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Jiang H, Wang S, Liu Y, Zheng C, Chen L, Zheng K, Xu Z, Dai Y, Jin H, Cheng Z, Zou C, Fu L, Liu K, Ma X. Targeting EFNA1 suppresses tumor progression via the cMYC-modulated cell cycle and autophagy in esophageal squamous cell carcinoma. Discov Oncol 2023; 14:64. [PMID: 37160815 PMCID: PMC10169935 DOI: 10.1007/s12672-023-00664-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/19/2023] [Indexed: 05/11/2023] Open
Abstract
PURPOSE Esophageal squamous cell carcinoma (ESCC) remains one of the most common causes of cancer death due to the lack of effective therapeutic options. New targets and the targeted drugs are required to be identified and developed. METHODS Highly expressed genes in ESCA were identified using the edgeR package from public datasets. Immunostaining assay verified the high expression level of EFNA1 in ESCC. CCK-8, colony formation and wound healing assays were performed to examine the role of EFNA1 and EPHA2 in ESCC progression. Cell cycle was analyzed by flow cytometry and autophagy activation was determined by autophagolysosome formation using transmission electron microscopy. The small molecule targeting to EFNA1 was identified by molecular docking and the anti-tumor effects were verified by in vitro and in vivo models with radiation treatment. RESULTS EFNA1 was highly expressed in esophageal cancer and significantly associated with poor prognosis. Downregulation of EFNA1 remarkably inhibited cell proliferation and migration. Furthermore, decreased EFNA1 significantly suppressed the expression of cMYC along with its representative downstream genes involved in cell cycle, and activated autophagy. Similar effects on ESCC progression were obtained from knockdown of the corresponding receptor, EPHA2. The potential small molecule targeting to EFNA1, salvianolic acid A (SAA), could significantly suppress ESCC progression and increase the sensitivity to radiotherapy. CONCLUSION We revealed that EFNA1 facilitated the ESCC progression via the possible mechanism of activating cMYC-modulated cell proliferation and suppressing autophagy, and identified SAA as a potential drug targeting EFNA1, providing new options for the future treatments for ESCC patients.
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Affiliation(s)
- Houxiang Jiang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, 241001, Anhui, China
- Anhui Province Clinical Research Center for Critical Respiratory Medicine, Wuhu, 241001, Anhui, China
| | - Shaoxiang Wang
- School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen, 518060, China
| | - Ying Liu
- Guangdong Provincial Clinical Research Center for Geriatrics, Shenzhen Clinical Research Center for Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College of Jinan University), Shenzhen, 518020, Guangdong, China
| | - Chaopan Zheng
- Department of Otolaryngology, Shenzhen People's Hospital (The Second Clinical Medical College of Jinan University), Shenzhen, 518020, Guangdong, China
| | - Lipeng Chen
- Guangdong Provincial Clinical Research Center for Geriatrics, Shenzhen Clinical Research Center for Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College of Jinan University), Shenzhen, 518020, Guangdong, China
| | - Kai Zheng
- School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen, 518060, China
| | - Zhenyu Xu
- Precision Medicine Center, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, 241001, Anhui, China
| | - Yong Dai
- Guangdong Provincial Clinical Research Center for Geriatrics, Shenzhen Clinical Research Center for Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College of Jinan University), Shenzhen, 518020, Guangdong, China
| | - Hongtao Jin
- Department of Pathology, Shenzhen People's Hospital (The Second Clinical Medical College of Jinan University), Shenzhen, 518020, Guangdong, China
| | - Zhiqiang Cheng
- Department of Pathology, Shenzhen People's Hospital (The Second Clinical Medical College of Jinan University), Shenzhen, 518020, Guangdong, China
| | - Chang Zou
- Guangdong Provincial Clinical Research Center for Geriatrics, Shenzhen Clinical Research Center for Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College of Jinan University), Shenzhen, 518020, Guangdong, China
- School of Medicine, Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, 518172, Guangdong, China
| | - Li Fu
- Department of Pharmacology, Shenzhen University School of Medicine, Shenzhen, 518060, Guangdong, China.
| | - Kaisheng Liu
- Guangdong Provincial Clinical Research Center for Geriatrics, Shenzhen Clinical Research Center for Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College of Jinan University), Shenzhen, 518020, Guangdong, China.
| | - Xiaoshi Ma
- Department of Urology, Shenzhen People's Hospital (The Second Clinical Medical College of Jinan University), Shenzhen, 518020, Guangdong, China.
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Chu LY, Huang BL, Huang XC, Peng YH, Xie JJ, Xu YW. EFNA1 in gastrointestinal cancer: Expression, regulation and clinical significance. World J Gastrointest Oncol 2022; 14:973-988. [PMID: 35646281 PMCID: PMC9124989 DOI: 10.4251/wjgo.v14.i5.973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 09/17/2021] [Accepted: 04/04/2022] [Indexed: 02/06/2023] Open
Abstract
Ephrin-A1 is a protein that in humans is encoded by the EFNA1 gene. The ephrins and EPH-related receptors comprise the largest subfamily of receptor protein-tyrosine kinases which play an indispensable role in normal growth and development or in the pathophysiology of various tumors. The role of EFNA1 in tumorigenesis and development is complex and depends on the cell type and microenvironment which in turn affect the expression of EFNA1. This article reviews the expression, prognostic value, regulation and clinical significance of EFNA1 in gastrointestinal tumors.
