Identification of genomic targets of transcription factor Aebp1 and its role in survival of glioma cells

Molecular Cancer Research

Volumn 10, Issue 8, 2012, Pages 1039-1051

  Ladha, Jayashree ^a   Sinha, Swati ^a   Bhat, Vasudeva ^a   Donakonda, Sainitin ^a   Rao, Satyanarayana M R ^a  

^a JAWAHARLAL NEHRU CENTRE FOR ADVANCED SCIENTIFIC RESEARCH   (India)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; RNA; SMALL INTERFERING RNA; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR AEBP1; TRANSCRIPTOME; UNCLASSIFIED DRUG;

APOPTOSIS; ARTICLE; BINDING SITE; BIOINFORMATICS; CELL CYCLE; CELL PROLIFERATION; CELL SURVIVAL; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; DNA BINDING; GENE EXPRESSION; GENE REPRESSION; GENE SILENCING; GENETIC TRANSCRIPTION; GLIOBLASTOMA; GLIOMA; GLIOMA CELL; HUMAN; HUMAN CELL; MICROARRAY ANALYSIS; PRIORITY JOURNAL; PROMOTER REGION; REAL TIME POLYMERASE CHAIN REACTION; REPORTER GENE; RNA INTERFERENCE; TRANSCRIPTION REGULATION;

ADIPOGENESIS; APOPTOSIS; BINDING SITES; CARBOXYPEPTIDASES; CELL LINE, TUMOR; CELL PROLIFERATION; CELL SURVIVAL; DNA-BINDING PROTEINS; FATTY ACID-BINDING PROTEINS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENOME, HUMAN; GLIOMA; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROMOTER REGIONS, GENETIC; PROTEIN BINDING; REPRESSOR PROTEINS;

EID: 84865289234     PISSN: 15417786     EISSN: 15573125     Source Type: Journal    
DOI: 10.1158/1541-7786.MCR-11-0488     Document Type: Article

References (50)

