis. Here, we investigated the role of tumor suppressor WWOX in suppressing pulmonary OS metastasis bothin vitroandin vivo. We demonstrated that ectopic expression of WWOX in OS cells, HOS and LM-7, inhibits OS invasion and cell migration in vitro. Furthermore, WWOX expression reduced tumor burden in vivo and inhibited metastases’ seeding and colonization. Mechanistically, WWOX function is associated with reduced levels of RUNX2 metastatic target genes implicated in adhesion and motility. Our results suggest that WWOX plays a critical role in determining the aggressive phenotype of OS, and its expression could be an attractive therapeutic target to combat this devastating adolescent disease.
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Affiliation(s)
- Sara Del Mare
- The Lautenberg Center for Immunology and Cancer Research, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Israel 91220
| | - Rami I Aqeilan
- The Lautenberg Center for Immunology and Cancer Research, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Israel 91220
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Yu H, Luo L, Wu L, Zheng M, Zhang L, Liu Y, Li H, Cao Q, Kijlstra A, Yang P. FASGene Copy Numbers are Associated with Susceptibility to Behçet Disease and VKH Syndrome in Han Chinese. Hum Mutat 2015; 36:1064-9. [PMID: 26136352 DOI: 10.1002/humu.22829] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 06/23/2015] [Indexed: 01/26/2023]
Affiliation(s)
- Hongsong Yu
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute; Chongqing P. R. China
| | - Le Luo
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute; Chongqing P. R. China
| | - Lili Wu
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute; Chongqing P. R. China
| | - Minming Zheng
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute; Chongqing P. R. China
| | - Lijun Zhang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute; Chongqing P. R. China
| | - Yunjia Liu
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute; Chongqing P. R. China
| | - Hua Li
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute; Chongqing P. R. China
| | - Qingfeng Cao
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute; Chongqing P. R. China
| | - Aize Kijlstra
- University Eye Clinic Maastricht; Maastricht The Netherlands
| | - Peizeng Yang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute; Chongqing P. R. China
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35
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Huang C, Tian Y, Peng R, Zhang C, Wang D, Han S, Jiao C, Wang X, Zhang H, Wang Y, Li X. Association of downregulation of WWOX with poor prognosis in patients with intrahepatic cholangiocarcinoma after curative resection. J Gastroenterol Hepatol 2015; 30:421-33. [PMID: 25168293 DOI: 10.1111/jgh.12722] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/03/2014] [Indexed: 12/30/2022]
Abstract
BACKGROUND AND AIM Downregulation of the WW domain containing oxidoreductase (WWOX) has been reported to be involved in tumorigenesis in several neoplasms. This study sought to investigate the expression and role of WWOX in intrahepatic cholangiocarcinoma (ICC). METHODS WWOX expression was measured by quantitative real-time polymerase chain reaction (PCR), immunoblot, immunofluorescence, and immunohistochemistry. The prognostic significance was assessed by Kaplan-Meier and Cox regression analyses. The role of WWOX in proliferation, anchorage-independent growth, gene expression regulation, and tumorigenesis was assessed by WWOX re-expression using lentivirus. Methylation-specific PCR was performed to evaluate the methylation status of the WWOX gene regulatory region. A DNA methyltransferase inhibitor, 5-aza-2'-deoxycytidine (AZA), was used to activate the endogenous WWOX gene in ICC cells both in vitro and in vivo. RESULTS The expression of WWOX in ICC tissues was much lower than that in nontumorous samples and showed reverse correlation with proliferative status. Restoration of WWOX expression resulted in suppression of the growth of WWOX-deficient ICC cells through activation of the intrinsic apoptotic signaling pathway, but did not affect growth of WWOX-sufficient human intrahepatic biliary epithelial derived non-cancer cells. Multivariate analyses revealed that downregulation of WWOX was an unfavorable predictor for overall survival and cumulative recurrence rates. The WWOX gene regulatory region was frequently methylated in ICC tissues and cell lines, and intratumoral WWOX restoration, through AZA injection, suppressed tumor growth in nude mice. CONCLUSION Downregulation of WWOX may occur as a result of hypermethylation and implies a poor prognosis in ICC; WWOX re-expression may be a potential molecular therapeutic target for ICC.
