Acknowledgement
We express our gratitude to Dubravka Germ and Ursa Adamic for their technical assistance with DNA isolation.
References
- Sung H, Ferlay J, Siegel RL, Laversanne M, Soerjomataram I, Jemal A, et al. Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin 2021;71:209-249. https://doi.org/10.3322/caac.21660
- Oliveira C, Pinheiro H, Figueiredo J, Seruca R, Carneiro F. Familial gastric cancer: genetic susceptibility, pathology, and implications for management. Lancet Oncol 2015;16:e60-e70. https://doi.org/10.1016/S1470-2045(14)71016-2
- Cancer Genome Atlas Research Network. Comprehensive molecular characterization of gastric adenocarcinoma. Nature 2014;513:202-209. https://doi.org/10.1038/nature13480
- Maleki SS, Rocken C. Chromosomal instability in gastric cancer biology. Neoplasia 2017;19:412-420. https://doi.org/10.1016/j.neo.2017.02.012
- Bakhoum SF, Silkworth WT, Nardi IK, Nicholson JM, Compton DA, Cimini D. The mitotic origin of chromosomal instability. Curr Biol 2014;24:R148-R149. https://doi.org/10.1016/j.cub.2014.01.019
- Burrell RA, McClelland SE, Endesfelder D, Groth P, Weller MC, Shaikh N, et al. Replication stress links structural and numerical cancer chromosomal instability. Nature 2013;494:492-496. https://doi.org/10.1038/nature11935
- Gao L, Nieters A, Brenner H. Cell proliferation-related genetic polymorphisms and gastric cancer risk: systematic review and meta-analysis. Eur J Hum Genet 2009;17:1658-1667. https://doi.org/10.1038/ejhg.2009.102
- Jiang N, Wang X, Jhanwar-Uniyal M, Darzynkiewicz Z, Dai W. Polo box domain of Plk3 functions as a centrosome localization signal, overexpression of which causes mitotic arrest, cytokinesis defects, and apoptosis. J Biol Chem 2006;281:10577-10582. https://doi.org/10.1074/jbc.M513156200
- Burns TF, Fei P, Scata KA, Dicker DT, El-Deiry WS. Silencing of the novel p53 target gene Snk/Plk2 leads to mitotic catastrophe in paclitaxel (taxol)-exposed cells. Mol Cell Biol 2003;23:5556-5571. https://doi.org/10.1128/MCB.23.16.5556-5571.2003
- Syed N, Smith P, Sullivan A, Spender LC, Dyer M, Karran L, et al. Transcriptional silencing of Polo-like kinase 2 (SNK/PLK2) is a frequent event in B-cell malignancies. Blood 2006;107:250-256. https://doi.org/10.1182/blood-2005-03-1194
- Benetatos L, Dasoula A, Hatzimichael E, Syed N, Voukelatou M, Dranitsaris G, et al. Polo-like kinase 2 (SNK/PLK2) is a novel epigenetically regulated gene in acute myeloid leukemia and myelodysplastic syndromes: genetic and epigenetic interactions. Ann Hematol 2011;90:1037-1045. https://doi.org/10.1007/s00277-011-1193-4
- Pellegrino R, Calvisi DF, Ladu S, Ehemann V, Staniscia T, Evert M, et al. Oncogenic and tumor suppressive roles of polo-like kinases in human hepatocellular carcinoma. Hepatology 2010;51:857-868.
- Chichirau BE, Scheidt T, Diechler S, Neuper T, Horejs-Hoeck J, Huber CG, et al. Dissecting the Helicobacter pylori-regulated transcriptome of B cells. Pathog Dis 2020;78:ftaa049. https://doi.org/10.1093/femspd/ftaa049
- Li B, Ouyang B, Pan H, Reissmann PT, Slamon DJ, Arceci R, et al. Prk, a cytokine-inducible human protein serine/threonine kinase whose expression appears to be down-regulated in lung carcinomas. J Biol Chem 1996;271:19402-19408. https://doi.org/10.1074/jbc.271.32.19402
- Dai W, Li Y, Ouyang B, Pan H, Reissmann P, Li J, et al. PRK, a cell cycle gene localized to 8p21, is downregulated in head and neck cancer. Genes Chromosomes Cancer 2000;27:332-336. https://doi.org/10.1002/(SICI)1098-2264(200003)27:3<332::AID-GCC15>3.0.CO;2-K
- Dai W, Liu T, Wang Q, Rao CV, Reddy BS. Down-regulation of PLK3 gene expression by types and amount of dietary fat in rat colon tumors. Int J Oncol 2002;20:121-126.
