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Depmap – A Cancer Dependency Map to systematically identify genetic and pharmacologic dependencies and the biomarkers that predict them.
Cancer Dependency Map
The mutations that cause cancer cells to grow also confer specific vulnerabilities that normal cells lack. Some of these acquired alterations represent compelling therapeutic targets. The challenge is that, for the overwhelming majority of cancers, we do not fully understand the relationship between the genetic alterations of cancer and the dependencies they cause. To solve this problem, we are creating a “cancer dependency map” by systematically identifying genetic dependencies and small molecule sensitivities and discovering the biomarkers that predict them.
DepMap scientists are profiling hundreds of cancer cell line models for genomic information and sensitivity to genetic and small molecule perturbations. By triangulating information from these and other large-scale datasets, the hope is to define a landscape of genetic targets for therapeutic development, identify patients that who respond to these therapies, and develop a better understanding of the vulnerabilities of cancer.
The DepMap project at the Broad Institute is part of a strategic collaboration with theWellcome Sanger Institute (Hinxton, UK). By leveraging the expertise and infrastructure available at both organisations, we aim to more rapidly deliver a high-quality DepMap. We anticipate that this foundational dataset will catalyse a new wave of precision cancer medicines.
Using Excel is not recommended for analyzing your CRISPR screen data. I recommend to instead using CRISPRAnalyzer (http://crispr-analyzer.dkfz.de/). However, using Excel could be an easy way to get an overview of the result as the video hopefully shows.
CRISPR RNAs trigger innate immune responses in human cells.
Kim S, Koo T, Jee HG, Cho HY, Lee G, Lim DG, Shin HS, Kim JS.
Genome Res. 2018 Feb 22. doi: 10.1101/gr.231936.117. [Epub ahead of print]
Here, we report that CRISPR guide RNAs (gRNAs) with a 5′-triphosphate group (5′-ppp gRNAs) produced via in vitro transcription triggerRNA-sensing innate immune responses in human and murine cells, leading to cytotoxicity. 5′-ppp gRNAs in the cytosol are recognized by DDX58, which in turn activates type I interferon responses, causing up to ∼80% cell death. We show that the triphosphate group can be removed by a phosphatase in vitro and that the resulting 5′-hydroxyl gRNAs in complex with Cas9 or Cpf1 avoid innate immune responses and can achieve targeted mutagenesis at a frequency of 95% in primary human CD4+ T cells. These results are in line with previous findings that chemically synthesized sgRNAs with a 5′-hydroxyl group are much more efficient than in vitro-transcribed (IVT) sgRNAs in human and other mammalian cells. The phosphatase treatment of IVT sgRNAs is a cost-effective method for making highly active sgRNAs, avoiding innate immune responses in human cells.
I just started to read this book: