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Oketch DJA, Giulietti M, Piva F. Copy Number Variations in Pancreatic Cancer: From Biological Significance to Clinical Utility. Int J Mol Sci 2023; 25:391. [PMID: 38203561 PMCID: PMC10779192 DOI: 10.3390/ijms25010391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 12/20/2023] [Accepted: 12/24/2023] [Indexed: 01/12/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is the most common type of pancreatic cancer, characterized by high tumor heterogeneity and a poor prognosis. Inter- and intra-tumoral heterogeneity in PDAC is a major obstacle to effective PDAC treatment; therefore, it is highly desirable to explore the tumor heterogeneity and underlying mechanisms for the improvement of PDAC prognosis. Gene copy number variations (CNVs) are increasingly recognized as a common and heritable source of inter-individual variation in genomic sequence. In this review, we outline the origin, main characteristics, and pathological aspects of CNVs. We then describe the occurrence of CNVs in PDAC, including those that have been clearly shown to have a pathogenic role, and further highlight some key examples of their involvement in tumor development and progression. The ability to efficiently identify and analyze CNVs in tumor samples is important to support translational research and foster precision oncology, as copy number variants can be utilized to guide clinical decisions. We provide insights into understanding the CNV landscapes and the role of both somatic and germline CNVs in PDAC, which could lead to significant advances in diagnosis, prognosis, and treatment. Although there has been significant progress in this field, understanding the full contribution of CNVs to the genetic basis of PDAC will require further research, with more accurate CNV assays such as single-cell techniques and larger cohorts than have been performed to date.
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Affiliation(s)
| | - Matteo Giulietti
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, 60131 Ancona, Italy
| | - Francesco Piva
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, 60131 Ancona, Italy
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Gao J, Zhang LX, Ao YQ, Jin C, Zhang PF, Wang HK, Wang S, Lin M, Jiang JH, Ding JY. Elevated circASCC3 limits antitumor immunity by sponging miR-432–5p to upregulate C5a in non-small cell lung cancer. Cancer Lett 2022; 543:215774. [DOI: 10.1016/j.canlet.2022.215774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 05/20/2022] [Accepted: 05/31/2022] [Indexed: 11/02/2022]
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Kong L, Liu P, Zheng M, Xue B, Liang K, Tan X. Multi-omics analysis based on integrated genomics, epigenomics and transcriptomics in pancreatic cancer. Epigenomics 2020; 12:507-524. [PMID: 32048534 DOI: 10.2217/epi-2019-0374] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Aim: Integrated analysis of genomics, epigenomics, transcriptomics and clinical information contributes to identify specific molecular subgroups and find novel biomarkers for pancreatic cancer. Materials & methods: The DNA copy number variation, the simple nucleotide variation, methylation and mRNA data of pancreatic cancer patients were obtained from The Cancer Genome Atlas. Four molecular subgroups (iC1, iC2, iC3 and iC4) of pancreatic cancer were identified by integrating analysis. Results: The iC1 subgroup harbors better prognosis, higher immune score, lesser DNA copy number variation mutations and better genomic stability compared with iC2, iC3 and iC4 subgroups. Three new genes (GRAP2, ICAM3 and A2ML1) correlated with prognosis were identified. Conclusion: Integrated multi-omics analysis provides fresh insight into molecular classification of pancreatic cancer, which may help discover new prognostic biomarkers and reveal the underlying mechanism of pancreatic cancer.
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Affiliation(s)
- Lingming Kong
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China
| | - Peng Liu
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China
| | - Mingjun Zheng
- Department of Obstetrics & Gynecology, University Hospital, LMU Munich, Marchioninistr. 15, 81377 Munich, Germany
| | - Busheng Xue
- Department of Pediatrics, Children's Cancer Research Center, Kinderklinik München Schwabing, School of Medicine, Technical University of Munich, Munich 80804, Germany
| | - Keke Liang
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China
| | - Xiaodong Tan
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China
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Karim MR, Rahman A, Jares JB, Decker S, Beyan O. A snapshot neural ensemble method for cancer-type prediction based on copy number variations. Neural Comput Appl 2019. [DOI: 10.1007/s00521-019-04616-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
AbstractAn accurate diagnosis and prognosis for cancer are specific to patients with particular cancer types and molecular traits, which needs to address carefully. The discovery of important biomarkers is becoming an important step toward understanding the molecular mechanisms of carcinogenesis in which genomics data and clinical outcomes need to be analyzed before making any clinical decision. Copy number variations (CNVs) are found to be associated with the risk of individual cancers and hence can be used to reveal genetic predispositions before cancer develops. In this paper, we collect the CNVs data about 8000 cancer patients covering 14 different cancer types from The Cancer Genome Atlas. Then, two different sparse representations of CNVs based on 578 oncogenes and 20,308 protein-coding genes, including genomic deletions and duplication across the samples, are prepared. Then, we train Conv-LSTM and convolutional autoencoder (CAE) networks using both representations and create snapshot models. While the Conv-LSTM can capture locally and globally important features, CAE can utilize unsupervised pretraining to initialize the weights in the subsequent convolutional layers against the sparsity. Model averaging ensemble (MAE) is then applied to combine the snapshot models in order to make a single prediction. Finally, we identify most significant CNVs biomarkers using guided-gradient class activation map plus (GradCAM++) and rank top genes for different cancer types. Results covering several experiments show fairly high prediction accuracies for the majority of cancer types. In particular, using protein-coding genes, Conv-LSTM and CAE networks can predict cancer types correctly at least 72.96% and 76.77% of the cases, respectively. Contrarily, using oncogenes gives moderately higher accuracies of 74.25% and 78.32%, whereas the snapshot model based on MAE shows overall 2.5% of accuracy improvement.
