Identification of genes and candidate agents associated with pancreatic cancer

Tumor Biology

Volumn 35, Issue 1, 2014, Pages 81-88

  Wang, Bao Sheng ^a   Liu, Zhen ^a   Sun, Shao Long ^a   Zhao, Yi ^a  

^a CHINA MEDICAL UNIVERSITY   (China)

Author keywords

Connectivity map; Differentially expressed genes; Drug discovery; Pancreatic cancer

Indexed keywords

SMAD4 PROTEIN; TRANSCRIPTION FACTOR;

APOPTOSIS; ARTICLE; BIOINFORMATICS; CANCER GROWTH; CANCER PROGNOSIS; CELL CYCLE PROGRESSION; CLINICAL ARTICLE; DIFFERENTIALLY EXPRESSED GENE; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENETIC ASSOCIATION; GENETIC IDENTIFICATION; HUMAN; HUMAN CELL; MICROARRAY ANALYSIS; NUCLEOTIDE SEQUENCE; ONCOGENE K RAS; PANCREAS CANCER; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; SIGNAL TRANSDUCTION; TRANSCRIPTION REGULATION;

COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENE REGULATORY NETWORKS; HUMANS; PANCREATIC NEOPLASMS; PROTEIN INTERACTION MAPS; SIGNAL TRANSDUCTION; TRANSCRIPTION FACTORS;

EID: 84893796928     PISSN: 10104283     EISSN: 14230380     Source Type: Journal    
DOI: 10.1007/s13277-013-1009-3     Document Type: Article

References (48)