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Affiliation(s)
- Ling-Yu Chu
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, Guangdong Province, China
| | - Bin-Liang Huang
- Department of Clinical Laboratory Medicine, The Cancer Hospital of Shantou University Medical College, Shantou 515041, Guangdong Province, China
| | - Xu-Chun Huang
- Department of Clinical Laboratory Medicine, The Cancer Hospital of Shantou University Medical College, Shantou 515041, Guangdong Province, China
| | - Yu-Hui Peng
- Department of Clinical Laboratory Medicine, The Cancer Hospital of Shantou University Medical College, Shantou 515041, Guangdong Province, China
- Guangdong Esophageal Cancer Research Institute, The Cancer Hospital of Shantou University Medical College, Shantou 515041, Guangdong Province, China
| | - Jian-Jun Xie
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, Guangdong Province, China
| | - Yi-Wei Xu
- Department of Clinical Laboratory Medicine, The Cancer Hospital of Shantou University Medical College, Shantou 515041, Guangdong Province, China
- Guangdong Esophageal Cancer Research Institute, The Cancer Hospital of Shantou University Medical College, Shantou 515041, Guangdong Province, China
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Alsheikh AJ, Wollenhaupt S, King EA, Reeb J, Ghosh S, Stolzenburg LR, Tamim S, Lazar J, Davis JW, Jacob HJ. The landscape of GWAS validation; systematic review identifying 309 validated non-coding variants across 130 human diseases. BMC Med Genomics 2022; 15:74. [PMID: 35365203 PMCID: PMC8973751 DOI: 10.1186/s12920-022-01216-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 03/17/2022] [Indexed: 02/08/2023] Open
Abstract
Background The remarkable growth of genome-wide association studies (GWAS) has created a critical need to experimentally validate the disease-associated variants, 90% of which involve non-coding variants. Methods To determine how the field is addressing this urgent need, we performed a comprehensive literature review identifying 36,676 articles. These were reduced to 1454 articles through a set of filters using natural language processing and ontology-based text-mining. This was followed by manual curation and cross-referencing against the GWAS catalog, yielding a final set of 286 articles. Results We identified 309 experimentally validated non-coding GWAS variants, regulating 252 genes across 130 human disease traits. These variants covered a variety of regulatory mechanisms. Interestingly, 70% (215/309) acted through cis-regulatory elements, with the remaining through promoters (22%, 70/309) or non-coding RNAs (8%, 24/309). Several validation approaches were utilized in these studies, including gene expression (n = 272), transcription factor binding (n = 175), reporter assays (n = 171), in vivo models (n = 104), genome editing (n = 96) and chromatin interaction (n = 33). Conclusions This review of the literature is the first to systematically evaluate the status and the landscape of experimentation being used to validate non-coding GWAS-identified variants. Our results clearly underscore the multifaceted approach needed for experimental validation, have practical implications on variant prioritization and considerations of target gene nomination. While the field has a long way to go to validate the thousands of GWAS associations, we show that progress is being made and provide exemplars of validation studies covering a wide variety of mechanisms, target genes, and disease areas. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01216-w.
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Affiliation(s)
- Ammar J Alsheikh
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA.
| | - Sabrina Wollenhaupt
- Information Research, AbbVie Deutschland GmbH & Co. KG, 67061, Knollstrasse, Ludwigshafen, Germany
| | - Emily A King
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - Jonas Reeb
- Information Research, AbbVie Deutschland GmbH & Co. KG, 67061, Knollstrasse, Ludwigshafen, Germany
| | - Sujana Ghosh
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | | | - Saleh Tamim
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - Jozef Lazar
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - J Wade Davis
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - Howard J Jacob
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
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Xie R, Yuan M, Jiang Y. The Pan-Cancer Crosstalk Between the EFNA Family and Tumor Microenvironment for Prognosis and Immunotherapy of Gastric Cancer. Front Cell Dev Biol 2022; 10:790947. [PMID: 35309935 PMCID: PMC8924469 DOI: 10.3389/fcell.2022.790947] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 02/08/2022] [Indexed: 12/24/2022] Open
Abstract
Background: EFNA1-5 have important physiological functions in regulating tumorigenesis and metastasis. However, correlating EFNA genes in the tumor immune microenvironment (TIME), and the prognosis of patients with gastric cancer remains to be determined. Methods: Using public databases, the expression of EFNA1-5 in pan-cancer and gastric cancer was comprehensively analyzed using UCSC Xena, the Oncomine dataset and UALCAN. We further completed survival analysis by Kaplan-Meier plotter to evaluate the prognosis of the high and low expression groups of the EFNAs gene in patients with gastric cancer. The TIMER tool was used to reveal the correlation between immune cell infiltration and genes of interest. Spearman correlation was used to find an association between the EFNA genes and tumor stem cells, TIME, microsatellite instability (MSI) or tumor mutational burden (TMB). We also used cBioportal, GeneMANIA and STRINGS to explore the types of changes in these genes and the protein interactions. Finally, we described the TIME based on QUANTISEQ algorithm, predicted the relationship between the EFNA genes and half-maximal inhibitory concentration (IC50), and analyzed the relationship between the EFNA family genes and immune checkpoints. Results: The expression of EFNA1, EFNA3, EFNA4, and EFNA5 was elevated in pan-cancer. Compared with normal adjacent tissues, EFNA1, EFNA3, and EFNA4 were up-regulated in gastric cancer. In terms of the influence on the survival of patients, the expression of EFNA3 and EFNA4 were related to overall survival (OS) and disease-free survival (DFS) for patients with gastric cancer. High expression of EFNA5 often predicted poor OS and DFS. In gastric cancer, the expression of EFNA3 and EFNA4 showed a significant negative correlation with B cells. The higher the expression of EFNA5, the higher the abundance of B cells, CD4+T cells and macrophages. CD8+T cells, dendritic cells infiltration and EFNA1-4 expression were negatively correlated. The infiltration of CD4+T cells, macrophages and neutrophils was negatively correlated with the expression of EFNA1, EFNA3, and EFNA4. TMB and MSI were positively correlated with EFNA3/EFNA4 expression. In the tumor microenvironment and drug sensitivity, EFNA3/4/5 also showed a significant correlation. In addition, we explored the relationship between the EFNA family genes and the immune microenvironment (B cells, M2 macrophages, monocytes, CD8+ T cells, regulatory T cells, myeloid dendritic cells, natural killer cells, non-regulatory CD4+ T cells), immune checkpoint (PDCD1, PDCD1LG2, CD274, CTLA4), and IC50 of common chemotherapeutic drugs for gastric cancer (5-fluorouracil, cisplatin, docetaxel and gemcitabine). Conclusions: Our study provides new ideas for tumor treatment and prognosis from the perspective of TIME, and nominates EFNA1-5 to become potential therapeutic targets for gastric cancer.
