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Quraishi R, Sanyal S, Dwivedi M, Moitra M, Dwivedi M. Genetic Factors and MicroRNAs in the Development of Gallbladder Cancer: The Prospective Clinical Targets. Curr Drug Targets 2024; 25:375-387. [PMID: 38544392 DOI: 10.2174/0113894501182288240319074330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 01/14/2024] [Accepted: 02/01/2024] [Indexed: 07/19/2024]
Abstract
Gallbladder cancer (GBC) is an uncommon condition in which malignant (cancer) cells are detected in gallbladder tissue. Cancer is often triggered when normal cells turn malignant and begin to spread. Cancer can also be caused by genetic anomalies that result in uncontrolled cell proliferation and tumor development. MicroRNAs (also known as miRNAs or miRs) are a group of small, endogenous, non-coding RNAs of 19-23 nucleotides in length, which play a key role in post-transcriptional gene regulation. These miRNAs serve as negative gene regulators by supervising target genes and regulating biological processes, including cell proliferation, migration, invasion, and apoptosis. Cancer development and progression relate to aberrant miRNA expression. This review demonstrated the implication of various genetic factors and microRNAs in developing and regulating GBC. This suggests the potential of genes and RNAs as the diagnostic, prognostic, and therapeutic targets in gallbladder cancer.
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Affiliation(s)
- Roshni Quraishi
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Gomtinagar Extension, Lucknow-226028, India
| | - Somali Sanyal
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Gomtinagar Extension, Lucknow-226028, India
| | - Medha Dwivedi
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Gomtinagar Extension, Lucknow-226028, India
| | - Monika Moitra
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Gomtinagar Extension, Lucknow-226028, India
| | - Manish Dwivedi
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Gomtinagar Extension, Lucknow-226028, India
- Research Cell, Amity University Uttar Pradesh, Lucknow Campus, Gomtinagar Extension, Lucknow-226028, India
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2
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Mumlek I, Ozretić P, Sabol M, Leović M, Glavaš-Obrovac L, Leović D, Musani V. BIRC5 Gene Polymorphisms Are Associated with a Higher Stage of Local and Regional Disease in Oral and Oropharyngeal Squamous Cell Carcinomas. Int J Mol Sci 2023; 24:17490. [PMID: 38139318 PMCID: PMC10743484 DOI: 10.3390/ijms242417490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 12/17/2023] Open
Abstract
Oral squamous cell carcinoma (OSCC) and oropharyngeal squamous cell carcinoma (OPSCC) are the most common types of cancers in the head and neck region (HNSCC). Despite very aggressive treatment modalities, the five-year survival rate has not changed for decades and is still around 60%. The search for potential specific biomarkers of aggressiveness or outcome indicators could be of great benefit in improving the treatment of these patients. One of the potential biomarkers is survivin, the protein product of the BIRC5 gene. In this study, we investigated the occurrence of BIRC5 gene polymorphisms in 48 patients with OSCC and OPSCC compared with healthy controls. A total of 18 polymorphisms were found, 11 of which occurred in HNSCC with a minor allele frequency (MAF) of more than 5%. Five polymorphisms (rs3764383, rs9904341, rs2071214, rs2239680, rs2661694) were significantly associated with tumor size, tumor stage, and advanced regional disease, but had no impact on survival.
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Affiliation(s)
- Ivan Mumlek
- Department of Maxillofacial and Oral Surgery, University Hospital Centre Osijek, Josipa Huttlera 4, 31000 Osijek, Croatia;
- Faculty of Medicine, Josip Juraj Strossmayer University of Osijek, Josipa Huttlera 4, 31000 Osijek, Croatia;
| | - Petar Ozretić
- Laboratory for Hereditary Cancer, Division of Molecular Medicine, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (P.O.); (M.S.)
| | - Maja Sabol
- Laboratory for Hereditary Cancer, Division of Molecular Medicine, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (P.O.); (M.S.)
| | - Matko Leović
- Clinical Hospital Centre Zagreb, Kišpatićeva 12, 10000 Zagreb, Croatia;
| | - Ljubica Glavaš-Obrovac
- Faculty of Medicine, Josip Juraj Strossmayer University of Osijek, Josipa Huttlera 4, 31000 Osijek, Croatia;
| | - Dinko Leović
- Maxillofacial Surgery Unit, Department of Otorhinolaryngology and Head and Neck Surgery, Clinical Hospital Centre Zagreb, Kišpatićeva Ulica 12, 10000 Zagreb, Croatia
| | - Vesna Musani
- Laboratory for Hereditary Cancer, Division of Molecular Medicine, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (P.O.); (M.S.)
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Pan-Cancer Study on Variants of Canonical miRNA Biogenesis Pathway Components: A Pooled Analysis. Cancers (Basel) 2023; 15:cancers15020338. [PMID: 36672288 PMCID: PMC9856462 DOI: 10.3390/cancers15020338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/23/2022] [Accepted: 01/03/2023] [Indexed: 01/06/2023] Open
Abstract
Single nucleotide polymorphisms in genes involved in microRNA processing/maturation and release may deregulate the microRNAome expression levels. We aimed to assess the relationship between miRNA machinery genetic variants and human cancer risk using integrative bioinformatics analyses to identify the role of these genes in cancer aggressiveness. Mutations of 8176 pan-cancer samples were retrieved from 33 studies in "TCGA" database, and a Cox regression model for survival was performed. Next, 22 computationally identified variants within 11 genes were selected based on their high citation rate and MAF. Relevant articles through March 2020 were included. Pooled estimates under the five genetic association models were calculated. Publication bias and heterogeneity between articles were evaluated. Trial Sequential Analysis (TSA) was applied to assess the power and reliability of the draw conclusions. TCGA patients with different cancer types revealed significant alterations in miRNA machinery genes, with mutation frequency ranging from 0.6-13% of samples. RAN was associated with LN metastasis, while TARBP2 and PIWIL1 gene mutations exhibited better overall survival. In the meta-analysis, 45 articles (74,593 cases and 89,198 controls) met the eligibility criteria. Pooled analysis revealed an increased cancer risk with DROSHArs10719*G, RANrs3803012*G, DGCR8rs417309*A, and GEMIN3rs197414*A. In contrast, both DICER1rs1057035*T and GEMIN4rs2743048*G conferred protection against developing cancer. TSA showed the cumulative evidence is inadequate, and the addition of further primary studies is necessary. This study suggests a potential role of miRNA biogenesis genes in cancer development/prognosis. Further functional studies may reveal biological explanations for the differential risks of the machinery variants in different cancer types.
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Xin Y, Peng J, Hong YY, Chao QC, Na S, Pan S, Zhao LF. Advances in research on the effects of platelet activation in acute lung injury (Review). Biomed Rep 2022; 16:17. [PMID: 35154701 PMCID: PMC8814673 DOI: 10.3892/br.2022.1500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 01/05/2022] [Indexed: 11/17/2022] Open
Abstract
Acute lung injury (ALI) is an acute hypoxic respiratory insufficiency or failure caused by various factors inside and outside the lungs. ALI is associated with high morbidity and a poor prognosis in hospitalized patients. The lungs serve as a reservoir for platelet precursor megakaryocytes and are closely associated with platelets. Platelets not only play a central role in hemostasis, coagulation and wound healing, but can also act as inflammatory cells capable of stimulating non-hemostatic immune functions under inflammatory conditions, participating in the progression of various inflammatory diseases, and can result in tissue damage. Therefore, it was speculated that platelets may play an important role in the pathogenesis of ALI. In this review, the latest research progress on secretion of bioactive mediators from platelets, platelet activation-related signaling pathways, and the direct contact reactions between platelets and neutrophils with endothelial cells that result in ALI are described, providing evidence to support the importance of the consideration of platelets in the search for ALI interventional targets.