1. Jemal A, Siegel R, Xu J, Ward E. Cancer statistics, 2010. CA Cancer J Clin. 2010;60(5):277-300. doi: 10.3322/caac.20073.
2. Li D, Xie K, Wolff R, Abbruzzese JL. Pancreatic cancer. Lancet. 2004;363(9414):1049-57. doi: 10.1016/S0140-6736(04)15841-8S0140-6736(04)15841-8.
3. Jimeno A, Hidalgo M. Molecular biomarkers: their increasing role in the diagnosis, characterization, and therapy guidance in pancreatic cancer. Mol Cancer Ther. 2006;5(4):787-96. doi: 10.1158/1535-7163.MCT-06-0005.
4. Maitra A, Kern SE, Hruban RH. Molecular pathogenesis of pancreatic cancer. Best Pract Res Clin Gastroenterol. 2006;20(2):211-26. doi: 10.1016/j.bpg.2005.10.002.
5. Mimeault M, Brand RE, Sasson AA, Batra SK. Recent advances on the molecular mechanisms involved in pancreatic cancer progression and therapies. Pancreas. 2005;31(4):301-16.
6. Goggins M. Molecular markers of early pancreatic cancer. J Clin Oncol. 2005;23(20):4524-31. doi: 10.1200/JCO.2005.19.711.
7. Nelson WG, De Marzo AM, Yegnasubramanian S. Epigenetic alterations in human prostate cancers. Endocrinology. 2009;150(9):3991-4002. doi: 10.1210/en.2009-0573.
8. Zhang G, Schetter A, He P, Funamizu N, Gaedcke J, Ghadimi BM, et al. DPEP1 inhibits tumor cell invasiveness, enhances chemosensitivity and predicts clinical outcome in pancreatic ductal adenocarcinoma. PLoS One. 2012;7(2):e31507. doi: 10.1371/journal.pone.0031507PONE-D-11-21687.
9. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, et al. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003;4(2):249-64. doi: 10.1093/biostatistics/4.2.2494/2/249.
10. Tusher VG, Tibshirani R, Chu G. Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA. 2001;98(9):5116-21. doi: 10.1073/pnas.091062498091062498.
11. Benjamini YH Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B (Methodol). 1995;57:289-300.
12. Tarca AL, Draghici S, Khatri P, Hassan SS, Mittal P, Kim JS, et al. A novel signaling pathway impact analysis. Bioinformatics. 2009;25(1):75-82. doi: 10.1093/bioinformatics/btn577btn577.
13. Roider HG, Manke T, O'Keeffe S, Vingron M, Haas SA. PASTAA: identifying transcription factors associated with sets of co-regulated genes. Bioinformatics. 2009;25(4):435-42. doi: 10.1093/bioinformatics/btn627btn627.
14. Roider HG, Kanhere A, Manke T, Vingron M. Predicting transcription factor affinities to DNA from a biophysical model. Bioinformatics. 2007;23(2):134-41. doi: 10.1093/bioinformatics/btl565.
15. Das J, Yu H. HINT: High-quality protein interactomes and their applications in understanding human disease. BMC Syst Biol. 2012;6:92. doi: 10.1186/1752-0509-6-92.
16. Lamb J, Crawford ED, Peck D, Modell JW, Blat IC, Wrobel MJ, et al. The connectivity map: using gene-expression signatures to connect small molecules, genes, and disease. Science. 2006;313(5795):1929-35. doi: 10.1126/science. 1132939.
17. Hariharan D, Saied A, Kocher HM. Analysis of mortality rates for pancreatic cancer across the world. HPB (Oxford). 2008;10(1):58-62. doi: 10.1080/13651820701883148.
18. Tan M, Yu D. Molecular mechanisms of erbB2-mediated breast cancer chemoresistance. Adv Exp Med Biol. 2007;608:119-29.
19. Santin AD, Bellone S, Siegel ER, Palmieri M, Thomas M, Cannon MJ, et al. Racial differences in the overexpression of epidermal growth factor type II receptor (HER2/neu): a major prognostic indicator in uterine serous papillary cancer. Am J Obstet Gynecol. 2005;192(3):813-8. doi: 10.1016/j.ajog.2004.10.605.
20. Almoguera C, Shibata D, Forrester K, Martin J, Arnheim N, Perucho M. Most human carcinomas of the exocrine pancreas contain mutant c-K-ras genes. Cell. 1988;53(4):549-54.
21. Collins MA, Brisset JC, Zhang Y, Bednar F, Pierre J, Heist KA, et al. Metastatic pancreatic cancer is dependent on oncogenic kras in mice. PLoS One. 2012;7(12):e49707. doi: 10.1371/journal.pone.0049707PONE-D-12-09212.
22. Hruban RH, Adsay NV. Molecular classification of neoplasms of the pancreas. Hum Pathol. 2009;40(5):612-23. doi: 10.1016/j.humpath.2009.01.008.
23. Dergham ST, Dugan MC, Sarkar FH, Vaitkevicius VK. Molecular alterations associated with improved survival in pancreatic cancer patients treated with radiation or chemotherapy. J Hepatobiliary Pancreat Surg. 1998;5(3):269-72.
24. Hezel AF, Deshpande V, Zimmerman SM, Contino G, Alagesan B, O'Dell MR, et al. TGF-beta and alphavbeta6 integrin act in a common pathway to suppress pancreatic cancer progression. Cancer Res. 2012;72(18):4840-5. doi: 10.1158/0008-5472.CAN-12-06340008-5472.CAN-12-0634.
25. Hahn SA, Hoque AT, Moskaluk CA, da Costa LT, Schutte M, Rozenblum E, et al. Homozygous deletion map at 18q21.1 in pancreatic cancer. Cancer Res. 1996;56(3):490-4.
26. Morgan MA, Parsels LA, Zhao L, Parsels JD, Davis MA, Hassan MC, et al. Mechanism of radiosensitization by the Chk1/2 inhibitor AZD7762 involves abrogation of the G2 checkpoint and inhibition of homologous recombinational DNA repair. Cancer Res. 2010;70(12):4972-81. doi: 10.1158/0008-5472.CAN-09-3573.
27. Parsels LA, Qian Y, Tanska DM, Gross M, Zhao L, Hassan MC, et al. Assessment of chk1 phosphorylation as a pharmacodynamic biomarker of chk1 inhibition. Clin Cancer Res. 2011;17(11):3706-15. doi: 10.1158/1078-0432.CCR-10- 3082.
