Prospective Detection and Monitoring of NF1 peripheral nerve sheath tumors using cell-free DNA

Malignant peripheral nerve sheath tumor (MPNST) – the leading cause of death in the most common cancer predisposition syndrome (NF1) worldwide – kills 80% of patients within 5 years. NF1 MPNSTs typically arise from within plexiform neurofibroma (PN) precursor lesions, yet clinicians have no reliable way to track transformation from benign PN to pre-malignant (atypical) PN to MPNST. Although benign PN, atypical PN, and MPNST are radiographically similar, they have unique genomic and epigenomic features. In our published work (Szymanski et al. PLOS Medicine, 2021), we showed that a plasma cell-free DNA copy number approach accurately distinguishes MPNST from benign PN, and facilitated both MPNST detection and disease burden monitoring. Our more recent data (Sundby et al. Clinical Cancer Research, 2024) suggest that fragmentomic features of cell-free DNA including genome-wide fragment size profiles and end motifs could further distinguish atypical PN from benign PN and MPNST. We thus hypothesize that integrative multi-omic approaches to analyzing cell-free DNA will revolutionize our ability to detect atypical PN with high malignant potential early, and facilitate ultra-sensitive therapeutic monitoring of MPNST including minimal residual disease (MRD) detection and dynamic clonal evolution analysis. To address this hypothesis, we will 1) Determine whether the trajectory of benign PN, atypical PN, and MPNST can be discriminated using an integrative genome-wide cell-free DNA epigenomic approach; 2) Determine whether MRD can be detected after surgery for localized MPNST using an optimized cell-free DNA size-selected copy number approach; and 3) Determine if clonal and phenotypic evolution of metastatic MPNST treated with MEK/MDM2 inhibition can be monitored using integrative methylation sequencing and targeted analysis of resistance mechanisms in cell-free DNA. We will also explore whether methylation levels underlie cell-free DNA fragment size differences between NF1 disease states. By performing these aims, we will lay the foundation for future clinical trials where plasma cell-free DNA genomics, epigenomics and fragmentomics form the basis for early detection and monitoring of the deadliest malignancy associated with the most common cancer predisposition syndrome worldwide. Project Number: 1U01CA299909-01A1 | Fiscal Year: 2026 | NIH Institute/Center: National Cancer Institute (NCI) | Principal Investigator: Aadel Chaudhuri (+1 co-PI) | Institution: MAYO CLINIC ROCHESTER, ROCHESTER, MN | Award Amount: $688,661 | Activity Code: U01 | Study Section: Molecular Cancer Diagnosis and Classification Study Section[MCDC] View on NIH RePORTER: https://reporter.nih.gov/project-details/11305093