An integrated mRNA and microRNA expression signature for glioblastoma multiforme prognosis

PLoS ONE

Volumn 9, Issue 5, 2014, Pages

  Xiong, Jie ^a   Bing, Zhitong ^b   Su, Yanlin ^a   Deng, Defeng ^c   Peng, Xiaoning ^a  

^a HUNAN NORMAL UNIVERSITY   (China)

^b INSTITUTE OF MODERN PHYSICS   (China)

^c UNIVERSITY OF TEXAS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; MICRORNA; TRANSCRIPTOME;

APOPTOSIS; ARTICLE; CANCER PROGNOSIS; CANCER SURVIVAL; CONTROLLED STUDY; GENE EXPRESSION; GLIOBLASTOMA; HUMAN; MAJOR CLINICAL STUDY; OVERALL SURVIVAL; PROPORTIONAL HAZARDS MODEL; RECEIVER OPERATING CHARACTERISTIC; REPRODUCIBILITY; RNA ANALYSIS; SURVIVAL RATE; AREA UNDER THE CURVE; COHORT ANALYSIS; GENE ONTOLOGY; GENETICS; KAPLAN MEIER METHOD; METABOLISM; PROGNOSIS; VALIDATION STUDY;

AREA UNDER CURVE; COHORT STUDIES; GENE ONTOLOGY; GLIOBLASTOMA; HUMANS; KAPLAN-MEIER ESTIMATE; MICRORNAS; PROGNOSIS; PROPORTIONAL HAZARDS MODELS; RNA, MESSENGER; TRANSCRIPTOME;

EID: 84901604240     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0098419     Document Type: Article

References (48)