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Affiliation(s)
- Yuan Xin
- Institute of Blood Transfusion, Chinese Academy of Medical Science and Peking Union Medical College, Chengdu, Sichuan 610052, P.R. China
| | - Jiang Peng
- Institute of Blood Transfusion, Chinese Academy of Medical Science and Peking Union Medical College, Chengdu, Sichuan 610052, P.R. China
| | - Yu Yun Hong
- Institute of Blood Transfusion, Chinese Academy of Medical Science and Peking Union Medical College, Chengdu, Sichuan 610052, P.R. China
| | - Qiao Cong Chao
- Institute of Blood Transfusion, Chinese Academy of Medical Science and Peking Union Medical College, Chengdu, Sichuan 610052, P.R. China
| | - Su Na
- Institute of Blood Transfusion, Chinese Academy of Medical Science and Peking Union Medical College, Chengdu, Sichuan 610052, P.R. China
| | - Sun Pan
- Institute of Blood Transfusion, Chinese Academy of Medical Science and Peking Union Medical College, Chengdu, Sichuan 610052, P.R. China
| | - Lin Fang Zhao
- Institute of Blood Transfusion, Chinese Academy of Medical Science and Peking Union Medical College, Chengdu, Sichuan 610052, P.R. China
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Jin Y, Chen Z, Chen Q, Sha L, Shen C. [Role and Significance of Bioactive Substances in Sputum
in the Diagnosis of Lung Cancer]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2021; 24:867-873. [PMID: 34923805 PMCID: PMC8695240 DOI: 10.3779/j.issn.1009-3419.2021.102.46] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
肺癌是我国目前发病率最高的恶性肿瘤之一,其诊断的金标准需要进行组织活检的病理学检查或脱落细胞学检查,二者的有创性和敏感性限制了他们的使用。痰液中含有大量核酸、蛋白质,是肺功能的良好反映物,肺癌组织也会影响痰液中的生物成分,检测其中的生物活性物质可有助于肺癌的诊断。本文综合目前国内外的研究结果,对痰液中可用于肺癌诊断的生物活性物质做一综述。
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Affiliation(s)
- Yuming Jin
- West China School of Medicine, Sichuan University, Chengdu 610041, China
| | - Zixuan Chen
- West China School of Medicine, Sichuan University, Chengdu 610041, China
| | - Quan Chen
- West China School of Medicine, Sichuan University, Chengdu 610041, China
| | - Leihao Sha
- West China School of Medicine, Sichuan University, Chengdu 610041, China
| | - Cheng Shen
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
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Chen X, Zhang H, Ou S, Chen H. Von Hippel-Lindau gene single nucleotide polymorphism (rs1642742) may be related to the occurrence and metastasis of HBV-related hepatocellular carcinoma. Medicine (Baltimore) 2021; 100:e27187. [PMID: 34477178 PMCID: PMC8415925 DOI: 10.1097/md.0000000000027187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 08/22/2021] [Indexed: 01/05/2023] Open
Abstract
It is well-known that microRNAs are able to regulate the expression of target mRNAs through complementary base-pairing to their 3'-untranslated regions (3'UTR) sequences. This study aimed to investigate whether single nucleotide polymorphisms resided in the 3'UTR sequences in patients with chronic hepatitis B viruses (HBV) infection are associated with the development and metastasis of hepatocellular carcinoma (HCC). Seventeen single nucleotide polymorphisms in the 3'UTR sequence of 10 genes regulated or affected by hepatitis B virus X protein were found by bioinformatics methods. Two hundred fifteen patients with HBV-related HCC and 216 patients with chronic HBV infection were recruited. Through case-control study, only found that the von Hippel-Lindau gene rs1642742 (G>A) may be associated with the occurrence and metastasis of HCC. The ORs of the frequencies of rs1642742 A allele versus G allele were 1.424 (P = .038, 95% confidence interval [CI] = 1.019-1.989) between HBV-related HCC and chronic HBV infection group and were 2.004 (P = .037, 95%CI = 1.031-3.895) between tumor metastasis and non-metastasis group, respectively. Through multivariate regression analysis, we also found that rs1642742 AA genotype was an independent risk factor for tumor metastasis (odds ratio = 2.227, 95% CI = 1.043-4.752, P = .038) in HBV-related HCC group. Our study suggested that Von Hippel-Lindau rs1642742 contributed to susceptibility to developing HCC and correlated with tumor metastasis.
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He D, Huang K, Liang Z. Prognostic value of baculoviral IAP repeat containing 5 expression as a new biomarker in lung adenocarcinoma: a meta-analysis. Expert Rev Mol Diagn 2021; 21:973-981. [PMID: 34176418 DOI: 10.1080/14737159.2021.1947798] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
BACKGROUND BIRC5 is associated with the prognosis of a variety of tumors. This meta-analysis aimed to identify whether BIRC5 is associated with the prognosis of lung adenocarcinoma (LUAD). RESEARCH DESIGN AND METHODS We conducted an in-depth review of seven Chinese and English databases and two high-throughput sequencing databases according to inclusion and exclusion criteria to find relevant studies. The pooled standardized mean differences (SMDs) and 95% confidence intervals (CIs) for the associations between the BIRC5 expression level and clinicopathological characteristics were calculated, and the pooled hazard ratios (HRs) and 95% CIs were calculated to estimate associations between the BIRC5 expression level and survival outcomes. RESULTS In total, 17 studies involving 2887 LUAD patients whose BIRC5 expression level was known were included in this meta-analysis. The BIRC5 expression level was higher in younger patients, males, and smokers and correlated with advanced AJCC, T and N stages but not M stage. A high BIRC5 expression level also correlated with poor overall survival (OS) and progression-free survival (PFS). There was no publication bias in this study. CONCLUSIONS This meta-analysis indicates that BIRC5 is a significant biomarker for a poor prognosis and poor clinicopathological outcomes in patients with LUAD.
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Affiliation(s)
- Dingxiu He
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Kaisen Huang
- Department of Cardiology, The People's Hospital of Deyang, Deyang, Sichuan, China
| | - Zongan Liang
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
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8
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Naghiyan Fesharaki S, Naghiyan Fesharaki S, Esmaeili A, Azadeh M, Ghaedi K. SNP rs1803622 in hsa-miR-548g binding site at GAPDH alters susceptibility to breast cancer. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Dobrijević Z, Matijašević S, Išić Denčić T, Savić-Pavićević D, Nedić O, Brajušković G. Association between genetic variants in DICER1 and cancer risk: An updated meta-analysis. Gene 2020; 766:145132. [PMID: 32911029 DOI: 10.1016/j.gene.2020.145132] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 08/01/2020] [Accepted: 09/01/2020] [Indexed: 02/06/2023]
Abstract
Dysfunctions in mechanisms of gene regulation based on RNA interference are recognized as a common feature of the molecular basis of cancer pathogenesis. Therefore, as one of the crucial components of the machinery involved in the biogenesis of both siRNAs and microRNA molecules, DICER was recognized as one of the candidates for the research in the field of carcinogenesis. Due to their potential functional properties, several genetic variants located within DICER1 gene were analyzed for their possible association with the susceptibility to cancer through case-control studies. In order to elucidate their effect on the overall cancer risk, we conducted an updated meta-analysis of all eligible association studies. The publications were selected based on PubMed database search, while OpenMeta-analyst and MetaGenyo software were used for quantitative data synthesis. Statistically significant results were found for the association of rs1057035 with the overall cancer risk under multiple genetic models (PCT vs. TT < 0.001, ORCT vs. TT = 0.870, 95% CI = 0.812-0.933; Pallelic = 0.009, ORallelic = 0.896, 95% CI = 0.825-0.973; Pdom < 0.001, ORdom = 0.874, 95% CI = 0.817-0.934; Poverdom = 0.004, ORoverdom = 0.858, 95% CI = 0.773-0.953). Other selected genetic variants within DICER1, rs13078, rs1209904 and rs3742330, did not show the association with the overall susceptibility to malignant diseases. We conclude that rs1057035 may represent a potential biomarker associated with the risk of developing cancer, which requires a confirmation in a larger set of studies.
