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Ahsan T, Shoily SS, Ahmed T, Sajib AA. Role of the redox state of the Pirin-bound cofactor on interaction with the master regulators of inflammation and other pathways. PLoS One 2023; 18:e0289158. [PMID: 38033031 PMCID: PMC10688961 DOI: 10.1371/journal.pone.0289158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 07/10/2023] [Indexed: 12/02/2023] Open
Abstract
Persistent cellular stress induced perpetuation and uncontrolled amplification of inflammatory response results in a shift from tissue repair toward collateral damage, significant alterations of tissue functions, and derangements of homeostasis which in turn can lead to a large number of acute and chronic pathological conditions, such as chronic heart failure, atherosclerosis, myocardial infarction, neurodegenerative diseases, diabetes, rheumatoid arthritis, and cancer. Keeping the vital role of balanced inflammation in maintaining tissue integrity in mind, the way to combating inflammatory diseases may be through identification and characterization of mediators of inflammation that can be targeted without hampering normal body function. Pirin (PIR) is a non-heme iron containing protein having two different conformations depending on the oxidation state of the iron. Through exploration of the Pirin interactome and using molecular docking approaches, we identified that the Fe2+-bound Pirin directly interacts with BCL3, NFKBIA, NFIX and SMAD9 with more resemblance to the native binding pose and higher affinity than the Fe3+-bound form. In addition, Pirin appears to have a function in the regulation of inflammation, the transition between the canonical and non-canonical NF-κB pathways, and the remodeling of the actin cytoskeleton. Moreover, Pirin signaling appears to have a critical role in tumor invasion and metastasis, as well as metabolic and neuro-pathological complications. There are regulatory variants in PIR that can influence expression of not only PIR but also other genes, including VEGFD and ACE2. Disparity exists between South Asian and European populations in the frequencies of variant alleles at some of these regulatory loci that may lead to differential occurrence of Pirin-mediated pathogenic conditions.
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Affiliation(s)
- Tamim Ahsan
- Molecular Biotechnology Division, National Institute of Biotechnology, Savar, Dhaka, Bangladesh
| | - Sabrina Samad Shoily
- Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Tasnim Ahmed
- Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Abu Ashfaqur Sajib
- Department of Genetic Engineering & Biotechnology, University of Dhaka, Dhaka, Bangladesh
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2
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Niu Z, Jiang D, Shen J, Liu W, Tan X, Cao G. Potential Role of the Fragile Histidine Triad in Cancer Evo-Dev. Cancers (Basel) 2023; 15:cancers15041144. [PMID: 36831487 PMCID: PMC9954361 DOI: 10.3390/cancers15041144] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/07/2023] [Accepted: 02/09/2023] [Indexed: 02/15/2023] Open
Abstract
Cancer development follows an evolutionary pattern of "mutation-selection-adaptation" detailed by Cancer Evolution and Development (Cancer Evo-Dev), a theory that represents a process of accumulating somatic mutations due to the imbalance between the mutation-promoting force and the mutation-repairing force and retro-differentiation of the mutant cells to cancer initiation cells in a chronic inflammatory microenvironment. The fragile histidine triad (FHIT) gene is a tumor suppressor gene whose expression is often reduced or inactivated in precancerous lesions during chronic inflammation or virus-induced replicative stress. Here, we summarize evidence regarding the mechanisms by which the FHIT is inactivated in cancer, including the loss of heterozygosity and the promoter methylation, and characterizes the role of the FHIT in bridging macroevolution and microevolution and in facilitating retro-differentiation during cancer evolution and development. It is suggested that decreased FHIT expression is involved in several critical steps of Cancer Evo-Dev. Future research needs to focus on the role and mechanisms of the FHIT in promoting the transformation of pre-cancerous lesions into cancer.
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Affiliation(s)
- Zheyun Niu
- Shanghai East Hospital, Key Laboratory of Arrhythmias, Ministry of Education, Tongji University School of Medicine Tongji University, Shanghai 200120, China
| | - Dongming Jiang
- Shanghai East Hospital, Key Laboratory of Arrhythmias, Ministry of Education, Tongji University School of Medicine Tongji University, Shanghai 200120, China
| | - Jiaying Shen
- Shanghai East Hospital, Key Laboratory of Arrhythmias, Ministry of Education, Tongji University School of Medicine Tongji University, Shanghai 200120, China
| | - Wenbin Liu
- Shanghai Key Laboratory of Medical Bioprotection, Shanghai 200433, China
- Key Laboratory of Biological Defense, Ministry of Education, Shanghai 200433, China
- Department of Epidemiology, Second Military Medical University, Shanghai 200433, China
| | - Xiaojie Tan
- Shanghai Key Laboratory of Medical Bioprotection, Shanghai 200433, China
- Key Laboratory of Biological Defense, Ministry of Education, Shanghai 200433, China
- Department of Epidemiology, Second Military Medical University, Shanghai 200433, China
| | - Guangwen Cao
- Shanghai East Hospital, Key Laboratory of Arrhythmias, Ministry of Education, Tongji University School of Medicine Tongji University, Shanghai 200120, China
- Shanghai Key Laboratory of Medical Bioprotection, Shanghai 200433, China
- Key Laboratory of Biological Defense, Ministry of Education, Shanghai 200433, China
- Department of Epidemiology, Second Military Medical University, Shanghai 200433, China
- Correspondence: ; Tel.: +86-21-81871060
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Zhao S, Wu Y, Dai Z, Chen Y, Zhou X, Zhao J. Risk factors for antibiotic resistance and mortality in patients with bloodstream infection of Escherichia coli. Eur J Clin Microbiol Infect Dis 2022; 41:713-721. [PMID: 35190911 DOI: 10.1007/s10096-022-04423-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 02/11/2022] [Indexed: 12/19/2022]
Abstract
This study aimed to investigate the risk factors for bloodstream infection (BSI) caused by extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli (E. coli) and related mortality. The clinical data of 388 patients with E. coli BSI were analyzed. Blood cultures were performed and the antimicrobial susceptibility profiles of the resulting isolates were determined. Four single-nucleotide polymorphisms (rs231775, rs12343816, rs16944, and rs2233406) were genotyped using real-time PCR. ESBL were detected by disk diffusion confirmatory testing. Univariate and multivariate regression analyses were applied to identify the risk factors for ESBL-producing isolates and the BSI-induced mortality. The prevalence of ESBL-producing E. coli in BSI patients was 40.98%. E. coli isolates were commonly susceptible to carbapenem and β-lactam/β-lactamase inhibitor combinations. The major ESBL genes were CTX-M-14, CTX-M-55, CTX-M-15, and CTX-M-27. The proportion of CTX-M-15 was significantly higher in patients over 70 years and those receiving stomach tube catheterization. Nosocomial infection, biliary tract infection, stomach tube catheterization, and previous cephalosporin administration were independent risk factors for ESBL-producing isolates. ESBL positivity, nosocomial infection, and cancer were independent risk factors of mortality. Two genetic polymorphisms associated with inflammation activation, rs231775 A allele and rs2233406 T allele, significantly increased the mortality risk of E. coli BSI with a risk ratio (95% CI) of 1.93 (1.05-3.55) and 4.38 (2.07-9.29), respectively. For patients with nosocomial infection, biliary tract infection, and cancer, the monitor of BSI and antibiotic susceptibility should be enhanced. The invasive procedures should be minimized. rs231775 and rs2233406 are promising prognostic markers for E. coli BSI patients.