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 Oncol 10: 459-466.
2. Krex D, Klink B, Hartmann C, von Deimling A, Pietsch T, et al. (2007) Long-term survival with glioblastomamultiforme. Brain 130: 2596-2606.
3. Dong S, Nutt CL, Betensky RA, Stemmer-Rachamimov AO, Denko NC, et al. (2005) Histology-based expression profiling yields novel prognostic markers in human glioblastoma. J NeuropatholExpNeurol 64: 948.
4. Ohka F, Natsume A, Wakabayashi T (2012) Current trends in targeted therapies for glioblastomamultiforme. Neurol Res Int 2012.
5. McLendon R, Friedman A, Bigner D, Van Meir EG, Brat DJ, et al. (2008) Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455: 1061-1068.
6. 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.
7. Kawaguchi A, Yajima N, Tsuchiya N, Homma J, Sano M, et al. (2013) Gene expression signature-based prognostic risk score in patients with glioblastoma. Cancer Sci 104: 1205-1210.
8. Arimappamagan A, Somasundaram K, Thennarasu K, Peddagangannagari S, Srinivasan H, et al. (2013) A Fourteen Gene GBM Prognostic Signature Identifies Association of Immune Response Pathway and Mesenchymal Subtype with High Risk Group. PLoS ONE 8: e62042.
9. Srinivasan S, Patric IRP, Somasundaram K (2011) A ten-microRNA expression signature predicts survival in glioblastoma. PLoS ONE 6: e17438.
10. 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.
11. Yoshihara K, Tajima A, Yahata T, Kodama S, Fujiwara H, et al. (2010) Gene expression profile for predicting survival in advanced-stage serous ovarian cancer across two independent datasets. PLoS ONE 5: e9615.
12. Harrell F, Lee KL, Mark DB (1996) Tutorial in biostatistics multivariable prognostic models: issues in developing models, evaluating assumptions and adequacy, and measuring and reducing errors. Stat Med 15: 361-387 (Pubitemid 26072233)
13. Yuan M, Lin Y (2006) Model selection and estimation in regression with grouped variables. J R Stat Soc Series B Stat Methodol (Statistical Methodology) 68: 49-67. (Pubitemid 43415335)
14. Bøvelstad HM, Nygård S, Størvold HL, Aldrin M, Borgan Ø, et al. (2007) Predicting survival from microarray data - a comparative study. Bioinformatics 23: 2080-2087. (Pubitemid 47394107)
15. Friedman J, Hastie T, Tibshirani R (2010) Regularization paths for generalized linear models via coordinate descent. J Stat Softw33: 1.
16. Simon N, Friedman J, Hastie T, Tibshirani R (2011) Regularization paths for Cox's proportional hazards model via coordinate descent. J Stat Softw 39: 1-13.
17. Tibshirani R, Bien J, Friedman J, Hastie T, Simon N, et al. (2012) Strong rules for discarding predictors in lasso-type problems. J R Stat Soc Series B Stat Methodol (Statistical Methodology) 74: 245-266.
18. Gautier L, Cope L, Bolstad BM, Irizarry RA (2004) affy - analysis of AffymetrixGeneChip data at the probe level. Bioinformatics 20: 307-315. (Pubitemid 38262761)
19. López-Romero P (2011) Pre-processing and differential expression analysis of Agilent microRNA arrays using the AgiMicroRna Bioconductor library. BMC Genomics 12: 64.
20. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Series B Stat Methodol (Methodological): 289-300.
21. Liu WM, Mei R, Di X, Ryder T, Hubbell E, et al. (2002) Analysis of high density expression microarrays with signed-rank call algorithms. Bioinformatics 18: 1593-1599. (Pubitemid 36097724)
22. Heagerty PJ, Lumley T, Pepe MS (2000) Time-dependent ROC curves for censored survival data and a diagnostic marker. Biometrics 56: 337-344. (Pubitemid 30422619)
23. Ihaka R, Gentleman R (1996) R: A language for data analysis and graphics. J Comput Graph Stat 5: 299-314.
24. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, et al. (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5:R80.
25. 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. (Pubitemid 39297907)
26. 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. (Pubitemid 43357943)
27. 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. (Pubitemid 40775641)
28. Lee Y, Scheck AC, Cloughesy TF, Lai A, Dong J, et al. (2008) Gene expression analysis of glioblastomas identifies the major molecular basis for the prognostic benefit of younger age. BMC Med Genomics 1: 52.
29. Da Wei Huang BTS, Lempicki RA (2008) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4: 44-57.
30. Grimson A, Farh KK-H, Johnston WK, Garrett-Engele P, Lim LP, et al. (2007) MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Molecular Cell 27: 91-105. (Pubitemid 46991392)
31. Lin Y, Jiang T, Zhou K, Xu L, Chen B, et al. (2009) Plasma IGFBP-2 levels predict clinical outcomes of patients with high-grade gliomas. NeuroOncol11: 468-476.
32. Cheng W-Y, Kandel JJ, Yamashiro DJ, Canoll P, Anastassiou D (2012) A multicancer mesenchymal transition gene expression signature is associated with prolonged time to recurrence in glioblastoma. PLoS ONE 7:e34705.
33. Kim H, Bredel M (2012) Predicting survival by cancer pathway gene expression profiles in the TCGA. In: Bioinformatics and Biomedicine Workshops (BIBMW), 2012 IEEE International Conference on: 2012: 872-875.
34. Kawaguchi A, Yajima N, Komohara Y, Aoki H, Tsuchiya N, et al. (2012)Identification and validation of a gene expression signature that predicts outcome in malignant glioma patients. Int J Oncol 40.: 721-730.
35. 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 ONE 4.:e6274.
36. Mizoguchi M, Betensky RA, Batchelor TT, Bernay DC, Louis DN, et al. (2006) Activation of STAT3, MAPK, and AKT in malignant astrocyticgliomas: correla tion with EGFR s tatus, tumor grade, and survival . J NeuropatholExpNeurol 65: 1181-1188. (Pubitemid 44885942)
37. Wiley SE, Paddock ML, Abresch EC, Gross L, van der Geer P, et al. (2007) The outer mitochondrial membrane protein mitoNEET contains a novel redoxactive 2Fe-2S cluster. J BiolChem 282: 23745-23749. (Pubitemid 47327996)
38. Shinoura N, Paradies N, Warnick R, Chen H, Larson J, et al. (1995) Expression of N-cadherin and alpha-catenin in astrocytomas and glioblastomas. Br J Cancer 72: 627.
39. Sun S, Lee D, Ho AS, Pu JK, Zhang X, et al. (2013) Inhibition of prolyl 4-hydroxylase, beta polypeptide (P4HB) attenuates temozolomide resistance in malignant glioma via the endoplasmic reticulum stress response (ERSR) pathways. NeuroOncol15: 562-577.
40. Marimuthu A, Subbannayya Y, Sahasrabuddhe NA, Balakrishnan L, Syed N, et al. (2012) SILAC-based quantitative proteomic analysis of gastric cancer secretome. Proteomics ClinAppl 7: 355-366
41. Varki A, Cummings RD, Esko JD, Freeze HH, Stanley P, et al. (2009) Glycosylation changes in cancer.
42. Taminelli GL, Sotomayor V, Valdivieso ÁG, Teiber ML, Marín MC, et al. (2008) CISD1 codifies a mitochondrial protein upregulated by the CFTR channel. BiochemBiophys Res Commun365: 856-862. (Pubitemid 350245381)
43. Cameron A, Fortenberry Y, Lindberg I (2000) The SAAS granin exhibits structural and functional homology to 7B2 and contains a highly potent hexapeptide inhibitor of PC1. FEBS Letters 473: 135-138. (Pubitemid 30254276)
44. Qian Y, Devi LA, Mzhavia N, Munzer S, Seidah NG, et al. (2000) The C-terminal region of proSAAS is a potent inhibitor of prohormoneconvertase 1. J BiolChem 275: 23596-23601. (Pubitemid 30624643)
45. Jin B, Yao B, Li J-L, Fields CR, Delmas AL, et al. (2009) DNMT1 and DNMT3B modulate distinct polycomb-mediated histone modifications in colon cancer. Cancer Res 69: 7412-7421.
46. Hua D, Mo F, Ding D, Li L, Han X, et al. (2012) A catalogue of glioblastoma and brain MicroRNAs identified by deep sequencing. OMICS 16: 690-699.
47. Roth P, Wischhusen J, Happold C, Chandran PA, Hofer S, et al. (2011) A specific miRNA signature in the peripheral blood of glioblastoma patients. J Neurochem118: 449-457.
48. Kim J ZY, Guessous F, Abounader R (2012) microRNA-148a: A novel oncogenic microRNA in glioblastoma. Proceedings of the 103rd Annual Meeting of the American Association for Cancer Res: 2012: 3165.