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Affiliation(s)
- Rongrong Xie
- Department of Radiotherapy, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Mengping Yuan
- Department of Gastroenterology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yiyan Jiang
- Department of Medical Oncology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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Pleiotropic Effects of Functional MUC1 Variants on Cardiometabolic, Renal, and Hematological Traits in the Taiwanese Population. Int J Mol Sci 2021; 22:ijms221910641. [PMID: 34638981 PMCID: PMC8509060 DOI: 10.3390/ijms221910641] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 09/09/2021] [Accepted: 09/27/2021] [Indexed: 12/27/2022] Open
Abstract
MUC1 is a transmembrane mucin involved in carcinogenesis and cell signaling. Functional MUC1 variants are associated with multiple metabolic and biochemical traits. This study investigated the association of functional MUC1 variants with MUC1 DNA methylation and various metabolic, biochemical, and hematological parameters. In total, 80,728 participants from the Taiwan Biobank were enrolled for association analysis using functional MUC1 variants and a nearby gene regional plot association study. A subgroup of 1686 participants was recruited for MUC1 DNA methylation analysis. After Bonferroni correction, we found that two MUC1 variants, rs4072037 and rs12411216, were significantly associated with waist circumference, systolic blood pressure, hemoglobin A1C, renal functional parameters (blood urea nitrogen, serum creatinine levels, and estimated glomerular filtration rate), albuminuria, hematocrit, hemoglobin, red blood cell count, serum uric acid level, and gout risk, with both favorable and unfavorable effects. Causal inference analysis revealed that the association between the variants and gout was partially dependent on the serum uric acid level. Both gene variants showed genome-wide significant associations with MUC1 gene-body methylation. Regional plot association analysis further revealed lead single-nucleotide polymorphisms situated at the nearby TRIM46-MUC1-THBS3-MTX1 gene region for the studied phenotypes. In conclusion, our data demonstrated the pleiotropic effects of MUC1 variants with novel associations for gout, red blood cell parameters, and MUC1 DNA methylation. These results provide further evidence in understanding the critical role of TRIM46-MUC1-THBS3-MTX1 gene region variants in the pathogenesis of cardiometabolic, renal, and hematological disorders.
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6
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Pu Y, Wen X, Jia Z, Xie Y, Luan C, Yu Y, Chen F, Chen P, Li D, Sun Y, Zhao J, Lv H. Association Between Polymorphisms in Gastric Cancer Related Genes and Risk of Gastric Cancer: A Case-Control Study. Front Mol Biosci 2021; 8:690665. [PMID: 34079823 PMCID: PMC8166284 DOI: 10.3389/fmolb.2021.690665] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 04/30/2021] [Indexed: 11/13/2022] Open
Abstract
Gastric cancer has the second highest incidence among all the malignancies in China, just below lung cancer. Gastric cancer is likewise one of the main sources of cancer related passings. Gastric cancer therefore remains a huge threat to human health. The primary reason is absence of high sensitivity and specificity for early detection while the pathogenesis of GC is stayed muddled. During the last few decades, a lot of GC related genes have been identified. To find candidate GC related variant in these GC related genes, we conducted this case-control study. 29 tagSNPs located in 7 GC related genes were included. 228 gastric cancer patients and 299 healthy controls were enrolled. Significant differences were found between the genotype frequencies of EFNA1 rs4971066 polymorphism between gastric cancer patients and healthy controls. The result indicated that ephrin-A1 tagSNP rs4971066 GT/TT genotypes was significantly associated with reduced susceptibility of gastric cancer development.
