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Absence of SMARCB1 in rhabdoid tumor cells increases sensitivity to translation inhibition and alters translation efficiency of specific mRNAs (RNA-Seq)

ABSTRACT: Absence of SMARCB1 in rhabdoid tumor cells increases sensitivity to translation inhibition and alters translation efficiency of specific mRNAs (RNA-Seq)

PROVIDER: PRJNA1116207 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR29165265_1.fastq.gz	Fastqsanger.gz
	SRR29165265_2.fastq.gz	Fastqsanger.gz
	SRR29165266_1.fastq.gz	Fastqsanger.gz
	SRR29165266_2.fastq.gz	Fastqsanger.gz
	SRR29165267_1.fastq.gz	Fastqsanger.gz

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Similar Datasets

Absence of SMARCB1 in rhabdoid tumor cells increases sensitivity to translation inhibition and alters translation efficiency of specific mRNAs (RNA-Seq)

Project description:Rhabdoid tumors, characterized and driven by the loss of the mSWI/SNF (mammalian SWItch/Sucrose Non-Fermentable) subunit SMARCB1, are very aggressive childhood cancers that can arise in the brain, the kidney, or soft tissues. Cell lines derived from these tumors are specifically sensitivity to the translation inhibitor homoharringtonin (HHT). Having recently demonstrated mSWI/SNF roles in translation, we assessed SMARCB1 potential roles in translation in rhabdoid tumor cells. We first revealed by cell viability assays that rhabdoid tumor cells’ sensitivity to HHT were dependent on the absence of SMARCB1. Polysome profiling and immunoprecipitation experiments demonstrated the interaction of SMARCB1 with the translation machinery. Global translation assays and ribosome profiling experiments further revealed that SMARCB1 re-expression increased global translation and altered translation efficiency of specific mRNAs. Most regulated mRNAs presented an increased translation efficiency and were involved in differentiation. In comparison with the entire transcriptome, these mRNAs presented a longer coding sequence and were enriched in GC. Finally, we demonstrated that SMARCB1 re-expression increased cytoplasmic localization of these mRNAs and that gene encoding these transcripts were bound by SMARCA4 and SMARCC1. In conclusion, this study reveals that the loss of SMARCB1 in rhabdoid tumors has specific consequences on mRNAs translation with potential to unveil new dependencies.

2024-10-31 | GSE268317 | GEO

Absence of SMARCB1 in rhabdoid tumor cells increases sensitivity to translation inhibition and alters translation efficiency of specific mRNAsn (Ribo-Seq)

2024-10-31 | GSE268315 | GEO

Absence of SMARCB1 in rhabdoid tumor cells increases sensitivity to translation inhibition and alters translation efficiency of specific mRNAsn

Project description:Absence of SMARCB1 in rhabdoid tumor cells increases sensitivity to translation inhibition and alters translation efficiency of specific mRNAsn

| PRJNA1116205 | ENA

Absence of SMARCB1 in rhabdoid tumor cells increases sensitivity to translation inhibition and alters translation efficiency of specific mRNAsn (Ribo-Seq)

Project description:Absence of SMARCB1 in rhabdoid tumor cells increases sensitivity to translation inhibition and alters translation efficiency of specific mRNAsn (Ribo-Seq)

| PRJNA1116206 | ENA

Mouse Smarcb1-deficient models recapitulate subtypes of human rhabdoid tumors.

Project description:Rhabdoid Tumors (RT) are highly aggressive tumors that are frequently localized in the central nervous system (CNS) where they are termed atypical teratoid and rhabdoid tumors (ATRT). We generated conditional Smarcb1-deficient mouse model leads to CNS Smarcb1-deficient tumors. We used microarrays to compared gene expression profilings of various human and mouse tumors. Our data demonstrate that the Smarcb1-deficient mouse model recapitulates the diversity of human RT.

2016-01-27 | GSE64019 | GEO

Absence of SMARCB1 in rhabdoid tumor cells increases sensitivity to translation inhibition and alters translation efficiency of specific mRNAsn

Project description:This SuperSeries is composed of the SubSeries listed below.

