Biology subjects

De Vleeschouwer, S.

Publications and source records attributed to De Vleeschouwer, S..

8 recordsLinked to original sources

bioRxiv2026

Macrophage-instructed GSDME couples glioblastoma cell-state plasticity with inflammatory cell death

Glioblastoma (GBM) cell states reflect spatial microenvironmental interactions. Here, using COMET spatial proteomics and RNAscope across multiregional human GBM tissue, spanning tumor cores with pseudopalisading regions, infiltrative margins and peripheral regions, together with multiplex spatial profiling of 202 specimens from 33 patients with matched primary and recurrent tumors, we identify full-length gasdermin E (GSDME-FL) as a macrophage-instructed regulator of malignant cell plasticity. Integration with single-cell transcriptomics and functional perturbation shows that GSDME-high tumor cells localize to macrophage-rich perivascular niches and are associated with delayed recurrence and longer patient survival. Mechanistically, macrophage-derived S100A4 activates EGFR-Sp1 signaling to induce GSDME-FL in neighboring GBM cells. GSDME-FL restrains hypoxia-associated mesenchymal plasticity and shapes macrophage-induced tumor state transitions independently of caspase activation. During immunogenic cell death (ICD), cleaved GSDME promotes pre-lytic swelling, early ATP efflux, and the release of canonical ICD-associated cytokines and chemokines. NLRP3 signaling further supports ATP release and licenses macrophage phagocytosis of dying GBM cells, whereas NINJ1-dependent membrane rupture enables terminal HMGB1 release. Vaccination with ICD-treated glioma cells elicits tumor rejection in a prophylactic intracranial challenge model. Notably, co-expression of GSDME and NINJ1 in macrophage-rich perivascular niches provides a spatial correlate of pathway convergence in patient tumors. Thus, our findings define how a spatial macrophage niche induces GSDME-FL, thereby coupling malignant cell state plasticity to the inflammatory properties of GBM cell death.

cancer biology↗

bioRxiv2026

Spatial Single Cell Lipid-Transcriptomic Coupling Reveals Metabolic Niches in Glioblastoma

Glioblastoma is characterized by spatial heterogeneity, with tumor-core and invasive-edge regions differing in cellular composition, transcriptional state, and metabolic context. Spatial transcriptomics has improved understanding of glioblastoma tissue organization. However, cellular transcriptional programs and metabolic interpretation remain poorly resolved. Here, single-cell matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI-MSI) with spatial transcriptomics were integrated on the same tissue sections to map lipid and transcriptomic organization across matched tumor-core and invasive-region samples from 10 glioblastoma patients. Common region-dependent cellular organization along the core - versus invasive regions were identified after accounting for patient specific signatures. Tumor cores were enriched with astrocyte-like malignant and immune cell types, whereas invasive regions showed increased contribution from oligodendrocyte (progenitor cells). Despite these compositional differences, tumor and invasive cells had a shared transcriptional state space, indicating that regional identity is shaped by altered spatial organization of shared cell states. Transcriptional programs associated with proliferation, hypoxia, extracellular matrix remodeling, tumor associated macrophages and microglia (TAMs) phagocytic activity, T-cell infiltration, and lipid synthesis were spatially structured and differed between tumor and invasive compartments. MALDI-MSI revealed broad lipidomic remodeling across these regions. Tumor regions were enriched in membrane and storage lipid classes, whereas invasive regions showed relative enrichment of lipid species associated with membrane turnover. Integrating lipid and transcriptomic layers revealed spatial lipid-gene program coupling, with tumor cores showing stronger and more coherent coupling than invasive regions. TAM phagocytic activity co-localized with cholesteryl ester abundance, while lipid synthesis coupled to phosphatidylcholine-rich astrocyte-like tumor niches. Exploratory analysis indicated that MGMT promoter methylation may be associated with this altered lipid-transcriptional coupling, particularly in TAM-associated lipid-handling programs. Together, these findings imply that spatial coordination between lipid states and transcriptional programs is a key feature of glioblastoma metabolic heterogeneity.