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Affiliation(s)
- Changjun Huang
- Department of General Surgery, Luohe Central Hospital Affiliated to Luohe Medical College, Luohe, China; Liver Transplantation Center, First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Living Donor Liver Transplantation, Ministry of Public Health, Nanjing, China
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Seiser EL, Innocenti F. Hidden Markov Model-Based CNV Detection Algorithms for Illumina Genotyping Microarrays. Cancer Inform 2015; 13:77-83. [PMID: 25657572 PMCID: PMC4310714 DOI: 10.4137/cin.s16345] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 11/18/2014] [Accepted: 11/21/2014] [Indexed: 12/24/2022] Open
Abstract
Somatic alterations in DNA copy number have been well studied in numerous malignancies, yet the role of germline DNA copy number variation in cancer is still emerging. Genotyping microarrays generate allele-specific signal intensities to determine genotype, but may also be used to infer DNA copy number using additional computational approaches. Numerous tools have been developed to analyze Illumina genotype microarray data for copy number variant (CNV) discovery, although commonly utilized algorithms freely available to the public employ approaches based upon the use of hidden Markov models (HMMs). QuantiSNP, PennCNV, and GenoCN utilize HMMs with six copy number states but vary in how transition and emission probabilities are calculated. Performance of these CNV detection algorithms has been shown to be variable between both genotyping platforms and data sets, although HMM approaches generally outperform other current methods. Low sensitivity is prevalent with HMM-based algorithms, suggesting the need for continued improvement in CNV detection methodologies.
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Affiliation(s)
- Eric L Seiser
- Center for Pharmacogenomics and Individualized Therapy, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Federico Innocenti
- Center for Pharmacogenomics and Individualized Therapy, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. ; UNC Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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Richards RI, Choo A, Lee CS, Dayan S, O'Keefe L. WWOX, the chromosomal fragile site FRA16D spanning gene: its role in metabolism and contribution to cancer. Exp Biol Med (Maywood) 2015; 240:338-44. [PMID: 25595186 DOI: 10.1177/1535370214565990] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The WWOX gene spans the common chromosomal fragile site FRA16D that is located within a massive (780 kb) intron. The WWOX gene is very long, at 1.1 Mb, which may contribute to the very low abundance of the full-length 1.4 kb mRNA. Alternative splicing also accounts for a variety of aberrant transcripts, most of which are devoid of C-terminal sequences required for WWOX to act as an oxidoreductase. The mouse WWOX gene also spans a chromosomal fragile site implying some sort of functional relationship that confers a selective advantage. The encoded protein domains of WWOX are conserved through evolution (between humans and Drosophila melanogaster) and include WW domains, an NAD -binding site, short-chain dehydrogenase/reductase enzyme and nuclear compartmentalization signals. This homology has enabled functional analyses in D. melanogaster that demonstrate roles for WWOX in reactive oxygen species regulation and metabolism. Indeed the human WWOX gene is also responsive to altered metabolism. Cancer cells typically exhibit altered metabolism (Warburg effect). Many cancers exhibit FRA16D DNA instability that results in aberrant WWOX expression and is associated with poor prognosis for these cancers. It is therefore thought that aberrant WWOX expression contributes to the altered metabolism in cancer. In addition, others have found that a specific (low-expression) allele of WWOX genotype contributes to cancer predisposition.
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Affiliation(s)
- Robert I Richards
- Discipline of Genetics and Centre for Molecular Pathology, School of Molecular and Biomedical Sciences, The University of Adelaide, Adelaide, SA 5000, Australia
| | - Amanda Choo
- Discipline of Genetics and Centre for Molecular Pathology, School of Molecular and Biomedical Sciences, The University of Adelaide, Adelaide, SA 5000, Australia
| | - Cheng Shoou Lee
- Discipline of Genetics and Centre for Molecular Pathology, School of Molecular and Biomedical Sciences, The University of Adelaide, Adelaide, SA 5000, Australia
| | - Sonia Dayan
- Discipline of Genetics and Centre for Molecular Pathology, School of Molecular and Biomedical Sciences, The University of Adelaide, Adelaide, SA 5000, Australia
| | - Louise O'Keefe
- Discipline of Genetics and Centre for Molecular Pathology, School of Molecular and Biomedical Sciences, The University of Adelaide, Adelaide, SA 5000, Australia
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Yang L, Qiu F, Fang W, Zhang L, Xie C, Lu X, Huang D, Guo Y, Pan M, Zhang H, Zhou Y, Lu J. The Functional Copy Number Variation-67048 in WWOX Contributes to Increased Risk of COPD in Southern and Eastern Chinese. COPD 2014; 12:494-501. [PMID: 25517572 DOI: 10.3109/15412555.2014.948993] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Recent studies have recognized the genetic variants in the WW domain-containing oxidoreductase (WWOX) gene as genetic determinants of lung function, reflecting that the WWOX gene may be a susceptible factor of chronic obstructive pulmonary disease (COPD), which characters as poor lung function. We have previously showed that the copy number variation-67048 (CNV-67048) of WWOX was associated with lung cancer risk. Here, we hypothesized that the CNV-67048 affects COPD susceptibility. Based on a two-stage case-control study with a total of 1791 COPD patients and 1940 controls of southern and eastern Chinese, we found that the loss genotypes (0-copy and 1-copy) of CNV-67048 harbored a significantly increased risk of COPD, with an odds ratio (OR) as 1.29 (1.11-1.49) when compared with the common 2-copy genotype. The pre-forced expiratory volume in one second (pre-FEV1) to pre-forced vital capacity (pre-FVC) of carriers with loss genotypes (0.729 ± 0.130) was significantly lower than carriers with 2-copy genotype (0.747 ± 0.124; p = 7.93 × 10(-5)). However, no significant difference was observed on pre-FEV1, pre-FVC and the annual decline of pre-FEV1 between the loss genotypes and 2-copy genotype carriers. Our data suggest that the loss genotypes of CNV-67048 in WWOX predispose their carriers to COPD, which might be a genetic biomarker to predict risk of COPD in Chinese.