28. Vance S, Liu E, Zhao L, Parsels JD, Parsels LA, Brown JL, et al. Selective radiosensitization of p53 mutant pancreatic cancer cells by combined inhibition of Chk1 and PARP1. Cell Cycle. 2011;10(24):4321-9. doi: 10.4161/cc.10.24.1866118661.
29. Rajkumar T, Soumittra N, Nancy NK, Swaminathan R, Sridevi V, Shanta V. BRCA1, BRCA2 and CHEK2 (1100 del C) germline mutations in hereditary breast and ovarian cancer families in South India. Asian Pac J Cancer Prev. 2003;4(3):203-8.
30. Antoniou A, Pharoah P, Narod S, Risch HA, Eyfjord JE, Hopper J, et al. Average risks of breast and ovarian cancer associated with BRCA1 or BRCA2 mutations detected in case series unselected for family history: a combined analysis of 22 studies. Am J Hum Genet. 2003;72(5):1117.
31. Greer JB, Whitcomb DC. Role of BRCA1 and BRCA2 mutations in pancreatic cancer. Gut. 2007;56(5):601-5. doi: 10.1136/gut.2006.101220.
32. Iqbal J, Ragone A, Lubinski J, Lynch HT, Moller P, Ghadirian P, et al. The incidence of pancreatic cancer in BRCA1 and BRCA2 mutation carriers. Br J Cancer. 2012;107(12):2005-9. doi: 10.1038/bjc.2012.483bjc2012483.
33. Liu R, Zhou A, Ren D, He A, Hu X, Zhang W, et al. Transcription factor specificity protein 1 (SP1) and activating protein 2alpha (AP-2alpha) regulate expression of human KCTD10 gene by binding to proximal region of promoter. FEBS J. 2009;276(4):1114-24. doi: 10.1111/j.1742-4658.2008.06855.x.
34. Li B, Wang X, Zhou F, Saunders NA, Frazer IH, Zhao KN. Up-regulated expression of Sp1 protein coincident with a viral protein in human and mouse differentiating keratinocytes may act as a cell differentiation marker. Differentiation. 2008;76(10):1068-80. doi: 10.1111/j.1432-0436.2008.00300.x.
35. Nichols AF, Itoh T, Zolezzi F, Hutsell S, Linn S. Basal transcriptional regulation of human damage-specific DNA-binding protein genes DDB1 and DDB2 by Sp1, E2F, N-myc and NF1 elements. Nucleic Acids Res. 2003;31(2):562-9.
36. Yuan P, Wang L, Wei D, Zhang J, Jia Z, Li Q, et al. Therapeutic inhibition of Sp1 expression in growing tumors by mithramycin a correlates directly with potent antiangiogenic effects on human pancreatic cancer. Cancer. 2007;110(12):2682-90. doi: 10.1002/cncr.23092.
37. Won J, Yim J, Kim TK. Sp1 and Sp3 recruit histone deacetylase to repress transcription of human telomerase reverse transcriptase (hTERT) promoter in normal human somatic cells. J Biol Chem. 2002;277(41):38230-8. doi: 10.1074/jbc.M206064200.
38. Tang S, Bhatia B, Zhou J, Maldonado CJ, Chandra D, Kim E, et al. Evidence that Sp1 positively and Sp3 negatively regulate and androgen does not directly regulate functional tumor suppressor 15-lipoxygenase 2 (15-LOX2) gene expression in normal human prostate epithelial cells. Oncogene. 2004;23(41):6942-53. doi: 10.1038/sj.onc.1207913.
39. Lin SY, Black AR, Kostic D, Pajovic S, Hoover CN, Azizkhan JC. Cell cycle-regulated association of E2F1 and Sp1 is related to their functional interaction. Mol Cell Biol. 1996;16(4):1668-75.
40. Jungert K, Buck A, von Wichert G, Adler G, König A, Buchholz M, et al. Sp1 is required for transforming growth factor-β-induced mesenchymal transition and migration in pancreatic cancer cells. Cancer Res. 2007;67(4):1563-70.
41. Rotheneder H, Geymayer S, Haidweger E. Transcription factors of the Sp1 family: interaction with E2F and regulation of the murine thymidine kinase promoter. J Mol Biol. 1999;293(5):1005-15. doi: 10.1006/jmbi.1999.3213.
42. Karlseder J, Rotheneder H, Wintersberger E. Interaction of Sp1 with the growth- and cell cycle-regulated transcription factor E2F. Mol Cell Biol. 1996;16(4):1659-67.
43. Jia Z, Gao Y, Wang L, Li Q, Zhang J, Le X, et al. Combined treatment of pancreatic cancer with mithramycin A and tolfenamic acid promotes Sp1 degradation and synergistic antitumor activity. Cancer Res. 2010;70(3):1111-9. doi: 10.1158/0008-5472.CAN-09-3282.
44. Jutooru I, Chadalapaka G, Lei P, Safe S. Inhibition of NFkappaB and pancreatic cancer cell and tumor growth by curcumin is dependent on specificity protein down-regulation. J Biol Chem. 2010;285(33):25332-44. doi: 10.1074/jbc.M109.095240.
45. Jenal M, Trinh E, Britschgi C, Britschgi A, Roh V, Vorburger SA, et al. The tumor suppressor gene hypermethylated in cancer 1 is transcriptionally regulated by E2F1. Mol Cancer Res. 2009;7(6):916-22. doi: 10.1158/1541-7786.MCR- 08-0359.
46. Shaw J, Yurkova N, Zhang T, Gang H, Aguilar F, Weidman D, et al. Antagonism of E2F-1 regulated Bnip3 transcription by NF-kappaB is essential for basal cell survival. Proc Natl Acad Sci USA. 2008;105(52):20734-9. doi: 10.1073/pnas.0807735105.
47. Xu Y, Shi QL, Ma H, Zhou H, Lu Z, Yu B, et al. High thymidine kinase 1 (TK1) expression is a predictor of poor survival in patients with pT1 of lung adenocarcinoma. Tumour Biol. 2012;33(2):475-83. doi: 10.1007/s13277-011-0276-0.
48. Prochazka V, Faber E, Raida L, Langova K, Indrak K, Papajik T. High baseline serum thymidine kinase 1 level predicts unfavorable outcome in patients with follicular lymphoma. Leuk Lymphoma. 2012;53(7):1306-10. doi: 10.3109/10428194.2011.654339.