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Affiliation(s)
- Zorana Dobrijević
- Department for Metabolism, Institute for the Application of Nuclear Energy (INEP), University of Belgrade, Belgrade, Serbia.
| | - Suzana Matijašević
- Centre for Human Molecular Genetics, Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Tijana Išić Denčić
- Department for Endocrinology and Radioimmunology, Institute for the Application of Nuclear Energy (INEP), University of Belgrade, Belgrade, Serbia
| | - Dušanka Savić-Pavićević
- Centre for Human Molecular Genetics, Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Olgica Nedić
- Department for Metabolism, Institute for the Application of Nuclear Energy (INEP), University of Belgrade, Belgrade, Serbia
| | - Goran Brajušković
- Centre for Human Molecular Genetics, Faculty of Biology, University of Belgrade, Belgrade, Serbia
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Xie W, Luo J, Pan C, Liu Y. SG-LSTM-FRAME: a computational frame using sequence and geometrical information via LSTM to predict miRNA-gene associations. Brief Bioinform 2020; 22:2032-2042. [PMID: 32181478 DOI: 10.1093/bib/bbaa022] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 02/10/2020] [Accepted: 02/11/2020] [Indexed: 12/19/2022] Open
Abstract
MOTIVATION MircroRNAs (miRNAs) regulate target genes and are responsible for lethal diseases such as cancers. Accurately recognizing and identifying miRNA and gene pairs could be helpful in deciphering the mechanism by which miRNA affects and regulates the development of cancers. Embedding methods and deep learning methods have shown their excellent performance in traditional classification tasks in many scenarios. But not so many attempts have adapted and merged these two methods into miRNA-gene relationship prediction. Hence, we proposed a novel computational framework. We first generated representational features for miRNAs and genes using both sequence and geometrical information and then leveraged a deep learning method for the associations' prediction. RESULTS We used long short-term memory (LSTM) to predict potential relationships and proved that our method outperformed other state-of-the-art methods. Results showed that our framework SG-LSTM got an area under curve of 0.94 and was superior to other methods. In the case study, we predicted the top 10 miRNA-gene relationships and recommended the top 10 potential genes for hsa-miR-335-5p for SG-LSTM-core. We also tested our model using a larger dataset, from which 14 668 698 miRNA-gene pairs were predicted. The top 10 unknown pairs were also listed. AVAILABILITY Our work can be download in https://github.com/Xshelton/SG_LSTM. CONTACT luojiawei@hnu.edu.cn. SUPPLEMENTARY INFORMATION Supplementary data are available at Briefings in Bioinformatics online.
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Affiliation(s)
- Weidun Xie
- College of Computer Science and Electronic Engineering, Hunan University, Changsha 410082, Hunan, China
| | - Jiawei Luo
- College of Computer Science and Electronic Engineering, Hunan University, Changsha 410082, Hunan, China
| | - Chu Pan
- College of Computer Science and Electronic Engineering, Hunan University, Changsha 410082, Hunan, China
| | - Ying Liu
- College of Computer Science and Electronic Engineering, Hunan University, Changsha 410082, Hunan, China
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Yang JH, Lin LK, Zhang S. Epigenetic silencing of microRNA-335 contributes to nasopharyngeal carcinoma metastasis. Am J Otolaryngol 2020; 41:102302. [PMID: 31732311 DOI: 10.1016/j.amjoto.2019.102302] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 09/11/2019] [Accepted: 09/12/2019] [Indexed: 02/04/2023]
Abstract
BACKGROUND MircoRNA-335 (miR-335), a member of mircoRNAs (miRNAs) family, has been found to be correlated with tumor invasion and metastasis. In this study, we aimed to detect the effect of miR-335 methylation on metastasis of nasopharyngeal carcinoma. METHODS RT-PCR and methylation-specific PCR were applied to detect the expression levels of miR-335 and miR-335 methylation in nasopharyngeal carcinoma tissues. RESULTS The levels of miR-335 expression were significantly lower in nasopharyngeal cancer tissues with promoter methylation, compared to those with promoter unmethylation. The levels of miR-335 gene promoter methylation were higher in 14 (46.7%) out of 30 nasopharyngeal cancer tissues. Furthermore, the patients with cervical lymph node metastasis had higher methylation rate in miR-335 promoter (66.7% versus 16.7%) than those without cervical lymph node metastasis. CONCLUSION Gene methylation contributes the expression of miR-335 in nasopharyngeal carcinoma. The expression of miR-335 methylation is correlated with the metastasis of nasopharyngeal carcinoma.
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12
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Gene and lncRNA co-expression network analysis reveals novel ceRNA network for triple-negative breast cancer. Sci Rep 2019; 9:15122. [PMID: 31641220 PMCID: PMC6805880 DOI: 10.1038/s41598-019-51626-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 10/03/2019] [Indexed: 12/31/2022] Open
Abstract
Breast cancer is the most frequently diagnosed malignancy among women, and triple-negative breast cancer (TNBC) is a highly aggressive subtype. Increasing evidence has shown that lncRNAs are involved in tumor growth, cell-cycle, and apoptosis through interactions with miRNAs or mRNAs. However, there is still limited data on ceRNAs involved in the molecular mechanisms underlying TNBC. In this study, we applied the weighted gene co-expression network analysis to the existing microarray mRNA and lncRNA expression data obtained from the breast tissues of TNBC patients to find the hub genes and lncRNAs involved in TNBC. Functional enrichment was performed on the module that correlated with Ki-67 status the most (Turquoise module). The hub genes in the Turquoise module were found to be associated with DNA repair, cell proliferation, and the p53 signaling pathway. We performed co-expression analysis of the protein-coding and lncRNA hub genes in the Turquoise module. Analysis of the RNA-seq data obtained from The Cancer Genome Atlas database revealed that the protein-coding genes and lncRNAs that were co-expressed were also differentially expressed in the TNBC tissues compared with the normal mammary tissues. On the basis of establishing the ceRNA network, two mRNAs (RAD51AP1 and TYMS) were found to be correlated with overall survival in TNBC. These results suggest that TNBC-specific mRNA and lncRNAs may participate in a complex ceRNA network, which represents a potential therapeutic target for the treatment of TNBC.