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Affiliation(s)
- Shunjin Zhao
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Lanxi Branch (Lanxi People's Hospital), Lanxi, 321100, China
| | - Yingjing Wu
- Emergency Department, The Second Affiliated Hospital of Zhejiang University School of Medicine, Lanxi Branch (Lanxi People's Hospital), Lanxi, 321100, China
| | - Zhong Dai
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Lanxi Branch (Lanxi People's Hospital), Lanxi, 321100, China
| | - Yijing Chen
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Zhejiang University School of Medicine, Lanxi Branch (Lanxi People's Hospital), Lanxi, 321100, China
| | - Xiaojuan Zhou
- Bacterium Room, The Second Affiliated Hospital of Zhejiang University School of Medicine, Lanxi Branch (Lanxi People's Hospital), Lanxi, 321100, China
| | - Jun Zhao
- Department of Respiratory and Critical Care Medicine, Zhejiang Medical & Health Group Hangzhou Hospital, 1 Banshan Road, Hangzhou, 310022, China.
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4
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Wang H, Zhang J, Lu Z, Dai W, Ma C, Xiang Y, Zhang Y. Identification of potential therapeutic targets and mechanisms of COVID-19 through network analysis and screening of chemicals and herbal ingredients. Brief Bioinform 2022; 23:bbab373. [PMID: 34505138 PMCID: PMC8499921 DOI: 10.1093/bib/bbab373] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/06/2021] [Accepted: 08/23/2021] [Indexed: 12/12/2022] Open
Abstract
After experiencing the COVID-19 pandemic, it is widely acknowledged that a rapid drug repurposing method is highly needed. A series of useful drug repurposing tools have been developed based on data-driven modeling and network pharmacology. Based on the disease module, we identified several hub proteins that play important roles in the onset and development of the COVID-19, which are potential targets for repositioning approved drugs. Moreover, different network distance metrics were applied to quantify the relationship between drug targets and COVID-19 disease targets in the protein-protein-interaction (PPI) network and predict COVID-19 therapeutic effects of bioactive herbal ingredients and chemicals. Furthermore, the tentative mechanisms of candidates were illustrated through molecular docking and gene enrichment analysis. We obtained 15 chemical and 15 herbal ingredient candidates and found that different drugs may play different roles in the process of virus invasion and the onset and development of the COVID-19 disease. Given pandemic outbreaks, our method has an undeniable immense advantage in the feasibility analysis of drug repurposing or drug screening, especially in the analysis of herbal ingredients.
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Affiliation(s)
- Hong Wang
- Chongqing Key Research Laboratory for Drug Metabolism, College of Pharmacy, Chongqing Medical University, Chongqing, 400016, China
- Medical Data Science Academy, Chongqing Medical University, Chongqing, 400016, China
- Chongqing Engineering Research Center for Clinical Big-data and Drug Evaluation, Chongqing Medical University, Chongqing, 401331, China
| | - Jingqing Zhang
- Chongqing Key Research Laboratory for Drug Metabolism, College of Pharmacy, Chongqing Medical University, Chongqing, 400016, China
| | - Zhigang Lu
- Department of Neurology, The First People's Hospital of Jingmen affiliated to Hubei Minzu University, Jingmen, 448000, China
| | - Weina Dai
- Chongqing Key Research Laboratory for Drug Metabolism, College of Pharmacy, Chongqing Medical University, Chongqing, 400016, China
| | - Chuanjiang Ma
- Chongqing Key Research Laboratory for Drug Metabolism, College of Pharmacy, Chongqing Medical University, Chongqing, 400016, China
| | - Yun Xiang
- Gynaecology and Obstetrics, Guangzhou Women and Children's Medical Center, Guangzhou, 510623, China
| | - Yonghong Zhang
- Chongqing Key Research Laboratory for Drug Metabolism, College of Pharmacy, Chongqing Medical University, Chongqing, 400016, China
- Medical Data Science Academy, Chongqing Medical University, Chongqing, 400016, China
- Chongqing Engineering Research Center for Clinical Big-data and Drug Evaluation, Chongqing Medical University, Chongqing, 401331, China
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5
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Liu W, Deng Y, Li Z, Chen Y, Zhu X, Tan X, Cao G. Cancer Evo-Dev: A Theory of Inflammation-Induced Oncogenesis. Front Immunol 2021; 12:768098. [PMID: 34880864 PMCID: PMC8645856 DOI: 10.3389/fimmu.2021.768098] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/04/2021] [Indexed: 12/13/2022] Open
Abstract
Chronic inflammation is a prerequisite for the development of cancers. Here, we present the framework of a novel theory termed as Cancer Evolution-Development (Cancer Evo-Dev) based on the current understanding of inflammation-related carcinogenesis, especially hepatocarcinogenesis induced by chronic infection with hepatitis B virus. The interaction between genetic predispositions and environmental exposures, such as viral infection, maintains chronic non-resolving inflammation. Pollution, metabolic syndrome, physical inactivity, ageing, and adverse psychosocial exposure also increase the risk of cancer via inducing chronic low-grade smoldering inflammation. Under the microenvironment of non-resolving inflammation, pro-inflammatory factors facilitate the generation of somatic mutations and viral mutations by inducing the imbalance between the mutagenic forces such as cytidine deaminases and mutation-correcting forces including uracil-DNA glycosylase. Most cells with somatic mutations and mutated viruses are eliminated in survival competition. Only a small percentage of mutated cells survive, adapt to the hostile environment, retro-differentiate, and function as cancer-initiating cells via altering signaling pathways. These cancer-initiating cells acquire stem-ness, reprogram metabolic patterns, and affect the microenvironment. The carcinogenic process follows the law of "mutation-selection-adaptation". Chronic physical activity reduces the levels of inflammation via upregulating the activity and numbers of NK cells and lymphocytes and lengthening leukocyte telomere; downregulating proinflammatory cytokines including interleukin-6 and senescent lymphocytes especially in aged population. Anti-inflammation medication reduces the occurrence and recurrence of cancers. Targeting cancer stemness signaling pathways might lead to cancer eradication. Cancer Evo-Dev not only helps understand the mechanisms by which inflammation promotes the development of cancers, but also lays the foundation for effective prophylaxis and targeted therapy of various cancers.
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Affiliation(s)
- Wenbin Liu
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Yang Deng
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Tai’an, China
| | - Zishuai Li
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Yifan Chen
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Xiaoqiong Zhu
- Department of Nutrition, School of Public Health, Anhui Medical University, Hefei, China
| | - Xiaojie Tan
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Guangwen Cao
- Department of Epidemiology, Second Military Medical University, Shanghai, China
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6
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Nong W, Ma L, Lan B, Liu N, Yang H, Lao X, Deng Q, Huang Z. Comprehensive Identification of Bridge Genes to Explain the Progression from Chronic Hepatitis B Virus Infection to Hepatocellular Carcinoma. J Inflamm Res 2021; 14:1613-1624. [PMID: 33907440 PMCID: PMC8071210 DOI: 10.2147/jir.s298977] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 03/16/2021] [Indexed: 12/16/2022] Open
Abstract
Background Hepatitis B virus infection co-occurs in 33% of individuals with hepatocellular carcinoma worldwide. However, the molecular link between hepatitis B virus and hepatocellular carcinoma is unknown. Thus, we aimed to elucidate molecular linkages underlying pathogenesis through in-depth data mining analysis. Materials and Methods Differentially expressed genes were identified from patients with chronic hepatitis B virus infection, hepatocellular carcinoma, or both. Gene set enrichment analysis revealed signaling pathways involving differentially expressed genes. Protein-protein interaction networks, protein crosstalk, and enrichment were analyzed to determine whether differentially expressed gene products might serve as a bridge from hepatitis B virus infection to hepatocellular carcinoma pathogenesis. Prognostic potential and transcriptional and post-transcriptional regulators of bridge genes were also examined. Results We identified vital bridge factors in hepatitis B virus infection-associated hepatocellular carcinoma. Differentially expressed genes were clustered into modules based on relative protein function. Signaling pathways associated with cancer, inflammation, immune system, and microenvironment showed significant crosstalk between modules. Thirty-two genes were dysregulated in hepatitis B virus infection-mediated hepatocellular carcinoma. CPEB3, RAB26, SLCO1B1, ST3GAL6 and XK had higher connectivity in the modular network, suggesting significant associations with survival. CDC20 and NUP107 were identified as driver genes as well as markers of poor prognosis. Conclusion Our results suggest that the sustained inflammatory environment created by hepatitis B virus infection is a risk factor for hepatocellular carcinoma. The identification of hepatitis B virus infection-related hepatocellular carcinoma bridge genes provides testable hypotheses about the pathogenesis of hepatocellular carcinoma.