molecular biology↗

bioRxiv2026

Longitudinal tumor ecosystem mapping defines glioblastoma treatment trajectories

Glioblastoma remains an invariably recurring and lethal brain tumor shaped by complex interactions between malignant and microenvironmental cells. How these interactions evolve under first-line standard-of-care (SOC) therapy remains unclear. We performed spatial single-cell profiling of 671 paired newly diagnosed and recurrent glioblastoma samples from 96 patients to map tumor-ecosystem evolution and its clinical relevance. We delineated five distinct patient subgroups, each characterized by unique ecosystem trajectories that correlated with clinical outcome. Patients whose tumors transitioned into oligodendrocyte-progenitor-like niches with enhanced vascular integrity, oxygenation and an IL10/CCL/MHCII immunomodulatory environment experienced improved clinical prognosis. In contrast, progression towards hypoxic mesenchymal/astrocyte-like niches dominated by strong LGALS1/SPP1/TGF{beta} immunosuppression predicted poor outcome. Furthermore, a subgroup of early-relapsing patients on SOC therapy that was characterized by a depletion of an antigen-presenting myeloid-cell-rich niche, exhibited diminished responsiveness to second-line lomustine therapy. Overall, mapping evolutions in glioblastoma ecosystems offers a novel framework for prognostic stratification and therapeutic guidance.

cancer biology↗

bioRxiv2023

Single-cell profiling and zebrafish avatars reveal LGALS1 as immunomodulating target in glioblastoma

Glioblastoma (GBM) remains the most malignant primary brain tumor, with a median survival rarely exceeding 2 years. Tumor heterogeneity and an immunosuppressive microenvironment are key factors contributing to the poor response rates of current therapeutic approaches. GBM-associated macrophages (GAMs) often exhibit immunosuppressive features that promote tumor progression. However, their dynamic interactions with GBM tumor cells remain poorly understood. Here, we used patient-derived GBM stem cell cultures and combined single-cell RNA sequencing of GAM-GBM co-cultures and real-time in vivo monitoring of GAM-GBM interactions in orthotopic zebrafish xenograft models to provide insight into the cellular, molecular, and spatial heterogeneity. Our analyses revealed substantial heterogeneity across GBM patients in GBM-induced GAM polarization and the ability to attract and activate GAMs - features that correlated with patient survival. Differential gene expression analysis, immunohistochemistry on original tumor samples, and knock-out experiments in zebrafish subsequently identified LGALS1 as a primary regulator of immunosuppression. Overall, our work highlights that GAM-GBM interactions can be studied in a clinically relevant way using co-cultures and avatar models, while offering new opportunities to identify promising immune-modulating targets.

cancer biology↗

bioRxiv2023

A lymph node-to-tumour PD-L1+macrophage circuit antagonizes dendritic cell immunotherapy

Immune-checkpoint blockers (ICB) provide limited benefit against T cell-depleted tumours, calling for therapeutic innovation. Here, we aimed at designing a new type of dendritic cell (DC) vaccine by unbiased computational integration of multi-omics data from cancer patients. In a first attempt, a DC vaccine designed to present tumor antigens from cancer cells succumbing to immunogenic cancer cell death (ICD) and to elicit high type I interferon (IFN) responses failed to induce the regression of mouse tumors lacking T cell infiltrates. In lymph nodes (LNs), instead of activating CD4+ and CD8+T cells, DCs stimulated immunosuppressive PD-L1+LN-associated macrophages (LAMs) via a type I IFN response. Moreover, DC vaccines of this type stimulated pre-existing, T cell-suppressive, PD-L1+tumour-associated macrophages (TAMs). This created a T cell-suppressive circuit of PD-L1+macrophages, spanning across LNs and tumours. Accordingly, DC vaccines synergised with PD-L1 blockade to deplete PD-L1+macrophages, suppress myeloid inflammation affecting the tumor bed and draining lymph nodes, and de-inhibit effector/stem-like memory T cells, eventually causing tumour regression. The synergistic interaction between the DC vaccine and PD-L1 blockade was lost when DCs were manipulated to lose Ifnar1or Ccr7 or when macrophages were depleted. Interestingly, clinical DC vaccines also potentiated lymphocyte-suppressive PD-L1+TAMs in patients bearing T cell-depleted tumours. Altogether, our results reveal the existence of a novel PD-L1+LAM/TAM-driven immunosuppressive pathway that can be elicited by DC vaccines, yet can be subverted for improving the outcome of immunotherapy.

immunology↗

bioRxiv2022

Single-cell molecular profiling using ex vivo functional readouts fuels precision oncology in glioblastoma

