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Wu J, Wu C, Li G. Identifying common driver modules by equilibrating coverage and mutual exclusivity across pan-cancer data. Neurocomputing 2022. [DOI: 10.1016/j.neucom.2022.04.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Huang L, Xu W, Yan D, You X, Shi X, Zhang S, Hong H, Dai L. Genetic Predisposition to Glioma Mediated by a MAPKAP1 Enhancer Variant. Cell Mol Neurobiol 2020; 40:643-652. [PMID: 31773361 DOI: 10.1007/s10571-019-00763-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 11/18/2019] [Indexed: 12/12/2022]
Abstract
Mitogen-activated protein kinase-associated protein 1 (MAPKAP1) is a unique component of the mechanistic target of rapamycin (MTOR) pathway which plays a pivotal role in carcinogenesis. The role of enhancer variant in carcinogenesis receives increased attentions. However, the significance of enhancer variants of MAPKAP1 in glioma has not yet been investigated. The associations of enhancer variants of MAPKAP1 with glioma susceptibility were evaluated in a cohort of 400 glioma patients and 651 controls. The function of glioma susceptibility locus was examined by a set of biochemical assays. We found that an enhancer variant of MAPKAP1 rs473426 was associated with a significantly increased risk of glioma in a dominant manner (OR 1.53, 95% CI 1.13-2.06; P = 0.006). The association for rs1339499 located in the same enhancer approached the borderline of significance after multiple testing correction (OR 0.74, 95% CI 0.56-0.98; P = 0.037). Furthermore, cumulative associations of rs473426 and rs1339499 with glioma risk were observed (P = 0.011). Functional analyses showed that the risk allele rs473426 C downregulated the regulatory activity of enhancer by reducing the binding affinity of a transcriptional activator NFΙC, which resulted in lower gene expression both in vitro and in vivo. These results demonstrate for the first time that enhancer variant of MAPKAP1 confers susceptibility to glioma by downregulation of MAPKAP1 expression, and provide further evidence highlighting MAPKAP1 as a cancer suppressor in glioma carcinogenesis.
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Affiliation(s)
- Liming Huang
- Department of Medical Oncology (39th Section), The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China.
| | - Wenshen Xu
- Department of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
| | - Danfang Yan
- Department of Radiation Oncology, The First Affiliated Hospital, Zhejiang University, Hangzhou, 310003, China
| | - Xin You
- Department of Medical Oncology (39th Section), The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
| | - Xi Shi
- Department of Medical Oncology (39th Section), The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
| | - Shu Zhang
- Department of Medical Oncology (39th Section), The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
| | - Hualan Hong
- Department of Medical Oncology (39th Section), The First Affiliated Hospital, Fujian Medical University, Fuzhou, 350005, China
| | - Lian Dai
- Department of Medicine, The Third Affiliated People's Hospital, Fujian University of Traditional Chinese Medicine, Fuzhou, 350108, China.
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Tsuruoka K, Kurahara T, Kanamaru H, Takahashi H, Gotoh T. Effect of feeding rice whole crop silage on growth rate, levels of vitamin A, β-carotene, vitamin E and IGF-1 in plasma and skeletal muscle protein degradation in Japanese black calves. Anim Sci J 2019; 90:728-736. [PMID: 31006927 DOI: 10.1111/asj.13198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 01/04/2019] [Accepted: 01/30/2019] [Indexed: 11/29/2022]
Abstract
This study evaluated the effects of rice whole crop silage (RWCS) on growth, plasma levels of vitamin A, β-carotene, vitamin E and IGF-1, and expression of genes involved in muscle protein degradation and synthesis in Japanese Black calves. Eleven calves were divided into RWCS (fed RWCS ad libitum and concentrate, n = 5) and control groups (fed hay ad libitum and concentrate, n = 6). Final body weight and dairy gain were significantly larger in the RWCS group compared with the control group. Plasma β-carotene and vitamin E concentrations were significantly higher in the RWCS group compared with control group. Although plasma vitamin E concentration in the RWCS group significantly increased from 4 to 9 months of age, it did not increase in the control group. At 6 months of age in the RWCS group, ubiquitin B (p < 0.05) and calpain 1 (p = 0.097) mRNA expression were lower than control group, but they were not different between groups at 9 months of age. These results indicate that RWCS increases plasma β-carotene level and promotes muscle growth because of a decrease in the rate of protein degradation, but the effect is lost with the increase in plasma vitamin E level.
