NicheProt: Cell-type-resolved proteomics of tissue compartments.

Area of Science:

• Proteomics
• Cell Biology
• Immunology

Background:

• Spatial proteomics provides insights into cellular functions within tissues.
• Laser capture microdissection and mass spectrometry offer proteomic profiling but lack cell-type specificity.
• Analyzing specific cell types within defined tissue microenvironments remains challenging.

Purpose of the Study:

• To develop a novel method for cell-type and microregion-resolved spatial proteomics.
• To identify distinct dendritic cell phenotypes within specific niches of the inflamed mouse spleen.

Main Methods:

• Developed NicheProt, a 3D optical microscopy-guided, photobleaching-mediated cell barcoding technique.
• Applied sequential bottom-up proteomic analysis to isolated cell populations.
• Utilized NicheProt to analyze CD11c+ dendritic cells in the mouse spleen.

Main Results:

• Identified two distinct CD11c+ dendritic cell phenotypes based on spatial location in the inflamed mouse spleen.
• Characterized these compartment-specific populations by proteomic signatures with 54 protein level differences.
• Demonstrated the capability of NicheProt for high-resolution spatial proteomic analysis.

Conclusions:

• NicheProt enables precise isolation of specific cell types from defined tissue niches.
• This method facilitates the discovery of previously unrecognized cell subtypes and their functions.
• Spatial proteomics guided by 3D microscopy is powerful for understanding tissue complexity.