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Identification of the Potential Molecular Mechanisms Linking RUNX1 Activity with Nonalcoholic Fatty Liver Disease, by Means of Systems Biology. Biomedicines 2022; 10:biomedicines10061315. [PMID: 35740337 PMCID: PMC9219880 DOI: 10.3390/biomedicines10061315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/24/2022] [Accepted: 06/01/2022] [Indexed: 12/10/2022] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is the most prevalent chronic hepatic disease; nevertheless, no definitive diagnostic method exists yet, apart from invasive liver biopsy, and nor is there a specific approved treatment. Runt-related transcription factor 1 (RUNX1) plays a major role in angiogenesis and inflammation; however, its link with NAFLD is unclear as controversial results have been reported. Thus, the objective of this work was to determine the proteins involved in the molecular mechanisms between RUNX1 and NAFLD, by means of systems biology. First, a mathematical model that simulates NAFLD pathophysiology was generated by analyzing Anaxomics databases and reviewing available scientific literature. Artificial neural networks established NAFLD pathophysiological processes functionally related to RUNX1: hepatic insulin resistance, lipotoxicity, and hepatic injury-liver fibrosis. Our study indicated that RUNX1 might have a high relationship with hepatic injury-liver fibrosis, and a medium relationship with lipotoxicity and insulin resistance motives. Additionally, we found five RUNX1-regulated proteins with a direct involvement in NAFLD motives, which were NFκB1, NFκB2, TNF, ADIPOQ, and IL-6. In conclusion, we suggested a relationship between RUNX1 and NAFLD since RUNX1 seems to regulate NAFLD molecular pathways, posing it as a potential therapeutic target of NAFLD, although more studies in this field are needed.
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2
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Ren X, Cui H, Wu J, Zhou R, Wang N, Liu D, Xie X, Zhang H, Liu D, Ma X, Dang C, Kang H, Lin S. Identification of a combined apoptosis and hypoxia gene signature for predicting prognosis and immune infiltration in breast cancer. Cancer Med 2022; 11:3886-3901. [PMID: 35441810 PMCID: PMC9582692 DOI: 10.1002/cam4.4755] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 03/11/2022] [Accepted: 04/01/2022] [Indexed: 11/26/2022] Open
Abstract
Background Breast cancer (BC) is the most common malignant tumor worldwide. Apoptosis and hypoxia are involved in the progression of BC, but reliable biomarkers for these have not been developed. We hope to explore a gene signature that combined apoptosis and hypoxia‐related genes (AHGs) to predict BC prognosis and immune infiltration. Methods We collected the mRNA expression profiles and clinical data information of BC patients from The Cancer Genome Atlas database. The gene signature based on AHGs was constructed using the univariate Cox regression, least absolute shrinkage and selection operator, and multivariate Cox regression analysis. The associations between risk scores, immune infiltration, and immune checkpoint gene expression were studied using single‐sample gene set enrichment analysis. Besides, gene signature and independent clinicopathological characteristics were combined to establish a nomogram. Finally, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were performed on the potential functions of AHGs. Results We identified a 16‐AHG signature (AGPAT1, BTBD6, EIF4EBP1, ERRFI1, FAM114A1, GRIP1, IRF2, JAK1, MAP2K6, MCTS1, NFKBIA, NFKBIZ, NUP43, PGK1, RCL1, and SGCE) that could independently predict BC prognosis. The median score of the risk model divided the patients into two subgroups. By contrast, patients in the high‐risk group had poorer prognosis, less abundance of immune cell infiltration, and expression of immune checkpoint genes. The gene signature and nomogram had good predictive effects on the overall survival of BC patients. GO and KEGG analyses revealed that the differential expression of AHGs may be closely related to tumor immunity. Conclusion We established and verified a 16‐AHG BC signature which may help predict prognosis, assess potential immunotherapy benefits, and provide inspiration for future research on the functions and mechanisms of AHGs in BC.
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Affiliation(s)
- Xueting Ren
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Hanxiao Cui
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Jianhua Wu
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Ruina Zhou
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Nan Wang
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Dandan Liu
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Xin Xie
- Department of Surgical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Hao Zhang
- Department of Surgical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Di Liu
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Xiaobin Ma
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Chengxue Dang
- Department of Surgical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Huafeng Kang
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Shuai Lin
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
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Firoozi Z, Mohammadisoleimani E, Shahi A, Mansoori H, Naghizadeh MM, Bastami M, Nariman‐Saleh‐Fam Z, Daraei A, Raoofat A, Mansoori Y. Potential roles of hsa_circ_000839 and hsa_circ_0005986 in breast cancer. J Clin Lab Anal 2022; 36:e24263. [PMID: 35098570 PMCID: PMC8906031 DOI: 10.1002/jcla.24263] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/27/2021] [Accepted: 01/15/2022] [Indexed: 11/26/2022] Open
Abstract
Background Breast cancer (BC) is one of the leading causes of death among women around the world. Circular RNAs (circRNAs) are a newly discovered group of non‐coding RNAs that their roles are being investigated in BC and other cancer types. In this study, we evaluated the association of hsa_circ_0005986 and hsa_circ_000839 in tumor and adjacent normal tissues of BC patients with their clinicopathological characteristics. Materials and methods Total RNA was extracted from tumors and adjacent non‐tumor tissues by the Trizol isolation reagent, and cDNA was synthesized using First Strand cDNA Synthesis Kit (Thermo Scientific). The expression level of hsa_circ_0005986 and hsa_circ_000839 was quantified using RT‐qPCR. Online in silico tools were used for identifying potentially important competing endogenous RNA (ceRNA) networks of these two circRNAs. Results The expression level of hsa_circ_0005986 and hsa_circ_000839 was lower in the tumor as compared to adjacent tissues. The expression level of hsa_circ_0005986 in the patients who had used hair dye in the last 5 years was significantly lower. Moreover, a statistically significant negative correlation between body mass index (BMI) and hsa_circ_000839 expression was observed. In silico analysis of the ceRNA network of these circRNAs revealed mRNAs and miRNAs with crucial roles in BC. Conclusion Downregulation of hsa_circ_000839 and hsa_circ_0005986 in BC tumors suggests a tumor‐suppressive role for these circRNAs in BC, meriting the need for more experimentations to delineate the exact mechanism of their involvement in BC pathogenesis.
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Affiliation(s)
- Zahra Firoozi
- Department of Medical Genetics Fasa University of Medical Sciences Fasa Iran
| | | | - Abbas Shahi
- Department of Immunology School of Medicine Tehran University of Medical Science Tehran Iran
- Noncommunicable Diseases Research CenterFasa University of Medical Sciences Fasa Iran
| | - Hosein Mansoori
- Department of Medical Genetics Fasa University of Medical Sciences Fasa Iran
| | | | - Milad Bastami
- Noncommunicable Diseases Research CenterFasa University of Medical Sciences Fasa Iran
| | - Ziba Nariman‐Saleh‐Fam
- Women's Reproductive Health Research CenterTabriz University of Medical Sciences Tabriz Iran
| | - Abdolreza Daraei
- Department of Medical Genetics School of Medicine Babol University of Medical Sciences Babol Iran
| | - Atefeh Raoofat
- Department of Medical Genetics School of Medicine Shiraz University of Medical Sciences Shiraz Iran
| | - Yaser Mansoori
- Department of Medical Genetics Fasa University of Medical Sciences Fasa Iran
- Noncommunicable Diseases Research CenterFasa University of Medical Sciences Fasa Iran
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4
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Yuan J, Duan F, Zhai W, Song C, Wang L, Xia W, Hua X, Yuan Z, Bi X, Huang J. An Aging-Related Gene Signature-Based Model for Risk Stratification and Prognosis Prediction in Breast Cancer. Int J Womens Health 2021; 13:1053-1064. [PMID: 34785957 PMCID: PMC8578840 DOI: 10.2147/ijwh.s334756] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 10/24/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Aging, an inevitable process characterized by functional decline over time, is a significant risk factor for various tumors. However, little is known about aging-related genes (ARGs) in breast cancer (BC). We aimed to explore the potential prognostic role of ARGs and to develop an ARG-based prognosis signature for BC. METHODS RNA-sequencing expression profiles and corresponding clinicopathological data of female patients with BC were obtained from public databases in The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). An ARG-based risk signature was constructed in the TCGA cohort based on results of least absolute shrinkage and selection operator (LASSO) and multivariate Cox regression analysis, and its prognostic value was further validated in the GSE20685 cohort. RESULTS A six ARG-based signature, including CLU, DGAT1, MXI1, NFKBI, PIK3CA and PLAU, was developed in the TCGA cohort and significantly stratified patients into low- and high-risk groups. Patients in the former group showed significantly better prognosis than those in the latter. Multivariate Cox regression analysis demonstrated that the ARG risk score was an independent prognostic factor for BC. A predictive nomogram integrating the ARG risk score and three identified factors (age, N- and M-classification) was established in the TCGA cohort and validated in the GSE20685 cohort. Calibration plots showed good consistency between predicted survival probabilities and actual observations. CONCLUSION A novel ARG-based risk signature was developed for patients with BC, which can be used for individual prognosis prediction and promoting personalized treatment.
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Affiliation(s)
- Jing Yuan
- Departments of Experimental Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, People’s Republic of China
| | - Fangfang Duan
- Departments of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, People’s Republic of China
| | - Wenyu Zhai
- Departments of Thoracic Surgery, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, People’s Republic of China
| | - Chenge Song
- Departments of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, People’s Republic of China
| | - Li Wang
- Departments of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, People’s Republic of China
| | - Wen Xia
- Departments of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, People’s Republic of China
| | - Xin Hua
- Departments of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, People’s Republic of China
| | - Zhongyu Yuan
- Departments of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, People’s Republic of China
| | - Xiwen Bi
- Departments of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, People’s Republic of China
| | - Jiajia Huang
- Departments of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, People’s Republic of China
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5
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Liu J, Zhang J. T-cell receptors provide potential prognostic signatures for breast cancer. Cell Biol Int 2021; 45:1220-1230. [PMID: 33527533 DOI: 10.1002/cbin.11562] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 12/18/2020] [Accepted: 01/31/2021] [Indexed: 12/18/2022]
Abstract
Although T-cell receptors (TCRs) are related to the progression of breast cancer (BC), their prognostic values remain unclear. We downloaded the messenger RNA (mRNA) profiles and corresponding clinical information of 1413 BC patients from the Cancer Genome Atlas and Gene Expression Omnibus database, respectively. The different expression analysis of 104 TCRs in BC samples was performed, and the consensus clustering based on 104 TCRs was performed by using the K-mean method of R language. Univariate cox regression analysis was used to screen TCRs significantly associated with the prognosis of BC, and LASSO Cox analysis was applied to optimize key TCRs. The risk score was calculated using the prognostic model constructed based on six optimal TCRs, and multivariate Cox regression analysis was used to determine whether it was an independent prognostic signature. Finally, the nomogram was constructed to predict the overall survival of BC patients. Six optimal TCRs (ZAP70, GRAP2, NFKBIE, IFNG, NFKBIA, and PAK5), which were favorable for the prognosis of BC patients, were screened. Risk score could reliably predict the prognosis of BC patients as an independent prognostic signature. In addition, when bringing into two independent prognostic signatures, age and risk score, the nomogram model could better predict the overall survival of BC patients. Our results suggested that the poor prognosis of BC patients with high risk might be due to an immunosuppressive microenvironment. In summary, a prognostic risk model based on six TCRs was established and could efficiently predict the prognosis of BC patients.
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Affiliation(s)
- Jingjing Liu
- 3rd Department of Breast Cancer, China Tianjin Breast Cancer Prevention, Treatment and Research Center, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
- Key Laboratory of Breast Cancer Prevention and Therapy of Ministry of Education, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, China
- National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Jin Zhang
- 3rd Department of Breast Cancer, China Tianjin Breast Cancer Prevention, Treatment and Research Center, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
- Key Laboratory of Breast Cancer Prevention and Therapy of Ministry of Education, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Tianjin's Clinical Research Center for Cancer, Tianjin, China
- National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
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6
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Kancharla J, Prasad IDV, Bhaskar LV, Bramhachari PV, Alam A. Meta-analysis of NFKB1-94 ATTG Ins/Del Polymorphism and Risk of Breast Cancer. Curr Drug Metab 2020; 21:221-225. [DOI: 10.2174/1389200221666200310113118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 01/13/2020] [Accepted: 01/14/2020] [Indexed: 11/22/2022]
Abstract
Background:
Breast cancer (BC) accounts for one of the most prevalent malignancies in the world.
Inflammatory molecules modulate tumor microenvironment in BC that promotes tumor growth and metastasis.
NF-κB (a transcription factor) that regulates multiple immune functions and acts as a crucial mediator of inflammatory
responses.
