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Series GSE176457 Query DataSets for GSE176457
Status Public on Jun 22, 2023
Title DNA Methylation Signatures Differentiate Meningiomas from Normal Dura [OmniSNP]
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
SNP genotyping by SNP array
Summary Meningiomas are the most common primary brain tumor. Though typically benign with a low mutational burden, histopathologic analysis has poor predictive value for malignant behavior and there are no proven chemotherapies. Although DNA methylation patterns distinguish subgroups of meningiomas and have higher predictive value for tumor behavior than histologic classification, little is known about differences in DNA methylation between meningiomas and surrounding normal dura tissue. Using multimodal studies of meningioma/dura pairs, we identified 4 distinct DNA methylation patterns. Diffuse DNA hypomethylation of malignant meningiomas readily facilitated their identification from lower grade tumors by unsupervised clustering. All clusters and 12/12 meningioma-dura pairs exhibited hypomethylation of the gene promoters of a module associated with the craniofacial patterning transcription factor FOXC1 and its upstream lncRNA FOXCUT. Furthermore, we identified an epigenetic continuum of increasing hypermethylation of polycomb repressive complex target promoters with increased histopathologic grade suggesting progressive epigenetic dysregulation is associated with increasing tumor aggressiveness. These findings are a starting point for future investigations of the role of epigenetic dysregulation of FOXC1 and cranial patterning genes in early stages of meningioma formation as well as studies of the utility of polycomb inhibitors for treatment of aggressive meningiomas.
Overall design 19 meningiomas (11 WHO grade I, 6 WHO grade II, 4 WHO grade III) underwent genotyping with a HumanOmni-Express v12.
Contributor(s) Zada G, Rhie SK, Wedemeyer MA, Muskins I, Wiemels JL, Weisenberg DJ, Wang K, Mukerjee D, Strickland BA
Citation(s) 35769412
Submission date Jun 09, 2021
Last update date Jul 14, 2023
Contact name Michelle Ariana Wedemeyer
Organization name University of Southern California
Department Neurosurgery
Street address 1200 N State St, Suite 3300
City Los Angeles
State/province California
ZIP/Postal code 90033
Country USA
Platforms (1)
GPL18900 HumanOmniExpress-12v1 BeadChip
Samples (19)
GSM5365909 Patient13 meningioma
GSM5365910 Patient14 meningioma
GSM5365911 Patient15 meningioma
This SubSeries is part of SuperSeries:
GSE178143 DNA Methylation Signatures Differentiate Meningiomas from Normal Dura
BioProject PRJNA737456

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
GSE176457_Processed_OmniSNP.txt.gz 137.1 Mb (ftp)(http) TXT
GSE176457_RAW.tar 250.0 Mb (http)(custom) TAR (of IDAT)
GSE176457_Raw_OmniSNP.txt.gz 117.0 Mb (ftp)(http) TXT
Processed data are available on Series record

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