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Affiliation(s)
- Katsuhiko Tsuruoka
- Livestock Research Institute, Oita Prefectural Agriculture, Forestry and Fisheries Research Center, Oita, Japan
| | - Takami Kurahara
- Livestock Research Institute, Oita Prefectural Agriculture, Forestry and Fisheries Research Center, Oita, Japan
| | - Hidenobu Kanamaru
- Livestock Research Institute, Oita Prefectural Agriculture, Forestry and Fisheries Research Center, Oita, Japan
| | | | - Takafumi Gotoh
- Kuju Agricultural Research Center, Kyushu University, Oita, Japan.,Department of Agricultural Sciences and Natural Resources, Faculty of Agriculture, Kagoshima University, Kagoshima, Japan
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Huang L, Xu W, Dai L, Yan D, Zhang S, Shi X. An intronic genetic variation of MGMT affects enhancer activity and is associated with glioma susceptibility. Cancer Manag Res 2018; 10:3995-4003. [PMID: 30310321 PMCID: PMC6166748 DOI: 10.2147/cmar.s176622] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Purpose O6-methylguanine-DNA methyltransferase (MGMT) plays a crucial role in repairing damaged DNA caused by alkylating agents. A number of cancer susceptibility loci have been recognized as enhancer variants. This study aimed to explore the significance of enhancer variants of MGMT in glioma susceptibility. Patients and methods A retrospective case-control study consisting of 150 glioma patients and 327 controls was conducted to test whether enhancer variants of MGMT are associated with glioma susceptibility. Genotypes were determined by Sequenom MassARRAY technology. Associations were estimated by logistic regression. Biochemical assays were used to examine the function of glioma susceptibility locus. Results We found that the A allele of rs10764901, an intronic variant of MGMT, was associated with a significantly decreased risk of glioma. The rs10764901 AA genotype carriers had an OR of 0.49 (95% CI, 0.24-0.98; P=0.045) compared with the rs10764901 GG genotype. When the rs10764901 AG and AA genotypes were pooled for analysis, a significantly decreased risk of glioma was also found (OR, 0.63; 95% CI, 0.43-0.93; P=0.021). Functional analyses showed that the rs10764901 A allele drove a lower luciferase expression and had higher transcription factor binding affinity than the G allele. Conclusion An enhancer variant of MGMT rs10764901 affects the regulatory activity of enhancer by altering the binding affinity of transcription factors and is associated with glioma susceptibility.
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Affiliation(s)
- Liming Huang
- The First Department of Chemotherapy, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China,
| | - Wenshen Xu
- Department of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
| | - Lian Dai
- Department of Medicine, The Third Affiliated People's Hospital, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian, China
| | - Danfang Yan
- Department of Radiation Oncology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Shu Zhang
- The First Department of Chemotherapy, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China,
| | - Xi Shi
- The First Department of Chemotherapy, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China,
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Huang L, Dai L, Xu W, Zhang S, Yan D, Shi X. Identification of expression quantitative trait loci of MTOR associated with the progression of glioma. Oncol Lett 2018; 15:665-671. [PMID: 29387238 DOI: 10.3892/ol.2017.7319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 09/22/2017] [Indexed: 11/05/2022] Open
Abstract
Mechanistic target of rapamycin (MTOR) encodes a key modulator of cell growth, proliferation, and apoptosis. Previous studies have demonstrated that the dysregulation of MTOR is involved in the development and progression of several types of cancer, including glioma. In the present study, a comprehensive analysis was conducted to examine whether the expression quantitative trait loci (eQTLs) of MTOR are associated with the progression of glioma. Candidate eQTLs of MTOR were obtained from the Genotype-Tissue Expression eQTL Browser. The Kaplan-Meier method and multivariate Cox model were used to analyze the progression-free survival time of glioma patients. Based on the analysis of 138 glioma patients, one eQTL of MTOR, rs4845964, was demonstrated to be significantly associated with the progression of glioma in a dominant manner. The adjusted hazard ratios (HRs) for patients with the AG or AA genotype at rs4845964 were 2.82 [95% confidence interval (CI), 1.27-6.27; P=0.0111] and 2.79 (95% CI, 1.10-7.07; P=0.0312), respectively, compared with those with the GG genotype. When the rs4845964 AG and AA genotypes were combined for analysis, the HR was 2.70 (95% CI, 1.25-5.82; P=0.0114) vs. the GG genotype. Stratified analyses revealed similar associations between the rs4845964 genotypes and the progression of glioma in all subgroups (following stratification by age, sex and tumor grade). These results demonstrate for the first time that the MTOR eQTL rs4845964 is associated with the progression of glioma.