Objective:
The present study is aimed to quantitatively summarize the relation of NFKB1-94 ATTG (I, insertion/D,
deletion) variant and risk of BC.
Methods:
Further, the meta-analysis includes three independent case-control investigations that focus on NFKB1-94,
ATTG I/D polymorphism, and BC patients. Web of Science, PubMed and Embase databases were used to retrieve
relevant data. OR and 95% confidence interval of pooled studies were analyzed by using the MetaGenyo web tool.
Results:
This study revealed a high heterogeneity. In all three genetic comparison models, the NFKB1-94 ATTG I/D
variant is not related to the risk of BC. Further, no publication bias on the connection between NFKB1-94 ATTG I/D
variant and risk of BC was observed.
Conclusion:
To summarize, our meta-analysis demonstrates that the NFKB1-94 ATTG I/D polymorphism is not a
major risk factor for BC.
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Affiliation(s)
- Jyothsna Kancharla
- Department of Bioscience and Biotechnology, Banasthali University, Vanasthali, Rajasthan 304022, India
| | - I. Devi Vara Prasad
- Department of Physical Education and Sports Sciences, Acharya Nagarjuna University, Ongole 523001, Andhra Pradesh, India
| | | | | | - Afroz Alam
- Department of Bioscience and Biotechnology, Banasthali University, Vanasthali, Rajasthan 304022, India
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7
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Lu J, Lu Y, Ding Y, Xiao Q, Liu L, Cai Q, Kong Y, Bai Y, Yu T. DNLC: differential network local consistency analysis. BMC Bioinformatics 2019; 20:489. [PMID: 31874600 PMCID: PMC6929334 DOI: 10.1186/s12859-019-3046-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 08/21/2019] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND The biological network is highly dynamic. Functional relations between genes can be activated or deactivated depending on the biological conditions. On the genome-scale network, subnetworks that gain or lose local expression consistency may shed light on the regulatory mechanisms related to the changing biological conditions, such as disease status or tissue developmental stages. RESULTS In this study, we develop a new method to select genes and modules on the existing biological network, in which local expression consistency changes significantly between clinical conditions. The method is called DNLC: Differential Network Local Consistency. In simulations, our algorithm detected artificially created local consistency changes effectively. We applied the method on two publicly available datasets, and the method detected novel genes and network modules that were biologically plausible. CONCLUSIONS The new method is effective in finding modules in which the gene expression consistency change between clinical conditions. It is a useful tool that complements traditional differential expression analyses to make discoveries from gene expression data. The R package is available at https://cran.r-project.org/web/packages/DNLC.
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Affiliation(s)
- Jianwei Lu
- School of Software Engineering, Tongji University, Shanghai, China
- Institute of Advanced Translational Medicine, Tongji University, Shanghai, China
| | - Yao Lu
- School of Software Engineering, Tongji University, Shanghai, China
| | - Yusheng Ding
- School of Software Engineering, Tongji University, Shanghai, China
| | - Qingyang Xiao
- Department of Environmental Health, Emory University, Atlanta, GA USA
| | - Linqing Liu
- School of Software Engineering, Tongji University, Shanghai, China
| | - Qingpo Cai
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA USA
| | - Yunchuan Kong
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA USA
| | - Yun Bai
- Department of Pharmaceutical Sciences, School of Pharmacy, Philadelphia College of Osteopathic Medicine, Georgia Campus, Suwanee, GA USA
| | - Tianwei Yu
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA USA
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Denkiewicz M, Saha I, Rakshit S, Sarkar JP, Plewczynski D. Identification of Breast Cancer Subtype Specific MicroRNAs Using Survival Analysis to Find Their Role in Transcriptomic Regulation. Front Genet 2019; 10:1047. [PMID: 31798622 PMCID: PMC6837165 DOI: 10.3389/fgene.2019.01047] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 09/30/2019] [Indexed: 01/19/2023] Open
Abstract
The microRNA (miRNA) biomolecules have a significant role in the development of breast cancer, and their expression profiles are different in each subtype of breast cancer. Thus, our goal is to use the Next Generation Sequencing provided high-throughput miRNA expression and clinical data in an integrated fashion to perform survival analysis in order to identify breast cancer subtype specific miRNAs, and analyze associated genes and transcription factors. We select top 100 miRNAs for each of the four subtypes, based on the value of hazard ratio and p-value, thereafter, identify 44 miRNAs that are related to all four subtypes, which we call as four-star miRNAs. Moreover, 12, 14, 9, and 15 subtype specific, viz. one-star miRNAs, are also identified. The resulting miRNAs are validated by using machine learning methods to differentiate tumor cases from controls (for four-star miRNAs), and subtypes (for one-star miRNAs). The four-star miRNAs provide 95% average accuracy, while in case of one-star miRNAs 81% accuracy is achieved for HER2-Enriched. Differences in expression of miRNAs between cancer stages is also analyzed, and a subset of eight miRNAs is found, for which expression is increased in stage II relative to stage I, including hsa-miR-10b-5p, which contributes to breast cancer metastasis. Subsequently we prepare regulatory networks in order to identify the interactions among miRNAs, their targeted genes and transcription factors (TFs), that are targeting those miRNAs. In this way, key regulatory circuits are identified, where genes such as TP53, ESR1, BRCA1, MYC, and others, that are known to be important genetic factors for the cause of breast cancer, produce transcription factors that target the same genes as well as interact with the selected miRNAs. To provide further biological validation the Protein-Protein Interaction (PPI) networks are prepared and Kyoto Encyclopedia of Genes and Genomes pathway and gene ontology (GO) enrichment analysis are performed. Among the enriched pathways many are breast cancer-related, such as PI3K-Akt or p53 signaling pathways, and contain proteins such as TP53, also present in the regulatory networks. Moreover, we find that the genes are enriched in GO terms associated with breast cancer. Our results provide detailed analysis of selected miRNAs and their regulatory networks.
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Affiliation(s)
- Michał Denkiewicz
- Laboratory of Functional and Structural Genomics, Center of New Technologies, University of Warsaw, Warsaw, Poland
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Warsaw, Poland
- Faculty of Mathematics and Information Science, Warsaw University of Technology Warsaw, Poland
| | - Indrajit Saha
- Department of Computer Science and Engineering, National Institute of Technical Teachers’ Training and Research, Kolkata, India
| | - Somnath Rakshit
- Laboratory of Functional and Structural Genomics, Center of New Technologies, University of Warsaw, Warsaw, Poland
- Department of Computer Science and Engineering, National Institute of Technical Teachers’ Training and Research, Kolkata, India
| | - Jnanendra Prasad Sarkar
- Cognitive and Analytics, Larsen & Toubro Infotech Ltd., Pune, India
- Department of Computer Science & Engineering, Jadavpur University, Kolkata, India
| | - Dariusz Plewczynski
- Laboratory of Functional and Structural Genomics, Center of New Technologies, University of Warsaw, Warsaw, Poland
- Faculty of Mathematics and Information Science, Warsaw University of Technology Warsaw, Poland
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9
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Li M, Guo Y, Feng YM, Zhang N. Identification of Triple-Negative Breast Cancer Genes and a Novel High-Risk Breast Cancer Prediction Model Development Based on PPI Data and Support Vector Machines. Front Genet 2019; 10:180. [PMID: 30930932 PMCID: PMC6428707 DOI: 10.3389/fgene.2019.00180] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 02/19/2019] [Indexed: 12/20/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is a special subtype of breast cancer that is difficult to treat. It is crucial to identify breast cancer-related genes that could provide new biomarkers for breast cancer diagnosis and potential treatment goals. In the development of our new high-risk breast cancer prediction model, seven raw gene expression datasets from the NCBI gene expression omnibus (GEO) database (GSE31519, GSE9574, GSE20194, GSE20271, GSE32646, GSE45255, and GSE15852) were used. Using the maximum relevance minimum redundancy (mRMR) method, we selected significant genes. Then, we mapped transcripts of the genes on the protein-protein interaction (PPI) network from the Search Tool for the Retrieval of Interacting Genes (STRING) database, as well as traced the shortest path between each pair of proteins. Genes with higher betweenness values were selected from the shortest path proteins. In order to ensure validity and precision, a permutation test was performed. We randomly selected 248 proteins from the PPI network for shortest path tracing and repeated the procedure 100 times. We also removed genes that appeared more frequently in randomized results. As a result, 54 genes were selected as potential TNBC-related genes. Using 14 out the 54 genes, which are potential TNBC associated genes, as input features into a support vector machine (SVM), a novel model was trained to predict high-risk breast cancer. The prediction accuracy of normal tissues and TNBC tissues reached 95.394%, and the predictions of Stage II and Stage III TNBC reached 86.598%, indicating that such genes play important roles in distinguishing breast cancers, and that the method could be promising in practical use. According to reports, some of the 54 genes we identified from the PPI network are associated with breast cancer in the literature. Several other genes have not yet been reported but have functional resemblance with known cancer genes. These may be novel breast cancer-related genes and need further experimental validation. Gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed to appraise the 54 genes. It was indicated that cellular response to organic cyclic compounds has an influence in breast cancer, and most genes may be related with viral carcinogenesis.
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Affiliation(s)
- Ming Li
- Department of Biomedical Engineering, Tianjin Key Lab of BME Measurement, Tianjin University, Tianjin, China
| | - Yu Guo
- Department of Biomedical Engineering, Tianjin Key Lab of BME Measurement, Tianjin University, Tianjin, China
| | - Yuan-Ming Feng
- Department of Biomedical Engineering, Tianjin Key Lab of BME Measurement, Tianjin University, Tianjin, China
- Department of Radiation Oncology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Ning Zhang
- Department of Biomedical Engineering, Tianjin Key Lab of BME Measurement, Tianjin University, Tianjin, China
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10
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Gupta A, Ragumani S, Sharma YK, Ahmad Y, Khurana P. Analysis of Hypoxiamir-Gene Regulatory Network Identifies Critical MiRNAs Influencing Cell-Cycle Regulation Under Hypoxic Conditions. Microrna 2019; 8:223-236. [PMID: 30806334 DOI: 10.2174/2211536608666190219094204] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 01/14/2019] [Accepted: 02/06/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND Hypoxia is a pathophysiological condition which arises due to low oxygen concentration in conditions like cardiovascular diseases, inflammation, ascent to higher altitude, malignancies, deep sea diving, prenatal birth, etc. A number of microRNAs (miRNAs), Transcription Factors (TFs) and genes have been studied separately for their role in hypoxic adaptation and controlling cell-cycle progression and apoptosis during this stress. OBJECTIVE We hypothesize that miRNAs and TFs may act in conjunction to regulate a multitude of genes and play a crucial and combinatorial role during hypoxia-stress-responses and associated cellcycle control mechanisms. METHOD We collected a comprehensive and non-redundant list of human hypoxia-responsive miRNAs (also known as hypoxiamiRs). Their experimentally validated gene-targets were retrieved from various databases and a comprehensive hypoxiamiR-gene regulatory network was built. RESULTS Functional characterization and pathway enrichment of genes identified phospho-proteins as enriched nodes. The phospho-proteins which were localized both in the nucleus and cytoplasm and could potentially play important role as signaling molecules were selected; and further pathway enrichment revealed that most of them were involved in NFkB signaling. Topological analysis identified several critical hypoxiamiRs and network perturbations confirmed their importance in the network. Feed Forward Loops (FFLs) were identified in the subnetwork of enriched genes, miRNAs and TFs. Statistically significant FFLs consisted of four miRNAs (hsa-miR-182-5p, hsa- miR-146b-5p, hsa-miR-96, hsa-miR-20a) and three TFs (SMAD4, FOXO1, HIF1A) both regulating two genes (NFkB1A and CDKN1A). CONCLUSION Detailed BioCarta pathway analysis identified that these miRNAs and TFs together play a critical and combinatorial role in regulating cell-cycle under hypoxia, by controlling mechanisms that activate cell-cycle checkpoint protein, CDKN1A. These modules work synergistically to regulate cell-proliferation, cell-growth, cell-differentiation and apoptosis during hypoxia. A detailed mechanistic molecular model of how these co-regulatory FFLs may regulate the cell-cycle transitions during hypoxic stress conditions is also put forth. These biomolecules may play a crucial and deterministic role in deciding the fate of the cell under hypoxic-stress.
