A liquid biopsy-based proteomic assay to identify circulating tumor cell (CTC) –derived druggable targets in cancer patients.
Authors: Horrmann Alec , Arafa Ali , Kamalanathan Kaylee , Hesch Alexa , Schaap Grant , Izuora Zikora , Ahmadi Mahdi , Konety Badrinath R. , Scher Howard I. , Antonarakis Emmanuel S. , Hong Jiarong , Drake Justin 
Published: February 2025

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Background:
Cancers are often thought of as a disease of a specific tissue; however, the drugs designed to fight them are tissue agnostic. These drugs function by typically targeting mutant or amplified proteins such as kinases, transcription factors, or other cell surface proteins. An ever-growing body of research shows that many well characterized protein targets are commonly found across many cancer types and can serve as potential targets for pan-cancer therapies. Despite this, enrollment criteria for clinical trials often do not include any test to measure the presence of a particular protein drug target, and almost universally do not attempt to quantify the target. As a result, patient-specific protein profiles should be utilized to not only minimize patient harm but to categorize patients so that drug trials can be more intentional in identifying only the patients most likely to benefit from a selected drug. To that end, we developed a liquid biopsy-based proteomic assay to measure multiple proteins of interest simultaneously from enriched circulating tumor cells (CTCs) in blood and to detect druggable protein targets.
Methods:
CTCs were isolated using Astrin Bioscience’s proprietary enrichment system yielding matched CTC and white blood cell (WBC) fractions. Samples were then processed in parallel following a custom developed protein aggregation capture protocol followed by trypsin digestion to yield peptide samples for bottom-up targeted peptide analysis by mass spectrometry on a FAIMS equipped Exploris 480 instrument.
Results:
We prospectively enrolled 20 heavily-pretreated metastatic castration resistant prostate cancer (mCRPC) patients from whom matched CTC and WBC profiles were analyzed. 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. The mean CTC count was 10.4 cells/mL with a median of 4.9 CTCs/mL. After CTC enrichment, we observed vastly diverse intra- and inter-patient proteomic profiles. Highly relevant proteins to mCRPC were 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).
Conclusions:
The clear differences seen between the CTC and WBC fractions, combined with expected proteins observed in the CTC fraction, supports the successful isolation of CTCs. Together, this demonstrates a first of its kind assay able to probe multiple highly relevant proteins from CTCs that could be crucial to help minimize patient harm and better design precision therapeutics.