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Series GSE98642 Query DataSets for GSE98642
Status Public on May 01, 2018
Title EZH2 regulates neuroblastoma cell differentiation via NTRK1 promoter epigenetic modifications
Organism Homo sapiens
Experiment type Expression profiling by array
Summary The polycomb repressor complex 2 molecule EZH2 is now known to play a role in essential cellular processes, namely, cell fate decisions, cell cycle regulation, senescence, cell differentiation, and cancer development/progression. EZH2 inhibitors have recently been developed; however, their effectiveness and underlying molecular mechanisms in many malignancies have not yet been elucidated in detail. Although the functional role of EZH2 in tumorigenesis in neuroblastoma (NB) has been investigated, mutations of EZH2 have not been reported. A Kaplan-Meier analysis on the event free- and overall survival of NB patients indicated that the highexpression of EZH2 correlated with an unfavorable prognosis. In order to elucidate the functional roles of EZH2 in NB tumorigenesis and its aggressiveness, we knocked down EZH2 in NB cell lines using lentivirus systems. The knockdown of EZH2 significantly induced NB cell differentiation, e.g. neurite extension, and the neuronal differentiation markers, NF68 and GAP43. EZH2 inhibitors also induced NB cell differentiation. We performed a comprehensive transcriptome analysis using Human Gene Expression Microarrays and found that NTRK1 (TrkA) is one of the EZH2-related suppression targets. The depletion of NTRK1 canceled EZH2 knockdown-induced NB cell differentiation. Our integrative methylome, transcriptome, and chromatin immunoprecipitation assays using NB cell lines and clinical samples clarified that the NTRK1 P1 and P2 promoter regions were regulated differently by DNA methylation and EZH2-related histone modifications. The NTRK1 transcript variants 1/2, which were regulated by EZH2-related H3K27me3 modifications at the P1 promoter region, were strongly expressed in favorable, but not unfavorable NB. The depletion and inhibition of EZH2 successfully induced NTRK1 transcripts and functional proteins. Collectively, these results indicate that EZH2 plays important roles in preventing the differentiation of NB cells and also that EZH2-related NTRK1 transcriptional regulation may be the key pathway for NB cell differentiation.
 
Overall design RNA was extracted at two time points, 8 and 11 days after shEZH2-expressing lentiviral infection, and a microarray analysis was performed using the Agilent platform of 8x60 K design ID G4851B (Agilent Single Color. 39494, Agilent Technologies). Two hundred nanograms of total RNA was labeled with Cyanine3 using a Low Input Quick-Amp Labeling Kit (one color, Agilent Technologies) according to the manufacturer’s instructions. Purified labeled total RNA was hybridized to the expression microarray. Hybridization, the scanning of microarrays, and data extraction from scanned images were conducted according to Agilent protocol version 6.9.
 
Contributor(s) Li Z, Takenobu H, Setyawati AN, Akita N, Haruta M, Satoh S, Shinno Y, Chikaraishi K, Mukae K, Akter J, Sugino RP, Nakagawara A, Aburatani H, Ohira M, Kamijo T
Citation(s) 29507419
Submission date May 08, 2017
Last update date Jul 25, 2021
Contact name Hisanori Takenobu
Phone +81-48-722-1111
Organization name Saitama Cancer Center
Department Research Institute for Clinical Oncology
Street address 818, Komuro, Ina-machi
City Kitaadachi-gun
State/province Saitama
ZIP/Postal code 362-0806
Country Japan
 
Platforms (1)
GPL16699 Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray 039381 (Feature Number version)
Samples (18)
GSM2607460 NB-39-nu_pLKO.1_day8_rep1
GSM2607461 NB-39-nu_pLKO.1_day8_rep2
GSM2607462 NB-39-nu_pLKO.1_day8_rep3
Relations
BioProject PRJNA385803

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
GSE98642_RAW.tar 54.7 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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