Biology subjects

Patel, K. S.

Publications and source records attributed to Patel, K. S..

9 recordsLinked to original sources

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↗

bioRxiv2026

Critical role of cell competition in gliomagenesis

ABSTRACTMalignant glioma is incurable. Using a mouse genetic mosaic system to generate sporadic Trp53,Nf1-null OPCs, we previously identified oligodendrocyte precursor cell (OPC) as a cell-of-origin of glioma. Here, we report that pre-malignant Trp53,Nf1-null OPCs outcompete wildtype counterparts during their expansion. Blocking competition by mutating/strengthening wildtype OPCs impeded both pre-malignant progression and malignant expansion of glioma. "In-tissue" phosphoproteomic profiling revealed an enrichment of phosphopeptides related to RNA splicing and protein translation at the peak of cell competition, suggesting that competitiveness may stem from unique protein species. Among candidates was mTORC1, whose pharmacological inhibition or genetic disruption resulted in a loss of competitiveness in our mouse model. Finally, analysis of patient biopsies and interrogating the role of individual gliomagenic mutations in OPC competition supported its relevance in human gliomas. Together, these findings identified the driving role of competitive interactions among OPCs in gliomagenesis, and suggest unconventional therapeutic strategies to target this process.

cancer biology↗

bioRxiv2025

A combined Eulerian-Lagrangian and thin film approximation model to investigate the disease-specific drug delivery efficacy on realistic lung geometry and breathing profiles

This work presents a computational approach to investigate antiviral aerosol deposition in anatomically realistic human airways under various physiological inhalation conditions. Antiviral drugs are represented as fine liquid droplets that form a thin coating on airway surfaces, primarily targeting early infection sites. The suggested method combines an Eulerian-Lagrangian discrete phase model (DPM) to track droplet motion and an Eulerian wall film (EWF) model to mimic the evolution of deposited liquid films. This combination effectively addresses the shortcomings of previous studies that employed DPM exclusively, which ignored the post-deposition redistribution dynamics of liquid drugs on airway surfaces. Furthermore, the effects of the distressed breathing of patients with chronic obstructive pulmonary disease (COPD) are compared with both idealized and physiologically realistic breathing patterns in healthy individuals. The study assesses airflow parameters, film thickness, deposition efficiency, and surface area coverage for aerosol particles from 1 to 10 {micro}m. Results reveal that distressed breathing patterns of COPD patients significantly alter the deposition preferences between the upper (~5.28%) and lower lobes (~2.52%) compared to the equivalent ideal and realistic healthy inhalations. Moreover, the distressed breathing also limits the drug penetration into deeper generations, as the highest surface coverage is observed at the carinal region rather than the usual left lower lobe (LLL) found in ideal and realistic healthy breathing cases. Such deposition contrasts highlight the importance of optimizing inhalation therapy and device designs for individuals with obstructive airway diseases.

bioengineering↗

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↗

bioRxiv2025

Passive Acoustic Dynamic Differentiation and Mapping: A Time-Domain Passive Cavitation Localization and Classification Approach

1ObjectivePassive cavitation imaging and control has explored various beamforming algorithms to balance resolution, imaging artifacts, and computational speed. Optimizing these parameters is essential for clinical translation, as precise cavitation localization and dosage control are critical for Focused Ultrasound (FUS)-based targeted therapies, minimizing unintended tissue damage. Among commonly used methods, Delay-Sum-Integrate (DSI) and Robust Capon Beamforming (RCB) have demonstrated effectiveness but are limited by either significant artifacts or the need for extensive parameter tuning. MethodsThis work introduces Passive Acoustic Dynamic Differentiation and Mapping (PADAM), which adapts the Multiple Signal Classification algorithm to the time domain to improve cavitation localization. ResultsPADAM achieves up to a 6-fold improvement in lateral beam-width compared to RCB, and a 4-fold reduction in mean-square intensity of artifacts. It further unveils a novel physical insight: its input parameter dynamically gauges the richness of an incoming signals frequency content. This feature enables a more physically defined and intuitive parameter for distinguishing between stable and inertial cavitation based on spectral characteristics, simplifying parameter selection and enhancing the framework for cavitation monitoring and control. ConclusionWith its ability to improve resolution, reduce artifacts, and provide computational efficiency, PADAM represents a promising advancement for precise cavitation localization and therapy monitoring. SignificanceThis work introduces PADAM, a novel time-domain passive cavitation imaging method that offers superior resolution and artifact reduction compared to DSI and RCB. Its physically intuitive input parameter enables dynamic differentiation between stable and inertial cavitation, enhancing precision in the monitoring and control of FUS therapy.

bioengineering↗

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↗

bioRxiv2022

Single-cell analysis characterizes non-enhancing region of recurrent high-grade glioma

BackgroundNon-enhancing (NE) infiltrating tumor cells beyond the contrast-enhancing (CE) bulk of tumor are potential propagators of recurrence after gross total resection of high-grade glioma. MethodsWe leveraged single-nucleus RNA-sequencing on 15 specimens from 5 high grade gliomas to compare prospectively identified biopsy specimens acquired from CE and NE regions. Additionally, 24 CE and 22 NE biopsies had immunohistochemical staining for Ki67 to identify proliferative cell burden. ResultsTumor cells in NE regions are enriched in neural progenitor cell-like cellular states, while CE regions are enriched for mesenchymal-like states. These NE glioma cells have similar proportions of proliferative and putative glioma stem cells relative to CE regions, without significant differences in % Ki67 staining. Tumor cells in NE regions exhibit upregulation of genes previously associated with lower grade gliomas. Cell-, gene-, and pathway-level analyses of the tumor microenvironment in the NE region reveal relative downregulation of tumor-mediated neovascularization and presence of cell-mediated immune response, but increased glioma-to-non-pathological cellular interactions. ConclusionsThis comprehensive analysis illustrates differing tumor and non-tumor landscapes of CE and NE regions in high-grade gliomas, highlighting the NE region as an area harboring likely initiators of recurrence in a pro-tumor microenvironment and identifying possible targets for future design of NE-specific adjuvant therapy. Key PointsSignificant proliferating tumor burden exist in non-enhancing regions of glioma; non-enhancing regions have unique tumor and non-tumor expression properties Importance of StudyStandard of care treatment for glioblastoma relies on visualization of tumor via contrast-enhanced magnetic resonance imaging. However, non-enhancing regions harbor tumor cells that should be targets for adjuvant therapy given these regions are not resected in surgery. To begin addressing these infiltrating non-enhancing tumor cells, we thoroughly characterize the tumor and non-tumor microenvironment of non-enhancing regions in high grade gliomas. Understanding the total tumor burden, proliferating tumor ratio, and presence of putative glioma stem cells may help design adjuvant therapies for these unique population of tumor cells. Understanding the non-tumor immune and vascular microenvironment may help target these areas in regards to drug delivery and immunotherapy. Overall, in a disease marked by significant intratumoral heterogeneity, we focus identifying therapeutic strategies for areas not addressed at surgery.

neuroscience↗