title: Real-time PCR assay based on the differential expression of microRNAs and protein-coding genes for molecular classification of formalin-fixed paraffin embedded medulloblastomas.
abstract: BACKGROUND
  Medulloblastoma has recently been found to consist of 4 molecularly and clinically distinct subgroups: WNT, Sonce hedgehog (SHH), Group 3, and Group 4. Deregulated microRNA expression is known to contribute to pathogenesis and has been shown to have diagnostic and prognostic potential in the classification of various cancers.
  
  
  METHODS
  Molecular subgrouping and microRNA expression analysis of 44 frozen and 59 formalin-fixed paraffin embedded medulloblastomas from an Indian cohort were carried out by real-time RT-PCR assay.
  
  
  RESULTS
  The differential expression of 9 microRNAs in the 4 molecular subgroups was validated in a set of 101 medulloblastomas. The tumors in the WNT subgroup showed significant (P < .0001) overexpression of miR-193a-3p, miR-224, miR-148a, miR-23b, and miR-365. Reliable classification of medulloblastomas into the 4 molecular subgroups was obtained using a set of 12 protein-coding genes and 9 microRNAs as markers in a real-time RT-PCR assay with an accuracy of 97% as judged by the Prediction Analysis of Microarrays. Age at diagnosis, histology, gender-related incidence, and the relative survival rates of the 4 molecular subgroups in the present Indian cohort were found to be similar to those reported for medulloblastomas from the American and European subcontinent. Non-WNT, non-SHH medulloblastomas underexpressing miR-592 or overexpressing miR-182 were found to have significantly inferior survival rates, indicating utility of these miRNAs as markers for risk stratification.
  
  
  CONCLUSIONS
  The microRNA based real-time PCR assay is rapid, simple, inexpensive, and useful for molecular classification and risk stratification of medulloblastomas, in particular formalin-fixed paraffin embedded tissues, wherein the expression profile of protein-coding genes is often less reliable due to RNA fragmentation.
authors.affiliation: Corresponding Author: Dr Neelam Vishwanath Shirsat, PhD, Advanced Centre for Treatment, Research & Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210 India. nshirsat@actrec.gov.in.
authors.forename: Ratika
authors.initials: R
authors.lastname: Kunder
authors.forename: Rakesh
authors.initials: R
authors.lastname: Jalali
authors.forename: Epari
authors.initials: E
authors.lastname: Sridhar
authors.forename: Aliasgar
authors.initials: A
authors.lastname: Moiyadi
authors.forename: Naina
authors.initials: N
authors.lastname: Goel
authors.forename: Atul
authors.initials: A
authors.lastname: Goel
authors.forename: Tejpal
authors.initials: T
authors.lastname: Gupta
authors.forename: Rahul
authors.initials: R
authors.lastname: Krishnatry
authors.forename: Sadhana
authors.initials: S
authors.lastname: Kannan
authors.forename: Purna
authors.initials: P
authors.lastname: Kurkure
authors.forename: Chandrashekhar
authors.initials: C
authors.lastname: Deopujari
authors.forename: Prakash
authors.initials: P
authors.lastname: Shetty
authors.forename: Naresh
authors.initials: N
authors.lastname: Biyani
authors.forename: Andrey
authors.initials: A
authors.lastname: Korshunov
authors.forename: Stefan M
authors.initials: SM
authors.lastname: Pfister
authors.forename: Paul A
authors.initials: PA
authors.lastname: Northcott
authors.forename: Neelam Vishwanath
authors.initials: NV
authors.lastname: Shirsat
mesh_terms: D000293:Adolescent; D000328:Adult; D016022:Case-Control Studies; D002528:Cerebellar Neoplasms / Q000145:classification* / Q000235:genetics / Q000401:mortality / Q000473:pathology; D002531:Cerebellum / Q000378:metabolism / Q000473:pathology; D002648:Child; D002675:Child, Preschool; D005260:Female; D005500:Follow-Up Studies; D020869:Gene Expression Profiling; D053823:Hedgehog Proteins / Q000235:genetics / Q000378:metabolism; D006801:Humans; D007223:Infant; D008297:Male; D008527:Medulloblastoma / Q000145:classification* / Q000235:genetics / Q000401:mortality / Q000473:pathology; D035683:MicroRNAs / Q000235:genetics*; D008875:Middle Aged; D009367:Neoplasm Staging; D020411:Oligonucleotide Array Sequence Analysis; D016612:Paraffin Embedding; D011379:Prognosis; D012333:RNA, Messenger / Q000235:genetics; D060888:Real-Time Polymerase Chain Reaction / Q000379:methods*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D015996:Survival Rate; D051153:Wnt Proteins / Q000235:genetics / Q000378:metabolism; D055815:Young Adult
chemical_list: D053823:Hedgehog Proteins; D035683:MicroRNAs; D012333:RNA, Messenger; D051153:Wnt Proteins
keywords: Indian cohort, medulloblastoma; miRNA; molecular classification; risk stratification