A Fourteen Gene GBM Prognostic Signature Identifies Association of Immune Response Pathway and Mesenchymal Subtype with High Risk Group

PLoS ONE

Volumn 8, Issue 4, 2013, Pages

  Arimappamagan, Arivazhagan ^a   Somasundaram, Kumaravel ^b   Thennarasu, Kandavel ^a   Peddagangannagari, Sreekanthreddy ^b   Srinivasan, Harish ^b   Shailaja, Bangalore C ^a   Samuel, Cini ^c   Patric, Irene Rosita Pia ^b   Shukla, Sudhanshu ^b   Thota, Balaram ^a   Prasanna, Krishnarao Venkatesh ^c   Pandey, Paritosh ^a   Balasubramaniam, Anandh ^a   Santosh, Vani ^a   Chandramouli, Bangalore Ashwathnarayanara ^a   Hegde, Alangar Sathyaranjandas ^c   Kondaiah, Paturu ^b   Sathyanarayana Rao, Manchanahalli R ^d  

^a NATIONAL INSTITUTE OF MENTAL HEALTH AND NEUROSCIENCES   (India)

^b INDIAN INSTITUTE OF SCIENCE   (India)

^c SRI SATHYA SAI INSTITUTE OF HIGHER MEDICAL SCIENCES   (India)

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

Author keywords

[No Author keywords available]

Indexed keywords

ALPHA SYNUCLEIN; ANGIOTENSINOGEN; CARBOXYPEPTIDASE H; EPIDERMAL GROWTH FACTOR RECEPTOR; MONOCYTE CHEMOTACTIC PROTEIN 1; MYELIN BASIC PROTEIN; SOMATOMEDIN BINDING PROTEIN 1; PROTEOME; TRANSCRIPTOME;

ADULT; ANGIOTENSINOGEN GENE; ARTICLE; CALCITONIN RECEPTOR LIKE GENE; CANCER PROGNOSIS; CANCER RISK; CANCER SURVIVAL; CARBOXYPEPTIDASE E GENE; CHEMOKINE LIGAND 2 GENE; CHITINASE 3 LIKE 1 GENE; CONTROLLED STUDY; DNA TOPOISOMERASE II ALPHA GENE; EPIDERMAL GROWTH FACTOR RECEPTOR GENE; GENE EXPRESSION; GENE FUNCTION; GENE IDENTIFICATION; GENETIC ASSOCIATION; GENETIC RISK; GLIOBLASTOMA; HIGH RISK POPULATION; HUMAN; HUMAN TISSUE; IMMUNE RESPONSE; INSULIN LIKE GROWTH FACTOR BINDING PROTEIN LIKE 1 GENE; LOW RISK POPULATION; MAJOR CLINICAL STUDY; MCF GENE; MESENCHYME; MYELIN BASIC PROTEIN GENE; OLFACTOMEDIN 1 GENE; OVERALL SURVIVAL; PREDICTIVE VALUE; PROTEIN KINASE C AND CASEIN KINASE SUBSTRATE IN NEURON 1 GENE; REGULATOR GENE; RISK ASSESSMENT; SUPEROXIDE DISMUTASE 2 GENE; SURVIVAL PREDICTION; SURVIVAL RATE; SYNUCLEIN ALPHA GENE; BIOLOGY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETICS; IMMUNOLOGY; INFLAMMATION; METABOLISM; MOLECULAR GENETICS; MORTALITY; PROGNOSIS; REPRODUCIBILITY; RISK; SIGNAL TRANSDUCTION;

COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENE REGULATORY NETWORKS; GLIOBLASTOMA; HUMANS; INFLAMMATION; MOLECULAR SEQUENCE ANNOTATION; PROGNOSIS; PROTEOME; REPRODUCIBILITY OF RESULTS; RISK; SIGNAL TRANSDUCTION; TRANSCRIPTOME;

EID: 84876997136     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0062042     Document Type: Article

References (49)

