Biology subjects

Bergers, G.

Publications and source records attributed to Bergers, G..

8 recordsLinked to original sources

bioRxiv2026

Microglial lipid signaling drives glioblastoma invasion and represents a therapeutic vulnerability

Glioblastoma (GBM) is characterized by diffuse infiltration into the surrounding brain, which precludes complete surgical resection, the strongest determinant of patient survival. The mechanisms that drive this invasive growth remain incompletely understood. Here we identify a lipid-mediated paracrine signaling axis through which microglia, the resident macrophages of the brain, promote glioma invasion. Integrating single-cell transcriptomics, spatial lipidomics, and functional perturbation across mouse models and human GBM samples, we show that invading tumor cells engage and reprogram microglia via CSF1R-PI3K signaling. This induces a metabolic switch in microglia, leading to the secretion of bioactive lipids, including lysophosphatidylcholines (LPCs) and lysophosphatidic acids (LPAs), which act as pro-invasive cues across GBM subtypes through distinct downstream pathways. Disruption of the microglia-GBM axis, either by inhibiting CSF1R signaling or by blocking lipid mobilization, reduces lipid secretion and suppresses tumor invasion. Targeting downstream LPA-LPAR or YAP/TAZ signaling further constrains invasion in a context-dependent manner. Together, these findings define a lipid-driven signaling circuit that links the tumor microenvironment to glioma invasion and identify therapeutic strategies to limit tumor infiltration and improve surgical resectability.

cancer biology↗

bioRxiv2025

Distinct tumor immune microenvironmental (TIME) landscapes drive divergent immunotherapy responses in glioblastoma

BackgroundImmunotherapies have improved outcomes in many cancers but show limited efficacy in glioblastoma (GBM). This study aimed to determine whether immunotherapy could be tailored to GBM by functional subtyping of vascular-immune landscapes. MethodsWe employed single-cell RNA sequencing, multiplex immunohistochemistry to characterize three distinct TIME subtypes in human and murine GBMs. We evaluated responses to combination of anti-angiogenic immunomodulating therapies (CD40 Ag, anti-PDL1, PI3K{gamma}/{delta} inhibition) in orthotopic syngeneic GBM mouse models. ResultsWe identified three distinct functional TIME subtypes with unique vascular-immune landscapes in human and murine GBM: TIME-low (immune-low/deserted, leaky vasculature), TIME-med (intermediate immune-infiltration, angiogenic), and TIME-high (heavily infiltrated with immunosuppressive myeloid cells and dysfunctional T cells). Representative mouse models of TIME-GBMs responded in subtype specific ways to anti-angiogenic immunomodulating therapies. TIME-low GBMs enhanced T-cell activity but relapsed due to emerging myeloid immunosuppression, concomitant with mesenchymal transition. TIME-med displayed the most immune-activated, yet angiogenic phenotype, and showed overall good responses to various anti-angiogenic immunomodulating therapies. TIME-high GBMs were mostly non-responsive but improved when the myeloid-cell PI3K{gamma} was targeted. However, CD40 agonist treatment, expected to enhance APC function, unexpectedly worsened survival by promoting angiogenesis and heightening immunosuppression, leading to dysfunctional T cells and reduced NK cell recruitment, and subsequent enhanced tumor propagation. ConclusionsOur study reveals three GBM TIME subtypes with distinct vascular-immune landscapes that require tailored therapies. TIME-med tumors are predicted to respond best to immunotherapies, TIME-low tumors show transient effects with anti-angiogenic immunomodulating therapies, while TIME-high tumors, due to their profound immunosuppression, can even have worse outcomes. Key pointsO_LIThree TIME subtypes were identified in GBM with distinct vascular-immune landscapes C_LIO_LITIME subtypes show divergent immunotherapy responses C_LIO_LITIME classification supports personalized treatment strategy for GBM immunotherapy C_LI Importance of the StudyThis study advances glioblastoma immunotherapy by providing the first comprehensive single-cell characterization of TIME subtypes, moving beyond bulk RNA-sequencing to reveal detailed functional states of immune cells. We establish clinically relevant murine models that recapitulate human TIME subtypes, enabling preclinical testing of TIME-targeted therapies. Our findings identify TIME-low GBM as immune deserted and TIME-med tumors as the most immunotherapy-responsive subtype that should be prioritized for clinical selection. We found that high immune infiltration correlates with non-responsiveness and even unexpected detrimental effects with CD40 agonist treatment in TIME-high tumors--critical information given ongoing clinical trials. Identifying distinct immunosuppressive mechanisms across TIME subtypes and differential treatment responses provides a framework for personalized immunotherapy selection. The immediate translational impact of this work highlights the importance of TIME classification for treatment stratification and the urgent need to consider TIME status in clinical trial design, potentially explaining variable patient responses in previous GBM immunotherapy trials.

