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Yang W, Liu W, Zhu L, Lin Y, Meng Z, Wang Y. Association Between the XRCC1, GSTM1, and GSTT1 Polymorphisms in Model of Thyroid Cancer: A Meta-Analysis. Horm Metab Res 2023; 55:625-633. [PMID: 37678329 DOI: 10.1055/a-2135-6659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Thyroid cancer is the most common malignant tumor of the endocrine system, and its incidence is increasing worldwide each year. This study aimed to explore the association between XRCC1, GSTM1, and GSTT1 polymorphisms in the model of thyroid cancer. The experiment was conducted by searching PubMed, Embase, and Web of Science, with the last search performed in March 2022. A total of 12 studies were included in this meta-analysis, with sample sizes ranging from 211 to 1124. The proportion of XRCC1 polymorphisms (rs25489, GG) in thyroid cancer was slightly lower than that of the normal control group, but the difference was not statistically significant (Mean difference=1.13, 95% CI: 0.99-1.28, p=0.08). The proportion of XRCC1 polymorphisms (rs25489, GA) in thyroid cancer was significantly lower than that of the normal control group (Mean difference=1.32, 95% CI: 1.16-1.52, p<0.00001). The proportion of XRCC1 polymorphisms (rs25489, AA) in thyroid cancer was slightly lower than that of the normal control group, but again, the difference was not statistically significant (Mean difference=0.78, 95% CI: 0.61-1.01, p=0.06). Similarly, the proportion of XRCC1 polymorphisms (rs25487, GG) and (rs25487, GA) in thyroid cancer was lower than that of the normal control group, but the differences were not statistically significant (p=0.22 and p=0.49, respectively). In conclusion, this study found that the proportion of XRCC1 polymorphisms (rs25489, AA) in thyroid cancer was lower than that of the normal control group.
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Affiliation(s)
- Wenhan Yang
- Department of Maxillofacial Surgery, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
| | - Wanyu Liu
- Department of Maxillofacial Surgery, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
| | - Lei Zhu
- Department of Maxillofacial Surgery, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
| | - Yaqi Lin
- Department of Maxillofacial Surgery, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
| | - Zilu Meng
- Department of Maxillofacial Surgery, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
| | - Yudong Wang
- Department of Maxillofacial Surgery, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
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Yang X, Wang X, Zou Y, Zhang S, Xia M, Fu L, Vollger MR, Chen NC, Taylor DJ, Harvey WT, Logsdon GA, Meng D, Shi J, McCoy RC, Schatz MC, Li W, Eichler EE, Lu Q, Mao Y. Characterization of large-scale genomic differences in the first complete human genome. Genome Biol 2023; 24:157. [PMID: 37403156 PMCID: PMC10320979 DOI: 10.1186/s13059-023-02995-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 06/23/2023] [Indexed: 07/06/2023] Open
Abstract
BACKGROUND The first telomere-to-telomere (T2T) human genome assembly (T2T-CHM13) release is a milestone in human genomics. The T2T-CHM13 genome assembly extends our understanding of telomeres, centromeres, segmental duplication, and other complex regions. The current human genome reference (GRCh38) has been widely used in various human genomic studies. However, the large-scale genomic differences between these two important genome assemblies are not characterized in detail yet. RESULTS Here, in addition to the previously reported "non-syntenic" regions, we find 67 additional large-scale discrepant regions and precisely categorize them into four structural types with a newly developed website tool called SynPlotter. The discrepant regions (~ 21.6 Mbp) excluding telomeric and centromeric regions are highly structurally polymorphic in humans, where the deletions or duplications are likely associated with various human diseases, such as immune and neurodevelopmental disorders. The analyses of a newly identified discrepant region-the KLRC gene cluster-show that the depletion of KLRC2 by a single-deletion event is associated with natural killer cell differentiation in ~ 20% of humans. Meanwhile, the rapid amino acid replacements observed within KLRC3 are probably a result of natural selection in primate evolution. CONCLUSION Our study provides a foundation for understanding the large-scale structural genomic differences between the two crucial human reference genomes, and is thereby important for future human genomics studies.