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Affiliation(s)
- Yan Pu
- School of Medicine, Southeast University, Nanjing, China
| | - Xu Wen
- Department of General Surgery, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Zhangjun Jia
- Department of Clinical Laboratory, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Yu Xie
- Department of Geriatrics, Affiliated Nanjing Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Changxing Luan
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, China
| | - Youjia Yu
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, China
| | - Feng Chen
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, China
| | - Peng Chen
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, China
| | - Ding Li
- Department of Forensic Medicine, Nanjing Medical University, Nanjing, China
| | - Yan Sun
- Department of Medical Oncology, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Jian Zhao
- Department of Radiation Oncology, Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Haiqin Lv
- School of Medicine, Southeast University, Nanjing, China
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7
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Association of Epidermal Growth Factor 61A>G, Survivin -31G>C, and EFNA1 -1732G>A Polymorphisms with Susceptibility to Colorectal Cancer. J Gastrointest Cancer 2020; 53:78-83. [PMID: 33180239 DOI: 10.1007/s12029-020-00551-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/05/2020] [Indexed: 10/23/2022]
Abstract
BACKGROUND Genetic polymorphisms play an important role in the development of colorectal cancer (CRC). Functional variants in the epidermal growth factor (EGF), survivin, and Ephrin A1 (EFNA1) genes have been previously reported to play a potential role in susceptibility to CRC, but these polymorphisms have not been well replicated. The aim of this study was to assess the association of the EGF 61A>G, Survivin -31G>C, and EFNA1 -1732G>A polymorphisms with the susceptibility to CRC in an Iranian population. METHODS A total of 148 cases diagnosed with CRC and 160 healthy subjects were recruited. The EGF 61A>G, survivin -31G>C, and EFNA1 -1732G>A polymorphisms were genotyped using a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay. RESULTS Our data revealed that the homozygous mutant genotype (CC: OR = 2.895, 95% CI = 1.092-7.673, p = 0.033) and mutant allele (C: OR = 1.629, 95% CI = 1.152-2.303, p = 0.006) of the survivin -31G>C were associated with an increased risk of CRC in the Iranian population. However, our results failed to show an association between the EGF 61A>G and EFNA1 -1732G>A polymorphisms and CRC risk. CONCLUSION Our results revealed that the survivin -31G>C polymorphism might play an important role in development of CRC in Iranian population. However, no association of EGF 61A>G and EFNA1 -1732G>A polymorphisms with CRC risk was found.
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8
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Hao Y, Li G. Role of EFNA1 in tumorigenesis and prospects for cancer therapy. Biomed Pharmacother 2020; 130:110567. [PMID: 32745910 DOI: 10.1016/j.biopha.2020.110567] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 07/14/2020] [Accepted: 07/26/2020] [Indexed: 12/14/2022] Open
Abstract
Cancer is one of the major threats to human health. It is of vital importance to reveal the mechanisms of tumorigenesis, identify effective biomarkers and develop novel treatments to improve patient outcome. EFNA1 (ephrinA1) is a member of the EFN family, and it has been studied extensively since its discovery in 1990. Increasing evidence indicates that EFNA1 plays a pivotal role in the pathogenesis of tumors. We provide a detailed overview of the expression and prognostic value of EFNA1 in different types of human malignancies. We briefly discuss the mechanisms of EFNA1 induction in hypoxic environments and its pro-angiogenic function in different cancer cells. We describe the effects of EFNA1 on tumor growth, invasiveness and metastasis. We summarize recent advances in EFNA1-associated cancer therapeutics with emphasis on the prospect of novel anti-tumor methods based on EFNA1.
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Affiliation(s)
- Yongping Hao
- Department of Radiation Oncology, The First Affiliated Hospital of China Medical University, Liaoning, 110001, China.
| | - Guang Li
- Department of Radiation Oncology, The First Affiliated Hospital of China Medical University, Liaoning, 110001, China.
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9
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Guo F, Yuan Y. Tumor Necrosis Factor Alpha-Induced Proteins in Malignant Tumors: Progress and Prospects. Onco Targets Ther 2020; 13:3303-3318. [PMID: 32368089 PMCID: PMC7182456 DOI: 10.2147/ott.s241344] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 03/04/2020] [Indexed: 12/14/2022] Open
Abstract
Tumor necrosis factor (TNF) is the first cytokine used in tumor biotherapy, but TNF-related drugs are limited by the lack of specific targets. Tumor necrosis factor alpha-induced proteins (TNFAIPs), derived from TNF, is a protein family and participates in proliferation, invasion and metastasis of tumor cells. In order to better understand biological functions and potential roles of TNFAIPs in malignant tumors, this paper in the form of “Gene–Protein–Tumor correlation” summarizes the biological characteristics, physiological functions and mechanisms of TNFAIPs by searching National Center of Biotechnology Information, GeneCards, UniProt and STRING databases. The relationship between TNFAIPs and malignant tumors is analyzed, and protein–protein interaction diagram in members of TNFAIPs is drawn based on TNF for the first time. We find that TNF as a key factor is related to TNFAIP1, TNFAIP3, TNFAIP5, TNFAIP6, TNFAIP8 and TNFAIP9, which can be directly involved in activating TNFAIP1, TNFAIP5, TNFAIP8 and TNFAIP9. We confirm that the mechanism of TNFAIP1, TNFAIP2 and TNFAIP3 inducing tumors may be related to NF-κB signaling pathway, but the mechanism of tumor induction by other members of TNFAIPs is not clear. In the future, translational studies are needed to explore the mechanisms of TNF-TNFAIPs-tumors.
