Identification of regulatory SNPs associated with genetic modifications in lung adenocarcinoma
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- 作者：Tzu-Pin Lu (1)
Chuhsing K Hsiao (1) (2)
Liang-Chuan Lai (2) (3)
Mong-Hsun Tsai (2) (4)
Chung-Ping Hsu (5)
Jang-Ming Lee (6)
Eric Y Chuang (2) (7)
1. Department of Public Health ; Institute of Epidemiology and Preventive Medicine ; National Taiwan University ; Taipei ; Taiwan
2. Bioinformatics and Biostatistics Core ; Center of Genomic Medicine ; National Taiwan University ; Taipei ; Taiwan
3. Graduate Institute of Physiology ; National Taiwan University ; Taipei ; Taiwan
4. Institute of Biotechnology ; National Taiwan University ; Taipei ; Taiwan
5. Division of Thoracic Surgery ; Taichung Veterans General Hospital ; Taichung ; Taiwan
6. Department of Surgery ; National Taiwan University Hospital ; Taipei ; Taiwan
7. Graduate Institute of Biomedical Electronics and Bioinformatics and Department of Electrical Engineering ; National Taiwan University ; Taipei ; Taiwan - 关键词：Lung adenocarcinoma ; Integrated analysis ; Copy number variation ; Methylation ; Microarray ; SNP
- 刊名：BMC Research Notes
- 出版年：2015
- 出版时间：December 2015
- 年：2015
- 卷：8
- 期：1
- 全文大小：3,115 KB
- 参考文献：1. Siegel, R, Naishadham, D, Jemal, A (2013) Cancer statistics, 2013. CA Cancer J Clin 63: pp. 11-30 22/caac.21166" target="_blank" title="It opens in new window">CrossRef
2. Malvezzi, M, Bertuccio, P, Levi, F, Vecchia, C, Negri, E (2013) European cancer mortality predictions for the year 2013. Ann Oncol 24: pp. 792-800 CrossRef
3. Molina, JR, Yang, P, Cassivi, SD, Schild, SE, Adjei, AA (2008) Non-small cell lung cancer: epidemiology, risk factors, treatment, and survivorship. Mayo Clin Proc 83: pp. 584-94 25-6196(11)60735-0" target="_blank" title="It opens in new window">CrossRef
4. Beer, DG, Kardia, SL, Huang, CC, Giordano, TJ, Levin, AM, Misek, DE (2002) Gene-expression profiles predict survival of patients with lung adenocarcinoma. Nat Med 8: pp. 816-24
5. Shedden, K, Taylor, JM, Enkemann, SA, Tsao, MS, Yeatman, TJ (2008) Gene expression-based survival prediction in lung adenocarcinoma: a multi-site, blinded validation study. Nat Med 14: pp. 822-7 CrossRef
6. Lu, TP, Tsai, MH, Lee, JM, Hsu, CP, Chen, PC, Lin, CW (2010) Identification of a novel biomarker, SEMA5A, for non-small cell lung carcinoma in nonsmoking women. Cancer Epidemiol Biomarkers Prev 19: pp. 2590-7 2" target="_blank" title="It opens in new window">CrossRef
7. Lu, TP, Chuang, EY, Chen, JJ (2013) Identification of reproducible gene expression signatures in lung adenocarcinoma. BMC Bioinformatics 14: pp. 371 2105-14-371" target="_blank" title="It opens in new window">CrossRef
8. Lau, SK, Boutros, PC, Pintilie, M, Blackhall, FH, Zhu, CQ, Strumpf, D (2007) Three-gene prognostic classifier for early-stage non small-cell lung cancer. J Clin Oncol 25: pp. 5562-9 200/JCO.2007.12.0352" target="_blank" title="It opens in new window">CrossRef
9. Pollack, JR, Sorlie, T, Perou, CM, Rees, CA, Jeffrey, SS, Lonning, PE (2002) Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors. Proc Natl Acad Sci U S A 99: pp. 12963-8 2471999" target="_blank" title="It opens in new window">CrossRef
10. Weir, BA, Woo, MS, Getz, G, Perner, S, Ding, L, Beroukhim, R (2007) Characterizing the cancer genome in lung adenocarcinoma. Nature 450: pp. 893-8 CrossRef
11. Lu, TP, Lai, LC, Tsai, MH, Chen, PC, Hsu, CP, Lee, JM (2011) Integrated analyses of copy number variations and gene expression in lung adenocarcinoma. PLoS One 6: pp. e24829 24829" target="_blank" title="It opens in new window">CrossRef
12. Park, YJ, Claus, R, Weichenhan, D, Plass, C (2011) Genome-wide epigenetic modifications in cancer. Prog Drug Res 67: pp. 25-49
13. Watanabe, Y, Maekawa, M (2010) Methylation of DNA in cancer. Adv Clin Chem 52: pp. 145-67 2423(10)52006-7" target="_blank" title="It opens in new window">CrossRef
14. Taby, R, Issa, JP (2010) Cancer epigenetics. CA Cancer J Clin 60: pp. 376-92 22/caac.20085" target="_blank" title="It opens in new window">CrossRef
15. Belinsky, SA, Klinge, DM, Dekker, JD, Smith, MW, Bocklage, TJ, Gilliland, FD (2005) Gene promoter methylation in plasma and sputum increases with lung cancer risk. Clin Cancer Res 11: pp. 6505-11 2.CCR-05-0625" target="_blank" title="It opens in new window">CrossRef
16. Tycko, B (2010) Allele-specific DNA methylation: beyond imprinting. Hum Mol Genet 19: pp. R210-20 CrossRef
