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Jing Zhu,
Yang Yu,
Xiangning Meng,
Yihui Fan,
Yu Zhang,
Chunshui Zhou,
Zhichao Yue,
Yan Jin,
Chunyu Zhang,
Lisa Yu, [......], Xueyuan Jia,
Rongwei Guan,
Jie Wu,
Jingcui Yu,
Jing Bai,
Xin-Yuan Guan,
Mingrong Wang,
Ki-Young Lee,
Wenjing Sun,
Songbin Fu
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ABSTRACT: Double minutes (DMs) are hallmarks of gene amplification. However, their molecular structure and the mechanisms of formation are largely unknown. To elucidate the structure and underlying molecular mechanism of DMs, we obtained and cloned DMs using micro-dissection and degenerated oligonucleotide primed PCR (DOP-PCR) from the ovarian cancer cell line UACC-1598. Two large amplicons, the 284 Kb AmpMYCN, originating from locus 2p24.3, and the 391 Kb AmpEIF5A2, from locus 3q26.2, were found co-amplified on the same DMs. The two amplicons are joined through a complex 7 Kb junction DNA sequence. Analysis of the junction has revealed three de novo created small palindromes surrounding the six breakpoints. Consistent with these observations, we further found that 70% of the 57 reported DM junction sequences have de novo creation of small palindromic sequences surrounding the breakpoints. Together, our findings indicate that de novo-generated small palindromic sequences are characteristic of amplicon boundary junctions on DMs. It is possible that the de novo-generated small palindromic sequences, which may be generated through non-homologous end joining in concert with a novel DNA repair machinery, play a common role in amplicon rejoining and gene amplification.
International Journal of Cancer 02/2013; · 5.44 Impact Factor
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Lidan Xu,
Weiguang Yuan,
Haiming Sun,
Xuelong Zhang, Xueyuan Jia,
Chao Shen,
Yanling Zhao,
Donglin Sun,
Yang Yu,
Yan Jin,
Songbin Fu
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ABSTRACT: The association between multiple sclerosis (MS) and tumor necrosis factor-alpha gene (TNF-α) polymorphisms has been analyzed in several studies, but conflicting results have been reported. The main purpose of this study was to integrate previous findings and explore whether the three single nucleotide polymorphisms (SNPs; -238G/A, -308G/A, and -376G/A) of TNF-α are associated with susceptibility to MS. A total of 2,639 patients and 3,303 controls from 21 studies, which were identified by searching the ISI Web of Knowledge database and the PubMed database up to December 2009, were collected for this meta-analysis. The association between MS and TNF-α -238G/A, -308G/A, and -376G/A was previously analyzed in 4, 18, and 4 studies, respectively. Overall, no associations were identified for the TNF-α -238G/A polymorphism and MS in any of genetic model. Similarly, no associations were found for the TNF-α -308G/A polymorphism and MS or between the TNF-α -376G/A polymorphism and MS. Furthermore, no significant association between the three SNPs and MS was identified using subgroup analyses examining ethnicity and clinical manifestation. The results of the present study indicated that TNF-α -238G/A, -308G/A, or -376G/A may not be the main risk factor for MS, which should be interpret with caution for the limited study numbers.
Molecular Biology Reports 12/2010; 38(6):4137-44. · 2.93 Impact Factor
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Chao Shen,
Haiming Sun,
Donglin Sun,
Lidan Xu,
Xuelong Zhang,
An Liu, Xueyuan Jia,
Jing Bai,
Feng Chen,
Yang Yu,
Yan Jin,
Jingcui Yu,
Songbin Fu
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ABSTRACT: We conducted a meta-analysis to assess the association between tumor necrosis factor-alpha (TNF-alpha) gene TNFA -308 (G>A), TNFA -238 (G>A), TNFA -857 (C>T), TNFA -863 (C>A), TNFA -1031 (T>C), TNFA -1210 (A>T) polymorphisms and breast cancer(BC) susceptibility. We also performed subgroup analyses based on ethnicity (Caucasian, Asian, and African). An extensive search was performed to identify all case-control studies investigating such association. Thirteen eligible studies, including 10,236 BC patients and 13,143 controls, were identified. No significant association was observed in all genotypes in worldwide populations, but stratification by ethnicity indicated that the TNFA -308 A allele was associated with a decreased risk of BC compared with the G allele in Caucasian individuals (OR = 0.927, 95%CI = 0.879-0.978). Similar results were obtained when the A/A +A/G genotype was compared with the G/G genotype. In addition, meta-analysis results indicated that the A/A genotype of TNFA -308 was a risk factor for BC in African (A/A vs. G/G OR = 4.085 95%CI = 1.460-11.425; A/A vs. G/A OR = 4.861 95%CI = 1.746-13.527; A/A vs. G/A + G/G OR = 4.246 95%CI = 1.551-11.625), but not in Caucasian or Asian individuals. In conclusion, the results of this meta-analysis indicate that the TNFA -308 A allele may be an important protective factor for BC in European individuals, but it is not likely to confer susceptibility to BC in worldwide populations. In addition, the AA genotype of TNFA -308 may be a risk factor for BC in African individuals. Besides, other polymorphisms were not associated with BC susceptibility.
