Cellular and spatial continuum of TAM functional states governs immune exclusion and dictates immune checkpoint resistance in melanoma
7 affiliations
- 1Institute of Medical Bioinformatics and Systems Medicine (IBSM), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Breisacherstr. 153, 79110 Freiburg, Germany
- 2Institute of Molecular Medicine and Cell Research (IMMZ), University of Freiburg, Stefan-Meier-Str. 17, 79104 Freiburg, Germany
- 3Department of Internal Medicine, Medical Center - University of Freiburg, Hugstetter Str. 55, 79106 Freiburg, Germany
- 4Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
- 5Department of Dermatology and Venereology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Hauptstr. 7, 79104 Freiburg, Germany
- 6German Cancer Consortium (DKTK), Partner Site Freiburg, a partnership between DKFZ and Medical Center - University of Freiburg, Heidelberg, Germany
- 7BIOSS and Centre for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany
Abstract
Background: Immune checkpoint inhibitor (ICI) therapy has transformed melanoma treatment, yet many patients either fail to respond or develop resistance after an initial response. The cellular and spatial determinants within the tumor microenvironment (TME) that underlie these divergent ICI therapy outcomes remain poorly defined. Here, we aimed to characterize the immune composition and spatial organization of the TME associated with ICI response and resistance.
Methods: We integrated public scRNA-seq data (N = 32) with in-house spatial transcriptomics and imaging mass cytometry from an independent melanoma cohort (N = 6) to achieve high-resolution spatial profiling of the TME. This multimodal approach allowed us to map cellular heterogeneity within discrete spatial neighborhoods. To validate our findings, we constructed a scRNA-seq derived signature-matrix and deconvoluted a bulk RNA-seq cohort (N = 334). Clinical associations were assessed using Kaplan–Meier survival analysis, Cox hazard models, and a machine-learning classifier.
Results: We identified a distinct tumor-associated macrophage (TAM) state, termed lipid-associated TAMs (LA-TAMs), characterized by conserved lipid metabolic programs and tumor-specific adaptations in glycolysis under hypoxic conditions. Deep spatial multi-omics profiling revealed divergent immune architectures associated with treatment outcomes. In non-responder patients, LA-TAMs colocalized with sparsely distributed TIM3⁺ exhausted CD8⁺ T cells within an immune-excluded TME. In contrast, responder patients harbored interferon-primed CCL4+ TAMs (IFN-TAMs) spatially associated with Granzyme B⁺ activated CD8⁺ T cells, reflecting an immune-active microenvironment. These findings define contrasting macrophage-centered immune neighborhoods linked to ICI response. Interestingly, patients with LA-TAM–enriched neighborhoods were consistently non-responders or progressed during follow-up, irrespective of the presence of IFN-TAM neighborhoods. Lastly, we constructed a single-cell–derived signature matrix that estimates TAM fractions from bulk RNA-seq data and revealed LA-TAM abundance as a robust, independent predictor of poor ICI response and survival in a validation cohort.
Conclusions: Our study defines the spatial landscapes of TAM-heterogeneity in melanoma and identifies LA-TAM neighborhoods as an important feature of ICI resistance. Although patients span a continuum of TAM-centered immune states, the presence of LA-TAM is likely to diminish the beneficial effects of IFN-TAM–associated immune activation. Finally, our proposed Melanoma-TME–derived signature-matrix provides a translatable framework to robustly predict ICI response and resistance.
Supplementary Information: The online version contains supplementary material available at https://doi.org/10.1186/s13073-026-01794-9.
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BibTeX
@article{chakraborty2026cellular,
title = {{Cellular and spatial continuum of TAM functional states governs immune exclusion and dictates immune checkpoint resistance in melanoma}},
author = {Sajib Chakraborty and Eyleen Corrales and Ira Godbole and Nawal Madkhali and Tonmoy Das and Christopher Krolla and Alexander Nystrom and Frank Meiss and David Rafei and Bertram Bengsch and Geoffroy Andrieux and Melanie Boerries},
journal = {Genome Medicine},
year = {2026},
month = nov,
doi = {10.1186/s13073-026-01794-9},
url = {https://doi.org/10.1186/s13073-026-01794-9},
note = {CC BY-NC-ND 4.0},
}
RIS
TY - JOUR
TI - Cellular and spatial continuum of TAM functional states governs immune exclusion and dictates immune checkpoint resistance in melanoma
AU - Sajib Chakraborty
AU - Eyleen Corrales
AU - Ira Godbole
AU - Nawal Madkhali
AU - Tonmoy Das
AU - Christopher Krolla
AU - Alexander Nystrom
AU - Frank Meiss
AU - David Rafei
AU - Bertram Bengsch
AU - Geoffroy Andrieux
AU - Melanie Boerries
PY - 2026
DA - 2026/11/03
JO - Genome Medicine
DO - 10.1186/s13073-026-01794-9
UR - https://doi.org/10.1186/s13073-026-01794-9
AB - Background: Immune checkpoint inhibitor (ICI) therapy has transformed melanoma treatment, yet many patients either fail to respond or develop resistance after an initial response. The cellular and spatial determinants within the tumor microenvironment (TME) that underlie these divergent ICI therapy outcomes remain poorly defined. Here, we aimed to characterize the immune composition and spatial organization of the TME associated with ICI response and resistance. Methods: We integrated public scRNA-seq data (N = 32) with in-house spatial transcriptomics and imaging mass cytometry from an independent melanoma cohort (N = 6) to achieve high-resolution spatial profiling of the TME. This multimodal approach allowed us to map cellular heterogeneity within discrete spatial neighborhoods. To validate our findings, we constructed a scRNA-seq derived signature-matrix and deconvoluted a bulk RNA-seq cohort (N = 334). Clinical associations were assessed using Kaplan–Meier survival analysis, Cox hazard models, and a machine-learning classifier. Results: We identified a distinct tumor-associated macrophage (TAM) state, termed lipid-associated TAMs (LA-TAMs), characterized by conserved lipid metabolic programs and tumor-specific adaptations in glycolysis under hypoxic conditions. Deep spatial multi-omics profiling revealed divergent immune architectures associated with treatment outcomes. In non-responder patients, LA-TAMs colocalized with sparsely distributed TIM3⁺ exhausted CD8⁺ T cells within an immune-excluded TME. In contrast, responder patients harbored interferon-primed CCL4+ TAMs (IFN-TAMs) spatially associated with Granzyme B⁺ activated CD8⁺ T cells, reflecting an immune-active microenvironment. These findings define contrasting macrophage-centered immune neighborhoods linked to ICI response. Interestingly, patients with LA-TAM–enriched neighborhoods were consistently non-responders or progressed during follow-up, irrespective of the presence of IFN-TAM neighborhoods. Lastly, we constructed a single-cell–derived signature matrix that estimates TAM fractions from bulk RNA-seq data and revealed LA-TAM abundance as a robust, independent predictor of poor ICI response and survival in a validation cohort. Conclusions: Our study defines the spatial landscapes of TAM-heterogeneity in melanoma and identifies LA-TAM neighborhoods as an important feature of ICI resistance. Although patients span a continuum of TAM-centered immune states, the presence of LA-TAM is likely to diminish the beneficial effects of IFN-TAM–associated immune activation. Finally, our proposed Melanoma-TME–derived signature-matrix provides a translatable framework to robustly predict ICI response and resistance. Supplementary Information: The online version contains supplementary material available at https://doi.org/10.1186/s13073-026-01794-9.
SN - 1756-994X
ER -