1. Park CK, Jung JH, Park SH, Jung HW, Cho BK. Multifarious proteomic signatures and regional heterogeneity in glioblastomas. J Neuro Oncol 2009;94:31-9.
2. Somasundaram K, Reddy SP, Vinnakota K, Britto R, Subbarayan M, Nambiar S, et al. Upregulation of ASCL1 and inhibition of Notch signaling pathway characterize progressive astrocytoma. Oncogene 2005;24:7073-83.
3. Li A, Walling J, Ahn S, Kotliarov Y, Su Q, Quezado M, et al. Unsupervised analysis of transcriptomic profiles reveals six glioma subtypes. Cancer Res 2009;69:2091-9.
4. Kroes RA, Dawson G, Moskal JR. Focused microarray analysis of glycol-gene expression in human glioblastomas. J Neurochem 2007;1:14-24.
5. Kleihues P, Ohgaki H. Primary and secondary glioblastomas: from concept to clinical diagnosis. Neuro Oncol 1999;1:44-51.
6. Zhu Y, Parada LF. The molecular and genetic basis of neurological tumors. Nat Rev Cancer 2002;2:616-26.
7. Phillips HS, Kharbanda S, Chen R, Forrest WF, Soriano RH, Wu TD, et al. Molecular subclasses of high-grade glioma predict prognosis, delineate a pattern of disease progression, and resemble stages in neurogenesis. Cancer Cell 2006;9 157-73.
8. Verhaak RG, Hoadley KA, Purdom E, Wang V, Qi Y, Wilkerson MD, et al. Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell 2010;17 98-110.
9. Reddy SP, Britto R, Vinnakota K, Aparna H, Sreepathi HK, Thota B, et al. Novel glioblastoma markers with diagnostic and prognostic value identified through transcriptome analysis. Clin Cancer Res 2008;14: 2978-87.
10. He GP, Muise A, Li AW, Ro HS. A eukaryotic transcriptional repressor with carboxypeptidase activity. Nature 1995;378:92-6.
11. Li Z, Szabolcs M, Terwilliger JD, Efstratiadis A. Prostatic intraepithelial neoplasia and adenocarcinoma in mice expressing a probasin-Neu oncogenic transgene. Carcinogenesis 2006;27:1054-67.
12. Ren B, Dynlacht BD. Use of chromatin immunoprecipitation assays in genome wide location analysis of mammalian transcription factors. Methods Enzymol 2004;376:304-15.
13. Benjamini Y, Hochberg Y. Controlling the false discovery rate: practical and powerful approach to multiple testing. J R Stat Soc B (Methodological) 1995;57:289-300.
14. R Development Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0. Available from: www.R-project.org/
15. Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome wide expression patterns. Proc Natl Acad Sci U S A 1998;95:14893-8.
16. Saldanha AJ. Java Treeview - extensible visualization of microarray data. Bioinformatics 2004;20:3246-8.
17. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000;25 25-9.
18. Huang da W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large lists using DAVID bioinformatics resources. Nat Protoc 2009;4:44-57.
19. Huang da W, Sherman BT, Lempicki RA. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 2009;37:1-13.
20. Jiang C, Xuan Z, Zhao F, Zhang MQ. TRED: a transcriptional regulatory element database, new entries and other development. Nucleic Acids Res 2007;35 (Database issue):D137-40.
21. Schmid CD, Perier R, Praz V, Bucher P. EPD in its twentieth year: towards complete promoter coverage of selected model organisms. Nucleic Acids Res 2006;34(Database issue):D82-5.
22. Karolchik D, Hinrichs AS, Furey TS. The UCSC Table browser data retrieval tool. Nucleic Acids Res 2004;32(Database issue):D493-6.
23. Sharov AA, Ko MS. Exhaustive search for over-represented DNA sequence motifs with CisFinder. DNA Res 2009;16:261-73.
24. Crooks GE, Hon G, Chandonia JN, Brenner SE. Weblogo: a sequence logo generator. Genome Res 2004;14:1188-90.
25. Thomas-Chollier M, Defrance M, Medina-Rivera A, Sand O, Herrmann C, Thieffry D, et al. RSAT: regulatory sequence analysis tools. Nucleic Acid Res 2011;39(Web Server issue):W86-91.
26. Ro HS, Roncari DA. The C/EBP-binding and adjacent sites regulate expression of the adipose P2 gene in human preadiopocytes. Mol Cell Biol 1991;11:2303-06.
27. Hunt CR, Ro JH, Dobson DE, Min HY, Spiegelman BM. Adipocyte P2 Gene: developmental expression and homology of 5′-flanking sequences among fat cell-specific genes. Proc Natl Acad Sci U S A 1986;83:3786-90.
28. Majdalawieh A, Zhang L, Fuki IV, Rader DJ, Ro HS. Adipocyte enhancer-binding protein 1 is a potential novel atherogenic factor involved in macrophage cholesterol homeostasis and inflammation. Proc Natl Acad Sci U S A 2006;103:2346-51.
29. Farnham PJ. Insights from genomic profiling of transcription factors. Nat Rev Genet 2009;10:605-16.
