Spatially-resolved single-cell imaging of melanoma brain metastases identifies localized immune patterns predictive of immune checkpoint blockade response

Stefanos Voglis; Daniel Schulz; Nils Eling; Natalie De Souza; Luca Regli; Marian Christoph Neidert; Marcus Czabanka; Michael Weller; Emilie Le Rhun; Daniela Mihic-Probst; Mitchell Levesque; Bernd Bodenmiller

doi:10.1093/neuonc/noag128

Spatially-resolved single-cell imaging of melanoma brain metastases identifies localized immune patterns predictive of immune checkpoint blockade response

Neuro Oncol. 2026 May 28:noag128. doi: 10.1093/neuonc/noag128. Online ahead of print.

Authors

Stefanos Voglis^{1

2

3}, Daniel Schulz^{1

2}, Nils Eling^{1

2}, Natalie De Souza^{1

2}, Luca Regli³, Marian Christoph Neidert⁴, Marcus Czabanka⁵, Michael Weller⁶, Emilie Le Rhun⁷, Daniela Mihic-Probst⁸, Mitchell Levesque⁹, Bernd Bodenmiller^{1

2}

Affiliations

¹ Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland.
² Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland.
³ Department of Neurosurgery, Clinical Neuroscience Center, University Hospital Zurich, University of Zurich, Zurich, Switzerland.
⁴ Department of Neurosurgery, HOCH Health Ostschweiz, Cantonal Hospital of St. Gallen, St. Gallen, Switzerland.
⁵ Department of Neurosurgery, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt, Germany.
⁶ Department of Neurology, Clinical Neuroscience Center, University Hospital Zurich, University of Zurich, Zurich, Switzerland.
⁷ Department of Medical Oncology and Hematology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.
⁸ Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.
⁹ Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.

PMID: 42209753
DOI: 10.1093/neuonc/noag128

Abstract

Background: A subset of patients with advanced-stage melanoma with brain metastases respond intracranially to immune-checkpoint inhibitors (ICIs). We reasoned that features of the spatial architecture of the tumor microenvironment correlates with treatment responses.

Methods: We used highly-multiplexed single-cell imaging to characterize the TME in 44 samples of MBM patients; both treatment naïve subjects and subjects who had received ICI were included in the cohort. Samples were stained with a 42-plex metal-isotope tagged antibody panel and subsequently imaged using imaging mass cytometry. Downstream analysis focused on phenotypic and spatial characteristics of the tumor microenvironments of ICI responders and non-responders and on correlations of protein expression with overall and local progression-free survival.

Results: Single-cell phenotyping identified more than 1.1 million cells, predominantly tumor (67%) and immune cells (29%). ICI responders exhibited higher baseline proportions of B cells, IDO+ macrophages, and specific T cell subsets (regulatory and exhausted/activated CD8+). Conversely, neutrophil infiltration was negatively associated with intracranial response and survival. Spatial analysis revealed that responders possess a more localized, clustered immune cell pattern compared to the dispersed patterns seen in non-responders. Modeling CD8+ T cell distribution showed that localized infiltration was positively associated with overall and local progression-free survival, while dispersed patterns correlated with poorer outcomes. Furthermore, ICI-pretreated samples showed higher immune-tumor co-localization than treatment-naïve samples.

Conclusions: Our single-cell, spatially resolved characterization of the tumor microenvironment of human melanoma brain metastases demonstrated distinct phenotypic and spatial infiltration patterns of various immune cells that are associated with ICI response and survival outcomes.

Keywords: melanoma brain metastases; precision oncology; predictive biomarkers; proteomics; tumor microenvironment.

Plain language summary

While immunotherapy helps some patients with melanoma brain metastases, predicting success is difficult. This study analyzed over one million individual cells to map the tissue architecture of these brain tumors. This study discovered that the spatial arrangement of immune cells, rather than just their quantity, predicts treatment response and survival. Specifically, spatial T cell pattern matter, while the presence of neutrophils—a different immune cell—indicates a poorer outcome. This detailed atlas provides a vital resource for future research, helping doctors identify which patients will benefit from therapy and paving the way for more effective, targeted treatments.