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Affiliation(s)
- Apoorv Gupta
- Defence Institute of Physiology and Allied Sciences (DIPAS), Defence R&D Organization (DRDO), Timarpur, Delhi- 110054, India
| | - Sugadev Ragumani
- Defence Institute of Physiology and Allied Sciences (DIPAS), Defence R&D Organization (DRDO), Timarpur, Delhi- 110054, India
| | - Yogendra Kumar Sharma
- Defence Institute of Physiology and Allied Sciences (DIPAS), Defence R&D Organization (DRDO), Timarpur, Delhi- 110054, India
| | - Yasmin Ahmad
- Defence Institute of Physiology and Allied Sciences (DIPAS), Defence R&D Organization (DRDO), Timarpur, Delhi- 110054, India
| | - Pankaj Khurana
- Defence Institute of Physiology and Allied Sciences (DIPAS), Defence R&D Organization (DRDO), Timarpur, Delhi- 110054, India
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11
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Deng L, Wang J, Xiao Y, Wang Z, Liu H. Accurate prediction of protein-lncRNA interactions by diffusion and HeteSim features across heterogeneous network. BMC Bioinformatics 2018; 19:370. [PMID: 30309340 PMCID: PMC6182872 DOI: 10.1186/s12859-018-2390-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 09/19/2018] [Indexed: 12/12/2022] Open
Abstract
Background Identifying the interactions between proteins and long non-coding RNAs (lncRNAs) is of great importance to decipher the functional mechanisms of lncRNAs. However, current experimental techniques for detection of lncRNA-protein interactions are limited and inefficient. Many methods have been proposed to predict protein-lncRNA interactions, but few studies make use of the topological information of heterogenous biological networks associated with the lncRNAs. Results In this work, we propose a novel approach, PLIPCOM, using two groups of network features to detect protein-lncRNA interactions. In particular, diffusion features and HeteSim features are extracted from protein-lncRNA heterogenous network, and then combined to build the prediction model using the Gradient Tree Boosting (GTB) algorithm. Our study highlights that the topological features of the heterogeneous network are crucial for predicting protein-lncRNA interactions. The cross-validation experiments on the benchmark dataset show that PLIPCOM method substantially outperformed previous state-of-the-art approaches in predicting protein-lncRNA interactions. We also prove the robustness of the proposed method on three unbalanced data sets. Moreover, our case studies demonstrate that our method is effective and reliable in predicting the interactions between lncRNAs and proteins. Availability The source code and supporting files are publicly available at: http://denglab.org/PLIPCOM/.
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Affiliation(s)
- Lei Deng
- School of Software, Central South University, Changsha, 410075, China
| | - Junqiang Wang
- School of Software, Central South University, Changsha, 410075, China
| | - Yun Xiao
- School of Software, Central South University, Changsha, 410075, China
| | - Zixiang Wang
- School of Software, Central South University, Changsha, 410075, China
| | - Hui Liu
- Lab of Information Management, Changzhou University, Jiangsu, 213164, China.
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12
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Ghali RM, Mahjoub S, Zaied S, Bhiri H, Bahia W, Mahjoub T, Almawi WY. Association of Genetic Variants in NF-kB with Susceptibility to Breast Cancer: a Case Control Study. Pathol Oncol Res 2018; 25:1395-1400. [PMID: 30027470 DOI: 10.1007/s12253-018-0452-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 07/10/2018] [Indexed: 01/10/2023]
Abstract
Insofar as altered NF-κB signaling stemming from the presence of specific genetic variants in NF-κB gene contribute to cancer pathogenesis, this study evaluated the association between NF-κB rs147574894/I552V, rs148626207/M860T rs3774937 and rs1598859 variants and breast cancer and associated features and complications. This was a retrospective case-control study, which involved 207 women with breast cancer, and 214 cancer-free women who served as controls. NF-κB genotyping was done by real-time PCR. Significantly higher rs3774937 minor allele frequencies (MAF), and lower rs147574894 MAF were seen among breast cancer patients, thereby imparting disease susceptibility and protective nature to these variants, respectively. Significant association of rs3774937 and rs147574894 genotypes with breast cancer was seen under the dominant model. Histological type and grade, molecular type, Her2 positivity and ER+/Her2- correlated positively, while distant metastasis negatively correlated with rs3774937. On the other hand, rs147574894 negatively correlated with histological type and grade, tumor size, Her2 positivity, molecular type, and ER+/Her2-, while rs148626207 correlated positively with histological grade, but negatively with distant metastasis and triple-negative status. Breast cancer-susceptible and -protective 4-locus haplotypes were also identified. This is the first report that addresses the contribution of NF-κB variants to the pathogenesis of breast cancer in Middle Eastern-North African population, and the first to document positive association of rs3774937 with breast cancer.
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Affiliation(s)
- Rabeb M Ghali
- Laboratory of Human Genome and Multifactorial Diseases (LR12ES07), Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia.,Faculty of Sciences of Bizerte, University of Carthage, Carthage, Tunisia
| | - Sana Mahjoub
- Laboratory of Human Genome and Multifactorial Diseases (LR12ES07), Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia
| | - Sonia Zaied
- Department of Clinical Oncology, CHU Fattouma Bourguiba, Monastir, Tunisia
| | - Hanen Bhiri
- Department of Clinical Oncology, CHU Fattouma Bourguiba, Monastir, Tunisia
| | - Wael Bahia
- Laboratory of Human Genome and Multifactorial Diseases (LR12ES07), Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia
| | - Touhami Mahjoub
- Laboratory of Human Genome and Multifactorial Diseases (LR12ES07), Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia
| | - Wassim Y Almawi
- Faculty of Sciences of Tunis (FST), El-Manar University, Tunis, Tunisia. .,School of Pharmacy, Lebanese American University, Byblos, Lebanon.
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13
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Dimitrakopoulos FID, Antonacopoulou AG, Kottorou AE, Maroussi S, Panagopoulos N, Koukourikou I, Scopa C, Kalofonou M, Koutras A, Makatsoris T, Papadaki H, Dougenis D, Brock M, Kalofonos HP. NF-kB2 Genetic Variations are Significantly Associated with Non-Small Cell Lung Cancer Risk and Overall Survival. Sci Rep 2018; 8:5259. [PMID: 29588475 PMCID: PMC5869671 DOI: 10.1038/s41598-018-23324-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 02/20/2018] [Indexed: 01/16/2023] Open
Abstract
During the last decade, a growing number of publications implicate NF-kB2 in NSCLC pathogenesis. Here, we investigated the clinical relevance of NF-kB2 single nucleotide polymorphisms (SNPs) rs7897947, rs11574852 and rs12769316 in NSCLC and their association with NF-kB2 protein and mRNA levels. Our data show that TT (rs7897947T >G) and AA (rs12769316G >A) genotypes were strongly associated with an increased risk for NSCLC (P = 0.019 and P = 0.003, respectively). Additionally, in multivariate analysis, TT (rs7897947T >G) homozygosity was associated with worse 2- and 3-year survival rates (P = 0.030 and P = 0.028, respectively), especially among patients with stages III/IV, who had worse 2, 3 and 5-year survival (P = 0.001, P = 0.022 and P = 0.035, respectively). In chemotherapy-treated patients, TT (rs12769316G >A) homozygosity was also associated with worse 2- and 3-year survival compared to G allele carriers (P = 0.006 and P = 0.014, respectively). Furthermore, rs12769316 was correlated with survival outcome of stage I and II patients (P = 0.031 and P = 0.006, respectively). Interestingly, amongst the patients who developed metastases, A allele carriers had better 5-year survival (P = 0.020). In addition, rs12769316 was associated with NF-kB2 protein (P = 0.001) and mRNA expression (P = 0.017) as well as with tumor maximum diameter (P = 0.025). Overall, this study suggests that rs7897947 and rs12769316 are involved in NSCLC susceptibility, in treatment response and in clinical outcome.
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Affiliation(s)
- Foteinos-Ioannis D Dimitrakopoulos
- Molecular Oncology Laboratory, Division of Oncology, Department of Internal Medicine, Medical School, University of Patras, Patras, Greece
| | - Anna G Antonacopoulou
- Molecular Oncology Laboratory, Division of Oncology, Department of Internal Medicine, Medical School, University of Patras, Patras, Greece
| | - Anastasia E Kottorou
- Molecular Oncology Laboratory, Division of Oncology, Department of Internal Medicine, Medical School, University of Patras, Patras, Greece
| | - Stella Maroussi
- "G. Gennimatas" General Hospital of Athens, Neurology Department, Athens, Greece
| | - Nikolaos Panagopoulos
- Department of Cardiothoracic Surgery, Medical School, University of Patras, Patras, Greece
| | - Ioulia Koukourikou
- Molecular Oncology Laboratory, Division of Oncology, Department of Internal Medicine, Medical School, University of Patras, Patras, Greece
| | - Chrisoula Scopa
- Department of Pathology, Medical School, University of Patras, Patras, Greece
| | - Melpomeni Kalofonou
- Institute of Biomedical Engineering, Imperial College London, London, United Kingdom
| | - Angelos Koutras
- Molecular Oncology Laboratory, Division of Oncology, Department of Internal Medicine, Medical School, University of Patras, Patras, Greece
| | - Thomas Makatsoris
- Molecular Oncology Laboratory, Division of Oncology, Department of Internal Medicine, Medical School, University of Patras, Patras, Greece
| | - Helen Papadaki
- Department of Anatomy, Medical School, University of Patras, Patras, Greece
| | - Dimitrios Dougenis
- Department of Cardiothoracic Surgery, Medical School, University of Patras, Patras, Greece
| | - Malcolm Brock
- Division of Thoracic Surgery, Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Haralabos P Kalofonos
- Molecular Oncology Laboratory, Division of Oncology, Department of Internal Medicine, Medical School, University of Patras, Patras, Greece.
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Gupta A, Agnihotri V, Kumar R, Upadhyay AD, Bhaskar S, Dwivedi S, Dey S. Effects of Tobacco Habits on the Polymorphism of NFKB1 and NFKB1A Gene of Head and Neck Squamous Cell Carcinoma in Indian Population. Asian Pac J Cancer Prev 2017; 18:1855-1859. [PMID: 28749120 PMCID: PMC5648390 DOI: 10.22034/apjcp.2017.18.7.1855] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Background: Polymorphism of NFKB1 and NFKB1A are highly associated with cancer. We have assessed
polymorphism in the promoter region of NFKB1 -94 del/ins ATTG (rs28362491) and NFKB1A -826 C/T (rs2233406)
with the risk of HNSCC in Indian population. Methods: Polymerase chain reaction–restriction fragment length
polymorphism (PCR-RFLP) method was used for the genotyping NFKB1 -94 del/ins ATTG and NFKB1A -826 C/T.
Sequencing was done to validate the results of PCR-RFLP. Statistical analysis of data was done by Stata/SE-14.0
software. Results: ins/ins genotype was observed to be a risk factor of HNSCC as compared del/del genotype of NFKB1
-94 ATTG. Interactive effects of smoking and chewing on ins/ins genotype showed 13.96 and 10.92 fold increased
risk of HNSCC. NFKB1A -826 C/T polymorphism, TT genotype showed no association with the risk of HNSCC as
compared to wild type CC genotype. Conclusion: Our results showed NFKB1 -94 del/ins ATTG with smoking and
tobacco chewing may increase the risk of HNSCC while NFKB1A -826 C/T plays a protective role in Indian population.
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Affiliation(s)
- Abhishek Gupta
- Department of Biophysics, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India.
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15
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Fu X, Fang J, Lian M, Zhong Q, Ma H, Feng L, Wang R, Wang H. Identification of microRNAs associated with medullary thyroid carcinoma by bioinformatics analyses. Mol Med Rep 2017; 15:4266-4272. [PMID: 28487941 DOI: 10.3892/mmr.2017.6547] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 01/19/2017] [Indexed: 11/05/2022] Open
Abstract
The present study aimed to investigate the microRNA (miRNA) profile in human medullary thyroid carcinoma (MTC) tissue. The GSE40807 data profile was downloaded from the Gene Expression Omnibus database. Following preprocessing, differentially expressed microRNAs (DEMs) between MTC and healthy tissues were identified. Based on the obtained DEMs, transcription factor (TF)‑miRNA and miRNA‑target gene regulatory association pairs were predicted. Finally, functional enrichment analysis was performed on target genes of DEMs. Fifteen upregulated and 17 downregulated DEMs were identified. In the constructed TF‑miRNA regulatory network, hsa‑miR‑9‑5p was regulated by 9 TFs and hsa‑miR‑1 was regulated by 8 TFs. TFs of nuclear factor of κ light polypeptide gene enhancer in B‑cells 1 (NF‑κB1) and v‑myc avian myelocytomatosis viral oncogene homolog (MYC) regulated 4 and 3 DEMs, respectively. In the miRNA‑target gene regulatory network, hsa‑miR‑1, hsa‑miR‑9‑5p, hsa‑miR‑96‑5p and hsa‑miR‑590‑5p were most upregulated. The target genes of these 4 miRNAs were primarily enriched in the mitogen activated protein kinase (MAPK) signaling pathway. Therefore, MAPK signaling pathway may serve important roles in MTC progression. In conclusion, the DEMs hsa‑miR‑1 and hsa‑miR‑9‑5p, and TFs of NF‑κB1 and MYC may be used as biomarkers for the diagnosis and treatment of MTC.