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Affiliation(s)
- Lei Yang
- a The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis , Guangzhou Medical University , Guangzhou , China
| | - Fuman Qiu
- a The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis , Guangzhou Medical University , Guangzhou , China
| | - Wenxiang Fang
- a The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis , Guangzhou Medical University , Guangzhou , China
| | - Lisha Zhang
- a The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis , Guangzhou Medical University , Guangzhou , China
| | - Chenli Xie
- a The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis , Guangzhou Medical University , Guangzhou , China.,b Dongguan Taiping People Hospital , Dongguan , China
| | - Xiaoxiao Lu
- a The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis , Guangzhou Medical University , Guangzhou , China
| | - Dongsheng Huang
- c Department of Respiratory Medicine , Guangzhou Chest Hospital , Guangzhou , China
| | - Yuan Guo
- d The Third Affiliated Hospital of Guangzhou Medical University , Guangzhou , China
| | - Mingan Pan
- e Department of Respiratory Medicine , the third Affiliated Hospital of Sun Yat-sen University , Guangzhou , China
| | - Haibo Zhang
- f Department of Respiratory Medicine , Guangzhou Red Cross Hospital , Guangzhou , China
| | - Yifeng Zhou
- g Department of Genetics , Medical College of Soochow University , Suzhou , China
| | - Jiachun Lu
- a The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis , Guangzhou Medical University , Guangzhou , China
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Yang L, Lu X, Deng J, Zhou Y, Huang D, Qiu F, Yang X, Yang R, Fang W, Ran P, Zhong N, Zhou Y, Fang S, Lu J. Risk factors shared by COPD and lung cancer and mediation effect of COPD: two center case–control studies. Cancer Causes Control 2014; 26:11-24. [DOI: 10.1007/s10552-014-0475-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 10/07/2014] [Indexed: 02/07/2023]
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Yang L, Lu X, Qiu F, Fang W, Zhang L, Huang D, Xie C, Zhong N, Ran P, Zhou Y, Lu J. Duplicated copy of CHRNA7 increases risk and worsens prognosis of COPD and lung cancer. Eur J Hum Genet 2014; 23:1019-24. [PMID: 25407004 DOI: 10.1038/ejhg.2014.229] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Revised: 07/21/2014] [Accepted: 09/19/2014] [Indexed: 12/11/2022] Open
Abstract
Recent genome-wide association studies implicated that the nicotinic acetylcholine receptors (nAChRs) are common susceptible genes of two contextual diseases: chronic obstructive pulmonary disease (COPD) and lung cancer. We aimed to test whether the copy number variations (CNVs) in nAChRs have hereditary contributions to development of the two diseases. In two, two-stage, case-control studies of southern and eastern Chinese, a common CNV-3956 that duplicates the cholinergic receptor, nicotinic, α7 (CHRNA7) gene was genotyped in a total of 7880 subjects and its biological phenotype was assessed. The ≥4-copy of CNV-3956 increased COPD risk (≥4-copy vs 2/3-copy: OR=1.44, 95% CI=1.23-1.68) and caused poor lung function, and it similarly augmented risk (OR=1.49, 95% CI=1.29-1.73) and worsened prognosis (hazard ratio (HR)=1.25, 95% CI=1.07-1.45) of lung cancer. The ≥4-copy was estimated to account for 1.56% of COPD heritability and 1.87% of lung cancer heritability, respectively. Phenotypic analysis further showed that the ≥4-copy of CNV-3956 improved CHRNA7 expression in vivo and increased the carriers' smoking amount. The CNV-3956 of CHRNA7 contributed to increased risks and poor prognoses of both COPD and lung cancer, and this may be a genetic biomarker of the two diseases.
