Abstract B045: Single cell proteomics as a method to analyze circulating tumor cells in prostate cancer patients

Abstract The purpose of this study was to develop a single-cell proteomic protocol capable of analyzing single circulating tumor cells (CTCs). Despite the numerous benefits possible from the analysis of CTCs they have not migrated into clinical use due to difficulty of purification and their minute numbers. Combined, this results in only miniscule amounts of sample, if any, for analysis. Most clinical assays primarily focus on genomic and/or transcriptomic assays, while only a select number of proteomic assays are used and these analyze a handful of targets at most. Recent developments in single-cell proteomics using liquid chromatography tandem mass spectrometry (LC-MS/MS) promise to solve this latter issue and increase the depth of proteome coverage. To analyze CTCs we adapted previously developed single-cell methodologies to be amenable for the analysis of CTCs. Our novel method uses a separately prepared carrier channel as opposed to traditional methods which rely on a large pool of the single-cells of interest. This is necessary since collected CTC’s will not have a large pool of similar cells to draw upon to form a carrier. As the carrier is prepared in bulk it allows for improved quality control measurements to be implemented. This is critical as for clinical use these metrics will be vital for ensuring repeatability and reliability of results. Using our developed protocol, we are able to analyze hundreds of proteins from each simulated CTC. Additionally, we demonstrate that a separately prepared carrier composed of cells from a different lineage still permits the identification of a wide array of proteins within single-cells as well as allows for better quality control over the digestion and TMT labeling efficiencies. In conclusion, our protocol demonstrates its capability to detect and quantify hundreds of proteins from individual cells. If this method was applied towards the analysis of CTCs it would represent by far the most comprehensive method for analysis of the proteome of single CTCs. Together, this provides a foundation for translating proteomic analysis of single CTCs towards guiding individualized cancer treatment in the clinic. Citation Format: Alec Horrmann, Zoi Sychev, Justin M. Drake. Single cell proteomics as a method to analyze circulating tumor cells in prostate cancer patients [abstract]. In: Proceedings of the AACR Special Conference: Advances in Prostate Cancer Research; 2023 Mar 15-18; Denver, Colorado. Philadelphia (PA): AACR; Cancer Res 2023;83(11 Suppl):Abstract nr B045.