BackgroundFunctional profiling of freshly isolated glioblastoma cells is being evaluated as a next-generation method for precision oncology. While promising, its success largely depends on the method to evaluate treatment activity which requires sufficient resolution and specificity. MethodsHere, we describe the precision oncology by single-cell profiling using ex vivo readouts of functionality (PROSPERO) assay to evaluate the intrinsic susceptibility of high- grade brain tumor cells to respond to therapy. Different from other assays, PROSPERO extends beyond life/death screening by rapidly evaluating acute molecular drug responses at single-cell resolution. ResultsThe PROSPERO assay was developed by correlating short-term single-cell molecular signatures using CyTOF to long-term cytotoxicity readouts in representative patient- derived glioblastoma cell cultures (n=14) that were exposed to radiotherapy and the small- molecule p53/MDM2 inhibitor AMG232. The predictive model was subsequently projected to evaluate drug activity in freshly resected GBM samples from patients (n=34). Here, PROSPERO revealed an overall limited capacity of tumor cells to respond to therapy, as reflected by the inability to induce key molecular markers upon ex vivo treatment exposure, while retaining proliferative capacity, insights that were validated in PDX models. This approach also allowed the investigation of cellular plasticity, which in PDCLs highlighted therapy-induced proneural-to-mesenchymal transitions, while in patients samples this was more heterogeneous. ConclusionPROSPERO provides a precise way to evaluate therapy efficacy by measuring molecular drug responses using specific biomarker changes in freshly resected brain tumor samples, in addition to providing key functional insights in cellular behavior, which may ultimately complement standard, clinical biomarker evaluations.

cancer biology↗

bioRxiv2021

Immunogenomic, single-cell and spatial dissection of CD8+T cell exhaustion reveals critical determinants of cancer immunotherapy

Tumoural-CD8+T cells exhibit exhausted or dysfunctional states. Contrary to immunotherapy-responsive exhausted-CD8+T cells, the clinical features of dysfunctional-CD8+T cells are disputed. Hence, we conducted large-scale multi-omics and multi-dimensional mapping of CD8+T cell-states across multiple cancer patient-cohorts. This identified tumour-specific continuum of CD8+T cell-states across 6 human cancers, partly imprinted by organ-specific immuno-modulatory niches. Herein, melanoma and glioblastoma enriched prototypical exhausted (CD8+TEXT) and severely-dysfunctional (CD8+TSDF) states, respectively. Contrary to CD8+TEXT, CD8+TSDF displayed transcriptomic and epigenetic effector/cytolytic dysfunctions, and dysregulated effector/memory single-cell trajectories, culminating into maladaptive prodeath stress and cell-cycle defects. Suboptimal antigen-priming underscored CD8+TSDF, which was distinct from immune-checkpoints "rich" CD8+TEXT, reflecting chronic antigen-stimulation. Continuum variation also existed on tumour spatial-level, with convergent (CD8+TEXT-supportive vascular regions) and divergent features (dysfunctional CD4+T::CD8+TSDFcell-to-cell interactions) between melanoma and glioblastoma. Globally, IFN{gamma}-IL2 disparities, paucity of intra-tumoural CD4+/CD8+T cells, and myeloid TGF{beta}/wound healing responses, distinguished CD8+TSDF-landscape. Within immuno-oncology clinical-trials, anti-PD1 immunotherapy failed to "reinvigorate" CD8+TSDF-landscape, and instead facilitated effector-dysfunction and TGF{beta}/wound healing. However, cellular immunotherapies (dendritic cell-vaccines, adoptive T-cell therapy) ameliorated assorted CD8+TSDF-landscape disparities, highlighting a roadmap for anti-glioblastoma multimodal-immunotherapy. Collectively, our study comprehensively expands clinical-knowledge on CD8+T cell-exhaustion and suggests that tumour-specific, pre-existing CD8+TEXT/TSDF-states, determine immunotherapy-responses.

immunology↗

bioRxiv2021

SLIT2-ROBO signaling in tumor-associated microglia/macrophages drives glioblastoma immunosuppression and vascular dysmorphia

SLIT2 is a secreted polypeptide that guides migration of cells expressing ROBO1&2 receptors. Herein, we investigated SLIT2/ROBO signaling effects in gliomas. In patients with glioblastoma (GBM), SLIT2 expression increased with malignant progression and correlated with poor survival and immunosuppression. Knockdown of SLIT2 in mouse glioma cells and patient derived GBM xenografts reduced tumor growth and synergized with immunotherapy to prolong survival. Tumor cell SLIT2 knockdown inhibited macrophage invasion and promoted a cytotoxic gene expression profile, which improved tumor vessel function and enhanced efficacy of chemotherapy and immunotherapy. Mechanistically, SLIT2 promoted microglia/macrophage chemotaxis and tumor-supportive polarization via ROBO1&2-mediated PI3K{gamma} activation. Macrophage Robo1&2 deletion and systemic SLIT2 trap delivery mimicked SLIT2 knockdown effects on tumor growth and the tumor microenvironment (TME), revealing SLIT2 signaling through macrophage ROBOs as a novel regulator of the GBM microenvironment and a potential immunotherapeutic target for brain tumors.

cancer biology↗