cancer biology↗

bioRxiv2025

LipidQMap - An Open-Source Tool for Quantitative Mass Spectrometry Imaging of Lipids

Mass spectrometry imaging (MSI) is a powerful tool in both basic and clinical research, enabling spatial visualization of biomolecules and drugs in tissue sections. However, factors influencing mass spectrometric response during imaging are increasingly recognized for their impact on apparent molecular distribution. Quantitative mass spectrometry imaging (qMSI) addresses this variability by incorporating analytical standards that undergo the same processes as analytes. While qMSI sample preparation protocols for omics-scale quantitative lipidomics are actively evolving, software solutions for downstream data processing remain scarce. Here, we introduce LipidQMap, the first open-source platform for processing omics-scale qMSI lipidomics data. LipidQMap applies one-point calibration, normalizing annotated lipid signals against class-specific standards on a pixel-by-pixel basis, and generates concentration heat maps in pmol/mm2. The software supports centroided data import, recalibration, and lipid identification using a built-in, user-modifiable lipid database. LipidQMap resolves Na/H adduct isobaric overlaps by leveraging sodiated-to-protonated adduct ratios of standards, validated across several MSI platforms using mouse brain sections. Type II isobaric overlaps are corrected using predicted isotopic patterns. Extensive validation demonstrates that LipidQMap is robust across MSI platforms and harmonizes qMSI data, enabling more accurate and reproducible spatial lipid quantification.

bioinformatics↗

bioRxiv2025

Autophagy maintains HEV identity and function during inflammation

High endothelial venules (HEVs) play a crucial role in adaptive immune responses in secondary and tertiary lymphoid organs. They are uniquely equipped with high levels of peripheral node addressins (PNAd), harboring carbohydrate structures that serve as L-Selectin ligands to efficiently facilitate lymphocyte homing. During inflammation, the HEV network expands in SLOs, increasing lymphocyte infiltration, but the underlying mechanisms maintaining HEVs remain underexplored. Here, we report that autophagy is essential for HEV function and expansion. Using single-cell transcriptomics, intravital imaging, and an inducible HEV tracer system in mice, we demonstrate that autophagy deficiency compromises LT{beta}R-signaling and the Unfolded Protein Response in HEVs, leading to disrupted PNAd production, dedifferentiation, and reduced lymphocyte homing. Autophagy deficiency and LT{beta}R blockade impaired HEV function and reduced skin inflammation in psoriasis-bearing mice by limiting immune infiltration and cytokine release. Our work uncovers an unprecedented role of autophagy in safeguarding HEV identity and function during inflammation. HighlightsO_LIHigh endothelial venules (HEVs) exhibit heightened autophagy in comparison to non-HEV blood endothelial cells, which further increases during inflammation. C_LIO_LIAutophagy is pivotal in maintaining HEV fate and function, specifically during inflammation, via LT{beta}R signaling and the Unfolded Protein Response (UPR), ensuring the proper production of peripheral node addressins (PNAd) that serve as L-selectin ligands for the efficient influx of naive lymphocytes. C_LIO_LIBlocking autophagy in HEVs leads to disrupted PNAd production, HEV flattening and dedifferentiation, and reduced lymphocyte homing. C_LIO_LIGenetic and pharmacological perturbation of HEV function in the lymph nodes and skin lesions of psoriasis-bearing mice impaired neutrophil and lymphocyte recruitment, as well as cytokine secretion, thereby alleviating skin inflammation. C_LI

cell biology↗

bioRxiv2023

An autophagy program that promotes T cell egress from the lymph node controls responses to immune checkpoint blockade

