Multiplex digital spatial profiling of proteins and RNA in fixed tissue

Area of Science:

• Biotechnology
• Molecular Biology
• Genomics
• Proteomics

Background:

• Digital Spatial Profiling (DSP) is an advanced technique for highly multiplexed spatial analysis of proteins and RNAs.
• It is particularly suitable for formalin-fixed, paraffin-embedded (FFPE) samples, preserving tissue integrity.
• The method utilizes oligonucleotide tags attached to affinity reagents via photocleavable linkers for spatial readout.

Discussion:

• DSP allows for precise spatial patterning of photocleavage within regions of interest (ROIs) comprising 1 to 5,000 cells.
• Single-cell sensitivity is achievable for protein profiling using antibody readouts.
• RNA detection is feasible down to approximately 600 individual mRNA transcripts.

Key Insights:

• The study demonstrates spatial profiling of up to 44 proteins and 96 genes using the nCounter system.
• Advanced RNA profiling of 1,412 genes was achieved using next-generation sequencing (NGS).
• DSP successfully profiled lymphoid, colorectal tumor, and autoimmune tissues.

Outlook:

• DSP can analyze proteins and RNAs in biobanked samples.
• The technology can profile immune markers in patient samples.
• This spatial profiling approach holds significant prognostic and predictive potential for clinical decision-making.