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Affiliation(s)
- Xiangyu Yang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Xuankai Wang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Yawen Zou
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Shilong Zhang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Manying Xia
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Lianting Fu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Mitchell R Vollger
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Nae-Chyun Chen
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Dylan J Taylor
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - William T Harvey
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Glennis A Logsdon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Dan Meng
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Junfeng Shi
- Shanghai Engineering Research Center of Advanced Dental Technology and Materials, Shanghai, China
- Shanghai Key Laboratory of Stomatology, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Rajiv C McCoy
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Michael C Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Weidong Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Qing Lu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Yafei Mao
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China.
- Shanghai Key Laboratory of Stomatology, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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Zheng M, Li J, Fang W, Luo L, Ding R, Zeng H, Luo H, Lin X, Duan C. The TNF-α rs361525 and IFN-γ rs2430561 polymorphisms are associated with liver cirrhosis risk: a comprehensive meta-analysis. Front Immunol 2023; 14:1129767. [PMID: 37122734 PMCID: PMC10140545 DOI: 10.3389/fimmu.2023.1129767] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 03/30/2023] [Indexed: 05/02/2023] Open
Abstract
Background Inflammation serves as an essential driver of liver cirrhosis (LC) incidence. Accordingly, a meta-analysis was carried out to explore the association between specific polymorphisms in the interferon-γ (IFN-γ) and tumor necrosis factor-α (TNF-α) genes and the incidence of LC based on comparisons of genotype and allele frequencies. Objectives To study the relationship between TNF-α rs361525 and IFN-γ rs2430561 polymorphisms and the risk of LC. Methods A database search was performed for all studies published as of September 10, 2022. The strength of risk relationships was assessed based on odds ratios (ORs) with 95% confidence intervals (CIs). Results Pooled analyses were conducted for one common TNF-α polymorphism (rs361525) as well as one common IFN-γ polymorphism (rs2430561). Both of these SNPs were identified as LC-related risk factors. Specifically, rs361525 was related to LC incidence in both alcoholic liver cirrhosis (OR: 1.86, 95%CI: 1.03-3.34) and hepatitis B virus (HBV)-related cirrhosis cases (OR: 1.44, 95%CI: 1.00-2.06) when using an allelic contrast model. Moreover, rs2430561 was significantly related to LC in an Asian population (OR: 1.45, 95%CI: 1.13-1.86) and in the context of HBV-related cirrhosis (OR: 1.48, 95%CI: 1.13-1.93) when using an allelic contrast model. Conclusion These findings indicate that rs361525 and rs2430561 represent LC-related risk factors, although additional large-scale clinical and case-control studies will be vital to confirm these results.
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Affiliation(s)
- Minghui Zheng
- Department of Clinical Laboratory, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
| | - Jing Li
- Department of Clinical Laboratory, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
| | - Weizhen Fang
- Department of Clinical Laboratory, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
| | - Ling Luo
- Department of Clinical Laboratory, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
| | - Rui Ding
- Department of Clinical Laboratory, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
| | - Hua Zeng
- Department of Clinical Laboratory, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
| | - Hong Luo
- Department of Clinical Laboratory, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xianghua Lin
- Department of Clinical Laboratory, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
- *Correspondence: Xianghua Lin, ; Chaohui Duan,
| | - Chaohui Duan
- Department of Clinical Laboratory, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, China
- *Correspondence: Xianghua Lin, ; Chaohui Duan,
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Liu M, Gu Y, Ma JN, Bao KN, Ao L, Ni X. An updated analysis on the association of GSTM1 polymorphism and smoking exposure with the increased risk of coronary heart disease. J Int Med Res 2022; 50:3000605221123697. [PMID: 36112810 PMCID: PMC9478701 DOI: 10.1177/03000605221123697] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/06/2022] Open
Abstract
Objective To undertake a meta-analysis to investigate if there is an association
between the glutathione S-transferase mu 1 (GSTM1) gene
polymorphism, coronary artery disease (CAD) susceptibility and smoking. Methods Electronic databases, including PubMed®, Web of Science and Embase®, were
searched for relevant case–control studies. Data were extracted and the odds
ratio (OR) was calculated and appropriate statistical methods were used for
the meta-analysis. Results The analysis included eight studies with a total of 1880 cases with CAD and
1758 control subjects. The results of this meta-analysis demonstrated that
there is no association between the GSTM1 null and CAD (OR
1.24, 95% confidence interval [CI] 1.00, 1.55). An increased risk of CAD was
observed in the smoking population with the GSTM1 null
genotype (OR 1.48, 95% CI 1.02, 2.15). Subgroup analyses of geographical
region, genotyping method and publication language category demonstrated
potential relationships among gene polymorphism, smoking and CAD. Conclusions Based on the current literature, the GSTM1 null genotype was
associated to CAD in the smoking population. The interaction between smoking
and GSTM1 polymorphism may contribute to the susceptibility
of CAD.