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Affiliation(s)
- Xiangjun Fu
- Department of Otorhinolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, P.R. China
| | - Jugao Fang
- Department of Otorhinolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, P.R. China
| | - Meng Lian
- Department of Otorhinolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, P.R. China
| | - Qi Zhong
- Department of Otorhinolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, P.R. China
| | - Hongzhi Ma
- Department of Otorhinolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, P.R. China
| | - Ling Feng
- Department of Otorhinolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, P.R. China
| | - Ru Wang
- Department of Otorhinolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, P.R. China
| | - Haizhou Wang
- Department of Otorhinolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, P.R. China
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16
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Youssef MR, Attia ZI, El-Baz RA, Roshdy S, Settin A. Genetic polymorphisms of NFκB1-94ins/delATTG and NFκBIA-881A/G genes in Egyptian patients with colorectal cancer. Fam Cancer 2017; 16:517-524. [DOI: 10.1007/s10689-017-9992-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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17
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Fakhir FZ, Lkhider M, Badre W, Alaoui R, Pineau P, Ezzikouri S, Benjelloun S. The -94Ins/DelATTG polymorphism in NFκB1 promoter modulates chronic hepatitis C and liver disease progression. INFECTION GENETICS AND EVOLUTION 2016; 39:141-146. [DOI: 10.1016/j.meegid.2016.01.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 12/22/2015] [Accepted: 01/26/2016] [Indexed: 12/26/2022]
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18
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Zhang M, Huang J, Tan X, Bai J, Wang H, Ge Y, Xiong H, Shi J, Lu W, Lv Z, Liang C. Common Polymorphisms in the NFKBIA Gene and Cancer Susceptibility: A Meta-Analysis. Med Sci Monit 2015; 21:3186-96. [PMID: 26488500 PMCID: PMC4621165 DOI: 10.12659/msm.895257] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background NFKBIA encodes the inhibitors of nuclear factor-κB (NF-κB), which regulate the translation of the genes involved in the inflammatory and immune reactions. Polymorphisms (rs2233406, rs3138053, and rs696) of NFKBIA have been implicated in susceptibility to many cancer types. Material/Methods To evaluate the association between polymorphisms of NFKBIA and cancer susceptibility, a meta-analysis including a total of 7182 cancer cases and 10 057 controls from 28 case-control studies was performed. Data were extracted and pooled odds ratios (ORs) with 95% confidence intervals (CIs) were calculated. Results Combined data demonstrated that rs3138053 polymorphism of NFKBIA was associated with cancer susceptibility in an allelic model (C vs. T: OR=10.754, 95%CI=4.175–27.697, Pheterogeneity=0.000), while the polymorphism of rs696 appeared to play a protective role in tumorigenesis (CC+CT vs. TT: OR=0.879, 95%CI=0.787–0.982, Pheterogeneity=0.107). When stratification analysis was performed by cancer type, an increased association of rs3138053 was recognized in hepatocarcinoma (C vs. T: OR=42.180, 95%CI=27.970–63.612, Pheterogeneity=0.007), while a decreased association of rs696 was identified in Hodgkin lymphoma (C vs. T: OR=0.792, 95%CI=0.656–0.956, Pheterogeneity=0.116; CC vs. TT: OR=0.658, 95%CI=0.448–0.965, Pheterogeneity=0.076; CC vs. CT+TT: OR=0.734, 95%CI=0.562–0.958, Pheterogeneity=0.347). By ethnicity, rs696 appears to be a protective candidate among Caucasians (CT vs. TT: OR=0.809, 95%CI=0.676–0.969, Pheterogeneity=0.459). Conclusions Our data demonstrated that the rs3138053 polymorphism of NFKBIA gene is a candidate for susceptibility to overall cancers, while rs696 plays a protective role.
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Affiliation(s)
- Meng Zhang
- Department of Urology, Shenzhen Second People's Hospital, Clinical Medicine College of Anhui Medical University, Shenzhen, Anhui, China (mainland)
| | - Junjie Huang
- Department of Medicine, Shenzhen University, Shenzhen, Anhui, China (mainland)
| | - Xiuxiu Tan
- Department of Urology, Shenzhen Second People's Hospital, Clinical Medicine College of Anhui Medical University, Shenzhen, Anhui, China (mainland)
| | - Jian Bai
- Department of Urology, Shenzhen Second People's Hospital, Clinical Medicine College of Anhui Medical University, Shenzhen, Anhui, China (mainland)
| | - Hao Wang
- Department of Urology, Shenzhen Second People's Hospital, Clinical Medicine College of Anhui Medical University, Shenzhen, Anhui, China (mainland)
| | - Yukun Ge
- Department of Urology, Shenzhen Second People's Hospital, Clinical Medicine College of Anhui Medical University, Shenzhen, Anhui, China (mainland)
| | - Hu Xiong
- Department of Urology, Shenzhen Second People's Hospital, Clinical Medicine College of Anhui Medical University, Shenzhen, Anhui, China (mainland)
| | - Jizhou Shi
- Department of Medicine, Shengli Oilfield Central Hospital, Dongying, Shandong, China (mainland)
| | - Wei Lu
- Department of Urology, Shenzhen Second People's Hospital, Clinical Medicine College of Anhui Medical University, Shenzhen, Anhui, China (mainland)
| | - Zhaojie Lv
- Department of Urology, Shenzhen Second People's Hospital, Clinical Medicine College of Anhui Medical University, Shenzhen, Anhui, China (mainland)
| | - Chaozhao Liang
- Department of Urology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China (mainland)
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Liang K, Zhu L, Tan J, Shi W, He Q, Yu B. Identification of autophagy signaling network that contributes to stroke in the ischemic rodent brain via gene expression. Neurosci Bull 2015; 31:480-90. [PMID: 26254060 DOI: 10.1007/s12264-015-1547-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 07/09/2015] [Indexed: 11/24/2022] Open
Abstract
Autophagy plays a vital role in cerebral ischemia and may be a potential target for developing novel therapy for stroke. In this study, we constructed an autophagy-related pathway network by analyzing the genes related to autophagy and ischemic stroke, and the risk genes were screened. Two autophagy-related modules were significantly up-regulated and clustered to influence cerebral ischemia. Besides, three key modular genes (NFKB1, RELA, and STAT3) were revealed. With 5-fold cross validation, the ROC curves of NFKB1, RELA, and STAT3 were 0.8256, 0.8462, and 0.8923. They formed a complex module and competitively mediated the activation of autophagy in cerebral ischemia. In conclusion, a module containing NFKB1, RELA, and STAT3 mediates autophagy, serving as a potential biomarker for the diagnosis and therapy of ischemic stroke.
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Affiliation(s)
- Kun Liang
- Department of Vascular Surgery, Huashan Hospital, Fudan University, Shanghai, 200040, China
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20
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Geng P, Ou J, Li J, Liao Y, Wang N, Sa R, Xiang L, Liang H. Genetic Association Between NFKBIA -881A>G Polymorphism and Cancer Susceptibility. Medicine (Baltimore) 2015; 94:e1024. [PMID: 26252270 PMCID: PMC4616602 DOI: 10.1097/md.0000000000001024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Several epidemiological studies have focused on the role of nuclear factor-kappa-B inhibitor-alpha (NFKBIA) -881 A>G polymorphism in cancer susceptibility. However, the published data have led to contentious results. This study was designed to examine the association between -881 A>G polymorphism and cancer risk.Comprehensive search of PubMed, Web of science and Embase, identified a total of 5 case-control studies. To assess the association, comparison among all subjects plus subgroup analysis by ethnicity was performed and odds ratio (OR) along with 95% confidence interval (CI) was calculated with the fixed-effect model or the random-effects model dependent on the heterogeneity.The pooling data consisting of 1965 cancer cases and 2717 cancer-free controls demonstrated no significant association with overall cancer risk. However, the subgroup of Asian populations showed statistical evidence for an increase in risk of cancer (GG vs. AA, OR, 2.14; 95% CI, 1.03-4.46; GG + GA vs. AA, OR, 1.22; 95% CI, 1.01-1.47; GG vs. GA + AA, OR, 2.09; 95% CI, 1.01-4.34).This investigation on the association of -881 A>G polymorphism and cancer susceptibility reveals that -881 A>G polymorphism may act as a candidate for cancer development in Asian populations.
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Affiliation(s)
- Peiliang Geng
- From the Department of Oncology and Southwest Cancer Center, Southwest Hospital Third Military Medical University, Chongqing, China
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Arslan S, Korkmaz Ö, Özbilüm N, Berkan Ö. Association between NF-κBI and NF-κBIA polymorphisms and coronary artery disease. Biomed Rep 2015; 3:736-740. [PMID: 26405555 DOI: 10.3892/br.2015.499] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 07/22/2015] [Indexed: 12/31/2022] Open
Abstract
Coronary artery disease (CAD) is the leading cause of fatalities worldwide. Nuclear factor (NF)-κB is a transcription factor that controls cell proliferation, differentiation and immunity. To the best of our knowledge, the present study is the first investigation of the association between CAD and NF-κB1 -94 W/D/NF-κBIA 3'-untranslated region (3'-UTR) A→G polymorphisms. The study population comprised 226 CAD patients and 201 controls. There was no significant difference in NF-κB1A 3'-UTR A→G in the allele and genotype frequencies between case and control populations. The D allele frequency of NF-κB1 -94 in the case group was significantly higher compared to the control group (P=0.028, odds ratio=1.37). The genotype frequency of NF-κB1 -94 DD in the case group was significantly higher compared to the controls (P=0.028). Linkage analysis showed a close linkage among these 2 genes (P<0.001 for case and control), and AD and GD haplotypes were associated with CAD (P<0.001; P=0.015, respectively). NF-κB1 -94 DD genotype can be a significant risk factor for the development of CAD.
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Affiliation(s)
- Serdal Arslan
- Department of Medical Biology, Cumhuriyet University, 58140 Sivas, Turkey
| | - Özge Korkmaz
- Department of Cardiovascular Surgery, Faculty of Medicine, Cumhuriyet University, 58140 Sivas, Turkey
| | - Nil Özbilüm
- Department of Molecular Biology and Genetics, Faculty of Science, Cumhuriyet University, 58140 Sivas, Turkey
| | - Öcal Berkan
- Department of Cardiovascular Surgery, Faculty of Medicine, Cumhuriyet University, 58140 Sivas, Turkey
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22
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Han X, Zhang JJ, Yao N, Wang G, Mei J, Li B, Li C, Wang ZA. Polymorphisms in NFKB1 and NFKBIA Genes Modulate the Risk of Developing Prostate Cancer among Han Chinese. Med Sci Monit 2015; 21:1707-15. [PMID: 26068031 PMCID: PMC4473804 DOI: 10.12659/msm.893471] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Background Nuclear factor kappa B (NF-κB) pathway proteins play an important role in modulating inflammation and other carcinogenic processes. Polymorphisms within NF-κB pathway genes may influence cancer risk. This study aimed to examine the association between NFKB19-4 ATTG ins→del, NFKBIA 3′ UTR A→G, -826CT and -881AG polymorphisms and prostate cancer risk among Chinese. Material/Methods The polymorphisms were genotyped via PCR-RFLP technique on 936 prostate cancer patients and 936 population-based healthy controls. Logistic regression model was used to measure the risk association present. Results With the exception of NFKBIA 3′ UTR polymorphism, the heterozygous and mutant genotypes of the other polymorphisms were significantly associated with prostate cancer risk. For NFKB1 polymorphism, a decreased risk was observed, with adjusted OR: 0.69; 95% CI: 0.44, 0.98; P=0.01 (heterozygous) and adjusted OR: 0.60; 95% CI: 0.37, 0.91; P=0.02 (mutant). NFKBIA -826CT and -881AG polymorphisms were in complete linkage disequilibrium and shared the same risk association, with adjusted OR: 1.34; 95% CI: 1.09, 1.62; P=0.02 (heterozygous) and adjusted OR: 2.83; 95% CI: 1.79, 4.50; P=0.01 (mutants). Interestingly, the impact of the NFKB1 polymorphism was not present in nonsmokers and younger (<60 years) subjects (P<0.05). Conclusions In conclusion, polymorphisms in NFKB1 and NFKBIA genes may modulate the risk of developing prostate cancer among Chinese.
