Identification and validation of a gene expression signature that predicts outcome in malignant glioma patients

International Journal of Oncology

Volumn 40, Issue 3, 2012, Pages 721-730

  Kawaguchi, Atsushi ^c   Yajima, Naoki ^a   Komohara, Yoshihiro ^b   Aoki, Hiroshi ^a   Tsuchiya, Naoto ^a   Homma, Jumpei ^a   Sano, Masakazu ^a   Natsumeda, Manabu ^a   Uzuka, Takeo ^a   Saitoh, Akihiko ^a   Takahashi, Hideaki ^a   Sakai, Yuko ^d   Takahashi, Hitoshi ^a   Fujii, Yukihiko ^a   Kakuma, Tatsuyuki ^c   Yamanaka, Ryuya ^d  

^a NIIGATA UNIVERSITY   (Japan)

^b KUMAMOTO UNIVERSITY   (Japan)

^c KURUME UNIVERSITY   (Japan)

^d KYOTO PREFECTURAL UNIVERSITY OF MEDICINE   (Japan)

Author keywords

Gene expression profile; Glioma; Prognostic marker

Indexed keywords

RNA;

ARTICLE; CANCER GRADING; CANCER STAGING; CANCER SURVIVAL; CLINICAL ARTICLE; CONTROLLED STUDY; DISEASE COURSE; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GLIOBLASTOMA; HUMAN; HUMAN TISSUE; IMMUNOHISTOCHEMISTRY; MICROARRAY ANALYSIS; OUTCOME ASSESSMENT; OVERALL SURVIVAL; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROGNOSIS; SURVIVAL PREDICTION; SURVIVAL TIME;

AGED; FEMALE; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENETIC TESTING; GLIOMA; HUMANS; MALE; NEOPLASM STAGING; PROGNOSIS; RNA; SURVIVAL RATE;

EID: 84857181925     PISSN: 10196439     EISSN: 17912423     Source Type: Journal    
DOI: 10.3892/ijo.2011.1240     Document Type: Article

References (49)

