Abstract C002: Identification of biomarkers predictive of sensitivity to the CHK1/2 inhibitor ACR-368 using high-resolution phosphoproteomics and development of an ACR-368-tailored patient responder identification 3-marker test, ACR-368 OncoSignature
Authors: Wigerup Caroline , Shipitsin Michail , Murshid Ayesha , Shi Lei , Jakobsson Magnus E. , Bekker-Jensen Dorte , Choudry Sibgat , Dunyak James , Proia David , Olsen Jesper V. , Masson Kristina , Blume-Jensen Peter 
Published: December 2023

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 protein-based, predictive biomarkers that measure the ACR-368-sensitive dysregulated signaling driving tumorigenesis using our proprietary approach, AP3 (Acrivon Predictive Precision Proteomics).

Methods ACR-368 anticancer activity was measured in a panel of ovarian cancer cell lines using CellTiter-Glo. Quantitative phosphoproteomics was performed on ACR-368 sensitive and resistant ovarian cancer cell lines using data-independent acquisition mass spectrometry (DIA-MS). Kinase activity inference analysis and signaling pathway analyses were conducted to uncover ACR-368-regulated pathways associated with tumorigenesis. A quantitative, multiplexed immunofluorescent (IF) assay was developed based on three biomarkers, termed ACR-368 OncoSignature. Ovarian PDX studies were conducted in female athymic nude or CB-17 Scid mice.  

Results ACR-368 demonstrated diverse anti-proliferative activity in ovarian cancer cell lines. Phosphoproteome-profiling analysis from ACR-368 sensitive and resistant cells exposed to ACR-368 yielded &gt;17,000 confidently localized phospho-sites (localization probability &gt; 0.75), with 8272 being significantly regulated by ACR-368 (FC &gt; 1.5, Q-value &lt; 0.05, Limma t-test). Unsupervised hierarchical clustering analysis revealed overrepresentation of ATM/ATR and CDK1/2-associated substrate sites in the upregulated group, while the downregulated group showed overrepresentation of CHK1-associated sites. Pathway enrichment analysis highlighted the differential regulation of the homology-directed repair (HDR) pathway between sensitive and non-sensitive ovarian cancer cells. Through analysis of HDR-related signaling networks, three functionally orthogonal predictive biomarkers were assembled into a quantitative multiplex in situ assay for FFPE tissue that provides a direct readout of a tumor’s dependency on the signaling axis inhibited by ACR-368. Quantitation of these biomarkers in cancer cell lines using the IF-based OncoSignature demonstrated efficient classification based on ACR-368 sensitivity. The assay accurately predicted sensitivity to ACR-368 across ovarian cancer PDX models with an AUC of 0.9 (95% confidence interval: 0.71 to 1; p-value = 0.025).

Conclusions Employing our AP3 platform, which combines MS-based phosphoproteomics and quantitative multiplexed-IF staining of drug-tailored biomarkers, we developed a response-predictive test for ACR-368 that enables identification of responders to ACR-368 treatment. A clinical trial (NCT05548296) evaluating the efficacy of ACR-368 based on the OncoSignature test status is currently recruiting in patients with platinum-resistant ovarian, endometrial, and urothelial cancer.

Citation Format: Caroline Wigerup, Michail Shipitsin, Ayesha Murshid, Lei Shi, Magnus E. Jakobsson, Dorte Bekker-Jensen, Sibgat Choudry, James Dunyak, David Proia, Jesper V. Olsen, Kristina Masson, Peter Blume-Jensen. Identification of biomarkers predictive of sensitivity to the CHK1/2 inhibitor ACR-368 using high-resolution phosphoproteomics and development of an ACR-368-tailored patient responder identification 3-marker test, ACR-368 OncoSignature [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 C002.