Acrivon Predictive Precision Proteomics (AP3)-guided development and prospective clinical Phase 2 validation of the response-predictive OncoSignature test for the CHK1/2 inhibitor, ACR-368

Introduction

ACR-368 (prexasertib) is a potent and selective CHK1/2 inhibitor with demonstrated durable, single-agent activity in patients with advanced solid tumors. Genomic biomarkers have been unsuccessful in predicting response to ACR-368 due in part to the complex genetic changes in cancer that translate into dysregulated protein signaling pathways. To address this challenge, we sought to identify and clinically validate protein-based predictive biomarkers that measure the ACR-368-sensitive dysregulated signaling driving tumorigenesis using our proprietary approach, termed Acrivon Predictive Precision Proteomics (AP3).

Methods

Ovarian cancer cells with differential ACR-368 sensitivity were profiled with phosphoproteomics. Kinase activity inference and signaling pathway activity analyses were conducted to uncover ACR-368-regulated pathways associated with tumorigenesis and biomarkers predictive of drug sensitivity. A quantitative, multiplexed immunofluorescent (IF) assay was developed based on three biomarkers, termed ACR-368 OncoSignature™, and validated in prospective clinical studies.

Results

AP3 phospho-proteomic profiling of ACR-368-sensitive and non-sensitive cells exposed to ACR-368 uncovered >17,000 confidently localized phospho-sites (localization probability > 0.75), with 8272 being significantly regulated by ACR-368 (FC > 1.5, Q-value < 0.05, Limma t-test). Upon ACR-368 treatment, annotated ATM/ATR and CDK1/2 substrate consensus sites were strongly upregulated and CHK1 substrates downregulated. Global phospho-pathway analyses revealed three functionally orthogonal biomarkers that were assembled into a predictive quantitative multiplex in situ assay, ACR-368 OncoSignature™, developed for routine-processed FFPE biopsy tissue to provide a direct readout of a tumor"s dependency on the signaling axis inhibited by ACR-368.

The ACR-368 OncoSignature™ test was robustly validated in preclinical studies, including 2 prospectively designed, blinded studies on biopsies from past ACR-368 Phase 2 trials on platinum-resistant ovarian cancer. The test demonstrated segregation of responders from non-responders across studies, including an ORR enrichment to 47% (p=0.01, Wilcoxon), and significant increase in progression free survival (p=0.006, CoxPH) in biopsies from Phase 2 trials at NCI.

Acrivon has shown initial prospective validation of the AP3-based ACR-368 OncoSignature™ test in the ongoing, registrational-intent Phase 2b clinical trial in ovarian and endometrial cancers (NCT05548296), demonstrating clear segregation of RECIST responders in the OncoSignature™-positive (50% confirmed ORR in 10 patients) versus OncoSignature™-negative (0% ORR in 16 patients) arms (p-value=0.0038).

Conclusions

Employing AP3, we have developed a response-predictive test for the CHK1/2 clinical stage inhibitor, ACR-368, and demonstrated initial prospective validation for patient responder identification in the ongoing Phase 2 registrational intent trial.