Abstract Background: Neurofibromatosis type 1 (NF1) is a neurogenetic condition characterized by neurocognitive symptoms, cutaneous findings, and a predisposition for benign and malignant tumors including peripheral nerve sheath tumors (PNST). About half of patients with NF1 develop plexiform neurofibromas (pNF), non-malignant tumors that often grow rapidly during childhood and can cause significant deformity, disruption of function, and pain. Some lesions, denoted atypical neurofibromatous neoplasms of uncertain biologic potential (ANNUBP), exhibit atypia, loss of neurofibroma architecture, high cellularity and mitotic activity, as an immediate precursor to malignant transformation. For people with NF1 there is a 10-15% overall lifetime risk of developing the aggressive soft tissue sarcoma malignant peripheral nerve sheath tumors (MPNST). Despite many clinical trials of chemotherapy and targeted agents, there has been little advancement in treatment outcomes and overall patient survival remains poor; therefore, new therapeutic approaches are needed. PNST are made up of transformed Schwann cell precursors, which do not grow and survive in isolation but rather interact with infiltrating immune cells. A deeper understanding of the relationship between the pre-existing immunity and the tumor microenvironment (TME) will help unveil potential for new combinations and adjuvant therapies for patients with PNST. Methods: We have developed a unique Johns Hopkins biospecimen repository of human NF1-associated PNST specimens. We use quantitative and spatial resolution of the geography and nature of tumor infiltrating immune cells in human PNST and have determined the interactions of T cells, myeloid cells, and immunoregulatory molecules, using a combination of multiplex chromogenic, high-dimensional flow cytometry and gene expression profiling studies. We have also analyzed existing transcriptomic datasets from 21 pNF and 34 MPNST cases. Results: RNA sequence analysis revealed an accumulation of immunosuppressive Th2 cells and tumor infiltrating myeloid cells (TIM) in the TME of PNST, which we postulate generates an anti-inflammatory response against tumors. Immunophenotyping of 17 pNF, 8 ANNUBP, and 15 MPNST human specimens confirmed the higher presence of infiltrating myeloid compared to lymphoid cells, with a predominance of CD163+ myeloid cells (TIM) during progression to malignancy. We also detected a significant increase in regulatory T cells and cytotoxic CD8+ T cells in MPNST vs ANNUBP vs pNF and near absence of CD19+ B cells in all tumor types. Multiparameter flow cytometry of single cells suspensions are being studied to further investigate the association of myeloid inflammation leading to the immune evasion of PNST. Conclusions: An immunosuppressive microenvironment characterizes PNST during the process of malignant transformation, generating an immune-excluded phenotype. Leveraging the immune contexture and the mechanisms of immune modulation in PNST will inform interventions to stimulate anti-tumor immunity in this dire disease. Citation Format: Lindy Zhang, Kai Pollard, Ana Calizo, Alexandre Maalouf, Aditya Suru, Jiawan Wang, Jineeta Banerjee, Christine A. Pratilas, Nicolas J. Llosa. Mechanisms of immune escape in NF1-associated peripheral nerve sheath tumors [abstract]. In: Proceedings of the AACR Special Conference: Sarcomas; 2022 May 9-12; Montreal, QC, Canada. Philadelphia (PA): AACR; Clin Cancer Res 2022;28(18_Suppl):Abstract nr A008.