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Affiliation(s)
- Wenwei Nong
- Department of General Surgery, Affiliated Minzu Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Liping Ma
- Department of Clinical Laboratory, Affiliated Minzu Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Biyang Lan
- Department of General Surgery, Affiliated Minzu Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Ning Liu
- Department of General Surgery, Affiliated Minzu Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Hongzhi Yang
- Department of General Surgery, Affiliated Minzu Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Xiaoxia Lao
- Department of Clinical Laboratory, Affiliated Minzu Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Qiaomei Deng
- Department of Clinical Laboratory, Affiliated Minzu Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Zhihu Huang
- Department of Clinical Laboratory, Affiliated Minzu Hospital of Guangxi Medical University, Nanning, People's Republic of China
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7
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Zhang Z, Wang C, Liu Z, Zou G, Li J, Lu M. Host Genetic Determinants of Hepatitis B Virus Infection. Front Genet 2019; 10:696. [PMID: 31475028 PMCID: PMC6702792 DOI: 10.3389/fgene.2019.00696] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 07/03/2019] [Indexed: 12/14/2022] Open
Abstract
Chronic hepatitis B virus (HBV) infection is still a major health problem worldwide. Recently, a great number of genetic studies based on single nucleotide polymorphisms (SNPs) and genome-wide association studies have been performed to search for host determinants of the development of chronic HBV infection, clinical outcomes, therapeutic efficacy, and responses to hepatitis B vaccines, with a focus on human leukocyte antigens (HLA), cytokine genes, and toll-like receptors. In addition to SNPs, gene insertions/deletions and copy number variants are associated with infection. However, conflicting results have been obtained. In the present review, we summarize the current state of research on host genetic factors and chronic HBV infection, its clinical type, therapies, and hepatitis B vaccine responses and classify published results according to their reliability. The potential roles of host genetic determinants of chronic HBV infection identified in these studies and their clinical significance are discussed. In particular, HLAs were relevant for HBV infection and pathogenesis. Finally, we highlight the need for additional studies with large sample sizes, well-matched study designs, appropriate statistical methods, and validation in multiple populations to improve the treatment of HBV infection.
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Affiliation(s)
- Zhenhua Zhang
- Department of Infectious Diseases, the Second Affiliated Hospital of Anhui Medical University, Hefei, China
- College of Pharmacy, Anhui Medical University, Hefei, China
| | - Changtai Wang
- Department of Infectious Diseases, the Affiliated Anqing Hospital of Anhui Medical University, Anqing, China
| | - Zhongping Liu
- Department of Infectious Diseases, the Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Guizhou Zou
- Department of Infectious Diseases, the Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Jun Li
- College of Pharmacy, Anhui Medical University, Hefei, China
| | - Mengji Lu
- Institute of Virology, University Hospital of Duisburg-Essen, Essen, Germany
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Yang F, Ma L, Yang Y, Liu W, Zhao J, Chen X, Wang M, Zhang H, Cheng S, Shen F, Wang H, Zhou W, Cao G. Contribution of Hepatitis B Virus Infection to the Aggressiveness of Primary Liver Cancer: A Clinical Epidemiological Study in Eastern China. Front Oncol 2019; 9:370. [PMID: 31179237 PMCID: PMC6537574 DOI: 10.3389/fonc.2019.00370] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 04/23/2019] [Indexed: 12/25/2022] Open
Abstract
Background and aims: The contribution of hepatitis B virus (HBV) infection to the aggressiveness of primary liver cancer (PLC) remains controversial. We aimed to characterize this in eastern China. Methods: We enrolled 8,515 PLC patients whose specimens were reserved at the BioBank of the hepatobiliary hospital (Shanghai, China) during 2007-2016. Of those, 3,124 who received primary radical resection were involved in survival analysis. A nomogram was constructed to predict the survivals using preoperative parameters. Results: Hepatocellular carcinoma (HCC), intrahepatic cholangiocarcinoma (ICC), and combined hepatocellular cholangiocarcinoma (CHC) accounted for 94.6, 3.7, and 1.7%, respectively. The rates of HBV infection were 87.5, 49.2, and 80.6%, respectively. HBV infection was significantly associated with 10-year earlier onset, more cirrhosis, higher α-fetoprotein, higher carbohydrate antigen 19-9 (CA19-9), more microvascular invasion (MVI), lower neutrophil-to-lymphocyte ratio (NLR), and lower platelet-to-lymphocyte ratio (PLR) in HCC. HBV infection was also associated with 7-year earlier onset, more cirrhosis, higher α-fetoprotein, more MVI, and lower PLR in ICC. In the multivariate Cox analysis, high circulating HBV DNA, α-fetoprotein, CA19-9, NLR, tumor size, number, encapsulation, Barcelona Clinic Liver Cancer (BCLC) stage, and MVI predicted an unfavorable prognosis in HCC; only CA19-9 and BCLC stage, rather than HBV-related parameters, had prognostic values in ICC. A nomogram constructed with preoperative HBV-related parameters including HBV load, ultrasonic cirrhosis, and α-fetoprotein perform better than the current staging systems in predicting postoperative survival in HCC. Conclusion: HBV promotes the aggressiveness of HCC in Chinese population. The contributions of HBV to ICC and other etiological factors to HCC might be indirect via arousing non-resolving inflammation.
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Affiliation(s)
- Fan Yang
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Longteng Ma
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Yuan Yang
- Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Wenbin Liu
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Jun Zhao
- Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Xi Chen
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Mengchao Wang
- Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Hongwei Zhang
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Shuqun Cheng
- Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Feng Shen
- Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Hongyang Wang
- Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Weiping Zhou
- Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Guangwen Cao
- Department of Epidemiology, Second Military Medical University, Shanghai, China
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Chen QY, Hu YL, Wang XY, Harrison TJ, Wang C, Hu LP, Yang QL, Ren CC, Jia HH, Fang AZL. Locus 5p13.1 may be associated with the selection of cancer-related HBV core promoter mutations. Int J Med Sci 2019; 16:990-997. [PMID: 31341412 PMCID: PMC6643130 DOI: 10.7150/ijms.34297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 05/21/2019] [Indexed: 11/16/2022] Open
Abstract
Background: The basal core promoter (BCP) double mutations (A1762T and G1764A) of hepatitis B virus (HBV) have been reported to be an aetiological factor of hepatocellular carcinoma (HCC). What distinguishes the subset of HBV carriers in whom these mutations are selected? Methods: A genome-wide association study (GWAS) was carried out on 218 asymptomatic HBsAg carriers infected with HBV with BCP double mutations and 191 controls infected with HBV with the wild type BCP. The highest ranking nucleotide polymorphisms (SNPs) were validated with other study subjects, 203 cases and 181 controls. The expression of the gene nearest a SNP found to be significant was examined using RT-PCR. Results: Forty-five candidate SNPs were identified in the GWAS. Three SNPs were found to be associated with the selection of HBV BCP double mutations in the replication stage, including rs7717457 at 5p13.1, rs670011 at 17q21.2, rs2071611 at 6p22.2. Especially, rs7717457 (P= 4.57×10-5 combined P) reached the potential GWAS significance level. The expression of gene complement component 7 (C7), nearest to SNP rs7717457, differed significantly between the case and control groups (t=2.045, P=0.04), suggesting that SNP rs7717457 was associated with the expression of its nearest gene. Conclusions: SNP rs7717457 is associated with the selection of HBV BCP double mutations, providing an important clue to understanding the mechanisms of oncogenesis of HBV BCP double mutations.
