Abstract 2744: Interrogating the functional roles of differential CTCF-binding sites in IDH-mutant gliomas using a novel CRISPR library

Abstract Isocitrate dehydrogenase (IDH) mutations are frequently observed in gliomas, and their mutation status is accepted as a CNS tumor classification marker. IDHs are enzymes that convert isocitrate into alpha-ketoglutarate (α-KG). Mutations in IDHs cause neomorphic enzymatic activity, by which D-2-hydroxyglutarate (2- HG), the oncometabolite, is produced from α-KG. This leads to the inhibition of α-KG-dependent enzymes, such as DNA and histone demethylases, thus altering chromatin structure and gene expression profile. CTCF is a methylation-sensitive structural protein that recognizes specific DNA motifs. It dimerizes, together with cohesin, forms chromatin loops, and determines the boundaries of topologically associated domains. Previous work demonstrated that IDH-mutant gliomas have hypermethylation at CTCF-binding sites, leading to reduced CTCF binding and permitting a constitutive enhancer to interact aberrantly with a glioma oncogene. Despite the unique epigenetic features of IDH-mutant gliomas and the ever-increasing importance of IDH mutation in patient prognosis, there has been no comprehensive study on the functional roles of CTCF binding sites in these tumors.We reanalyzed publicly available CTCF ChIP-seq data of three IDH-wild type (wt) and three IDH-mutant glioma cell lines, determined differential CTCF ChIP-seq regions, and aimed to explore their functional roles in glioma survival. To investigate the effect of methylation and demethylation of a specific CTCF binding site in both IDH-wt and -mutant gliomas, we developed a novel paired gRNA library targeting the left and right sides of these differential regions, which consists of 899 paired gRNAs. The CRISPR droplet screens are being conducted using dCas9-fused DNMT3A&3 and TET1 effector proteins, causing DNA methylation and demethylation, respectively. Beyond the alterations of gRNAs in the population, the single-cell transcriptomic readout will be obtained at the end of the screen.Our library design offers advantages over available libraries as it can be utilized with different CRISPR approaches. This high-throughput epigenome editing approach will allow for identifying regulatory interactions leading to tumor cell survival in IDH-wild type and -mutant gliomas. Citation Format: Ebru Yilmaz, Alisan Kayabolen, Dogancan Ozturan, Tahsin E. Tekoglu, Ester Calvo Fernández, Sedef Sarac Yalcinkaya, Nathan A. Lack, Mario L. Suvà, Tugba Bagci Onder. Interrogating the functional roles of differential CTCF-binding sites in IDH-mutant gliomas using a novel CRISPR library [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 2744.