- Abraham RT. Cell cycle checkpoint signaling through the ATM and ATR kinases. Genes Dev 2001;15:2177-2196. https://doi.org/10.1101/gad.914401
- Giunta S, Belotserkovskaya R, Jackson SP. DNA damage signaling in response to double-strand breaks during mitosis. J Cell Biol 2010;190:197-207. https://doi.org/10.1083/jcb.200911156
- Suarez F, Mahlaoui N, Canioni D, Andriamanga C, Dubois d'Enghien C, Brousse N, et al. Incidence, presentation, and prognosis of malignancies in ataxia-telangiectasia: a report from the French national registry of primary immune deficiencies. J Clin Oncol 2015;33:202-208.
- Helgason H, Rafnar T, Olafsdottir HS, Jonasson JG, Sigurdsson A, Stacey SN, et al. Loss-of-function variants in ATM confer risk of gastric cancer. Nat Genet 2015;47:906-910. https://doi.org/10.1038/ng.3342
- Xu Z, Taylor JA. SNPinfo: integrating GWAS and candidate gene information into functional SNP selection for genetic association studies. Nucleic Acids Res 2009;37:W600-5. https://doi.org/10.1093/nar/gkp290
- Barrett JC. Haploview: visualization and analysis of SNP genotype data. Cold Spring Harb Protoc 2009;2009:pdb.ip71.
- Chen B, Wilkening S, Drechsel M, Hemminki K. SNP_tools: a compact tool package for analysis and conversion of genotype data for MS-Excel. BMC Res Notes 2009;2:214. https://doi.org/10.1186/1756-0500-2-214
- Ruiz-Larranaga O, Garrido JM, Iriondo M, Manzano C, Molina E, Koets AP, et al. Genetic association between bovine NOD2 polymorphisms and infection by Mycobacterium avium subsp. paratuberculosis in Holstein-Friesian cattle. Anim Genet 2010;41:652-655. https://doi.org/10.1111/j.1365-2052.2010.02055.x
- Farre D, Roset R, Huerta M, Adsuara JE, Rosello L, Alba MM, et al. Identification of patterns in biological sequences at the ALGGEN server: PROMO and MALGEN. Nucleic Acids Res 2003;31:3651-3653. https://doi.org/10.1093/nar/gkg605
- Messeguer X, Escudero R, Farre D, Nunez O, Martinez J, Alba MM. PROMO: detection of known transcription regulatory elements using species-tailored searches. Bioinformatics 2002;18:333-334. https://doi.org/10.1093/bioinformatics/18.2.333
- Liu C, Zhang F, Li T, Lu M, Wang L, Yue W, et al. MirSNP, a database of polymorphisms altering miRNA target sites, identifies miRNA-related SNPs in GWAS SNPs and eQTLs. BMC Genomics 2012;13:661. https://doi.org/10.1186/1471-2164-13-661
- Riolo G, Cantara S, Marzocchi C, Ricci C. miRNA targets: from prediction tools to experimental validation. Methods Protoc 2020;4:1. https://doi.org/10.3390/mps4010001
- Aken BL, Achuthan P, Akanni W, Amode MR, Bernsdorff F, Bhai J, et al. Ensembl 2017. Nucleic Acids Res 2017;45:D635-D642. https://doi.org/10.1093/nar/gkw1104
- Team R. RStudio: Integrated Development Environment for R. Boston (MA): RStudio, Inc., 2016.
- Gonzalez JR, Armengol L, Sole X, Guino E, Mercader JM, Estivill X, et al. SNPassoc: an R package to perform whole genome association studies. Bioinformatics 2007;23:644-645.
- Vrieze SI. Model selection and psychological theory: a discussion of the differences between the Akaike information criterion (AIC) and the Bayesian information criterion (BIC). Psychol Methods 2012;17:228-243. https://doi.org/10.1037/a0027127
- Nagy A, Munkacsy G, Gyorffy B. Pancancer survival analysis of cancer hallmark genes. Sci Rep 2021;11:6047. https://doi.org/10.1038/s41598-021-84787-5
- Xu F, Wang Y, Ling Y, Zhou C, Wang H, Teschendorff AE, et al. dbDEMC 3.0: Functional exploration of differentially expressed miRNAs in cancers of human and model organisms. Genomics Proteomics Bioinformatics 2022;S1672-0229(22)00068-7.
