Biology subjects

Nathanson, D. A.

Publications and source records attributed to Nathanson, D. A..

10 recordsLinked to original sources

bioRxiv2026

High-throughput spheroid profiling reveals BMP-driven rewiring of glioma cell death responses

The mechanisms regulating glioma cell death are poorly understood. Here, we developed a high-throughput method to study cell death in patient-derived glioblastoma (GBM) and diffuse intrinsic pontine glioma (DIPG) spheroids. Using this method, we systematically profiled how extracellular ligands modulate compound-induced cell death. We find that bone morphogenetic protein 2 (BMP2) and BMP4 potently rewire cell death sensitivity. These ligands suppress killing by standard-of-care DNA alkylating agents and kinase inhibitors by inhibiting cell cycle progression. Simultaneously, BMP2/4 prime spheroids for lipid-dependent necrosis (LiDN), a palmitate-dependent form of non-apoptotic cell death that can be triggered by the clinical drug candidate tegavivint. Activating mutations in the BMP receptor ACVR1, found in ~25% of DIPG tumors, are sufficient to prime cells for LiDN in the absence of BMP ligand. Together, these findings identify a cell death switch that can be activated in glioma cells by BMP signaling.

cancer biology↗

bioRxiv2026

Glutamatergic neuron-tumor synapses shape human glioblastoma cell states through radial glia plasticity

Glioblastoma (GBM) is a devastating primary brain tumor with remarkable inter- and intra-tumoral heterogeneity. GBM cells assume a spectrum of neurodevelopmental-like phenotypes and co-opt normal neurophysiological processes, which include synaptic integration with their neuronal microenvironment. This is mediated by neuron-tumor synapses (NTS) that predominantly involve glutamatergic receptors, which drive calcium elevations that promote tumor proliferation and invasion. The exact relationship between synaptic signaling and tumor cell fate specification, however, remains largely unexplored. Here, we develop and leverage a synapse-optimized human organoid tumor transplantation (so-HOTT) model of GBM to decipher how glutamatergic signaling impacts GBM lineage trajectories. so-HOTT preserves patient tumor heterogeneity, features excitatory NTS, and enables clonal lineage tracing of tumor cells after NTS perturbations. Genetic and pharmacological inhibition of AMPA and kainate receptors in so-HOTT shifts tumor cell composition from neuronal fates toward progenitor-proximal astrocytic/mesenchymal states. This occurs through the attenuation of calcium signaling and reduced plasticity of malignant radial glia (RG)-like progenitors, a previously unrecognized target of NTS. Through the integration of inputs from the neuronal microenvironment into glutamatergic signaling, progenitor populations modulate their transcriptional programs and cell fate, ultimately shaping GBM tumor heterogeneity. Targeting synaptic input may thus constrain the heterogeneity that fuels GBM adaptation and therapeutic escape.

cancer biology↗

bioRxiv2026

Predictable clonal hierarchies from restricted progenitors provide a framework for cell type-specific therapies in glioblastoma

Extensive molecular profiling has revealed profound heterogeneity in glioblastoma (GBM), yet how cellular lineages organize over time to govern tumor propagation and therapeutic response remains poorly understood. Existing single-cell approaches define transcriptional states but provide limited insight into how clonal dynamics shape functional tumor behavior. Here, we integrate high-complexity combinatorial DNA barcoding with single-cell transcriptomics in direct-from-patient IDH1-wild-type GBM, enabling lineage-resolved mapping of progenitor organization in a human microenvironmental context. Across 235,155 malignant cells from nine tumors, clonal relationships form reproducible lineage tracks in which distinct progenitor populations give rise to specific differentiated cell types, revealing that tumor growth is sustained by multiple non-redundant progenitors rather than a single dominant population. These progenitors exhibit distinct propensities for self-renewal, fate restriction, and cross-compartment interactions, collectively accounting for the full spectrum of tumor states. Using this lineage-resolved framework, we identify complementary drug targets in distinct progenitor compartments and demonstrate that hierarchy-informed combination therapies disrupt progenitor-progenitor interactions and reshape lineage output. These findings move beyond descriptive heterogeneity to define functional logic underlying GBM propagation and establish a generalizable framework for rational, cell type-specific combinatorial therapies.

