Abstract

Malignant peripheral nerve sheath tumors (MPNSTs) are aggressive sarcomas that arise sporadically or in the setting of neurofibromatosis type 1 (NF1). Although benign plexiform neurofibromas (PNs) are common in NF1, only a subset undergo malignant transformation, and the molecular events that define high-risk progression remain incompletely understood. A major axis of biological heterogeneity in MPNST is loss of Polycomb Repressive Complex 2 (PRC2), commonly detected through loss of H3K27me3 and frequently mediated by alterations in SUZ12 or EED. This dissertation integrates three manuscript-based studies to define genomic resources, tumor-intrinsic vulnerabilities, and immune microenvironmental remodeling in NF1-associated peripheral nerve sheath tumors, with emphasis on PRC2-loss versus PRC2-retained disease. Chapter 1 presents an updated Johns Hopkins NF1 biospecimen repository dataset, including whole-exome and RNA sequencing from NF1-associated peripheral nerve sheath tumors. This resource provides standardized, reusable genomic data from cutaneous neurofibromas, plexiform neurofibromas, atypical neurofibromatous neoplasms of uncertain biologic potential, diffuse neurofibromas, and MPNSTs. The dataset validates expected NF1-associated genomic patterns and supports broad reanalysis by the NF1 research community. Chapter 2 investigates the chromatin and signaling consequences of PRC2 deficiency in MPNST. Integrative epigenomic, transcriptomic, and proteomic profiling demonstrates that PRC2 loss produces coordinated depletion of H3K27me3 and gain of active chromatin features, activating a fetal-like growth program centered on IGF2 and IGF2BP family members. Functional experiments show that PRC2-deficient MPNST cells are selectively dependent on IGF2 signaling, nominating the IGF2-IGF2BP axis as a therapeutic vulnerability. Chapter 3 integrates whole-exome sequencing, bulk and single-cell transcriptomics, quantitative proteomics, histone post-translational modification profiling, and imaging mass cytometry in paired PN and MPNST specimens. These analyses reveal that PRC2-loss tumors follow distinct evolutionary routes and establish an immunosuppressive spatial ecosystem marked by M2 macrophages, regulatory T cells, reduced cytotoxic T-cell access, and attenuated interferon and antigen-presentation programs. In vivo validation in immunocompetent syngeneic models demonstrates selective suppression of SUZ12KO tumor growth by the CSF1R inhibitor pexidartinib, supporting macrophage-directed therapeutic strategies for PRC2-deficient MPNST. Together, these studies support a model in which PRC2 loss is coupled to aggressive tumor evolution, chromatin-state remodeling, fetal growth factor dependency, and spatially organized immune suppression. This dissertation provides a framework for PRC2-stratified risk assessment and for rational therapeutic strategies that combine tumor-intrinsic targeting with approaches designed to remodel suppressive myeloid niches and restore effective antitumor immunity. Introduction Neurofibromatosis type 1 (NF1) is a common autosomal-dominant tumor predisposition syndrome caused by pathogenic alterations in NF1, which encodes neurofibromin, a negative regulator of RAS signaling. Loss of neurofibromin promotes activation of RAS/MAPK and PI3K pathway signaling and establishes a permissive context for development of peripheral nerve sheath tumors. In individuals with NF1, benign plexiform neurofibromas can arise early in life and may progress through atypical neurofibromatous neoplasms of uncertain biologic potential to malignant peripheral nerve sheath tumors. MPNSTs are highly aggressive sarcomas with frequent recurrence, metastatic spread, limited systemic treatment options, and poor long-term survival. The malignant transformation of PN to MPNST is a multistep process. Biallelic NF1 inactivation is necessary for tumor initiation but is not sufficient for malignant progression. Additional genetic events affecting cell-cycle control, chromosomal stability, DNA damage response, and chromatin regulation accumulate during transformation. Recurrent alterations in CDKN2A/B, TP53, PRC2 components, and copy-number or structural events collectively shape the genomic landscape of NF1-associated MPNST. Because individual tumors often follow distinct evolutionary routes, paired precursor and malignant specimens are particularly valuable for resolving when key alterations emerge and how they influence subsequent tumor behavior. PRC2 loss is one of the most clinically and biologically important events in MPNST. PRC2, composed of core members including SUZ12, EED, and EZH2, catalyzes trimethylation of histone H3 lysine 27 (H3K27me3), a repressive chromatin modification that maintains lineage identity and constrains inappropriate enhancer activation. Loss of PRC2 function results in global H3K27me3 depletion and broad transcriptional reprogramming. In clinical pathology, loss of H3K27me3 immunostaining is used as a practical marker of PRC2-deficient MPNST, and PRC2-deficient tumors are often associated with more aggressive behavior. However, PRC2 loss should not be viewed only as a diagnostic feature; it represents an epigenetic state that can reshape tumor evolution, growth factor signaling, extracellular matrix remodeling, and immune interactions. A central challenge is identifying downstream vulnerabilities created by PRC2 loss. Because loss-of-function events in chromatin regulators are difficult to target directly, therapeutic development requires defining pathways that become activated or essential in the PRC2-deficient state. One such pathway is the insulin-like growth factor network. IGF2 is a fetal growth factor whose expression is normally tightly controlled by imprinting and epigenetic regulation. Reactivation of IGF2 and its post-transcriptional regulators can promote proliferation, survival, and developmental plasticity in cancer. Integrating chromatin profiling with transcriptomic and proteomic measurements provides a powerful strategy for determining whether PRC2 loss directly derepresses such fetal growth programs in MPNST. The tumor immune microenvironment is equally important. MPNSTs are not composed only of malignant Schwann-lineage cells; they contain macrophages, T cells, regulatory T cells, stromal cells, endothelial cells, extracellular matrix, and cytokine networks that together shape tumor growth and treatment response. A cold or immunosuppressive microenvironment may limit the effectiveness of immunotherapy and allow tumor cells to evade cytotoxic killing. In PRC2-loss tumors, emerging evidence supports reduced cytotoxic T-cell infiltration, attenuation of interferon and antigen-presentation programs, and enrichment of immunosuppressive macrophage and regulatory T-cell states. Spatial profiling further suggests that immune exclusion can be organized anatomically, with macrophage- and stromal-rich niches forming barriers that prevent cytotoxic lymphocytes from reaching malignant cells. This dissertation brings together three complementary studies. The first chapter presents an updated public genomic resource for NF1-associated peripheral nerve sheath tumors, providing a foundation for community-wide reanalysis and validation. The second chapter defines how PRC2 deficiency remodels chromatin and activates the IGF2-IGF2BP growth factor axis in MPNST. The third chapter integrates genomic, transcriptomic, proteomic, histone modification, single-cell, spatial, and in vivo therapeutic analyses to compare PRC2-loss versus PRC2-retained PN-to-MPNST progression. Across these chapters, the unifying hypothesis is that PRC2 loss coordinates aggressive tumor evolution with tumor-intrinsic signaling vulnerabilities and spatially organized immune suppression.

Committee Chair

Angela Hirbe

Degree

Doctor of Philosophy (PhD)

Author's Department

Biology & Biomedical Sciences (Human & Statistical Genetics)

Author's School

Graduate School of Arts and Sciences

Document Type

Dissertation

Date of Award

8-17-2026

Language

English (en)

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