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Affiliation(s)
- Xiao Han
- Internal Medicine-Oncology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, China (mainland)
| | - Jia-Jun Zhang
- Department of Urology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, China (mainland)
| | - Nan Yao
- Department of Pathology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, China (mainland)
| | - Gang Wang
- Department of Urology, Bengbu Third People's Hospital, Bengbu, Anhui, China (mainland)
| | - Juan Mei
- Department of Pathology, The Second Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, China (mainland)
| | - Bo Li
- Department of Urology, The People's Liberation Army 123rd Hospital China, Bengbu, Anhui, China (mainland)
| | - Chao Li
- Department of Urology, Bengbu First People's Hospital, Bengbu, Anhui, China (mainland)
| | - Zi-An Wang
- Internal Medicine-Oncology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, China (mainland)
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Wang Z, Liu QL, Sun W, Yang CJ, Tang L, Zhang X, Zhong XM. Genetic polymorphisms in inflammatory response genes and their associations with breast cancer risk. Croat Med J 2015; 55:638-46. [PMID: 25559835 PMCID: PMC4295076 DOI: 10.3325/cmj.2014.55.638] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Aim To explore the association of NFKB1 c.-798_-795delATTG (rs28362491), NFKBIA c.-949C>T (rs2233406), IL-8 c.-352A>T (rs4073), IL-10 c.-854T>C (rs1800871), TNF c.-418G>A (rs361525), and TNF c.-488G>A (rs1800629) polymorphisms with breast cancer risk in an East Chinese population. Methods We conducted a case-control study including 975 study participants (474 breast cancer patients and 501 female controls without cancer) and genotyped the polymorphisms employing polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Logistic regression was used to assess the association of the polymorphisms with breast cancer risk. Results We found that the ins/del and del/del genotypes of NFKB1 polymorphism and TT genotype of IL-10 polymorphism significantly increased breast cancer risk (NFKB1 ins/del odds ratio [OR] 1.69, 95% [CI] 1.23-2.33, P = 0.001; NFKB1 del/del OR 2.42, 95% CI 1.72-3.42, P < 0.001; IL-10 TT OR 2.36, 95% CI 1.58-3.52, P < 0.001). On the other hand, the TT genotype of IL-8 polymorphism, GA and AA genotypes of TNF c.-418G>A polymorphism, and GA genotype of TNF c.-488G>A polymorphism significantly reduced breast cancer risk (IL-8 TT OR 0.48, 95% CI 0.33-0.72, P < 0.001; TNF c.-418 GA OR 0.58, 95% CI 0.41-0.80, P = 0.001; TNF c.-418 AA OR 0.38, 95% CI 0.14-0.98, P = 0.044; TNF c.-488 GA OR 0.68, 95% CI 0.48-0.96, P = 0.029). When stratified by menopausal status, the CT genotype of NFKBIA polymorphism significantly reduced the risk among pre-menopausal women (OR 0.63, 95% CI 0.40-0.99, P = ,043), but not among post-menopausal women. Conclusions NFKB1, NFKBIA, IL-8, IL-10, and TNF polymorphisms could serve as useful predictive biomarkers for breast cancer risk among women in East China.
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Affiliation(s)
| | | | | | | | | | | | - Xiao-Ming Zhong
- Xiao-Ming Zhong, Department of Radiotherapy, Jiangxi Province Cancer Hospital, No. 519, Beijing East Road, Nanchang, Jiangxi 330029, China,
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Zhen Y, Pan W, Hu F, Wu H, Feng J, Zhang Y, Chen J. Exogenous hydrogen sulfide exerts proliferation/anti-apoptosis/angiogenesis/migration effects via amplifying the activation of NF-κB pathway in PLC/PRF/5 hepatoma cells. Int J Oncol 2015; 46:2194-204. [PMID: 25738635 DOI: 10.3892/ijo.2015.2914] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 02/13/2015] [Indexed: 01/08/2023] Open
Abstract
Hydrogen sulfide (H2S) takes part in a diverse range of intracellular pathways and hss physical and pathological properties in vitro and in vivo. However, the effects of H2S on cancer are controversial and remain unclear. The present study investigates the effects of H2S on liver cancer progression via activating NF-κB pathway in PLC/PRF/5 hepatoma cells. PLC/PRF/5 hepatoma cells were pretreated with 500 µmol/l NaHS (a donor of H2S) for 24 h. The expression levels of CSE, CBS, phosphosphorylate (p)-NF-κB p65, caspase-3, COX-2, p-IκB and MMP-2 were measured by western blot assay. Cell viability was detected by cell counter kit 8 (CCK-8). Apoptotic cells were observed by Hoechst 33258 staining assay. The production level of H2S in cell culture medium was measured by using the sulfur-sensitive electrode method. The production of vascular endothelial growth factor (VEGF) was tested by enzyme-linked immunosorbent assay (ELISA). Our results showed that the production of H2S was dramatically increased in the PLC/PRF/5 hepatoma cells, compared with human LO2 hepatocyte cells group, along with the overexpression levels of CSE and CBS. Treatment of PLC/PRF/5 hepatoma cells with 500 µmol/l NaHS (a donor of H2S) for 24 h markedly increased the expression levels of CSE, CBS, p-IκB and NF-κB activation, leading to COX-2 and MMP-2 overexpression, and decreased caspase-3 production, as well as increased cell viability and decreased number of apoptotic cells. Otherwise, the production level of H2S and VEGF were also significantly increased. Furthermore, co-treatment of PLC/PRF/5 hepatoma cells with 500 µmol/l NaHS and 200 µmol/l PDTC for 24 h significantly overturned these indexes. The findings of the present study provide evidence that the NF-κB is involved in the NaHS-induced cell proliferation, anti-apoptisis, angiogenesis, and migration in PLC/PRF/5 hepatoma cells, and that the PDTC against the NaHS-induced effects were by inhibition of the NF-κB pathway.
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Affiliation(s)
- Yulan Zhen
- Oncology Center, Affiliated Hospital of Guangdong Medical College, Zhanjiang, Guangdong 524001, P.R. China
| | - Wanying Pan
- Department of Anesthesiology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510700, P.R. China
| | - Fen Hu
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510700, P.R. China
| | - Hongfu Wu
- Department of Physiology, Guangdong Medical College, Zhanjiang, Guangdong 524001, P.R. China
| | - Jianqiang Feng
- Department of Physiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, P.R. China
| | - Ying Zhang
- Oncology Center, Affiliated Hospital of Guangdong Medical College, Zhanjiang, Guangdong 524001, P.R. China
| | - Jingfu Chen
- Department of Cardiovasology and Cardiac Care Unit (CCU), Huangpu Division, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510700, P.R. China
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Gao J, Xu HL, Gao S, Zhang W, Tan YT, Rothman N, Purdue M, Gao YT, Zheng W, Shu XO, Xiang YB. Genetic polymorphism of NFKB1 and NFKBIA genes and liver cancer risk: a nested case-control study in Shanghai, China. BMJ Open 2014; 4:e004427. [PMID: 24578542 PMCID: PMC3939648 DOI: 10.1136/bmjopen-2013-004427] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
OBJECTIVES Genetic variations of nuclear factor-κB (NF-κB) signalling pathway were found to be associated with inflammatory diseases and several malignancies. However, little is known about NF-κB pathway gene polymorphisms and susceptibility of liver cancer. The aim of this study was to investigate whether genetic variants of NFKB1 and NFKBIA were associated with risk of liver cancer in a Chinese population. DESIGN The study was designed as a nested case-control study within two prospective cohorts (the Shanghai Women's Health Study, SWHS, 1996-2000 and the Shanghai Men's Health Study, SMHS, 2002-2006). SETTINGS This population-based study was conducted in urban Shanghai, China. PARTICIPANTS A total of 217 incident liver cancer cases diagnosed through 31 December 2009 and 427 healthy controls matched by sex, age at baseline (±2 years) and date (±30 days) of sample collection were included in the study. PRIMARY AND SECONDARY OUTCOME MEASURES Genetic polymorphisms of NFKB1 and NFKBIA were determined blindly by TaqMan single-nucleotide polymorphism (SNP) genotyping assay. OR and its 95% CIs were estimated by an unconditional logistic regression model to measure the association between selected SNPs and the risk of liver cancer. RESULTS After adjusted for potential confounding factors, rs28362491 ins/del or del/del genotypes were associated with higher risk of liver cancer with an adjusted OR 1.54 (95% CI 1.04 to 2.28). rs230496 AG and GG genotypes were also noted with higher risk of liver cancer with an adjusted OR 1.53 (95% CI 1.03 to 2.26). Haplotype analysis indicated that carriers of the NFKB1 GA and AA (rs230525-rs230530) haplotypes had higher risk of liver cancer under an additive model. No association was observed between NFKBIA variants and risk of live cancer. CONCLUSIONS Our results suggest that genetic variants of NFKB1 influence liver cancer susceptibility in Chinese population, although replication in other studies is needed.
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Affiliation(s)
- Jing Gao
- State Key Laboratory of Oncogene and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
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Mahajanakatti AB, Murthy G, Sharma N, Skariyachan S. Exploring inhibitory potential of Curcumin against various cancer targets by in silico virtual screening. Interdiscip Sci 2014; 6:13-24. [DOI: 10.1007/s12539-014-0170-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2013] [Revised: 06/04/2013] [Accepted: 06/17/2013] [Indexed: 12/17/2022]
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Effects of NFKB1 and NFKBIA gene polymorphisms on hepatocellular carcinoma susceptibility and clinicopathological features. PLoS One 2013; 8:e56130. [PMID: 23457512 PMCID: PMC3573054 DOI: 10.1371/journal.pone.0056130] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 01/05/2013] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Constitutive activation of nuclear factor (NF)-κB is frequently observed in hepatocellular carcinoma (HCC). The current study examined associations of polymorphisms within promoter regions of NFKB1 encoding NF-κB1 and NFKBIA encoding IκBα with the susceptibility of developing HCC and clinicopathological characteristics of the tumors. METHODOLOGY AND PRINCIPAL FINDINGS Genetic polymorphisms of NFKB1 and NFKBIA were analyzed by a real-time polymerase chain reaction (PCR) in 135 HCC patients and 520 healthy controls. The genotypic frequency of the NFKB1 -94 Ins polymorphism in HCC patients was significantly higher than that of the controls (adjusted odds ratio (AOR) = 2.23; 95% confidence interval (CI) 1.32∼3.77). No statistical significance was observed for the distribution frequency of the NFKBIA --519 C/T, -826 C/T, or -881 A/G genotype and haplotype polymorphisms between HCC patients and controls. Furthermore, female HCC patients carrying the NFKB1 -94 Ins polymorphism were associated with lower clinical stages and smaller tumor sizes. CONCLUSIONS Our results indicate that the NFKB1 -94 Ins promoter polymorphism increased the risk of HCC, and may be applied as a predictive factor for the clinical stage and tumor size in female HCC patients.
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Slattery ML, John EM, Torres-Mejia G, Lundgreen A, Herrick JS, Baumgartner KB, Hines LM, Stern MC, Wolff RK. Genetic variation in genes involved in hormones, inflammation and energetic factors and breast cancer risk in an admixed population. Carcinogenesis 2012; 33:1512-21. [PMID: 22562547 DOI: 10.1093/carcin/bgs163] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Breast cancer incidence rates are characterized by unique racial and ethnic differences. Native American ancestry has been associated with reduced breast cancer risk. We explore the biological basis of disparities in breast cancer risk in Hispanic and non-Hispanic white women by evaluating genetic variation in genes involved in inflammation, insulin and energy homeostasis in conjunction with genetic ancestry. Hispanic (2111 cases, 2597 controls) and non-Hispanic white (1481 cases, 1586 controls) women enrolled in the 4-Corner's Breast Cancer Study, the Mexico Breast Cancer Study and the San Francisco Bay Area Breast Cancer Study were included. Genetic admixture was determined from 104 ancestral informative markers that discriminate between European and Native American ancestry. Twenty-one genes in the CHIEF candidate pathway were evaluated. Higher Native American ancestry was associated with reduced risk of breast cancer (odds ratio = 0.79, 95% confidence interval 0.65, 0.95) but was limited to postmenopausal women (odds ratio = 0.66, 95% confidence interval 0.52, 0.85). After adjusting for genetic ancestry and multiple comparisons, four genes were significantly associated with breast cancer risk, NFκB1, NFκB1A, PTEN and STK11. Within admixture strata, breast cancer risk among women with low Native American ancestry was associated with IkBKB, NFκB1, PTEN and RPS6KA2, whereas among women with high Native American ancestry, breast cancer risk was associated with IkBKB, mTOR, PDK2, PRKAA1, RPS6KA2 and TSC1. Higher Native American ancestry was associated with reduced breast cancer risk. Breast cancer risk differed by genetic ancestry along with genetic variation in genes involved in inflammation, insulin, and energy homeostasis.
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Affiliation(s)
- Martha L Slattery
- University of Utah, Department of Medicine295 Chipeta Way Salt Lake City, Utah 84108, USA.
