Aligned ECM influences neuroblastoma cell plasticity via YAP-WT1 association

Introduction Neuroblastoma (NB) is the most common extracranial pediatric solid tumor and is comprised of two interconvertible cell states: the less-aggressive adrenergic (ADRN) and the aggressive, therapy-resistant mesenchymal (MES) subtypes. Through an ADRN-to-MES transition (AMT), NB cells become more refractory to existing therapeutics, as is often observed in high-risk (HR) and relapsed NB. We previously identified that aligned extracellular matrix (ECM) proteins, featured in HR and relapsed NB, drive AMT in NB by facilitating epigenetic silencing of ADRN signatures. Our study aims to further characterize the underlying mechanisms driving AMT in NB, specifically how aligned ECM increases MES signatures through activation of yes-associated protein (YAP), which interacts with Wilm's Tumor 1 (WT1) to regulate activity of the MES driver, paired related homeobox 1 (PRRX1). Experimental Procedures To interrogate how aligned ECM influences MES signatures, we employ a nanogrooved collagen-coated array (NGCA) that models the aligned collagen observed in HR and relapsed NB. Cells plated on this in vitro platform are assessed for differences in MES signatures and expression of YAP, WT1, and PRRX1 via biochemical analyses including Western blot, immunofluorescent (IF) staining, and chromatin immunoprecipitation sequencing (ChIP-seq). We also use cells with knockdown and overexpression of YAP as well as knockdown of WT1 to determine their roles in our proposed AMT mechanism. The association of YAP and WT1 is physically evaluated using proximity ligation assay (PLA) and co-immunoprecipitation (co-IP). Results Our data demonstrate that aligned ECM modeled in vitro with NGCA increases MES signatures and YAP expression in NB. NGCA additionally promotes expression of the MES driver PRRX1 in a YAP-dependent manner, suggesting its recruitment by YAP to increase MES signatures. Furthermore, ChIP-seq highlights an association between YAP and WT1 that promotes PRRX1 expression. Computational analysis identifies WT1 as a transcription factor interacting with PRRX1, an association we confirm through reduction of PRRX1 expression following WT1 knockdown. We show that WT1 expression and nuclear localization are associated with YAP activity; indeed, PLA and co-IP analyses reveal that YAP and WT1 form a complex in response to NGCA, which then translocates to the nucleus. Conclusions Together our data support a mechanism by which YAP and WT1 interact in response to aligned ECM to promote PRRX1 expression, thereby increasing MES signatures. Identification of this process uncovers pharmacological and therapeutic targets for re-sensitization of HR and relapsed NB to existing treatments to improve clinical outcomes.