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Series GSE36082 Query DataSets for GSE36082
Status Public on Aug 22, 2013
Title Small RNA-seq and gene expression analysis reveal a miRNA profile of cancer-susceptibility in ATM deficient human mammary epithelial cells (mRNA)
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Deficiencies in the ATM gene are the underlying cause for ataxia telangiectasia, a congenital syndrome characterized by neurological, motor and immunological defects, as well as a predisposition to cancer risks. MicroRNAs (miRNAs) are small regulators of post-transcriptional gene expression and a useful tool for cancer diagnosis, staging, and prediction of therapeutic responses to clinical regimens. In particular, miRNAs have been used to develop signatures for breast cancer profiling. We are interested in the consequences of ATM deficiency on miRNA expression in breast epithelial cells and the potential contribution to cancer predisposition. In this study we investigate the effects of ATM loss on the miRNA expression and related gene expression changes in normal human mammary epithelial cells (HME-CC). We have identified 81 significantly differently expressed miRNAs in the ATM-deficient HME-CCs using small RNA sequencing. Many of these differentially expressed miRNAs have been described and implicated in tumorigenesis and proliferation. These changes include down-regulation of tumor suppressor miRNAs, such as hsa-miR-29c and hsa-miR-16, as well as the over-expression of pro-oncogenic miRNAs hsa-miR-93 and hsa-mir-221. All 81 miRNAs were combined with genome wide gene expression profiles to investigate possible targets of miRNA regulation. We identified messenger RNA (mRNA) targets of these miRNAs that were also significantly regulated after the depletion of ATM. Predicted targets included many genes implicated in cancer formation and progression, including SOCS1 and the proto-oncogene MAF. Integrated analysis of miRNA and mRNA expression allows us to build a more complete understanding of the pathways and networks involved in the breast cancer predisposition observed in individuals deficient in ATM. This study highlights miRNA and predicted mRNA target expression changes in ATM-deficient HME-CCs and suggests a mechanism for the breast cancer-prone phenotype seen in ATM deficient cells and patients. Additionally, this study provides preliminary data for defining miRNA profiles that may be used prognostic biomarkers for breast cancer predisposition.
 
Overall design Examination of small RNA population in human mammary epithelial cell lines. Each condition was preformed in triplicate.

This submission represents the transcriptome component of study.
 
Contributor(s) Hesse JE, Liu L, Innes CL, Paules RS
Citation(s) 23741392
Submission date Feb 25, 2012
Last update date Feb 22, 2018
Contact name NIEHS Microarray Core
E-mail(s) microarray@niehs.nih.gov, liuliw@niehs.nih.gov
Organization name NIEHS
Department DIR
Lab Microarray Core
Street address 111 T.W. Alexander Drive
City RTP
State/province NC
ZIP/Postal code 27709
Country USA
 
Platforms (1)
GPL4133 Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Feature Number version)
Samples (6)
GSM880854 HME-CC-LacZ_Untreated_Replicate1
GSM880855 HME-CC-LacZ_Untreated_Replicate2
GSM880856 HME-CC-LacZ_Untreated_Replicate3
This SubSeries is part of SuperSeries:
GSE36267 Small RNA-seq and gene expression analysis reveal a miRNA profile of cancer-susceptibility in ATM deficient human mammary epithelial cells
Relations
BioProject PRJNA155733

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
GSE36082_RAW.tar 60.1 Mb (http)(custom) TAR (of TXT)
GSE36082_US23502387_251485042559_S01_H.tif.gz 60.4 Mb (ftp)(http) TIFF
GSE36082_US23502387_251485042559_S01_L.tif.gz 45.6 Mb (ftp)(http) TIFF
GSE36082_US23502387_251485042560_S01_H.tif.gz 60.3 Mb (ftp)(http) TIFF
GSE36082_US23502387_251485042560_S01_L.tif.gz 45.5 Mb (ftp)(http) TIFF
GSE36082_US23502387_251485042561_S01_H.tif.gz 60.5 Mb (ftp)(http) TIFF
GSE36082_US23502387_251485042561_S01_L.tif.gz 45.8 Mb (ftp)(http) TIFF
Raw data provided as supplementary file
Processed data included within Sample table
Raw data are available on Series record
Processed data provided as supplementary file

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