- Jash A, Yun K, Sahoo A, So JS, Im SH. Looping mediated interaction between the promoter and 3' UTR regulates type II collagen expression in chondrocytes. PLoS One 2012;7:e40828. https://doi.org/10.1371/journal.pone.0040828
- Degtyareva AO, Antontseva EV, Merkulova TI. Regulatory SNPs: altered transcription factor binding sites implicated in complex traits and diseases. Int J Mol Sci 2021;22:6454. https://doi.org/10.3390/ijms22126454
- Steri M, Idda ML, Whalen MB, Orru V. Genetic variants in mRNA untranslated regions. Wiley Interdiscip Rev RNA 2018;9:e1474. https://doi.org/10.1002/wrna.1474
- Ma G, Dai W, Sang A, Yang X, Gao C. Upregulation of microRNA-23a/b promotes tumor progression and confers poor prognosis in patients with gastric cancer. Int J Clin Exp Pathol 2014;7:8833-8840.
- Hu X, Wang Y, Liang H, Fan Q, Zhu R, Cui J, et al. miR-23a/b promote tumor growth and suppress apoptosis by targeting PDCD4 in gastric cancer. Cell Death Dis 2017;8:e3059. https://doi.org/10.1038/cddis.2017.447
- Johnson SA, Dubeau L, White RJ, Johnson DL. The TATA-binding protein as a regulator of cellular transformation. Cell Cycle 2003;2:442-444.
- Lin J, Liu W, Luan T, Yuan L, Jiang W, Cai H, et al. High expression of PU.1 is associated with Her-2 and shorter survival in patients with breast cancer. Oncol Lett 2017;14:8220-8226.
- Xu Y, Gu S, Bi Y, Qi X, Yan Y, Lou M. Transcription factor PU.1 is involved in the progression of glioma. Oncol Lett 2018;15:3753-3759.
- Antony-Debre I, Paul A, Leite J, Mitchell K, Kim HM, Carvajal LA, et al. Pharmacological inhibition of the transcription factor PU.1 in leukemia. J Clin Invest 2017;127:4297-4313. https://doi.org/10.1172/JCI92504
- Bufill E, Roura-Poch P, Sala-Matavera I, Anton S, Lleo A, Sanchez-Saudinos B, et al. Reelin signaling pathway genotypes and Alzheimer disease in a Spanish population. Alzheimer Dis Assoc Disord 2015;29:169-172. https://doi.org/10.1097/WAD.0000000000000002
- Balmer JE, Blomhoff R. Gene expression regulation by retinoic acid. J Lipid Res 2002;43:1773-1808. https://doi.org/10.1194/jlr.R100015-JLR200
- Hu KW, Chen FH, Ge JF, Cao LY, Li H. Retinoid receptors in gastric cancer: expression and influence on prognosis. Asian Pac J Cancer Prev 2012;13:1809-1817. https://doi.org/10.7314/APJCP.2012.13.5.1809
- Mohsenzadeh M, Sadeghi RN, Vahedi M, Kamani F, Hashemi M, Asadzadeh H, et al. Promoter hypermethylation of RAR-β tumor suppressor gene in gastric carcinoma: Association with histological type and clinical outcomes. Cancer Biomark 2017;20:7-15. https://doi.org/10.3233/CBM-160331
- Odrowaz Z, Sharrocks AD. The ETS transcription factors ELK1 and GABPA regulate different gene networks to control MCF10A breast epithelial cell migration. PLoS One 2012;7:e49892. https://doi.org/10.1371/journal.pone.0049892
- Kasza A. IL-1 and EGF regulate expression of genes important in inflammation and cancer. Cytokine 2013;62:22-33. https://doi.org/10.1016/j.cyto.2013.02.007
- Majid S, Dar AA, Saini S, Arora S, Shahryari V, Zaman MS, et al. miR-23b represses proto-oncogene Src kinase and functions as methylation-silenced tumor suppressor with diagnostic and prognostic significance in prostate cancer. Cancer Res 2012;72:6435-6446. https://doi.org/10.1158/0008-5472.CAN-12-2181
- Majid S, Dar AA, Saini S, Deng G, Chang I, Greene K, et al. MicroRNA-23b functions as a tumor suppressor by regulating Zeb1 in bladder cancer. PLoS One 2013;8:e67686. https://doi.org/10.1371/journal.pone.0067686
- Ono M, Kosaka N, Tominaga N, Yoshioka Y, Takeshita F, Takahashi RU, et al. Exosomes from bone marrow mesenchymal stem cells contain a microRNA that promotes dormancy in metastatic breast cancer cells. Sci Signal 2014;7:ra63.