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Affiliation(s)
- Qin-Yan Chen
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, China
| | - Yan-Ling Hu
- Center for Genomic and Personalized Medicine, Guangxi Medical University, 22 ShuangYong Road, Nanning, Guangxi 530021, China
| | - Xue-Yan Wang
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, China
| | | | - Chao Wang
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, China
| | - Li-Ping Hu
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, China
| | - Qing-Li Yang
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, China
| | - Chuang-Chuang Ren
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, China.,School of Preclinical Medicine, Guangxi Medical University, 22 ShuangYong Road, Nanning, Guangxi 530021, China
| | - Hui-Hua Jia
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, China.,School of Preclinical Medicine, Guangxi Medical University, 22 ShuangYong Road, Nanning, Guangxi 530021, China
| | - And Zhong-Liao Fang
- Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Guangxi Key Laboratory for the Prevention and Control of Viral Hepatitis, Nanning, Guangxi 530028, China
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10
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Song XM, Li QL, Guo F, Peng H, Guo JJ. The Effect of ICOS Polymorphism Interactions with HBV Mutations on HBV Subtype Infection Outcomes. Ann Hepatol 2018; 17:940-947. [PMID: 30600290 DOI: 10.5604/01.3001.0012.7194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
INTRODUCTION AND AIM Hepatitis B virus (HBV) infection remains a public health problem worldwide. In addition, HBV infection results are influenced by various virological, immunological, and genetic factors. Inducible T-cell costimulator (ICOS) polymorphisms involving chronic HBV infection have been confirmed in previous studies. This study was to explore the effects of ICOS single nucleotide polymorphisms in HBV subtypes and their interactions with viral mutations on HBV infection outcomes. MATERIAL AND METHODS A total of 1,636 Han Chinese individuals were recruited, including 47 asymptomatic HBV carriers (ASC), 353 chronic hepatitis B (CHB) patients, 327 HBV-related liver cirrhosis (LC) patients, 193 HBV-related hepatocellular carcinoma (HCC) patients, 464 patients with spontaneous recovery from HBV infection (SR), and 252 healthy controls (HC). DNA samples from these subjects were genotyped for four ICOS SNPs (rs11883722, rs10932029, rs1559931, and rs4675379). Direct sequencing was used to determine the HBV mutations in the enhancer II, basal core promoter, and pre-core regions. RESULTS We found that the genotype "TC" of ICOS rs10932029 SNP was associated with decreased HBV-related LC risk in the genotype C group. Additionally, the A1762T, G1764A and A1762T/G1764A mutations were associated with an increased risk of LC in the genotype C group. Further study indicated that interactions between ICOS rs10932029 genotype "TC" and A1762T or A1762T/G1764A mutations significantly decreased the LC risk in the genotype C group. CONCLUSION The rs10932029 genotype "TC" might be an LC-protective factor for HBV genotype C infection. The interactions between the rs10932029 genotype "TC" and A1762T or A1762T/G1764A mutations could decrease the risk of LC.
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Affiliation(s)
- Xiao-Mei Song
- Department of Gastroenterology and Hepatology, the Fourth People's Hospital of Chongqing (Chongqing Emergency Medical Center), Chongqing, China
| | - Qing-Ling Li
- Institute of Life Sciences, Chongqing Medical University, Chongqing, China
| | - Feng Guo
- Department of Gastroenterology and Hepatology, the Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Hong Peng
- Department of Gastroenterology and Hepatology, the People's Hospital of Bishan District, Chongqing, China
| | - Jin-Jun Guo
- Department of Gastroenterology and Hepatology, the Fourth People's Hospital of Chongqing (Chongqing Emergency Medical Center), Chongqing, China
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11
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Luo YQ, Wang D, Gong T, Zhu J. An updated meta-analysis of 37 case-control studies on the association between NFKB1 -94ins/del ATTG promoter polymorphism and cancer susceptibility. Oncotarget 2018; 7:58659-58670. [PMID: 27463002 PMCID: PMC5295460 DOI: 10.18632/oncotarget.10808] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Accepted: 07/10/2016] [Indexed: 02/05/2023] Open
Abstract
As a cell survival signal, nuclear factor-kappa B (NFKB) is associated with the pathogenesis of numerous malignancies. According to several studies, NFKB1 −94ins/del ATTG promoter polymorphism is associated with the risk of different malignancies, but the results were not consistent. Therefore, we performed an updated meta-analysis based on 37 case-control studies from 33 articles (16,271 cases and 22,781 controls) to clarify the relationship. The odds ratio (OR) and 95% confidence interval (CI) were used to determine the strength of the association. We found that the NFKB1 −94ins/del ATTG promoter polymorphism was significantly associated with increased susceptibility to cancer in the recessive (II vs. ID+DD, OR = 1.140, 95% CI = 1.029–1.263, p =0.012), homozygote (II vs. DD, OR = 1.259, 95% CI = 1.068–1.485, p =0.006), and allele (I vs. D, OR = 1.109, 95% CI = 1.025–1.199, p =0.010) genetic models. The subgroup analysis for ethnicity found that the NFKB1 −94ins/del ATTG promoter polymorphism was significantly associated with an increased susceptibility to cancer in Asians and with a decreased susceptibility in Caucasians. The stratified analyses revealed significant associations between the polymorphism and increased susceptibility to ovarian cancer, oral squamous cell carcinoma, and nasopharyngeal carcinoma.
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Affiliation(s)
- Yi-Qiao Luo
- Department of Thoracic Oncology, West China Hospital/West China School of Medicine, Sichuan University, Chengdu, China
| | - Duan Wang
- Department of Orthopaedics, West China School of Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Teng Gong
- Sichuan Mianyang 404 Hospital, Mianyang, China
| | - Jiang Zhu
- Department of Thoracic Oncology, West China Hospital, Sichuan University, Chengdu, China
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12
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Lin Y, Su C, Niu J, Guo Z, Lu Y. The Association between NFKBIA Polymorphisms and the Progression of Chronic Hepatitis B Virus Infection among the Chinese Han Population. Jpn J Infect Dis 2017; 71:21-27. [PMID: 29093318 DOI: 10.7883/yoken.jjid.2017.161] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Based on the involvement of nuclear factor-κB inhibitor alpha (NFKIBA) in the NF-κ B pathway, which is closely related to host immunity, we evaluated whether NFKIBA polymorphisms are associated with the disease progression of chronic hepatitis B virus (HBV) infection. We collected blood samples from a total of 212 treatment-naïve patients with chronic HBV infection. NFKBIA polymorphisms were determined by Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry. Enzyme-linked immunosorbent assays were employed to quantify the serum levels of tumor necrosis factor-α (TNF-α) and interleukin-6(IL-6). Unconditional logistic regression revealed that carriers of the TT genotype at rs2233406 had a greater risk (OR = 5.57, 95% CI = 2.14-14.52) of chronic HBV infection progression. A similar association was observed for the rs2233409 polymorphism, in which the OR for the TT genotype was 4.06 (95% CI = 1.70-9.71) compared to that for the wildtype CC genotype. Mutations at rs2233406 and rs2233409 also impact liver function parameters and cytokine levels. However, null associations were observed between these parameters and rs696 polymorphism. These findings suggest that reduced NFKBIA function leads to activation of the NF-κB pathway, and consequently causes inflammation and liver damage among patients with chronic HBV infection.
