NIH grant: Echinocandin Cross-resistance and Hetero-resistance (1R21AI199117-01)

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NIH grant 1R21AI199117-01: Echinocandin Cross-resistance and Hetero-resistance
Institute: {'code': 'AI', 'abbreviation': 'NIAID', 'name': 'National Institute of Allergy and Infectious Diseases', 'admin_org_id': '12500003', 'admin_funding_url': ''}. PI: KYLE W CUNNINGHAM. Award: $412324.
Start: 2026-06-25T00:00:00.
Summary
Echinocandins are an important class of antifungals used to treat life-threatening fungal infections such as
candidemia and invasive candidiasis. Though usually effective, mortality still ranges from 20% to 40% largely
due to mutations that arise within the drug targets (encoded by FKS genes) that cause resistance. Mutations in
the hotspot-1 region of FKS genes generally confer cross-resistance (CR) to all echinocandins and are
associated with poor clinical outcomes. This project investigates the question of whether echinocandin
susceptibility can be restored to CR mutants by targeting other gene products. Such genes will be identified by
performing the genome-wide Tn-seq screens in two different CR derivatives of the yeast Candida glabrata, a
common opportunistic pathogen. Preliminary Tn-seq screens identified dozens of candidate genes and several
known inhibitors that will be evaluated judiciously for their ability to mitigate CR to echinocandins.
Surprisingly, super-cross-resistance (super-CR) was conferred in both the FKS1F625∆ and FKS2F659∆ derivatives
by disrupting a small number of genes with transposons, suggesting that endogenous inhibitors of the FKS
genes were lost. The strongest inhibitor of FKS1F625∆ was FKS2 and the strongest inhibitor of FKS2F659∆ was
FKS1, which confirms earlier reports of mutual antagonism between the FKS gene products. Similar super-CR
derivatives of C. glabrata and C. albicans have been recovered previously from echinocandin-treated patients
and from in vitro evolution experiments. To better understand the mutual antagonism mechanism that
prevents super-CR and to determine whether other genes and their inhibitors can mitigate super-CR,
additional Tn-seq screens will be performed. The results will also shed light on the mechanism responsible for
FKS mutual antagonism. In another surprise, only one of the two CR derivatives (FKS2F659∆ mutant) was found
to exhibit heteroresistance (HR) to echinocandins while the other (FKS1F625∆ mutant) did not. HR occurs when
the majority of cells in a clonal population remain susceptible to echinocandins, and a small minority exhibit
the resistance phenotype. Though HR contributes to breakthrough infections of C. parapsilosis, the mechanism
that governs phenotypic switching between susceptible and resistant states is not understood. To help
elucidate this mechanism, the Tn-seq experiments described above in C. glabrata will be reanalyzed and
candidate genes will be retested using specific assays of HR in addition to CR. Preliminary results indicate an
FDA approved compound can prevent this type of HR in vitro and potentially can be repurposed to mitigate
HR and CR in patients. This pioneering project may quickly lead to improved clinical outcomes and serve as a
paradigm for researching similar processes in other human pathogens.

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