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Zhang H, Zeng J, Tan Y, Lu L, Sun C, Liang Y, Zou H, Yang X, Tan Y. Subgroup analysis reveals molecular heterogeneity and provides potential precise treatment for pancreatic cancers. Onco Targets Ther 2018; 11:5811-5819. [PMID: 30254473 PMCID: PMC6140745 DOI: 10.2147/ott.s163139] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Background The relationship between molecular heterogeneity and clinical features of pancreatic cancer remains unclear. In this study, pancreatic cancer was divided into different subgroups to explore its specific molecular characteristics and potential therapeutic targets. Patients and methods Expression profiling data were downloaded from The Cancer Genome Atlas database and standardized. Bioinformatics techniques such as unsupervised hierarchical clustering was used to explore the optimal molecular subgroups in pancreatic cancer. Clinical pathological features and pathways in each subgroup were also analyzed to find out the potential clinical applications and initial promotive mechanisms of pancreatic cancer. Results Pancreatic cancer was divided into three subgroups based on different gene expression features. Patients included in each subgroup had specific biological features and responded significantly different to chemotherapy. Conclusion Three distinct subgroups of pancreatic cancer were identified, which means that patients in each subgroup might benefit from targeted individual management.
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Affiliation(s)
- Heying Zhang
- Department of Oncology, Shengjing Hospital, China Medical University, Shenyang, People's Republic of China,
| | - Juan Zeng
- Department of Oncology, Shengjing Hospital, China Medical University, Shenyang, People's Republic of China,
| | | | - Lin Lu
- Department of Radiology, Columbia University Medical Center, New York, NY, USA
| | - Cheng Sun
- Department of Oncology, Shengjing Hospital, China Medical University, Shenyang, People's Republic of China,
| | - Yusi Liang
- Department of Oncology, Shengjing Hospital, China Medical University, Shenyang, People's Republic of China,
| | - Huawei Zou
- Department of Oncology, Shengjing Hospital, China Medical University, Shenyang, People's Republic of China,
| | - Xianghong Yang
- Department of Pathology, Shengjing Hospital, China Medical University, Shenyang, People's Republic of China
| | - Yonggang Tan
- Department of Oncology, Shengjing Hospital, China Medical University, Shenyang, People's Republic of China,
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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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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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Recurrent amplification of MYC and TNFRSF11B in 8q24 is associated with poor survival in patients with gastric cancer. Gastric Cancer 2016; 19:116-27. [PMID: 25618371 DOI: 10.1007/s10120-015-0467-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 01/12/2015] [Indexed: 02/07/2023]
Abstract
BACKGROUND Gastric cancer (GC) is an aggressive malignancy whose mechanisms of development and progression are poorly understood. The identification of prognosis-related genomic loci and genes may suffer from the relatively small case numbers and a lack of systematic validation in previous studies. METHODS Array-based comparative genomic hybridization (aCGH) coupled with patient clinical information was applied to identify prognosis-related loci and genes with high-frequency recurrent gains in 129 GC patients. The candidate loci and genes were then validated using an independent cohort of 384 patients through branched DNA signal amplification analysis (QuantiGene assays). RESULTS In the 129 patients, a copy number gain of three chromosome regions-namely, 8q22 (including ESRP1 and CCNE2), 8q24 (including MYC and TNFRSF11B), and 20q11-q13 (including SRC, MMP9, and CSE1L)--conferred poor survival for patients. In addition, the correlation between the branched DNA signal amplification analysis results and the aCGH results was analyzed in 73 of these 129 patients, and MYC, TNFRSF11B, ESRP1, CSE1L, and MMP9 were found to be well correlated. Further validation using an independent cohort (n = 384) verified that only MYC and TNFRSF11B within 8q24 are related to survival. Patients with gains in both MYC and TNFRSF11B had poorer survival than those with no gains, particularly those with noncardia GC. Gains in both of these genes were also a significant independent prognostic indicator. CONCLUSIONS Our results revealed that copy number gains in MYC and TNFRSF11B located at 8q24 are associated with survival in GC, particularly noncardia GC.
