LAUSR

Immuno-oncology (IO) has substantially improved the survival of cancer patients over the past several years encouraging the discovery of novel IO targets which are typically proteins expressed on the surface of immune cells. Sensitive quantification of proteins in complex biological samples is routinely achieved by immunoassays that use antibodies specific to target proteins. Such approaches can be a limitation in IO drug discovery and development as de novo development of antibodies is associated with long lead times, high costs, and high failure rates. Protein quantification using mass spectrometry (MS) is agnostic to species and matrices and removes the barriers of availability or specificity of antibody-based assay. Further, MS proteomics workflows can support both large scale discovery studies but also represent an attractive alternative to targeted quantitative studies. The main purpose of this work is to assess the performance of the TrueDiscovery™ and TrueSignature™ MS-proteomics platforms for the deep proteome and surfaceome profiling of human primary and immortalized immune cells compared to flow cytometry solutions. We assess the number of quantified proteins and specifically the coverage of immune cell marker proteins in primary human immune cells across cell count groups from 2 million down to 2500 immune cells. In addition, we compared the quantification of a multiplexed surface antigens panel using TrueSignature™ and QIFI® flow cytometry platforms. We found that the applied MS-based proteomics workflows achieve high sensitivity and robustness in detection and quantification of immune cell markers down to 2500 primary immune cells. Additionally, we observed a strong correlation of the quantitative data derived from our MS-based proteomics workflows with flow cytometry supporting the substitution of immunoassays by MS-based proteomics workflows in target discovery and validation. Citation Format: Yu-Wah Au, David Satijn, Martin Mehnert, Amaury Lachaud, Yuehan Feng, Jakob Vowinckel, Hélène Bon. Discovery and validation of therapeutic targets in immune cells by mass spectrometry-based proteomics. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3974.