The Science

The human body comprises trillions of cells with hundreds of different cell types, which are spatially organized along with their extracellular matrix to form tissues and organs with diverse functionalities. Spatial proteomics for proteome mapping of human tissues at high spatial resolution is crucial for phenotypic characterization of tissue heterogeneity and the microenvironment within a spatial context. Currently, there are no spatial proteomics technologies commonly accessible for robust, cost-effective proteome mapping of tissues. We developed a robust, easy-to-use spatial proteomics technique. This innovative approach enables deep proteome mapping of tissues and profiling of specific regions of interest, advancing our understanding of spatial biology and tissue organization. 

The Impact

Existing antibody-based spatial proteomics methods are limited by issues such as low multiplexing capacity and non-specific binding, which provide only a narrow view of the proteome. The new spatial proteomics technique has addressed this issue and can be broadly applied to different types of tissues for enabling deep proteome mapping of tissues at high spatial resolutions. With its easy implementation, robustness, and cost effectiveness, this new technique may pave the way for routine proteome mapping of tissues and profiling of regions of interest. This could make significant contributions to spatial biology.          

Summary

With advanced mass spectrometry (MS)-based proteomics, genome-scale proteome coverage can be achieved from bulk tissues. However, bulk tissue analysis lacks the spatial resolution needed to study tissue heterogeneity and microenvironments. Researchers developed a new spatial proteomics technique with effective integration of wet collection of single microscale tissue voxels and Surfactant-assisted One-Pot voxel processing termed wcSOP for robust, cost-effective single voxel (pixel) proteomics. wcSOP capitalizes on buffer droplet-assisted wet collection of single voxels dissected by LCM to the tube cap and SOP voxel processing in the same collection cap. This technique allows reproducible label-free quantification of ~900 and ~4,600 proteins for single voxels at 20 µm × 20 µm × 10 µm (~1 cell region) and 200 µm × 200 µm × 10 µm (~100 cell region), respectively. 100s-1000s of protein signatures, as well as region-specific pathways, were spatially resolved between diseased (breast cancer tumor or AD[ST1]  amyloid plaque) and adjacent normal regions. Its robustness and sensitivity were demonstrated by 2-D proteome mapping of tissues at high spatial resolutions. With its easy implementation, robustness, and cost effectiveness, this new technique may pave the way for routine robust single-voxel proteomics and spatial proteomics.     

PNNL Contact

Tujin Shi, tujin.shi@pnnl.gov 

Funding

This work was supported bya  grant (to T.S.) from the National Institutes of Health (NIH) Common Fund, Human Biomolecular Atlas Program (HuBMAP) grant. PNNL is a multi-program national laboratory operated by Battelle for the Department of Energy (DOE) under Contract DE-AC05-76RLO 1830.