Abstract SY34-02: Developing therapeutics for cancers driven by fusion proteins: Lessons from fibrolamellar carcinoma

Abstract Many cancers, such as fibrolamellar carcinoma (FLC), Ewing’s sarcoma, chronic myelogenous leukemia and rhabdomyosarcoma, are driven by fusion oncoproteins (1-6). Since each fusion partner originates from a native protein with essential functions, it is important but difficult to selectively target fusion oncoproteins while sparing native components. FLC is a usually lethal primary liver tumor of adolescents and young adults driven by an oncogenic fusion DNAJB1::PRKACA, which results from the fusion of the first exon of DNAJB1, a heat shock protein, to the bulk of the coding region of PRKACA, the catalytic subunit of protein kinase A (PKA) (7-10), forming DNAJB1::PRKACA. The fusion protein not only triggers the tumor, but drives the tumor and the tumor is oncogenically addicted to the fusion oncoprotein. Elimination of the mRNA encoding DNAJB1::PRKACA with an shRNA (11) or an siRNA (12) is sufficient to stop growth and kill the tumor. However, because the active sites of the DNAJB1::PRKACA and native PRKACA are structurally indistinguishable (13), designing inhibitors specific to the fusion protein is challenging. To test therapeutics, we developed a number of model systems including organoids and patient-derived xenografts grown in mice, genetically engineered mouse models, genetically engineered human hepatocytes and FLC tumors cells directly from patient surgical resection. These were validated for their transcriptome, proteome, phosphoproteome, metabolome and drug-sensitivity. Currently, there is no accepted therapy for FLC. Our testing of agents that are currently being tried in the clinic, found no therapeutic window between the FLC cells and normal human hepatocytes. We identified several potential upregulated targets in FLC tumors at both the transcriptomic and proteomic level (14,15). However, inhibitors against these targets showed no therapeutic advantage (16). Here, we present three therapeutic strategies that were successful and are applicable to other Fusion Oncoprotein-driven Malignancies. Each of these three approaches are in, or moving towards, clinical trials and each of these pipelines are applicable to other Fusion Oncoprotein-driven Malignancies. References1. Verma, S.K., Witkin, K.L., Sharman, A., and Smith, M.A. (2024). Targeting fusion oncoproteins in childhood cancers: challenges and future opportunities for developing therapeutics. Journal of the National Cancer Institute 116, 1012-1018. 10.1093/jnci/djae075. 2. Wachtel, M., Surdez, D., Grunewald, T.G.P., and Schafer, B.W. (2024). Functional Classification of Fusion Proteins in Sarcoma. Cancers (Basel) 16. 10.3390/cancers16071355. 3. Gao, Q., Liang, W.W., Foltz, S.M., Mutharasu, G., Jayasinghe, R.G., Cao, S., Liao, W.W., Reynolds, S.M., Wyczalkowski, M.A., Yao, L., et al. (2018). Driver Fusions and Their Implications in the Development and Treatment of Human Cancers. Cell Rep 23, 227-238 e223. 10.1016/j.celrep.2018.03.050. 4. Simon, S.M. (2023). Fighting rare cancers: lessons from fibrolamellar hepatocellular carcinoma. Nature reviews. Cancer 23, 335-346. 10.1038/s41568-023-00554-w. 5. Crompton, B.D., Stewart, C., Taylor-Weiner, A., Alexe, G., Kurek, K.C., Calicchio, M.L., Kiezun, A., Carter, S.L., Shukla, S.A., Mehta, S.S., et al. (2014). The genomic landscape of pediatric Ewing sarcoma. Cancer Discov 4, 1326-1341. 10.1158/2159-8290.CD-13-1037. 6. Delattre, O., Zucman, J., Plougastel, B., Desmaze, C., Melot, T., Peter, M., Kovar, H., Joubert, I., de Jong, P., Rouleau, G., and et al. (1992). Gene fusion with an ETS DNA-binding domain caused by chromosome translocation in human tumours. Nature 359, 162-165. 