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Affiliation(s)
- Lei Yang
- The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, Guangzhou, China
| | - Xiaoxiao Lu
- 1] The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, Guangzhou, China [2] Colby-Sawyer College, New London, NH, USA
| | - Fuman Qiu
- The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, Guangzhou, China
| | - Wenxiang Fang
- The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, Guangzhou, China
| | - Lisha Zhang
- The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, Guangzhou, China
| | - Dongsheng Huang
- Department of Respiratory Medicine, Guangzhou Chest Hospital, Guangzhou, China
| | - Chenli Xie
- 1] The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, Guangzhou, China [2] Dongguan Taiping People Hospital, Dongguan, China
| | - Nanshan Zhong
- The First Affiliated Hospital, The State Key Lab of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Pixin Ran
- The First Affiliated Hospital, The State Key Lab of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
| | - Yifeng Zhou
- Department of Genetics, Medical College of Soochow University, Suzhou, China
| | - Jiachun Lu
- The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, Guangzhou, China
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Wang B, Zhang L, Qiu F, Fang W, Deng J, Zhou Y, Lu J, Yang L. A Newfound association between MDC1 functional polymorphism and lung cancer risk in Chinese. PLoS One 2014; 9:e106794. [PMID: 25198518 PMCID: PMC4157800 DOI: 10.1371/journal.pone.0106794] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 08/02/2014] [Indexed: 12/18/2022] Open
Abstract
Mediator of DNA damage checkpoint protein 1 (MDC1) plays an early and core role in Double-Strand Break Repair (DDR) and ataxia telangiectasia-mutated (ATM) mediated response to DNA double-strand breaks (DSBs), and thus involves the pathogenesis of several DNA damage-related diseases such as cancer. We hypothesized that the single nucleotide polymorphisms (SNPs) of MDC1 which have potencies on affecting MDC1 expression or function were associated with risk of lung cancer. In a two-stage case-control study, we tested the association between 5 putatively functional SNPs of MDC1 and lung cancer risk in a southern Chinese population, and validated the promising association in an eastern Chinese population. We found the SNP rs4713354A>C that is located in the 5′-untranslated region of MDC1 was significantly associated with lung cancer risk in both populations (P = 0.001), with an odds ratio as 1.33(95% confidence interval = 1.14–1.55) for the rs4713354C (CA+CC) genotypes compared to the rs4713354AA genotype. The correct sixth sentence is: The gene-based analysis rested with these SNPs suggested the MDC1 as a susceptible gene for lung cancer (P = 0.057) [corrected]. Moreover, by querying the gene expression database, we further found that the rs4713354C genotypes confer a significantly lower mRNA expression of MDC1 than the rs4713354AA genotype in 260 cases of lymphoblastoid cells (P = 0.002). Our data suggested that the SNP rs4713354A>C of MDC1 may be a functional genetic biomarker for susceptibility to lung cancer in Chinese.
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Affiliation(s)
- Bo Wang
- The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou, China
| | - Lisha Zhang
- The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou, China
| | - Fuman Qiu
- The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou, China
| | - Wenxiang Fang
- The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou, China
| | - Jieqiong Deng
- Soochow University Laboratory of Cancer Molecular Genetics, Medical College of Soochow University, Suzhou, China
| | - Yifeng Zhou
- Soochow University Laboratory of Cancer Molecular Genetics, Medical College of Soochow University, Suzhou, China
| | - Jiachun Lu
- The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou, China
| | - Lei Yang
- The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou, China
- * E-mail:
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Ding X, Tsang SY, Ng SK, Xue H. Application of Machine Learning to Development of Copy Number Variation-based Prediction of Cancer Risk. GENOMICS INSIGHTS 2014. [PMID: 26203258 PMCID: PMC4504076 DOI: 10.4137/gei.s15002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In the present study, recurrent copy number variations (CNVs) from non-tumor blood cell DNAs of Caucasian non-cancer subjects and glioma, myeloma, and colorectal cancer-patients, and Korean non-cancer subjects and hepatocellular carcinoma, gastric cancer, and colorectal cancer patients, were found to reveal for each of the two ethnic cohorts highly significant differences between cancer patients and controls with respect to the number of CN-losses and size-distribution of CN-gains, suggesting the existence of recurrent constitutional CNV-features useful for prediction of predisposition to cancer. Upon identification by machine learning, such CNV-features could extensively discriminate between cancer-patient and control DNAs. When the CNV-features selected from a learning-group of Caucasian or Korean mixed DNAs consisting of both cancer-patient and control DNAs were employed to make predictions on the cancer predisposition of an unseen test group of mixed DNAs, the average prediction accuracy was 93.6% for the Caucasian cohort and 86.5% for the Korean cohort.