Breast Cancer Research and Treatment 09/2010; 126(3):763-70. · 4.43 Impact Factor
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Haiming Sun,
Yuandong Qiao,
Xuelong Zhang,
Lidan Xu, Xueyuan Jia,
Donglin Sun,
Chao Shen,
An Liu,
Yanling Zhao,
Yan Jin,
Yang Yu,
Jing Bai,
Songbin Fu
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ABSTRACT: Several studies have investigated the associations between X-ray repair cross-complementing group 3 (XRCC3) Thr241Met polymorphism and the susceptibility to lung cancer and bladder cancer, but results have been inconclusive. In order to derive a more precise estimation of the relationship, a meta-analysis was performed. A total of 22 case control studies, including 2976 cases and 4495 controls for lung cancer, and 3445 cases and 4599 controls for bladder cancer, met the inclusion criteria and were selected. Overall, there was no evidence showing a significant association between XRCC3 Thr241Met polymorphism and lung cancer risk. Furthermore, the results for bladder cancer showed that significant decreased risk was found for the additive model (odds ratio [OR] = 0.959, 95% confidence interval [CI], 0.924-0.996) and dominant model (OR = 0.982, 95% CI, 0.963-1.000) but not for the recessive model (OR = 0.958, 95% CI, 0.905-1.014). In summary, our meta-analysis indicates that XRCC3 Thr241Met polymorphism may be weakly associated with the risk of bladder cancer. (Cancer Sci 2010).
Cancer Science 08/2010; 101(8):1777-82. · 3.33 Impact Factor
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Lidan Xu,
Yuandong Qiao,
Xuelong Zhang,
Haiming Sun,
Jingwei Wang,
Donglin Sun, Xueyuan Jia,
Chao Shen,
Yanling Zhao,
Yan Jin,
Yang Yu,
Hong Ling,
Kaili Wang,
Songbin Fu
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ABSTRACT: It has been reported that single nucleotide polymorphisms (SNPs) in the promoter of the CCR5 gene are associated with the risk for HIV-1 infection and AIDS progression. Using resequencing, we performed a systematic survey of 78 HIV-1 seropositive individuals and 70 population-matched healthy control individuals from northern China to investigate SNPs of the CCR5 gene promoter and evaluated their effects on HIV-1 infection and the progression of AIDS. Linkage disequilibrium (LD) plots and haplotypes were generated using Haploview software. The association analyses were statistically compared using the Chi-square test with SPSS13.0 software for Windows. Seven SNPs (58755A>G, 58791C>T, 58934G>T, 59029A>G, 59353C>T, 59402A>G and 59653C>T) in the region of the CCR5 gene promoter were evaluated in this study. Among the seven SNPs, the minor allele frequencies of 58755G and 58791T were less than 2%. The differences in frequencies of the other five SNPs were not significant between case and control cohorts (P>0.05). In the case cohort, the association between these SNPs and clinical features (CD4+ T-lymphocyte counts and clinical categories) was not significant (P>0.05); however, there was a significant association between the haplotype GGTAC and susceptibility to HIV-1 infection (P<0.05), which is not consistent with other reports studied in different populations. The results suggest that the haplotype GGTAC may have a role in the process of HIV-1 infection in the northern Chinese population.
Molecular Biology Reports 04/2010; 38(1):327-32. · 2.93 Impact Factor