1. Stupp R, Hegi ME, Mason WP, van den Bent MJ, Taphoorn MJ, et al. (2009) Effects of radiotherapy with concomitant and adjuvant temozolomide versus radiotherapy alone on survival in glioblastoma in a randomised phase III study: 5-year analysis of the EORTC-NCIC trial. Lancet Oncol10: 459-466.
2. Lacroix M, bi-Said D, Fourney DR, Gokaslan ZL, Shi W, et al. (2001) A multivariate analysis of 416 patients with glioblastoma multiforme: prognosis, extent of resection, and survival. J Neurosurg95: 190-198.
3. Stupp R, Mason WP, van den Bent MJ, Weller M, Fisher B, et al. (2005) Radiotherapy plus concomitant and adjuvant temozolomide for glioblastoma. N Engl J Med 352: 987-996.
4. Nagarajan RP, Costello JF, (2009) Epigenetic mechanisms in glioblastoma multiforme. Semin Cancer Biol19: 188-197.
5. Mizoguchi M, Betensky RA, Batchelor TT, Bernay DC, Louis DN, et al. (2006) Activation of STAT3, MAPK, and AKT in malignant astrocytic gliomas: correlation with EGFR status, tumor grade, and survival. J Neuropathol Exp Neurol65: 1181-1188.
6. Hegi ME, Liu L, Herman JG, Stupp R, Wick W, et al. (2008) Correlation of O6-methylguanine methyltransferase (MGMT) promoter methylation with clinical outcomes in glioblastoma and clinical strategies to modulate MGMT activity. J Clin Oncol 26: 4189-4199.
7. Nutt CL, Mani DR, Betensky RA, Tamayo P, Cairncross JG, et al. (2003) Gene expression-based classification of malignant gliomas correlates better with survival than histological classification. Cancer Res 63: 1602-1607.
8. Godard S, Getz G, Delorenzi M, Farmer P, Kobayashi H, et al. (2003) Classification of human astrocytic gliomas on the basis of gene expression: a correlated group of genes with angiogenic activity emerges as a strong predictor of subtypes. Cancer Res 63: 6613-6625.
9. Freije WA, Castro-Vargas FE, Fang Z, Horvath S, Cloughesy T, et al. (2004) Gene expression profiling of gliomas strongly predicts survival. Cancer Res 64: 6503-6510.
10. Colman H, Zhang L, Sulman EP, McDonald JM, Shooshtari NL, et al. (2010) A multigene predictor of outcome in glioblastoma. Neuro Oncol 12: 49-57.
11. Sreekanthreddy P, Srinivasan H, Kumar DM, Nijaguna MB, Sridevi S, et al. (2010) Identification of potential serum biomarkers of glioblastoma: serum osteopontin levels correlate with poor prognosis. Cancer Epidemiol Biomarkers Prev19: 1409-1422.
12. Srinivasan S, Patric IR, Somasundaram K, (2011) A ten-microRNA expression signature predicts survival in glioblastoma. PLoS One6: e17438.
13. deTayracM, Aubry M, Saikali S, Etcheverry A, Surbled C, et al. (2011) A 4-gene signature associated with clinical outcome in high-grade gliomas. Clin Cancer Res 17: 317-327.
14. Somasundaram K, Reddy SP, Vinnakota K, Britto R, Subbarayan M, et al. (2005) Upregulation of ASCL1 and inhibition of Notch signaling pathway characterize progressive astrocytoma. Oncogene 24: 7073-7083.
15. Reddy SP, Britto R, Vinnakota K, Aparna H, Sreepathi HK, et al. (2008) Novel glioblastoma markers with diagnostic and prognostic value identified through transcriptome analysis. Clin Cancer Res 14: 2978-2987.
16. Santosh V, Arivazhagan A, Sreekanthreddy P, Srinivasan H, Thota B, et al. (2010) Grade-specific expression of insulin-like growth factor-binding proteins-2,-3, and-5 in astrocytomas: IGFBP-3 emerges as a strong predictor of survival in patients with newly diagnosed glioblastoma. Cancer Epidemiol Biomarkers Prev19: 1399-1408.
17. Liang Y, Diehn M, Watson N, Bollen AW, Aldape KD, et al. (2005) Gene expression profiling reveals molecularly and clinically distinct subtypes of glioblastoma multiforme. Proc Natl Acad Sci U S A 102: 5814-5819.
18. Hastie T, Tibshirani R, Sherlock G, Eisen M, Brown P, et al. (1999) Imputing Missing Data for Gene Expression Arrays. Technical report. Stanford University Statistics Department.
19. Bair E, Tibshirani R, (2004) Semi-supervised methods to predict patient survival from gene expression data. PLoS Biol2: E108.
20. R Devleopment Core Team, (2010) R: A Language and Environment for Statistical Computing [http://www.R-project.org].R Foundation for Statistical Computing, Vienna, Austria.
21. Cox DR (1972) Regression models and life tables (with discussion). J Royal Stat Soc B34, 187-220.
22. Tibshirani RJ, Efron B, (2002) Pre-validation and inference in microarrays. Stat Appl Genet Mol Biol1: Article1.
23. Heagerty PJ, Lumley T, Pepe MS, (2000) Time-dependent ROC curves for censored survival data and a diagnostic marker. Biometrics 56: 337-344.