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Giorgio E, Robyr D, Spielmann M, Ferrero E, Di Gregorio E, Imperiale D, Vaula G, Stamoulis G, Santoni F, Atzori C, Gasparini L, Ferrera D, Canale C, Guipponi M, Pennacchio LA, Antonarakis SE, Brussino A, Brusco A. A large genomic deletion leads to enhancer adoption by the lamin B1 gene: a second path to autosomal dominant adult-onset demyelinating leukodystrophy (ADLD). Hum Mol Genet 2015; 24:3143-54. [PMID: 25701871 PMCID: PMC4424952 DOI: 10.1093/hmg/ddv065] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 02/13/2015] [Indexed: 01/23/2023] Open
Abstract
Chromosomal rearrangements with duplication of the lamin B1 (LMNB1) gene underlie autosomal dominant adult-onset demyelinating leukodystrophy (ADLD), a rare neurological disorder in which overexpression of LMNB1 causes progressive central nervous system demyelination. However, we previously reported an ADLD family (ADLD-1-TO) without evidence of duplication or other mutation in LMNB1 despite linkage to the LMNB1 locus and lamin B1 overexpression. By custom array-CGH, we further investigated this family and report here that patients carry a large (∼660 kb) heterozygous deletion that begins 66 kb upstream of the LMNB1 promoter. Lamin B1 overexpression was confirmed in further ADLD-1-TO tissues and in a postmortem brain sample, where lamin B1 was increased in the frontal lobe. Through parallel studies, we investigated both loss of genetic material and chromosomal rearrangement as possible causes of LMNB1 overexpression, and found that ADLD-1-TO plausibly results from an enhancer adoption mechanism. The deletion eliminates a genome topological domain boundary, allowing normally forbidden interactions between at least three forebrain-directed enhancers and the LMNB1 promoter, in line with the observed mainly cerebral localization of lamin B1 overexpression and myelin degeneration. This second route to LMNB1 overexpression and ADLD is a new example of the relevance of regulatory landscape modifications in determining Mendelian phenotypes.
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Affiliation(s)
- Elisa Giorgio
- Department of Medical Sciences, University of Torino, via Santena, 19, Torino 10126, Italy
| | - Daniel Robyr
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva 1211, Switzerland
| | - Malte Spielmann
- Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, Berlin 14195, Germany
| | - Enza Ferrero
- Department of Medical Sciences, University of Torino, via Santena, 19, Torino 10126, Italy
| | - Eleonora Di Gregorio
- Department of Medical Sciences, University of Torino, via Santena, 19, Torino 10126, Italy Medical Genetics Unit and
| | - Daniele Imperiale
- Centro Regionale Malattie Da Prioni - Domp (ASLTO2), Torino 10144, Italy
| | - Giovanna Vaula
- Department of Neurology, Città della Salute e della Scienza University Hospital, Torino 10126, Italy
| | - Georgios Stamoulis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva 1211, Switzerland
| | - Federico Santoni
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva 1211, Switzerland
| | - Cristiana Atzori
- Centro Regionale Malattie Da Prioni - Domp (ASLTO2), Torino 10144, Italy
| | | | | | - Claudio Canale
- Department of Nanophysics, Istituto Italiano di Tecnologia, Genoa 16163, Italy and
| | - Michel Guipponi
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva 1211, Switzerland
| | - Len A Pennacchio
- Genomics Division, Lawrence Berkeley National Laboratory, MS 84-171, Berkeley, CA 9472, USA
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva 1211, Switzerland
| | - Alessandro Brussino
- Department of Medical Sciences, University of Torino, via Santena, 19, Torino 10126, Italy
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, via Santena, 19, Torino 10126, Italy Medical Genetics Unit and
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Suppression of CYP2C9 by microRNA hsa-miR-128-3p in human liver cells and association with hepatocellular carcinoma. Sci Rep 2015; 5:8534. [PMID: 25704921 PMCID: PMC4336941 DOI: 10.1038/srep08534] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 01/23/2015] [Indexed: 01/08/2023] Open
Abstract
Published studies have identified genetic variants, somatic mutations, and changes in gene expression profiles that are associated with hepatocellular carcinoma (HCC), particularly involving genes that encode drug metabolizing enzymes (DMEs). CYP2C9, one of the most abundant and important DMEs, is involved in the metabolism of many carcinogens and drugs and is down-regulated in HCC. To investigate the molecular mechanisms that control CYP2C9 expression, we applied integrative approaches including in silico, in vitro, and in vivo analyses to elucidate the role of microRNA hsa-miR-128-3p in the regulation of CYP2C9 expression and translation. RNA electrophoresis mobility shift assays demonstrated a direct interaction between hsa-miR-128-3p and its cognate target, the CYP2C9 transcript. Furthermore, the expression of a luciferase reporter gene containing the 3′-UTR of CYP2C9 and the endogenous expression of CYP2C9 were suppressed by transfection of hsa-miR-128-3p. Importantly, chemically-induced up- or down-regulation of hsa-miR-128-3p correlated inversely with the expression of CYP2C9. Finally, an association analysis revealed that the expression of hsa-miR-128-3p is inversely correlated with the expression of CYP2C9 in HCC tumor tissues. Altogether, the study helped to elucidate the mechanism of CYP2C9 regulation by hsa-miR-128-3p, and the inverse association in HCC.