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Affiliation(s)
- Yong Lin
- Clinical Laboratory, Zhongshan Hospital, Medical College of Xiamen University
| | - Chenghao Su
- Xiamen Branch of Zhongshan Hospital, Fudan University.,School of Public Health, Xiamen University
| | - Jianjun Niu
- Clinical Laboratory, Zhongshan Hospital, Medical College of Xiamen University
| | - Zhinan Guo
- Xiamen Center for Disease Control and Prevention
| | - Yapi Lu
- Department of Gastroenterology, Zhongshan Hospital, Medical College of Xiamen University
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13
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Plantinga TS, Petrulea MS, Oosting M, Joosten LAB, Piciu D, Smit JW, Netea-Maier RT, Georgescu CE. Association of NF-κB polymorphisms with clinical outcome of non-medullary thyroid carcinoma. Endocr Relat Cancer 2017; 24:307-318. [PMID: 28428267 DOI: 10.1530/erc-17-0033] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 04/20/2017] [Indexed: 12/15/2022]
Abstract
The NF-κB inflammatory pathway plays a major role in cancer development and clinical progression. Activation of NF-κB signaling is promoted by NFKB1 and inhibited by NFKBIA. The present study aimed to determine the relevance of NFKB1 rs4648068 and NFKBIA rs2233406 genetic variants for non-medullary thyroid cancer (NMTC) susceptibility, progression and clinical outcome. This case-control and cohort study consists of a Romanian discovery cohort (157 patients and 258 controls) and a Dutch validation cohort (138 patients and 188 controls). In addition, patient cohorts were analyzed further for the association of genetic variants with clinical parameters. Functional studies were performed on human peripheral blood mononuclear cells. No associations were observed between the studied genetic variants and TC susceptibility. Although no statistically significant associations with clinical parameters were observed for NFKB1 rs4648068, the heterozygous genotype of NFKBIA rs2233406 was correlated with decreased radioactive iodide sensitivity requiring higher cumulative dosages to achieve clinical response. These findings were discovered in the Romanian cohort (P < 0.001) and confirmed in the Dutch cohort (P = 0.01). Functional studies revealed that this NFKBIA rs2233406 genotype was associated with elevated TLR4-mediated IL-1β production. In conclusion, genetic variation in NFKBIA, an inhibitor of NF-κB signaling, is associated with clinical response to RAI therapy and with increased production of the pro-inflammatory cytokine IL-1β, providing a potential mechanism for the observed clinical associations. These data suggest that NF-κB signaling is involved in NMTC pathogenesis and that the inflammatory tumor microenvironment could contribute to RAI resistance.
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Affiliation(s)
- Theo S Plantinga
- Department of Internal MedicineRadboud University Medical Center, Nijmegen, The Netherlands
- Department of PathologyRadboud University Medical Center, Nijmegen, The Netherlands
| | - Mirela S Petrulea
- Department of EndocrinologyIuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Marije Oosting
- Department of Internal MedicineRadboud University Medical Center, Nijmegen, The Netherlands
| | - Leo A B Joosten
- Department of Internal MedicineRadboud University Medical Center, Nijmegen, The Netherlands
| | | | - Johannes W Smit
- Department of Internal MedicineRadboud University Medical Center, Nijmegen, The Netherlands
| | - Romana T Netea-Maier
- Department of Internal MedicineRadboud University Medical Center, Nijmegen, The Netherlands
| | - Carmen E Georgescu
- Department of EndocrinologyIuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
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14
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Fu W, Zhuo ZJ, Chen YC, Zhu J, Zhao Z, Jia W, Hu JH, Fu K, Zhu SB, He J, Liu GC. NFKB1 -94insertion/deletion ATTG polymorphism and cancer risk: Evidence from 50 case-control studies. Oncotarget 2017; 8:9806-9822. [PMID: 28039461 PMCID: PMC5354772 DOI: 10.18632/oncotarget.14190] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 11/22/2016] [Indexed: 02/07/2023] Open
Abstract
Nuclear factor-kappa B1 (NF-κB1) is a pleiotropic transcription factor and key contributor to tumorigenesis in many types of cancer. Numerous studies have addressed the association of a functional insertion (I)/deletion (D) polymorphism (-94ins/delATTG, rs28362491) in the promoter region of NFKB1 gene with the risk of various types of cancer; however, their conclusions have been inconsistent. We therefore conducted a meta-analysis to reevaluate this association. PubMed, EMBASE, China National Knowledge infrastructure (CNKI), and WANFANG databases were searched through July 2016 to retrieve relevant studies. After careful assessment, 50 case-control studies, comprising 18,299 cases and 23,484 controls were selected. Crude odds ratios (ORs) and 95% confidence intervals (CIs) were used to determine the strength of the association. The NFKB1 -94ins/delATTG polymorphism was associated with a decreased risk of overall cancer in the homozygote model (DD vs. II): OR = 0.75, 95% CI = 0.64-0.87); heterozygote model (ID vs. II): OR = 0.91, 95% CI = 0.83-0.99; recessive model (DD vs. ID/II): OR = 0.81, 95% CI = 0.71-0.91; dominant model (ID/DD vs. II): OR = 0.86, 95% CI = 0.78-0.95; and allele contrast model (D vs. I): OR = 0.88, 95% CI = 0.81-0.95). Subgroup and stratified analyses revealed decreased risks for lung cancer, nasopharyngeal carcinoma, prostate cancer, ovarian cancer, and oral squamous cell carcinoma, and this association held true also for Asians (especially Chinese subjects) in hospital-based studies, and in studies with quality scores less than nine. Well-designed, large-scale case-control studies are needed to confirm these results.
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Affiliation(s)
- Wen Fu
- Department of Pediatric Urology, Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China
| | - Zhen-Jian Zhuo
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong 999077, China
| | - Yung-Chang Chen
- Department of Gastroenterology, The First People's Hospital of Foshan (Affiliated Foshan Hospital of Sun Yat-sen University), Foshan 528000, Guangdong, China
| | - Jinhong Zhu
- Molecular Epidemiology Laboratory and Department of Laboratory Medicine, Harbin Medical University Cancer Hospital, Harbin 150040, Heilongjiang, China
| | - Zhang Zhao
- Department of Pediatric Urology, Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China
| | - Wei Jia
- Department of Pediatric Urology, Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China
| | - Jin-Hua Hu
- Department of Pediatric Urology, Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China
| | - Kai Fu
- Department of Pediatric Urology, Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China
| | - Shi-Bo Zhu
- Department of Pediatric Urology, Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China
| | - Jing He
- Department of Pediatric Urology, Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China
| | - Guo-Chang Liu
- Department of Pediatric Urology, Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China
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15
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Wang D, Xie T, Xu J, Wang H, Zeng W, Rao S, Zhou K, Pei F, Zhou Z. Genetic association between NFKB1 -94 ins/del ATTG Promoter Polymorphism and cancer risk: a meta-analysis of 42 case-control studies. Sci Rep 2016; 6:30220. [PMID: 27443693 PMCID: PMC4957149 DOI: 10.1038/srep30220] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 06/30/2016] [Indexed: 02/05/2023] Open
Abstract
Accumulating evidences have indicated that the functional -94 ins/del ATTG polymorphism in the promoter region of human nuclear factor-kappa B1 (NFKB1) gene may be associated with cancer risk. However, some studies yielded conflicting results. To clarify precise association, we performed a comprehensive meta-analysis of 42 case-control studies involving 43,000 subjects (18,222 cases and 24,778 controls). The overall results suggested that the -94 ins/del ATTG polymorphism had a decreased risk for cancer, reaching significant levels in five genetic models (dominant model: OR = 0.86, 95% CI = 0.79–0.95, P = 0.002; recessive model: OR = 0.84, 95% CI = 0.74–0.94, P = 0.003; homozygous model: OR = 0.77, 95% CI = 0.66–0.90, P = 0.001; heterozygous model: OR = 0.90, 95% CI = 0.83–0.98, P = 0.011; allelic model: OR = 0.89, 95% CI = 0.83–0.96, P = 0.002). Furthermore, the -94 ins/del ATTG polymorphism could confer a decreased or increased risk for cancer development among Asians and Caucasians, respectively. Additionally, the stratification analysis revealed a significant association between the variant and decreased risk of oral, ovarian, and nasopharyngeal cancer in Asians. After we adjusted p values using the Benjamini-Hochberg false discovery rate method to account for multiple comparisons, these associations remained.
