Abstract 3564: SNAI2 enhances oncogenesis in malignant peripheral nerve sheath tumors
Authors: Jafarah Hilda , Murray Béga , Shern Jack , Zhang Xiyuan 
Published: April 2023

Abstract
Background: MPNSTs are highly aggressive soft tissue sarcomas. Recurrent genetic mutations have been linked to its tumorigenesis, including the loss of functional polycomb repressive complex 2 (PRC2). This results in an altered transcription landscape characterized by the global loss of methylation on histone H3 lysine 27 (H3K27me3) and increased super-enhancer (SE) -associated histone acetylation. We have previously identified SNAI2 as a core SE-driven transcription factor (TF) that is essential for the growth of MPNST. Although SNAI2 is known to be critical for oncogenic processes, including epithelial-to-mesenchymal transition (EMT) and dedifferentiation, its role in maintaining MPNST survival through transcriptomic and epigenetic regulation has not been explored.
Methods: Using CRISPR mediated knockout (KO), we targeted the SNAI2 DNA binding domain and confirmed KO via western blot, followed by in vitro phenotypic characterization, including 2D growth assays, anchorage-independent colony formation assays, and scratch assays. Additionally, an integrative analysis of SNAI2 genomic distribution and the transcriptomic effect of its KO was performed using chromatin immunoprecipitation coupled with DNA sequencing (ChIPseq) and RNA sequencing (RNAseq). Finally, an inducible re-expression system was employed to examine the effects on the chromatin landscape with SNAI2 rescue.
Results: Genetic loss of SNAI2 slowed the growth of MPNST cells by 50% in comparison to the control. In vitro tumorigenic assays revealed that SNAI2 KO diminished the cells’ capacity in invasion but not in anchorage-independent cell growth. Analysis of the RNAseq results revealed that SNAI2 loss upregulated 790 genes and downregulated 1623 genes (log2fold change&gt; 1, p&lt;0.01), indicating a dominant transcriptional activation role. Gene Set Enrichment Analysis of these SNAI2-regulated genes revealed upregulation of hallmark Myc targets (normalized enrichment score (NES)=2.6, FDR=0.0), whilst genes involved in response to alpha interferon proteins were downregulated (NES=-1.87, FDR=0.002). Interestingly, genes defining EMT were upregulated (NES=1.6, FDR=0.006) in cells upon SNAI2 loss, contrasting its known repressive role in this biological process in other systems. Through integrative analysis of the RNAseq and ChIPseq data, we demonstrate SNAI2 binding to promoters of its regulated targets. Downstream targets of interest include CRELD1, a gene involved in cell adhesion, where SNAI2 KO caused loss of promoter binding and gene downregulation (p&lt;0.001).
Conclusion: SNAI2 is an essential SE-driven TF in MPNST cells. Transcriptomic and genomic profiling of SNAI2 through loss- and gain-of-function experiments revealed that it is a critical TF that is involved in key biological processes. Future efforts will focus on designing methods to employ targeted degradation of this essential TF and test preclinical efficacy in treating MPNST.
Citation Format: Hilda Jafarah, Béga Murray, Jack Shern, Xiyuan Zhang. SNAI2 enhances oncogenesis in malignant peripheral nerve sheath tumors. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3564.