Single-cell (phospho-)proteomics platform for functional analysis of tumor microenvironment - ABSTRACT Tumor microenvironment (TME) is a complex ecosystem comprised of cancer cells, immune cells, stromal cells, and other cell types. They interact and collectively determine disease progression and response to therapy. To achieve a complete picture of TME, multi-omics single-cell technologies are needed to characterize diverse individual cells within TME at both genotype and phenotype levels. Such analysis holds promise to move towards precision medicine. However, single-cell proteomics technologies are lagging far behind other single-cell omics technologies. Many studies have shown that mRNA abundance is a poor surrogate for protein abundance and cannot provide any insights into protein activity regulated by protein phosphorylation. Therefore, single-cell (phospho-)proteomics is critically important to provide complementary data that cannot be achieved by other omics technologies. Antibody-based immunoassays are primarily used for functional analysis of single cells, but they only can open a small window into the complex TME ecosystem due to their inherent limitations. Mass spectrometry (MS)-based (phospho-)proteomics is a powerful tool for genome-scale proteome profiling and site-specific quantification of 1,000s of phosphorylation sites. However, it does not meet the merit for single-cell (phospho-)proteomics analysis. There are three major challenges that need to be addressed: 1) low recovery for phospho-enrichment, 2) insufficient MS sensitivity, 3) low sample throughput. We propose to develop a single-cell (phospho-)proteomics platform to address these three challenges for robust rapid analysis of single cells at both proteome and phosphoproteome levels. The project feasibility is strongly supported by our recent progress in many aspects of technology development. The new platform will be developed through integration of a high-recovery sample preparation platform for single-cell processing and phospho-enrichment with a high-efficiency MS platform to enhance MS detection sensitivity and sample multiplexing to improve sample throughput. We envision that the single-cell MS platform will eventually become an indispensable tool for robust, rapid, deep (phospho-)proteomic analysis of single cells and TME. In turn, it will make substantial contributions to improve our understanding of cancer biology and accelerate the movement towards precision medicine.