24. Cancer Genome Atlas Research Network, et al. (2008) Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455: 1061-1068.
25. Huang dW, Sherman BT, Lempicki RA, (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4: 44-57.
26. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29.
27. Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M, (2010) KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res 38: D355-D360.
28. Phillips HS, Kharbanda S, Chen R, Forrest WF, Soriano RH, et al. (2006) Molecular subclasses of high-grade glioma predict prognosis, delineate a pattern of disease progression, and resemble stages in neurogenesis. Cancer Cell 9: 157-173.
29. Gravendeel LA, Kouwenhoven MC, Gevaert O, de Rooi JJ, Stubbs AP, et al. (2009) Intrinsic gene expression profiles of gliomas are a better predictor of survival than histology. Cancer Res 69: 9065-9072.
30. Verhaak RG, Hoadley KA, Purdom E, Wang V, Qi Y, et al. (2010) Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell 17: 98-110.
31. Li A, Walling J, Ahn S, Kotliarov Y, Su Q, et al. (2009) Unsupervised analysis of transcriptomic profiles reveals six glioma subtypes. Cancer Res 69: 2091-2099.
32. Zhang J, Liu B, Jiang X, Zhao H, Fan M, et al. (2009) A systems biology-based gene expression classifier of glioblastoma predicts survival with solid tumors. PLoS One4: e6274.
33. Rich JN, Hans C, Jones B, Iversen ES, McLendon RE, et al. (2005) Gene expression profiling and genetic markers in glioblastoma survival. Cancer Res 65: 4051-4058.
34. Maher EA, Brennan C, Wen PY, Durso L, Ligon KL, et al. (2006) Marked genomic differences characterize primary and secondary glioblastoma subtypes and identify two distinct molecular and clinical secondary glioblastoma entities. Cancer Res 66: 11502-11513.
35. Cai Z, Chen HT, Boyle B, Rupp F, Funk WD, et al. (2005) Identification of a novel insulin-like growth factor binding protein gene homologue with tumor suppressor like properties. Biochem Biophys Res Commun 331: 261-266.
36. Komai K, Okayama R, Kitagawa M, Yagi H, Chihara K, et al. (2002) Alternative splicing variants of the human DBL (MCF-2) proto-oncogene. Biochem Biophys Res Commun 299: 455-458.
37. Jarvinen TA, Liu ET, (2003) HER-2/neu and topoisomerase IIalpha in breast cancer. Breast Cancer Res Treat78: 299-311.
38. Arivazhagan A, Kumar DM, Sagar V, Patric IR, Sridevi S, et al. (2012) Higher topoisomerase 2 alpha gene transcript levels predict better prognosis in GBM patients receiving temozolomide chemotherapy: identification of temozolomide as a TOP2A inhibitor. J Neurooncol 107: 289-97.
39. Chigurupati S, Kulkarni T, Thomas S, Shah G, (2005) Calcitonin stimulates multiple stages of angiogenesis by directly acting on endothelial cells. Cancer Res 65: 8519-8529.
40. Mennel HD, Hallier-Neelsen M, Hagner S, Benes L, (2006) Two novel cell specific receptor proteins, CRLR and CD 117 in human glial tumors. Clin Neuropathol 25: 107-114.
41. Wheeler DL, Dunn EF, Harari PM, (2010) Understanding resistance to EGFR inhibitors-impact on future treatment strategies. Nat Rev Clin Oncol 7: 493-507.
42. Johansen JS, Jensen BV, Roslind A, Nielsen D, Price PA, (2006) Serum YKL-40, a new prognostic biomarker in cancer patients? Cancer Epidemiol Biomarkers Prev 15: 194-202.
43. Conti I, Rollins BJ, (2004) CCL2 (monocyte chemoattractant protein-1) and cancer. Semin Cancer Biol 14: 149-154.
44. Takei H, Yogeswaren ST, Wong KK, Mehta V, Chintagumpala M, et al. (2008) Expression of oligodendroglial differentiation markers in pilocytic astrocytomas identifies two clinical subsets and shows a significant correlation with proliferation index and progression free survival. J Neurooncol 86: 183-190.
45. Li W, Lee MK, (2005) Antiapoptotic property of human alpha-synuclein in neuronal cell lines is associated with the inhibition of caspase-3 but not caspase-9 activity. J Neurochem 93: 1542-1550.
46. Grivennikov SI, Greten FR, Karin M, (2010) Immunity, inflammation, and cancer. Cell 140: 883-899.
47. Aggarwal BB, Shishodia S, Sandur SK, Pandey MK, Sethi G, (2006) Inflammation and cancer: how hot is the link? Biochem Pharmacol 72: 1605-1621.
48. Mantovani A, Allavena P, Sica A, Balkwill F, (2008) Cancer-related inflammation. Nature 454: 436-444.
49. Engler JR, Robinson AE, Smirnov I, Hodgson JG, Berger MS, et al. (2012) Increased microglia/macrophage gene expression in a subset of adult and pediatric astrocytomas. PLoS One7: e43339.