Benign peripheral nerve sheath tumors are the clinical hallmark of Neurofibromatosis Type 1. They account for substantial morbidity and mortality in NF1. Cutaneous (CNF) and plexiform neurofibromas (PNF) share nearly identical histology, but maintain different growth rates and risk of malignant conversion. The reasons for this disparate clinical behavior are not well explained by recent genome or transcriptome profiling studies. We hypothesized that CNFs and PNFs are epigenetically distinct tumor types that exhibit differential signaling due to genome-wide and site-specific methylation events. We interrogated the methylation profiles of 45 CNFs and 17 PNFs from NF1 subjects with the Illumina EPIC 850K methylation array. Based on these profiles, we confirm that CNFs and PNFs are epigenetically distinct tumors with broad differences in higher-order chromatin states and specific methylation events altering genes involved in key biological and cellular processes, such as inflammation, RAS/MAPK signaling, actin cytoskeleton rearrangement, and oxytocin signaling. Based on our identification of two separate DMRs associated with alternative leading exons in MAP2K3, we demonstrate differential RAS/MKK3/p38 signaling between CNFs and PNFs. Epigenetic reinforcement of RAS/MKK/p38 was a defining characteristic of CNFs leading to pro-inflammatory signaling and chromatin conformational changes, whereas PNFs signaled predominantly through RAS/MEK. Tumor size also correlated with specific CpG methylation events. Taken together, these findings confirm that NF1 deficiency influences the epigenetic regulation of RAS signaling fates, accounting for observed differences in CNF and PNF clinical behavior. The extension of these findings is that CNFs may respond differently than PNFs to RAS-targeted therapeutics raising the possibility of targeting p38-mediated inflammation for CNF treatment.
Abstract Benign peripheral nerve sheath tumors are the clinical hallmark of Neurofibromatosis Type 1. They account for substantial morbidity and mortality in NF1. Cutaneous (CNF) and plexiform neurofibromas (PNF) share nearly identical histology but maintain different growth rates and risk of malignant conversion. The reasons for this disparate clinical behavior are not well explained by recent genome or transcriptome profiling studies. We hypothesized that CNFs and PNFs are epigenetically distinct tumor types that exhibit differential signaling due to genome-wide and site-specific methylation events. We interrogated the methylation profiles of 45 CNFs and 17 PNFs from NF1 subjects with the Illumina EPIC 850K methylation array. Based on these profiles, we confirm that CNFs and PNFs are epigenetically distinct tumors with broad differences in higher order chromatin states and specific methylation events altering genes involved in key biological and cellular processes, such as inflammation, RAS/MAPK signaling, actin cytoskeleton rearrangement, and oxytocin signaling. Based on our identification of two separate DMRs associated with alternative leading exons in MAP2K3, we demonstrate differential RAS/MKK3/p38 signaling between CNFs and PNFs. Epigenetic reinforcement of RAS/MKK/p38 was a defining characteristic of CNFs leading to pro-inflammatory signaling and chromatin conformational changes, whereas PNFs signaled predominantly through RAS/MEK. Tumor size also correlated with specific CpG methylation events. Taken together, these findings confirm that NF1 deficiency influences the epigenetic regulation of RAS signaling fates, accounting for observed differences in CNF and PNF clinical behavior. The extension of these findings is that CNFs may respond differently than PNFs to RAS-targeted therapeutics raising the possibility of targeting p38-mediated inflammation for CNF treatment.
<div>Abstract<p>Malignant peripheral nerve sheath tumors often arise in patients with neurofibromatosis type 1 and are among the most treatment-refractory types of sarcoma. Overall survival in patients with relapsed disease remains poor, and thus novel therapeutic approaches are needed. NF1 is essential for negative regulation of RAS activity and is altered in about 90% of malignant peripheral nerve sheath tumors (MPNST). A complex interplay of upstream signaling and parallel RAS-driven pathways characterizes NF1-driven tumorigenesis, and inhibiting more than one RAS effector pathway is therefore necessary. To devise potential combination therapeutic strategies, we identified actionable alterations in signaling that underlie adaptive and acquired resistance to MEK inhibitor (MEKi). Using a series of proteomic, biochemical, and genetic approaches in an <i>in vitro</i> model of MEKi resistance provided a rationale for combination therapies. HGF/MET signaling was elevated in the MEKi-resistant model. HGF overexpression conferred resistance to MEKi in parental cells. Depletion of HGF or MET restored sensitivity of MEKi-resistant cells to MEKi. Finally, a combination of MEK and MET inhibition demonstrated activity in models of MPNST and may therefore be effective in patients with MPNST harboring genetic alterations in <i>NF1</i>.</p>Significance:<p>This study demonstrates that MEKi plus MET inhibitor may delay or prevent a novel mechanism of acquired MEKi resistance, with clinical implications for MPNST patients harboring <i>NF1</i> alterations.</p></div>