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Hu L, Wu Y, Tan D, Meng H, Wang K, Bai Y, Yang K. Up-regulation of long noncoding RNA MALAT1 contributes to proliferation and metastasis in esophageal squamous cell carcinoma. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2015; 34:7. [PMID: 25613496 PMCID: PMC4322446 DOI: 10.1186/s13046-015-0123-z] [Citation(s) in RCA: 187] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Accepted: 01/04/2015] [Indexed: 01/26/2023]
Abstract
BACKGROUND Metastasis Associated Lung Adenocarcinoma Transcript 1 (MALAT1) has been demonstrated to be an important player in various human malignancies; it is thought to promote tumor growth by cell cycle regulating. However, the roles of MALAT1 in esophageal squamous cell carcinoma(ESCC), and the mechanisms involved in cell cycle regulation remain poorly understood. Moreover, the factors contributing to its up-regulation in tumor tissues are still largely unclear. METHODS Expression of MALAT1 was determined from cell lines and clinical samples by qRT-PCR. The effects of MALAT1 knockdown on cell proliferation, cell cycle, apoptosis, migration, and invasion were evaluated by in vitro and in vivo assays. The potential protein expression changes were investigated by Western-blotting. The methylation status of the CpG island in the MALAT1 promoter was explored by bisulfite sequencing, while the copy numbers in tumor tissues and blood samples were detected by a well-established AccuCopy(TM) method. RESULTS MALAT1 was over-expressed in 46.3% of ESCC tissues, mostly in the high-stage tumor samples. Enhanced MALAT1 expression levels were positively correlated with clinical stages, primary tumor size, and lymph node metastasis. Inhibition of MALAT1 suppressed tumor proliferation in vitro and in vivo, as well as the migratory and invasive capacity. MALAT1 depletion also induced G2/M phase arrest and increased the percentage of apoptotic cells. Western-blotting results implicated that the ATM-CHK2 pathway which is associated with G2/M arrest was phosphorylated by MALAT1 knockdown. No effects of CpG island methylation status on MALAT1 expression were found, whereas amplification of MALAT1 was found in 22.2% of tumor tissues, which correlated significantly with its over-expression. However, neither association between tissue copy number amplification and germline copy number variation, nor correlation between germline copy number variation and ESCC risk were identified in the case-control study. CONCLUSIONS Our data suggest that MALAT1 serves as an oncogene in ESCC, and it regulates ESCC growth by modifying the ATM-CHK2 pathway. Moreover, amplification of MALAT1 in tumor tissues may play an important role for its up-regulation, and it seems that the gene amplification in tumor tissues emerges during ESCC progression, but is not derived from germline origins.
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Affiliation(s)
- Liwen Hu
- Department of Cardiothoracic Surgery, Southwest Hospital, Third Military Medical University, Gaotanyan St., Shapingba District, Chongqing, People's Republic of China.
| | - Yuanyuan Wu
- Department of Medical Genetics, College of Basic Medical Science, Third Military Medical University, Gaotanyan St., Shapingba District, Chongqing, People's Republic of China.
| | - Deli Tan
- Department of Cardiothoracic Surgery, Southwest Hospital, Third Military Medical University, Gaotanyan St., Shapingba District, Chongqing, People's Republic of China.
| | - Hui Meng
- Department of Medical Genetics, College of Basic Medical Science, Third Military Medical University, Gaotanyan St., Shapingba District, Chongqing, People's Republic of China.
| | - Kai Wang
- Department of Medical Genetics, College of Basic Medical Science, Third Military Medical University, Gaotanyan St., Shapingba District, Chongqing, People's Republic of China.
| | - Yun Bai
- Department of Medical Genetics, College of Basic Medical Science, Third Military Medical University, Gaotanyan St., Shapingba District, Chongqing, People's Republic of China.
| | - Kang Yang
- Department of Cardiothoracic Surgery, Southwest Hospital, Third Military Medical University, Gaotanyan St., Shapingba District, Chongqing, People's Republic of China.
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Association of melanoma with intraepithelial neoplasia of the pancreas in three patients. Exp Mol Pathol 2014; 97:144-7. [DOI: 10.1016/j.yexmp.2014.06.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 06/27/2014] [Indexed: 12/20/2022]
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13
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Li MJ, Yan B, Sham PC, Wang J. Exploring the function of genetic variants in the non-coding genomic regions: approaches for identifying human regulatory variants affecting gene expression. Brief Bioinform 2014; 16:393-412. [PMID: 24916300 DOI: 10.1093/bib/bbu018] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 04/23/2014] [Indexed: 12/13/2022] Open
Abstract
Understanding the genetic basis of human traits/diseases and the underlying mechanisms of how these traits/diseases are affected by genetic variations is critical for public health. Current genome-wide functional genomics data uncovered a large number of functional elements in the noncoding regions of human genome, providing new opportunities to study regulatory variants (RVs). RVs play important roles in transcription factor bindings, chromatin states and epigenetic modifications. Here, we systematically review an array of methods currently used to map RVs as well as the computational approaches in annotating and interpreting their regulatory effects, with emphasis on regulatory single-nucleotide polymorphism. We also briefly introduce experimental methods to validate these functional RVs.