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Affiliation(s)
- Duan Wang
- West China Hospital/West China School of Medicine, Sichuan University, Chengdu, 610041, China
| | - Tianhang Xie
- West China Hospital/West China School of Medicine, Sichuan University, Chengdu, 610041, China
| | - Jin Xu
- Tianjin Hospital, Tianjin, 300211, China
| | - Haoyang Wang
- Department of Orthopaedics, West China Hospital/West China School of Medicine, Sichuan University, Chengdu, 610041, China
| | - Weinan Zeng
- Center for Joint Surgery, Southwest Hospital, Third Military Medical University, Chongqing, 400038, China
| | - Shuquan Rao
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Kai Zhou
- West China Hospital/West China School of Medicine, Sichuan University, Chengdu, 610041, China
| | - Fuxing Pei
- Department of Orthopaedics, West China Hospital/West China School of Medicine, Sichuan University, Chengdu, 610041, China
| | - Zongke Zhou
- Department of Orthopaedics, West China Hospital/West China School of Medicine, Sichuan University, Chengdu, 610041, China
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Li J, Yu L, Shen Z, Li Y, Chen B, Wei W, Chen X, Wang Q, Tong F, Lou H, Chu M, Wei L. miR-34a and its novel target, NLRC5, are associated with HPV16 persistence. INFECTION GENETICS AND EVOLUTION 2016; 44:293-299. [PMID: 27423514 DOI: 10.1016/j.meegid.2016.07.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Revised: 07/08/2016] [Accepted: 07/12/2016] [Indexed: 01/05/2023]
Abstract
Persistent infection with human papillomavirus (HPV), particularly type 16, is causally associated with cervical cancer and its precursors. The role of miRNAs in HPV16 persistence currently remains unclear. Preliminary analysis of miRNA profile demonstrated that HPV16 infection caused a striking downregulation of miR-34a. Through bioinformatics analysis and dual-luciferase assay with site-directed mutagenesis strategy, NLRC5, a negative regulator of NF-κB signaling, was identified to be a novel interactor of miR-34a. Transfection of miR-34a mimic strikingly downregulated NLRC5 in the HPV16-positive cervical cells, which might result in the nuclear accumulation of NF-κB p65. However, transfection of miR-34a inhibitor exhibited an opposite effect. The antagonistic expressions of NLRC5 and miR-34a were also observed in keratinocytes harboring HPV16 genome as well as in human cervical samples with persistent infection of HPV16. Our data uncover a previously unknown connection among HPV16 persistence, miR-34a and its interactor NLRC5.
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Affiliation(s)
- Jinyuan Li
- Department of Microbiology, Harbin Medical University, Immunity and Infection, Pathogenic Biology Key Laboratory in Heilongjiang Province, Harbin 150081, Heilongjiang, PR China
| | - Libo Yu
- Department of Gynaecology, The Third Affiliated Hospital of Harbin Medical University, Harbin 150001, Heilongjiang, PR China
| | - Zhenji Shen
- Department of Microbiology, Harbin Medical University, Immunity and Infection, Pathogenic Biology Key Laboratory in Heilongjiang Province, Harbin 150081, Heilongjiang, PR China
| | - Yushu Li
- Department of Neurosurgery, The First Affiliated Hospital, Harbin Medical University, Harbin 150001, Heilongjiang, PR China
| | - Beibei Chen
- Department of Gynaecology, The Third Affiliated Hospital of Harbin Medical University, Harbin 150001, Heilongjiang, PR China
| | - Wei Wei
- Department of Orthopedic Surgery, ,The First Affiliated Hospital of Jiamusi University, Jiamusi 154002, Heilongjiang, PR China
| | - Xiaohang Chen
- Department of Microbiology, Harbin Medical University, Immunity and Infection, Pathogenic Biology Key Laboratory in Heilongjiang Province, Harbin 150081, Heilongjiang, PR China
| | - Qingyi Wang
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Fangjia Tong
- Department of Microbiology, Harbin Medical University, Immunity and Infection, Pathogenic Biology Key Laboratory in Heilongjiang Province, Harbin 150081, Heilongjiang, PR China
| | - Huihuang Lou
- Department of Microbiology, Harbin Medical University, Immunity and Infection, Pathogenic Biology Key Laboratory in Heilongjiang Province, Harbin 150081, Heilongjiang, PR China
| | - Ming Chu
- Department of Neurosurgery, The First Affiliated Hospital, Harbin Medical University, Harbin 150001, Heilongjiang, PR China
| | - Lanlan Wei
- Department of Microbiology, Harbin Medical University, Immunity and Infection, Pathogenic Biology Key Laboratory in Heilongjiang Province, Harbin 150081, Heilongjiang, PR China.
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17
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Lee SM, Kim-Ha J, Choi WY, Lee J, Kim D, Lee J, Choi E, Kim YJ. Interplay of genetic and epigenetic alterations in hepatocellular carcinoma. Epigenomics 2016; 8:993-1005. [PMID: 27411963 DOI: 10.2217/epi-2016-0027] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Genetic and epigenetic alterations play prominent roles in hepatocarcinogenesis and their appearance varies depending on etiological factors, race and tumor progression. Intriguingly, distinct patterns of these genetic and epigenetic mutations are coupled not only to affect each other, but to trigger different types of tumorigenesis. The patterns and frequencies of somatic variations vary depending on the nature of the surrounding chromatin. On the other hand, epigenetic alterations often induce genomic instability prone to mutation. Therefore, genetic mutations and epigenetic alterations in hepatocellular carcinoma appear to be inseparable factors that accelerate tumorigenesis synergistically. We have summarized recent findings on genetic and epigenetic modifications, their influences on each other's alterations and putative roles in liver tumorigenesis.
