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KDM4B regulates alternative splicing in castration resistant prostate cancer

ABSTRACT: KDM4B regulates alternative splicing in castration resistant prostate cancer

PROVIDER: PRJNA540817 | ENA |

REPOSITORIES: ENA

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KDM4B regulates alternative splicing in castration resistant prostate cancer

Project description:We studied the alternative splicing function of KDM4B and found that KDM4B can act as a bona fide trans-acting splicing factor that binds RNA and signal-responsive scaffold protein that binds spliceosome.

2020-04-01 | GSE130620 | GEO

Whole Transcriptomic Sequencing of Metastatic Castration Resistant Prostate Cancer Samples

Project description:We report the gene expression profile of 8 metastatic castration resisistant prostate cancer samples analyzed by paired-end RNA-seq. We found evidence of extensive abnormal splicing as well as several novel fusion genes. Finally, we also observed several recurrent high-confidence somatic mutations. Paired-end RNA-seq by rRNA depletion

2014-09-06 | E-GEOD-50630 | biostudies-arrayexpress

RNA splicing factors SRRM3 and SRRM4 distinguish molecular phenotypes of castration-resistant neuroendocrine prostate cancer [methylation]

Project description:Neuroendocrine (NE) differentiation in metastatic castration-resistant prostate cancer (mCRPC) usually develops through cellular plasticity. We recently characterized two mCRPC phenotypes with NE features; Androgen receptor (AR)-positive, NE-positive amphicrine prostate cancer (AMPC) and AR-negative small cell or neuroendocrine prostate cancer (SCNPC). Here, we interrogate the RE-1 silencing transcription factor (REST) pathway in mCRPC and demonstrate that SRRM3 has analogous functions to SRRM4 and mediates NE differentiation through alternative splicing of REST. We scrutinize transcriptome datasets across species and tumor types and discover that SRRM3 and SRRM4 expression define molecular phenotypes in AMPC and SCNPC. Notably, we characterize two AMPC phenotypes driven by either REST attenuation or ASCL1 activity and three SCNPC phenotypes with progressive activation of neuronal transcription factor programs. Together, our data provides a biological framework for classifying NE phenotypes in mCRPC that could be useful for future therapeutic development and precision medicine applications.

2021-07-14 | GSE158598 | GEO

Whole Transcriptomic Sequencing of Metastatic Castration Resistant Prostate Cancer Samples

2014-09-06 | GSE50630 | GEO

RNA splicing factors SRRM3 and SRRM4 distinguish molecular phenotypes of castration-resistant neuroendocrine prostate cancer [RNA-seq]

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Position-dependent alternative splicing activity revealed by global profiling of alternative splicing events regulated by PTB

Project description:This SuperSeries is composed of the following subset Series: GSE23513: Position-dependent alternative splicing activity revealed by global profiling of alternative splicing events regulated by PTB (HJAY) GSE23514: Position-dependent alternative splicing activity revealed by global profiling of alternative splicing events regulated by PTB (Exon array) Refer to individual Series

2010-09-01 | E-GEOD-23522 | biostudies-arrayexpress

Transcriptomic analysis of KDM4B-mediated gene in C4-2B prostate cancer cells

Project description:Histone lysine demethylase KDM4B is often overexpressed in prostate cancer and links to poor survival outcome. Recent evidence suggests that KDM4B serves as a potential therapeutic target. The global transcriptomic analysis between control and KDM4B-knockdown C4-2B cells reveals the metabolic genes involved in Warburg effect are downregulated after knocking down the expression of KDM4B, indicating its role in tumor growth.

2023-03-24 | GSE147481 | GEO

Transcription profiling by array of castration-resistant prostate cancer PC-3 cells treated with Hsp27-siRNA or control siRNA to study the role of Heat shock protein (Hsp) 27 in splicing

Project description:In order to investigate the involvement of Hsp27 in splicing, we performed a whole-genome exonic expression profiling of the castration-resistant prostate cancer PC-3 cells treated by Hsp27-siRNA or CTL-siRNA (both in biological duplicates).

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Coupling between alternative polyadenylation and alternative splicing is limited to terminal introns

Project description:Alternative polyadenylation has been implicated as an important regulator of gene expression. In some cases, alternative polyadenylation is known to couple with alternative splicing to influence last intron removal. However, it is unknown whether alternative polyadenylation events influence alternative splicing decisions at upstream exons. Knockdown of the polyadenylation factors CFIm25 or CstF64 was used as an approach in identifying alternative polyadenylation and alternative splicing events on a genome-wide scale. Although hundreds of alternative splicing events were found to be differentially spliced in the knockdown of CstF64, genes associated with alternative polyadenylation did not exhibit an increased incidence of alternative splicing. These results demonstrate that the coupling between alternative polyadenylation and alternative splicing is usually limited to defining the last exon. The striking influence of CstF64 knockdown on alternative splicing can be explained through its effects on UTR selection of known splicing regulators such as hnRNP A2/B1, thereby indirectly influencing splice site selection. We conclude that changes in the expression of the polyadenylation factor CstF64 influences alternative splicing through indirect effects. HeLa cell line was stably transfected with shRNA plasmids targeting CstF64. Total RNA was isolated from CstF64 KD cells and wild-type control cells using Trizol according to manufacturerâs protocols. Samples were deep sequenced in duplicate using the Illumina GAIIx system.

2016-03-14 | E-GEOD-79157 | biostudies-arrayexpress

FOXA1 regulates splicing-related gene expression and alternative splicing in prostate cancer cells

Project description:Dysregulation of alternative splicing in prostate cancer is linked to transcriptional programs activated by canonical oncogenic transcription factors. However, the relative contribution of these factors to alternative splicing regulation is yet to be defined. We investigated the role of FOXA1 by performing deep RNA-seq on siRNA-treated (i.e. siFOXA1) and control (i.e. NSI) samples from prostate cancer cell lines. Using this data, we performed canonical parametric differential expression analysis between NSI and siFOXA1 samples to determine the effect of FOXA1 depletion on splicing related gene expression. We also identified FOXA1-regulated differentially alternatively spliced exons between NSI and siFOXA1 samples.

2022-09-27 | GSE193127 | GEO

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