Real-time PCR assay based on the differential expression of microRNAs and protein-coding genes for molecular classification of formalinfixed paraffin embedded medulloblastomas

Neuro-Oncology

Volumn 15, Issue 12, 2013, Pages 1644-1651

  Kunder, Ratika ^a   Jalali, Rakesh ^a   Sridhar, Epari ^a   Moiyadi, Aliasgar ^a   Goel, Naina ^b   Goel, Atul ^c   Gupta, Tejpal ^a   Krishnatry, Rahul ^a   Kannan, Sadhana ^a   Kurkure, Purna ^a   Deopujari, Chandrashekhar ^d   Shetty, Prakash ^a   Biyani, Naresh ^d   Korshunov, Andrey ^e   Pfister, Stefan M ^e   Northcott, Paul A ^e   Shirsat, Neelam Vishwanath ^a  

^a TATA MEMORIAL HOSPITAL   (India)

^b Department of Neurosurgery ^*  (United States)

^c KEM HOSPITAL   (India)

^d BOMBAY HOSPITAL   (India)

^e GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER; FORMALDEHYDE; MICRORNA; MICRORNA 10B; MICRORNA 148A; MICRORNA 182; MICRORNA 193A; MICRORNA 224; MICRORNA 23B; MICRORNA 365; MICRORNA 592; MYC PROTEIN; PARAFFIN; TRANSCRIPTION FACTOR OTX2; UNCLASSIFIED DRUG;

ARTICLE; CANCER SURVIVAL; CONTROLLED STUDY; DKK2 GENE; EOMES GENE; EYA1 GENE; FROZEN SECTION; GENE; GENE OVEREXPRESSION; GRM8 GENE; HHIP GENE; HISTOPATHOLOGY; HUMAN; HUMAN TISSUE; IMPG2 GENE; INDIAN; MAJOR CLINICAL STUDY; MEDULLOBLASTOMA; MICROARRAY ANALYSIS; MYCN GENE; NPR3 GENE; ONCOGENE MYC; OVERALL SURVIVAL; PROTEIN CODING GENE; REAL TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RISK REDUCTION; SURVIVAL RATE; TRANSCRIPTION FACTOR OTX2 GENE; TUMOR CLASSIFICATION; UNC5D GENE;

INDIAN COHORT, MEDULLOBLASTOMA; MIRNA; MOLECULAR CLASSIFICATION; RISK STRATIFICATION;

ADOLESCENT; ADULT; CASE-CONTROL STUDIES; CEREBELLAR NEOPLASMS; CEREBELLUM; CHILD; CHILD, PRESCHOOL; FEMALE; FOLLOW-UP STUDIES; GENE EXPRESSION PROFILING; HEDGEHOG PROTEINS; HUMANS; INFANT; MALE; MEDULLOBLASTOMA; MICRORNAS; MIDDLE AGED; NEOPLASM STAGING; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PARAFFIN EMBEDDING; PROGNOSIS; REAL-TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, MESSENGER; SURVIVAL RATE; WNT PROTEINS; YOUNG ADULT;

EID: 84891853105     PISSN: 15228517     EISSN: 15235866     Source Type: Journal    
DOI: 10.1093/neuonc/not123     Document Type: Article

References (23)