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Trnski D, Gregorić M, Levanat S, Ozretić P, Rinčić N, Vidaković TM, Kalafatić D, Maurac I, Orešković S, Sabol M, Musani V. Regulation of Survivin Isoform Expression by GLI Proteins in Ovarian Cancer. Cells 2019; 8:cells8020128. [PMID: 30736319 PMCID: PMC6406444 DOI: 10.3390/cells8020128] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 02/01/2019] [Accepted: 02/04/2019] [Indexed: 02/05/2023] Open
Abstract
Ovarian cancer (OC) is the most lethal female gynecological malignancy, mostly due to diagnosis in late stages when treatment options are limited. Hedgehog-GLI (HH-GLI) signaling is a major developmental pathway involved in organogenesis and stem cell maintenance, and is activated in OC. One of its targets is survivin (BIRC5), an inhibitor of apoptosis protein (IAP) that plays a role in multiple processes, including proliferation and cell survival. We wanted to investigate the role of different GLI proteins in the regulation of survivin isoform expression (WT, 2α, 2B, 3B, and Δex3) in the SKOV-3 OC cell line. We demonstrated that survivin isoforms are downregulated in GLI1 and GLI2 knock-out cell lines, but not in the GLI3 knock-out. Treatment of GLI1 knock-out cells with GANT-61 shows an additional inhibitory effect on several isoforms. Additionally, we examined the expression of survivin isoforms in OC samples and the potential role of BIRC5 polymorphisms in isoform expression. Clinical samples showed the same pattern of survivin isoform expression as in the cell line, and several BIRC5 polymorphisms showed the correlation with isoform expression. Our results showed that survivin isoforms are regulated both by different GLI proteins and BIRC5 polymorphisms in OC.
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Affiliation(s)
- Diana Trnski
- Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia.
| | - Maja Gregorić
- Zagreb Health School, Medvedgradska 55, 10000 Zagreb, Croatia.
| | - Sonja Levanat
- Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia.
| | - Petar Ozretić
- Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia.
| | - Nikolina Rinčić
- Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia.
| | - Tajana Majić Vidaković
- Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia.
- PP Orahovica, Pustara 1, 33513 Zdenci, Croatia.
| | - Držislav Kalafatić
- Department of Obstetrics and Gynaecology, University Hospital Centre Zagreb, Petrova 13, 10000 Zagreb, Croatia.
- School of Medicine, University of Zagreb, Petrova 13, 10000 Zagreb, Croatia.
| | - Ivana Maurac
- Department of Obstetrics and Gynaecology, University Hospital Centre Zagreb, Petrova 13, 10000 Zagreb, Croatia.
| | - Slavko Orešković
- Department of Obstetrics and Gynaecology, University Hospital Centre Zagreb, Petrova 13, 10000 Zagreb, Croatia.
- School of Medicine, University of Zagreb, Petrova 13, 10000 Zagreb, Croatia.
| | - Maja Sabol
- Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia.
| | - Vesna Musani
- Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia.
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Li Y, Nowak CM, Withers D, Pertsemlidis A, Bleris L. CRISPR-Based Editing Reveals Edge-Specific Effects in Biological Networks. CRISPR J 2018; 1:286-293. [PMID: 31021219 DOI: 10.1089/crispr.2018.0018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Unraveling the properties of biological networks is central to understanding both normal and disease cellular phenotypes. Networks consist of functional elements (nodes) that form a variety of diverse connections (edges), with each node being a hub for multiple edges. Herein, in contrast to node-centric network perturbation and analysis approaches, we present a high-throughput CRISPR-based methodology for delineating the role of network edges. Ablation of network edges using a library targeting 93 miRNA target sites in 71 genes reveals numerous edges that control, with variable importance, cellular growth and survival under stress. To compare the impact of removing nodes versus edges in a biological network, we dissect a specific p53-microRNA pathway. We show that removal of the miR-34a target site from the anti-apoptotic gene BCL2 desensitizes the cell to ectopic delivery of miR-34a in a p53-dependent manner. In summary, we demonstrate that network edges are critical to the function and stability of biological networks. Our results introduce a novel genetic screening opportunity via edge ablation and highlight a new dimension in biological network analysis.
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Affiliation(s)
- Yi Li
- 1 Department of Bioengineering, The University of Texas at Dallas, Richardson, Texas.,2 Center for Systems Biology, The University of Texas at Dallas, Richardson, Texas
| | - Chance M Nowak
- 2 Center for Systems Biology, The University of Texas at Dallas, Richardson, Texas.,3 Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas
| | - Daniel Withers
- 1 Department of Bioengineering, The University of Texas at Dallas, Richardson, Texas.,2 Center for Systems Biology, The University of Texas at Dallas, Richardson, Texas
| | - Alexander Pertsemlidis
- 4 Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio , San Antonio, Texas
| | - Leonidas Bleris
- 1 Department of Bioengineering, The University of Texas at Dallas, Richardson, Texas.,2 Center for Systems Biology, The University of Texas at Dallas, Richardson, Texas.,3 Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas
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15
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Karimian M, Aftabi Y, Mazoochi T, Babaei F, Khamechian T, Boojari H, Nikzad H. Survivin polymorphisms and susceptibility to prostate cancer: A genetic association study and an in silico analysis. EXCLI JOURNAL 2018; 17:479-491. [PMID: 30034311 PMCID: PMC6046628 DOI: 10.17179/excli2018-1234] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 05/07/2018] [Indexed: 12/27/2022]
Abstract
Survivin is a member of the apoptosis inhibitor protein family and its polymorphisms may lead to susceptibility to cancer. The aim of this study was to investigate the possible association of c.-31G>C (rs9904341), c.454G>A (rs2071214), c.*148T>C (rs2239680) and c.*571T>C (rs1042489) polymorphisms of survivin gene with prostate cancer risk and provide some justification using in silico analysis. The 157 men with prostate cancer and 145 healthy controls were included in a case-control study. The studied polymorphisms were genotyped using PCR-RFLP method. An in silico approach was employed to show the possible effects of the polymorphisms on the survivin gene function. The study revealed that there are significant associations between c.-31CC genotype (OR= 2.29, 95 % CI= 1.20-4.37, p= 0.012), c.-31C allele (OR= 1.62, 95 % CI= 1.17-2.26, p= 0.004), c.454AG genotype (OR= 2.03, 95 % CI= 1.02-4.04, p= 0.043), and c.*148C allele (OR= 1.49, 95 % CI= 1.04-2.15, p= 0.031) with prostate cancer. Using stratified analysis, we found also significant effects of age distribution on the association of c.-31G>C with prostate cancer risk (OR= 2.10, 95 % CI= 1.08-4.10, p= 0.030). Also as a preliminary study, it was shown that smoking status has significant effects on the association of c.-31G>C (OR= 1.94, 95 % CI= 1.08-3.49, p= 0.027) and c.*148T>C (OR= 2.60, 95 % CI= 1.47-4.60, p= 0.001) polymorphisms with prostate cancer risk. Finally, in silico analysis revealed that c.-31G>C, which is located in a CpG island of the promoter may change transcriptional regulation of survivin gene and c.454G>A and *148T>C could affect protein structure and possible miRNA interaction with 3'-UTR of survivin transcript respectively. According to the results, c.-31G>C, c.454G>A, and c.*148T>C polymorphisms could be genetic risk factors for prostate cancer in an Iranian population. However, further studies with larger sample size and different ethnicities are required to obtain more comprehensive results.
