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SMARCB1 loss interacts with neuronal differentiation state to block maturation in an organoid model

ABSTRACT: SMARCB1 loss interacts with neuronal differentiation state to block maturation in an organoid model

PROVIDER: PRJNA661565 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12594375.fastq.gz	Fastqsanger.gz
	SRR12594376.fastq.gz	Fastqsanger.gz
	SRR12594377.fastq.gz	Fastqsanger.gz
	SRR12594378.fastq.gz	Fastqsanger.gz
	SRR12594379.fastq.gz	Fastqsanger.gz

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SMARCB1 loss interacts with neuronal differentiation state to block maturation and impact cell stability

Project description:SMARCB1 loss interacts with neuronal differentiation state to block maturation and impact cell stability

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SMARCB1 loss interacts with neuronal differentiation state to block maturation in an organoid model

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SMARCB1 loss interacts with neuronal differentiation state to block maturation and impact cell stability

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SMARCB1 loss interacts with neuronal differentiation state to block maturation and impact cell stability.

Project description:Atypical teratoid rhabdoid tumors (ATRTs) are challenging pediatric brain cancers that are predominantly associated with inactivation of the gene SMARCB1, a conserved subunit of the chromatin remodeling BAF complex, which has known contributions to developmental processes. To identify potential interactions between SMARCB1 loss and the process of neural development, we introduced an inducible SMARCB1 loss-of-function system into human induced pluripotent stem cells (iPSCs) that were subjected to either directed neuronal differentiation or differentiation into cerebral organoids. Using this system, we identified substantial differences in the downstream effects of SMARCB1 loss depending on differentiation state and identified an interaction between SMARCB1 loss and neural differentiation pressure that causes a resistance to terminal differentiation and a defect in maintenance of a normal cell state. Our results provide insight into how SMARCB1 loss might interact with neural development in the process of ATRT tumorigenesis.

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Phosphoproteomic response underpinning cardiac organoid maturation by electronic pacing and directed maturation media

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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

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SIRT2 is a regulator of the differentiation block driven by SMARCB1 loss in ATRT.

Project description:SIRT2 is a regulator of the differentiation block driven by SMARCB1 loss in ATRT.

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Gene expression analysis of human haploid cells (HAP1) depleted of SMARCB1 and SMARCA4

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SIRT2 is a regulator of the differentiation block driven by SMARCB1 loss in ATRT. [CUT&Run]

Project description:Atypical teratoid rhabdoid tumor (ATRT) is a highly aggressive brain tumor of childhood with a poor overall survival. The salient molecular feature of ATRT is the loss of SMARCB1 which results in epigenetic dysregulation of the genome. SMARCB1 loss affects lineage commitment and differentiation by controlling gene expression. We hypothesized that additional epigenetic factors co-operate with SMARCB1 loss to control cell self-renewal and drive ATRT. We identified SIRT2 as a primary dependency in ATRT. Using a combination of RNA-seq, CUT&RUN and single RNA sequencing in model systems ATRT, we observed genome-wide reorganization of active chromatin and significantly changes in genes expression in ATRT cells with genetic (with shRNA) or chemical (with Tenovin or Thiomyristoyl (TM)) SIRT2 deactivation. Single-cell RNA transcriptome analysis of xenograft tumors revealed the elimination of tumor cells expressing stem cell genes and expansion of tumor cells expressing differentiated genes in vivo. Furthermore, SIRT2 inhibition induced apoptosis, decreased tumor growth and prolonged survival in orthotopic xenograft models. In summary we demonstrated that SIRT2 inhibition is a molecular vulnerability in SMARCB1-deleted tumors with therapeutic potential.

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