Multi-pronged analysis of pediatric low-grade glioma and ganglioglioma reveals a unique tumor microenvironment associated with BRAF alterations

Shadi Zahedi; Kent Riemondy; Tian Liu; Andrea M Griesinger; Andrew M Donson; April A Apfelbaum; Rui Fu; Julian Grandvallet Contreras; Michele Crespo; John DeSisto; Madeline M Groat; Emil Bratbak; Adam Green; Todd C Hankinson; Michael Handler; Rajeev Vibhakar; Nicholas Willard; Nicholas K Foreman; Tzu Phang; Jean Mulcahy Levy

doi:10.1111/bpa.70023

Multi-pronged analysis of pediatric low-grade glioma and ganglioglioma reveals a unique tumor microenvironment associated with BRAF alterations

Brain Pathol. 2025 Jun 30:e70023. doi: 10.1111/bpa.70023. Online ahead of print.

Authors

Shadi Zahedi^{1

2

3}, Kent Riemondy⁴, Tian Liu¹, Andrea M Griesinger^{1

2

3}, Andrew M Donson^{1

2}, April A Apfelbaum^{5

6}, Rui Fu⁴, Julian Grandvallet Contreras¹, Michele Crespo^{1

2}, John DeSisto^{1

2}, Madeline M Groat^{1

2}, Emil Bratbak^{1

2}, Adam Green^{1

2}, Todd C Hankinson^{1

2

7}, Michael Handler^{2

7}, Rajeev Vibhakar^{1

2}, Nicholas Willard⁸, Nicholas K Foreman^{1

2

7}, Tzu Phang¹, Jean Mulcahy Levy^{1

2

9}

Affiliations

¹ Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA.
² Department of Pediatrics, Morgan Adams Foundation Pediatric Brain Tumor Research Program, Children's Hospital Colorado, Aurora, Colorado, USA.
³ Clinical Science Program, Graduate School, Anschutz Medical Campus, University of Colorado, Denver, Colorado, USA.
⁴ RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA.
⁵ Department of Pediatric Oncology, Broad Institute Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Dana-Farber Cancer/Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts, USA.
⁶ Department of Pediatrics, Harvard Medical School, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
⁷ Department of Neurosurgery, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA.
⁸ Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA.
⁹ Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA.

PMID: 40588233
DOI: 10.1111/bpa.70023

Abstract

Pediatric low-grade gliomas (pLGG) comprise 35% of all brain tumors. Despite favorable survival, patients experience significant morbidity from disease and treatments. A deeper understanding of pLGG biology is essential to identify novel, more effective, and less toxic therapies. We utilized single-cell RNA sequencing (scRNA-seq), spatial transcriptomics, and cytokine analyses to characterize and understand tumor and immune cell heterogeneity of pilocytic astrocytoma (PA) and ganglioglioma (GG). scRNA-seq revealed tumor and immune cells within the tumor microenvironment (TME). Tumor cell subsets include both progenitor and mature cell populations. Immune cells included myeloid and lymphocytic cells. There was a significant difference between the prevalence of two major myeloid subclusters between PA and GG. Bulk and single-cell cytokine analyses evaluated the immune cell signaling cascade with distinct immune phenotypes among tumor samples. KIAA1549-BRAF tumors appeared more immunogenic, secreting higher levels of immune cell activators and chemokines, compared to BRAF V600E tumors. Spatial transcriptomics revealed the differential gene expression of these chemokines and their location within the TME. A multi-pronged analysis demonstrated the complexity of the PA and GG TME and differences between genetic drivers that may influence their response to immunotherapy. Further investigation of immune cell infiltration and tumor-immune interactions is warranted.

Keywords: Pilocytic astrocytoma; chemokine; ganglioglioma; scRNA‐sequencing; spatial transcriptomics.

Abstract

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