Comparison of spatial transcriptomics technologies using tumor cryosections

Background: Spatial 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 of ST methods, each with unique features, presents a challenge in selecting the most appropriate technology for specific research objectives. Here, we compare four imaging-based ST methods – RNAscope HiPlex, Molecular Cartography, MERFISH/Merscope, and Xenium – together with sequencing-based ST (Visium). These technologies were used to study cryosections of medulloblastoma with extensive nodularity (MBEN), a tumor chosen for its distinct microanatomical features.