Therapeutic vulnerabilities of the drug-resistant fungal meningitis pathogen Cryptococcus neoformans
- 1Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
Abstract
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{triangleup} mutants lack {beta}-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.
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BibTeX
@misc{huang2026therapeutic,
title = {{Therapeutic vulnerabilities of the drug-resistant fungal meningitis pathogen Cryptococcus neoformans}},
author = {M. Y. Huang and P. Hecht and K. Cesar and M. Ciranni and A. L. Wei and M. J. Boucher and S. L. Briner and L. Lortal and V. Nayak and A. Ankur and T. Wang and T. L. Doering and V. P. Pastore and H. D. Madhani},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.31.763343},
url = {https://www.biorxiv.org/content/10.64898/2026.10.31.763343v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - Therapeutic vulnerabilities of the drug-resistant fungal meningitis pathogen Cryptococcus neoformans
AU - M. Y. Huang
AU - P. Hecht
AU - K. Cesar
AU - M. Ciranni
AU - A. L. Wei
AU - M. J. Boucher
AU - S. L. Briner
AU - L. Lortal
AU - V. Nayak
AU - A. Ankur
AU - T. Wang
AU - T. L. Doering
AU - V. P. Pastore
AU - H. D. Madhani
PY - 2026
DA - 2026/10/31
PB - bioRxiv
DO - 10.64898/2026.10.31.763343
UR - https://www.biorxiv.org/content/10.64898/2026.10.31.763343v1
AB - 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{triangleup} mutants lack {beta}-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.
ER -