# RNAi-dependent epimutation roles in antimicrobial drug resistance and pathogenesis

> **NIH NIH R01** · DUKE UNIVERSITY · 2024 · $726,611

## Abstract

Abstract. This proposal focuses on the human fungal pathogenic Mucor species complex, a group of related
pathogens that cause devastating infections that are difficult to treat, with limited drug treatment options, and
requiring surgical debridement in some patients. Over the past decade, we and others have advanced genomics,
genetics, and animal models for this understudied group of microbial pathogens. We discovered the protein
phosphatase calcineurin controls the dimorphic transition from yeast to hyphae required for Mucor pathogenesis,
and through studies of FK506-resistant isolates discovered a novel mechanism of antimicrobial drug resistance.
 In previously published and preliminary studies, significant advances were achieved through our discovery
of a novel mechanism of antifungal drug resistance called epimutation, whereby the RNAi pathway is activated
and silences drug target genes. This pathway confers transient, unstable drug resistance, and resistant isolates
rapidly revert to drug sensitivity in the absence of drug. Through genetic and molecular studies, we defined
RNAi components required for epimutation, those that are dispensable for epimutation, and a novel category
that inhibits formation of epimutations. The discovery of antimicrobial drug resistance mediated via epimutations
has been generalized: 1) showing epimutation occurs in two different pathogenic Mucor species, 2) defining an
alternative RNAi pathway controlling epimutation frequency and stability, 3) identifying epimutations in additional
genes causing resistance to antifungal agents, and 4) documenting that epimutations persist during animal
infection or arise after animal passage. These insights set the stage for studies proposed here to further define
mechanisms of epimutation, and elucidate the impact of epimutations on microbial pathogen interactions with
the host. In the current proposal, we hypothesize epimutation is a general process that operates across many
eukaryotic microbial pathogens, and acts as a major force in antimicrobial drug resistance that controls target
genes involved in drug action, genome stability, and pathogenesis of eukaryotic microbial pathogens.
 Our studies will reveal unique facets of RNAi that lead to epimutations, which mediate antimicrobial drug
resistance in ubiquitous fungal pathogens of humans. Aim 1 will 1) elucidate molecular mechanisms of
epimutation and targets, including genes involved in drug resistance (including clinically used antifungal drugs)
and transposable elements, and their impact on genome stability, 2) define conditions, including stress, sexual
reproduction, and infection, that may drive the emergence of epimutations, and 3) establish the generalizability
of these findings to other pathogenic fungal species. Aim 2 will define the impact of epimutation on antimicrobial
drug resistance and pathogenicity in microbe interactions with immune cells, the blood-brain barrier, organoids,
and whole-animal models. These st...

## Key facts

- **NIH application ID:** 10883738
- **Project number:** 5R01AI170543-03
- **Recipient organization:** DUKE UNIVERSITY
- **Principal Investigator:** JOSEPH HEITMAN
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $726,611
- **Award type:** 5
- **Project period:** 2022-07-01 → 2027-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10883738

## Citation

> US National Institutes of Health, RePORTER application 10883738, RNAi-dependent epimutation roles in antimicrobial drug resistance and pathogenesis (5R01AI170543-03). Retrieved via AI Analytics 2026-06-23 from https://api.ai-analytics.org/grant/nih/10883738. Licensed CC0.

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