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Affiliation(s)
- Liming Huang
- The First Department of Chemotherapy, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, P.R. China
| | - Lian Dai
- Department of Medicine, The Third Affiliated People's Hospital, Fujian University of Traditional Chinese Medicine, Fuzhou, Fujian 350108, P.R. China
| | - Wenshen Xu
- Department of Laboratory Medicine, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, P.R. China
| | - Shu Zhang
- The First Department of Chemotherapy, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, P.R. China
| | - Danfang Yan
- Department of Radiation Oncology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
| | - Xi Shi
- The First Department of Chemotherapy, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, P.R. China
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Odhams CA, Cortini A, Chen L, Roberts AL, Viñuela A, Buil A, Small KS, Dermitzakis ET, Morris DL, Vyse TJ, Cunninghame Graham DS. Mapping eQTLs with RNA-seq reveals novel susceptibility genes, non-coding RNAs and alternative-splicing events in systemic lupus erythematosus. Hum Mol Genet 2017; 26:1003-1017. [PMID: 28062664 PMCID: PMC5409091 DOI: 10.1093/hmg/ddw417] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 12/05/2016] [Indexed: 12/19/2022] Open
Abstract
Studies attempting to functionally interpret complex-disease susceptibility loci by GWAS and eQTL integration have predominantly employed microarrays to quantify gene-expression. RNA-Seq has the potential to discover a more comprehensive set of eQTLs and illuminate the underlying molecular consequence. We examine the functional outcome of 39 variants associated with Systemic Lupus Erythematosus (SLE) through the integration of GWAS and eQTL data from the TwinsUK microarray and RNA-Seq cohort in lymphoblastoid cell lines. We use conditional analysis and a Bayesian colocalisation method to provide evidence of a shared causal-variant, then compare the ability of each quantification type to detect disease relevant eQTLs and eGenes. We discovered the greatest frequency of candidate-causal eQTLs using exon-level RNA-Seq, and identified novel SLE susceptibility genes (e.g. NADSYN1 and TCF7) that were concealed using microarrays, including four non-coding RNAs. Many of these eQTLs were found to influence the expression of several genes, supporting the notion that risk haplotypes may harbour multiple functional effects. Novel SLE associated splicing events were identified in the T-reg restricted transcription factor, IKZF2, and other candidate genes (e.g. WDFY4) through asQTL mapping using the Geuvadis cohort. We have significantly increased our understanding of the genetic control of gene-expression in SLE by maximising the leverage of RNA-Seq and performing integrative GWAS-eQTL analysis against gene, exon, and splice-junction quantifications. We conclude that to better understand the true functional consequence of regulatory variants, quantification by RNA-Seq should be performed at the exon-level as a minimum, and run in parallel with gene and splice-junction level quantification.
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Affiliation(s)
| | - Andrea Cortini
- Department of Medical & Molecular Genetics, King's College London, London, UK
| | - Lingyan Chen
- Department of Medical & Molecular Genetics, King's College London, London, UK
| | - Amy L Roberts
- Department of Medical & Molecular Genetics, King's College London, London, UK
| | - Ana Viñuela
- Department of Twin Research, King's College London, London, UK
| | | | - Kerrin S Small
- Department of Twin Research, King's College London, London, UK
| | | | - David L Morris
- Department of Medical & Molecular Genetics, King's College London, London, UK
| | - Timothy J Vyse
- Department of Medical & Molecular Genetics, King's College London, London, UK.,Division of Immunology, Infection and Inflammatory Disease, King's College London, London, UK
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