cancer biology↗

bioRxiv2025

Beyond Cell Cycle Control: CDKN2A Loss Orchestrates NAD⁺ Metabolic Plasticity and NAMPT Inhibitor Sensitivity in Glioblastoma

While CDKN2A loss is classically associated with cell cycle deregulation through the p16-Cdk4-Rb axis, our findings suggest an additional layer of metabolic vulnerability arising from altered NAD homeostasis in CDKN2A-deleted glioblastoma, revealing a previously unrecognized metabolic-genetic interface for rationally revisiting NAD+ targeting strategies, moving beyond the broad inhibition approaches.

cancer biology↗

bioRxiv2025

A Human Tumor-Immune Organoid Model of Glioblastoma

A major obstacle to identifying effective therapies for the aggressive brain tumor glioblastoma is the lack of human-specific, immunocompetent models that reflect the human tumor microenvironment. To address this, we developed the immune-Human Organoid Tumor Transplantation (iHOTT) model. This is an autologous co-culture platform that integrates patient-derived tumor cells and matched peripheral blood mononuclear cells (PBMCs) within human cortical organoids, enabling the study of the patient-specific immune response to the tumor and tumor-immune interactions. This platform preserves tumor and immune populations, immune signaling, and cell-cell interactions observed in patient tumors. Treatment of iHOTT with pembrolizumab, a checkpoint inhibitor, mirrored cell type shifts and cell interactions observed in patients. TCR sequencing further revealed pembrolizumab-driven expansion of stem-like CD4-T-cell clonotypes exhibiting patient-specific repertoires. These findings establish iHOTT as a physiologically relevant platform for exploring autologous tumor-immune interactions and underscore the critical need for antigen-targeted strategies to enhance immunotherapy in glioblastoma.

cancer biology↗

bioRxiv2024

Glioblastoma Neurovascular Progenitor Orchestrates Tumor Cell Type Diversity

Glioblastoma (GBM) exhibits developmental programs and marked cellular heterogeneity, yet how these features are organized into connected lineage hierarchies remains unclear. Here we identify a rare tumor-intrinsic population, termed the neurovascular progenitor (NVP), that occupies an intermediate position between the major GBM organizational axes. NVP cells co-express neural progenitor and perivascular transcriptional features, are consistently detected across independent patient cohorts, retain canonical GBM copy-number alterations, and localize in situ in both vessel-associated and parenchymal niches. Using direct-from-patient lineage tracing in a human organoid tumor transplantation system, we show that individual NVP cells clonally generate both neural-like and mesenchymal/vascular-like malignant progeny, providing a concrete lineage link between states that are commonly considered mutually exclusive. Despite comprising [~]1% of tumor cells, NVP-derived lineages account for a majority of observed tumor cell types and disproportionately contribute to cycling compartments. Orthogonally, ablation of NVP-associated programs in an in vivo GBM model remodels tumor composition, elicits compensatory progenitor states, and significantly prolongs survival. Together, these findings position NVP as a fate-restricted yet highly influential lineage intermediate that serves as a functional bridge and organizational nexus within GBM hierarchies, linking population-level lineage architecture to the behavior of a specific progenitor cell type.

cancer biology↗

bioRxiv2024

Human Organoid Tumor Transplantation Identifies Functional Glioblastoma - Microenvironmental Communication Mediated by PTPRZ1

Glioblastoma, the most aggressive and deadly form of primary brain cancer, is driven by both intrinsic cellular properties and external factors from the tumor microenvironment. Here, we leverage our novel human organoid tumor transplantation (HOTT) system to explore how extrinsic cues modulate glioblastoma cell type specification, heterogeneity, and migration. We show that HOTT recapitulates the core features of major patient tumor cell types and key aspects of peritumor cell types, while providing a human microenvironment that uniquely enables perturbations in both the patient tumor and its microenvironment. Our exploration of patient tumor - microenvironmental interactions in HOTT highlighted PTPRZ1, a receptor tyrosine phosphatase implicated in tumor migration, as a key player in intercellular communication. We observed that tumor knockdown of PTPRZ1 recapitulated previously described roles in migration and maintaining progenitor identity. Unexpectedly, environmental PTPRZ1 knockdown drove opposite migration and cell fate changes in the tumor, even when the tumor was not manipulated. This previously undiscovered mode of tumor-microenvironmental communication highlights the need to study human glioblastoma in the context of a human microenvironment such as HOTT.