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Affiliation(s)
- Mohammad Karimian
- Gametogenesis Research Center, Kashan University of Medical Sciences, Kashan, Iran
| | - Younes Aftabi
- Anatomical Sciences Research Center, Kashan University of Medical Sciences, Kashan, Iran
| | - Tahereh Mazoochi
- Anatomical Sciences Research Center, Kashan University of Medical Sciences, Kashan, Iran
| | - Faezeh Babaei
- Gametogenesis Research Center, Kashan University of Medical Sciences, Kashan, Iran
| | - Tahereh Khamechian
- Department of Pathology, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Hossein Boojari
- Department of Statistics, Faculty of Sciences, Islamic Azad University, Kashan Branch, Kashan, Iran
| | - Hossein Nikzad
- Gametogenesis Research Center, Kashan University of Medical Sciences, Kashan, Iran
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16
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He J, Zhao J, Zhu W, Qi D, Wang L, Sun J, Wang B, Ma X, Dai Q, Yu X. MicroRNA biogenesis pathway genes polymorphisms and cancer risk: a systematic review and meta-analysis. PeerJ 2016; 4:e2706. [PMID: 27957388 PMCID: PMC5147022 DOI: 10.7717/peerj.2706] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 10/20/2016] [Indexed: 12/25/2022] Open
Abstract
MicroRNAs (miRNAs) may promote the development and progression of human cancers. Therefore, components of the miRNA biogenesis pathway may play critical roles in human cancer. Single nucleotide polymorphisms (SNPs) or mutations in genes involved in the miRNA biogenesis pathway may alter levels of gene expression, affecting disease susceptibility. Results of previous studies on genetic variants in the miRNA biogenesis pathway and cancer risk were inconsistent. Therefore, a meta-analysis is needed to assess the associations of these genetic variants with human cancer risk. We searched for relevant articles from PubMed, Web of Science, CNKI, and CBM through Jun 21, 2016. In total, 21 case-control articles met all of the inclusion criteria for the study. Significant associations were observed between cancer risk and the DGCR8polymorphism rs417309 G >A (OR 1.22, 95% CI [1.04-1.42]), as well as the DICER1 polymorphism rs1057035 TT (OR 1.13, 95% CI [1.05-1.22]). These SNPs exhibit high potential as novel diagnostic markers. Future studies with larger sample sizes and more refined analyses are needed to shed more light on these findings.
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Affiliation(s)
- Jieyu He
- Southeast University, Department of Public Health, Nanjing, China
| | - Jun Zhao
- National Research Institute for Family Planning, Beijing, China.,Graduate School of Peking Union Medical College, Beijing, China
| | - Wenbo Zhu
- Southeast University, Department of Public Health, Nanjing, China
| | - Daxun Qi
- National Research Institute for Family Planning, Beijing, China
| | - Lina Wang
- Southeast University, Department of Public Health, Nanjing, China
| | - Jinfang Sun
- Southeast University, Department of Public Health, Nanjing, China
| | - Bei Wang
- Southeast University, Department of Public Health, Nanjing, China
| | - Xu Ma
- National Research Institute for Family Planning, Beijing, China.,Graduate School of Peking Union Medical College, Beijing, China
| | - Qiaoyun Dai
- National Research Institute for Family Planning, Beijing, China
| | - Xiaojin Yu
- Southeast University, Department of Public Health, Nanjing, China
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17
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Luo LJ, Wang DD, Wang J, Yang F, Tang JH. Diverse roles of miR-335 in development and progression of cancers. Tumour Biol 2016; 37:10.1007/s13277-016-5385-3. [PMID: 27718128 DOI: 10.1007/s13277-016-5385-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 09/09/2016] [Indexed: 12/16/2022] Open
Abstract
MicroRNAs (miRNAs), a series of small noncoding RNAs that regulate gene expression at the post-transcriptional/translational level, are pivotal in cell differentiation, biological development, occurrence, and development of diseases, especially in cancers. Early studies have shown that miRNA-335 (miR-335) is widely dysregulated in human cancers and play critical roles in tumorigenesis and tumor progression. In this review, we aim to summarize the regulation of miR-335 expression mechanisms in cancers. We focus on the target genes regulated by miR-335 and its downstream signaling pathways involved in the biological effects of tumor growth, invasion, and metastasis both in vitro and in vivo, and analyze the relationships between miR-335 expression and the clinical characteristics of tumors as well as its effects on prognosis. The collected evidences support the potential use of miR-335 in prognosis and diagnosis as well as the therapeutic prospects of miR-335 in cancers.
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Affiliation(s)
- Long-Ji Luo
- Department of General Surgery, Xuzhou Medical University, Xuzhou, Jiangsu, China
- Department of General Surgery, Jiangsu Cancer Hospital Affiliated to Nanjing Medical University, Baiziting 42, Nanjing, 210009, China
| | - Dan-Dan Wang
- Department of General Surgery, Jiangsu Cancer Hospital Affiliated to Nanjing Medical University, Baiziting 42, Nanjing, 210009, China
- Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jing Wang
- Department of General Surgery, Jiangsu Cancer Hospital Affiliated to Nanjing Medical University, Baiziting 42, Nanjing, 210009, China
- Nanjing Medical University, Nanjing, Jiangsu, China
| | - Fan Yang
- Department of General Surgery, Xuzhou Medical University, Xuzhou, Jiangsu, China
- Department of General Surgery, Jiangsu Cancer Hospital Affiliated to Nanjing Medical University, Baiziting 42, Nanjing, 210009, China
| | - Jin-Hai Tang
- Department of General Surgery, Jiangsu Cancer Hospital Affiliated to Nanjing Medical University, Baiziting 42, Nanjing, 210009, China.
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18
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Qu Z, Yuan CH, Yin CQ, Guan Q, Chen H, Wang FB. Meta-analysis of the prognostic value of abnormally expressed lncRNAs in hepatocellular carcinoma. Onco Targets Ther 2016. [PMID: 27574455 DOI: 10.2147/ott] [Citation(s) in RCA: 193] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Many long noncoding RNAs (lncRNAs) have been reported to be abnormally expressed in hepatocellular carcinoma (HCC), and may have the potential to serve as prognostic markers. In this study, a meta-analysis was conducted to systematically evaluate the prognostic value of various lncRNAs in HCC. Eligible literatures were systematically collected from PubMed, Embase, Web of Science, and Cochrane Library (up to December 30, 2015). The main outcomes including overall survival, relapse-free survival, and disease-free survival were analyzed. Pooled hazard ratios (HRs) and 95% confidence intervals (95% CIs) were calculated using random- or fixed-effects models. A total of 2,991 patients with HCC in People's Republic of China from 27 studies were included in the analysis. The level of lncRNAs showed a significant association with clinical outcomes. Abnormally elevated lncRNA transcription level predicted poor overall survival (HR: 1.68, 95% CI: 1.20-2.34, P=0.002; I (2)=75.5%, P=0.000) and relapse-free survival (HR: 2.08, 95% CI: 1.65-2.61, P<0.001; I (2)=24.0%, P=0.215), while no association was observed with disease-free survival of HCC patients (HR: 1.39, 95% CI: 0.51-3.78, P=0.524; I (2)=81.3%, P=0.005). Subgroup analysis further showed that lncRNA transcription level was significantly associated with tumor size (relative risk [RR]: 1.19, 95% CI: 1.01-1.39, P=0.035), microvascular invasion (RR: 1.44, 95% CI: 1.10-1.89, P=0.009), and portal vein tumor thrombus (RR: 1.50, 95% CI: 1.03-2.20, P=0.036). Publication bias and sensitivity analysis further confirmed the stability of our results. Our present meta-analysis indicates that abnormal lncRNA transcription level may serve as a promising indicator for prognostic evaluation of patients with HCC in People's Republic of China.
