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Penha Mesquita A, Victor Oliveira Monteiro A, Luiz Araújo Bentes Leal A, Dos Santos Pessoa L, de Siqueira Amorim Júnior J, Rogério Souza Monteiro J, Andrade de Sousa A, Fernando Pereira Vasconcelos D, Carolina Alves de Oliveira A, Leão Pereira A, Rodolfo Pereira da Silva F. Gene variations related to the hepatocellular carcinoma: Results from a field synopsis and Bayesian revaluation. Gene 2023; 869:147392. [PMID: 36966980 DOI: 10.1016/j.gene.2023.147392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/28/2023] [Accepted: 03/21/2023] [Indexed: 04/22/2023]
Abstract
Hepatocellular carcinoma (HCC) is considered as the second cause of cancer-related deaths worldwide. Genetic variations are associated with HCC risk, an issue that has been the subject of several meta-analyses. However, meta-analyses have an important limitation on the likelihood of false positive data. Henceforth, this study aimed to assess the level of noteworthiness in the meta-analyses by means of a Bayesian approach. A systematic search was performed for meta-analyses with associations between gene polymorphisms and HCC. The calculations for the False-Positive Rate Probability (FPRP) and the Bayesian False Discovery Probability (BFDP) were performed to assess the noteworthiness with a statistical power of 1.2 and 1.5 of Odds Ratio at a prior probability of 10-3 and 10-5. The quality of studies was evaluated by the Venice criteria. As additional analyses, the gene-gene and protein-protein networks were designed for these genes and products. As results, we found 33 meta-analytic studies on 45 polymorphisms occurring in 35 genes. A total of 1,280 values for FPRP and BFDP were obtained. Seventy-five for FPRP (5.86%) and 95 for BFDP (14.79%) were noteworthy. In conclusion, the polymorphisms in CCND1, CTLA4, EGF, IL6, IL12A, KIF1B, MDM2, MICA, miR-499, MTHFR, PNPLA3, STAT4, TM6SF2, and XPD genes were considered as noteworthy biomarkers for HCC risk.
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Affiliation(s)
- Abel Penha Mesquita
- Medicine College, Altamira University Campus, Federal University of Para, Altamira, PA, Brazil
| | | | | | - Larissa Dos Santos Pessoa
- Parnaiba Delta Federal University, Parnaiba, PI, Brazil; Laboratory of Histological Analysis and Preparation (LAPHIs), Parnaiba Delta Federal University, Parnaiba, PI, Brazil
| | | | | | - Aline Andrade de Sousa
- Medicine College, Altamira University Campus, Federal University of Para, Altamira, PA, Brazil
| | - Daniel Fernando Pereira Vasconcelos
- Parnaiba Delta Federal University, Parnaiba, PI, Brazil; Laboratory of Histological Analysis and Preparation (LAPHIs), Parnaiba Delta Federal University, Parnaiba, PI, Brazil
| | | | - Adenilson Leão Pereira
- Medicine College, Altamira University Campus, Federal University of Para, Altamira, PA, Brazil
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Zhang XQ, Li L. A meta-analysis of XRCC1 single nucleotide polymorphism and susceptibility to gynecological malignancies. Medicine (Baltimore) 2021; 100:e28030. [PMID: 34918657 PMCID: PMC8677953 DOI: 10.1097/md.0000000000028030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 11/11/2021] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Gynecological malignant tumor is a serious threat to women's health, cervical cancer, endometrial cancer and ovarian cancer are the most common. The eponymous protein encoded by the XRCC1 (X-ray repair cross complementation 1) gene is an important functional protein in the process of single-stranded DNA damage. Non-synonymous mutations of XRCC1 gene cause amino acid sequence changes that affect protein function and DNA repair ability, and may affect the interaction with other DNA repair proteins, leading to increased risk of tumor development. Many studies have assessed the association between XRCC1 gene polymorphism and the risk of cancer in the female reproductive system, but the results have been inconclusive. In this study, the relationship between XRCC1 Arg399Gln, Arg194Trp, Arg280His single nucleotide polymorphisms and susceptibility to gynecological malignancies was further explored by meta-analysis. METHODS English database: Pubmed, Medline, Excerpta Medica Database, Cochrance, etc; Chinese database: China national knowledge infrastructure, Wanfang Database, etc. STATA14 was used for statistical analysis, such as odd ratio (OR) value, subgroup analysis, heterogeneity test, sensitivity analysis, and publication bias. RESULTS In gynecologic cancers, the allele frequency difference of Arg399Gln case control group was statistically significant (GvsA: P = .007). There was no significant difference in allele frequency in the Arg194Trp and Arg280His case control groups (P = .065, 0.198). In different gene models, Arg399Gln was significantly correlated with gynecologic cancers susceptibility (GGvs AA: OR 0.91; 95% confidence interval [CI], 0.85 0.98); Arg194Trp was significantly correlated with gynecologic cancers susceptibility (CCvs TT: OR 0.94; 95% CI 0.88,1.00; CCvs CT: OR 0.97; 95% CI 0.90, 1.05); Arg280His was significantly correlated with gynecologic cancers susceptibility (GGvs AA: OR 0.98; 95% CI 0.94, 1.02; GGvs GA: OR 1.00;95% CI 0.97, 1.04). In the subgroup analysis, Arg399Gln and Arg194Trp were significantly correlated with gynecologic cancers susceptibility in the Asian race (P = .000, 0.049). In the analysis of different cancer subgroups, Arg399Gln and cervical cancer susceptibility were statistically significant (P = .039). Arg194Trp and endometrial cancer susceptibility were statistically significant (P = .033, 0.001). CONCLUSIONS XRCC1 Arg399Gln, Arg194Trp, Arg280His single nucleotide polymorphisms were associated with gynecologic cancer susceptibility. Arg399Gln genotype was statistically significant in relation to cervical cancer susceptibility. Arg194Trp genotype was statistically significant in relation to endometrial cancer susceptibility.
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Singh N, Kazim SN, Sultana R, Tiwari D, Borkotoky R, Kakati S, Nath Das N, Kumar Saikia A, Bose S. Oxidative stress and deregulations in base excision repair pathway as contributors to gallbladder anomalies and carcinoma - a study involving North-East Indian population. Free Radic Res 2019; 53:473-485. [PMID: 31117842 DOI: 10.1080/10715762.2019.1606423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Gallbladder cancer (GBC) is a fatal condition with dismal prognosis and aggressive local invasiveness; and with uncharacterised molecular pathology relating to non-specific therapeutic modalities. Given the importance of oxidative stress in chronic diseases and carcinogenesis, and the lacunae in literature regarding its role in gallbladder diseases, this study aimed to study the involvement of oxidative stress and deregulation in the base excision repair (BER) pathway in the pathogenesis of gallbladder diseases including GBC. This study involved patients from the North-East Indian population, where the numbers of reported cases are increasing rapidly and alarmingly. Oxidative stress, based on 8-OH-dG levels, was found to be significantly higher in gallbladder anomalies (cholelithiasis [CL] and cholecystitis [CS]) and GBC at the plasma and DNA level, and was associated with GBC severity. The expressions of key BER pathway genes were downregulated in gallbladder anomalies and GBC compared to controls, and in GBC compared to both non-neoplastic controls and gallbladder anomalies. Expression of XRCC1 and hOGG1 was significantly associated with both susceptibility and severity of GBC. The XRCC1 codon280 polymorphism was associated with disease susceptibility; and significantly higher oxidative stress was observed in hOGG1 genotypic variants. The genomes of GBC patients were found to be more hypermethylated compared to controls, with the promoters of XRCC1 and hOGG1 being hypermethylated and, therefore, being silenced. This study underlined the prognostic significance of the oxidative stress marker 8-OH-dG and BER pathway genes, especially hOGG1 and XRCC1, in gallbladder anomalies and GBC, as well as stated their potential for therapeutic targeting.
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Affiliation(s)
- Nidhi Singh
- a Department of Biotechnology , Gauhati University , Guwahati , India
| | - Syed Naqui Kazim
- b Centre for Interdisciplinary Research in Basic Sciences , Jamia Millia Islamia , New Delhi , India
| | - Rizwana Sultana
- c Bioengineering and Technology , Gauhati University , Guwahati , India
| | - Diptika Tiwari
- c Bioengineering and Technology , Gauhati University , Guwahati , India
| | - Raktim Borkotoky
- a Department of Biotechnology , Gauhati University , Guwahati , India
| | | | | | - Anjan Kumar Saikia
- e Central Railway Hospital , Guwahati , India.,f GNRC Hospital , Guwahati , India
| | - Sujoy Bose
- a Department of Biotechnology , Gauhati University , Guwahati , India
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Krupa R, Czarny P, Wigner P, Wozny J, Jablkowski M, Kordek R, Szemraj J, Sliwinski T. The Relationship Between Single-Nucleotide Polymorphisms, the Expression of DNA Damage Response Genes, and Hepatocellular Carcinoma in a Polish Population. DNA Cell Biol 2017; 36:693-708. [PMID: 28598207 DOI: 10.1089/dna.2017.3664] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The molecular mechanism of hepatocellular carcinoma (HCC) is related to DNA damage caused by oxidative stress products induced by hepatitis B virus (HBV) or C (HCV) infection and exposure to environmental pollutants. Single-nucleotide polymorphisms (SNPs) of DNA damage response (DDR) genes may influence individual susceptibility to environmental risk factors and affect DNA repair efficacy, which, in turn, can influence the risk of HCC. The study evaluates a panel of 15 SNPs in 11 DDR genes (XRCC1, XRCC3, XPD, MUTYH, LIG1, LIG3, hOGG1, PARP1, NFIL1, FEN1, and APEX1) in 65 HCC patients, 50 HBV- and 50 HCV-infected non-cancerous patients, and 50 healthy controls. It also estimates the mRNA expression of nine DDR genes in cancerous and adjacent healthy liver tissues. Two of the investigated polymorphisms (rs1052133 and rs13181) were associated with HCC risk. For all investigated genes, the level of mRNA was significantly lower in HCC cancer tissue than in non-cancerous liver tissue. Seven of the investigated polymorphisms were statistically related to gene expression in cancer tissues. The disruption of DDR genes may be responsible for hepatocellular transformation in HCV-infected patients.
