An integrative spatial multi-omic workflow for unified analysis of tumor tissue

Kriel, J; Moffet, JJD; Lu, T; Fatunla, OE; Narayana, VK; Valkovic, A; Maluenda, A; McConville, MJ; Tsui, E; Whittle, JR; Best, SA; Freytag, S

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;
Details: Publication Year 2026-02-23,Volume 6,Issue #2,Page 101306
Journal Title: Cell Reports Methods
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.
Publisher: Cell Press
Keywords: Humans; Workflow; *Glioma/genetics/pathology/metabolism; *Metabolomics/methods; *Brain Neoplasms/genetics/pathology/metabolism; Mutation; Transcriptome; Gene Expression Profiling/methods; Multiomics; CP: cancer biology; CP: systems biology; CosMx; Maldi-tof; Merscope; Xenium; alignment; cell segmentation; glioma; spatial metabolomics; spatial multi-omics; spatial transcriptomics
Research Division(s): Personalised 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: 2026-03-16 01:38:20

Last Modified: 2026-03-16 01:52:35