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@ARTICLE{Rademacher:302142,
      author       = {A. Rademacher$^*$ and A. Huseynov$^*$ and M.
                      Bortolomeazzi$^*$ and S. J. Wille$^*$ and S. Schumacher$^*$
                      and P. Sant$^*$ and D. Keitel$^*$ and K. Okonechnikov$^*$
                      and D. R. Ghasemi$^*$ and K. W. Pajtler$^*$ and J.-P.
                      Mallm$^*$ and K. Rippe$^*$},
      title        = {{C}omparison of spatial transcriptomics technologies using
                      tumor cryosections.},
      journal      = {Genome biology},
      volume       = {26},
      number       = {1},
      issn         = {1465-6906},
      address      = {London},
      publisher    = {BioMed Central},
      reportid     = {DKFZ-2025-01260},
      pages        = {176},
      year         = {2025},
      note         = {#EA:B066#LA:W192#LA:B066#},
      abstract     = {Spatial transcriptomics technologies are revolutionizing
                      our understanding of intra-tumor heterogeneity and the tumor
                      microenvironment by revealing single-cell molecular profiles
                      within their spatial tissue context. The rapid development
                      of spatial transcriptomics methods, each with unique
                      characteristics, makes it challenging to select the most
                      suitable technology for specific research objectives. Here,
                      we compare four imaging-based approaches-RNAscope HiPlex,
                      Molecular Cartography, Merscope, and Xenium-alongside
                      Visium, a sequencing-based method. These technologies were
                      employed to study cryosections of medulloblastoma with
                      extensive nodularity (MBEN), a tumor chosen for its distinct
                      microanatomical features.Our analysis reveals that automated
                      imaging-based spatial transcriptomics methods are
                      well-suited to delineate the intricate MBEN microanatomy and
                      capture cell-type-specific transcriptome profiles. We devise
                      approaches to compare the sensitivity and specificity of
                      different methods, along with their unique attributes, to
                      guide method selection based on the research objective.
                      Furthermore, we demonstrate how reimaging slides after the
                      spatial transcriptomics analysis can significantly improve
                      cell segmentation accuracy and integrate additional
                      transcript and protein readouts, expanding the analytical
                      possibilities and depth of insight.This study underscores
                      important distinctions between spatial transcriptomics
                      technologies and offers a framework for evaluating their
                      performance. Our findings support informed decisions
                      regarding methods and outline strategies to improve the
                      resolution and scope of spatial transcriptomic analyses,
                      ultimately advancing spatial transcriptomics applications in
                      solid tumor research.},
      keywords     = {MERFISH (Other) / Medulloblastoma (Other) / Merscope
                      (Other) / Molecular Cartography (Other) / RNAscope (Other) /
                      Spatial transcriptomics (Other) / Visium (Other) / Xenium
                      (Other)},
      cin          = {B066 / W192 / B062 / HD01},
      ddc          = {570},
      cid          = {I:(DE-He78)B066-20160331 / I:(DE-He78)W192-20160331 /
                      I:(DE-He78)B062-20160331 / I:(DE-He78)HD01-20160331},
      pnm          = {312 - Funktionelle und strukturelle Genomforschung
                      (POF4-312)},
      pid          = {G:(DE-HGF)POF4-312},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:40542418},
      pmc          = {pmc:PMC12180266},
      doi          = {10.1186/s13059-025-03624-4},
      url          = {https://inrepo02.dkfz.de/record/302142},
}