SIRT2 is a regulator of the differentiation block driven by SMARCB1 loss in ATRT. [RNA-Seq]
Atypical teratoid rhabdoid tumor (ATRT) is a highly aggressive brain tumor of childhood with a poor overall survival. The salient molecular feature of ATRT is the loss of SMARCB1 which results in epigenetic dysregulation of the genome. SMARCB1 loss affects lineage commitment and differentiation by controlling gene expression. We hypothesized that additional epigenetic factors co-operate with SMARCB1 loss to control cell self-renewal and drive ATRT. We identified SIRT2 as a primary dependency in ATRT. Using a combination of RNA-seq, CUT&RUN and single RNA sequencing in model systems ATRT, we observed genome-wide reorganization of active chromatin and significantly changes in genes expression in ATRT cells with genetic (with shRNA) or chemical (with Tenovin or Thiomyristoyl (TM)) SIRT2 deactivation. Single-cell RNA transcriptome analysis of xenograft tumors revealed the elimination of tumor cells expressing stem cell genes and expansion of tumor cells expressing differentiated genes in vivo. Furthermore, SIRT2 inhibition induced apoptosis, decreased tumor growth and prolonged survival in orthotopic xenograft models. In summary we demonstrated that SIRT2 inhibition is a molecular vulnerability in SMARCB1-deleted tumors with therapeutic potential. Overall design: CUT&RUN data comparing peak height in Atypical teratoid rhabdoid tumor (ATRT) BT16 cells treated with Thiomyristoyl (TM) and DMSO. Thiomyristoyl was bought from MedChem express (HY-101278) and reconstituted in DMSO. BT16 ATRT cells were treated with 20 uM of TM for 24 hours followed by CUT&RUN assay with antibodies for H3K4me (positive control; EpiCypher #13-0041), H3K27ac (Cell signaling #8173), HeK27me3 (Cell signaling#, 9733), IgG (negative control; EpiCypher#13-0042K). For bulk RNA-seq experiment BT16 ATRT cells were treated with DMSO or 30uM TM for 72hrs. RNA-Seq data comparing gene expression in pediatric ATRT treated with TM vs DMSO. Single-cell RNA sequencing on GFP-positive BT16ATRT cells. To study the impact of TM on differentiation in vivo, we performed single-cell RNA sequencing on GFP-positive BT16 ATRT cells. Cell were growing in mice cerebellum and treatment started when tumors were established. Mice were treated with either TM (50 mg/kg IP 3/week for 4 weeks) or Vehichle control.