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Affiliation(s)
- Zhen Qu
- Department of Laboratory Medicine and Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University
| | - Chun-Hui Yuan
- Department of Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Chang-Qing Yin
- Department of Laboratory Medicine and Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University
| | - Qing Guan
- Department of Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Hao Chen
- Department of Laboratory Medicine and Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University
| | - Fu-Bing Wang
- Department of Laboratory Medicine and Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University
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19
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Yang G, Zhang L, Li R, Wang L. The role of microRNAs in gallbladder cancer. Mol Clin Oncol 2016; 5:7-13. [PMID: 27330755 DOI: 10.3892/mco.2016.905] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 03/21/2016] [Indexed: 01/17/2023] Open
Abstract
MicroRNAs (also referred to as miRNAs or miRs) play a crucial role in post-transcriptional gene regulation and serve as negative gene regulators by controlling a variety of target genes and regulating diverse biological processes, such as cell proliferation, invasion, migration and apoptosis. Aberrant expression of miRNAs is associated with the development and progression of cancer. Recent studies have reported that miRNAs may repress or promote the expression of cancer-related genes via several different signaling pathways in gallbladder cancer (GBC) patients and may function as tumor suppressors or oncogenes, thus providing a promising tool for the diagnosis and therapeutics of GBCs. In this review, we summarize the role of dysregulawted miRNA expression in the signaling pathways implicated in GBC and discuss the significant role of circulating miRNAs in GBC. Therefore, miRNAs may serve as novel therapeutic targets as well as diagnostic or prognostic markers in GBC.
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Affiliation(s)
- Ganghua Yang
- Department of Geriatric Surgery, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Lei Zhang
- Department of Geriatric Surgery, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Ruixiang Li
- Department of Geriatric Surgery, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Lin Wang
- Department of Geriatric Surgery, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
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20
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Võsa U, Esko T, Kasela S, Annilo T. Altered Gene Expression Associated with microRNA Binding Site Polymorphisms. PLoS One 2015; 10:e0141351. [PMID: 26496489 PMCID: PMC4619707 DOI: 10.1371/journal.pone.0141351] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 10/06/2015] [Indexed: 02/03/2023] Open
Abstract
Allele-specific gene expression associated with genetic variation in regulatory regions can play an important role in the development of complex traits. We hypothesized that polymorphisms in microRNA (miRNA) response elements (MRE-SNPs) that either disrupt a miRNA binding site or create a new miRNA binding site can affect the allele-specific expression of target genes. By integrating public expression quantitative trait locus (eQTL) data, miRNA binding site predictions, small RNA sequencing, and Argonaute crosslinking immunoprecipitation (AGO-CLIP) datasets, we identified genetic variants that can affect gene expression by modulating miRNA binding efficiency. We also identified MRE-SNPs located in regions associated with complex traits, indicating possible causative mechanisms associated with these loci. The results of this study expand the current understanding of gene expression regulation and help to interpret the mechanisms underlying eQTL effects.
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Affiliation(s)
- Urmo Võsa
- Estonian Genome Center, University of Tartu, Riia 23b, 51010 Tartu, Estonia
- * E-mail:
| | - Tõnu Esko
- Estonian Genome Center, University of Tartu, Riia 23b, 51010 Tartu, Estonia
- Division of Endocrinology, Children's Hospital, Boston, MA, United States of America
- Department of Genetics, Harvard Medical School, Boston, MA, United States of America
- Broad Institute, Cambridge, MA, United States of America
| | - Silva Kasela
- Estonian Genome Center, University of Tartu, Riia 23b, 51010 Tartu, Estonia
| | - Tarmo Annilo
- Estonian Genome Center, University of Tartu, Riia 23b, 51010 Tartu, Estonia
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21
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Pu F, Shao Z, Yang S, Liu J, Lin S, Ma X, Yang H. Association between functional variants in BIRC5/survivin gene 3' untranslated region and mRNA expression in lymphoblastoid cell lines. Oncol Lett 2015; 10:2319-2322. [PMID: 26622842 DOI: 10.3892/ol.2015.3507] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 06/25/2015] [Indexed: 11/06/2022] Open
Abstract
Baculoviral inhibitor of apoptosis repeat-containing 5 (BIRC5)/survivin genetic microRNA (miRNA) binding site variants in the 3' untranslated region (3'UTR) are known to be significantly associated with cancer risk. However, the roles of genetic variants in BIRC5/survivin gene 3'UTRs and post-transcriptional regulation have not been elucidated. In the present study, we revealed that rs1042489, rs1042542, rs17882360, rs2239680, rs2661694 and rs4789560 in the BIRC5/survivin 3'UTR have potential miRNA binding sites using bioinformatics analysis. However, only rs1042489 was significantly associated with BIRC5/survivin mRNA expression in lymphoblastoid cell lines (P=0.030); rs1042489 may be a putative variant mediating the post-transcriptional regulation of the target BIRC5/survivin gene. An in-depth understanding of how 3'UTR variants regulate BIRC5/survivin activity is expected to pave the way to targeting the BIRC5/survivin pathway in cancer therapy.
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Affiliation(s)
- Feifei Pu
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Zengwu Shao
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Shuhua Yang
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Jianxiang Liu
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Song Lin
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Xiucai Ma
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Haofei Yang
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
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22
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Yuan L, Zhang TT, Ren Y. miR-27a rs895819 polymorphism and risk of cancer in Chinese population: a meta-analysis. J Evid Based Med 2015; 8:75-83. [PMID: 25976406 DOI: 10.1111/jebm.12152] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 03/24/2015] [Indexed: 02/05/2023]
Abstract
OBJECTIVE Previous studies have evaluated the association between miR-27a rs895819 polymorphism and cancer risk in Chinese population, but the results were inconclusive. The present meta-analysis was conducted to clarify these controversies. METHODS A comprehensive search was conducted to identify all relevant case-control studies of miR-27a rs895819 polymorphism and cancer risk in Chinese participants. We calculated odds ratios (ORs) with 95% confidence intervals (CIs) to assess the strength of any association. RESULTS A total of 12 case-control studies involving 2655 cases and 3106 controls were included. Overall, the results suggested that there was no significant association between miR-27a rs895819 polymorphism and cancer risk in Chinese population (OR = 1.14, 95%CI 0.86 to1.15, P = 0.85 for GG vs. AA). In the subgroup analysis by the source of controls, no significant association was found either among hospital-based group (OR = 1.16, 95%CI 0.78 to 1.73) or population-based group (OR = 1.06, 95%CI 0.74 to 1.35). However, when stratified by cancer types, we found a significant association between the polymorphism with colorectal cancer (OR = 1.56, 95%CI 1.01 to 2.40 for GG vs. AA). CONCLUSION miR-27a rs895819 polymorphism was associated with increased risk of colorectal cancer in Chinese population.
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Affiliation(s)
- Lu Yuan
- Department of Endocrinology and Metabolism, West China Hospital, Sichuan University, China
| | - Ting-ting Zhang
- Department of Endocrinology and Metabolism, West China Hospital, Sichuan University, China
| | - Yan Ren
- Department of Endocrinology and Metabolism, West China Hospital, Sichuan University, China
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23
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MicroRNA signatures in total peripheral blood of gallbladder cancer patients. Tumour Biol 2015; 36:6985-90. [PMID: 25861754 DOI: 10.1007/s13277-015-3412-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 03/30/2015] [Indexed: 12/21/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNA molecules that function as negative regulators of gene expression. Expression analysis of miRNAs can reflect the developmental lineage and differentiation state of the tumor. Thus, the miRNA profiles could play essential roles in gallbladder cancer (GBC). However, their role as novel biomarkers for the diagnosis of GBC is unclear yet. We assessed here for the first time whole-genome miRNA expression in peripheral blood samples of 40 GBC patients using microRNA microarray. We identified 11 miRNAs, which are significantly dysregulated in GBC patients in comparison to 40 healthy controls. Among these, the expression of let-7a, miR-21, miR-187, miR-143, miR-202, and miR-335 are in agreement with those measured by real-time PCR (p < 0.05). Furthermore, dysregulated miR-187, miR-143, and miR-202 demonstrate a significant correlation with clinicopathologic features (p < 0.05). Our results suggest a possible pathological relationship between the differential expression of miRNA in peripheral blood and GBC, and these dysregulated miRNAs could be novel tumor biomarkers for early detection of GBC.