10.1038/359162a0. 7. Honeyman, J.N., Simon, E.P., Robine, N., Chiaroni-Clarke, R., Darcy, D.G., Lim, II, Gleason, C.E., Murphy, J.M., Rosenberg, B.R., Teegan, L., et al. (2014). Detection of a recurrent DNAJB1-PRKACA chimeric transcript in fibrolamellar hepatocellular carcinoma. Science 343, 1010-1014. 10.1126/science.1249484. 8. Kastenhuber, E.R., Lalazar, G., Houlihan, S.L., Tschaharganeh, D.F., Baslan, T., Chen, C.C., Requena, D., Tian, S., Bosbach, B., Wilkinson, J.E., et al. (2017). DNAJB1-PRKACA fusion kinase interacts with beta-catenin and the liver regenerative response to drive fibrolamellar hepatocellular carcinoma. Proceedings of the National Academy of Sciences of the United States of America 114, 13076-13084. 10.1073/pnas.1716483114. 9. Shirani, M., Levin, S., Shebl, B., Requena, D., Finkelstein, T.M., Johnson, D.S., Ng, D., Lalazar, G., Heissel, S., Hojrup, P., et al. (2024). Increased Protein Kinase A Activity Induces Fibrolamellar Hepatocellular Carcinoma Features Independent of DNAJB1. Cancer research 84, 2626-2644. 10.1158/0008-5472.CAN-23-4110. 10. Graham, R.P., Lackner, C., Terracciano, L., Gonzalez-Cantu, Y., Maleszewski, J.J., Greipp, P.T., Simon, S.M., and Torbenson, M.S. (2018). Fibrolamellar carcinoma in the Carney complex: PRKAR1A loss instead of the classic DNAJB1-PRKACA fusion. Hepatology 68, 1441-1447. 10.1002/hep.29719. 11. Neumayer, C., Ng, D., Jiang, C.S., Qureshi, A., Lalazar, G., Vaughan, R., and Simon, S.M. (2023). Oncogenic Addiction of Fibrolamellar Hepatocellular Carcinoma to the Fusion Kinase DNAJB1-PRKACA. Clinical cancer research : an official journal of the American Association for Cancer Research 29, 271-278. 10.1158/1078-0432.CCR-22-1851. 12. Neumayer, C., Ng, D., Requena, D., Jiang, C.S., Qureshi, A., Vaughan, R., Prakash, T.P., Revenko, A., and Simon, S.M. (2024). GalNAc-conjugated siRNA targeting the DNAJB1-PRKACA fusion junction in Fibrolamellar Hepatocellular Carcinoma. Molecular therapy : the journal of the American Society of Gene Therapy 32, 140-151. 10.1016/j.ymthe.2023.11.012. 13. Tomasini, M.D., Wang, Y., Karamafrooz, A., Li, G., Beuming, T., Gao, J., Taylor, S.S., Veglia, G., and Simon, S.M. (2018). Conformational Landscape of the PRKACA-DNAJB1 Chimeric Kinase, the Driver for Fibrolamellar Hepatocellular Carcinoma. Scientific reports 8, 720. 10.1038/s41598-017-18956-w. 14. Simon, E.P., Freije, C.A., Farber, B.A., Lalazar, G., Darcy, D.G., Honeyman, J.N., Chiaroni-Clarke, R., Dill, B.D., Molina, H., Bhanot, U.K., et al. (2015). Transcriptomic characterization of fibrolamellar hepatocellular carcinoma. Proceedings of the National Academy of Sciences of the United States of America 112, E5916-5925. 10.1073/pnas.1424894112. 15. Requena, D., Medico, J.A., Soto-Ugaldi, L.F., Shirani, M., Saltsman, J.A., 3rd, Torbenson, M.S., Coffino, P., and Simon, S.M. (2024). Liver cancer multiomics reveals diverse protein kinase A disruptions convergently produce fibrolamellar hepatocellular carcinoma. Nature communications 15, 10887. 10.1038/s41467-024-55238-2. 16. Lalazar, G., Requena, D., Ramos-Espiritu, L., Ng, D., Bhola, P.D., de Jong, Y.P., Wang, R., Narayan, N.J.C., Shebl, B., Levin, S., et al. (2021). Identification of Novel Therapeutic Targets for Fibrolamellar Carcinoma Using Patient-Derived Xenografts and Direct-from-Patient Screening. Cancer Discov 11, 2544-2563. 10.1158/2159-8290.CD-20-0872. Citation Format: Sanford M. Simon. Developing therapeutics for cancers driven by fusion proteins: Lessons from fibrolamellar carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_2):Abstract nr SY34-02.