Abstract 4252: Genetic and pharmacological disruption of the HBS1L/PELO complex impairs mRNA homeostasis and leads to in vivo tumor regressions in FOCAD-deleted cancers

Abstract Loss of tumor suppressor genes in cancer often results in the co-deletion of nearby genes around the chromosomal locus, creating potential collateral damage contexts for targeted therapy. One such example is the loss of MTAP, which is frequently co-deleted with the tumor suppressor genes CDKN2A/B and creates a synthetic lethal dependency on PRMT5 and susceptibility to MTA-cooperative PRMT5 inhibitors. To identify additional novel drug targets for patients with chromosome 9p21 loss, we first conducted unbiased, combinatorial CRISPR screens evaluating the pairwise knockout of ‘context’ genes lost on Ch9p21 against a focused library of ∼5, 000 ‘target’ genes. We identified loss of FOCAD, the gene encoding the SKI complex interacting exonuclease, as synthetic lethal with loss of PELO, a ribosome rescue factor. To expand on this genetic interaction, we conducted genome-wide CRISPR screens in FOCAD isogenic cell lines discovering both PELO and its binding partner HBS1L as synthetic lethal targets in FOCAD-null cells. In FOCAD-deleted xenografts, knockout of HBS1L eliminates tumor growth and results in protein loss of PELO, likely through destabilization of the HBS1L/PELO protein complex. The dependency of FOCAD-null cells on HBS1L/PELO could be rescued by exogenous cDNA expression of FOCAD, and conversely, knockout of FOCAD in WT cells rendered them dependent on HBS1L, demonstrating the robustness of this interaction and validating the HBS1L/PELO protein complex as a promising target for drug discovery. Through cellular phenotypic screens and a medicinal chemistry campaign, we identified pharmacological disruptors of the HBS1L/PELO complex that selectively kill FOCAD-deleted, but not FOCAD-proficient, cells across diverse models. Oral dosing of mice harboring FOCAD-deleted xenografts with our leading compound led to dose-dependent tumor regression and modulation of PD biomarkers. Mechanistically, HBS1L and PELO form a complex responsible for resolving stalled elongation complexes during protein translation. We propose a model in which loss of FOCAD (and/or other SKI complex members) leads to accumulation of aberrant mRNAs on which ribosomes become stalled, leading to hyperdependence on HBS1L/PELO for ribosome rescue. This model is supported by the observation of translational arrest and activation of the unfolded protein response upon HBS1L/PELO inactivation. Clinically, FOCAD loss occurs in ∼30% of all MTAP deleted tumors, representing ∼3% of all solid tumors (including ∼7% of NSCLC). Our lead molecule provides preclinical validation for targeting the HBS1L/PELO complex as a novel strategy for the potential treatment of a large population of patients with FOCAD-deleted tumors. Citation Format: Lauren Catherine M. Martires, Matthew Tonini, Hongxiang Zhang, Minjie Zhang, Chengyin Min, Charlotte B. Pratt, Katherine Lazarides, Frank J. Bruzzese, Douglas A. Whittington, Patrick McCarren, Teng Teng, Madhavi Bandi, Shanchuan Zhao, Stephen Paik, Eden Gordon, Shangtao Liu, Alvin Lu, Maria Dam Ferdinez, Binzheng Shen, Hannah Stowe, Yi Yu, Samuel R. Meier, Ashley H. Choi, Lauren Grove, Alan Huang, Alice Tsai, William D. Mallender, Wenhai Zhang, Jannik N. Andersen, Ed Wu, Hilary E. Nicholson. Genetic and pharmacological disruption of the HBS1L/PELO complex impairs mRNA homeostasis and leads to in vivo tumor regressions in FOCAD-deleted cancers [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 4252.