At-20integrated Pathway Analysis of Rhabdoid Tumor Subtypes Identifies Key Smarcb1-Dependencies and Therapeutic Opportunities

Abstract

Atypical Teratoid Rhabdoid Tumor are aggressive pediatric malignancies characterized by biallelic inactivation of a single gene; SMARCB1 a core subunit of the hSWI/SNF chromatin remodelling complex regulating hundreds of downstream genes/pathways. We performed RNA-seq/ Methylation profiling on primary Rhabdoid Tumors (RT) and a panel of RT cell lines re-expressing SMARCB1 to identify and characterise the molecular profiles of primary RT subtypes and downstream SMARCB1-dependent pathways that may be critical to RT tumorigenesis. We identified by integrated network-based pathway analysis key genes/pathways which are deregulated at the transcriptional/methylation level and are characteristic of primary RT or particular RT subtypes but also SMARCB1-dependent in our functional models. These SMARCB1-dependent pathways were further validated by quantitative proteomic analysis (LC-MS/MS) performed in our RT model and protein abundance cross-referenced with RNA-seq to give insight into the similarities in regulation at both proteomic and transcriptomic level and drug-targeting opportunities in RT. SMARCB1-dependent gene/pathway deregulation was verified and validated by targeted pathway manipulation and quantified by qRT-PCR and phenotypic changes. Key pathways/genes include but are not limited to E2F1, AURKA, BMI1, PLK1, SHH, Rho, TGF-Beta, PDGFRa, FGFR1, Wnt and STAT3/IL-6. PDGFRa, FGFR1, STAT3/IL-6 and Wnt mechanisms were further investigated in vitro using available inhibitors. Rhabdoid cells showed sensitivity to pathway inhibition and cell death by dysregulation of several downstream SMARCB1-dependent oncogenes. Integrative analysis of -omics data allows us to collate a detailed catalogue of the effect of SMARCB1 loss within RT subtypes revealing key regulators/effectors among differentially expressed and methylated genes that may ultimately be targetable therapeutically.