An integrative spatial multi-omic workflow for unified analysis of tumor tissue
- Author(s)
- Kriel, J; Moffet, JJD; Lu, T; Fatunla, OE; Narayana, VK; Valkovic, A; Maluenda, A; McConville, MJ; Tsui, E; Whittle, JR; Best, SA; Freytag, S;
- Journal Title
- Cell Reports Methods
- Publication Type
- Online publication before print
- Abstract
- Combining molecular profiling with imaging techniques has advanced the field of spatial biology, offering new insights into complex biological processes. Focusing on diffuse IDH-mutated glioma, this study presents a workflow for spatial multi-omics integration (SMINT) specifically combining spatial transcriptomics and spatial metabolomics. Our workflow incorporates both existing and custom-developed computational tools to enable cell segmentation and registration of spatial coordinates from both modalities to a common coordinate framework. During our investigation of cell segmentation strategies, we found that nuclei-only segmentation, while containing only 40% of segmented cell transcripts, enables accurate cell-type annotation but does not account for scenarios including delineation of multinucleated cells. Our integrative workflow including cell-morphology segmentation identified distinct cellular neighborhoods at the infiltrating edge of IDH-mutated gliomas, which were enriched in multinucleated and oligodendrocyte-lineage tumor cells and associated with differentially abundant metabolites.
- Keywords
- CP: cancer biology; CP: systems biology; CosMx; Maldi-tof; Merscope; Xenium; alignment; cell segmentation; glioma; spatial metabolomics; spatial multi-omics; spatial transcriptomics
- Department(s)
- Medical Oncology
- Publisher's Version
- https://doi.org/10.1016/j.crmeth.2026.101306
- Open Access at Publisher's Site
https://doi.org/10.1016/j.crmeth.2026.101306- Terms of Use/Rights Notice
- Refer to copyright notice on published article.
Creation Date: 2026-02-24 05:56:03
Last Modified: 2026-02-24 05:56:10