Abstract 3877: Multi-modal analysis of paracrine signaling in group 3/4 medulloblastoma

Abstract

Abstract Medulloblastoma (MB) is the most common primary brain malignancy in kids, with the group 3 and 4 subtypes (G3/4) being the most aggressive. Recent single-cell genomics studies have identified the G3/4 MB cell of origin and point to disrupted stem-cell differentiation as a key factor in MB pathogenesis. However, surprisingly little is known about the contribution of tumor-supportive paracrine signaling to the ontogeny of this disease. The spatial organization of MB cellular hierarchies is not completely understood. We profiled N=24 G3/4 MBs from UCSF patients via single-nucleus RNA sequencing (snRNA-seq). Of these cases, N=10 were profiled via single-cell assay for transposase-accessible chromatin by sequencing (scATAC-seq). To capture the spatial context, we profiled an additional 20 samples via spatial transcriptomics using the Visium and Xenium platforms. We found that the standard Xenium brain capture set was inadequate, and we developed a highly specific capture set for G3/4 MBs. In particular, our panel resolves cell-type differences in the stage of MB lineage commitment, from rhombic-lip progenitors to more differentiated unipolar brush-like cells. Altogether, over 110,000 nuclear-sequencing libraries and over 1,898,000 spatially-resolved single-cell libraries were generated. We inferred cell-cell communication signals from our snRNA-seq data by identifying co-expressed receptors and their cognate ligands. We then performed an integrated analysis of our snRNA-seq and scATAC-seq data to infer the cis-regulatory enhancers of those signaling genes, as well as the transcription factors that bind them. We employed our spatial transcriptomics data to confirm paracrine signaling networks inferred from nuclear-sequencing data. We found that distinct MB cell types corresponding to different stages of differentiation occupied specific spatial domains. The results of our ongoing analysis of this spatially-resolved single-cell atlas will be presented. This study paves the way for innovative therapeutic strategies targeting paracrine signaling in G3/4 MB. Citation Format: Bohyeon Yu, Jangham Jung, Aaron Diaz. Multi-modal analysis of paracrine signaling in group 3/4 medulloblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3877.