Association between RAD51, XRCC2 and XRCC3 gene polymorphisms and risk of ovarian cancer: a case control and an in silico study
Tóm tắt
Từ khóa
Tài liệu tham khảo
Li J, Sun H, Huang Y et al (2019) Pathways and assays for DNA double-strand break repair by homologous recombination. Acta Biochim Biophys Sin (Shanghai) 51:879–889. https://doi.org/10.1093/abbs/gmz076
Khanna KK, Jackson SP (2001) DNA double-strand breaks: signaling, repair and the cancer connection. Nat Genet 27:247–254. https://doi.org/10.1038/85798
Lengauer C, Kinzler KW, Vogelstein B (1998) Genetic instabilities in human cancers. Nature 396:643–649. https://doi.org/10.1038/25292
Hustedt N, Durocher D (2017) The control of DNA repair by the cell cycle. Nat Cell Biol 19:1–9. https://doi.org/10.1038/ncb3452
Cerbinskaite A, Mukhopadhyay A, Plummer ER et al (2012) Defective homologous recombination in human cancers. Cancer Treat Rev 38:89–100. https://doi.org/10.1016/j.ctrv.2011.04.015
West SC, Blanco MG, Chan YW et al (2016) Resolution of recombination intermediates: mechanisms and regulation. Cold Spring Harb Symp Quant Biol 80:103–109. https://doi.org/10.1101/sqb.2015.80.027649
Suwaki N, Klare K, Tarsounas M (2011) RAD51 paralogs: roles in DNA damage signalling, recombinational repair and tumorigenesis. Semin Cell Dev Biol 22:898–905. https://doi.org/10.1016/j.semcdb.2011.07.019
Mao CF, Qian WY, Wu JZ et al (2014) Association between the XRCC3 Thr241Met polymorphism and breast cancer risk: an updated meta-analysis of 36 casecontrol studies. Asian Pac J Cancer Prev 15:6613–6618. https://doi.org/10.7314/APJCP.2014.15.16.6613
Kadouri L, Kote-Jarai Z, Hubert A et al (2004) A single-nucleotide polymorphism in the RAD51 gene modifies breast cancer risk in BRCA2 carriers, but not in BRCA1 carriers or noncarriers. Br J Cancer 90:2002–2005. https://doi.org/10.1038/sj.bjc.6601837
Griffin CS, Simpson PJ, Wilson CR, Thacker J (2000) Mammalian recombination-repair genes XRCC2 and XRCC3 promote correct chromosome segregation. Nat Cell Biol 2:757–761. https://doi.org/10.1038/35036399
Thacker J (2005) The RAD51 gene family, genetic instability and cancer. Cancer Lett 219:125–135. https://doi.org/10.1016/j.canlet.2004.08.018
Takata M, Sasaki MS, Tachiiri S et al (2001) Chromosome Instability and defective recombinational repair in knockout mutants of the five Rad51 paralogs. Mol Cell Biol 21:2858–2866. https://doi.org/10.1128/mcb.21.8.2858-2866.2001
Clarkson SG, Wood RD (2005) Polymorphisms in the human XPD (ERCC2) gene, DNA repair capacity and cancer susceptibility: an appraisal. DNA Repair (Amst) 4:1068–1074. https://doi.org/10.1016/j.dnarep.2005.07.001
Deans B, Griffin CS, Maconochie M, Thacker J (2000) Xrcc2 is required for genetic stability, embryonic neurogenesis and viability in mice. EMBO J 19:6675–6685. https://doi.org/10.1093/emboj/19.24.6675
Zhang Y, Wang H, Peng Y et al (2014) The Arg188His polymorphism in the XRCC2 gene and the risk of cancer. Tumor Biol 35:3541–3549. https://doi.org/10.1007/s13277-013-1468-6
Ramadan RA, Desouky LM, Elnaggar MA et al (2014) Association of DNA repair genes XRCC1 (Arg399Gln), (Arg194Trp) and XRCC3 (Thr241Met) polymorphisms with the risk of breast cancer: a case-control study in Egypt. Genet Test Mol Biomark 18:754–760. https://doi.org/10.1089/gtmb.2014.0191
