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Series GSE57342 Query DataSets for GSE57342
Status Public on May 08, 2014
Title Immune regulation by low doses of the DNA methyltransferase inhibitor 5-azacitidine in common human epithelial cancers [methylation]
Organism Homo sapiens
Experiment type Methylation profiling by array
Summary Epigenetic therapy is emerging as a potential therapy for solid tumors. To investigate its mechanism of action, we performed integrative expression and methylation analysis of 63 cancer cell lines (breast, colorectal, and ovarian) after treatment with the DNA methyltransferase inhibitor 5-azacitidine (AZA). Gene Set Enrichment Analysis demonstrated significant enrichment for immunomodulatory pathways in all three cancers (14.4-31.3%) including interferon signaling, antigen processing and presentation, and cytokines/chemokines. Strong upregulation of cancer testis antigens was also observed.
An AZA IMmune gene set (AIMs) derived from the union of these immunomodulatory pathway genes classified primary tumors from all three types, into “high” and “low” AIM gene expression subsets in tumor expression data from both TCGA and GEO (GSE42284, GSE10893, and GSE26712 for the colon, breast, and ovarian samples, respectively). Samples from selected patient biopsies showed upregulation of AIM genes after treatment with epigenetic therapy. These results point to a broad immune stimulatory role for DNA demethylating drugs in multiple cancers.
 
Overall design A total of 338 samples were analyzed.
 
Contributor(s) Li H, Chiappinelli KB, Guzzetta AA, Yen RC, Vatapalli R, Baylin SB, Zahnow CA, Ahuja N
Citation(s) 24583822
Submission date May 06, 2014
Last update date Mar 22, 2019
Contact name Stephen Baylin
E-mail(s) sbaylin@jhmi.edu
Phone 4109558506
Organization name Johns Hopkins UniversityJohns Hopkins Medical Institutions
Department Oncology
Street address 1650 Orleans St CRB I RM 541
City Baltimore
State/province Maryland
ZIP/Postal code 21287
Country USA
 
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (338)
GSM1380380 genomic dna from breast_MDA231_Mock_day1
GSM1380381 genomic dna from breast_MDA231_AZA_day1
GSM1380382 genomic dna from breast_MDA231_Mock_day3
This SubSeries is part of SuperSeries:
GSE57343 Immune regulation by low doses of the DNA methyltransferase inhibitor 5-azacitidine in common human epithelial cancers
Relations
BioProject PRJNA246413

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
GSE57342_RAW.tar 183.1 Mb (http)(custom) TAR
GSE57342_processed_data.txt.gz 1.3 Gb (ftp)(http) TXT
GSE57342_signal_intensities.txt.gz 777.2 Mb (ftp)(http) TXT
Processed data are available on Series record
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