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Affiliation(s)
- Sun-Min Lee
- Department of Biochemistry, College of Life Science & Technology, Yonsei University, Seoul, Korea
| | - Jeongsil Kim-Ha
- Department of Integrative Bioscience & Biotechnology, College of Life Sciences, Sejong University, Seoul, Korea
| | - Won-Young Choi
- Department of Integrated Omics for Biomedical Science, Graduate School, Yonsei University, Seoul, Korea
| | - Jungwoo Lee
- Department of Integrated Omics for Biomedical Science, Graduate School, Yonsei University, Seoul, Korea
| | - Dawon Kim
- Department of Integrated Omics for Biomedical Science, Graduate School, Yonsei University, Seoul, Korea
| | - Jinyoung Lee
- Department of Integrated Omics for Biomedical Science, Graduate School, Yonsei University, Seoul, Korea
| | - Eunji Choi
- Department of Integrated Omics for Biomedical Science, Graduate School, Yonsei University, Seoul, Korea
| | - Young-Joon Kim
- Department of Biochemistry, College of Life Science & Technology, Yonsei University, Seoul, Korea.,Department of Integrated Omics for Biomedical Science, Graduate School, Yonsei University, Seoul, Korea
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18
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Liu WB, Wu JF, Du Y, Cao GW. Cancer Evolution-Development: experience of hepatitis B virus-induced hepatocarcinogenesis. ACTA ACUST UNITED AC 2016; 23:e49-56. [PMID: 26966413 DOI: 10.3747/co.23.2836] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Here, we present the basic concept and theoretical framework of a scientific hypothesis called Cancer Evolution-Development ("Cancer Evo-Dev"), based on our recent studies of the molecular mechanisms by which chronic infection with the hepatitis B virus induces hepatocarcinogenesis, together with related advances in that field. Several aspects central to our hypothesis are presented: ■ Immune imbalance-caused by the interaction of genetic predispositions and environmental exposures such as viral infection-is responsible for the maintenance of chronic non-resolving inflammation. Non-resolving inflammation promotes the occurrence and progression of cancers, characterized by an evolutionary process of "mutation-selection-adaptation" for both viruses and host cells.■ Under a microenvironment of non-resolving inflammation, proinflammatory factors promote mutations in viral or host genomes by transactivation of the expression of cytidine deaminases and their analogues. Most cells with genomic mutations and mutated viruses are eliminated in the competition for survival in the inflammatory microenvironment. Only a small percentage of the mutated cells that alter their survival signal pathways and exhibit the characteristics of "stem-ness" can survive and function as cancer-initiating cells.■ Cancers generally develop with properties of "backward evolution" and "retro-differentiation," indicating the indispensability of stem-like signal pathways in the evolution and development of cancers. The hypothesis of Cancer Evo-Dev not only lays the theoretical foundation for understanding the mechanisms by which inflammation promotes the development of cancers, but also plays an important role in specific prophylaxis, prediction, early diagnosis, and targeted treatment of cancers.
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Affiliation(s)
- W B Liu
- Department of Epidemiology, Second Military Medical University, Shanghai, P.R.C
| | - J F Wu
- Department of Epidemiology, Second Military Medical University, Shanghai, P.R.C
| | - Y Du
- Department of Epidemiology, Second Military Medical University, Shanghai, P.R.C
| | - G W Cao
- Department of Epidemiology, Second Military Medical University, Shanghai, P.R.C
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19
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Association and interaction of NFKB1 rs28362491 insertion/deletion ATTG polymorphism and PPP1R13L and CD3EAP related to lung cancer risk in a Chinese population. Tumour Biol 2015; 37:5467-73. [PMID: 26563375 DOI: 10.1007/s13277-015-4373-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 11/03/2015] [Indexed: 01/02/2023] Open
Abstract
The nuclear factor of kappa light polypeptide gene enhancer in B cells 1 (NFKB1) gene encodes p105 and p50 kD which are both subunits of the transcription factor NF-kB, involved in a wide variety of diseases and pathological states associated with inflammation, immunity, and tumorigenesis. The NFKB1 rs28362491 polymorphism in the promoter region (-94 insertion/deletion ATTG) has been associated with risk of various cancers. Our study aims were to evaluate the associations of NFKB1 rs28362491 polymorphism and interactions of this single-nucleotide polymorphism (SNP) and PPP1R13L and CD3EAP and smoking duration in relation to lung cancer risk in a Chinese population. The study population consisted of 544 Chinese lung cancer cases and 550 cancer-free matched (age, sex, and ethnicity) controls. No associations were found between NFKB1 rs28362491 and lung cancer risk. CD3EAP rs967591 was associated with increased lung cancer risk in the dominant model [OR (95 % CI) = 1.38 (1.05-1.80), P = 0.018]. The common haplotype containing PPP1R13L rs1970764(G), CD3EAP rs967591(A), and CD3EAP rs735482(C) was associated with lung cancer [adjusted OR (95 % CI) = 1.29 (1.03-1.62), P = 0.028]. Multifactor dimensionality reduction (MDR) analysis revealed two-way and three-way interactions between CD3EAP rs735482 and smoking and between NFKB1 rs28362491, PPP1R13L rs1970764, and smoking. In conclusion, we were able to reproduce previously found associations between PPP1R13L and CD3EAP polymorphisms and lung cancer risk in an increased study group, and we found interactions between NFKB1 rs28362491-PPP1R13L rs1970764 and smoking duration and between CD3EAP rs735482 and smoking duration. These results suggest that these genes and smoking are part of the same biological pathway leading to smoking-induced lung cancer.
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20
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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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21
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Du Y, Zhang YW, Pu R, Han X, Hu JP, Zhang HW, Wang HY, Cao GW. Phosphatase and tensin homologue genetic polymorphisms and their interactions with viral mutations on the risk of hepatocellular carcinoma. Chin Med J (Engl) 2015; 128:1005-13. [PMID: 25881591 PMCID: PMC4832937 DOI: 10.4103/0366-6999.155057] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Background: Chronic hepatitis B virus (HBV) infection is the major cause of hepatocellular carcinoma (HCC). Some HBV mutants and dysregulation of phosphatase and tensin homolog (PTEN) may promote the development of HCC synergistically. We aimed to test the effects of PTEN genetic polymorphisms and their interactions with important HBV mutations on the development of HCC in HBV-infected subjects. Methods: Quantitative polymerase chain reaction was applied to genotype PTEN polymorphisms (rs1234220, rs2299939, rs1234213) in 1012 healthy controls, 302 natural clearance subjects, and 2011 chronic HBV-infected subjects including 1021 HCC patients. HBV mutations were determined by sequencing. The associations of PTEN polymorphisms and their interactions with HBV mutations with HCC risk were assessed using multivariate logistic regression analysis. Results: Rs1234220 C allele was significantly associated with HCC risk compared to healthy controls (adjusted odds ratio [AOR] = 1.35, 95% confidence interval [CI] = 1.07–1.69) and HCC-free HBV-infected subjects (AOR = 1.27, 95% CI = 1.01–1.57). rs1234220 C allele was significantly associated with increased frequencies of HCC-risk A1652G, C1673T, and C1730G mutations in genotype B HBV-infected subjects. Rs2299939 GT genotype was inversely associated with HCC risk in HBV-infected patients (AOR = 0.75, 95% CI = 0.62–0.92). The interaction of rs2299939 variant genotypes (GT+TT) with A3054T mutation significantly increased HCC risk (AOR = 2.41, 95% CI = 1.08–5.35); whereas its interaction with C3116T mutation significantly reduced HCC risk (AOR = 0.34, 95% CI = 0.18–0.66). These significant effects were only evident in males after stratification. Conclusions: PTEN polymorphisms and their interactions with HBV mutations may contribute to hepatocarcinogenesis in males. The host-virus interactions are important in identifying HBV-infected subjects who are more likely to develop HCC.