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24
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Ryan BM, Robles AI, McClary AC, Haznadar M, Bowman ED, Pine SR, Brown D, Khan M, Shiraishi K, Kohno T, Okayama H, Modali R, Yokota J, Harris CC. Identification of a functional SNP in the 3'UTR of CXCR2 that is associated with reduced risk of lung cancer. Cancer Res 2014; 75:566-75. [PMID: 25480945 DOI: 10.1158/0008-5472.can-14-2101] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Global changes in gene expression accompany the development of cancer. Thus, inherited variants in miRNA-binding sites are likely candidates for conferring inherited susceptibility. Using an in silico approach, we compiled a comprehensive list of SNPs predicted to modulate miRNA binding in genes from several key lung cancer pathways. We then investigated whether these SNPs were associated with lung cancer risk in two independent populations. In general, SNPs in miRNA-binding sites are rare. However, some allelic variation was observed. We found that rs1126579 in CXCR2 was associated with a reduced risk of lung cancer in both European American [ORTT vs. CC 0.56 (0.37-0.88); P = 0.008] and Japanese [ORTT vs. CC 0.62 (0.38-1.00); P = 0.049] populations. Furthermore, we found that the SNP disrupted a novel binding site for miR-516a-3p, led to a moderate increase in CXCR2 mRNA and protein expression, and increased MAPK signaling. Moreover, analysis of rs1126579 with serum levels of IL8, its endogenous ligand, supported an interaction whereby rs1126579-T and high serum IL8 conferred synergistic protection from lung cancer. Our findings demonstrate a function for a 3'UTR SNP in modulating CXCR2 expression, signaling, and susceptibility to lung cancer.
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Affiliation(s)
- Bríd M Ryan
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Ana I Robles
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Andrew C McClary
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland. Department of Pathology, Stanford University Hospital and Clinics, Stanford, California
| | - Majda Haznadar
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Elise D Bowman
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Sharon R Pine
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, New Jersey
| | - Derek Brown
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Mohammed Khan
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Kouya Shiraishi
- Division of Genome Biology, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan
| | - Hirokazu Okayama
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland. Division of Genome Biology, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan
| | | | - Jun Yokota
- Division of Genome Biology, National Cancer Center Research Institute, Chuo-ku, Tokyo, Japan
| | - Curtis C Harris
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland.
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25
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Cipollini M, Landi S, Gemignani F. MicroRNA binding site polymorphisms as biomarkers in cancer management and research. Pharmgenomics Pers Med 2014; 7:173-91. [PMID: 25114582 PMCID: PMC4126202 DOI: 10.2147/pgpm.s61693] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs (miRNAs) are important regulators of eukaryotic gene expression. They have been implicated in a broad range of biological processes, and miRNA-related genetic alterations probably underlie several human diseases. Single nucleotide polymorphisms of transcripts may modulate the posttranscriptional regulation of gene expression by miRNAs and explain interindividual variability in cancer risk and in chemotherapy response. On the basis of recent association studies published in the literature, the present review mainly summarizes the potential role of miRNAs as molecular biomarkers for disease susceptibility, diagnosis, prognosis, and drug-response prediction in tumors. Many clues suggest a role for polymorphisms within the 3' untranslated regions of KRAS rs61764370, SET8 rs16917496, and MDM4 rs4245739 as SNPs in miRNA binding sites highly promising in the biology of human cancer. However, more studies are needed to better characterize the composite spectrum of genetic determinants for future use of markers in risk prediction and clinical management of diseases, heading toward personalized medicine.
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Affiliation(s)
| | - Stefano Landi
- Department of Biology, University of Pisa, Pisa, Italy
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Sun Z, Zhang Z, Liu Z, Qiu B, Liu K, Dong G. MicroRNA-335 inhibits invasion and metastasis of colorectal cancer by targeting ZEB2. Med Oncol 2014; 31:982. [PMID: 24829139 DOI: 10.1007/s12032-014-0982-8] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 04/25/2014] [Indexed: 12/01/2022]
Abstract
MicroRNAs have been suggested to play a vital role in regulate tumor progression and invasion. However, the expression of miR-335 in colorectal cancer (CRC) and its clinical significance are not known. Here, we report that miR-335 is a tumor suppressor by regulating expression of ZEB2. In this study, we showed that downregulated miR-335 levels in highly invasive CRC cell lines and tissues. Kaplan-Meier survival analysis indicated that patients with reduced miR-335 had a poor overall survival. Furthermore, enhancing the expression of miR-335 inhibited CRC cell migration and invasion in vitro and lung and liver metastasis in vivo, while silencing its expression resulted in increased migration and invasion. Additionally, we identified a novel miR-335 target, ZEB2, and the direct interaction between them was verified by 3'-untranslated region dual-luciferase reporter assay. In conclusion, our results demonstrate that miR-335 functions as a tumor suppressor and play a role in inhibiting metastasis of CRC cells through targeting ZEB2. These findings suggest that miR-335 may be useful as a new potential therapeutic target for CRC.
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Affiliation(s)
- ZhiFeng Sun
- Department of Gastrointestinal Surgery, Xi Jing Digestive Hospital, Fourth Military Medical University, Xi'an, Shan Xi Province, China
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He F, Zheng LL, Luo WT, Yang R, Xu XQ, Cai L. Inferring Single Nucleotide Polymorphisms in MicroRNA Binding Sites of Lung Cancer-related Inflammatory Genes. Asian Pac J Cancer Prev 2014; 15:3601-6. [DOI: 10.7314/apjcp.2014.15.8.3601] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Chen X, Chen S, Hang W, Huang H, Ma H. MiR-95 induces proliferation and chemo- or radioresistance through directly targeting sorting nexin1 (SNX1) in non-small cell lung cancer. Biomed Pharmacother 2014; 68:589-95. [PMID: 24835695 DOI: 10.1016/j.biopha.2014.04.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 04/16/2014] [Indexed: 10/25/2022] Open
Abstract
MicroRNAs are emerging as a class of small regulatory RNAs whose specific roles and significant functions in the majority of carcinomas have yet to be entirely illustrated. The aim of this study is to explore the effect of miR-95 and determine whether miR-95 could be a potential therapeutic target for human non-small cell lung cancer. First of all, our study showed that miR-95 was highly expressed in both NSCLC cell lines (compared with normal cells) and tumor tissues (compared with corresponding normal tissues), whereas the protein level of SNX1 was downregulated in NSCLC cell lines. Next, we found that ectopic overexpression of miR-95 in A549 or H226 contributed to tumor growth in xenograft mouse models. In addition, the results also indicated that upregulation of miR-95 could significantly enhance the susceptibilities of NSCLC cells to chemo- or radiotherapy. Furthermore, using the luciferase reporter, we demonstrated that SNX1 is a direct target of miR-95. Meanwhile, overexpression of SNX1 could abrogate the growth of NSCLC cells induced by miR-95. Taken together, these results suggest that miR-95 functions as an oncogene role in NSCLC cells by directly targeting SNX1.