Nissar S, Baba SM, Akhtar T et al (2014) RAD51 G135C gene polymorphism and risk of colorectal cancer in Kashmir. Eur J Cancer Prev 23:264–268. https://doi.org/10.1097/CEJ.0000000000000049
Sobhan MR, Yazdi MF, Mazaheri M et al (2017) Association between the DNA repair gene XRCC3 rs861539 polymorphism and risk of osteosarcoma: a systematic review and meta-analysis. Asian Pac J Cancer Prev 18:549–555. https://doi.org/10.22034/APJCP.2017.18.2.549
Braybrooke JP, Spink KG, Thacker J, Hickson ID (2000) The RAD51 family member, RAD51L3, is a DNA-stimulated ATPase that forms a complex with XRCC2. J Biol Chem 275:29100–29106. https://doi.org/10.1074/jbc.M002075200
Jiao L, Hassan MM, Bondy ML et al (2008) XRCC2 and XRCC3 gene polymorphismand risk of pancreatic cancer. Am J Gastroenterol 103:360–367. https://doi.org/10.1111/j.1572-0241.2007.01615.x
Auranen A, Song H, Waterfall C et al (2005) Polymorphisms in DNA repair genes and epithelial ovarian cancer risk. Int J Cancer 117:611–618. https://doi.org/10.1002/ijc.21047
Beesley J, Jordan SJ, Spurdle AB et al (2007) Association between single-nucleotide polymorphisms in hormone metabolism and DNA repair genes and epithelial ovarian cancer: results from two Australian studies and an additional validation set. Cancer Epidemiol Biomark Prev 16:2557–2565. https://doi.org/10.1158/1055-9965.EPI-07-0542
Yen CY, Liu SY, Chen CH et al (2008) Combinational polymorphisms of four DNA repair genes XRCC1, XRCC2, XRCC3, and XRCC4 and their association with oral cancer in Taiwan. J Oral Pathol Med 37:271–277. https://doi.org/10.1111/j.1600-0714.2007.00608.x
Sliwinski T, Krupa R, Majsterek I et al (2005) Polymorphisms of the BRCA2 and RAD51 genes in breast cancer. Breast Cancer Res Treat 94:105–109. https://doi.org/10.1007/s10549-005-0672-5
Blasiak J, Przybyłowska K, Czechowska A et al (2003) Analysis of the G/C polymorphism in the 5′-untranslated region of the RAD51 gene in breast cancer. Acta Biochim Pol 50:249–253. https://doi.org/10.18388/abp.2003_3733
Krupa R, Synowiec E, Pawlowska E et al (2009) Polymorphism of the homologous recombination repair genes RAD51 and XRCC3 in breast cancer. Exp Mol Pathol 87:32–35. https://doi.org/10.1016/j.yexmp.2009.04.005
Waterhouse A, Bertoni M, Bienert S et al (2018) SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res 46:W296–W303. https://doi.org/10.1093/nar/gky427
Kelley LA, Mezulis S, Yates CM et al (2015) The Phyre2 web portal for protein modeling, prediction and analysis. Nat Protoc 10:845–858. https://doi.org/10.1038/nprot.2015.053
Sim NL, Kumar P, Hu J et al (2012) SIFT web server: predicting effects of amino acid substitutions on proteins. Nucleic Acids Res 40:W452–W457. https://doi.org/10.1093/nar/gks539
Adzhubei I, Jordan DM, Sunyaev SR (2013) Predicting functional effect of human missense mutations using PolyPhen-2. Curr Protoc Hum Genet Chapter. https://doi.org/10.1002/0471142905.hg0720s76
Choi Y, Sims GE, Murphy S et al (2012) Predicting the functional effect of amino acid substitutions and indels. PLoS ONE 7:e46688. https://doi.org/10.1371/journal.pone.0046688
Hecht M, Bromberg Y, Rost B (2015) Better prediction of functional effects for sequence variants. BMC Genom. https://doi.org/10.1186/1471-2164-16-S8-S1
Tang H, Thomas PD (2016) PANTHER-PSEP: predicting disease-causing genetic variants using position-specific evolutionary preservation. Bioinformatics 32:2230–2232. https://doi.org/10.1093/bioinformatics/btw222
