Applying genome-wide CRISPR screens for therapeutic discovery in FSHD

The emergence of CRISPR gene-editing technologies and genome-wide CRISPR libraries enables a new mechanism to efficiently perform unbiased genetic screens that can accelerate the process of therapeutic discovery for genetic disorders. This represents a significant leap forward from the extensive studies of genetic and biochemical interactions typically required to understand disease pathogenesis and development of targeted therapy. In this study, we demonstrate the utility of a genome-wide CRISPR loss-of-function library to identify therapeutic targets for facioscapulohumeral muscular dystrophy (FSHD), a genetically complex subtype of muscular dystrophy for which there is currently no treatment available. In FSHD, both genetic and epigenetic changes can lead to misexpression of DUX4, the FSHD causal gene that encodes the highly cytotoxic DUX4 protein. We performed a genome-wide CRISPR screen to identify genes whose loss-of-function conferred survival when DUX4 was expressed, thus reducing the pathogenic impact of the genetic defect. Emerging genes from our screen illuminated 'druggable' pathways that can be targeted with small molecule inhibitors. Treatment with PI3K/Akt/mTOR signaling inhibitors resulted in reduced DUX4 protein expression and a reduction of FSHD disease biomarkers in patient myogenic lines, as well as improved structural and functional properties of a zebrafish model of FSHD. Our genome-wide perturbation of pathways affecting DUX4 expression has empowered us to rapidly identify existing compounds with potential therapeutic benefit for FSHD. Thus, the experimental pipeline described in this paper presents an accelerated paradigm towards therapeutic discovery and is translatable to other genetic diseases with well-established phenotypic selection assays. Overall design: Identifying genes and pathways that rescue DUX4 induced toxicity in myoblast