An integrated protocol for multiplexed DNA FISH and protein detection in large tissue sections

Area of Science:

• Spatial biology
• Molecular pathology
• Single-cell analysis

Background:

• Omics technologies like genomics and proteomics are crucial for understanding biological systems.
• Integrating spatial context with omics data provides in situ biological insights at the single-cell level.

Purpose of the Study:

• To present a protocol for combined multiplexed gene and protein detection in large tissue sections.
• To enable high-throughput single-cell analysis of tumor heterogeneity and microenvironment.

Main Methods:

• Utilized DNA FISH for multiplexed targeted gene detection.
• Employed multiplexed immunofluorescence for protein detection.
• Integrated both methods on the PhenoCycler Fusion platform for unified data generation.

Main Results:

• Generated a single dataset with simultaneous gene and protein readouts at the single-cell level.
• Achieved high-throughput analysis of thousands to millions of cells in large tissue sections.
• Enabled characterization of malignant cells based on genetic aberrations and deciphering of the cellular microenvironment.

Conclusions:

• The presented protocol offers a powerful tool for spatial omics analysis in large tissue samples.
• This integrated approach facilitates comprehensive understanding of tumor biology and cellular interactions.