Enhancer reprogramming in PRC2-deficient malignant peripheral nerve sheath tumors induces a targetable de-differentiated state

Abstract

Malignant peripheral nerve sheath tumors (MPNSTs) are soft tissue sarcomas that frequently harbor genetic alterations in polycomb repressor complex 2 (PRC2) components-SUZ12 and EED. Here, we show that PRC2 loss confers a dedifferentiated early neural-crest phenotype which is exclusive to PRC2-mutant MPNSTs and not a feature of neurofibromas. Neural crest phenotype in PRC2 mutant MPNSTs was validated via cross-species comparative analysis using spontaneous and transgenic MPNST models. Systematic chromatin state profiling of the MPNST cells showed extensive epigenomic reprogramming or chromatin states associated with PRC2 loss and identified gains of active enhancer states/super-enhancers on early neural crest regulators in PRC2-mutant conditions around genomic loci that harbored repressed/poised states in PRC2-WT MPNST cells. Consistently, inverse correlation between H3K27me3 loss and H3K27Ac gain was noted in MPNSTs. Epigenetic editing experiments established functional roles for enhancer gains on DLX5-a key regulator of neural crest phenotype. Consistently, blockade of enhancer activity by bromodomain inhibitors specifically suppressed this neural crest phenotype and tumor burden in PRC2-mutant PDXs. Together, these findings reveal accumulation of dedifferentiated neural crest like state in PRC2-mutant MPNSTs that can be targeted by enhancer blockade.

CDX2 expression in malignant peripheral nerve sheath tumour: a potential diagnostic pitfall associated with PRC2 inactivation

“…To confirm that the anti‐CDX2 immunoreactivity observed in MPNSTs with PRC2 inactivation reflects expression of the CDX2 locus itself, we analysed the association between CDX2 expression and PRC2 inactivation in an independent RNA‐sequencing dataset. CDX2 expression was analysed in publicly available RNA‐sequencing data (GSE141439) from 6 PRC2‐mutant MPNST cell lines and 6 PRC2‐intact MPNST cell lines 20 . In all cell lines, the status of PRC2 function was previously confirmed by next‐generation sequencing: SUZ12 mutation was present in 4 cell lines, EED mutation in 1 cell line, and combined SUZ12/EED mutation in 1 cell line.…”

“…Previously published RNA‐sequencing data (GSE141439) from 12 cultured MPNST cell lines (6 PRC2‐mutant, 6 PRC2‐wild‐type) were accessed between 1 October 2021 and 27 December 2021 20 . Ten cell lines were derived from NF1‐associated MPNST (MPNST007, MPNST181, SNF02.2, MPNST4970, ST88, S462, MPNST642, MPNST3813E, T265, SNF96.2); two cell lines were derived from sporadic MPNST (STS26T, MPNST724).…”

“…Ten cell lines were derived from NF1‐associated MPNST (MPNST007, MPNST181, SNF02.2, MPNST4970, ST88, S462, MPNST642, MPNST3813E, T265, SNF96.2); two cell lines were derived from sporadic MPNST (STS26T, MPNST724). It has been reported that T265 was contaminated by ST88 at very early passage, so these cell lines may be clonally related, although they appear to exhibit non‐identical genomic and transcriptomic features at current passage 20,21 . Fisher's exact test was used to assess the association between CDX2 expression and PRC2 inactivation among cases analysed by immunohistochemistry.…”

“…Despite the insight that PRC2 inactivation may influence cellular plasticity in MPNST, 20 the effect of PRC2 inactivation on histopathologic variability in MPNST remains incompletely characterized. Having observed prominent CDX2 expression that caused diagnostic confusion in cases of MPNST referred to us for evaluation, we aimed to further explore this phenomenon and its relationship to PRC2 inactivation.…”

“…13 As many as 80% of high-grade MPNSTs show complete loss of H3K27me3 by immunohistochemistry (IHC) as a surrogate marker of EED or SUZ12 alterations leading to PRC2 dysfunction. [14][15][16][17][18][19] Despite the insight that PRC2 inactivation may influence cellular plasticity in MPNST, 20 the effect of PRC2 inactivation on histopathologic variability in MPNST remains incompletely characterized. Having observed prominent CDX2 expression that caused diagnostic confusion in cases of MPNST referred to us for evaluation, we aimed to further explore this phenomenon and its relationship to PRC2 inactivation.…”