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Affiliation(s)
- Xiaofan Ding
- Applied Genomics Center and Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Shui-Ying Tsang
- Applied Genomics Center and Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Siu-Kin Ng
- Applied Genomics Center and Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Hong Xue
- Applied Genomics Center and Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
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Wang H, Yang L, Deng J, Wang B, Yang X, Yang R, Cheng M, Fang W, Qiu F, Zhang X, Ji W, Ran P, Zhou Y, Lu J. Genetic variant in the 3'-untranslated region of VEGFR1 gene influences chronic obstructive pulmonary disease and lung cancer development in Chinese population. Mutagenesis 2014; 29:311-7. [PMID: 24891316 DOI: 10.1093/mutage/geu020] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Lung inflammation and epithelial to mesenchymal transition (EMT) are two pathogenic features for the two contextual diseases: chronic obstructive pulmonary disease (COPD) and lung cancer. VEGFR1 (or FLT1) plays a certain role in promoting tumour growth, inflammation and EMT. To simultaneously test the association between the single nucleotide polymorphisms (SNPs) in VEGFR1 and risk of COPD and lung cancer would reveal genetic mechanisms shared by these two diseases and joint aetiology. We conducted a two-population hospital-based case-control study. Three potential functional SNPs (rs664393, rs7326277 and rs9554314) were genotyped in southern Chinese and validated in eastern Chinese to explore their associations with COPD risk in 1511 COPD patients and 1677 normal lung function controls, and with lung cancer risk in 1559 lung cancer cases and 1679 cancer-free controls. We also detected the function of the promising SNP. Individuals carrying the rs7326277C (CT+CC) variant genotypes of VEGFR1 had a significant decrease in risk of both COPD (OR = 0.78; 95% CI = 0.68-0.90) and lung cancer (OR = 0.79; 95% CI = 0.64-0.98), compared with those carrying the rs7326277TT genotype. Functional assays further showed that the rs7326277C genotypes had lower transcriptional activity and caused decreased VEGFR expression, compared with the rs7326277TT genotype. However, no significant association was observed for the other two SNPs (rs664393 and rs9554314) and either COPD or lung cancer risk. Our data suggested that the rs7326277C variant of VEGFR1 could reduce both COPD and lung cancer risk by lowering VEGFR1 mRNA expression; the SNP might be a common susceptible locus for both COPD and lung cancer.
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Affiliation(s)
- Hui Wang
- The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis, School of Public Health, Guangzhou Medical University, Guangzhou 510182, Guangdong, China, School of Public Health, Guangdong Key Laboratory of Molecular Epidemiology, Guangdong Pharmaceutical University, Guangzhou 510310, Guangdong, China
| | - Lei Yang
- The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis, School of Public Health, Guangzhou Medical University, Guangzhou 510182, Guangdong, China
| | - Jieqiong Deng
- Soochow University Laboratory of Cancer Molecular Genetics, Medical College of Soochow University, Suzhou 215123, China and
| | - Bo Wang
- The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis, School of Public Health, Guangzhou Medical University, Guangzhou 510182, Guangdong, China
| | - Xiaorong Yang
- The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis, School of Public Health, Guangzhou Medical University, Guangzhou 510182, Guangdong, China
| | - Rongrong Yang
- The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis, School of Public Health, Guangzhou Medical University, Guangzhou 510182, Guangdong, China
| | - Mei Cheng
- The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis, School of Public Health, Guangzhou Medical University, Guangzhou 510182, Guangdong, China
| | - Wenxiang Fang
- The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis, School of Public Health, Guangzhou Medical University, Guangzhou 510182, Guangdong, China
| | - Fuman Qiu
- The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis, School of Public Health, Guangzhou Medical University, Guangzhou 510182, Guangdong, China
| | - Xin Zhang