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Alisoltani A, Fallahi H, Ebrahimi M, Ebrahimi M, Ebrahimie E. Prediction of potential cancer-risk regions based on transcriptome data: towards a comprehensive view. PLoS One 2014; 9:e96320. [PMID: 24796549 PMCID: PMC4010480 DOI: 10.1371/journal.pone.0096320] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 04/07/2014] [Indexed: 12/20/2022] Open
Abstract
A novel integrative pipeline is presented for discovery of potential cancer-susceptibility regions (PCSRs) by calculating the number of altered genes at each chromosomal region, using expression microarray datasets of different human cancers (HCs). Our novel approach comprises primarily predicting PCSRs followed by identification of key genes in these regions to obtain potential regions harboring new cancer-associated variants. In addition to finding new cancer causal variants, another advantage in prediction of such risk regions is simultaneous study of different types of genomic variants in line with focusing on specific chromosomal regions. Using this pipeline we extracted numbers of regions with highly altered expression levels in cancer condition. Regulatory networks were also constructed for different types of cancers following the identification of altered mRNA and microRNAs. Interestingly, results showed that GAPDH, LIFR, ZEB2, mir-21, mir-30a, mir-141 and mir-200c, all located at PCSRs, are common altered factors in constructed networks. We found a number of clusters of altered mRNAs and miRNAs on predicted PCSRs (e.g.12p13.31) and their common regulators including KLF4 and SOX10. Large scale prediction of risk regions based on transcriptome data can open a window in comprehensive study of cancer risk factors and the other human diseases.
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Affiliation(s)
- Arghavan Alisoltani
- Department of Plant Breeding and Biotechnology, University of Shahrekord, Shahrekord, Iran
| | - Hossein Fallahi
- Department of Biology, School of Sciences, Razi University, Kermanshah, Iran
| | - Mahdi Ebrahimi
- Department of Informatics, Saarland University, Saarbrucken, Germany
| | - Mansour Ebrahimi
- Bioinformatics Research Group and Department of Biology, University of Qom, Qom, Iran
| | - Esmaeil Ebrahimie
- School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, Australia
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Borchers CH, Kast J, Foster LJ, Siu KWM, Overall CM, Binkowski TA, Hildebrand WH, Scherer A, Mansoor M, Keown PA. The Human Proteome Organization Chromosome 6 Consortium: integrating chromosome-centric and biology/disease driven strategies. J Proteomics 2014; 100:60-7. [PMID: 23933161 PMCID: PMC4096956 DOI: 10.1016/j.jprot.2013.08.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 08/01/2013] [Indexed: 11/20/2022]
Abstract
The Human Proteome Project (HPP) is designed to generate a comprehensive map of the protein-based molecular architecture of the human body, to provide a resource to help elucidate biological and molecular function, and to advance diagnosis and treatment of diseases. Within this framework, the chromosome-based HPP (C-HPP) has allocated responsibility for mapping individual chromosomes by country or region, while the biology/disease HPP (B/D-HPP) coordinates these teams in cross-functional disease-based groups. Chromosome 6 (Ch6) provides an excellent model for integration of these two tasks. This metacentric chromosome has a complement of 1002-1034 genes that code for known, novel or putative proteins. Ch6 is functionally associated with more than 120 major human diseases, many with high population prevalence, devastating clinical impact and profound societal consequences. The unique combination of genomic, proteomic, metabolomic, phenomic and health services data being drawn together within the Ch6 program has enormous potential to advance personalized medicine by promoting robust biomarkers, subunit vaccines and new drug targets. The strong liaison between the clinical and laboratory teams, and the structured framework for technology transfer and health policy decisions within Canada will increase the speed and efficacy of this transition, and the value of this translational research. BIOLOGICAL SIGNIFICANCE Canada has been selected to play a leading role in the international Human Proteome Project, the global counterpart of the Human Genome Project designed to understand the structure and function of the human proteome in health and disease. Canada will lead an international team focusing on chromosome 6, which is functionally associated with more than 120 major human diseases, including immune and inflammatory disorders affecting the brain, skeletal system, heart and blood vessels, lungs, kidney, liver, gastrointestinal tract and endocrine system. Many of these chronic and persistent diseases have a high population prevalence, devastating clinical impact and profound societal consequences. As a result, they impose a multi-billion dollar economic burden on Canada and on all advanced societies through direct costs of patient care, the loss of health and productivity, and extensive caregiver burden. There is no definitive treatment at the present time for any of these disorders. The manuscript outlines the research which will involve a systematic assessment of all chromosome 6 genes, development of a knowledge base, and development of assays and reagents for all chromosome 6 proteins. We feel that the informatic infrastructure and MRM assays developed will place the chromosome 6 consortium in an excellent position to be a leading player in this major international research initiative. This article is part of a Special Issue: Can Proteomics Fill the Gap Between Genomics and Phenotypes?
