Abstract B169: Retrospective baseline biomarker analyses in a first-in-human Phase 1 trial of the PKMYT1 inhibitor lunresertib (RP-6306) in pts with advanced solid tumors harboring CCNE1 amplification and/or deleterious alterations in FBXW7 or PPP2R1A
Authors: Aguado-Fraile Elia , Sethuraman Sunantha , Petrone Adam , Bacque Emeline , Schram Alison , Lheureux Stephanie , Lee Elizabeth K , Koehler Maria , Silverman Ian M , Rimkunas Victoria , Yap Timothy A 
Published: December 2023

Abstract
Background: Lunresertib (RP-6306) is a first-in-class membrane-associated tyrosine- and threonine-specific Cdc2-inhibitory kinase (PKMYT1) inhibitor that disrupts the G2/M checkpoint leading to premature mitosis and catastrophic DNA damage in cells harboring synthetic lethal genomic alterations. The safety and tolerability of lunresertib alone and in combination with camonsertib (RP-3500) is being investigated in the Phase 1 MYTHIC study in patients with advanced solid tumors with either CCNE1 amplifications (amp) or deleterious alterations in FBXW7 or PPP2R1A (NCT04855656). Here, we present a comprehensive retrospective biomarker analysis aimed at understanding concordance between local vs. central and tissue- vs. plasma-based next generation sequencing (NGS). The correlation between CCNE1 copy number assessment by NGS and fluorescence in situ hybridization (FISH), as well as the relationship between CCNE1 amp and Cyclin E1 protein levels, was investigated.
Methods: Patients were enrolled based on results from sponsor-approved local tumor NGS and plasma circulating tumor DNA (ctDNA) tests. To ensure molecular eligibility criteria were met, local NGS reports were centrally reviewed and functionally annotated prior to enrollment. Tumor tissue and plasma samples collected at screening were retrospectively analyzed by SNiPDx™ and Tempus xF(+), respectively. Tissue samples were further evaluated by FISH and immunohistochemistry.
Results: As of June 1, 2023, 145 patients were screened with uterine (23%), colorectal (CRC, 15%), ovarian (13%), and upper GI (6%) as the most frequent cancers. Ninety-four percent (137/145) of patients screened had local NGS results available (98% tissue, 2% plasma). CCNE1 amp (40.1%) were most frequently observed in ovarian, uterine, and upper GI malignancies. FBXW7 (39.4%) and PPP2R1A (16.0%) alterations were enriched in CRC and uterine cancer, respectively. TP53 alterations were frequent across all biomarker groups (76% CCNE1, 54% FBXW7, and 88% PPP2R1A). Central tissue NGS confirmed 94% (47/50) of the enrollment alterations. Central plasma ctDNA confirmed 83.0% (39/47) of FBXW7 and PPP2R1A mutations and had high positive predictive value (100%, 17/17) but low sensitivity (42.5%; 17/40) for CCNE1 amp. CCNE1 amp call and copy number estimation by tissue NGS and FISH were highly correlated (Spearman ρ=0.65, p=0.006). Seventy-five percent of tumors with CCNE1 amp had Cyclin E1 overexpression (H-score ≥100; mean=168; range [0, 300]).
Conclusion: In this study, local NGS tests were an efficient and robust strategy for directing patients into a molecularly defined Phase 1 trial. Plasma ctDNA reliably detected alterations in all 3 genes, but caution should be taken when interpreting CCNE1 amplification negative results due to a high false negative rate. FISH and genomics are appropriate methods to estimate CCNE1 amp copy number. These retrospective analyses enable the testing of the synthetic lethal hypothesis of lunresertib and CCNE1, PPP2R1A and FBXW7, assuring reliable interpretation of the clinical data.
Citation Format: Elia Aguado-Fraile, Sunantha Sethuraman, Adam Petrone, Emeline Bacque, Alison Schram, Stephanie Lheureux, Elizabeth K Lee, Maria Koehler, Ian M Silverman, Victoria Rimkunas, Timothy A Yap. Retrospective baseline biomarker analyses in a first-in-human Phase 1 trial of the PKMYT1 inhibitor lunresertib (RP-6306) in pts with advanced solid tumors harboring CCNE1 amplification and/or deleterious alterations in FBXW7 or PPP2R1A [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr B169.