Abstract 6357: A liquid biopsy-based targeted proteomic assay to identify druggable proteins from circulating tumor cells (CTCs)
Authors: Alec Horrmann, Ali T. Arafa, Kaylee Kamalanathan, Alexa Hesch, Grant Schaap, Mahdi Ahmadi, Nathaniel Bristow, Badrinath Konety, Howard Scher, Emmanuel S. Antonarakis, Jiarong Hong, Justin M. Drake
Journal: Cancer Research (2025)

Abstract Background: While cancers often arise from a specific tissue the drugs designed to fight them are largely tissue agnostic. Drugs most commonly target mutant or amplified proteins such as transcription factors, kinases, or other cell surface proteins. An ever-growing body of research shows that these well characterized protein targets are commonly found across many cancer types and can serve as potential targets for pan-cancer therapies. Despite this growing consensus, enrollment criteria for clinical trials often do not include any test to detect or quantify the presence of the drug’s target protein. However, patient-specific protein profiles should be utilized as a tool to not only minimize patient harm but also to categorize patients so drug trials can be designed to identify only the patients most likely to benefit in mind. To that end, we developed A liquid biopsy-based proteomic assay to identify druggable targets from CTCs from cancer patients’ blood. Methods: CTCs were isolated using Astrin Bioscience’s proprietary enrichment system yielding matched CTC and white blood cell (WBC) fractions. Following enrichment, samples were processed in parallel using a custom developed protein aggregation capture protocol followed by protein digestion to yield peptide samples ready for bottom-up targeted peptide analysis on a FAIMS equipped Exploris 480 instrument with internal normalization to heavy labeled peptide standards. Results: We prospectively enrolled 20 heavily-pretreated metastatic castration resistant prostate cancer (mCRPC) patients from whom matched CTC and WBC profiles were analyzed. The mean CTC count was 10.4 cells/mL with a median of 4.9 CTCs/mL. The median age of these patients was 74 years, 80% had Gleason GG4-5, 30% had visceral metastases, median number of prior systemic therapies was 5, and median PSA level was 135 ng/mL. Following CTC enrichment, we observed vastly diverse inter- and intra-patient proteomic profiles. Some of the highly relevant proteins to mCRPC identified and quantified from CTCs in 100% of patients for androgen receptor (AR) and B7 homolog 3 (B7-H3), 57% of patients for trophoblast cell surface antigen-2 (TROP2), 43% of patients for prostate specific membrane antigen (PSMA), 28% of patients for programmed cell death antigen 1 (PD-L1), and 14% of patients for neuroendocrine markers chromogranin A (CHGA) and delta like ligand 3 (DLL3) with significantly less or no detection of these proteins in the WBC fraction. Conclusions: With the clear differences seen between the CTC and WBC fractions, combined with expected proteins observed in the CTC fraction, this demonstrates the successful isolation of CTCs. Together, this shows a first of its kind assay able to probe multiple highly relevant proteins from a patient's own CTCs that could be crucial to help minimizing patient harm and designing better precision therapeutics. Citation Format: Alec Horrmann, Ali T. Arafa, Kaylee Kamalanathan, Alexa Hesch, Grant Schaap, Mahdi Ahmadi, Nathaniel Bristow, Badrinath Konety, Howard Scher, Emmanuel S. Antonarakis, Jiarong Hong, Justin M. Drake. A liquid biopsy-based targeted proteomic assay to identify druggable proteins from circulating tumor cells (CTCs) [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 6357.