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Affiliation(s)
- C H Borchers
- University of Victoria/Genome BC Proteomics Centre, Victoria, BC, Canada
| | - J Kast
- Biomedical Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - L J Foster
- Centre for High Throughput Biology, University of British Columbia, BC, Canada
| | - K W M Siu
- Centre for Research in Mass Spectrometry, York University, Ontario, Canada
| | - C M Overall
- Centre for Blood Research, Faculty of Dentistry, University of British Columbia, Canada
| | - T A Binkowski
- Midwest Centre for Structural Genomics, Argonne National Laboratory and Computation Institute, University of Chicago, USA
| | - W H Hildebrand
- Department of Microbiology and Immunology, University of Oklahoma, OK, USA
| | - A Scherer
- Australian Genome Research Facility, Walter and Eliza Hall Institute, Parkville, Australia
| | - M Mansoor
- Department Medicine, University of British Columbia, Vancouver, BC, Canada
| | - P A Keown
- Department Medicine, University of British Columbia, Vancouver, BC, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.
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Hu XY, Bai XM, Qiao X, Zhu YQ. Copy number variation at 6q13 is associated with lung cancer risk in a Han Chinese population. Exp Lung Res 2013; 39:427-33. [PMID: 24245924 DOI: 10.3109/01902148.2013.822946] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Copy number variations (CNVs), a major source of human genetic polymorphism, have been suggested to have an important role in genetic susceptibility to common diseases such as cancer, immune diseases, and neurological disorders. Lung cancer is a multifactorial tumor closely associated with genetic background. Previous genome-wide association studies have identified single nucleotide polymorphisms (SNPs) that are associated with lung cancer susceptibility. This study examined the CNVR2966.1 at 6q13 and its association with lung cancer susceptibility. The CNVR2966.1 was found to be a 10,379 bp nucleotides deletion/insertion within the uniform boundaries chromosome 6: 74,648,791-74,659,169. The risk of lung cancer observed in 503 cases and 623 controls was significantly associated with copy number of CNVR2966.1, with the odds ratio (OR) being 1.38 [95% confidence interval (CI) = 1.05-1.79; P = .007] for one copy genotype compared with two copies genotype. These results suggest that CNVR2966.1 is associated with lung cancer risk.
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Affiliation(s)
- Xiao-Yun Hu
- 1Department of Respiratory Medicine, The First People's Hospital, Wujiang, Jiangsu, China
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17
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Fanale D, Iovanna JL, Calvo EL, Berthezene P, Belleau P, Dagorn JC, Ancona C, Catania G, D'Alia P, Galvano A, Gulotta E, Lo Dico S, Passiglia F, Bronte G, Midiri M, Lo Re G, Cicero G, Bazan V, Russo A. Analysis of Germline Gene Copy Number Variants of Patients with Sporadic Pancreatic Adenocarcinoma Reveals Specific Variations. Oncology 2013; 85:306-11. [DOI: 10.1159/000354737] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 07/27/2013] [Indexed: 12/15/2022]
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18
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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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19
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Gutiérrez-Camino Á, López-López E, Martín-Guerrero I, Sánchez-Toledo J, García de Andoin N, Carboné Bañeres A, García-Miguel P, Navajas A, García-Orad Á. Intron 3 of the ARID5B gene: a hot spot for acute lymphoblastic leukemia susceptibility. J Cancer Res Clin Oncol 2013; 139:1879-86. [PMID: 24013273 DOI: 10.1007/s00432-013-1512-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 08/30/2013] [Indexed: 11/30/2022]
Abstract
PURPOSE Single-nucleotide polymorphisms (SNPs) in AT-rich interactive domain 5B (ARID5B) have been associated with risk for pediatric acute lymphoblastic leukemia (ALL). After reviewing previous studies, we realized that the most significant associations were restricted to intron 3, but the mechanism(s) by which those SNPs affect ALL risk remain to be elucidated. Therefore, the aim of this study was to analyze the association between genetic variants of the intron 3 region of ARID5B and the incidence of B-ALL in a Spanish population. We also aimed to find a functional explanation for the association, searching for copy number variations (CNVs), and changes in ARID5B expression associated with the genotypes of the SNPs. METHODS We analyzed 10 SNPs in intron 3 of ARID5B in a Spanish population of 219 B-ALL patients and 397 unrelated controls with the Taqman Open Array platform. CNVs were analyzed in 23 patients and 17 controls using the Cytogenetics Whole-genome 2.7 M platform. Expression of ARID5B transcript 1 was quantified by qPCR and related to SNPs genotype in seven ALL cell lines. RESULTS Association between intron 3 and B-ALL risk was confirmed for all of the SNPs evaluated in our Spanish population. We could not explain this association by the presence of CNVs. We neither detected changes in the expression of ARID5B isoform associated with the genotype of the SNPs. CONCLUSIONS The intron 3 of ARID5B gene was found to be strongly associated with B-ALL risk in the Spanish population examined. However, neither CNVs nor changes in mRNA expression were found to be responsible for this association.
