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Updated: Jan 10, 2026

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection
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Systematic benchmarking of imaging spatial transcriptomics platforms in FFPE tissues.

Huan Wang1, Ruixu Huang2, Jack Nelson1

  • 1Spatial Technology Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.

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|November 20, 2025
PubMed
Summary
This summary is machine-generated.

This study benchmarks three imaging spatial transcriptomics (iST) platforms for analyzing formalin-fixed paraffin-embedded (FFPE) tissues. Xenium showed higher transcript counts, while Xenium and CosMx aligned well with single-cell transcriptomics for spatial cell typing.

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Area of Science:

  • Spatial transcriptomics
  • Molecular pathology
  • Biotechnology

Background:

  • Emerging imaging spatial transcriptomics (iST) platforms analyze cell interactions and gene expression in tissues.
  • These platforms are valuable for formalin-fixed paraffin-embedded (FFPE) tissues, commonly used in pathology.
  • Benchmarking is crucial for selecting appropriate iST methods for FFPE sample analysis.

Purpose of the Study:

  • To benchmark the performance of three commercial iST platforms: 10X Xenium, Vizgen MERSCOPE, and Nanostring CosMx.
  • To evaluate their technical and biological performance on tissue microarrays (TMAs) with diverse tumor and normal tissues.
  • To guide researchers in choosing the optimal iST method for FFPE samples.

Main Methods:

  • Comparative analysis of 10X Xenium, Vizgen MERSCOPE, and Nanostring CosMx platforms.
  • Utilized serial sections from TMAs containing 17 tumor and 16 normal tissue types.
  • Assessed transcript counts, specificity, concordance with single-cell transcriptomics, and cell typing capabilities.

Main Results:

  • 10X Xenium consistently yielded higher transcript counts per gene without compromising specificity.
  • Xenium and CosMx demonstrated concordance with orthogonal single-cell transcriptomics for RNA transcript measurement.
  • All platforms performed spatially resolved cell typing, with Xenium and CosMx identifying more sub-clusters than MERSCOPE, despite variations in error rates.

Conclusions:

  • The study provides a comprehensive benchmark of three leading iST platforms for FFPE tissue analysis.
  • 10X Xenium offers high transcript yield and specificity, while Xenium and CosMx excel in spatially resolved cell typing.
  • The findings will aid researchers in selecting the most suitable iST platform for their specific FFPE-based studies.