All-at-once spatial proteome profiling of complex tissue context with single-cell-type resolution by proximity...

Area of Science:

• Proteomics
• Spatial Biology
• Biotechnology

Background:

• Spatial proteomics methods like laser microdissection-mass spectrometry (LMD-MS) and antibody imaging have limitations in sampling precision, throughput, and proteome coverage.
• Existing strategies struggle to balance detailed tissue architecture mapping with comprehensive proteome analysis.

Purpose of the Study:

• To introduce proximity labeling for spatial proteomics (PSPro) as a novel method for high-resolution cell-type proteome capture.
• To overcome the trade-offs associated with current spatial proteomics techniques.

Main Methods:

• PSPro combines antibody-targeted biotinylation with affinity purification for simultaneous proteome capture from single tissue slices.
• The method achieves sub-micrometer resolution and was benchmarked against flow cytometry and LMD-based workflows.
• Laser microdissection was integrated into PSPro to enable comparative analysis of cell subpopulations within the same tissue.

Main Results:

• PSPro demonstrated reliable performance in benchmarking studies.
• Thousands of proteins, including known cell markers, were enriched from ten distinct cell types in tumor and spleen tissues.
• Spatial proteome heterogeneity in pancreatic tumors, specifically in cancer and immune cells, was revealed through integrated LMD-PSPro analysis.

Conclusions:

• PSPro offers a user-friendly approach to spatial biology, shifting from an "antibody-epitope" to an "antibody-cell-type proteome" paradigm.
• The method enhances the ability to map tissue architectures and understand cell-type-specific proteomes in complex biological systems.
• PSPro provides a powerful tool for investigating spatial proteome heterogeneity and its implications in diseases like cancer.