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Affiliation(s)
- Ángela Gutiérrez-Camino
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Dentistry, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, 48940, Leioa, Spain
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Yang L, Liu B, Huang B, Deng J, Li H, Yu B, Qiu F, Cheng M, Wang H, Yang R, Yang X, Zhou Y, Lu J. A functional copy number variation in the WWOX gene is associated with lung cancer risk in Chinese. Hum Mol Genet 2013; 22:1886-94. [DOI: 10.1093/hmg/ddt019] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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21
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Huang L, Wu C, Yu D, Wang C, Che X, Miao X, Zhai K, Chang J, Jiang G, Yang X, Cao G, Hu Z, Zhou Y, Zuo C, Wang C, Zhang X, Zhou Y, Yu X, Dai W, Li Z, Shen H, Liu L, Chen Y, Zhang S, Wang X, Liu Y, Sun M, Cao W, Gao J, Ma Y, Zheng X, Cheung ST, Jia Y, Tan W, Wu T, Lin D. Identification of common variants in BRCA2 and MAP2K4 for susceptibility to sporadic pancreatic cancer. Carcinogenesis 2013; 34:1001-5. [PMID: 23299404 DOI: 10.1093/carcin/bgt004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Germline mutations in genes that cause hereditary syndromes are highly predisposed to familial pancreatic cancer. However, genetic susceptibility to sporadic pancreatic cancer is largely uncovered. We conducted a two-stage association study on pancreatic cancer that included 981 cases and 1991 controls in the first stage followed by a second stage (2603 cases and 2877 controls). Using an approach based on candidate genes whose roles in pancreatic cancer have been well known, we identified two new susceptibility loci. rs11571836 located in the BRCA2 3'-untranslated region was significantly associated with lower expression of BRCA2 transcript and increased pancreatic cancer risk [odds ratio = 1.30, 95% confidence interval = 1.14-1.47, P = 7.64 × 10(-5)] in a recessive manner. rs12939944 located in the MAP2K4 intron was associated with decreased risk (odds ratio = 0.82, 95% confidence interval = 0.74-0.91, P = 0.0001) in a dominant manner. Our results demonstrate for the first time that common variants in BRCA2 and MAP2K4 are susceptibility to sporadic pancreatic cancer.
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Affiliation(s)
- Liming Huang
- State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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22
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Xu MJ, Ai L, Fu JH, Nisbet AJ, Liu QY, Chen MX, Zhou DH, Zhu XQ. Comparative characterization of microRNAs from the liver flukes Fasciola gigantica and F. hepatica. PLoS One 2012; 7:e53387. [PMID: 23300925 PMCID: PMC3534066 DOI: 10.1371/journal.pone.0053387] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2012] [Accepted: 11/27/2012] [Indexed: 11/18/2022] Open
Abstract
MicroRNAs (miRNAs) are key regulators of gene expression at the post-transcription level. The present study specifically explored and compared the miRNA expression profiles of F. gigantica and F. hepatica using an integrated sequencing and bioinformatics platform and quantitative real-time PCR. Nineteen and 16 miRNA candidates were identified from F. gigantica and F. hepatica, respectively. The two parasites shared 11 miRNAs, with 8 also showing similarity to miRNAs of Schistosoma japonicum. Another 8 miRNAs were identified as F. gigantica-specific and 5 as F. hepatica-specific, most of which were novel. Predicted target analysis with 11465 mRNA and EST sequences of F. hepatica and F. gigantica revealed that all of the miRNAs had more than one target, ranging from 2 to 398 with an average of 51 targets. Some functions of the predicted targets were only found in F. gigantica, such as “transcription regulator”, while some others were only found in F. hepatica, such as “reproduction” and “response to stimulus”, indicating the different metabolism and gene regulation patterns of the two parasites. The present study represents the first global comparative characterization of miRNA expression profiles of F. gigantica and F. hepatica, which has provided novel valuable resources for a better understanding of the two zoonotic trematodes.