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Affiliation(s)
- Fang Guo
- Liaoning Provincial Education Department, Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, and Key Laboratory of Cancer Etiology and Prevention (China Medical University), Shenyang City, Liaoning Province, People's Republic of China.,Department of Oncology, PLA Cancer Center, General Hospital of Northern Theater Command, Shenyang City, Liaoning Province, People's Republic of China
| | - Yuan Yuan
- Liaoning Provincial Education Department, Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, and Key Laboratory of Cancer Etiology and Prevention (China Medical University), Shenyang City, Liaoning Province, People's Republic of China
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10
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Zeng ZN, Liu LL, He YL, Shi X, Wei YS. A functional variant rs12904 in the miR-200c binding site was associated with a decreased risk of ischemic stroke. Lipids Health Dis 2019; 18:110. [PMID: 31077198 PMCID: PMC6511201 DOI: 10.1186/s12944-019-1060-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 04/29/2019] [Indexed: 11/10/2022] Open
Abstract
Genome-wide association study (GWAS) identified chromosome 12p13 rs12425791 and rs11833579 as susceptibility loci of ischemic stroke (IS) in a European population. However, conflicting results were obtained in subsequent replication analysis. miR-200c, located on chromosome 12p13, was found to have a neuroprotective effect on ischemia. Our aim of this study was to investigate the association of the rs12425791, rs11833579 and rs12904 in the binding site of miR-200c with the risk of IS. The rs12425791, rs11833579, and rs12904 were genotyped using a TaqMan allelic discrimination assay. The results were verified by Sanger sequencing. We found that the rs12904 AG/GG genotypes and G allele were associated with a decreased risk of IS (AG/GG vs. AA: adjusted OR = 0.64; 95% CI, 0.44-0.95; G vs. A: adjusted OR = 0.65; 95% CI, 0.46-0.93). The combined genotypes of the rs11833579AG/AA and rs12904AG/GG were also associated with a reduced risk of IS (OR = 0.65; 95% CI, 0.46-0.93). These findings suggest that the rs12904 may have a jointly protective effect against the risk of IS.
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Affiliation(s)
- Zhi-Neng Zeng
- Department of Clinical Laboratory, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi, China
| | - Ling-Ling Liu
- Department of Neonatology, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi, China
| | - Yong-Ling He
- Department of Clinical Laboratory, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi, China
| | - Xiang Shi
- Department of Clinical Laboratory, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi, China
| | - Ye-Sheng Wei
- Department of Clinical Laboratory, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi, China.
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Alur VC, Raju V, Vastrad B, Vastrad C. Mining Featured Biomarkers Linked with Epithelial Ovarian CancerBased on Bioinformatics. Diagnostics (Basel) 2019; 9:diagnostics9020039. [PMID: 30970615 PMCID: PMC6628368 DOI: 10.3390/diagnostics9020039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/31/2019] [Accepted: 04/05/2019] [Indexed: 11/16/2022] Open
Abstract
Epithelial ovarian cancer (EOC) is the18th most common cancer worldwide and the 8th most common in women. The aim of this study was to diagnose the potential importance of, as well as novel genes linked with, EOC and to provide valid biological information for further research. The gene expression profiles of E-MTAB-3706 which contained four high-grade ovarian epithelial cancer samples, four normal fallopian tube samples and four normal ovarian epithelium samples were downloaded from the ArrayExpress database. Pathway enrichment and Gene Ontology (GO) enrichment analysis of differentially expressed genes (DEGs) were performed, and protein-protein interaction (PPI) network, microRNA-target gene regulatory network and TFs (transcription factors) -target gene regulatory network for up- and down-regulated were analyzed using Cytoscape. In total, 552 DEGs were found, including 276 up-regulated and 276 down-regulated DEGs. Pathway enrichment analysis demonstrated that most DEGs were significantly enriched in chemical carcinogenesis, urea cycle, cell adhesion molecules and creatine biosynthesis. GO enrichment analysis showed that most DEGs were significantly enriched in translation, nucleosome, extracellular matrix organization and extracellular matrix. From protein-protein interaction network (PPI) analysis, modules, microRNA-target gene regulatory network and TFs-target gene regulatory network for up- and down-regulated, and the top hub genes such as E2F4, SRPK2, A2M, CDH1, MAP1LC3A, UCHL1, HLA-C (major histocompatibility complex, class I, C), VAT1, ECM1 and SNRPN (small nuclear ribonucleoprotein polypeptide N) were associated in pathogenesis of EOC. The high expression levels of the hub genes such as CEBPD (CCAAT enhancer binding protein delta) and MID2 in stages 3 and 4 were validated in the TCGA (The Cancer Genome Atlas) database. CEBPD andMID2 were associated with the worst overall survival rates in EOC. In conclusion, the current study diagnosed DEGs between normal and EOC samples, which could improve our understanding of the molecular mechanisms in the progression of EOC. These new key biomarkers might be used as therapeutic targets for EOC.
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Affiliation(s)
- Varun Chandra Alur
- Department of Endocrinology, J.J. M Medical College, Davanagere, Karnataka 577004, India.
| | - Varshita Raju
- Department of Obstetrics and Gynecology, J.J. M Medical College, Davanagere, Karnataka 577004, India.
| | - Basavaraj Vastrad
- Department of Pharmaceutics, SET`S College of Pharmacy, Dharwad, Karnataka 580002, India.
| | - Chanabasayya Vastrad
- Biostatistics and Bioinformatics,Chanabasava Nilaya, Bharthinagar,Dharwad, Karanataka 580001, India.
