Spatial pharmaco-multiomics reveals drug distribution, metabolic niches, and spatially constrained resistance in medulloblastoma

This dataset contains the raw spatial multi-omics data generated for a same-section spatial pharmaco-multiomics study of Sonic Hedgehog medulloblastoma (SHH-MB). The dataset integrates matrix-assisted laser desorption/ionisation mass spectrometry imaging (MALDI-MSI)–based spatial metabolomics, 10x Genomics Visium whole-transcriptome spatial profiling, and 10x Genomics Xenium high-resolution in situ transcriptomics acquired from the same histological tissue sections.

Samples include SHH-MB patient-derived orthotopic xenograft (PDOX) mouse tumours treated with the CDK4/6 inhibitor palbociclib, as well as primary human SHH-MB tumour specimens where indicated. MALDI-MSI data capture the spatial distribution of palbociclib and endogenous metabolites across tumour bulk, tumour–brain interface, and perivascular regions. Visium data provide spatially resolved whole-transcriptome expression profiles aligned to corresponding histological contexts. Xenium data deliver single-cell–scale spatial transcriptomic maps of selected gene panels, enabling high-resolution characterisation of tumour, stromal, and vascular compartments.

Raw data files include:

1. MALDI-MSI raw spectral and imaging files acquired in positive ion modes, preserving full mass-to-charge and spatial information.

2. Visium raw sequencing files (FASTQ) and associated spatial metadata, including spot coordinates and histology images.

3. Xenium raw output files, including molecule-level transcript detections, cell segmentation data, and spatial coordinates.

These data enable independent reanalysis of spatial drug penetration, metabolic landscapes, transcriptional programs, and resistance states within SHH-MB, and support reproducibility of the integrated same-section spatial pharmaco-multiomics framework described in the accompanying study.