# Cryptococcus genomic resources

> **NIH NIH R01** · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · 2022 · $763,656

## Abstract

Effective diagnosis and treatment of invasive fungal infections is a major unmet clinical challenge. Annotated
genomic sequences of the major fungal pathogens create an opportunity to revolutionize medical mycology
through the application of systematic approaches. To be maximally useful, genome sequences must be coupled
with genome-wide biological resources. The availability of genome-wide knockout and tagged gene collections
as well as a global genetic interaction map have been instrumental in catalyzing research progress in the model
yeast Saccharomyces cerevisiae. The generation of analogous resources in pathogenic fungi creates
experimental tools enabling comprehensive approaches to elucidating the basis of fungal virulence in the
mammalian host and to develop drugs. Cryptococcus neoformans is an encapsulated budding yeast that causes
fungal meningitis, resulting in ~200,000 fatalities each year. C. neoformans has haploid genetics, homologous
recombination, and excellent animal models of disease. In the last period, we used biolistic transformation and
long homology targeting constructs to complete a gene knockout collection, performed extensive quality control
work, developed quantitative methods for screening the library in pools, and performed pooled screens both in
mice and in vitro. We have made the strains available without restriction to the community via the Fungal Genetic
Stock Center (FGSC). This resource has already been used in over 30 publications. To accelerate genome
modification, we developed the first short-homology CRISPR-Cas9 methods for C. neoformans. We have also
created an effective combined localization and purification tag. Preliminary work demonstrates that these
methods can be deployed at scale to enable construction of a tagged strain collection. In addition, we have
devised a novel method that enables pooled CRISPR-Cas9 screens in C. neoformans. Capitalizing on these
technical advances, we will 1) complete the Cryptococcus whole-genome tag collection including production of
an image resource, and 2) construct a first-generation genetic interaction map focused on virulence
determinants. Accomplishment of the first aim will enable the cell biological and/or biochemical investigations of
any protein. Completion of the second aim will deorphanize large fraction genes through membership in clusters
of genes with known functions while defining new modules/pathways. This information will be integrated into the
searchable and web accessible VEuPathDB database. Together these new genomic resources will accelerate
the ability of the research community to understand and develop therapies against the most common cause of
human fungal meningitis.

## Key facts

- **NIH application ID:** 10444326
- **Project number:** 2R01AI100272-11
- **Recipient organization:** UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
- **Principal Investigator:** Hiten D Madhani
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $763,656
- **Award type:** 2
- **Project period:** 2012-06-01 → 2027-05-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10444326

## Citation

> US National Institutes of Health, RePORTER application 10444326, Cryptococcus genomic resources (2R01AI100272-11). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10444326. Licensed CC0.

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