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Zhou ZX, Zhang ZP, Tao ZZ, Tan TZ. miR-632 Promotes Laryngeal Carcinoma Cell Proliferation, Migration, and Invasion Through Negative Regulation of GSK3β. Oncol Res 2018; 28:21-31. [PMID: 29562960 PMCID: PMC7851529 DOI: 10.3727/096504018x15213142076069] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Laryngeal cancer, one of the most common head and neck malignancies, is an aggressive neoplasm. Increasing evidence has demonstrated that microRNAs (miRNAs) exert important roles in oncogenesis and progression of diverse types of human cancers. miR-632, a tumor-related miRNA, has been reported to be dysregulated and implicated in human malignancies; however, its biological role in laryngeal carcinoma remains to be elucidated. The present study aimed at exploring the role of miR-632 in laryngeal cancer and clarifying the potential molecular mechanisms involved. In the current study, miR-632 was found to be significantly upregulated both in laryngeal cancer tissues and laryngeal cancer cell lines. Functional studies demonstrated that miR-632 accelerated cell proliferation and colony formation, facilitated cell migration and invasion, and enhanced the expression of cell proliferation-associated proteins, cyclin D1 and c-myc. Notably, miR-632 could directly bind to the 3′-untranslated region (3′-UTR) of glycogen synthase kinase 3β (GSK3β) to suppress its expression in laryngeal cancer cells. Mechanical studies revealed that miR-632 promoted laryngeal cancer cell proliferation, migration, and invasion through negative modulation of GSK3β. Pearson’s correlation analysis revealed that miR-632 expression was inversely correlated with GSK3β mRNA expression in laryngeal cancer tissues. Taken together, our findings suggest that miR-632 functions as an oncogene in laryngeal cancer and may be used as a novel therapeutic target for laryngeal cancer.
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Affiliation(s)
- Zhong-Xin Zhou
- Department of Otorhinolaryngology, Renmin Hospital of Wuhan UniversityWuhan, HubeiP.R. China
| | - Zu-Ping Zhang
- Department of Otorhinolaryngology, Liaocheng People's HospitalLiaocheng, ShandongP.R. China
| | - Ze-Zhang Tao
- Department of Otorhinolaryngology, Renmin Hospital of Wuhan UniversityWuhan, HubeiP.R. China
| | - Ting-Zhao Tan
- Department of Oncology, Liaocheng Tumor HospitalLiaocheng, ShandongP.R. China
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Yu SR, Huang XJ, Zhang YP. Gastric cancer related genes. Shijie Huaren Xiaohua Zazhi 2016; 24:4381-4388. [DOI: 10.11569/wcjd.v24.i32.4381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Gastric cancer is one of the most common malignant tumors. In addition to environmental, socioeconomic, and dietary factors, hereditary factors also play an important role in the development of gastric cancer. Although some driver genes have been identified in gastric cancer, the molecular compositions of gastric cancer have not been fully understood. Genome-wide association studies, copy number variations and next-generation sequencing provide systematic methods to identify all genetic alterations in the cancer genome, especially in the field of mutation detection. Here we make a brief review of the current status of research on gastric cancer genetics.
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da Silva Oliveira KC, Thomaz Araújo TM, Albuquerque CI, Barata GA, Gigek CO, Leal MF, Wisnieski F, Rodrigues Mello Junior FA, Khayat AS, de Assumpção PP, Rodriguez Burbano RM, Smith MC, Calcagno DQ. Role of miRNAs and their potential to be useful as diagnostic and prognostic biomarkers in gastric cancer. World J Gastroenterol 2016; 22:7951-7962. [PMID: 27672290 PMCID: PMC5028809 DOI: 10.3748/wjg.v22.i35.7951] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Revised: 06/14/2016] [Accepted: 08/01/2016] [Indexed: 02/06/2023] Open
Abstract
Alterations in epigenetic control of gene expression play an important role in many diseases, including gastric cancer. Many studies have identified a large number of upregulated oncogenic miRNAs and downregulated tumour-suppressor miRNAs in this type of cancer. In this review, we provide an overview of the role of miRNAs, pointing to their potential to be useful as diagnostic and/or prognostic biomarkers in gastric cancer. Moreover, we discuss the influence of polymorphisms and epigenetic modifications on miRNA activity.
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Levran O, Peles E, Randesi M, Correa da Rosa J, Ott J, Rotrosen J, Adelson M, Kreek MJ. Synaptic Plasticity and Signal Transduction Gene Polymorphisms and Vulnerability to Drug Addictions in Populations of European or African Ancestry. CNS Neurosci Ther 2015; 21:898-904. [PMID: 26384852 PMCID: PMC4619135 DOI: 10.1111/cns.12450] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 08/01/2015] [Accepted: 08/14/2015] [Indexed: 12/23/2022] Open
Abstract
AIM Drug addiction is characterized, in part, by deregulation of synaptic plasticity in circuits involved in reward, stress, cue learning, and memory. This study was designed to assess whether 185 variants in 32 genes central to synaptic plasticity and signal transduction contribute to vulnerability to develop heroin and/or cocaine addiction. METHODS Analyses were conducted in a sample of 1860 subjects divided according to ancestry (African and European) and drug of abuse (heroin or cocaine). RESULTS Eighteen SNPs in 11 genes (CDK5R1, EPHA4, EPHA6, FOSL2, MAPK3, MBP, MPDZ, NFKB1, NTRK2, NTSR1, and PRKCE) showed significant associations (P < 0.01), but the signals did not survive correction for multiple testing. SNP rs230530 in the NFKB1 gene, encoding the transcription regulator NF-kappa-B, was the only SNP indicated in both ancestry groups and both addictions. This SNP was previously identified in association with alcohol addiction. SNP rs3915568 in NTSR1, which encodes neurotensin receptor, and SNP rs1389752 in MPDZ, which encodes the multiple PDZ domain protein, were previously associated with heroin addiction or alcohol addiction, respectively. CONCLUSIONS The study supports the involvement of genetic variation in signal transduction pathways in heroin and cocaine addiction and provides preliminary evidence suggesting several new risk or protective loci that may be relevant for diagnosis and treatment success.
