SWI/SNF complex heterogeneity relates with polyphenotypic differentiation, prognosis and immune response in rhabdoid tumors.

BACKGROUND Rhabdoid tumors (RTs) arise within (Atypical Teratoid/Rhabdoid Tumor-AT/RT) or outside the brain (extraCNS-RT-eCNS-RT) and are driven mainly by inactivation of the SWI/SNF complex subunit SMARCB1. A pathognomonic hallmark of RTs is heterogenous multilineage differentiation including anomalous neuronal differentiation in some eCNS-RTs. Because remodeling of the SWI/SNF complex regulates differentiation, we hypothesized that SWI/SNF-BAF and PBAF complex heterogeneity correlates with both multilineage differentiation and clinical outcome. METHODS We performed an integrated analysis of SWI/SNF complex alterations in the developing kidney and cerebellum (most common regions of RT origin) in comparison to eCNS-RT (n=14) and AT/RT (n=25) tumors. RT samples were interrogated using immunohistochemistry, DNA methylation and gene expression analyses. RESULTS (A) The SWI/SNF-BAF paralogs ACTL6A/ACTL6B were expressed in a mutually exclusive manner in the developing cerebellum and kidney. In contrast, a subset of eCNS-RTs lost mutual exclusivity and co-expressed both subunits. These tumors showed aberrant DNA methylation of genes that regulate neuronal and renal development and demonstrated immunohistochemical evidence of neuronal differentiation. (B) Low expression of the PBAF subunit-PBRM1 identified a group of AT/RTs in younger children with better overall prognosis. PBRM1-low AT/RT and eCNS-RTs showed altered DNA methylation and gene expression in immune-related genes. PBRM1 knockdown resulted in lowering immunosuppressive cytokines and PBRM1 levels in tumor samples tumor showed an inverse relationship with CD8 cytotoxic T-cell infiltration. CONCLUSIONS Heterogeneity in SWI/SNF BAF (ACTL6A/ACTL6B) and PBAF (PBRM1) subunits correlates with histogenesis, contributes to the immune microenvironment and prognosis in RTs and may inform opportunities to develop immunotherapies.

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