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de Jong OG, Verhaar MC, Chen Y, Vader P, Gremmels H, Posthuma G, Schiffelers RM, Gucek M, van Balkom BWM. Cellular stress conditions are reflected in the protein and RNA content of endothelial cell-derived exosomes. J Extracell Vesicles 2012; 1:18396. [PMID: 24009886 PMCID: PMC3760650 DOI: 10.3402/jev.v1i0.18396] [Citation(s) in RCA: 456] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Revised: 03/21/2012] [Accepted: 03/21/2012] [Indexed: 12/14/2022] Open
Abstract
Background The healthy vascular endothelium, which forms the barrier between blood and the surrounding tissues, is known to efficiently respond to stress signals like hypoxia and inflammation by adaptation of cellular physiology and the secretion of (soluble) growth factors and cytokines. Exosomes are potent mediators of intercellular communication. Their content consists of RNA and proteins from the cell of origin, and thus depends on the condition of these cells at the time of exosome biogenesis. It has been suggested that exosomes protect their target cells from cellular stress through the transfer of RNA and proteins. We hypothesized that endothelium-derived exosomes are involved in the endothelial response to cellular stress, and that exosome RNA and protein content reflect the effects of cellular stress induced by hypoxia, inflammation or hyperglycemia. Methods We exposed cultured endothelial cells to different types of cellular stress (hypoxia, TNF-α-induced activation, high glucose and mannose concentrations) and compared mRNA and protein content of exosomes produced by these cells by microarray analysis and a quantitative proteomics approach. Results We identified 1,354 proteins and 1,992 mRNAs in endothelial cell-derived exosomes. Several proteins and mRNAs showed altered abundances after exposure of their producing cells to cellular stress, which were confirmed by immunoblot or qPCR analysis. Conclusion Our data show that hypoxia and endothelial activation are reflected in RNA and protein exosome composition, and that exposure to high sugar concentrations alters exosome protein composition only to a minor extend, and does not affect exosome RNA composition.
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Affiliation(s)
- Olivier G de Jong
- Department of Nephrology and Hypertension, UMC Utrecht, Utrecht, The Netherlands
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Effects of NFKB1 and NFKBIA gene polymorphisms on susceptibility to environmental factors and the clinicopathologic development of oral cancer. PLoS One 2012; 7:e35078. [PMID: 22509384 PMCID: PMC3324415 DOI: 10.1371/journal.pone.0035078] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Accepted: 03/08/2012] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Oral cancer, which is the fourth most common cancer in Taiwanese men, is associated with environmental carcinogens. The possibility that genetic predisposition in nuclear factor-kappa B (NF-κB)-signaling pathways activation is linked to the development of oral squamous cell carcinoma (OSCC) requires investigation. The current study examines associations between polymorphisms within promoter regions of NFKB1 encoding NF-κB1 and NFKBIA encoding IkappaBalpha (IκBα) with both the susceptibility to develop OSCC and the clinicopathological characteristics of the tumors. METHODOLOGY/PRINCIPAL FINDINGS Genetic polymorphisms of NFKB1 and NFKBIA were analyzed by a real-time polymerase chain reaction (real-time PCR) for 462 patients with oral cancer and 520 non-cancer controls. We found that NFKB1 -94 ATGG1/ATGG2, -94 ATGG2/ATGG2, and the combination of -94 ATGG1/ATGG2 and ATGG2/ATGG2 genotypes NFKBIA -826 T (CT+TT) and -881 G (AG+GG) allelic carriages, were more prevalent in OSCC patients than in non-cancer participants. Moreover, we found that NFKB1 or NFKBIA gene polymorphisms seem to be related to susceptibility to develop oral cancer linked to betel nut and tobacco consumption. Finally, patients with oral cancer who had at least one -519 T allele of the NFKBIA gene were at higher risk for developing distant metastasis (P<.05), compared with those patients CC homozygotes. CONCLUSIONS Our results suggest that NFKB1 -94 ATTG2, NFKBIA -826 T, and -881 G alleles are associated with oral carcinogenesis. The combination of NFKB1 or NFKBIA gene polymorphisms and environmental carcinogens appears related to an increased risk of oral cancer. More importantly, the genetic polymorphism of NFKBIA -519 might be a predictive factor for the distal metastasis of OSCC in Taiwanese.
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Arslan S, Engin A. Relationship between NF-κB1 and NF-κBIA genetic polymorphisms and Crimean-Congo hemorrhagic fever. ACTA ACUST UNITED AC 2011; 44:138-43. [DOI: 10.3109/00365548.2011.623313] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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Fujii M, Honma M, Takahashi H, Ishida-Yamamoto A, Iizuka H. The nuclear factor kappa B p50 subunit and cortactin as markers to distinguish between keratoacanthoma and well-differentiated squamous cell carcinoma. Clin Exp Dermatol 2011; 36:788-92. [PMID: 21883393 DOI: 10.1111/j.1365-2230.2011.04118.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND Distinguishing keratoacanthoma (KA) from well-differentiated squamous cell carcinoma (SCC) is sometimes difficult. Recent evidence indicates that the nuclear factor kappa B p50 subunit (p50) and cortactin might be useful to distinguish between these two conditions. AIM To verify whether p50 and cortactin are useful differentiation markers to distinguish between subungual KA and well-differentiated SCC. METHODS Immunohistochemistry using p50, cortactin and Ki-67 was performed on 20 patients with KA and 20 patients with facial well-differentiated SC. Ki-67 staining was also evaluated and scored. RESULTS Both p50 and cortactin had higher levels of expression in KA than in SCC. Both were localized to the basal-cell layer of KA, whereas they were scattered without polarity throughout the SCC lesions. Although the Ki-67 index was not significantly different between KA and SCC, the staining pattern also showed loss of polarity in SCC. CONCLUSION p50 and cortactin might be useful makers to distinguish between KA and well-differentiated SCC.
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Affiliation(s)
- M Fujii
- Department of Dermatology, Asahikawa Medical University, Asahikawa, Japan.
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Song S, Chen D, Lu J, Liao J, Luo Y, Yang Z, Fu X, Fan X, Wei Y, Yang L, Wang L, Wang J. NFκB1 and NFκBIA polymorphisms are associated with increased risk for sporadic colorectal cancer in a southern Chinese population. PLoS One 2011; 6:e21726. [PMID: 21738780 PMCID: PMC3128094 DOI: 10.1371/journal.pone.0021726] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Accepted: 06/06/2011] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Nuclear factor κB (NFκB) plays a key role in the regulation of apoptosis. The function of NFκB is inhibited by binding to NFκB inhibitor (IκB), and disruption of the balance of NFκB and IκB is related to the development of many diseases, including tumors. Therefore, we hypothesized that the NFκB1 (-94del/insATTG) and NFκBIA (2758 A>G) polymorphisms were associated with colorectal cancer (CRC) susceptibility. METHODS In a hospital-based case-control study of 1001 CRC patients and 1005 cancer-free controls frequency matched by age and sex, we genotyped polymorphisms using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method and performed luciferase assays and Western blotting analysis to identify whether genetic variants in NFκBIA alter its gene expressions and functions and thus cancer risk. RESULTS We found that both NFκB1-94 ins/delATTG and NFκBIA 2758 A>G polymorphisms were correlated with CRC risk (OR = 1.47; 95%CI = 1.14-1.86, and OR = 1.38; 95% CI = 1.14-1.66, respectively). Furthermore, when evaluated these two polymorphisms together, the combined genotypes with 2 variant (risk) alleles (2758GG and -94ins/ins+del/ins) were associated with an increased risk of CRC (OR = 1.71; 95% CI = 1.23-2.38) compared to 0 variant, and the significant trend for 2 variant (risk) alleles were more pronounced among subgroups of aged <60 years, women, never drinkers, never smokers, persons with a normal BMI and those with a family history of cancer(P(trend)<0.01). Moreover, luciferase assays showed that the G allele in the 3'UTR significantly decreased NFκBIA mRNA stability and the A allele regulation by miRNA449a in vitro and that the NFκBIA protein expression levels of the AA+AG variant carriers were significantly higher in peritumoral tissues than those of the 2758GG genotype. CONCLUSION NFκB1 and NFκBIA polymorphisms appear to jointly contribute to risk of CRC. These two variants may be a genetic modifier for CRC susceptibility in this southern Chinese population.
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Affiliation(s)
- Shunxin Song
- Gastrointestinal Institute of Sun Yat-Sen University, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
- Department of Colorectal Surgery, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Dianke Chen
- Gastrointestinal Institute of Sun Yat-Sen University, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Jiachun Lu
- The Institute for Chemical Carcinogenesis, The State Key Laboratory of Respiratory Disease, Guangzhou Medical College, Guangzhou, People's Republic of China
| | - Jiawei Liao
- Gastrointestinal Institute of Sun Yat-Sen University, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Yanxin Luo
- Gastrointestinal Institute of Sun Yat-Sen University, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
- Department of Colorectal Surgery, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Zuli Yang
- Gastrointestinal Institute of Sun Yat-Sen University, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
- Department of Colorectal Surgery, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Xinhui Fu
- Gastrointestinal Institute of Sun Yat-Sen University, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Xinjuan Fan
- Gastrointestinal Institute of Sun Yat-Sen University, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Yisheng Wei
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Guangzhou Medical College, Guangzhou, People's Republic of China
| | - Lei Yang
- The Institute for Chemical Carcinogenesis, The State Key Laboratory of Respiratory Disease, Guangzhou Medical College, Guangzhou, People's Republic of China
| | - Lei Wang
- Gastrointestinal Institute of Sun Yat-Sen University, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
- Department of Colorectal Surgery, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
- * E-mail: (JW); (LW)
| | - Jianping Wang
- Gastrointestinal Institute of Sun Yat-Sen University, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
- Department of Colorectal Surgery, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, People's Republic of China
- * E-mail: (JW); (LW)
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Zou YF, Yuan FL, Feng XL, Tao JH, Ding N, Pan FM, Wang F. Association Between NFKB1 -94ins/delATTG Promoter Polymorphism and Cancer Risk: A Meta-Analysis. Cancer Invest 2010; 29:78-85. [DOI: 10.3109/07357907.2010.535054] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Honma M, Kato N, Hashimoto M, Takahashi H, Ishida-Yamamoto A, Iizuka H. Subungual keratoacanthoma: analysis of cell proliferation and copy number variation of oncogenes compared with periungual squamous cell carcinoma. Clin Exp Dermatol 2010; 36:57-62. [DOI: 10.1111/j.1365-2230.2010.03841.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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A combined analysis of genome-wide association studies in breast cancer. Breast Cancer Res Treat 2010; 126:717-27. [PMID: 20872241 DOI: 10.1007/s10549-010-1172-9] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2010] [Accepted: 09/09/2010] [Indexed: 01/03/2023]
Abstract
In an attempt to identify common disease susceptibility alleles for breast cancer, we performed a combined analysis of three genome-wide association studies (GWAS), involving 2,702 women of European ancestry with invasive breast cancer and 5,726 controls. Tests for association were performed for 285,984 SNPs. Evidence for association with SNPs in genes in specific pathways was assessed using a permutation-based approach. We confirmed associations with loci reported by previous GWAS on 1p11.2, 2q35, 3p, 5p12, 8q24, 10q23.13, 14q24.1 and 16q. Six SNPs with the strongest signals of association with breast cancer, and which have not been reported previously, were typed in two further studies; however, none of the associations could be confirmed. Suggestive evidence for an excess of associations was found for genes involved in the regulation of actin cytoskeleton, glycan degradation, alpha-linolenic acid metabolism, circadian rhythm, hematopoietic cell lineage and drug metabolism. Androgen and oestrogen metabolism, a pathway previously found to be associated with the development of postmenopausal breast cancer, was marginally significant (P = 0.051 [unadjusted]). These results suggest that further analysis of SNPs in these pathways may identify associations that would be difficult to detect through agnostic single SNP analyses. More effort focused in these aspects of oncology can potentially open up promising avenues for the understanding of breast cancer and its prevention.
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Rajaraman P, Brenner AV, Neta G, Pfeiffer R, Wang SS, Yeager M, Thomas G, Fine HA, Linet MS, Rothman N, Chanock SJ, Inskip PD. Risk of meningioma and common variation in genes related to innate immunity. Cancer Epidemiol Biomarkers Prev 2010; 19:1356-61. [PMID: 20406964 DOI: 10.1158/1055-9965.epi-09-1151] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND The etiology of meningioma, the second most common type of adult brain tumor in the United States, is largely unknown. Prior studies indicate that history of immune-related conditions may affect the risk of meningioma. METHODS To identify genetic markers for meningioma in genes involved with innate immunity, we conducted an exploratory association study of 101 meningioma cases and 330 frequency-matched controls of European ancestry using subjects from a hospital-based study conducted by the National Cancer Institute. We genotyped 1,407 "tag" single nucleotide polymorphisms (SNP) in 148 genetic regions chosen on the basis of an r2>0.8 and minor allele frequency of >5% in Caucasians in HapMap1. Risk of meningioma was estimated by odds ratios and 95% confidence intervals. RESULTS Seventeen SNPs distributed across 12 genetic regions (NFKB1 (3), FCER1G (3), CCR6 (2), VCAM1, CD14, TNFRSF18, RAC2, XDH, C1D, TLR1/TLR10/TLR6, NOS1, and DEFA5) were associated with the risk of meningioma with P<0.01. Although individual SNP tests were not significant after controlling for multiple comparisons, gene region-based tests were statistically significant (P<0.05) for TNFRSF18, NFKB1, FCER1G, CD14, C1D, CCR6, and VCAM1. CONCLUSIONS AND IMPACT Our results indicate that common genetic polymorphisms in innate immunity genes may be associated with risk of meningioma. Given the small sample size, replication of these results in a larger study of meningioma is needed.
