Spatial-Resolution Cell Type Proteome Profiling of Cancer Tissue by Fully Integrated Proteomics Technology

Abstract

Increasing attention has been focused on cell type proteome profiling for understanding the heterogeneous multicellular microenvironment in tissue samples. However, current cell type proteome profiling methods need large amounts of starting materials which preclude their application to clinical tumor specimens with limited access. Here, by seamlessly combining laser capture microdissection and integrated proteomics sample preparation technology SISPROT, specific cell types in tumor samples could be precisely dissected with single cell resolution and processed for high-sensitivity proteome profiling. Sample loss and contamination due to the multiple transfer steps are significantly reduced by the full integration and noncontact design. H&E staining dyes which are necessary for cell type investigation could be selectively removed by the unique two-stage design of the spintip device. This easy-to-use proteome profiling technology achieved high sensitivity with the identification of more than 500 proteins from only 0.1 mm and 10 μm thickness colon cancer tissue section. The first cell type proteome profiling of four cell types from one colon tumor and surrounding normal tissue, including cancer cells, enterocytes, lymphocytes, and smooth muscle cells, was obtained. 5271, 4691, 4876, and 2140 protein groups were identified, respectively, from tissue section of only 5 mm and 10 μm thickness. Furthermore, spatially resolved proteome distribution profiles of enterocytes, lymphocytes, and smooth muscle cells on the same tissue slices and across four consecutive sections with micrometer distance were successfully achieved. This fully integrated proteomics technology, termed LCM-SISPROT, is therefore promising for spatial-resolution cell type proteome profiling of tumor microenvironment with a minute amount of clinical starting materials.

Mutual regulation of JAG2 and PRAF2 promotes migration and invasion of colorectal cancer cells uncoupled from epithelial–mesenchymal transition

“…Protein concentration was determined by Pierce Micro BCA Kit (Thermo). The obtained tissue lysate was processed by using SISPROT protocol as previously described [17]. Briefly, the samples were firstly acidified to pH 2–3 and loaded onto 200 μL or 10 μL spintip device packed with one plug of C18 disk (3 M Empore, USA) and 0.6 mg of 20 μm POROS SCX beads (Applied Biosystems, USA) in tandem.…”

Proteomic Profiling and Artificial Intelligence for Hepatocellular Carcinoma Translational Medicine

“…For example, LCM-SISPROT technology based on immunochemistry has been used to identify HCC cell population specific spatial proteome [26]. Moreover, single cell resolution multiomics technologies provide valuable opportunity to measure various biomolecules at their low concentrations [27,28].…”

Unraveling Heterogeneity in Transcriptome and Its Regulation Through Single-Cell Multi-Omics Technologies

“…Following the advent of spatial transcriptomic era, methods to spatially resolve proteome are also being developed (Angelo et al, 2014;Giesen et al, 2014). Recent improvements include greater multiplexing capabilities (up to thousands of proteins) and reduced input requirements, albeit not at a single-cell level (Xu et al, 2018;Davis et al, 2019). Spatially resolved methods are also moving toward increased versatility.…”