- Guangzhou Institute of Respiratory Diseases, The First Affiliated Hospital, The State Key Lab of Respiratory Disease, Guangzhou Medical University, Guangzhou 510120, Guangdong, China
| | - Weidong Ji
- Guangzhou Institute of Respiratory Diseases, The First Affiliated Hospital, The State Key Lab of Respiratory Disease, Guangzhou Medical University, Guangzhou 510120, Guangdong, China
| | - Pixin Ran
- Guangzhou Institute of Respiratory Diseases, The First Affiliated Hospital, The State Key Lab of Respiratory Disease, Guangzhou Medical University, Guangzhou 510120, Guangdong, China
| | - Yifeng Zhou
- Soochow University Laboratory of Cancer Molecular Genetics, Medical College of Soochow University, Suzhou 215123, China and
| | - Jiachun Lu
- The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis, School of Public Health, Guangzhou Medical University, Guangzhou 510182, Guangdong, China,
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Yu K, Fan J, Ding X, Li C, Wang J, Xiang Y, Wang QS. Association study of a functional copy number variation in theWWOXgene with risk of gliomas among Chinese people. Int J Cancer 2014; 135:1687-91. [PMID: 24585490 DOI: 10.1002/ijc.28815] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2013] [Indexed: 01/24/2023]
Affiliation(s)
- Ke Yu
- Department of Neurology; Chengdu Military General Hospital; Chengdu China
| | - Jin Fan
- Department of Neurology; Chengdu Military General Hospital; Chengdu China
| | - Xin Ding
- Department of Neurology; Chengdu Military General Hospital; Chengdu China
| | - CongYang Li
- Department of Neurology; Chengdu Military General Hospital; Chengdu China
| | - Jun Wang
- Department of Neurology; Chengdu Military General Hospital; Chengdu China
| | - Yang Xiang
- Department of Neurology; Chengdu Military General Hospital; Chengdu China
| | - Qing Song Wang
- Department of Neurology; Chengdu Military General Hospital; Chengdu China
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Admixture fine-mapping in African Americans implicates XAF1 as a possible sarcoidosis risk gene. PLoS One 2014; 9:e92646. [PMID: 24663488 PMCID: PMC3963923 DOI: 10.1371/journal.pone.0092646] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 02/25/2014] [Indexed: 12/23/2022] Open
Abstract
Sarcoidosis is a complex, multi-organ granulomatous disease with a likely genetic component. West African ancestry confers a higher risk for sarcoidosis than European ancestry. Admixture mapping provides the most direct method to locate genes that underlie such ethnic variation in disease risk. We sought to identify genetic risk variants within four previously-identified ancestry-associated regions—6p24.3–p12.1, 17p13.3–13.1, 2p13.3–q12.1, and 6q23.3–q25.2—in a sample of 2,727 African Americans. We used logistic regression fit by generalized estimating equations and the MIX score statistic to determine which variants within ancestry-associated regions were associated with risk and responsible for the admixture signal. Fine mapping was performed by imputation, based on a previous genome-wide association study; significant variants were validated by direct genotyping. Within the 6p24.3–p12.1 locus, the most significant ancestry-adjusted SNP was rs74318745 (p = 9.4*10−11), an intronic SNP within the HLA-DRA gene that did not solely explain the admixture signal, indicating the presence of more than a single risk variant within this well-established sarcoidosis risk region. The locus on chromosome 17p13.3–13.1 revealed a novel sarcoidosis risk SNP, rs6502976 (p = 9.5*10−6), within intron 5 of the gene X-linked Inhibitor of Apoptosis Associated Factor 1 (XAF1) that accounted for the majority of the admixture linkage signal. Immunohistochemical expression studies demonstrated lack of expression of XAF1 and a corresponding high level of expression of its downstream target, X-linked Inhibitor of Apoptosis (XIAP) in sarcoidosis granulomas. In conclusion, ancestry and association fine mapping revealed a novel sarcoidosis susceptibility gene, XAF1, which has not been identified by previous genome-wide association studies. Based on the known biology of the XIAP/XAF1 apoptosis pathway and the differential expression patterns of XAF1 and XIAP in sarcoidosis granulomas, we suggest that this pathway may play a role in the maintenance of sarcoidosis granulomas.
