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Liao Z, Yi M, Li J, Zhang Y. DNA repair in lung cancer: a large-scale quantitative analysis for polymorphisms in DNA repairing pathway genes and lung cancer susceptibility. Expert Rev Respir Med 2022; 16:997-1010. [PMID: 35984915 DOI: 10.1080/17476348.2022.2115361] [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: 12/30/2022]
Abstract
BACKGROUND The results of associations between single nucleotide polymorphisms (SNPs) of genes in DNA repairing pathway and lung cancer (LC) risk are inconsistent. METHODS We applied allele, dominant and recessive models to explore the risk of researched variants to LC in total LC and subgroups by ethnicity or LC subtypes with a cutoff point of p < 0.05. RESULTS A total of 76,935 cases and 88,649 controls from 192 articles were included. Among the analyzed 40 variants from 20 genes, we found 9 statistically significant variants in overall populations by allele model, including five SNPs (rs1760944, rs9344, rs13181, rs1001581, and rs915927) increasing LC risk (odd ratios [ORs] = 1.10-1.71) and four SNPs (rs1042522, rs3213245, rs11615, and rs238406) decreasing the risk (ORs = 0.75-0.94). We identified rs1042522 and rs13181 as significant variants for LC in three models. Additionally, we identified differential significant SNPs in ethnic and subtype's analysis with comparison to total population. CONCLUSIONS There are five SNPs in DNA repairing pathway associated with increased LC risk and four others decreased LC risk. Besides, the risky SNPs in different ethnicities and various LC subtypes were partly different, and the contribution of different genotypes to risk alleles were various as well.
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Affiliation(s)
- Zexi Liao
- Department of Respiratory Medicine, Central South University, Changsha, Hunan, China.,Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Xiangya Medical School, Central South University, Changsha, Hunan, China
| | - Minhan Yi
- Department of Respiratory Medicine, Central South University, Changsha, Hunan, China.,School of Life Sciences, Central South University, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jiaxin Li
- Department of Respiratory Medicine, Central South University, Changsha, Hunan, China.,Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Xiangya Medical School, Central South University, Changsha, Hunan, China
| | - Yuan Zhang
- Department of Respiratory Medicine, Central South University, Changsha, Hunan, China.,Center of Respiratory Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
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Yin J, Wang H, Vogel U, Wang C, Ma Y, Hou W, Zhang Y, Guo L, Li X. Fine-mapping markers of lung cancer susceptibility in a sub-region of chromosome 19q13.3 among Chinese. Oncotarget 2018; 7:60929-60939. [PMID: 27183913 PMCID: PMC5308627 DOI: 10.18632/oncotarget.9279] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 04/19/2016] [Indexed: 12/11/2022] Open
Abstract
Linkage disequilibrium-mapping studies in Caucasians have indicated anassociation of Chr19q13.3 sub-region spanning ERCC2, PPP1R13L, CD3EAP and ERCC1 with several cancers. To refine the region of association and identify potential causal variations among Asians, we performed a fine-mapping study using 32 (39) SNPs in a 71.654kb sub-region. The study included 384 Chinese lung cancer cases and 387 controls. Seven closely situated SNPs showed significant associations with lung cancer risk in five different genetic models of single-locus associations (adjusted for smoking duration). These were PPP1R13L rs1970764 [OR (95% CI) = 1.58 (1.09-2.29), P = 0.014] in a recessive model and PPP1R13L rs1005165 [OR (95% CI) = 1.25 (1.01-1.54), P = 0.036], CD3EAP rs967591 [OR (95% CI) = 1.40 (1.13-1.75), P = 0.0023], rs735482 [OR (95% CI) = 1.29 (1.03-1.61), P = 0.026], rs1007616 [OR (95% CI) = 0.78 (0.61-1.00), P = 0.046], and rs62109563 [OR (95% CI) = 1.28 (1.03-1.59), P = 0.024] in a log-additive model and ERCC1 rs3212965 [OR (95% CI) = 0.70 (0.52-0.94), P = 0.019] in an over-dominant model. Six-haplotype blocks were determined in the sub-region. Using an alternative approach where we performed a haplotype analysis of all significant polymorphisms, rs1970764 was found to be most consistently associated with lung cancer risk. The combined data suggest that the sub-region with the strongest association to lung cancer susceptibility might locate to the 23.173kb from PPP1R13L intron8 rs1970764 to rs62109563 3′ to CD3EAP. Limited risk loci and span on lung cancer in this sub-region are initially defined among Asians.
