Abstract P21: Advancing Translational and Clinical Research through Quantitative Proteomics

Abstract

Abstract Quantitative proteomics is a cornerstone in unraveling complex biological systems and elucidating disease mechanisms, where proteins serve as critical effectors. At our Quantitative Proteomics Core (QPC) at the Cancer Science Institute of Singapore (CSI Singapore), NUS, we are committed to facilitating high-impact translational and clinical research through cutting-edge proteomics technologies. We utilized label-free quantitative (LFQ) proteomics to characterize forty gastric cancer cell lines, aiming to explore whether molecular classification based on proteomic profiles could offer novel insights beyond existing classification methods. Unsupervised clustering revealed two distinct groups, with differentially expressed proteins distinguishing these clusters. Notably, a protein of interest emerged that was also differentially expressed in a small cohort of 23 gastric cancer patients who underwent standard chemotherapy, stratified by median overall survival. This finding is currently under investigation to determine its role and function in gastric cancer progression. To explore potential therapeutic targets, we implemented a technique of labeling cell surface proteins with aminooxy-biotin, facilitating the subsequent enrichment of these labeled proteins via streptavidin for detailed characterization of surface membrane proteomes using LFQ proteomics. We are now applying this approach to fresh sarcoma tissue samples to discover new therapeutic targets. Recognizing the value of formalin-fixed, paraffin-embedded (FFPE) tissues in translational research, we established an in-house workflow for LFQ proteomics on FFPE samples in our core facility. In a proof-of-concept study comparing paired fresh-frozen and FFPE tissues across various mouse organs, our workflow demonstrated only a ∼10 % reduction in peptide and protein identifications in FFPE tissues while consistently delivering robust data and significant proteome depth. Our ongoing efforts focus on enabling reproducible and high-quality proteomics analyses, with a particular emphasis on translational and clinical research. The QPC is dedicated to empowering the scientific community by offering our expertise and technologies to drive forward innovative investigations and breakthroughs. Citation Format: Wai Khang Yong, Vartika Khanchandani, Jie Min Lee, Sumedha Pundrik, Sakshi Rajoria, & Dennis Kappei. Advancing Translational and Clinical Research through Quantitative Proteomics [abstract]. In: Proceedings of Frontiers in Cancer Science 2024; 2024 Nov 13-15; Singapore. Philadelphia (PA): AACR; Cancer Res 2025;85(15_Suppl):Abstract nr P21.