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Genome-wide CRISPR-Cas9 knockout screens identify DNMT1 as a druggable dependency in sonic hedgehog medulloblastoma [RNA-seq]

ABSTRACT: Sonic hedgehog subgroup of medulloblastoma (SHH-MB) is characterized by aberrant activation of the SHH signaling pathway. An inhibition of the positive SHH regulator Smoothened (SMO) has demonstrated promising clinical efficacy. Yet, primary and acquired resistance to SMO inhibitors limit their efficacy. An understanding of underlying molecular mechanisms of resistance to therapy is warranted to bridge this unmet need. Here, we make use of genome-wide CRISPR-Cas9 knockout screens in SMB21 and DAOY cells, in order to unravel genetic dependencies and drug-related genetic interactors that could serve as alternative therapeutic targets for SHH-MB. Our screens reinforce SMB21 cells as a faithful model system for SHH-MB, as opposed to DAOY cells, and identify members of the epigenetic machinery including DNA methyltransferase 1 (DNMT1) as druggable targets in SHH-dependent tumors. We show that Dnmt1 plays a crucial role in normal murine cerebellar development and is required for SHH-MB growth in vivo. Additionally, DNMT1 pharmacological inhibition alone and in combination with SMO inhibition effectively inhibits tumor growth in murine and human SHH-MB cell models and prolongs survival of SHH-MB mouse models by inhibiting SHH signaling output downstream of SMO. In conclusion, our data highlight the potential of inhibiting epigenetic regulators as a novel therapeutic avenue in SMO-inhibitor sensitive as well as resistant SHH-MBs.

ORGANISM(S): Mus musculus

PROVIDER: GSE269462 | GEO | 2024/06/13

REPOSITORIES: GEO

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Project description:Purpose: Medulloblastoma (MB) is the most common malignant brain tumor in children. About 30% MB isreleated to the abnormally activation of the Hedgehog signaling pathway. Smoothened(SMO) is a G protein-coupled receptor that interacts with the patched protein(PTCH) to transduce the hedgehog's proteins signal.This study analyzed the differential expression gene and obtained GO(Gene Ontology) terms and KEGG of these genes after SMO knockdown in Daoy medulloblastoma cells by transcriptome profiling (RNA-seq) .This study aims to provide the basis for subsequent study on medulloblastoma's driven genes. Methods: Cultured Daoy medulloblastoma cells were transfected with 50nM SMO small interference RNA(siRNA) or negtive control siRNA using Lipofectamine 2000 for 48 hours, and transfection efficiency was analyzed by reverse transcription polymerase chain reaction (qRT–PCR) and Western Blot. Then the transriptome profiles of siNC and siSMO cell were sequenced with high-throughput sequencing technology. Results: Using a standardized data analysis workflow, we mapped about 45 million sequence reads per sample. With comparative analysis of transcriptome of siNC and siSMO samples that each repeated three times, 216 differentially expressed genes (DEGs) were found, including 79 up-regulated and 137 down-regulated genes.Genes with q≤0.05 and |log2_ratio|≥1 are identified as DEGs. The ratio that sequence data mapping into reference genome is above 97%. Gene sequences were aligned to public datases such as GO, KEGG(kyoto Encyclopedia of Genes and Genomes) and STRING (Protein-Protein Interaction Networks Functional Enrichment Analysis). 47 genes were matched to GO database. 158 genes were up regulate in 114 pathways and 306 genes were down regulate in 179 pathways in KEGG database. Conclusions: In cancer research, cancer cell lines are important for examining and manipulating molecular and cellular process. DAOY cell line is grouped in the TP53 mutant SHH subgroup MB.Our study represents the first detailed analysis of SMO transcriptomes in Daoy medulloblastoma cells, with biologic replicates, generated by RNA-seq technology. We conclude that knockdown of SMO could participate in transcriptional regulation of many genes and lead to changes in many signaling pathways, witch provises important basis for further investigation of molecular mechanism in SHH subtype MS.

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Genome-wide CRISPR-Cas9 knockout screens identify DNMT1 as a druggable dependency in sonic hedgehog medulloblastoma [RNA-seq]

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