The emergence of CRISPR-Cas9 gene-editing technologies and genome-wide CRISPR-Cas9 libraries enables efficient unbiased genetic screening that can accelerate the process of therapeutic discovery for genetic disorders. Here, we demonstrate the utility of a genome-wide CRISPR-Cas9 loss-of-function library to identify therapeutic targets for facioscapulohumeral muscular dystrophy (FSHD), a genetically complex type of muscular dystrophy for which there is currently no treatment. In FSHD, both genetic and epigenetic changes lead to misexpression of DUX4, the FSHD causal gene that encodes the highly cytotoxic DUX4 protein. We performed a genome-wide CRISPR-Cas9 screen to identify genes whose loss-of-function conferred survival when DUX4 was expressed in muscle cells. Genes emerging from our screen illuminated a pathogenic link to the cellular hypoxia response, which was revealed to be the main driver of DUX4-induced cell death. Application of hypoxia signaling inhibitors resulted in increased DUX4 protein turnover and subsequent reduction of the cellular hypoxia response and cell death. In addition, these compounds proved successful in reducing FSHD disease biomarkers in patient myogenic lines, as well as improving structural and functional properties in two zebrafish models of FSHD. Our genome-wide perturbation of pathways affecting DUX4 expression has provided insight into key drivers of DUX4-induced pathogenesis and has identified existing compounds with potential therapeutic benefit for FSHD. Our experimental approach presents an accelerated paradigm toward mechanistic understanding and therapeutic discovery of a complex genetic disease, which may be translatable to other diseases with well-established phenotypic selection assays.

Facioscapulohumeral Muscular Dystrophy (FSHD) is an autosomal dominant neuromuscular disease affecting 1 in 20,000 to 1 in 15,000 individuals and is characterized by progressive weakness in the facial, scapular, humeral, truncal, and lower extremity muscles (Tawil and Van Der Maarel Muscle Nerve 2006). FSHD is associated with the contraction of the D4Z4 microsatellite repeat below a threshold number of repeats (Wijmenga et al., Nat. Genet, 1992), allowing the transcription of the DUX4 gene contained within the last repeat (Snider et al., PLoS Gen, 2010). The disease only develops when DUX4 is expressed from a chromosome with the permissive 4qA allele, which contains a polyadenylation signal (PAS) that stabilizes the DUX4 transcript (Lemmers et al., Science, 2010). We are using CRISPR technology to investigate the possibility that disruption of the PAS in cells derived from FSHD patients could prevent expression of the DUX4 protein and restore the cell to a less affected phenotype. We will then take advantage of the high reprogramming efficiency of FSHD cells and generate iPSC from FSHD muscle cells with the repressed DUX4 allele, and determine if they have a similar phenotype to iPS cells derived from non-affected individuals. Finally, we will use the highly-engraftable iPS cells in xenograft experiments to determine if the DUX4-silenced iPSCs repopulate injured muscle more efficiently than unaltered FSHD-derived iPSC, and evaluate their potential for use as therapeutics.