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Affiliation(s)
- Renata Krupa
- 1 Department of Molecular Genetics, University of Lodz , Lodz, Poland
| | - Piotr Czarny
- 2 Department of Medical Biochemistry, Medical University of Lodz , Lodz, Poland
| | - Paulina Wigner
- 1 Department of Molecular Genetics, University of Lodz , Lodz, Poland
| | - Joanna Wozny
- 3 Department of Infectious and Liver Diseases, Medical University of Lodz , Lodz, Poland
| | - Maciej Jablkowski
- 3 Department of Infectious and Liver Diseases, Medical University of Lodz , Lodz, Poland
| | - Radzislaw Kordek
- 4 Department of Pathology, Medical University of Lodz , Lodz, Poland
| | - Janusz Szemraj
- 2 Department of Medical Biochemistry, Medical University of Lodz , Lodz, Poland
| | - Tomasz Sliwinski
- 1 Department of Molecular Genetics, University of Lodz , Lodz, Poland
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XRCC1 Arg399Gln Gene Polymorphism and Hepatocellular Carcinoma Risk in the Italian Population. Int J Biol Markers 2017; 32:e190-e194. [DOI: 10.5301/jbm.5000241] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2016] [Indexed: 01/29/2023]
Abstract
Background The human X-ray repair cross-complementing protein 1 ( XRCC1) gene encodes for one of the major repair factors involved in base excision repair (BER), which is reported to be associated with the risk of several cancers. A few studies have explored the association between risk of hepatocellular carcinoma (HCC) and single-nucleotide polymorphisms (SNPs) in different DNA repair genes, with contradictory results. The purpose of this study was to evaluate the association between XRCC1 Arg399Gln polymorphism and susceptibility to HCC. Methods A total of 89 HCC patients and 99 randomly selected healthy controls were enrolled. Genotyping of XRCC1 rs25487 was performed by high-resolution melting analysis and Sanger sequencing. Results On univariate analysis, a statistically significant association was found between risk of HCC and XRCC1 399Arg/Gln genotype (odd ratio [OR] = 1.88; 95% CI, 1.04-3.43), which was confirmed after adjusting by sex (OR = 1.94; 95% CI, 1.04-3.63). Although not significant, Kaplan-Meier analysis showed a decreased median survival in Arg/Gln genotype carriers in comparison with Arg/Arg carriers. Conclusions To our knowledge, this is the first study reporting an association between BER SNP and HCC risk in a population of central-southern Italy.
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Jeng JE, Wu HF, Tsai MF, Tsai HR, Chuang LY, Lin ZY, Hsieh MY, Chen SC, Chuang WL, Wang LY, Yu ML, Dai CY, Tsai JF. Independent and additive interaction between tumor necrosis factor β +252 polymorphisms and chronic hepatitis B and C virus infection on risk and prognosis of hepatocellular carcinoma: a case-control study. Asian Pac J Cancer Prev 2014; 15:10209-10215. [PMID: 25556449 DOI: 10.7314/apjcp.2014.15.23.10209] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2023] Open
Abstract
To assess the contribution of tumor necrosis factor (TNF)β +252 polymorphisms to risk and prognosis of hepatocellular carcinoma (HCC), we enrolled 150 pairs of sex- and age-matched patients with HCC, patients with cirrhosis alone, and unrelated healthy controls. TNFβ +252 genotypes were determined by polymerase chain reaction with restriction fragment length polymorphism. Multivariate analysis indicated that TNFβ G/G genotype [odds ratio (OR), 3.64; 95%CI, 1.49-8.91], hepatitis B surface antigen (OR, 16.38; 95%CI, 8.30-32.33), and antibodies to hepatitis C virus (HCV) (OR, 39.11; 95%CI, 14.83-103.14) were independent risk factors for HCC. There was an additive interaction between TNFβ G/G genotype and chronic hepatitis B virus (HBV)/HCV infection (synergy index=1.15). Multivariate analysis indicated that factors associated with TNFβ G/G genotype included cirrhosis with Child-Pugh C (OR, 4.06; 95%CI, 1.34-12.29), thrombocytopenia (OR, 6.55; 95%CI, 1.46-29.43), and higher serum α-fetoprotein concentration (OR, 2.53; 95%CI, 1.14-5.62). Patients with TNFβ G/G genotype had poor cumulative survival (p=0.005). Cox proportional hazard model indicated that TNFβ G/G genotype was a biomarker for poor HCC survival (hazard ratio, 1.70; 95%CI, 1.07-2.69). In conclusion, there are independent and additive effects between TNFβ G/G genotype and chronic HBV/HCV infection on risk for HCC. It is a biomarker for poor HCC survival. Carriage of this genotype correlates with disease severity and advanced hepatic fibrosis, which may contribute to a higher risk and poor survival of HCC. Chronic HBV/HCV infected subjects with this genotype should receive more intensive surveillance for early detection of HCC.
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Affiliation(s)
- Jen-Eing Jeng
- Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan E-mail :
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