cancer biology↗

bioRxiv2023

Glioblastoma Mesenchymal Transition and Invasion are Dependent on a NF-κB/BRD2 Chromatin Complex

Glioblastoma (GBM) represents the most aggressive subtype of glioma, noted for its profound invasiveness and molecular heterogeneity. The mesenchymal (MES) transcriptomic subtype is frequently associated with therapy resistance, rapid recurrence, and increased tumor-associated macrophages. Notably, activation of the NF-{kappa}B pathway and alterations in the PTEN gene are both associated with this malignant transition. Although PTEN aberrations have been shown to be associated with enhanced NF-{kappa}B signaling, the relationships between PTEN, NF-{kappa}B and MES transition are poorly understood in GBM. Here, we show that PTEN regulates the chromatin binding of bromodomain and extraterminal (BET) family proteins, BRD2 and BRD4, mediated by p65/RelA localization to the chromatin. By utilizing patient-derived glioblastoma stem cells and CRISPR gene editing of the RELA gene, we demonstrate a crucial role for RelA lysine 310 acetylation in recruiting BET proteins to chromatin for MES gene expression and GBM cell invasion upon PTEN loss. Remarkably, we found that BRD2 is dependent on chromatin associated acetylated RelA for its recruitment to MES gene promoters and their expression. Furthermore, loss of BRD2 results in the loss of MES signature, accompanied by an enrichment of proneural signature and enhanced therapy responsiveness. Finally, we demonstrate that disrupting the NF-{kappa}B/BRD2 interaction with a brain penetrant BET-BD2 inhibitor reduces mesenchymal gene expression, GBM invasion, and therapy resistance in GBM models. This study uncovers the role of hitherto unexplored PTEN-NF-{kappa}B-BRD2 pathway in promoting MES transition and suggests inhibiting this complex with BET-BD2 specific inhibitors as a therapeutic approach to target the MES phenotype in GBM.

cancer biology↗

bioRxiv2022

Calculating ATP production rates from oxidative phosphorylation and glycolysis during cell activation

Oxidative phosphorylation and glycolysis are the dominant ATP-generating pathways in mammalian metabolism. The balance between these two pathways is often shifted to execute cell-specific functions in response to stimuli that promote activation, proliferation, or differentiation. However, measurement of these metabolic switches has remained mostly qualitative, making it difficult to discriminate between healthy, physiological changes in energy transduction or compensatory responses due to metabolic dysfunction. We therefore developed a broadly applicable method to calculate ATP production rates from oxidative phosphorylation and glycolysis using Seahorse XF Analyzer data. We quantified the bioenergetic changes observed during macrophage polarization as well as cancer cell adaptation to in vitro culture conditions. Additionally, we detected substantive changes in ATP utilization upon neuronal depolarization and T cell receptor activation that are not evident from steady-state ATP measurements. This method generates a single readout that allows the direct comparison of ATP produced from oxidative phosphorylation and glycolysis in live cells. Additionally, the manuscript provides a framework for tailoring the calculations to specific cell systems or experimental conditions.

biochemistry↗

bioRxiv2021

Pathway-based approach reveals differential sensitivity of glioblastoma to E2F1 inhibition

Targeting glioblastoma (GBM) based on molecular subtyping have not yet translated into successful therapies. Here, we used gene set enrichment analysis (GSEA) to conduct an unsupervised clustering analysis to condense the gene expression data from bulk patient samples and patient-derived gliomasphere lines into new gene lists. We then identified key molecular pathways differentially regulated between tumors. These gene lists associated not only with cell cycle and stemness signatures, but also with cell-type specific markers and different cellular states of GBM. We identified the transcription factor E2F1 as a key regulator of tumor cell proliferation and self-renewal in only the subset of proliferating gliomasphere cultures predicted to be E2F1-activated and validated its functional significance in tumor formation capacity. E2F1 inhibition also sensitized E2F1-activated gliomasphere cultures to radiation treatment. Our findings indicate that a pathway-based approach can be leveraged to deconstruct inter-tumoral heterogeneity and uncover key therapeutic vulnerabilities for targeting GBM.

cancer biology↗