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Series GSE148389 Query DataSets for GSE148389
Status Public on Apr 10, 2020
Title MiR-1253 exerts tumor-suppressive effects in medulloblastoma via inhibition of CDK6 and CD276 (B7-H3) (RNA-seq dataset)
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Of the four primary subgroups of medulloblastoma, the most frequent cytogenetic abnormality, i17q, distinguishes Groups 3 and 4 which carry the highest mortality; haploinsufficiency of 17p13.3 is a marker for particularly poor prognosis. At the terminal end of this locus lies miR-1253, a brain-enriched microRNA that regulates bone morphogenic proteins during cerebellar development. We hypothesized miR-1253 confers novel tumor-suppressive properties in medulloblastoma. Using two different cohorts of medulloblastoma samples, we first studied the expression and methylation profiles of miR-1253. We then explored the anti-tumorigenic properties of miR-1253, in parallel with a biochemical analysis of apoptosis and proliferation, and isolated oncogenic targets using high-throughput screening. Deregulation of miR-1253 expression was noted, both in medulloblastoma clinical samples and cell lines, by epigenetic silencing via hypermethylation; specific de-methylation of miR-1253 not only resulted in rapid recovery of expression but also a sharp decline in tumor cell proliferation and target gene expression. Expression restoration also led to a reduction in tumor cell virulence, concomitant with activation of apoptotic pathways, cell cycle arrest and reduction of markers of proliferation. We identified two oncogenic targets of miR-1253, CDK6 and CD276, whose silencing replicated the negative trophic effects of miR-1253. These data reveal novel tumor-suppressive properties for miR-1253, i.e., (i) loss of expression via epigenetic silencing; (ii) negative trophic effects on tumor aggressiveness; and (iii) downregulation of oncogenic targets.
 
Overall design RNA-seq analysis of 14 normal and 26 tumor tissues with subgroup classfication. Each sample was sequenced on 4 Illumina lanes.
 
Contributor(s) Sidharth M
Citation(s) 32145124
Submission date Apr 09, 2020
Last update date Oct 04, 2022
Contact name Pranita Atri
Organization name UNIVERSITY OF NEBRASKA MEDICAL CENTER
Department Biochemistry
Street address S 42nd and Emile St
City Omaha
State/province NE
ZIP/Postal code 68198
Country USA
 
Platforms (1)
GPL21697 NextSeq 550 (Homo sapiens)
Samples (160)
GSM4466846 NC1_1_RNA-seq
GSM4466847 NC1_2_RNA-seq
GSM4466848 NC1_3_RNA-seq
This SubSeries is part of SuperSeries:
GSE148390 MiR-1253 exerts tumor-suppressive effects in medulloblastoma via inhibition of CDK6 and CD276 (B7-H3)
Relations
BioProject PRJNA624128
SRA SRP255885

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE148389_allcounts_with_unk.csv.gz 5.8 Mb (ftp)(http) CSV
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Raw data are available in SRA
Processed data are available on Series record

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