NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE28547 Query DataSets for GSE28547
Status Public on May 29, 2013
Title Underexpression of miR-224 in methotrexate resistant human colon cancer cells
Organism Homo sapiens
Experiment type Non-coding RNA profiling by array
Summary A summary of the work associated to these microarrays is the following:

MicroRNAs (miRNAs) are small non-coding RNAs involved in RNA silencing that play a role in many biological processes. They are involved in the development of many diseases, including cancer. Extensive experimental data show that they play a role in the pathogenesis of cancer as well as the development of drug resistance during treatment. MiRNA microarrays of sensitive and MTX-resistant HT29 colon cancer cells were performed. The results were analyzed using the GeneSpring GX11.5 software. Differentially expressed microRNAs in resistant cells were identified and miR-224, which was greatly underexpressed and displayed robust raw signal values, was selected for further studies. Putative targets were predicted using TargetScan 5.1 software and intersected with the data from expression microarrays previously performed. This approach allowed us to identify miR-224 targets that were differentially expressed more than 2-fold in resistant cells. Among them, ARL3, CDS2, DCP2, HSPC159, MYST3 and SLC4A4 were validated at the mRNA level by qRT-PCR. Functional assays using an anti-miR against miR-224 desensitized the cells toward MTX, mimicking the resistant phenotype. On the other hand, siRNA treatment against SLC4A4 or incubation of Poly Purine Reverse Hoogsteen (PPRH) hairpins against CDS2 or HSPC159 increased sensitivity to MTX. These results revealed a role for miR-224 and its targets in MTX resistance in HT29 colon cancer cells.
KEYWORDS
Methotrexate, miRNAs, drug resistance, DHFR
 
Overall design Two cell lines are compared in the study, which are HT29 colon cancer cells sensitive to methotrexate and HT29 cells resistant to 10e-5M MTX. Six samples are provided which correspond to 3 samples for the control condition and 3 samples for the resistant condition. Data files from miRNA and mRNA (previously submitted to GEO as GSE11440) microarrays were analyzed with GeneSpring GX11.5 software (Agilent Technologies) to find differentially expressed miRNAs and their cellular target genes in the resistant cell lines compared to their sensitive counterparts.
 
Contributor(s) Mencia N, Selga E, Noe V, Ciudad CJ
Citation(s) 21864507
Submission date Apr 12, 2011
Last update date May 07, 2014
Contact name Carlos J Ciudad
E-mail(s) cciudad@ub.edu
Phone +34-93-403-4455
Organization name University of Barcelona
Department Biochemistry and Molecular Biology
Lab School of Pharmacy
Street address Av. Juan XXIII-27
City Barcelona
State/province Barcelona
ZIP/Postal code 08028
Country Spain
 
Platforms (1)
GPL8227 Agilent-019118 Human miRNA Microarray 2.0 G4470B (miRNA ID version)
Samples (6)
GSM706688 HT29 sensitive cells replicate 1
GSM706690 HT29 sensitive cells replicate 2
GSM706691 HT29 sensitive cells replicate 3
Relations
Affiliated with GSE11440 (mRNA data)
BioProject PRJNA139061

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
GSE28547_RAW.tar 5.7 Mb (http)(custom) TAR (of GPR, TXT)
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap