Abstract 461: Identifying potential immunotherapeutic targets on malignant peripheral nerve sheath tumors via surfaceomic profiling
Authors: Mo George , Zhang Xiyuan , Widemann Brigitte C. , Shern Jack F. 
Published: September 2020

Background: Malignant peripheral nerve sheath tumors (MPNSTs) are aggressive soft tissue sarcomas, with approximately 50% of these tumors arising in patients with neurofibromatosis type I (NF1). Polycomb repressive complex 2 (PRC2) inactivation due to loss of components EED or SUZ12 is thought to drive MPNST formation in NF1 patients and is associated with poor prognosis. PRC2 inactivation leads to histone H3 lysine 27 trimethylation (H3K27me3) loss and de-repression of various genes. These transcription alterations may lead to proteomic changes within the cell and at the cell surface, giving rise to surface expression of molecules not present in normal tissue. With the advent of immune-based therapies, unique, highly expressed surface markers on tumors are prime candidates for targetability. Thus, we use a systematic approach to characterize the surfaceome of MPNSTs to identify potential candidates for immunotherapeutic targeting.

Methods and Results: RNA sequencing data was obtained from 16 MPNST tumor samples and 5 MPNST cell lines. Expression data was compared to a panel of 42 normal tissues to generate a list of significantly differentially expressed genes to minimize potential off-targets (p &lt; 0.01). This gene list was then filtered using a cell surface protein prediction aggregated dataset of 11 annotated databases (genes were included in subsequent analysis if identified as a plasma membrane protein in at least 7 of the databases). A list of 357 genes differentially expressed on the surface of MPNSTs ranked by expression level was generated, with CD63, MMP14, and DAD1 at the top of the ranklist. We further subset this list by using RNA sequencing data obtained from 3 SUZ12-inducible MPNST cell lines. Genes that are downregulated after SUZ12 induction (and thus restored PRC2 functionality) in originally SUZ12-null MPNST cell lines may provide even more specificity as PRC2-loss associated MPNST targets. 27 genes on this list were found to be downregulated after SUZ12 restoration, with GJB2, IL17RD, PROM1, and LGR5 being top hits. Flow cytometry and immunohistochemistry were performed on our genes of interest to assess surface expression. Further validation of the global surfaceome is ongoing with mass spectrometry analysis of MPNST cell surface protein isolates via biotinylation.

Conclusion: We demonstrate here that the MPNST surfaceome can be surveyed at depth for the discovery of new immunotherapeutic targets and that there are unique and differentially expressed surface proteins that warrant further study. A proteogenomic integration of RNA and mass spectrometry datasets will allow us to gain further insight into the cell surface landscape of MPNST.

Citation Format: George Mo, Xiyuan Zhang, Brigitte C. Widemann, Jack F. Shern. Identifying potential immunotherapeutic targets on malignant peripheral nerve sheath tumors via surfaceomic profiling [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 461.