GSE116494
The effect of STAG2 loss in Ewing sarcoma [ATAC-Seq]
Ewing sarcoma is an aggressive malignancy characterized by oncogenic rearrangements of the EWS gene with an ETS-family transcription factor, most commonly FLI. Recent comprehensive next-generation sequencing efforts have revealed few other highly recurrent mutations in this disease apart from loss-of-function mutations in STAG2 which occur in 15-20% of tumors. STAG2 is a member of the cohesin complex, which regulates sister chromatid alignment during mitosis and epigenetic regulation of gene expression. While some studies suggest that loss of STAG2 is associated with the development of aneuploidy, this is not the case in Ewing sarcoma. To investigate whether STAG2 loss effects epigenetic regulation of gene expression in Ewing sarcoma, we developed isogenic Ewing sarcoma cell lines with STAG2 knockout. We found that Ewing sarcoma cells engineered for loss of STAG2 maintain an intact cohesion complex that alternately incorporates STAG1. Overall design: ATAC-seq  on isogenic clonally-selected   A673 cells treated with STAG2 targeting CRISPR Cas9,  and on  A673 cells with STAG2 wild-type. Reads mapped on the STAG2 wild-type clones (A673.sgNT-1c4 and  A673.sgNT-2c3) were merged  and labeled  “STAG2 WT”. Reads mapped on the STAG2 knockout clones (A673.sgSTAG2-1c6, A673.sgSTAG2-4c5) were merged and labeled  “STAG2 null”.