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Affiliation(s)
- Orna Levran
- The Laboratory of the Biology of Addictive DiseasesThe Rockefeller UniversityNew YorkNYUSA
| | - Einat Peles
- Dr. Miriam and Sheldon G. Adelson Clinic for Drug Abuse Treatment and ResearchTel Aviv Elias Sourasky Medical CenterTel AvivIsrael
- Sackler Faculty of MedicineTel Aviv UniversityTel AvivIsrael
| | - Matthew Randesi
- The Laboratory of the Biology of Addictive DiseasesThe Rockefeller UniversityNew YorkNYUSA
| | - Joel Correa da Rosa
- Center for Clinical and Translational ScienceThe Rockefeller UniversityNew YorkNYUSA
| | - Jurg Ott
- Institute of PsychologyChinese Academy of SciencesBeijingChina
- The Laboratory of Statistical GeneticsThe Rockefeller UniversityNew YorkNYUSA
| | - John Rotrosen
- VA New York Harbor Healthcare SystemNYU School of MedicineNew YorkNYUSA
| | - Miriam Adelson
- The Laboratory of the Biology of Addictive DiseasesThe Rockefeller UniversityNew YorkNYUSA
- Dr. Miriam and Sheldon G. Adelson Clinic for Drug Abuse Treatment and ResearchTel Aviv Elias Sourasky Medical CenterTel AvivIsrael
- Dr. Miriam and Sheldon G. Adelson Clinic for Drug Abuse Treatment and ResearchLas VegasNVUSA
| | - Mary Jeanne Kreek
- The Laboratory of the Biology of Addictive DiseasesThe Rockefeller UniversityNew YorkNYUSA
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Lee JH, Kim Y, Choi JW, Kim YS. Genetic variants and risk of gastric cancer: a pathway analysis of a genome-wide association study. SPRINGERPLUS 2015; 4:215. [PMID: 25992311 PMCID: PMC4431986 DOI: 10.1186/s40064-015-1005-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 04/28/2015] [Indexed: 12/12/2022]
Abstract
This study aimed to discover candidate single nucleotide polymorphisms (SNPs) for hypothesizing significant biological pathways of gastric cancer (GC). We performed an Identify Candidate Causal SNPs and Pathways (ICSNPathway) analysis using a GC genome-wide association study (GWAS) dataset, including 472,342 SNPs in 2,240 GC cases and 3,302 controls of Asian ethnicity. By integrating linkage disequilibrium analysis, functional SNP annotation, and pathway-based analysis, seven candidate SNPs, four genes and 12 pathways were selected. The ICSNPathway analysis produced 4 hypothetical mechanisms of GC: (1) rs4745 and rs12904 → EFNA1 → ephrin receptor binding; (2) rs1801019 → UMPS → drug and pyrimidine metabolism; (3) rs364897 → GBA → cyanoamino acid metabolism; and (4) rs11187870, rs2274223, and rs3765524 → PLCE1 → lipid biosynthetic process, regulation of cell growth, and cation homeostasis. This pathway analysis using GWAS dataset suggests that the 4 hypothetical biological mechanisms might contribute to GC susceptibility.
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Affiliation(s)
- Ju-Han Lee
- Department of Pathology, Korea University Ansan Hospital, 123, Jeokgeum-Ro, Danwon-Gu, Ansan-Si, Gyeonggi-Do 425-707 Republic of Korea
| | - Younghye Kim
- Department of Pathology, Korea University Ansan Hospital, 123, Jeokgeum-Ro, Danwon-Gu, Ansan-Si, Gyeonggi-Do 425-707 Republic of Korea
| | - Jung-Woo Choi
- Department of Pathology, Korea University Ansan Hospital, 123, Jeokgeum-Ro, Danwon-Gu, Ansan-Si, Gyeonggi-Do 425-707 Republic of Korea
| | - Young-Sik Kim
- Department of Pathology, Korea University Ansan Hospital, 123, Jeokgeum-Ro, Danwon-Gu, Ansan-Si, Gyeonggi-Do 425-707 Republic of Korea
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Zhu H, Yang M, Zhang H, Chen X, Yang X, Zhang C, Qin Q, Cheng H, Sun X. Genome-wide association pathway analysis to identify candidate single nucleotide polymorphisms and molecular pathways for gastric adenocarcinoma. Tumour Biol 2015; 36:5635-9. [PMID: 25687184 DOI: 10.1007/s13277-015-3236-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 02/06/2015] [Indexed: 01/19/2023] Open
Abstract
To demonstrate candidate single nucleotide polymorphisms that might affect susceptibility to gastric adenocarcinoma as well as their potential mechanisms and pathway hypotheses, we performed a genome-wide association study dataset of gastric adenocarcinoma. Our study included 472,342 single nucleotide polymorphisms from 2766 cases of gastric cardia adenocarcinoma cases and 11,013 subjects from north central China as control groups. The identify candidate causal SNPs and pathways (ICSNPathway) analysis was employed to identify 13 candidate single nucleotide polymorphisms, nine genes, and 15 pathways. The top three candidate SNPs were rs3765524 (-log10(p) = 8.556), rs2274223 (-log10(p) = 8.633), and rs2076472 (-log10(p) = 3.205). The strongest mechanism involved the modulation of rs4745 and rs12904, thereby affecting their regulatory roles in ephrin receptor binding (p = 0.001; FDR = 0.005). The second strongest hypothetical biological mechanism was that rs932972 and rs1052177 alters the regulatory role of the glycolysis pathway (p < 0.001; FDR = 0.013). The most significant pathway was the regulation of the ephrin receptor binding pathway, which involved EFNA1, TIAM1, EFNA5, EFNB2, and EFNB3.
