Journal Article

DKFZ-2025-01260

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Comparison of spatial transcriptomics technologies using tumor cryosections.

Rademacher, A. (First author)DKFZ* ; Huseynov, A. (First author)DKFZ* ; Bortolomeazzi, M. (First author)DKFZ* ; Wille, S. J.DKFZ* ; Schumacher, S.DKFZ* ; Sant, P.DKFZ* ; Keitel, D.DKFZ* ; Okonechnikov, K.DKFZ* ; Ghasemi, D. R.DKFZ* ; Pajtler, K. W.DKFZ* ; Mallm, J.-P.DKFZ* ; Rippe, K. (Last author)DKFZ*

2025
BioMed Central London

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Please use a persistent id in citations: doi:10.1186/s13059-025-03624-4

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.

Keyword(s): MERFISH ; Medulloblastoma ; Merscope ; Molecular Cartography ; RNAscope ; Spatial transcriptomics ; Visium ; Xenium

Note: #EA:B066#LA:W192#LA:B066#

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Contributing Institute(s):

1. B066 Chromatin-Netzwerke (B066)
2. Single-cell Open Lab (W192)
3. B062 Pädiatrische Neuroonkologie (B062)
4. DKTK HD zentral (HD01)

Research Program(s):

1. 312 - Funktionelle und strukturelle Genomforschung (POF4-312) (POF4-312)

Appears in the scientific report 2025

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Database coverage:
; ; Article Processing Charges ; BIOSIS Previews ; Biological Abstracts ; Clarivate Analytics Master Journal List ; Current Contents - Life Sciences ; DOAJ Seal ; Essential Science Indicators ; Fees ; IF >= 10 ; JCR ; SCOPUS ; Science Citation Index Expanded ; Web of Science Core Collection ; Zoological Record

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