Early-Stage Technology Development to Enable Rigorous and Reproducible Fungal Metatranscriptomics in Human Vaginal Samples

About This Grant

PROJECT SUMMARY Fungal diseases cost the U.S. an estimated $11 billion annually, yet the pathogenesis of many fungal diseases remains poorly understood because there is no reliable technology for measuring fungal activity directly in human samples. Sequencing fungal RNA directly from clinical samples is infeasible because fungal RNA accounts for <0.1% of total RNA. This technological limitation constrains understanding of fungal diseases and the development of better diagnostics and treatments for fungal diseases. Vulvovaginal candidiasis (VVC) is one example of how healthcare outcomes would be greatly improved by being able to determine which fungal and human genes and pathways are active during disease vs benign colonization. VVC afflicts ~75% of all women at least once in their lives; half will experience multiple episodes of VVC and 1 in 10 (tens of millions of women) have recurrent VVC (RVVC), a chronic disease defined as three or more episodes annually. VVC has significant negative impacts on a woman’s quality of life and also causes substantial economic burden. Diagnostics that detect vaginal Candida have limited utility because 20–50% of women are colonized by benign vaginal Candida. Diagnostics that can determine unambiguously when Candida is causative of disease are urgently needed. The standard treatments for VVC, fungistatic azoles, are also inadequate; more than half of women relapse within 6 months. The ongoing failures of diagnostics and treatments in VVC are due to scientific knowledge gaps that could be addressed if in vivo Candida gene-expression data could be obtained directly from vaginal samples. This technology-development R21 will create FRAMES (Fungal Ribonucleic Acid Metatranscriptomics via Enrichment and Stabilization), a low-cost (≤$5 per sample) workflow that enriches and stabilizes fungal RNA while retaining human RNA transcripts. By enabling simultaneous RNA-sequencing of fungi and human material from a single vaginal swab, this technology will enable, for the first time, a transcriptome-wide view of gene expression in both Candida and human host during commensalism and infection. Aim 1 will optimize FRAMES in fungi-negative human vaginal swabs by combining differential lysis, RNase treatment, and chemical fixation to achieve ≥ 1,000-fold depletion of host RNA and ≥30% recovery of fungal transcripts. FRAMES will be rigorously validated by digital PCR and RNA-sequencing. Aim 2 will leverage the menstrual cycle (as hormonal shifts correlate with many vaginal diseases) to demonstrate in a pilot cohort of healthy women that FRAMES yields rigorous, interpretable gene expression data. We will then apply FRAMES to a pilot RVVC cohort to identify the first set of fungal and human gene-expression signatures that distinguish benign Candida colonization from active disease. The VVC-associated fungal and human genes identified by FRAMES here (and validated in future, higher-powered studies) can serve as crucial targets for development of better VVC diagnostics and durable treatments. More broadly, FRAMES can be adapted in future to other human health conditions significantly impacted by fungi-human interactions and advance the NIH’s mission to improve public health.