2024-10-31 | GSE268318 | GEO

Molecular profiling of rhabdoid tumors in a Smarcb1-deficient mouse model

Project description:Germline mutations of the SMARCB1 gene predispose to two distinct tumor syndromes: rhabdoid tumor predisposition syndrome, with malignant pediatric tumors mostly developing in brain and kidney, and familial schwannomatosis, with adulthood benign tumors involving cranial and peripheral nerves. The mechanisms by which SMARCB1 germline mutations predispose to rhabdoid tumors versus schwannomas are still unknown. Here, to understand the origin of these two types of SMARCB1-associated tumors, we generated different tissue- and developmental stage-specific conditional knockout mice carrying Smarcb1 and/or Nf2 deletion. Smarcb1 loss in early neural crest was necessary to initiate tumorigenesis in the cranial nerves and meninges with typical histological features and molecular profiles of human rhabdoid tumors. By inducing Smarcb1 loss at later developmental stage in the Schwann cell lineage, in addition to biallelic Nf2 gene inactivation, we generated the first mouse model developing schwannomas with the same underlying gene mutations found in schwannomatosis patients.

2017-10-31 | GSE94082 | GEO

DNA methylation profiling of SMARCB1 reconstitution in malignant rhabdoid tumor organoids

Project description:We have generated DNA methylation profiles for patient-derived malignant rhabdoid tumor organoids and re-expressed SMARCB1 to assess SMARCB1-dependent changes in DNA methylation

2021-01-13 | GSE161814 | GEO

Transcriptional response to Smarcb1 re-expression in murine derived Smarcb1 deficient p53 null tumors

Project description:SMARCB1 (Snf5/Ini1/Baf47) is a potent tumor suppressor, the loss of which serves as the diagnostic feature in Malignant Rhabdoid Tumors (MRT) and Atypical Teratoid/Rhabdoid Tumors (AT/RT), two highly aggressive forms of pediatric neoplasms. Here, we restore Smarcb1 expression in cells derived from Smarcb1-deficient tumors which developed in Smarcb1-heterozygous p53-/- mice. Profiling Smarcb1 dependent gene expression we find genes which are dependent on Smarcb1 expression to be enriched for ECM and cell adhesion functions. We identify Igfbp7, which is related to the insulin-like growth factor binding proteins family, as a downstream target of Smarcb1 transcriptional activity, and show that re-introduction of Igfbp7 alone can hinder tumor development. Two cancer cell lines, 167 and 365, derived from Smarcb1-deficient tumors which developed in Smarcb1-heterozygous p53-/- mice were re-infected with a retro-viral vector for Smarcb1 re-expression or an empty retro-viral vector as control. Total-RNA was collected 3 days post infection so as to enrich for direct targets of Smarcb1 transcriptionaly regulated genes

2013-12-31 | E-GEOD-46017 | biostudies-arrayexpress

Genome-wide DNA methylation profiling of SCCOHT and SMARCB1-mutated rhabdoid tumours

Project description:Extracranial rhabdoid tumours (ECRT) are an aggressive malignancy of infancy and early childhood. The vast majority of cases demonstrate inactivation of SMARCB1 (ECRT_SMARCB1) but, rarely, ECRT can harbour the alternative inactivation of SMARCA4 (ECRT_SMARCA4) instead of SMARCB1. To explore the place of ECRTSMARCA4 in the "rhabdoid tumour" spectrum, we generated and collected from previous studies genome-wide DNA methylation array data (n = 85) from Atypical/Teratoid Rhabdoid Tumours (ATRT), ECRT_SMARCB1, ECRT_SMARCA4 and small cell carcinomas of the ovary, hypercalcaemic type (SCCOHT) tumours. Using dimensionality reduction and unsupervised clustering approaches, our results demonstrate that ECRT_SMARCA4 display an intermediate DNA methylation profile between SCCOHT and ECRT_SMARCB1.

2021-06-02 | GSE175892 | GEO

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