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Affiliation(s)
- Hongcheng Zhu
- Department of Radiation Oncology, The First Affiliated Hospital of Nanjing Medical University, 300 Guanzhou Road, Nanjing, 210029, China
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MicroRNA and signaling pathways in gastric cancer. Cancer Gene Ther 2014; 21:305-16. [PMID: 25060632 DOI: 10.1038/cgt.2014.37] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Revised: 06/19/2014] [Accepted: 06/20/2014] [Indexed: 02/08/2023]
Abstract
MicroRNAs (miRNAs) function as either oncogenes or tumor suppressors by inhibiting the expression of target genes, some of which are either directly or indirectly involved with canonical signaling pathways. The relationship between miRNAs and signaling pathways in gastric cancer is extremely complicated. In this paper, we determined the pathogenic mechanism of gastric cancer related to miRNA expression based on recent high-quality studies and then clarified the regulation network of miRNA expression and the correlated functions of these miRNAs during the progression of gastric cancer. We try to illustrate the correlation between the expression of miRNAs and outcomes of patients with gastric cancer. Understanding this will allow us to take a big step forward in the treatment of gastric cancer.
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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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Abstract
A multifactorial and multistep model of gastric cancer (GC) is currently accepted, according to which different environmental and genetic factors are involved at different stages in the cancer process. The aim of this article is to review the most relevant information published on the relative contribution of genetic and environmental factors. Large meta-analyses confirmed the association between IL8, IL10, TNF-b, TP53 and PSCA, while genetic variation at different genes such as XPG, PLCE1, HFE, ERCC5, EZH2, DOC2, CYP19A1, ALDH2, and CDH1 have been reported to be associated with GC risk. Several microRNAs have also been associated with GC and their prognosis. Cohort studies have shown the association between GC and fruit, flavonoid, total antioxidant capacity, and green tea intake. Obesity was associated with cardia GC, heme iron intake from meat with GC risk. Several large meta-analyses have confirmed the positive association of GC with salt intake and pickled foods and the negative association with aspirin use.
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Affiliation(s)
- Carlos A González
- Unit of Nutrition, Environment and Cancer, Catalan Institute of Oncology- Idibell, Barcelona, Spain
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Bulik-Sullivan B, Selitsky S, Sethupathy P. Prioritization of genetic variants in the microRNA regulome as functional candidates in genome-wide association studies. Hum Mutat 2013; 34:1049-56. [PMID: 23595788 PMCID: PMC3807557 DOI: 10.1002/humu.22337] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 04/03/2013] [Indexed: 02/06/2023]
Abstract
Comprehensive analyses of results from genome-wide association studies (GWAS) have demonstrated that complex disease/trait-associated loci are enriched in gene regulatory regions of the genome. The search for causal regulatory variation has focused primarily on transcriptional elements, such as promoters and enhancers. microRNAs (miRNAs) are now widely appreciated as critical posttranscriptional regulators of gene expression and are thought to impart stability to biological systems. Naturally occurring genetic variation in the miRNA regulome is likely an important contributor to phenotypic variation in the human population. However, the extent to which polymorphic miRNA-mediated gene regulation underlies GWAS signals remains unclear. In this study, we have developed the most comprehensive bioinformatic analysis pipeline to date for cataloging and prioritizing variants in the miRNA regulome as functional candidates in GWAS. We highlight specific findings, including a variant in the promoter of the miRNA let-7 that may contribute to human height variation. We also provide a discussion of how our approach can be expanded in the future. Overall, we believe that the results of this study will be valuable for researchers interested in determining whether GWAS signals implicate the miRNA regulome in their disease/trait of interest.
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Affiliation(s)
- Brendan Bulik-Sullivan
- Department of Genetics, University of North Carolina at Chapel HillChapel Hill, North Carolina
| | - Sara Selitsky
- Department of Genetics, University of North Carolina at Chapel HillChapel Hill, North Carolina
| | - Praveen Sethupathy
- Department of Genetics, University of North Carolina at Chapel HillChapel Hill, North Carolina
- Carolina Center for Genome Sciences, University of North Carolina at Chapel HillChapel Hill, North Carolina
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel HillChapel Hill, North Carolina
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