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Affiliation(s)
- Min-Jun Xu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, China
| | - Lin Ai
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, China
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, China
| | - Jing-Hua Fu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, China
- College of Animal Science, South China Agricultural University, Guangzhou, Guangdong Province, China
| | - Alasdair J. Nisbet
- Parasitology Division, Moredun Research Institute, Midlothian, Scotland, UK
| | - Qing-You Liu
- Animal Reproduction Institute, Guangxi Key Laboratory of Subtropical Bioresource Conservation and Utilization, Guangxi University, Nanning, Guangxi Zhuang Nationality Autonomous Region, China
| | - Mu-Xin Chen
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, China
| | - Dong-Hui Zhou
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, China
| | - Xing-Quan Zhu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province, China
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang Province, China
- * E-mail:
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Zhang T, Cai J, Chang J, Yu D, Wu C, Yan T, Zhai K, Bi X, Zhao H, Xu J, Tan W, Qu C, Lin D. Evidence of associations of APOBEC3B gene deletion with susceptibility to persistent HBV infection and hepatocellular carcinoma. Hum Mol Genet 2012; 22:1262-9. [PMID: 23213177 DOI: 10.1093/hmg/dds513] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
APOBEC3s are a family of cytidine deaminases involved in innate cellular immunity against virus including hepatitis B virus (HBV). A germline deletion across APOBEC3A and APOBEC3B (A3B) genes results in complete removal of the A3B coding region and destroys A3B expression. To determine whether this deletion affects susceptibility to HBV infection and HBV-related hepatocellular carcinoma (HCC), A3B genotypes were analyzed in 1124 individuals with HCC, 510 individuals with persistent HBV infection and 826 healthy controls and the association was estimated by odds ratio (OR) and 95% confidence interval (CI) computed by logistic regression. We also examined the effects of A3B on HBV genome hypermutation and replication in HCC cells. We observed a significantly higher frequency of the A3B deletion allele in persistent HBV carriers (33.3%; P = 0.0015) and HCC patients (37.9%; P = 1.28 × 10(-11)) compared with that in controls (27.5%). An increased risk for persistent HBV infection (OR = 1.35, 95% CI: 1.03-1.77) and HCC development (OR = 1.90, 95% CI: 1.58-2.28) was associated with at least one A3B deletion allele (+/- or -/- genotype) compared with the +/+ genotype. Transfection of A3B in HepG2 cells caused a substantial reduction of HBV RNA levels and G → A hypermutation in the HBV genome. Interestingly, a cytidine deaminase null mutant of A3B (E255A) also inhibited HBV RNA production although it was unable to edit HBV. These results suggest that the deletion of A3B attenuates HBV clearance, which in turn may result in persistent HBV infection and increased risk for developing HCC. Further studies are needed to verify our findings.
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Affiliation(s)
- Tongwen Zhang
- State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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A functional copy-number variation in MAPKAPK2 predicts risk and prognosis of lung cancer. Am J Hum Genet 2012; 91:384-90. [PMID: 22883146 DOI: 10.1016/j.ajhg.2012.07.003] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2012] [Revised: 05/22/2012] [Accepted: 07/02/2012] [Indexed: 02/06/2023] Open
Abstract
Mitogen-activated protein kinase-activated protein kinase 2 (MAPKAPK2) may promote cancer development and progression by inducing tumorigenesis and drug resistance. To assess whether the copy-number variation g.CNV-30450 located in the MAPKAPK2 promoter has any effect on lung cancer risk or prognosis, we investigated the association between g.CNV-30450 and cancer risk in three independent case-control studies of 2,332 individuals with lung cancer and 2,457 controls and the effects of g.CNV-30450 on cancer prognosis in 1,137 individuals with lung cancer with survival data in southern and eastern Chinese populations. We found that those subjects who had four copies of g.CNV-30450 had an increased cancer risk (odds ratio = 1.94, 95% confidence interval [CI] = 1.61-2.35) and a worse prognosis for individuals with lung cancer (with a median survival time of only 9 months) (hazard ratio = 1.47, 95% CI = 1.22-1.78) compared with those with two or three copies (with a median survival time of 14 months). Meanwhile, four copies of g.CNV-30450 significantly increased MAPKAPK2 expression, both in vitro and in vivo, compared with two or three copies. Our study establishes a robust association between the functional g.CNV-30450 in MAPKAPK2 and risk as well as prognosis of lung cancer, and it presents this functional copy-number variation as a potential biomarker for susceptibility to and prognosis for lung cancer.
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Al-Sukhni W, Joe S, Lionel AC, Zwingerman N, Zogopoulos G, Marshall CR, Borgida A, Holter S, Gropper A, Moore S, Bondy M, Klein AP, Petersen GM, Rabe KG, Schwartz AG, Syngal S, Scherer SW, Gallinger S. Identification of germline genomic copy number variation in familial pancreatic cancer. Hum Genet 2012; 131:1481-94. [PMID: 22665139 DOI: 10.1007/s00439-012-1183-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Accepted: 05/23/2012] [Indexed: 12/20/2022]
Abstract
Adenocarcinoma of the pancreas is a significant cause of cancer mortality, and up to 10 % of cases appear to be familial. Heritable genomic copy number variants (CNVs) can modulate gene expression and predispose to disease. Here, we identify candidate predisposition genes for familial pancreatic cancer (FPC) by analyzing germline losses or gains present in one or more high-risk patients and absent in a large control group. A total of 120 FPC cases and 1,194 controls were genotyped on the Affymetrix 500K array, and 36 cases and 2,357 controls were genotyped on the Affymetrix 6.0 array. Detection of CNVs was performed by multiple computational algorithms and partially validated by quantitative PCR. We found no significant difference in the germline CNV profiles of cases and controls. A total of 93 non-redundant FPC-specific CNVs (53 losses and 40 gains) were identified in 50 cases, each CNV present in a single individual. FPC-specific CNVs overlapped the coding region of 88 RefSeq genes. Several of these genes have been reported to be differentially expressed and/or affected by copy number alterations in pancreatic adenocarcinoma. Further investigation in high-risk subjects may elucidate the role of one or more of these genes in genetic predisposition to pancreatic cancer.
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Affiliation(s)
- Wigdan Al-Sukhni
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, ON, Canada.
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