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Affiliation(s)
- Jiaoyang Yin
- Key Laboratory of Environment and Population Health of Liaoning Education Ministry (Shenyang Medical College), Shenyang, Liaoning Province, People's Republic of China
| | - Huiwen Wang
- Key Laboratory of Environment and Population Health of Liaoning Education Ministry (Shenyang Medical College), Shenyang, Liaoning Province, People's Republic of China
| | - Ulla Vogel
- National Research Centre for The Working Environment, Lerso Parkalle, Copenhagen O, Denmark
| | - Chunhong Wang
- Key Laboratory of Environment and Population Health of Liaoning Education Ministry (Shenyang Medical College), Shenyang, Liaoning Province, People's Republic of China
| | - Yegang Ma
- Department of Thoracic Surgery, Liaoning Cancer Hospital, Shenyang, Liaoning Province, People's Republic of China
| | - Wei Hou
- Department of Pathology, School of Basic Medical Sciences, Health Science Center, Peking University, Beijing, People's Republic of China
| | - Ying Zhang
- Key Laboratory of Environment and Population Health of Liaoning Education Ministry (Shenyang Medical College), Shenyang, Liaoning Province, People's Republic of China
| | - Li Guo
- Key Laboratory of Environment and Population Health of Liaoning Education Ministry (Shenyang Medical College), Shenyang, Liaoning Province, People's Republic of China
| | - Xinxin Li
- Key Laboratory of Environment and Population Health of Liaoning Education Ministry (Shenyang Medical College), Shenyang, Liaoning Province, People's Republic of China
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Yin J, Vogel U, Wang H, Ma Y, Wang C, Liang D, Liu J, Yue L, Zhao Y, Ma J. HapMap-based study identifies risk sub-region on chromosome 19q13.3 in relation to lung cancer among Chinese. Cancer Epidemiol 2013; 37:923-9. [DOI: 10.1016/j.canep.2013.09.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Accepted: 09/22/2013] [Indexed: 10/26/2022]
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van Huis-Tanja LH, Kweekel DM, Lu X, Franken K, Koopman M, Gelderblom H, Antonini NF, Punt CJA, Guchelaar HJ, van der Straaten T. Excision Repair Cross-Complementation group 1 (ERCC1) C118T SNP does not affect cellular response to oxaliplatin. Mutat Res 2013; 759:37-44. [PMID: 24220697 DOI: 10.1016/j.mrfmmm.2013.11.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 10/21/2013] [Accepted: 11/01/2013] [Indexed: 01/29/2023]
Abstract
AIMS ERCC1 is involved in the repair of oxaliplatin-induced DNA damage. Studies for the association of the C118T SNP with clinical response to treatment with platinum drugs have rendered inconsistent results. We investigated the ERCC1 C118T SNP with respect to overall and progression-free survival in patients with advanced colorectal cancer (ACC) treated with oxaliplatin and in vitro DNA repair capacity after oxaliplatin exposure. In addition we discuss discrepancies from other studies concerning ERCC1 C118T. MATERIALS AND METHODS Progression-free survival was determined in 145 ACC patients treated with oxaliplatin-based chemotherapy in a phase 3 trial. For the in vitro studies regarding ERCC1 functionality, we transfected an ERCC1 negative cell line with 118C or 118T ERCC1. Cellular sensitivity and DNA repair capacity after exposure to oxaliplatin was examined by Sulphorodamine B growth inhibition assay, COMET assay and Rad51 foci staining. RESULTS We found no association between ERCC1 C118T and progression-free or overall survival. In addition, transfection of either 118C or 118T restores DNA-repair capacity of UV20 cells to the same level and chemosensitivity to oxaliplatin was similar in ERCC1 118C and 118T transfected cells. CONCLUSION This study shows that the ERCC1 C118T variants are not associated with survival in ACC patients treated with oxaliplatin or the in vitro sensitivity and DNA-repair capacity in 118C and 118T transfected cell lines. Therefore, ERCC1 C118T genotyping seems of no value in individualizing oxaliplatin based chemotherapy in ACC.
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Affiliation(s)
- Lieke H van Huis-Tanja
- Department of Clinical Oncology, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands.
| | - Dina M Kweekel
- Department of Clinical Pharmacy & Toxicology, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands.
| | - Xiaobo Lu
- Department of Clinical Pharmacy & Toxicology, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Kees Franken
- Department of Infectious Diseases, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands.
| | - Miriam Koopman
- Department of Medical Oncology, University Medical Center Utrecht, PO Box 85500, 3508 GA Utrecht, The Netherlands.
| | - Hans Gelderblom
- Department of Clinical Oncology, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands.
| | - Ninja F Antonini
- Department of Biometrics, Netherlands Cancer Institute (NKI), Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
| | - Cornelis J A Punt
- Department of Medical Oncology, Academic Medical Center, University of Amsterdam, PO BOX 22660, 1100 DD Amsterdam, The Netherlands.
| | - Henk-Jan Guchelaar
- Department of Clinical Pharmacy & Toxicology, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands.
| | - Tahar van der Straaten
- Department of Clinical Pharmacy & Toxicology, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands.
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Lanara Z, Giannopoulou E, Fullen M, Kostantinopoulos E, Nebel JC, Kalofonos HP, Patrinos GP, Pavlidis C. Comparative study and meta-analysis of meta-analysis studies for the correlation of genomic markers with early cancer detection. Hum Genomics 2013; 7:14. [PMID: 23738773 PMCID: PMC3686617 DOI: 10.1186/1479-7364-7-14] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 05/01/2013] [Indexed: 12/12/2022] Open
Abstract
A large number of common disorders, including cancer, have complex genetic traits, with multiple genetic and environmental components contributing to susceptibility. A literature search revealed that even among several meta-analyses, there were ambiguous results and conclusions. In the current study, we conducted a thorough meta-analysis gathering the published meta-analysis studies previously reported to correlate any random effect or predictive value of genome variations in certain genes for various types of cancer. The overall analysis was initially aimed to result in associations (1) among genes which when mutated lead to different types of cancer (e.g. common metabolic pathways) and (2) between groups of genes and types of cancer. We have meta-analysed 150 meta-analysis articles which included 4,474 studies, 2,452,510 cases and 3,091,626 controls (5,544,136 individuals in total) including various racial groups and other population groups (native Americans, Latinos, Aborigines, etc.). Our results were not only consistent with previously published literature but also depicted novel correlations of genes with new cancer types. Our analysis revealed a total of 17 gene-disease pairs that are affected and generated gene/disease clusters, many of which proved to be independent of the criteria used, which suggests that these clusters are biologically meaningful.
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Affiliation(s)
- Zoi Lanara
- Faculty of Mathematical, Physical and Natural Sciences, Department of Biological Sciences, University of Trieste, Trieste, 34128, Italy
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