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Affiliation(s)
- Min Liu
- Department of Scientific Research, Jiading District Central Hospital Affiliated Shanghai University of Medicine & Health Sciences, Shanghai, China.,Department of Hospital Infection Control, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province, China
| | - Ye Gu
- Department of Nursing, Jiading District Central Hospital Affiliated Shanghai University of Medicine & Health Sciences, Shanghai, China
| | - Jian-Ning Ma
- Department of Nursing, Jiading District Central Hospital Affiliated Shanghai University of Medicine & Health Sciences, Shanghai, China
| | - Ke-Na Bao
- Department of Nursing, Jiading District Central Hospital Affiliated Shanghai University of Medicine & Health Sciences, Shanghai, China
| | - Li Ao
- Department of Nursing, Jiading District Central Hospital Affiliated Shanghai University of Medicine & Health Sciences, Shanghai, China
| | - Xin Ni
- Department of Anaesthesiology, Jiading District Central Hospital Affiliated Shanghai University of Medicine & Health Sciences, Shanghai, China
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Zheng M, Fang W, Yu M, Ding R, Zeng H, Huang Y, Mi Y, Duan C. IL-6 and IL-10 gene polymorphisms and cirrhosis of liver risk from a comprehensive analysis. BMC Endocr Disord 2021; 21:242. [PMID: 34886817 PMCID: PMC8656043 DOI: 10.1186/s12902-021-00906-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 11/23/2021] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND Different inflammatory and immune cytokines play a key role in the development of cirrhosis of liver (CL). To investigate the association between interleukin-6,10 (IL-6,10) genes polymorphisms and CL risk through comparison of the allele and genotype distribution frequencies by meta-analysis. METHODS A literature search covered with the PubMed, Embase, Cochrane Library, Web of Science, Google Scholar, SinoMed (CNKI and Wanfang) through 20th April, 2021. Odds ratios (OR) and 95% confidence intervals (CI) were used to assess the strength of associations. RESULTS After a comprehensive search, three common polymorphisms (rs1800872, rs1800871, rs1800896) in IL-10 gene were selected, and three common polymorphisms (rs1800795, rs1800796, rs1800797) in IL-6 gene were also identified. The important finding was that IL-10 rs1800872 was a risk factor for CL development. For example, there has a significantly increased relationship between rs1800872 polymorphism and CL both in the whole group (OR: 1.30, 95%CI: 1.01-1.67 in heterozygote model), Asian population (OR: 1.40, 95%CI: 1.03-1.88 in heterozygote model) and hospital-based source of control (OR: 1.40, 95%CI: 1.01-1.96 in dominant model). In addition, significant association was found between rs1800896 and primary biliary cirrhosis subtype disease (OR: 1.30, 95%CI: 1.01-1.68 in allelic contrast model). No association was observed in all three polymorphisms in IL-6 gene. CONCLUSION Our present study suggests that the IL-10 rs1800872 and rs1800896 polymorphisms is potentially associated with the risk of CL susceptibility.
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Affiliation(s)
- Minghui Zheng
- Department of Clinical Laboratory, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, 510120, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, 510120, China
| | - Weizhen Fang
- Department of Clinical Laboratory, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, 510120, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, 510120, China
| | - Menglei Yu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, 510120, China
- Emergency Department, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, People's Republic of China
| | - Rui Ding
- Department of Clinical Laboratory, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, 510120, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, 510120, China
| | - Hua Zeng
- Department of Clinical Laboratory, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, 510120, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, 510120, China
| | - Yan Huang
- Department of Parasitology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China.
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Chinese Ministry of Education, Guangzhou, Guangdong, 510080, People's Republic of China.
| | - Yuanyang Mi
- Department of Urology, Affiliated Hospital of Jiangnan University, 1000 Hefeng Rd, Wuxi, 214000, People's Republic of China.
| | - Chaohui Duan
- Department of Clinical Laboratory, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, 510120, China.
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, 510120, China.
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