Imaging mass cytometry data from IDH wildtype glioblastomas

Myeloid cells are highly prevalent in glioblastoma (GBM), existing in a spectrum of phenotypic and activation states. We now have limited knowledge of the tumor microenvironment (TME) determinants that influence the localization and the functions of the diverse myeloid cell populations in GBM. In this dataset, we have used imaging mass cytometry to identify and map the various myeloid populations in the human GBM tumor microenvironment (TME) using known markers for myeloid and neoplastic cells in GBM. Our analyses of these data found that different myeloid populations had distinct and reproducible compartmentalization patterns in the GBM TME that were driven by tissue hypoxia and varied homotypic and heterotypic cellular interactions. This dataset consists of imaging mass cytometry data (16-bit TIFF images) for 8 glioblastomas and 1 tonsil sourced from the Salford Royal NHS Trust Biobank.

Methods
In brief, 5 um FFPE sections from 8 primary glioblastomas (see Cases.xls) and 1 tonsil (as a control) were stained using the protocol recommended by Standard BioTools (https://www.standardbio.com/products/instruments/hyperion) using a panel of metal-conjugated antibodies. They were then imaged on the Hyperion using the standard settings. Regions of interest were identified on serial-cut H&E stained sections by a neuropathologist, targeting regions either in the tumor or infiltrating the edge of the tumor. Raw TIFF images were then extracted from MCD files, and denoised using the IMC-Denoise method (https://www.nature.com/articles/s41467-023-37123-6). Single-cell information for each of the channels was extracted using the Bodenmiller pipeline (https://github.com/BodenmillerGroup/ImcSegmentationPipeline), with the resulting cell table (see cell_table.csv) detailing the single-cell expression of each of the markers in the panel, along with their X and Y locations in the region of interest. Details of whether the regions of interest (ROI) came from either edge or core regions (as defined by histopathological features by a neuropathologist) are detailed in edge_core.csv.