Reva B, Antipin Y, Sander C (2011) Predicting the functional impact of protein mutations: application to cancer genomics. Nucleic Acids Res 39:e118–e118. https://doi.org/10.1093/nar/gkr407
Shihab HA, Gough J, Mort M et al (2014) Ranking non-synonymous single nucleotide polymorphisms based on disease concepts. Hum Genom 8:11. https://doi.org/10.1186/1479-7364-8-11
Pejaver V, Urresti J, Lugo-Martinez J et al (2020) Inferring the molecular and phenotypic impact of amino acid variants with MutPred2. Nat Commun 11:1–13. https://doi.org/10.1038/s41467-020-19669-x
Capriotti E, Calabrese R, Casadio R (2006) Predicting the insurgence of human genetic diseases associated to single point protein mutations with support vector machines and evolutionary information. Bioinformatics 22:2729–2734. https://doi.org/10.1093/bioinformatics/btl423
Capriotti E, Calabrese R, Fariselli P et al (2013) WS-SNPs&GO: a web server for predicting the deleterious effect of human protein variants using functional annotation. BMC Genom 14(Suppl 3):S6. https://doi.org/10.1186/1471-2164-14-s3-s6
Niroula A, Urolagin S, Vihinen M (2015) PON-P2: prediction method for fast and reliable identification of harmful variants. PLoS ONE. https://doi.org/10.1371/journal.pone.0117380
Capriotti E, Altman RB, Bromberg Y (2013) Collective judgment predicts disease-associated single nucleotide variants. BMC Genom 14(Suppl 3):S2. https://doi.org/10.1186/1471-2164-14-s3-s2
Capriotti E, Altman RB (2011) A new disease-specific machine learning approach for the prediction of cancer-causing missense variants. Genomics 98:310–317. https://doi.org/10.1016/j.ygeno.2011.06.010
Capriotti E, Fariselli P, Casadio R (2005) I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure. Nucleic Acids Res. https://doi.org/10.1093/nar/gki375
Cheng J, Randall A, Baldi P (2006) Prediction of protein stability changes for single-site mutations using support vector machines. Proteins Struct Funct Genet 62:1125–1132. https://doi.org/10.1002/prot.20810
Ashkenazy H, Abadi S, Martz E et al (2016) ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules. Nucleic Acids Res 44:W344–W350. https://doi.org/10.1093/nar/gkw408
Geourjon C, Deléage G (1995) Sopma: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments. Bioinformatics 11:681–684. https://doi.org/10.1093/bioinformatics/11.6.681
Szklarczyk D, Gable AL, Lyon D et al (2019) STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res 47:D607–D613. https://doi.org/10.1093/nar/gky1131
Schrödinger LLC (2015) The PyMOL molecular graphics system, version~1.8
Han J, Haiman C, Niu T et al (2009) Genetic variation in DNA repair pathway genes and premenopausal breast cancer risk. Breast Cancer Res Treat 115:613–622. https://doi.org/10.1007/s10549-008-0089-z
Michalska MM, Samulak D, Romanowicz H et al (2016) Association between single nucleotide polymorphisms (SNPs) of XRCC2 and XRCC3 homologous recombination repair genes and ovarian cancer in Polish women. Exp Mol Pathol 100:243–247. https://doi.org/10.1016/j.yexmp.2016.01.007
Sliwinski T, Walczak A, Przybylowska K et al (2010) Polymorphisms of the XRCC3 C722T and the RAD51 G135C genes and the risk of head and neck cancer in a Polish population. Exp Mol Pathol 89:358–366. https://doi.org/10.1016/j.yexmp.2010.08.005
Krejci L, Altmannova V, Spirek M, Zhao X (2012) Homologous recombination and its regulation. Nucleic Acids Res 40:5795–5818. https://doi.org/10.1093/nar/gks270