17. Milani, L, Lundmark, A, Nordlund, J, Kiialainen, A, Flaegstad, T, Jonmundsson, G (2009) Allele-specific gene expression patterns in primary leukemic cells reveal regulation of gene expression by CpG site methylation. Genome Res 19: pp. 1-11 CrossRef
18. Loo, P, Nordgard, SH, Lingjaerde, OC, Russnes, HG, Rye, IH, Sun, W (2010) Allele-specific copy number analysis of tumors. Proc Natl Acad Sci U S A 107: pp. 16910-5 CrossRef
19. LaFramboise, T, Dewal, N, Wilkins, K, Pe'er, I, Freedman, ML (2010) Allelic selection of amplicons in glioblastoma revealed by combining somatic and germline analysis. PLoS Genet 6: pp. e1001086 CrossRef
20. Lai, LC, Tsai, MH, Chen, PC, Chen, LH, Hsiao, JH, Chen, SK (2014) SNP rs10248565 in HDAC9 as a novel genomic aberration biomarker of lung adenocarcinoma in non-smoking women. J Biomed Sci 21: pp. 24 23-0127-21-24" target="_blank" title="It opens in new window">CrossRef
21. Chari, R, Coe, BP, Vucic, EA, Lockwood, WW, Lam, WL (2010) An integrative multi-dimensional genetic and epigenetic strategy to identify aberrant genes and pathways in cancer. BMC Syst Biol 4: pp. 67 2-0509-4-67" target="_blank" title="It opens in new window">CrossRef
22. Sturn, A, Quackenbush, J, Trajanoski, Z (2002) Genesis: cluster analysis of microarray data. Bioinformatics 18: pp. 207-8 207" target="_blank" title="It opens in new window">CrossRef
23. Irizarry, RA, Ladd-Acosta, C, Wen, B, Wu, Z, Montano, C, Onyango, P (2009) The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat Genet 41: pp. 178-86 298" target="_blank" title="It opens in new window">CrossRef
24. Meissner, A, Mikkelsen, TS, Gu, H, Wernig, M, Hanna, J, Sivachenko, A (2008) Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454: pp. 766-70
25. Hayami, S, Yoshimatsu, M, Veerakumarasivam, A, Unoki, M, Iwai, Y, Tsunoda, T (2010) Overexpression of the JmjC histone demethylase KDM5B in human carcinogenesis: involvement in the proliferation of cancer cells through the E2F/RB pathway. Mol Cancer 9: pp. 59 CrossRef
26. Ren TN, Wang JS, He YM, Xu CL, Wang SZ, Xi T. Effects of SMYD3 over-expression on cell cycle acceleration and cell proliferation in MDA-MB-231 human breast cancer cells. Med Oncol. 2011. Suppl 1:S91鈥?. doi: 10.1007/s12032-010-9718-6. Epub 2010 Oct 19.
27. Berger, MF, Lawrence, MS, Demichelis, F, Drier, Y, Cibulskis, K, Sivachenko, AY (2011) The genomic complexity of primary human prostate cancer. Nature 470: pp. 214-20 CrossRef
28. Wu, X, Hepner, K, Castelino-Prabhu, S, Do, D, Kaye, MB, Yuan, XJ (2000) Evidence for regulation of the PTEN tumor suppressor by a membrane-localized multi-PDZ domain containing scaffold protein MAGI-2. Proc Natl Acad Sci U S A 97: pp. 4233-8 233" target="_blank" title="It opens in new window">CrossRef
29. Shackleton, M (2010) Moving targets that drive cancer progression. N Engl J Med 363: pp. 885-6 28" target="_blank" title="It opens in new window">CrossRef - 刊物主题：Biomedicine general; Medicine/Public Health, general; Life Sciences, general;
- 出版者：BioMed Central
- ISSN：1756-0500
文摘
Background Although much research effort has been devoted to elucidating lung cancer, the molecular mechanism of tumorigenesis still remains unclear. A major challenge to improve the understanding of lung cancer is the difficulty of identifying reproducible differentially expressed genes across independent studies, due to their low consistency. To enhance the reproducibility of the findings, an integrated analysis was performed to identify regulatory SNPs. Thirty-two pairs of tumor and adjacent normal lung tissue specimens were analyzed using Affymetrix U133plus2.0, Affymetrix SNP 6.0, and Illumina Infinium Methylation microarrays. Copy number variations (CNVs) and methylation alterations were analyzed and paired t-tests were used to identify differentially expressed genes. Results A total of 505 differentially expressed genes were identified, and their dysregulated patterns moderately correlated with CNVs and methylation alterations based on the hierarchical clustering analysis. Subsequently, three statistical approaches were performed to explore regulatory SNPs, which revealed that the genotypes of 551 and 66 SNPs were associated with CNV and changes in methylation, respectively. Among them, downstream transcriptional dysregulation was observed in 9 SNPs for CNVs and 4 SNPs for methylation alterations. Conclusions In summary, these identified SNPs concurrently showed the same direction of gene expression changes with genetic modifications, suggesting their pivotal roles in the genome for non-smoking women with lung adenocarcinoma.