A SOX2 engineered epigenetic silencer factor represses the glioblastoma genetic program

By rational engineering of the transcription factor SOX2, a key promoter of GBM malignancy, we generated a synthetic repressor named SOX2 Epigenetic Silencer (SES), which maintains the ability to bind to a large group of its original targets. Data from RNAseq, ATACseq, MeDIPseq, ChIPseq in GBM cells indicate that SES, through the KRAB and DNA methyltransferase 3A/L catalytic domains, epigenetically inhibits the SOX2 tumorigenic molecular network (rather than activating it as SOX2 does). This epigenetic long-term transcriptional silencing includes genes crucial for tumor maintenance and growth. Conversely, transcriptomic and epigenomic data show that SES is ineffective (thus not harmful) in healthy neural cells. Overall design: Human SNB19 cells: 3x SOX2 ATAC; 3x SES ATAC; 2x Mock H3K9me3; 2x SES H3K9me3; 2x Mock MeDIP; 2x SES MeDIP; 2x SOX2 V5 ChIP; 2x SES V5 ChIP; 3x SOX2 V5 Cut-n-Tag; 3x SES V5 Cut-n-Tag; 3x Mock RNA; 3x SES RNA. Mouse cortical neurons: 3x Mock RNA; 3x SES RNA