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Affiliation(s)
- Xiaochun Chen
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou 215006, Jiangsu Province, People's Republic of China
| | - Shaomu Chen
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou 215006, Jiangsu Province, People's Republic of China
| | - Weijie Hang
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou 215006, Jiangsu Province, People's Republic of China
| | - Haitao Huang
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou 215006, Jiangsu Province, People's Republic of China
| | - Haitao Ma
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou 215006, Jiangsu Province, People's Republic of China.
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Trott JF, Freking BA, Hovey RC. Variation in the coding and 3′ untranslated regions of the porcine prolactin receptor short form modifies protein expression and function. Anim Genet 2013; 45:74-86. [DOI: 10.1111/age.12100] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2013] [Indexed: 12/31/2022]
Affiliation(s)
- Josephine F. Trott
- Department of Animal Science; University of California, Davis; One Shields Ave Davis CA 95616 USA
| | - Bradley A. Freking
- USDA, ARS; US Meat Animal Research Center; PO Box 166 Clay Center NE 68933 USA
| | - Russell C. Hovey
- Department of Animal Science; University of California, Davis; One Shields Ave Davis CA 95616 USA
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Peng HH, Zhang YD, Gong LS, Liu WD, Zhang Y. Increased expression of microRNA-335 predicts a favorable prognosis in primary gallbladder carcinoma. Onco Targets Ther 2013; 6:1625-30. [PMID: 24250228 PMCID: PMC3829675 DOI: 10.2147/ott.s53030] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Background MicroRNAs (miRNAs) display aberrant expression patterns and functional abnormalities in many types of cancer. However, their roles in primary gallbladder carcinoma (PGC) have not been well documented. miR-335 has been demonstrated to be involved in tumorigenesis of several cancers in the digestive system. The aim of this study was to investigate the clinical significance of miR-335 in PGC. Methods miR-335 expression in 166 human PGC tissues and matched adjacent nondysplastic gallbladder epithelia was measured by real-time quantitative polymerase chain reaction (RT-PCR) assay. Results The expression level of miR-335 was significantly lower in PGC tissues than that in nondysplastic gallbladder epithelia (P<0.001). Of 166 PGC patients, 96 (57.83%) had reduced expression of miR-335. Additionally, the expression of miR-335 was significantly lower in PGC tissues with high histologic grade (P=0.02), advanced pathologic T stage (P=0.009) and clinical stage (P=0.008), and with positive lymph node metastasis (P=0.001). In univariate analysis by log-rank test, histologic grade (P=0.03), pathologic T stage (P=0.008), clinical stage (P=0.01), lymph node metastasis (P<0.001), and miR-335 expression (P<0.001) were significant prognostic factors for overall survival of PGC patients. Multivariate analysis further revealed that pathologic T stage (P=0.02), lymph node metastasis (P=0.008), and miR-335 expression (P=0.006) maintained independent prognostic influence on overall survival. Conclusion This study offers convincing evidence for the first time that miR-335 was downregulated in a majority of PGC patients and may be associated with the aggressive tumor behaviors. Loss of miR-335 expression may be a useful marker for clinical outcome and a therapeutic target for PGC.
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Affiliation(s)
- Hong-Hua Peng
- Department of Oncology, Third Xiangya Hospital, Central South University, Changsha, People's Republic of China
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Zhu Y, Li Y, Zhu S, Tang R, Liu Y, Li J. Association of survivin polymorphisms with tumor susceptibility: a meta-analysis. PLoS One 2013; 8:e74778. [PMID: 24098667 PMCID: PMC3787000 DOI: 10.1371/journal.pone.0074778] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 08/06/2013] [Indexed: 12/25/2022] Open
Abstract
Background The survivin polymorphisms have been shown to confer genetic susceptibility to various tumors, but the results are inconsistent. In order to accomplish a more precise estimation of the relationship, a meta-analysis was performed. Results For rs9904341, a significantly increased tumor risk was found in overall meta-analysis under C/C vs. G/G (OR = 1.40, 95% CI = 1.13–1.74, p = 0.002), dominant (OR = 1.18, 95% CI = 1.01–1.38, p = 0.039) and recessive (OR = 1.34, 95% CI = 1.13–1.58, p = 0.001) genetic models and Asians group. In subgroup analyses of tumor types, we found a significant association between this SNP and an increased risk of gastric, colorectal, bladder and other tumors as well as a decreased risk of hepatocellular cancer. For rs17878467, a significantly decreased tumor risk was identified in overall meta-analysis for allele contrast (T vs. C: OR = 0.69, 95% CI = 0.51–0.92, p = 0.012), C/T vs. C/C (OR = 0.61, 95% CI = 0.42–0.88, p = 0.009) and dominant (OR = 0.62, 95% CI = 0.43–0.88, p = 0.007) genetic models and Asians group. For rs2071214, we found a significant association between this SNP and an increased tumor risk in overall meta-analysis under G/G vs. A/A (OR = 1.51, 95% CI = 1.04–2.18, p = 0.029) and recessive (OR = 1.54, 95% CI = 1.07–2.22, p = 0.020) genetic models and Asians group. Besides, there was a significant association of rs8073069 with an increased tumor risk under recessive genetic model (OR = 1.37, 95% CI = 1.01–1.84, p = 0.040), while no significant association between rs1042489 and tumor risk was detected. Conclusions The survivin rs9904341 most likely contributed to increased susceptibility to tumor in Asians as well as to gastric, colorectal and bladder cancers. As for rs17878467, the T allele might be a protective factor for tumor, especially in Asians. Moreover, the survivin rs8073069 and rs2071214 seemed to be associated with an increased tumor risk in Asians, while there was no association between the survivin rs1042489 and tumor risk.
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Affiliation(s)
- Ying Zhu
- Department of Forensic Medicine, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing, China
| | - Yongguo Li
- Department of Forensic Medicine, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing, China
| | - Shisheng Zhu
- Department of Forensic Medicine, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing, China
| | - Renkuan Tang
- Department of Forensic Medicine, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing, China
| | - Yunzhi Liu
- Department of Forensic Medicine, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing, China
| | - Jianbo Li
- Department of Forensic Medicine, Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing, China
- * E-mail:
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Zhang WC, Liu J, Xu X, Wang G. The role of microRNAs in lung cancer progression. Med Oncol 2013; 30:675. [PMID: 23925663 DOI: 10.1007/s12032-013-0675-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 07/21/2013] [Indexed: 12/31/2022]
Abstract
Lung cancer is a heterogeneous disease with currently still unknown mechanisms of development. Besides genetic and epigenetic mechanisms, microRNAs (miRNAs) have recently been discovered as one of the crucial players in lung carcinogenesis through posttranscriptional regulation of tumor suppressor and oncogenes. A substantial number of deregulated miRNAs have been revealed in lung cancer, and the biological significance of those miRNAs has been confirmed in multiple functional experiments. A growing number of studies suggest involvement of miRNAs in various steps of lung carcinogenesis. Great biological stability of miRNAs opens novel fields in biomarker research with potential clinical implementation in screening, diagnosis and prediction of prognosis. In this review, we provide the basic knowledge of miRNA biogenesis and discuss extensively the role of miRNAs in lung carcinogenesis, including potential translational clinical implementations.
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Affiliation(s)
- Wen-Cheng Zhang
- Department of Oncology, Bao Di Hospital, Bao Di Clinical College of Tianjin Medical University, Guang Chuan road, Bao Di, Tianjin, People's Republic of China
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