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In vivo CRISPR screens reveal NOTCH regulators suppressing Head and Neck Squamous Cell Carcinoma in mice

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

ORGANISM(S): Mus musculus

PROVIDER: GSE140497 | GEO | 2020/02/04

REPOSITORIES: GEO

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In vivo CRISPR screens reveal NOTCH regulators suppressing Head and Neck Squamous Cell Carcinoma in mice [Cut&Run]

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In vivo CRISPR screens reveal NOTCH regulators suppressing Head and Neck Squamous Cell Carcinoma in mice [RNA-seq]

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In vivo CRISPR screens reveal NOTCH regulators suppressing Head and Neck Squamous Cell Carcinoma in mice

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Genome-wide CRISPR Screens in Primary Human T Cells Reveal Key Regulators of Immune Function.

Project description:Human T cells are central effectors of immunity and cancer immunotherapy. CRISPR-based functional studies in T cells could prioritize novel targets for drug development and improve the design of genetically reprogrammed cell-based therapies. However, large-scale CRISPR screens have been challenging in primary human cells. We developed a new method, single guide RNA (sgRNA) lentiviral infection with Cas9 protein electroporation (SLICE), to identify regulators of stimulation responses in primary human T cells. Genome-wide loss-of-function screens identified essential T cell receptor signaling components and genes that negatively tune proliferation following stimulation. Targeted ablation of individual candidate genes characterized hits and identified perturbations that enhanced cancer cell killing. SLICE coupled with single-cell RNA sequencing (RNA-seq) revealed signature stimulation-response gene programs altered by key genetic perturbations. SLICE genome-wide screening was also adaptable to identify mediators of immunosuppression, revealing genes controlling responses to adenosine signaling. The SLICE platform enables unbiased discovery and characterization of functional gene targets in primary cells.

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Single-cell heterogeneity analysis and CRISPR screens in MIN6 cell line reveal transcriptional regulators of insulin.

Project description:Diabetes mellitus is caused by either insulin resistance or insulin deficiency. The pancreatic β cells are the primary producers of insulin. Large-scale CRISPR screens combined with single-cell RNA sequencing (scRNA-seq) on β cells has identified novel insulin regulators and revealed the presence of a highly complex inner network. Here, we performed pooled CRISPR delivery with single-cell transcriptome analysis on the MIN6 cell line, a pancreatic β-cell line. We have presented the scRNA-seq readout and demonstrated that the MIN6 cell line might develop genetic heterogeneity with increasing passage number based on GO and KEGG pathway analysis. Both computational and biological analyses revealed that the function of MIN6 cell lines could be divided into five clusters, including endocrine cells, basal cells, epithelial cells, and neuroendocrine cells. The fifth cluster was different from the other four clusters due to the differentially expressed insulin transcription and was called the lncRNA-enriched cluster. The experiments also confirmed that uncharacterized lncRNAs GM26917 and Cenpw were associated with insulin transcription. This study provides information that can be used to systematically characterize insulin regulator genes and other genes that control protein folding and vesicle trafficking.

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