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Comparison of imaging based single-cell resolution spatial transcriptomics profiling platforms using formalin-fixed paraffin-embedded tumor samples

Author

Listed:
  • Nejla Ozirmak Lermi

    (The University of Texas MD Anderson Cancer Center)

  • Max Molina Ayala

    (The University of Texas MD Anderson Cancer Center)

  • Sharia Hernandez

    (The University of Texas MD Anderson Cancer Center)

  • Wei Lu

    (The University of Texas MD Anderson Cancer Center)

  • Khaja Khan

    (The University of Texas MD Anderson Cancer Center)

  • Alejandra Serrano

    (The University of Texas MD Anderson Cancer Center)

  • Idania Lubo

    (The University of Texas MD Anderson Cancer Center)

  • Leticia Hamana

    (The University of Texas MD Anderson Cancer Center)

  • Katarzyna Tomczak

    (The University of Texas MD Anderson Cancer Center)

  • Sean Barnes

    (The University of Texas MD Anderson Cancer Center)

  • Jinzhuang Dou

    (The University of Texas MD Anderson Cancer Center)

  • Qingnan Liang

    (The University of Texas MD Anderson Cancer Center)

  • Maria Gabriela Raso

    (The University of Texas MD Anderson Cancer Center)

  • Ximing Tang

    (The University of Texas MD Anderson Cancer Center)

  • Mei Jiang

    (The University of Texas MD Anderson Cancer Center)

  • Beatriz Sanchez-Espiridion

    (The University of Texas MD Anderson Cancer Center)

  • Annikka Weissferdt

    (The University of Texas MD Anderson Cancer Center)

  • John Heymach

    (The University of Texas MD Anderson Cancer Center)

  • Jianjun Zhang

    (The University of Texas MD Anderson Cancer Center)

  • Boris Sepesi

    (The University of Texas MD Anderson Cancer Center)

  • Tina Cascone

    (The University of Texas MD Anderson Cancer Center)

  • Anne Tsao

    (The University of Texas MD Anderson Cancer Center)

  • Mehmet Altan

    (The University of Texas MD Anderson Cancer Center)

  • Reza Mehran

    (The University of Texas MD Anderson Cancer Center)

  • Don Gibbons

    (The University of Texas MD Anderson Cancer Center)

  • Ignacio Wistuba

    (The University of Texas MD Anderson Cancer Center)

  • Cara Haymaker

    (The University of Texas MD Anderson Cancer Center)

  • Ken Chen

    (The University of Texas MD Anderson Cancer Center)

  • Luisa M. Solis Soto

    (The University of Texas MD Anderson Cancer Center)

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.

Suggested Citation

  • Nejla Ozirmak Lermi & Max Molina Ayala & Sharia Hernandez & Wei Lu & Khaja Khan & Alejandra Serrano & Idania Lubo & Leticia Hamana & Katarzyna Tomczak & Sean Barnes & Jinzhuang Dou & Qingnan Liang & M, 2025. "Comparison of imaging based single-cell resolution spatial transcriptomics profiling platforms using formalin-fixed paraffin-embedded tumor samples," Nature Communications, Nature, vol. 16(1), pages 1-16, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-63414-1
    DOI: 10.1038/s41467-025-63414-1
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    References listed on IDEAS

    as
    1. Amanda Janesick & Robert Shelansky & Andrew D. Gottscho & Florian Wagner & Stephen R. Williams & Morgane Rouault & Ghezal Beliakoff & Carolyn A. Morrison & Michelli F. Oliveira & Jordan T. Sicherman &, 2023. "High resolution mapping of the tumor microenvironment using integrated single-cell, spatial and in situ analysis," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    2. Valero-Mora, Pedro M., 2010. "ggplot2: Elegant Graphics for Data Analysis," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 35(b01).
    Full references (including those not matched with items on IDEAS)

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