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Affiliation(s)
- Preetha Rajaraman
- Division of Cancer Epidemiology and Genetics, Neuro-oncology Branch, National Cancer Institute, NIH, Department of Health and Human Services, 6120 Executive Boulevard, EPS Room 7058, Bethesda, MD 20892-7238, USA.
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Babar M, Ennis D, Abdel-Latif M, Byrne PJ, Ravi N, Reynolds JV. Differential molecular changes in patients with asymptomatic long-segment Barrett's esophagus treated by antireflux surgery or medical therapy. Am J Surg 2010; 199:137-43. [DOI: 10.1016/j.amjsurg.2008.11.032] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2008] [Revised: 11/21/2008] [Accepted: 11/21/2008] [Indexed: 12/17/2022]
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Senol Tuncay S, Okyay P, Bardakci F. Identification of NF-kappaB1 and NF-kappaBIAlpha polymorphisms using PCR-RFLP assay in a Turkish population. Biochem Genet 2009; 48:104-12. [PMID: 19941056 DOI: 10.1007/s10528-009-9302-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2008] [Accepted: 07/07/2009] [Indexed: 12/15/2022]
Abstract
A polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay was used in a Turkish population to determine the frequency of polymorphisms of the nuclear factor-kappa (NF-kappaB1) and NF-kappaBIA genes, which have been shown to be related to several inflammatory diseases and cancer pathogenesis. Total genomic DNA was isolated from peripheral blood samples taken from 565 healthy volunteers living in Aydin Province. The genomic regions in question were amplified by PCR, and the polymorphisms in these regions were detected by a PCR-RFLP assay. The frequencies were 10.3% for the NF-kappaB1 -94ins/delATTG del/del genotype, 49.1% for del/ins, and 40.6% for ins/ins. The genotype frequencies of the NF-kappaBIA 3'UTR A --> G genotypes were A/A 19.2%, A/G 42.3%, and G/G 38.5%. Distribution of genotype frequencies was tested by Hardy-Weinberg; the NF-kappaB1 gene was in Hardy-Weinberg equilibrium (chi(2) = 3.402, P > 0.05), the NF-kappaBIA gene was not (chi(2) = 8.293, P < 0.05).
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Affiliation(s)
- Serap Senol Tuncay
- Department of Biology, Faculty of Arts and Sciences, Adnan Menderes University, Aydin, Turkey
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He Y, Zhang H, Yin J, Xie J, Tan X, Liu S, Zhang Q, Li C, Zhao J, Wang H, Cao G. IkappaBalpha gene promoter polymorphisms are associated with hepatocarcinogenesis in patients infected with hepatitis B virus genotype C. Carcinogenesis 2009; 30:1916-22. [PMID: 19797428 PMCID: PMC2783005 DOI: 10.1093/carcin/bgp226] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Genetic predisposition of nuclear factor-kappa B (NF-κB)-signaling pathways linking inflammation to hepatitis B virus (HBV)-induced hepatocellular carcinoma (HCC) remains unresolved. We conducted a case–control study to determine the associations of the polymorphisms within the promoter regions of NFKB1 encoding NF-κB1 and NFKBIA encoding IkappaBalpha with the development of HCC. A total of 404 healthy controls, 482 non-HCC subjects with HBV infection and 202 patients with HCC were included. NFKB1 −94ATTG2 allele and GG allele in the 3′-untranslated region of NFKBIA were more prevalent in HCC patients than in the healthy controls. NFKBIA −826CT and NFKBIA −881AG allelic carriages were more prevalent in HCC patients than in the non-HCC subjects with HBV infection. The estimated haplotype frequency of NFKBIA promoter −881G−826T−519C was significantly higher in the patients with HCC than in the HBV-infected subjects without HCC (odds ratio = 3.142, P = 0.002). As compared with the HBV-infected subjects without HCC, NFKBIA −826 T and NFKBIA −881AG allelic carriages were only associated with HCC risk in the subjects with HBV genotype C. The association of NFKBIA −881AG allelic carriage with HCC risk was not affected by liver cirrhosis (LC) status, alanine aminotransferase level and hepatitis B e antigen status. By multivariate regression analysis, NFKB1 −94ATTG2, NFKBIA −826T, NFKBIA −881AG and HBV genotype C were independently associated with an increased risk of HCC. In conclusion, NFKB1 −94ATTG2 allele and haplotype −881G−826T−519C in NFKBIA promoter were associated with hepatocarcinogenesis. NFKBIA −826T and −881AG were associated with the risk of HCC in the subjects infected with HBV genotype C.
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Affiliation(s)
- Yongchao He
- Department of Epidemiology, the 1st Affiliated Hospital, Second Military Medical University, Shanghai 200433, People's Republic of China
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Gao J, Arbman G, He L, Qiao F, Zhang Z, Zhao Z, Rosell J, Sun XF. MANBA polymorphism was related to increased risk of colorectal cancer in Swedish but not in Chinese populations. Acta Oncol 2009; 47:372-8. [PMID: 17899454 DOI: 10.1080/02841860701644052] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
beta-mannosidase, encoded by MANBA, has been suggested to be implicated in cancers, while genetic variations in the MANBA in relation to colorectal cancer (CRC) risk has not been examined. In this study, we investigated the relationship of a polymorphic CA repeat in MANBA gene with CRC risk in 152 Swedish CRC patients and 441 Swedish controls, and 196 Chinese CRC patients and 577 Chinese controls, as well as the clinicopathologic significance of this polymorphism on CRC patients, by using capillary electrophoresis. The MANBA genotypes were related to CRC risk in the Swedish population (p=0.03), but not in the Chinese population. In the Swedish population, individuals with < 22 CAs/< 22 CAs had significantly increased risk for CRC compared with those with >or=22 CAs/>or= 22 CAs (gender-age-adjusted analysis: OR 1.93, 95% CI 1.06-3.51). There was no relationship between the polymorphism and clinicopathologic variables. These findings suggest the different susceptibilities of this polymorphism to CRC development in the two populations.
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Affiliation(s)
- Jingfang Gao
- Department of Oncology, Institute of Biomedicine and Surgery, Linköping University, Linköping, Sweden.
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Lee JY, Park AK, Lee KM, Park SK, Han S, Han W, Noh DY, Yoo KY, Kim H, Chanock SJ, Rothman N, Kang D. Candidate gene approach evaluates association between innate immunity genes and breast cancer risk in Korean women. Carcinogenesis 2009; 30:1528-31. [PMID: 19372141 DOI: 10.1093/carcin/bgp084] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES This study was conducted to investigate the role of common variation in innate immunity-related genes as susceptibility factors to breast cancer risk in Korean women. METHODS Total 1536 single-nucleotide polymorphisms (SNPs) in 203 genes were analyzed by Illumina GoldenGate assay in 209 cases and the same numbers of controls. Both SNP and gene-based tests were used to evaluate the association with breast cancer risk. The robustness of results was further evaluated with permutation method, false discovery rate and haplotype analyses. RESULTS Both SNP and gene-based analyses showed promising associations with breast cancer risk for 17 genes: OR10J3, FCER1A, NCF4, CNTNAP1, CTNNB1, KLKB1, ITGB2, ALOX12B, KLK2, IRAK3, KLK4, STAT6, NCF2, CCL1, C1QR1, MBP and NOS1. The most significant association with breast cancer risk was observed for the OR10J3 SNP (rs2494251, P-value = 1.2 x 10(-4)) and FCER1A SNP (rs7548864, P-value = 7.7 x 10(-4)). Gene-based permutation and false discovery rate P-values for OR10J3 SNP (rs2494251) with breast cancer risk were also significant (P = 4 x 10(-5) and 0.008, respectively). Haplotype analyses supported these findings that OR10J3 and FCER1A were most significantly associated with risk for breast cancer (P = 2 x 10(-4) and 0.004, respectively). CONCLUSION This study suggests that common genetic variants in the OR10J3 and FCER1A be strongly associated with breast cancer risk among Korean women.
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Affiliation(s)
- Ji-Young Lee
- Department of Preventive Medicine, Seoul National University College of Medicine, 103 Daehak-Ro, Jongno-Gu, Seoul 110-799, Korea
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Lo SS, Chen JH, Wu CW, Lui WY. Functional polymorphism of NFKB1 promoter may correlate to the susceptibility of gastric cancer in aged patients. Surgery 2009; 145:280-5. [PMID: 19231580 DOI: 10.1016/j.surg.2008.11.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2008] [Accepted: 11/13/2008] [Indexed: 11/29/2022]
Abstract
BACKGROUND Activated nuclear factor-kappaB (NF-kappaB) is associated reportedly with the pathogenesis of numerous malignancies. This study investigated whether a common insertion (ins)/deletion (del) polymorphism (-94 ins/del ATTG) in the NFKB1 promoter is associated with susceptibility to gastric cancer and its tumor behavior. METHODS Blood samples from 182 gastric cancer patients and 116 controls were examined by polymerase chain reaction-based genotyping. Allelotype and genotype (polymorphism) of NFKB1 promoter in gastric cancer patients were analyzed with controls and patients' clinicopathologic factors to evaluate their association using a multivariate analytical model. RESULTS The mean ages of patients and controls were 65.7 +/- 12.8, and 64.9 +/- 8.8 years old, respectively. Sex ratios (male to female) were 2.7:1 and 2.2:1, respectively. Insertion allelotype, genotypes with ins/ins, as well as ins allele carrier (ins/ins+ ins/del) were significantly greater in gastric cancer patients than in controls, especially in patients >65 years old, but not in younger patients. The polymorphism did not correlate with clinicopathologic factors and patient survival. CONCLUSION NFKB1 could be a susceptible gene for gastric cancer and its functional polymorphism in promoter is associated with the risk of gastric cancer, particularly in aged patients.
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Affiliation(s)
- Su-Shun Lo
- Department of Surgery, National Yang Ming University Hospital, I-Lan, Taiwan.
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Bu H, Rosdahl I, Sun XF, Zhang H. Importance of polymorphisms in NF-κB1 and NF-κBIα genes for melanoma risk, clinicopathological features and tumor progression in Swedish melanoma patients. J Cancer Res Clin Oncol 2007; 133:859-66. [PMID: 17492467 DOI: 10.1007/s00432-007-0228-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/10/2007] [Indexed: 01/29/2023]
Abstract
PURPOSE Importance of polymorphisms in NF-kappaB1 and NF-kappaBIalpha genes for melanoma risk, clinicopathological features and tumor progression is analyzed in Swedish melanoma patients. PATIENTS AND METHODS Functional polymorphisms of NF-kappaB1 and NF-kappaBIalpha genes were examined in 185 melanoma patients and 438 tumor-free individuals. Associations of the polymorphisms with melanoma risk, age and pigment phenotypes of the patients and clinicopathological tumor characteristics were analyzed. DNAs were isolated from mononuclear cells of venous blood. Polymorphisms of the genes were genotyped by a PCR-RFLP technique, and transcription level of NF-kappaBIalpha was examined by a quantitative real-time reverse transcription PCR. RESULTS Both ATTG insertion polymorphism of NF-kappaB1 and A to G polymorphism of NF-kappaBIalpha genes were correlated with melanoma risk, especially, in a combination of ATTG( 2 )/ATTGT(2) and GG. NF-kappaB1 ATTG(2)/ATTG(2) and NF-kappaBIalpha GG genotypes were associated with male gender and age >65 years (at diagnosis). Patients with ATTG(1)/ATTG(1 )genotype had thinner tumors and lower Clark levels at diagnosis. Frequency of ATTG(1)/ATTG(1) genotype was higher in patients with melanomas on intermittently sun-exposed pattern of the body and NF-kappaBIalpha GG was more frequent in the patients with melanomas at rarely exposed sites. There were no differences in the gene transcription level between patients with different NF-kappaBIalpha genotypes. CONCLUSION NF-kappaB1 and NF-kappaBIalpha genes might be susceptible genes for melanoma risk and functional polymorphisms of these genes might be biological predictors for melanoma progression.