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Affiliation(s)
| | | | | | | | | | | | | | - Guang-Wen Cao
- Department of Epidemiology, Second Military Medical University, Shanghai 200433, China
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22
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Yin J, Wang J, Pu R, Xin H, Li Z, Han X, Ding Y, Du Y, Liu W, Deng Y, Ji X, Wu M, Yu M, Zhang H, Wang H, Thompson TC, Ni W, Cao G. Hepatitis B Virus Combo Mutations Improve the Prediction and Active Prophylaxis of Hepatocellular Carcinoma: A Clinic-Based Cohort Study. Cancer Prev Res (Phila) 2015; 8:978-88. [PMID: 26290395 DOI: 10.1158/1940-6207.capr-15-0160] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Accepted: 07/31/2015] [Indexed: 12/21/2022]
Abstract
We aimed to evaluate whether hepatitis B virus (HBV) mutations at the core promoter region could improve the prediction and specific prophylaxis of hepatocellular carcinoma (HCC) in chronic HBV-infected patients. A total of 2,114 HBV-infected patients enrolled between August 1998 and December 2007 were followed-up for 18,406 person-years. Of those, 612 received ≥48 week treatments with nucleos(t)ide analogue (NA) and/or IFNα. Baseline HBV mutations were identified by sequencing. Propensity score matching was applied to reduce baseline differences between antiviral and control cohorts. Multivariate Cox regression analyses, including baseline characteristics of 2,114 patients, showed that age, male, cirrhosis, and HBV mutations (C1653T, T1753V, and A1762T/G1764A) independently increased HCC risk. In control patients carrying A1762T/G1764A, addition of C1653T and/or T1753V significantly increased HCC risk (HR, 1.57; P = 0.038); combo mutations with C1653T, T1753V, and A1762T/G1764A improved the validity of HCC prediction by age, male, and cirrhosis (P = 0.002). In the matched cohorts, antiviral treatment reduced HCC incidence (13.90/1,000 vs. 7.70/1,000 person-years, P = 0.005); NA treatment for ≥60 months was required for the prophylaxis of HCC in cirrhotic patients (P = 0.03); antiviral treatment reduced HCC risk in patients carrying A1762T/G1764A (HR, 0.40; P = 0.002) or C1653T (HR, 0.45; P = 0.04) and in those without T1753V (HR, 0.42; P = 0.005), but could not reduce HCC risk in patients without A1762T/G1764A or C1653T and in those with T1753V. In summary, HBV mutation A1762T/G1764A, C1653T, and T1753V in combination improve HCC prediction in HBV-infected patients. To prevent HCC, patients infected with HBV carrying A1762T/G1764A or C1653T, but not T1753V, should be given priority of receiving antiviral treatments.
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Affiliation(s)
- Jianhua Yin
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Junxue Wang
- Department of Infectious Diseases, The 2nd Affiliated Hospital, Second Military Medical University, Shanghai, China
| | - Rui Pu
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Haiguang Xin
- Department of Infectious Diseases, The 2nd Affiliated Hospital, Second Military Medical University, Shanghai, China
| | - Zixiong Li
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Xue Han
- Division of Chronic Diseases, Center for Disease Control and Prevention of Yangpu District, Shanghai, China
| | - Yibo Ding
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Yan Du
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Wenbin Liu
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Yang Deng
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Xiaowei Ji
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Ming Wu
- Division of Chronic Diseases, Provincial Center for Disease Control and Prevention of Jiangsu, Nanjing, China
| | - Min Yu
- Division of Chronic Diseases, Provincial Center for Disease Control and Prevention of Zhejiang, Hangzhou, China
| | - Hongwei Zhang
- Department of Epidemiology, Second Military Medical University, Shanghai, China
| | - Hongyang Wang
- International Cooperation Laboratory on Signal Transduction, The 3rd Affiliated Hospital, Second Military Medical University, Shanghai, China
| | - Timothy C Thompson
- Department of Genitourinary Medical Oncology-Research, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Wu Ni
- Department of Infectious Diseases, The 2nd Affiliated Hospital, Second Military Medical University, Shanghai, China
| | - Guangwen Cao
- Department of Epidemiology, Second Military Medical University, Shanghai, China.
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23
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Li Z, Hou X, Cao G. Is mother-to-infant transmission the most important factor for persistent HBV infection? Emerg Microbes Infect 2015; 4:e30. [PMID: 26060603 PMCID: PMC4451268 DOI: 10.1038/emi.2015.30] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 03/24/2015] [Accepted: 04/06/2015] [Indexed: 02/06/2023]
Abstract
Of the infants born to hepatitis B surface antigen (HBsAg)-positive mothers globally, 42.1% who did not receive hepatitis B virus (HBV) passive-active immunoprophylaxis and 2.9% of infants who received the immunoprophylaxis acquired HBV infection perinatally. Moreover, perinatal infection occurred in 84.2% (18.8%-100%) and 8.7% (0.0-21.0%) of infants born to hepatitis B e-antigen (HBeAg)-positive mothers who did not and did receive immunoprophylaxis, respectively; by contrast, the infection rates were 6.7% (0.0-15.4%) and 0.4% (0.0-2.5%) for infants born to HBeAg-negative-carrier mothers, respectively. The chronicity rates of HBV infection acquired perinatally were 28.2% (17.4%-33.9%) in infants born to HBeAg-negative mothers and 64.5% (53.5%-100%) in infants born to HBeAg-positive mothers. HBV mother-to-child transmission was more frequent in East Asia relative to other areas. In addition to differences in the endemic HBV genotype, the interchange of allelic dominance in genetic polymorphisms in HLA class II and NF-κB between the Chinese and European populations may explain why chronic HBV infection frequently affects the Chinese. The risk of progressing into chronic infection was inversely related to the age of children at the time of horizontal transmission. To further diminish HBV chronic infection, it is necessary to enforce antiviral treatment after the 28th week of gestation for HBeAg-positive mothers and to improve the health habits of carrier mothers and household sanitary conditions.
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Affiliation(s)
- Zixiong Li
- Department of Epidemiology, Second Military Medical University , Shanghai 200433, China
| | - Xiaomei Hou
- Department of Epidemiology, Second Military Medical University , Shanghai 200433, China
| | - Guangwen Cao
- Department of Epidemiology, Second Military Medical University , Shanghai 200433, China
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Itan Y, Casanova JL. Novel primary immunodeficiency candidate genes predicted by the human gene connectome. Front Immunol 2015; 6:142. [PMID: 25883595 PMCID: PMC4381650 DOI: 10.3389/fimmu.2015.00142] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 03/15/2015] [Indexed: 01/06/2023] Open
Abstract
Germline genetic mutations underlie various primary immunodeficiency (PID) diseases. Patients with rare PID diseases (like most non-PID patients and healthy individuals) carry, on average, 20,000 rare and common coding variants detected by high-throughput sequencing. It is thus a major challenge to select only a few candidate disease-causing variants for experimental testing. One of the tools commonly used in the pipeline for estimating a potential PID-candidate gene is to test whether the specific gene is included in the list of genes that were already experimentally validated as PID-causing in previous studies. However, this approach is limited because it cannot detect the PID-causing mutation(s) in the many PID patients carrying causal mutations of as yet unidentified PID-causing genes. In this study, we expanded in silico the list of potential PID-causing candidate genes from 229 to 3,110. We first identified the top 1% of human genes predicted by the human genes connectome to be biologically close to the 229 known PID genes. We then further narrowed down the list of genes by retaining only the most biologically relevant genes, with functionally enriched gene ontology biological categories similar to those for the known PID genes. We validated this prediction by showing that 17 of the 21 novel PID genes published since the last IUIS classification fall into this group of 3,110 genes (p < 10−7). The resulting new extended list of 3,110 predicted PID genes should be useful for the discovery of novel PID genes in patients.
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Affiliation(s)
- Yuval Itan
- Rockefeller Branch, St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University , New York, NY , USA
| | - Jean-Laurent Casanova
- Rockefeller Branch, St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University , New York, NY , USA ; Necker Branch, Laboratory of Human Genetics of Infectious Diseases, INSERM U1163 , Paris , France ; Imagine Institute, University Paris Descartes , Paris , France ; Howard Hughes Medical Institute , New York, NY , USA ; Pediatric Hematology-Immunology Unit, Necker Hospital for Sick Children , Paris , France
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