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. 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