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Affiliation(s)
- Huajie Bu
- Department of Dermatology, Institute of Biomedicine and Surgery, Linköping University, 581 85, Linköping, Sweden
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Gao J, Pfeifer D, He LJ, Qiao F, Zhang Z, Arbman G, Wang ZL, Jia CR, Carstensen J, Sun XF. Association of NFKBIA polymorphism with colorectal cancer risk and prognosis in Swedish and Chinese populations. Scand J Gastroenterol 2007; 42:345-50. [PMID: 17354114 DOI: 10.1080/00365520600880856] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
OBJECTIVE The inhibitory proteins, IkappaBs, regulate the activity of nuclear factor kappa-beta (NF-kappaB), which is implicated in tumorigenesis by regulating expression of a variety of genes involved in cellular transformation, proliferation, invasion, angiogenesis and metastasis. Variants in the genes encoding IkappaBs may be involved in cancer development through the activation of NF-kappaB. The objective of this study was to investigate the susceptibility of an A to G variation (rs696) in the 3' UTR of NFKBIA (encoding IkappaBalpha) to colorectal cancer (CRC) and the association of this polymorphism with clinicopathologic variables in CRC patients. MATERIAL AND METHODS A case-control study was carried out on a Swedish (155 CRCs, 438 controls) and a Chinese population (199 CRCs, 577 controls). The genotype of NFKBIA was determined by PCR-restriction fragment length polymorphism. RESULTS The frequency of the AG genotype was increased in the Chinese patients >or=50 years of age compared with the Chinese controls (odds ratio (OR)=3.06, 95% confidence interval (CI)=1.55-6.02, p=0.001), even when adjusted for age (OR=3.20, 95% CI=1.61-6.38, p=0.001). The GG genotype of NFKBIA was related to a poorer survival rate in the Swedish patients, independent of gender, age, tumour location, Dukes' stage and differentiation (hazard ratio = 3.10, 95% Cl=1.28-7.60, p=0.01). CONCLUSIONS Chinese individuals >or=50 years of age carrying the AG genotype of NFKBIA may be at an increased risk of developing CRC, and the GG genotype of NFKBIA may be considered as a prognostic factor for Swedish CRC patients.
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Affiliation(s)
- Jingfang Gao
- Department of Oncology, Institute of Biomedicine and Surgery, Linköping University, Linköping, Sweden
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Romzova M, Hohenadel D, Kolostova K, Pinterova D, Fojtikova M, Ruzickova S, Dostal C, Bosak V, Rychlik I, Cerna M. NFkappaB and its inhibitor IkappaB in relation to type 2 diabetes and its microvascular and atherosclerotic complications. Hum Immunol 2006; 67:706-13. [PMID: 17002901 DOI: 10.1016/j.humimm.2006.05.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2006] [Accepted: 05/23/2006] [Indexed: 02/06/2023]
Abstract
Nuclear factor kappa B (NFkappaB) is an important transcription factor that together with its inhibitor (IkappaB) participates in the activation of genes involved in immune responses. We examined the CA repeat polymorphism of the NFKB1 gene (encoding for NFkappaB) and A/G point variation in the 3'UTR region of the nuclear factor kappa B inhibitor alpha (NFKBIA) gene (encoding for IkappaB) in Czech and German patients with type 2 diabetes. The sample consisted of 211 patients, both with and without kidney complications, and 159 controls. Additionally, 152 patients with systemic lupus erythematosus (SLE) were genotyped for NFKBIA polymorphism. We observed a significant increase in the homozygous AA genotype of the NFKBIA gene when compared with the control group (the highest value was in diabetics without diabetic nephropathy [p(c)* = 0.0015, odds ratio = 3.59]). No differences were seen between the SLE and control groups. With regard to the polymorphism of the NFKB1 gene, we did not observe any significant differences between the groups. Since the AA genotype of the NFKBIA gene presents a risk for type 2 diabetes development but not for diabetic nephropathy alone, we believe that the NFkappaB gene polymorphism can influence the pathogenesis of diabetes mellitus and affect its complications. Negative findings relative to other inflammatory autoimmune diseases, such as SLE, suggest a specific relationship between NFkappaB and type 2 diabetes mellitus.
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Affiliation(s)
- Marianna Romzova
- Department of Cell and Molecular Biology, 3rd Medical Faculty of Charles University, Prague, Czech Republic.
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Lin SC, Liu CJ, Yeh WI, Lui MT, Chang KW, Chang CS. Functional polymorphism in NFKB1 promoter is related to the risks of oral squamous cell carcinoma occurring on older male areca (betel) chewers. Cancer Lett 2006; 243:47-54. [PMID: 16387424 DOI: 10.1016/j.canlet.2005.11.019] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2005] [Revised: 10/31/2005] [Accepted: 11/18/2005] [Indexed: 01/07/2023]
Abstract
Areca (betel)-chewing is tightly associated with the high prevalence of oral squamous cell carcinoma (OSCC) in Asians. NFKB1 encodes a 105kDa protein that can be processed to produce p50 subunit of nuclear factor-kappaB protein complex. A insertion (ins)/deletion (del) polymorphism (-94ins/delATTG) in NFKB1 promoter, which may drive the ins allele two-fold increase in NFKB1 transcription relative to del allele, was recently found. This study identified that the odds ratio in OSCC carrying ins allelotype were 1.78 relative to controls (56.7 vs 41.8%) in subjects more than 50 years old. L allelotype of Heme oxygenase-1 (HO-1), accounting for a long (GT)(n) repeat in HO-1 promoter, is associated with the risks of areca-related OSCC. Subjects carried both NFKB1 ins and HO-1 L allelotypes had significant risks for various subsets of OSCC. OSCC with lymph node metastasis or advanced stage had significantly higher frequency of NFKB1 ins and HO-1 L allelotypes. This study suggested that the functional NFKB1promoter polymorphism could be valuable for assessment of cancer risk.
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Affiliation(s)
- Shu-Chun Lin
- School of Dentistry, National Yang-Ming University, Li-Nong St, Sec. 2, Taipei 112, Taiwan, ROC
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Orozco G, Sánchez E, Collado MD, López-Nevot MA, Paco L, García A, Jiménez-Alonso J, Martín J. Analysis of the functional NFKB1 promoter polymorphism in rheumatoid arthritis and systemic lupus erythematosus. ACTA ACUST UNITED AC 2005; 65:183-6. [PMID: 15713218 DOI: 10.1111/j.1399-0039.2005.00341.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nuclear factor (NF)-kappaB plays an important role in inflammatory diseases such as rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE). A functional insertion/deletion polymorphism (-94ins/delATTG) has been identified in the promoter of the NFKB1 gene. In addition, a polymorphic dinucleotide repeat (CA) has been identified in proximity to the coding region of the human NFKB1 gene. The aim of the present study was to investigate the influence of both the -94ins/delATTG and the (CA) microsatellite NFKB1 polymorphisms in the susceptibility/severity of RA and SLE. We analyzed the distribution of -94ins/delATTG and the multiallelic (CA)(n) repeat in 272 RA patients, 181 SLE patients, and 264 healthy controls from Southern Spain, in both cases using a polymerase chain reaction-fluorescent method. No statistically significant difference in the distribution of the -94delATTG NFKB1 genotypes and alleles between RA patients, SLE patients, and control subjects was observed. Similarly, we found no statistically significant differences in the (CA)(n) microsatellite allele frequency between controls and RA patients or SLE patients. In addition, no association was found between the above mentioned NFKB1 polymorphisms with any of the demographic and clinical parameters tested either in RA or in SLE patients. From these results, it seems that the -94ins/delATTG and the (CA)(n) repeat of NFKB1 gene may not play a relevant role in RA and/or SLE in our population.
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Affiliation(s)
- G Orozco
- Instituto de Parasitología y Biomedicina, Granada, Spain
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Sun X, Wei L, Lidén J, Hui G, Dahlman-Wright K, Hjerpe A, Dobra K. Molecular characterization of tumour heterogeneity and malignant mesothelioma cell differentiation by gene profiling. J Pathol 2005; 207:91-101. [PMID: 16007577 DOI: 10.1002/path.1810] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Malignant mesothelioma is an aggressive tumour, characterized by a variable differentiation pattern and poor prognosis. At present, the clinical outcome in patients with malignant mesothelioma is mainly predicted by the morphological phenotype of the tumour. However, this conventional clinicopathological parameter is of limited value, partly because of the biological heterogeneity of this tumour and poor understanding of the regulatory mechanisms underlying the various patterns of growth. To elucidate the intrinsic molecular programmes that determine tumour differentiation, oligonucleotide arrays were used in an in vitro model of mesothelioma differentiation. The analysis of 2059 genes detected 102 genes that were significantly deregulated. Clustering of these genes into functional categories showed distinctive patterns for the two phenotypes, namely epithelioid and sarcomatoid. The molecular fingerprint of the sarcomatoid tumour component indicates overrepresentation of growth factor receptors and growth factor binding proteins, whereas epithelioid mesothelioma cells express other tumour-promoting factors involved in differentiation, metabolism, and regulation of apoptosis. These differences in the molecular phenotype may give a better basis for diagnosis and for designing novel therapies.
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Affiliation(s)
- Xiaojuan Sun
- Department of Laboratory Medicine, Division of Pathology, Huddinge University Hospital, F-46, Karolinska Institutet, S-141 86 Stockholm, Sweden
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Abba MC, Drake JA, Hawkins KA, Hu Y, Sun H, Notcovich C, Gaddis S, Sahin A, Baggerly K, Aldaz CM. Transcriptomic changes in human breast cancer progression as determined by serial analysis of gene expression. Breast Cancer Res 2004; 6:R499-513. [PMID: 15318932 PMCID: PMC549167 DOI: 10.1186/bcr899] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2004] [Revised: 05/21/2004] [Accepted: 05/25/2004] [Indexed: 11/17/2022] Open
Abstract
Introduction Genomic and transcriptomic alterations affecting key cellular processes such us cell proliferation, differentiation and genomic stability are considered crucial for the development and progression of cancer. Most invasive breast carcinomas are known to derive from precursor in situ lesions. It is proposed that major global expression abnormalities occur in the transition from normal to premalignant stages and further progression to invasive stages. Serial analysis of gene expression (SAGE) was employed to generate a comprehensive global gene expression profile of the major changes occurring during breast cancer malignant evolution. Methods In the present study we combined various normal and tumor SAGE libraries available in the public domain with sets of breast cancer SAGE libraries recently generated and sequenced in our laboratory. A recently developed modified t test was used to detect the genes differentially expressed. Results We accumulated a total of approximately 1.7 million breast tissue-specific SAGE tags and monitored the behavior of more than 25,157 genes during early breast carcinogenesis. We detected 52 transcripts commonly deregulated across the board when comparing normal tissue with ductal carcinoma in situ, and 149 transcripts when comparing ductal carcinoma in situ with invasive ductal carcinoma (P < 0.01). Conclusion A major novelty of our study was the use of a statistical method that correctly accounts for the intra-SAGE and inter-SAGE library sources of variation. The most useful result of applying this modified t statistics beta binomial test is the identification of genes and gene families commonly deregulated across samples within each specific stage in the transition from normal to preinvasive and invasive stages of breast cancer development. Most of the gene expression abnormalities detected at the in situ stage were related to specific genes in charge of regulating the proper homeostasis between cell death and cell proliferation. The comparison of in situ lesions with fully invasive lesions, a much more heterogeneous group, clearly identified as the most importantly deregulated group of transcripts those encoding for various families of proteins in charge of extracellular matrix remodeling, invasion and cell motility functions.
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Affiliation(s)
- Martin C Abba
- Department of Carcinogenesis, The University of Texas MD Anderson Cancer Center, Science Park – Research Division, Smithville, Texas, USA
| | - Jeffrey A Drake
- Department of Carcinogenesis, The University of Texas MD Anderson Cancer Center, Science Park – Research Division, Smithville, Texas, USA
| | - Kathleen A Hawkins
- Department of Carcinogenesis, The University of Texas MD Anderson Cancer Center, Science Park – Research Division, Smithville, Texas, USA
| | - Yuhui Hu
- Department of Carcinogenesis, The University of Texas MD Anderson Cancer Center, Science Park – Research Division, Smithville, Texas, USA
| | - Hongxia Sun
- Department of Carcinogenesis, The University of Texas MD Anderson Cancer Center, Science Park – Research Division, Smithville, Texas, USA
| | - Cintia Notcovich
- Department of Carcinogenesis, The University of Texas MD Anderson Cancer Center, Science Park – Research Division, Smithville, Texas, USA
| | - Sally Gaddis
- Department of Carcinogenesis, The University of Texas MD Anderson Cancer Center, Science Park – Research Division, Smithville, Texas, USA
| | - Aysegul Sahin
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Keith Baggerly
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - C Marcelo Aldaz
- Department of Carcinogenesis, The University of Texas MD Anderson Cancer Center, Science Park – Research Division, Smithville, Texas, USA
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