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

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 mm2 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 mm2 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.