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| Status |
Public on Nov 02, 2020 |
| Title |
The epithelial splicing regulator ESRP2 is epigenetically repressed by DNA hypermethylation in Wilms tumor and acts as a tumor suppressor |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Wilms tumor (WT), a childhood kidney cancer with embryonal origins, has been extensively characterised for genetic and epigenetic alterations, but a proportion of WTs still lack identifiable abnormalities. To uncover DNA methylation changes critical for WT pathogenesis, we compared the epigenome of fetal kidney with two WT cell lines, using methyl-CpG immunoprecipitation. We filtered our results to remove common cancer-associated epigenetic changes, and to enrich for genes involved in early kidney development. This identified four candidate genes that were hypermethylated in WT cell lines compared to fetal kidney, of which ESRP2 (epithelial splicing regulatory protein 2), was the most promising gene for further study. ESRP2 was commonly repressed by DNA methylation early in WT development (in nephrogenic rests) and could be reactivated by DNA methyltransferase inhibition in WT cell lines. When ESRP2 was expressed in WT cell lines, it acted as an inhibitor of cellular proliferation in vitro and in vivo it suppressed tumor growth of orthotopic xenografts in nude mice. RNA-seq of the ESRP2-expressing WT cell lines identified several novel splicing targets, in addition to well-characterised targets of ESRP2. One of these targets, LEF1, is a component of the Wnt signalling pathway that is essential for kidney development and commonly disrupted in WT. We propose a model in which the Wnt pathway can be disrupted in early kidney development to generate WT, either by genetic abnormalities such as WT1 mutations, or by epigenetic defects, such as ESRP2 methylation.
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| Overall design |
To discover splicing events induced by ESRP2 in Wilms tumor, we established a variant of the Wit49 Wilms tumor cell line that contained a doxycycline (DOX)-inducible ESRP2 expression construct (E200L). In biological duplicates, we extracted RNA from E200L cells that were DOX-induced (ESRP2-expressing) or uninduced (non-expressing), and sequenced them, obtaining between 70 and 80 million paired-end reads per sample. These reads were mapped onto the human genome and used in rMATS software to identify alternative splicing events.
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| Contributor(s) |
Legge D, Moriarty W, Lee D, Malik KT, Oltean S, Brown KW |
| Citation(s) |
34520622 |
| Submission date |
Jul 15, 2020 |
| Last update date |
Sep 30, 2021 |
| Contact name |
Keith William Brown |
| E-mail(s) |
keith.brown@bristol.ac.uk
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| Phone |
+441173312071
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| Organization name |
University of Bristol
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| Department |
School of Cellular and Molecular Medicine
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| Lab |
Cancer Epigenetics Laboratory
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| Street address |
Biomedical Sciences Building, University Walk
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| City |
Bristol |
| State/province |
- |
| ZIP/Postal code |
BS8 1TD |
| Country |
United Kingdom |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA646492 |
| SRA |
SRP272098 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE154496_MXE.MATS.JC_v2.xlsx |
274.2 Kb |
(ftp)(http) |
XLSX |
| GSE154496_RI.MATS.JC_v2.xlsx |
52.6 Kb |
(ftp)(http) |
XLSX |
| GSE154496_SE.MATS.JC_v2.xlsx |
1005.1 Kb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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