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Yang L, Yang X, Ji W, Deng J, Qiu F, Yang R, Fang W, Zhang L, Huang D, Xie C, Zhang H, Zhong N, Ran P, Zhou Y, Lu J. Effects of a functional variant c.353T>C in snai1 on risk of two contextual diseases. Chronic obstructive pulmonary disease and lung cancer. Am J Respir Crit Care Med 2014; 189:139-48. [PMID: 24354880 DOI: 10.1164/rccm.201307-1355oc] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
RATIONALE Epithelial-mesenchymal transition (EMT) plays a key role in the development of chronic obstructive pulmonary disease (COPD) and lung cancer. OBJECTIVES There are five major EMT regulatory genes (Snai1, Slug, Zeb1, Zeb2, and Twist1) involved in EMT. We hypothesized that germline variants in these genes may influence the development of both diseases. METHODS Seven genetic variants were genotyped in two two-stage case-control studies with 2,072 lung cancer cases and 2,077 control subjects, and 1,791 patients with COPD and 1,940 control subjects to show their associations with development of both diseases. MEASUREMENTS AND MAIN RESULTS An exon variant c.353T>C(p.Val118Ala) of Snai1 harbored decreased risks of lung cancer (CT/CC vs. TT: odds ratio [OR], 0.76; 95% confidence interval [CI], 0.65-0.90) and COPD (CC vs. CT vs. TT: OR, 0.75; 95% CI, 0.63-0.89), and c.353T>C affected lung cancer risk indirectly through COPD (COPD accounted for 6.78% of effect that the variant had on lung cancer). Moreover, c.353T>C was correlated with lung cancer stages in smoking patients (P = 0.013), and those with the c.353C genotypes were less likely to have metastasis at diagnosis than those with the c.353TT genotype (OR, 0.60; 95% CI, 0.41-0.88). The c.353C allele encoding p.118Ala attenuated Snai1's ability to up-regulate mesenchymal biomarkers (i.e., fibronectin and vimentin) expression, and to promote EMT-like changes, including morphologic changes, cell migration, and invasion. However, these effects were not observed for the other variants. CONCLUSIONS The functional germline variant c.353T>C (p.Val118Ala) of Snai1 confers consistently decreased risks of lung cancer and COPD, and this variant affects lung cancer risk through a mediation effect of COPD.
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Affiliation(s)
- Lei Yang
- 1 The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis, Guangzhou Institute of Respiratory Diseases, and
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Copy Number Variation in Chickens: A Review and Future Prospects. MICROARRAYS 2014; 3:24-38. [PMID: 27605028 PMCID: PMC5003453 DOI: 10.3390/microarrays3010024] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Revised: 01/22/2014] [Accepted: 01/23/2014] [Indexed: 12/19/2022]
Abstract
DNA sequence variations include nucleotide substitution, deletion, insertion, translocation and inversion. Deletion or insertion of a large DNA segment in the genome, referred to as copy number variation (CNV), has caught the attention of many researchers recently. It is believed that CNVs contribute significantly to genome variability, and thus contribute to phenotypic variability. In chickens, genome-wide surveys with array comparative genome hybridization (aCGH), SNP chip detection or whole genome sequencing have revealed a large number of CNVs. A large portion of chicken CNVs involves protein coding or regulatory sequences. A few CNVs have been demonstrated to be the determinant factors for single gene traits, such as late-feathering, pea-comb and dermal hyperpigmentation. The phenotypic effects of the majority of chicken CNVs are to be delineated.
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Role of WWOX and NF-κB in lung cancer progression. TRANSLATIONAL RESPIRATORY MEDICINE 2013; 1:15. [PMID: 27234396 PMCID: PMC4715152 DOI: 10.1186/2213-0802-1-15] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 11/04/2013] [Indexed: 01/28/2023]
Abstract
It is generally agreed that the pro-inflammatory, pro-survival transcription factor NF-κB is a tumor promoter. Tumor necrosis factor alpha (TNF-α or TNF) mediates NF-κB activation. Tumor suppressor WWOX (FOR or WOX1) is a downstream effector of the TNF signaling. Thus, activation of both WWOX (FOR or WOX1) and NF-κB may occur during TNF signaling and/or under stress conditions. Indeed, the first WW domain of WWOX induces the activation of NF-κB-responsive promoter without TNF participation. It appears that WWOX counteracts with NF-κB in regulating cell survival and death. For example, WWOX becomes activated with Tyr33 phosphorylation and relocates together with NF-κB and many transcription factors to the nucleus to cause neuronal death in sciatic nerve-transected rats. While WWOX is frequently lost in lung cancer and many other cancers, NF-κB activation-induced cancer promotion probably requires WWOX-independent signaling networks to induce expression of pro-survival factors. The antagonistic role of WWOX and NF-κB in the regulation of lung cancer progression is discussed.
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Yang R, Yang L, Qiu F, Zhang L, Wang H, Yang X, Deng J, Fang W, Zhou Y, Lu J. Functional genetic polymorphisms in PP2A subunit genes confer increased risks of lung cancer in southern and eastern Chinese. PLoS One 2013; 8:e77285. [PMID: 24204789 PMCID: PMC3812212 DOI: 10.1371/journal.pone.0077285] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Accepted: 09/02/2013] [Indexed: 12/28/2022] Open
Abstract
Protein phosphatase-2A (PP2A) is one of the major cellular serine-threonine phosphatases and functions as a tumor suppressor that negatively regulates the activity of some oncogenic kinases. Recent studies have reported that PP2A expression was suppressed during lung carcinogenesis, we there hypothesized that the single nucleotide polymorphisms (SNPs) in PP2A subunit genes may affect PP2A function and thus contribute to lung cancer susceptibility. In a two-stage case-control study with a total of 1559 lung cancer patients and 1679 controls, we genotyped eight putative functional SNPs and one identified functional SNP (i.e., rs11453459) in seven major PP2A subunits (i.e., PPP2R1A, PPP2R1B, PPP2CA, PPP2R2A, PPP2R2B, PPP2R5C, PPP2R5E) in southern and eastern Chinese. We found that rs11453459G (-G/GG) variant genotypes of PPP2R1A and the rs1255722AA variant genotype of PPP2R5E conferred increased risks of lung cancer (rs11453459, -G/GG vs. –: OR = 1.31, 95% CI = 1.13–1.51; rs1255722, AA vs. AG/GG: OR = 1.27, 95% CI = 1.07–1.51). After combined the two variants, the number of the adverse genotypes was positively associated with lung cancer risk in a dose-response manner (Ptrend = 5.63×10−6). Further functional assay showed that lung cancer tissues carrying rs1255722AA variant genotype had a significantly lower mRNA level of PPP2R5E compared with tissues carrying GG/GA genotypes. However, such effect was not observed for the other SNPs and other combinations. Our findings suggested that the two functional variants in PPP2R1A and PPP2R5E and their combination are associated with lung cancer risk in Chinese, which may be valuable biomarkers to predict risk of lung cancer.
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Affiliation(s)
- Rongrong Yang
- The Institute for Chemical Carcinogenesis, The State Key Lab of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
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Yang L, Liu B, Qiu F, Huang B, Li Y, Huang D, Yang R, Yang X, Deng J, Jiang Q, Zhou Y, Lu J. The effect of functional MAPKAPK2 copy number variation CNV-30450 on elevating nasopharyngeal carcinoma risk is modulated by EBV infection. Carcinogenesis 2013; 35:46-52. [PMID: 24056810 DOI: 10.1093/carcin/bgt314] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
UNLABELLED Mitogen-activated protein kinase-activated protein kinase 2 (MAPKAPK2) is recognized as oncogenic and simulative role on tumorigenesis by virtue of abnormal expression in cancer including nasopharyngeal carcinoma (NPC). We hypothesized that the copy number variation (CNV)-30450, which duplicates the MAPKAPK2 promoter, may affect MAPKAPK2 expression and be associated with NPC risk. In two independent case-control panels of southern and eastern Chinese with a total of 1590 NPC patients and 1979 cancer-free controls, we investigated the association between CNV-30450 and NPC risk by genotyping the CNV-30450 with the TaqMan assay, and tested its biological effect. Consistent findings were observed in the two populations, that the increased copy number of CNV-30450 was associated with increased risk of NPC (3/4-copy versus 2-copy: odds ratio = 1.28, 95% confidence interval = 1.10-1.49), in which lies a biological mechanism that the adverse genotypes enhanced the promoter activity of MAPKAPK2 and elevated MAPKAPK2 expression. Moreover, the CNV-30450 adverse genotypes significantly interacted with Epstein-Barr virus (EBV) infection on increasing NPC risk (P = 0.035), and the genotype-phenotype correlation was only significant in EBV-positive cases (P = 0.037) but not in EBV-negative ones (P = 0.366). These data suggest that the functional CNV-30450 in the MAPKAPK2 promoter elevates the NPC risk with a modulation by EBV infection, which may be an indicator of susceptibility to NPC. SUMMARY This case-control study suggests that the functional CNV-30450 in the MAPKAPK2 promoter elevates the NPC risk with a modulation by EBV infection, which may be an indicator of susceptibility to NPC.
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Affiliation(s)
- Lei Yang
- The Institute for Chemical Carcinogenesis, The State Key Lab of Respiratory Disease, Guangzhou Medical University, 195 Dongfengxi Road, Guangzhou 510182, People's Republic of China
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