Journal: Brain Tumor Pathology

Article Title: Comprehensive molecular characterization of craniopharyngiomas using whole transcriptome and spatial transcriptomics approaches

doi: 10.1007/s10014-025-00509-z

Figure Lengend Snippet: Cellular clustering and spatial localization in craniopharyngioma tissue sections using Xenium spatial transcriptomics. Left: UMAP plot display the distribution of 201,499 profiled cells from two ACP and one PCP. Cells are grouped into 13 distinct clusters based on dimensionality reduction and gene expression profiles from the Human Multi-tissue and Cancer Panel. Right: Adjacent high-resolution spatial maps for each sample depict the localization of the clusters directly on histologic sections of CP samples (top to bottom: one PCP, two ACP). Each cell cluster is color-coded consistently with the UMAP for visual correlation between transcriptional identity and tissue localization

Article Snippet: Our Xenium-based spatial transcriptomics analysis was limited to 377 genes included in the Human Multi-tissue and Cancer Panel.

Techniques: Gene Expression

Journal: Brain Tumor Pathology

Article Title: Comprehensive molecular characterization of craniopharyngiomas using whole transcriptome and spatial transcriptomics approaches

doi: 10.1007/s10014-025-00509-z

Figure Lengend Snippet: Differentially expressed genes between ACP and PCP obtained from Xenium-based spatial transcriptomics analysis. Bar plot illustrating the log2 fold change of 41 differentially expressed genes between ACP and PCP samples, with upregulated genes shown above and downregulated genes below the axis. Bar colors represent statistical significance, with a color gradient from blue (less significant) to red (highly significant) based on –log10 ( p value) ( a ). High-resolution spatial distribution maps display selected genes with significant expression differences between ACP and PCP, visualizing localization patterns of four upregulated (APCDD1, GATM, MCF2L, EPCAM) and seven downregulated (SERPINB3, CLCA2, ADAM28, SLC26A, GPRC5A, BASP1, TREM2) transcripts across tissue sections from two ACP and one PCP case. Red intensity indicates greater transcript abundance in spatial context ( b ) ( ACP adamantinomatous craniopharyngioma, PCP papillary craniopharyngioma)

Article Snippet: Our Xenium-based spatial transcriptomics analysis was limited to 377 genes included in the Human Multi-tissue and Cancer Panel.

Techniques: Expressing

Journal: Brain Tumor Pathology

Article Title: Comprehensive molecular characterization of craniopharyngiomas using whole transcriptome and spatial transcriptomics approaches

doi: 10.1007/s10014-025-00509-z

Figure Lengend Snippet: Reference-based clustering and spatial localization of brain cell populations in craniopharyngioma tissues using Xenium spatial transcriptomics. The left panel displays a UMAP plot of reference-based cluster annotation for Xenium-derived transcriptomes, generated by mapping spatial transcriptomic data from ACP and PCP to the Allen Brain Map RNA-Seq Data: Human MTG 10 × SEA-AD reference. Each color represents a distinct cell cluster identified in the tissue, revealing 24 separable clusters including perivascular macrophages (microglia-PVM), endothelial cells, astrocytes, and others. The right panels present high-resolution spatial images of whole tissue slides from PCP and ACP sections, where colored regions reflect the spatial expression and localization of these identified clusters within the tumor and adjacent brain tissue ( a ). Additional UMAP plots highlight the spatial distribution of three selected cell types: perivascular macrophages (microglia-PVM), endothelial cells, and astrocytes ( b ). Cell annotation was performed using existing brain and immune cell atlases due to the limited coverage of the gene panel, and not all clusters could be annotated with complete certainty ( ACP adamantinomatous craniopharyngioma, PCP papillary craniopharyngioma)

Article Snippet: Our Xenium-based spatial transcriptomics analysis was limited to 377 genes included in the Human Multi-tissue and Cancer Panel.

Techniques: Derivative Assay, Generated, RNA Sequencing, Expressing