San Filippo J, Sung P, Klein H (2008) Mechanism of eukaryotic homologous recombination. Annu Rev Biochem 77:229–257. https://doi.org/10.1146/annurev.biochem.77.061306.125255
Walsh CS (2015) Two decades beyond BRCA1/2: homologous recombination, hereditary cancer risk and a target for ovarian cancer therapy? Gynecol Oncol 137:343–350. https://doi.org/10.1016/j.ygyno.2015.02.017
Lin WY, Camp NJ, Cannon-Albright LA et al (2011) A role for XRCC2 gene polymorphisms in breast cancer risk and survival. J Med Genet 48:477–484. https://doi.org/10.1136/jmedgenet-2011-100018
Romanowicz-Makowska H, Smolarz B, Polać I, Sporny S (2012) Single nucleotide polymorphisms of RAD51 G135C, XRCC2 Arg188His and XRCC3 Thr241Met homologous recombination repair genes and the risk of sporadic endometrial cancer in Polish womenjog. J Obstet Gynaecol Res 38:918–924. https://doi.org/10.1111/j.1447-0756.2011.01811.x
Zdzienicka MZ (1999) Mammalian X-ray-sensitive mutants which are defective in non-homologous (illegitimate) DNA double-strand break repair. Biochimie 81:107–116. https://doi.org/10.1016/S0300-9084(99)80043-1
He Y, Zhang Y, Jin C et al (2014) Impact of XRCC2 Arg188His polymorphism on cancer susceptibility: a meta-analysis. PLoS ONE. https://doi.org/10.1371/journal.pone.0091202
Yuan C, Liu X, Yan S et al (2014) Analyzing association of the XRCC3 gene polymorphism with ovarian cancer risk. Biomed Res Int 2014:25–29. https://doi.org/10.1155/2014/648137
Hu X, Sun S (2015) RAD51 gene 135G/C polymorphism and ovarian cancer risk: a meta-analysis. Int J Clin Exp Med 8:22365–22370
Wang W, Li JL, He XF et al (2013) Association between the RAD51 135 G>C polymorphism and risk of cancer: a meta-analysis of 19,068 cases and 22,630 controls. PLoS ONE 8:1–9. https://doi.org/10.1371/journal.pone.0075153
Zhang B, bei, Wang D gang, Xuan C, et al (2014) Genetic 135G/C polymorphism of RAD51 gene and risk of cancer: a meta-analysis of 28,956 cases and 28,372 controls. Fam Cancer 13:515–526. https://doi.org/10.1007/s10689-014-9729-0
Van Der Velden AW, Thomas AAM (1999) The role of the 5′ untranslated region of an mRNA in translation regulation during development. Int J Biochem Cell Biol 31:87–106. https://doi.org/10.1016/S1357-2725(98)00134-4
Gray NK (1998) Translational control by repressor proteins binding to the 5′UTR of mRNAs. Methods Mol Biol 77:379–397. https://doi.org/10.1385/0-89603-397-x:379
Wang WW, Ebbers SM, Kaufman DJ et al (2001) A single nucleotide polymorphism in the 5′ untranslated region of RAD51 and risk of cancer among BRCA1/2 mutation carriers. Cancer Epidemiol Biomark Prev 10:955–960
Kayani MA, Khan S, Baig RM, Mahjabeen I (2014) Association of RAD 51 135 G/C, 172 G/T and XRCC3 Thr241Met gene polymorphisms with increased risk of head and neck cancer. Asian Pac J Cancer Prev 15:10457–10462. https://doi.org/10.7314/APJCP.2014.15.23.10457
Zhou GW, Hu J, Peng XD, Li Q (2011) RAD51 135G>C polymorphism and breast cancer risk: a meta-analysis. Breast Cancer Res Treat 125:529–535. https://doi.org/10.1007/s10549-010-1031-8
Michalska MM, Samulak D, Romanowicz H, Smolarz B (2015) Single nucleotide polymorphisms (SNPs) of RAD51-G172T and XRCC2-41657C/T homologous recombination repair genes and the risk of triple- negative breast cancer in Polish women. Pathol Oncol Res 21:935–940. https://doi.org/10.1007/s12253-015-9922-y