Lymphatic endothelial cells (LECs) lining the lymphatic vessels of the lymph node (LN) parenchyma orchestrate leukocyte trafficking and peripheral T cell dynamics. T cell responses to immunotherapy largely rely on peripheral T cell recruitment in tumors. Yet, a systematic and molecular understanding of how LECs within the LNs control T cell dynamics under steady state and tumor-bearing conditions is lacking. Using intravital and high-resolution imaging combined with immune phenotyping, we show that LEC-specific deletion of the essential autophagy gene Atg5 alters intranodal positioning of lymphocytes and accrues their persistence in the LNs, by increasing the availability of the main egress signal S1P. Single-cell RNA-sequencing of tumor-draining LNs from WT and ATG5LEC-KO mice unveils that loss of ATG5 remodels niche-specific LEC phenotypes, involved in molecular pathways regulating lymphocyte trafficking and LEC-T cell interactions. Functionally, loss of LEC-autophagy prevents recruitment of tumor-infiltrating T cells and NK cells and abrogates tumor regression in response to anti-PD-1 or anti-CTLA4-based immunotherapy. Thus, a unique LEC-autophagy program boosts immune-checkpoint responses by guiding systemic T cell dynamics. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=143 SRC="FIGDIR/small/549282v1_ufig1.gif" ALT="Figure 1"> View larger version (51K): org.highwire.dtl.DTLVardef@1a4bfe1org.highwire.dtl.DTLVardef@1317fe2org.highwire.dtl.DTLVardef@c2fa20org.highwire.dtl.DTLVardef@b35dba_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2023

TUMOR ENDOTHELIAL CELL AUTOPHAGY IS A KEY VASCULAR-IMMUNE CHECKPOINT IN MELANOMA

Tumor endothelial cells (TECs) actively repress inflammatory responses and maintain an immune-excluded tumor phenotype. However, the molecular mechanisms that sustain TEC-mediated immunosuppression remain largely elusive. Here, we show that autophagy ablation in TECs boosts antitumor immunity by supporting infiltration and effector function of T cells, thereby restricting melanoma growth. In melanoma-bearing mice, loss of TEC autophagy leads to the transcriptional expression of an immunostimulatory/inflammatory TEC phenotype driven by heightened NF-kB and STING signaling. In line, single-cell transcriptomic datasets from melanoma patients disclose an enriched InflammatoryHigh/AutophagyLow TEC phenotype in correlation with clinical responses to immunotherapy. Congruently, patients responding to immunotherapy exhibit an increased presence of inflamed vessels, interfacing with infiltrating CD8+ T cells. Mechanistically, STING-dependent immunity in TECs is not critical for the immunomodulatory effects of autophagy ablation, since NF-kB-driven inflammation remains functional in STING/ATG5 double knockout TECs. Hence, autophagy is a principal tumor vascular anti-inflammatory mechanism dampening melanoma antitumor immunity.

cancer biology↗

bioRxiv2021

Anticancer immunotherapies transition postcapillary venules into high-endothelial venules that generate TCF1+ T lymphocyte niches through a feed-forward loop

The lack of T-cell infiltrates is a major obstacle to effective immunotherapy in cancer. Conversely, the formation of tumor-associated tertiary-lymphoid-like structures (TA-TLS), which are the local site of humoral and cellular immune responses against cancers, are associated with good prognosis and have recently been detected in Immune Checkpoint Blockade (ICB)-responding patients. However, how these lymphoid aggregates develop remains poorly understood. By employing scRNA sequencing, endothelial fate mapping, and functional multiplex immune profiling, we demonstrate that antiangiogenic immune-modulating therapies evoke the transition of postcapillary venules into inflamed high endothelial venules (HEVs), which generate permissive TA-TLS-like lymphocyte niches with PD1neg and PD1+TCF1+CD8 T cell progenitors that differentiate into GrzB+TCF1neg TIM3+ PD1+ CD8 T effector cells. Tumor-HEVs require continuous CD8 and NK cell-derived lymphotoxin signals revealing that tumor-HEV maintenance is actively sculpted by the adaptive immune system through a feed-forward loop. In BriefHua & Vella et al. reveal that effective antiangiogenic immunotherapy transitions postcapillary venules into inflamed high-endothelial venules (HEV), sustained by CD8 T and NK cell-derived signals through a feed-forward loop. Thereby, tumoral HEVs establish perivascular niches in which TCF1+ PD1+ lymphocytes expand and produce cytolytic PD1+ TIM3+ CD8 T cells that facilitate anti-tumoral immunity. HighlightsO_LIHigh endothelial venule induction by anticancer immunotherapies generates perivascular immune niches permissive for TCF1+ PD1+ CD8 progenitor T cell expansion and production of TCF1neg PD1+ TIM3+ CD8 effector T cells C_LIO_LITumoral high-endothelial venules exhibit characteristics of inflamed lymph node HEVs and postcapillary venules C_LIO_LIPostcapillary venules dynamically transdifferentiate into high-endothelial venules in tumors, which requires continuous signals from surrounding immune cells C_LIO_LICD8 and NK cells drive tumoral high-endothelial venule formation during antiangiogenic immunotherapies in a feed-forward loop via lymphotoxin beta receptor signaling C_LI

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↗