# Nominating vulnerabilities in fusion oncoprotein-driven rhabdomyosarcoma

> **NIH NIH R21** · DUKE UNIVERSITY · 2024 · $182,090

## Abstract

Project Summary
This proposal focuses on the fact that 400 children and young adults develop rhabdomyosarcoma (RMS) each
year, and the vast majority of those with high-risk disease will not be long term, disease-free survivors. One of
the major drivers of high-risk disease is the presence of PAX3-FOXO1 fusion protein. In what is commonly
referred to as fusion-positive (FP) RMS, next generation DNA and RNA sequencing tools and molecular and cell
biological approaches have yet to uncover targetable cancer drivers. As such, the treatment for these children
and young adults has not fundamentally changed for several decades!
Major challenges to unraveling FP-RMS and the biology of PAX3-FOXO1 are at least two-fold: First, we know
much about the biology of the PAX3-FOXO1 fusion protein, including the fact that cooperating genetic or
epigenetic changes are needed for it to drive RMS formation and progression. But our knowledge is not
sophisticated enough to focus on the subset of cooperating genetic/epigenetic changes that can be leveraged
as therapeutic vulnerabilities. Second, though some elegant, experimental models exist for FP-RMS, pure
isogenic systems in which PAX3-FOXO1 expression can be quickly and completely turned “on” and “off” are not
available. We are convinced that solving both of these challenges will provide a foundational step toward
identifying actionable targets that are driven by the oncogenic fusion protein in FP-RMS.
Over the next two years, we can accomplish this by completing two complementary but independent aims. First,
we apply an innovative computational pipeline to nominate oncogenic drivers and tumor suppressors based on
genetic and epigenetic changes in FP-RMS, and functionally validate them in a CRISPR/Cas9-based “mini-pool”
assay using both FP and fusion-negative RMS models. Second, we will develop and validate a new degron-
based system in which human PAX3-FOXO1 can be controlled in a dynamic and reversible fashion in native
RMS cells and PDX models. Among other things, this system created in Aim 2 will be utilized to identify how the
key drivers and suppressors from Aim 1 are controlled by PAX3-FOXO1. Our success will lay the foundation for
future, hypothesis-directed studies of FP-RMS, generate sharable data and tools for the scientific community,
and illustrate a general approach to tackling other translocation-driven cancers that pose challenges similar to
FP-RMS.

## Key facts

- **NIH application ID:** 11200239
- **Project number:** 7R21CA273282-03
- **Recipient organization:** DUKE UNIVERSITY
- **Principal Investigator:** STEPHEN X SKAPEK
- **Activity code:** R21 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $182,090
- **Award type:** 7
- **Project period:** 2023-05-16 → 2026-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/11200239

## Citation

> US National Institutes of Health, RePORTER application 11200239, Nominating vulnerabilities in fusion oncoprotein-driven rhabdomyosarcoma (7R21CA273282-03). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/11200239. Licensed CC0.

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