Faculty, Staff and Student Publications

Publication Date

9-26-2025

Journal

Nature Communications

DOI

10.1038/s41467-025-63414-1

PMID

41006245

PMCID

PMC12474935

PubMedCentral® Posted Date

9-26-2025

PubMedCentral® Full Text Version

Post-print

Abstract

Imaging-based spatial transcriptomics (ST) is evolving as a pivotal technology in studying tumor biology and associated microenvironments. However, the strengths of the commercially available ST platforms in studying spatial biology have not been systematically evaluated using rigorously controlled experiments. We use serial 5 μm sections of formalin-fixed, paraffin-embedded surgically resected lung adenocarcinoma and pleural mesothelioma samples in tissue microarrays to compare the performance of the ST platforms (CosMx, MERFISH, and Xenium (uni/multi-modal)) in reference to bulk RNA sequencing, multiplex immunofluorescence, GeoMx, and hematoxylin and eosin staining data. In addition to an objective assessment of automatic cell segmentation and phenotyping, we perform a manual phenotyping evaluation to assess pathologically meaningful comparisons between ST platforms. Here, we show the intricate differences between the ST platforms, reveal the importance of parameters such as probe design in determining the data quality, and suggest reliable workflows for accurate spatial profiling and molecular discovery.

Keywords

Humans, Gene Expression Profiling, Paraffin Embedding, Formaldehyde, Single-Cell Analysis, Lung Neoplasms, Transcriptome, Tissue Array Analysis, Mesothelioma, Tissue Fixation, Adenocarcinoma of Lung, Sequence Analysis, RNA

Published Open-Access

yes

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