Comparison of spatial transcriptomics technologies using tumor cryosections

Abstract

AbstractBackgroundSpatial transcriptomics (ST) 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 evolution ofSTmethods, each with unique features, presents a challenge in selecting the most appropriate technology for specific research objectives. Here, we compare four imaging-basedSTmethods – RNAscope HiPlex, Molecular Cartography, MERFISH/Merscope, and Xenium – together with sequencing-basedST(Visium). These technologies were used to study cryosections of medulloblastoma with extensive nodularity (MBEN), a tumor chosen for its distinct microanatomical features.ResultsOur analysis reveals that automated imaging-basedSTmethods are well suited to delineating the intricate MBEN microanatomy, capturing cell-type-specific transcriptome profiles. We devise approaches to compare the sensitivity and specificity of the different methods together with their unique attributes to guide method selection based on the research aim. Furthermore, we demonstrate how reimaging of slides after theSTanalysis can markedly improve cell segmentation accuracy and integrate additional transcript and protein readouts to expand the analytical possibilities and depth of insights.ConclusionsThis study highlights key distinctions between variousSTtechnologies and provides a set of parameters for evaluating their performance. Our findings aid in the informed choice ofSTmethods and delineate approaches for enhancing the resolution and breadth of spatial transcriptomic analyses, thereby contributing to advancingSTapplications in solid tumor research.