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CRISPR/Cas9 genome-wide screen and transcriptome profiling in a MYC-conditional HCC model

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Mus musculus

PROVIDER: GSE205132 | GEO | 2023/10/30

REPOSITORIES: GEO

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CRISPR/Cas9 genome-wide screen and transcriptome profiling in a MYC-conditional HCC model [CRISPR]

Project description:The MYC oncogene is often dysregulated in human cancer, including hepatocellular carcinoma (HCC). However, MYC is considered undruggable to date. Here, we comprehensively identify genes essential for the survival of MYC-high but not MYC-low cells by performing a CRISPR/Cas9 genome-wide screen in a MYC-conditional HCC model. Our screen identifies novel MYC-synthetic lethal interactions, as well as most previously identified MYC-synthetic lethal genes. In particular, we found genes involved in nuclear to cytoplasmic transport to be MYC-synthetic lethal in HCC, and we show that many of these genes are transcriptionally upregulated in MYC-high murine HCC.

2023-10-30 | GSE205131 | GEO

CRISPR/Cas9 genome-wide screen and transcriptome profiling in a MYC-conditional HCC model [RNA-seq]

2023-10-30 | GSE205130 | GEO

CRISPR/Cas9 genome-wide screen and transcriptome profiling in a MYC-conditional HCC model [EC4 RNA-seq]

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CRISPR/Cas9 genome-wide screen and transcriptome profiling in a MYC-conditional HCC model [CRISPR]

Project description:CRISPR/Cas9 genome-wide screen and transcriptome profiling in a MYC-conditional HCC model [CRISPR]

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CRISPR/Cas9 genome-wide screen and transcriptome profiling in a MYC-conditional HCC model

Project description:CRISPR/Cas9 genome-wide screen and transcriptome profiling in a MYC-conditional HCC model

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CRISPR/Cas9 genome-wide screen and transcriptome profiling in a MYC-conditional HCC model [RNA-seq]

Project description:CRISPR/Cas9 genome-wide screen and transcriptome profiling in a MYC-conditional HCC model [RNA-seq]

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CRISPR/Cas9 genome-wide screen and transcriptome profiling in a MYC-conditional HCC model [EC4 RNA-seq]

Project description:CRISPR/Cas9 genome-wide screen and transcriptome profiling in a MYC-conditional HCC model [EC4 RNA-seq]

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CRISPR/Cas9 screen for genome-wide interrogation of essential MYC-bound E-boxes in cancer cells.

Project description:The transcription factor MYC is a proto-oncogene with a well-documented essential role in the pathogenesis and maintenance of several types of cancer. MYC binds to specific E-box sequences in the genome to regulate gene expression in a cell-type- and developmental-stage-specific manner. To date, a combined analysis of essential MYC-bound E-boxes and their downstream target genes important for growth of different types of cancer is missing. In this study, we designed a CRISPR/Cas9 library to destroy E-box sequences in a genome-wide fashion. In parallel, we used the Brunello library to knock out protein-coding genes. We performed high-throughput screens with these libraries in four MYC-dependent cancer cell lines-K562, ST486, HepG2, and MCF7-which revealed several essential E-boxes and genes. Among them, we pinpointed crucial common and cell-type-specific MYC-regulated genes involved in pathways associated with cancer development. Extensive validation of our approach confirmed that E-box disruption affects MYC binding, target-gene expression, and cell proliferation in vitro as well as tumor growth in vivo. Our unique, well-validated tool opens new possibilities to gain novel insights into MYC-dependent vulnerabilities in cancer cells.

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