- An Y, Zhang Z, Shang Y, Jiang X, Dong J, Yu P, et al. miR-23b-3p regulates the chemoresistance of gastric cancer cells by targeting ATG12 and HMGB2. Cell Death Dis 2015;6:e1766. https://doi.org/10.1038/cddis.2015.123
- Geng J, Luo H, Pu Y, Zhou Z, Wu X, Xu W, et al. Methylation mediated silencing of miR-23b expression and its role in glioma stem cells. Neurosci Lett 2012;528:185-189. https://doi.org/10.1016/j.neulet.2012.08.055
- Zhang H, Hao Y, Yang J, Zhou Y, Li J, Yin S, et al. Genome-wide functional screening of miR-23b as a pleiotropic modulator suppressing cancer metastasis. Nat Commun 2011;2:554. https://doi.org/10.1038/ncomms1555
- Tian L, Fang YX, Xue JL, Chen JZ. Four microRNAs promote prostate cell proliferation with regulation of PTEN and its downstream signals in vitro. PLoS One 2013;8:e75885. https://doi.org/10.1371/journal.pone.0075885
- Jin L, Wessely O, Marcusson EG, Ivan C, Calin GA, Alahari SK. Prooncogenic factors miR-23b and miR27b are regulated by Her2/Neu, EGF, and TNF-α in breast cancer. Cancer Res 2013;73:2884-2896.
- Qi P, Xu MD, Shen XH, Ni SJ, Huang D, Tan C, et al. Reciprocal repression between TUSC7 and miR-23b in gastric cancer. Int J Cancer 2015;137:1269-1278. https://doi.org/10.1002/ijc.29516
- Zhuang K, Han K, Tang H, Yin X, Zhang J, Zhang X, et al. Up-regulation of plasma miR-23b is associated with poor prognosis of gastric cancer. Med Sci Monit 2016;22:356-361. https://doi.org/10.12659/MSM.895428
- Xie Y, Liu Y, Li Q, Chen J. Polo-like kinase 2 promotes chemoresistance and predicts limited survival benefit from adjuvant chemotherapy in colorectal cancer. Int J Oncol 2018;52:1401-1414.
- Coley HM, Hatzimichael E, Blagden S, McNeish I, Thompson A, Crook T, et al. Polo Like Kinase 2 Tumour Suppressor and cancer biomarker: new perspectives on drug sensitivity/resistance in ovarian cancer. Oncotarget 2012;3:78-83. https://doi.org/10.18632/oncotarget.332
- Korns J, Liu X, Takiar V. A review of Plks: thinking outside the (polo) box. Mol Carcinog 2022;61:254-263. https://doi.org/10.1002/mc.23388
- Gorre M, Mohandas PE, Kagita S, Cingeetham A, Vuree S, Jarjapu S, et al. Significance of ATM gene polymorphisms in chronic myeloid leukemia - a case control study from India. Asian Pac J Cancer Prev 2016;17:815-821. https://doi.org/10.7314/APJCP.2016.17.2.815
- Koren M, Kimmel G, Ben-Asher E, Gal I, Papa MZ, Beckmann JS, et al. ATM haplotypes and breast cancer risk in Jewish high-risk women. Br J Cancer 2006;94:1537-1543. https://doi.org/10.1038/sj.bjc.6603062
- Zhao ZL, Xia L, Zhao C, Yao J. ATM rs189037 (G>A) polymorphism increased the risk of cancer: an updated meta-analysis. BMC Med Genet 2019;20:28. https://doi.org/10.1186/s12881-019-0760-8
- Tao Y, Mei Y, Ying R, Chen S, Wei Z. The ATM rs189037 G>A polymorphism is associated with the risk and prognosis of gastric cancer in Chinese individuals: a case-control study. Gene 2020;741:144578. https://doi.org/10.1016/j.gene.2020.144578
- Song CM, Kwon TK, Park BL, Ji YB, Tae K. Single nucleotide polymorphisms of ataxia telangiectasia mutated and the risk of papillary thyroid carcinoma. Environ Mol Mutagen 2015;56:70-76. https://doi.org/10.1002/em.21898
- Shen M, Xu Z, Xu W, Jiang K, Zhang F, Ding Q, et al. Inhibition of ATM reverses EMT and decreases metastatic potential of cisplatin-resistant lung cancer cells through JAK/STAT3/PD-L1 pathway. J Exp Clin Cancer Res 2019;38:149. https://doi.org/10.1186/s13046-019-1161-8