1. Bourdeaut F, Miquel C, Alapetite C, Roujeau T, Doz F. Medulloblastomas: update on a heterogeneous disease. Curr Opin Oncol. 2011;23: 630-637.
2. Rossi A, Caracciolo V, Russo G, Reiss K, Giordano A. Medulloblastoma: from molecular pathology to therapy. Clin Cancer Res. 2008;14: 971-976.
3. Kool M, Koster J, Bunt J, et al. Integrated genomics identifies five medulloblastoma subtypes with distinct genetic profiles,pathwaysignatures and clinicopathological features. PLoS ONE. 2008;3:e3088.
4. Northcott PA, Korshunov A, Witt H, et al. Medulloblastoma comprises four distinct molecular variants. J Clin Oncol. 2011;29:1408-1414.
5. Cho YJ, Tsherniak A, Tamayo P, et al. Integrative genomic analysis fmedulloblastoma identifies a molecular subgroup that drives poor clinical outcome. J Clin Oncol. 2011;29:1424-1430.
6. Taylor MD, Northcott PA, Korshunov A, et al. Molecular subgroups of medulloblastoma: the current consensus. Acta Neuropathol. 2012;123:465-472.
7. Northcott PA, Korshunov A, Pfister SM, Taylor MD. The clinical implications of medulloblastoma subgroups. Nat Rev Neurol. 2012;8:340-351.
8. Ambros V. MicroRNA pathways in flies and worms: growth, death, fat, stress, and timing. Cell. 2003;113:673-676.
9. Murchison EP, Hannon GJ. miRNAs on the move: miRNA biogenesis and the RNAi machinery. Curr Opin Cell Biol. 2004;16:223-229.
10. Croce CM, Calin GA. miRNAs, cancer, and stem cell division. Cell. 2005;122:6-7.
11. Iorio MV, Croce CM. microRNA involvement in human cancer. Carcinogenesis. 2012;33:1126-1133.
12. Calin GA, Croce CM. MicroRNA signatures in human cancers. Nat Rev Cancer. 2006;6:857-866.
13. Hall JS, Taylor J, Valentine HR, et al. Enhanced stability of microRNA expression facilitates classification of FFPE tumour samples exhibiting near total mRNA degradation. Br J Cancer. 2012;107:684-694.
14. Xi Y, Nakajima G, Gavin E, et al. Systematic analysis of microRNA expression of RNA extracted from fresh frozen and formalin-fixed paraffin-embedded samples. Rna. 2007;13:1668-1674.
15. Liu A, TetzlaffMT,VanbelleP, et al.MicroRNAexpression profiling outperforms mRNA expression profiling in formalin-fixed paraffin-embedded tissues. Int J Clin Exp Pathol. 2009;2:519-527.
16. Gokhale A, Kunder R, Goel A, et al. Distinctive microRNA signature of medulloblastomas associated with the WNT signaling pathway. J Cancer Res Ther. 2010;6:521-529.
17. Korbler T, Grskovic M, Dominis M, Antica M. A simple method for RNA isolation from formalin-fixed and paraffin-embedded lymphatic tissues. Exp Mol Pathol. 2003;74:336-340.
18. Chomczynski P, Sacchi N. Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chlorofrom extraction. Anal Biochem. 1987;162:156-159.
19. Tibshirani R, Hastie T, Narasimhan B, Chu G. Diagnosis of multiple cancer types by shrunken centroids of gene expression. Proc Natl Acad Sci U S A. 2002;99:6567-6572.
20. Northcott PA, Fernandez LA,Hagan JP, et al. The miR-17/92 polycistron is up-regulated in sonic hedgehog-drivenmedulloblastomasand induced by N-myc in sonic hedgehog-treated cerebellar neural precursors. Cancer Res. 2009;69:3249-3255.
21. Glazov EA, McWilliam S, Barris WC, Dalrymple BP. Origin, evolution, and biological role of miRNA cluster in DLK-DIO3 genomic region in placental mammals. Mol Biol Evol. 2008;25:939-948.
22. Northcott PA, Shih DJ, Remke M, et al. Rapid, reliable, and reproducible molecular sub-grouping of clinical medulloblastoma samples. Acta Neuropathol. 2012;123:615-626.
23. Kool M, Korshunov A, Remke M, et al. Molecular subgroups of medulloblastoma: An international meta-analysis of transcriptome, genetic aberrations, and clinical data of WNT, SHH, Group 3, and Group 4 medulloblastomas. Acta Neuropathol. 2012;123:473-484.