1. Stewart LA: Chemotherapy in adult high-grade glioma: a syste-matic review and meta-analysis of individual patient data from 12 randomised trials. Lancet 359: 1011-1018, 2002.
2. Stupp R, Hegi ME, Mason WP, et al: 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 Oncol 10: 459-466, 2009.
3. Kleihues P, Louis DN, Wiestler OD, et al: WHO grading of tumours of the central nervous system. In: World Health Organization Classification of Tumours of the Nervous System. Louis DN, Ohgaki H, Wiestler OD and Cavenee WK (eds). IARC Press, Lyon, pp10-11, 2007.
4. Ramaswamy S, Tamayo P, Rifkin R, et al: Multiclass cancer diagnosis using tumor gene expression signatures. Proc Natl Acad Sci USA 98: 15149-15154, 2001. (Pubitemid 34013984)
5. Rickman DS, Bobek MP, Misek DE, et al: Distinctive molecular profiles of high-grade and low-grade gliomas based on oligo-nucleotide microarray analysis. Cancer Res 61: 6885-6891, 2001. (Pubitemid 32896514)
6. Kim S, Dougherty ER, Shmulevich I, et al: Identification of combination gene sets for glioma classification. Mol Cancer Ther 1: 1229-1236, 2002.
7. Khan J, Wei JS, Ringner M, et al: Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks. Nat Med 7: 673-679, 2001. (Pubitemid 32588022)
8. Mischel PS, Shai R, Shi T, et al: Identification of molecular subtypes of glioblastoma by gene expression profiling. Oncogene 22: 2361-2273, 2003.
9. Nigro JM, Misra A, Zhang L, et al: Integrated array-comparative genomic hybridization and expression array profiles identify clinically relevant molecular subtypes of glioblastoma. Cancer Res 65: 1678-1686, 2005. (Pubitemid 40478592)
10. Shai R, Shi T, Kremen TJ, et al: Gene expression profiling identifies molecular subtypes of gliomas. Oncogene 22: 4918-4923, 2003. (Pubitemid 36981282)
11. Sorlie T, Tibshirani R, Parker J, et al: Repeated observation of breast tumor subtypes in independent gene expression data sets. Proc Natl Acad Sci USA 100: 8418-8423, 2003. (Pubitemid 36842560)
12. Liang Y, Diehn M, Watson N, et al: Gene expression profiling reveals molecularly and clinically distinct subtypes of glioblastoma multiforme. Proc Natl Acad Sci USA 102: 5814-5819, 2005. (Pubitemid 40559642)
13. Wong KK, Chang YM, Tsang YT, et al: Expression analysis of juvenile pilocytic astrocytomas by oligonucleotide microarray reveals two potential subgroups. Cancer Res 65: 76-84, 2005. (Pubitemid 40070797)
14. Shirahata M, Iwao-Koizumi K, Saito S, et al: Gene expression-based molecular diagnostic system for malignant gliomas is superior to histological diagnosis. Clin Cancer Res 13: 7341-7356, 2007.
15. Li A, Walling J, Ahn S, et al: Unsupervised analysis of transcriptomic profiles reveals six glioma subtypes. Cancer Res 69: 2091-2099, 2009.
16. Sallinen SL, Sallinen PK, Haapasalo HK, et al: Identification of differentially expressed genes in human gliomas by DNA microarray and tissue chip techniques. Cancer Res 60: 6617-6622, 2000.
17. Godard S, Getz G, Delorenzi M, et al: 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, 2003. (Pubitemid 37322939)
18. Rich JN, Hans C, Jones B, et al: Gene expression profiling and genetic markers in glioblastoma survival. Cancer Res 65: 4051-4058, 2005. (Pubitemid 40775641)
19. Somasundaram K, Reddy SP, Vinnakota K, et al: Upregulation of ASCL1 and inhibition of Notch signaling pathway characterize progressive astrocytoma. Oncogene 24: 7073-7083, 2005. (Pubitemid 41573636)
20. Horvath S, Zhang B, Carlson M, et al: Analysis of oncogenic signaling networks in glioblastoma identifies ASPM as a molecular target. Proc Natl Acad Sci USA 103: 17402-17407, 2006. (Pubitemid 44788981)
21. Yamanaka R, Arao T, Yajima N, et al: Identification of expressed genes characterizing long-term survival in malignant glioma patients. Oncogene 25: 5994-6002, 2006. (Pubitemid 44477293)
22. Soroceanu L, Kharbanda S, Chen R, et al: Identification of IGF2 signaling through phosphoinositide-3-kinase regulatory subunit 3 as a growth-promoting axis in glioblastoma. Proc Natl Acad Sci USA 104: 3466-3471, 2007. (Pubitemid 46364182)
23. Reddy SP, Britto R, Vinnakota K, et al: Novel glioblastoma markers with diagnostic and prognostic value identified through transcriptome analysis. Clin Cancer Res 14: 2978-2987, 2008.
24. Nutt CL, Mani DR, Betensky RA, et al: Gene expression-based classification of malignant gliomas correlates better with survival than histological classification. Cancer Res 63: 1602-1607, 2003. (Pubitemid 36373650)
25. Freije WA, Castro-Vargas FE, Fang Z, et al: Gene expression profiling of gliomas strongly predicts survival. Cancer Res 64: 6503-6510, 2004. (Pubitemid 39297907)
26. Petalidis LP, Oulas A, Backlund M, et al: Improved grading and survival prediction of human astrocytic brain tumors by artificial neural network analysis of gene expression microarray data. Mol Cancer Ther 7: 1013-1024, 2008.
27. Marko NF, Toms SA, Barnett GH and Weil R: Genomic expression patterns distinguish long-term from short-term glioblastoma survivors: a preliminary feasibility study. Genomics 91: 395-406, 2008.
28. Livak KJ and Schmittgen TD: Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method. Methods 25: 402-408, 2001. (Pubitemid 34164012)
29. R Development Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. 2009 ISBN 3-900051-07-0, URL http://www.R-project.org.
30. Gentleman R, Carey V, Bates D, et al: Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5: R80, 2004.
31. Ishwaran H, Kogalur UB, Blackstone EH and Lauer MS: Random survival forests. Ann Appl Statist 2: 841-860, 2008.
32. Harrel FE Jr, Lee KL and Mark DB: Tutorial in biostatistics: multivariable prognostic models: issues in developing models, evaluating assumptions and adequacy, and measuring and reducing error. Stat Med 15: 361-387, 1996. (Pubitemid 26072233)
33. Ripley BD: Pattern recognition and neural networks. Cambridge: Cambridge University Press, 2008.
34. Kaplan EL and Meier P: Nonparametric estimation from incomplete observations. J Am Statist Assoc 53: 457-481, 1958.
35. Efron B and Tibshirani R: On testing the significance of sets of genes. Ann Appl Stat 1: 107-129, 2007.
36. Kanehisa M, Goto S, Furumichi M, et al: KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res 38: 355-360, 2010.
37. Phillips HS, Kharbanda S, Chen R, et al: Molecular subclasses of high-grade glioma predict prognosis, delineate a pattern of disease progression, and resemble stages in neurogenesis. Cancer Cell 9: 157-173, 2006. (Pubitemid 43357943)
38. Cancer Genome Atlas Research Network: Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455: 1061-1068, 2008.
39. Haibe-Kains B, Desmedt C, Sotiriou C and Bontempi G: A comparative study of survival models for breast cancer prognostication based on microarray data: does a single gene beat them all? Bioinformatics 24: 2200-2208, 2008.
40. Breiman L: Random forests. Machine Learning 45: 5-32, 2001.
41. Tusher VG, Tibshirani R, Chu G: Significance analysis of micro-arrays applied to the ionizing radiation response. Proc Natl Acad Sci USA 98: 5116-5121, 2001. (Pubitemid 32397092)
42. Cordell HJ: Detecting gene-gene interactions that underlie human diseases. Nat Rev Genet 10: 392-404, 2009.
43. Diaz-Uriarte R and Alvarez de Andres S: Gene selection and classification of microarray data using random forest. BMC Bioinformatics 7: 3, 2006.
44. Ishwaran H, Kogalur UB, Gorodeski EZ, et al: High-dimensional variable selection for survival data. J Am Statist Assoc 105: 205-217, 2010.
45. Hlobilkova A, Ehrmann J, Knizetova P, et al: Analysis of VEGF, Flt-1, Flk-1, nestin and MMP-9 in relation to astrocytoma pathogenesis and progression. Neoplasma 56: 284-290, 2009.
46. Vredenburgh JJ, Desjardins A, Herndon JE II, et al: Bevacizumab plus irinotecan in recurrent glioblastoma multiforme. J Clin Oncol 25: 4722-4729, 2007. (Pubitemid 350086473)
47. Cheng CK, Fan QW and Weiss WA: PI3K signaling in glioma-animal models and therapeutic challenges. Brain Pathol 19: 112-120, 2009.
48. Ruano Y, Mollejo M, Camacho FI, et al: Identification of survival-related genes of the phosphatidylinositol 3′-kinase signaling pathway in glioblastoma multiforme. Cancer 112: 1575-1584, 2008. (Pubitemid 351441171)
49. Carro MS, Lim WK, Alvarez MJ, et al: The transcriptional network for mesenchymal transformation of brain tumours. Nature 463: 318-325, 2010.