Therapeutic vulnerabilities of the drug-resistant fungal meningitis pathogen Cryptococcus neoformans

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Abstract
SUMMARY: Treatment options are limited for the priority fungal pathogen Cryptococcus neoformans . We describe CRISPR-insert, a scalable gene inactivation method for global interrogation of drug targets. Genome-wide screens using this methodology combined with machine learning predict 1,297 essential genes under liberal criteria. Unexpectedly absent from this list is FKS1 , encoding the target of echinocandin drugs to which C. neoformans is resistant. Contrary to longstanding literature, targeted deletion shows that FKS1 is not essential. Solid-state NMR reveals that fks1 Δ mutants lack β-1,3-glucan, arguing against compensation by another synthase. We experimentally test essentiality predictions for genes lacking human orthologs, identifying high-priority drug target candidates. To uncover targets for combination therapies, we establish genome-scale quantitative genetic interaction mapping. We use this method to uncover synthetic lethal dependencies of echinocandin resistance determinants, including the druggable calcineurin and Cdc50-Apt1 pathways. CRISPR-insert illuminates therapeutic vulnerabilities of an invasive fungal pathogen.
Funding Information
  • NIH (R01AI100272)

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