Abstract PR003: KLIPP: Targeting fusion oncogenes with CRISPR

Abstract With the development of whole genome sequencing and CRISPR technology, it is now possible to identify sequence features that are unique to an individual’s cancer genome and to precisely target them. Such personalized precision therapy holds the promise of ushering in a new era of safe and effective cancer treatments with minimal side-effects. To specifically target the cancer genome, we have developed a CRISPR-based therapeutic approach, “KLIPP,” which is designed to target structural variants junctions (SVJs) specific to cancer genomes, with few, or no off-target effects expected in normal cell. KLIPP uses a “split enzyme” approach consisting of a dead Cas9 endonuclease (dCas9) fused to the endonuclease Fok1 where two Fok1 endonucleases need to homodimerize to become active. To “nucleate” and activate these complexes, sgRNAs are designed to bind sequences flanking cancer-specific SVJs, bringing two Fok1-dCas9 complexes together to induce double-strand breaks (DSBs). While any SVJ in the cancer genome may be targeted with KLIPP, we have found that junctions in oncogenic fusion genes represents a particularly valuable target. We show effective targeting of the EWS::FLI1 fusion oncogene in Ewing sarcoma cells using lipid nanoparticle delivery of the Fok1-dCas9 mRNA and SVJ-targeting sgRNA, leading to the induction of DSBs, diminished expression of the fusion oncogene and loss of cell survival. Other fusion oncogenes that we are currently targeting with KLIPP involve TMPSS2::ERG in prostate cancer, DNAJB1::PRKACA in fibrolamellar liver cancer and BCR::ABL1 in leukemia. We believe that KLIPP is a safe and cancer-specific approach for precision targeting of fusion oncogenes in cancer cells. This paradigm-shifting personalized therapy could revolutionize how we treat fusion-driven cancers without inflicting long-term side effects. Citation Format: Huibin Yang, Radhika Suhas. Hulbatte, Natalie Gratsch, Ann Urzynicok, Ashley Sutter, Meyer Cusnir, Mario Ashaka, Ishwarya Venkata. Narayanan, Michelle Paulsen, Anna Schwendeman, Tom E. Wilson, Erika Newman, Mats Ljungman. KLIPP: Targeting fusion oncogenes with CRISPR [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Fusion-Positive Cancer: From Discovery to Therapy; 2026 Jan 13-15; Philadelphia PA. Philadelphia (PA): AACR; Cancer Res 2026;86(1_Suppl):Abstract nr A008.