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| Status |
Public on Mar 23, 2018 |
| Title |
Modulation of ESRP2 and MBNL2 in normal kidney and clear cell renal cell carcinoma cell lines for analysis of stability programs |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
While analyzing mRNA expression profiles of clear cell renal cell carcinoma (ccRCC) tumors, we found that the mRNAs that are bound at their 3' UTRs by muscleblind-like splicing regulator 2 (Mbnl2) and epithelial splicing regulatory protein 2 (ESRP2) are up-regulated in tumor compared to patient-matched normal tissues. Given that MBNL2 increases the stability of its targets and ESRP2 destabilizes its targets, we predicted that, in ccRCC tumors, MBNL2 activity increases, while ESRP2 activity decreases. To investigate the effect of each of these two RNA-binding proteins (RBPs) on the transcriptome of the cell, we used shRNA to knockdown MBNL2 in two different cell line models of ccRCC (786-O and A-498), and also to knockdown ESRP2 in normal primary renal proximal tubule epithelial cells (PRPTEC). RNA-seq revealed that MBNL2 knockdown partially reverses the ccRCC-associated transcriptome in ccRCC cell lines, whereas ESRP2 knockdown shifts the transcriptome of PRPTEC toward that of ccRCC.
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| Overall design |
Two independent shRNAs were used for each protein in each cell line. Each cell line was also infected by a control shRNA in two replicates. The transcriptome after infection with MBNL2- or ESRP2-specific shRNA was compared to the transcriptome after infection with control shRNA.
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| Contributor(s) |
Najafabadi HS, Jandaghi P, Safisamghabadi M, Riazalhosseini Y |
| Citation(s) |
29742422 |
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| Submission date |
Jul 04, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Hamed S Najafabadi |
| Organization name |
McGill University
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| Department |
Human Genetics
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| Lab |
Computational and Statistical Genomics Lab
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| Street address |
740 Dr. Penfield Avenue, Room 7202
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| City |
Montreal |
| State/province |
QC |
| ZIP/Postal code |
H3A 0G1 |
| Country |
Canada |
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| Platforms (1) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA327769 |
| SRA |
SRP077885 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE83999_DESeq.average_10_reads_per_sample.log2fc.shRNA_vs_ctrl.matrix.txt.gz |
615.6 Kb |
(ftp)(http) |
TXT |
| GSE83999_RAW.tar |
2.7 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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