- Kang W, Tong JH, Chan AW, Zhao J, Dong Y, Wang S, et al. Yin Yang 1 contributes to gastric carcinogenesis and its nuclear expression correlates with shorter survival in patients with early stage gastric adenocarcinoma. J Transl Med 2014;12:80. https://doi.org/10.1186/1479-5876-12-80
- Bonavida B. Therapeutic YY1 inhibitors in cancer: ALL in ONE. Crit Rev Oncog 2017;22:37-47. https://doi.org/10.1615/CritRevOncog.2017020472
- Keld R, Guo B, Downey P, Cummins R, Gulmann C, Ang YS, et al. PEA3/ETV4-related transcription factors coupled with active ERK signalling are associated with poor prognosis in gastric adenocarcinoma. Br J Cancer 2011;105:124-130. https://doi.org/10.1038/bjc.2011.187
- Manicum T, Ni F, Ye Y, Fan X, Chen BC. Prognostic values of E2F mRNA expression in human gastric cancer. Biosci Rep 2018;38:BSR20181264. https://doi.org/10.1042/BSR20181264
- Xie Y, Wang C, Li L, Ma Y, Yin Y, Xiao Q. Overexpression of E2F-1 inhibits progression of gastric cancer in vitro. Cell Biol Int 2009;33:640-649. https://doi.org/10.1016/j.cellbi.2009.02.015
- Nishi M, Batsaikhan BE, Yoshikawa K, Higashijima J, Tokunaga T, Takasu C, et al. High STAT4 expression indicates better disease-free survival in patients with gastric cancer. Anticancer Res 2017;37:6723-6729.
- Teng Y, Cang B, Mao F, Chen W, Cheng P, Peng L, et al. Expression of ETS1 in gastric epithelial cells positively regulate inflammatory response in Helicobacter pylori-associated gastritis. Cell Death Dis 2020;11:498. https://doi.org/10.1038/s41419-020-2705-8
- Spiotto MT, Banh A, Papandreou I, Cao H, Galvez MG, Gurtner GC, et al. Imaging the unfolded protein response in primary tumors reveals microenvironments with metabolic variations that predict tumor growth. Cancer Res 2010;70:78-88.
- Dai W, Li Q, Liu BY, Li YX, Li YY. Differential networking meta-analysis of gastric cancer across Asian and American racial groups. BMC Syst Biol 2018;12 Suppl 4:51. https://doi.org/10.1186/s12918-018-0564-z
- Rong H, Gu S, Zhang G, Kang L, Yang M, Zhang J, et al. MiR-2964a-5p binding site SNP regulates ATM expression contributing to age-related cataract risk. Oncotarget 2017;8:84945-84957. https://doi.org/10.18632/oncotarget.17600
- Sandhu V, Bowitz Lothe IM, Labori KJ, Skrede ML, Hamfjord J, Dalsgaard AM, et al. Differential expression of miRNAs in pancreatobiliary type of periampullary adenocarcinoma and its associated stroma. Mol Oncol 2016;10:303-316. https://doi.org/10.1016/j.molonc.2015.10.011
- Moi L, Braaten T, Al-Shibli K, Lund E, Busund LR. Differential expression of the miR-17-92 cluster and miR-17 family in breast cancer according to tumor type; results from the Norwegian Women and Cancer (NOWAC) study. J Transl Med 2019;17:334. https://doi.org/10.1186/s12967-019-2086-x
- Wilkening S, Chen B, Bermejo JL, Canzian F. Is there still a need for candidate gene approaches in the era of genome-wide association studies? Genomics 2009;93:415-419. https://doi.org/10.1016/j.ygeno.2008.12.011
- Jorgensen TJ, Ruczinski I, Kessing B, Smith MW, Shugart YY, Alberg AJ. Hypothesis-driven candidate gene association studies: practical design and analytical considerations. Am J Epidemiol 2009;170:986-993. https://doi.org/10.1093/aje/kwp242
- Gorlov IP, Gorlova OY, Sunyaev SR, Spitz MR, Amos CI. Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms. Am J Hum Genet 2008;82:100-112. https://doi.org/10.1016/j.ajhg.2007.09.006