Work

Protocol to characterize tumor microenvironment in a diffuse midline glioma mouse model using multi-omics approach on sequential sections

Year: 2026

Type: article

Abstract: Diffuse midline glioma (DMG) tumors form complex tumor-immune microenvironments with marked cellular heterogeneity. Here, we present a protocol to generate orthotopic DMG tumors in immunocompetent neonatal mice and to spatially characterize the tumor ecosystem using a multi-omics workflow on sequential brain sections. We detail procedures for brain freezing, cryosectioning, single-nuclei RNA sequencing, and Visium spatial transcriptomics. We then describe steps for cyclic immunofluorescence and integrative computational analysis to resolve cellular states and spatial organization. For complete details on the use and execution of this protocol, please refer to Collot et al. 1 1. Collot, R. ∙ Ruiz-Moreno, C. ∙ Honhoff, C. ... IGSF11-VISTA is a critical and targetable immune checkpoint axis in diffuse midline glioma Cancer Cell. 2026; 44 :641-657.e9 Full Text Full Text (PDF) Scopus (1) PubMed Google Scholar

Source: STAR Protocols

DOI: 10.1016/j.xpro.2026.104801

Authors: Raphaël Collot, Celina Honhoff, Cristian Ruiz-Moreno, Ravian L. van Ineveld, Anne C. Rios

Institutions: Oncode Institute, Princess Máxima Center, Utrecht University

Language: English

Topic: Single-cell and spatial transcriptomics

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

SDG: Good health and well-being

Open Access status: gold

Estimated APC paid: $1,550