30. Kidokoro T, Tanikawa C, Furukawa Y, Katagiri T, Nakamura Y, Matsuda K, et al. CDC20, a potential cancer therapeutic target, is negatively regulated by p53. Oncogene 2008;27:1562-71.
31. Boutros R, Lobjois V, Ducommun B. CDC25 phosphatases in cancer cells: key players? Good targets? Nat Rev Cancer 2007;7:495-507.
32. Calzolari F, Appolloni I, Tutucci E, Caviglia S, Terrile M, Corte G, et al. Tumor progression and oncogene addiction in a PDGF-B-induced model of gliomagenesis. Neoplasia 2008;10:1373-82.
33. Jeuken J, van den Broecke C, Gijsen S, Boots-Sprenger S, Wesseling P. RAS/RAF pathway activation in gliomas: the result of copy number gains rather than activating mutations. Acta Neuropathol 2007;114: 121-33.
34. Park S, Zhao D, Hatanpaa KJ, Mickey BE, Saha D, Boothman DA, et al. RIP1 activates PI3K-Akt via a dual mechanism involving NF-kappaB-mediated inhibition of the mTOR-S6K-IRS1 negative feedback loop and down-regulation of PTEN. Cancer Res 2009;69: 4107-11.
35. Rahaman Shaik O, Vogelbaum Michael A, Haque Saikh J. Aberrant Stat3 signaling via IL-4R/IL-13R activation in malignant glioma cells: involvement of IL-13Ra2. Proc Amer Assoc Cancer Res 2005;65: 2956-63.
36. Ro HS, Zhang L, Majdalawieh A, Kim SW, Wu X, Lyons PJ, et al. Adipocyte enhancer-binding protein 1modulates adiposity and energy homeostasis. Obesity (Silver Spring) 2007;15:288-302.
37. Bie L, Zhao G, Cheng P, Rondeau G, Porwollik S, Ju Y, et al. The accuracy of survival time prediction for patients with glioma is improved by measuring mitotic spindle checkpoint gene expression. Plos One 2011;6:e25631.
38. Costello JF, Plass C, Arap W, Chapman VM, Held WA, Berger MS, et al. Cyclin-dependent kinase6 (CDK6) amplification in human gliomas identified using two-dimensional separation of genomic DNA. Cancer Res 1997;57:1250-54.
39. Lam PY, Di Tomaso E, Ng HK, Pang JC, Roussel MF, Hjelm NM. Expression of p19INK4d, CDK4, CDK6 in glioblastoma multiforme. Br J Neurosurg 2000;28-32.
40. Preusser M, Gelpi E, Matej R, Marosi C, Dieckmann K, Rössler K, et al. No prognostic impact of survivin expression in glioblastoma. Acta Neuropathol 2005;109:534-8.
41. Johannessen A, Torp S. The clinical value of Ki-67/MIB-1 labeling index in human astrocytomas. Pathol Oncol Res 2006;12: 143-7.
42. Mueller W, Nutt CL, Ehrich M, Riemenschneider MJ, von Deimling A, van den Boom D, et al. Downregulation of RUNX3 and TES by hypermethylation in glioblastoma. Oncogene 2007;26:583-93.
43. Piperi C, Themistocleous MS, Papavassiliou GA, Farmaki E, Levidou G, Korkolopoulou P, et al. High incidence of MGMT and RARβ promoter methylation in primary glioblastomas: association with histopathological characteristics, inflammatory mediators and clinical outcome. Mol Med 2010;16:1-9.
44. Petrova DT, Asif AR, Armstrong VW, Dimova I, Toshev S, Yaramov N, et al. Expression of chloride intracellular channel protein 1 (CLIC1) and tumor protein D52 (TPD52) as potential biomarkers for colorectal cancer. Clin. Biochem 2008;41:1224-36.
45. Scrideli CA, Carlotti CG Jr, Okamoto OK, Andrade VS, Cortez MA, Motta FJ, et al. Gene expression profile analysis of primary glioblastomas and non-neoplastic brain tissue: identification of potential target genes by oligonucleotide microarray and real-time quantitative PCR. J Neuro Oncol 2008;88:281-91.
46. Sato N, Fukushima N, Chang R, Matsubayashi H, Goggins M. Differential and epigenetic gene expression profiling identifies frequent disruption of the RELN pathway in pancreatic cancers. Gastroenterology 2006;130:548-65.
47. Rossi D, Deaglio S, Dominguez-Sola D, Rasi S, Vaisitti T, Agostinelli C, et al. Alteration of BIRC3 and multiple other NF-κB pathway genes in splenic marginal zone lymphoma. Blood 2011;118:4930-4.
48. Honma K, Tsuzuki S, Nakagawa M, Tagawa H, Nakamura S, Morishima Y, et al. TNFAIP3/A20 functions as a novel tumor suppressor gene in several subtypes of non-Hodgkin lymphomas. Blood 2009;114:2467-75.
49. Dong QZ, Zhao Y, Liu Y, Wang Y, Zhang PX, Jiang GY, et al. Overexpression of SCC-S2 correlates with lymph node metastasis and poor prognosis in patients with non-small-cell lung cancer. Cancer Sci 2010;101:1562-9.
50. van der Deen M, Akech J, Lapointe D, Gupta S, Young DW, Montecino MA, et al. Genomic promoter occupancy of Runt-related transcription factors RUNX2 in osteosarcoma cells identifies gene involved in cell adhesion and motility. J Biol Chem 2012;287:4503-17.