Biology subjects

Burns, T.

Publications and source records attributed to Burns, T..

8 recordsLinked to original sources

bioRxiv2026

CSF-Seq enables transcriptome-wide profiling of cerebrospinal fluid and identifies prognostic signature of leptomeningeal disease

Leptomeningeal disease (LMD) is a rapidly fatal complication of systemic cancer for which sensitive diagnostic tools and informative biomarkers remain limited. Here, we introduce CSF-Seq, a method for whole-transcriptome sequencing of cell-free RNA (cfRNA) from human cerebrospinal fluid (CSF), designed to enable molecular profiling of LMD and other central nervous system (CNS) conditions. Using a prospectively collected CSF biobank, we analyzed 125 samples spanning multiple pathologies, including breast and lung LMD, glioblastoma, traumatic brain injury, and non-cancer neurological controls. Through optimized RNA extraction, library preparation, and deep sequencing, CSF-Seq generated robust and reproducible transcriptome-wide profiles despite the low abundance and fragmentation of cfRNA in CSF. CSF transcriptomes exhibited disease-specific expression, separating LMD from non-cancer controls and from non-LMD cancers, independent of CSF collection modality. Tumor-associated epithelial transcripts, including CEACAM6 and MUC1, were consistently enriched in LMD samples, whereas immune and CNS-associated transcripts were broadly detected across disease states, consistent with contributions from both tumor and non-tumor sources. Cross-site processing of matched samples demonstrated high concordance, indicating preservation of sample-specific transcriptional signatures across independent workflows. Importantly, we identified a collection method- independent LMD gene expression signature that was significantly associated with overall survival, supporting its potential prognostic relevance. Together, these findings establish CSF-Seq as a technically robust and clinically informative platform for transcriptomic biomarker discovery in CNS metastatic disease, offering a minimally invasive approach for disease characterization, risk stratification, and longitudinal monitoring in patients with LMD.

cancer biology↗

bioRxiv2025

Continuous Production of Recombinant Adeno-Associated Virus in the Insect Cell/Baculovirus Expression Vector System

Continuous production processes may offer significant advantages for biotherapeutic manufacturing, including increased productivity, consistent product quality, reduced facility footprint, and decreased process turnaround time. Despite these benefits, the in-situ formation of defective recombinant baculovirus expression vectors (BEVs) hinders the continuous manufacturing of recombinant adeno-associated viruses (rAAV) in the baculovirus expression vector system. This study investigates an approach of reducing defective viruses through the infusion of standard recombinant baculovirus (rBV) and the compartmentalization of early- and late-stage infected cells, resulting in stable rAAV production. In this study, rAAVs were continuously produced in a series of cascading reactors, comprising a feeder reactor, an infection reactor, and a production reactor. Residence times and transfer rates across the three reactors were optimized based on the production kinetics of rBV and rAAV derived from our mechanistic model. The majority of rBV was produced within the production reactor, thereby reducing the impact of defective viruses in the infection reactor, enabling continuous rAAV production. This study demonstrates the successful implementation of a continuous rAAV production process, yielding over 5x1010 vg/mL per day for 4 weeks. This work represents the first reported continuous rAAV production process utilizing the Sf9/BEVS platform and establishes engineering know-how for overcoming manufacturing challenges associated with rAAV-based gene therapies.

bioengineering↗

bioRxiv2024

Detection of a reassortant swine- and human-origin H3N2 influenza A virus in farmed mink in British Columbia, Canada

In December 2021, influenza A viruses (IAV) were detected in a population of farmed mink in British Columbia, Canada. Based on genomic sequencing and phylogenetic analysis, these IAVs were subtyped as H3N2s that originated from reassortment of swine H3N2 (clade 1990.4h), human seasonal H1N1 (pdm09), and swine H1N2 (clade 1A.1.1.3). This reassortant has been subsequently observed in swine in several Midwest American states, as well as in swine and turkeys in Ontario, suggesting its spillover into farmed mink in British Columbia was incidental to its broader dissemination in North American swine populations. These detections reaffirm the need for extensive genomic surveillance of IAVs in swine populations to monitor reassortments that might become public health concerns. They also highlight the need for closer surveillance of IAVs in mink to preserve animal health, protect agricultural interests, and monitor potential zoonotic threats.

microbiology↗

bioRxiv2022

MRI-to-Synthetic 3D Gel Brain: Proof-of-Concept Fabrication For Intra-Parenchymal Diffusion Studies

Bioprinting technologies utilize hydrogel-based biomaterials to more accurately depict in vivo physical conditions within in vitro studies, yet, manufacturing the human brain from soft, poroelastic hydrogels remains a fundamental challenge. Conventional manufacturing routes to fabricate hydrogel brain models using techniques, i.e., 3D printing, seems challenging. This study aims to demonstrate an inverse replica molding fabrication technique that can overcome these challenges while maintaining the complex shape of an individual subjects brain in a miniaturized model--allowing for a more robust hydrogel model that can capture the interactions between diffusing molecules and brain boundaries. This is done by taking a subjects magnetic resonance imaging (MRI) scan and reconstructing the outer pial surface into a mesh surface. The mesh was then converted to an STL and printed out using an extrusion printer. A silicon mold was made from this print into which agarose was gelled. Once fully gelated, the synthetic gel brain was then carefully removed. Two infusion trials were run in the gel brain, each using a different infusion site. Then a diffusion profile was established and compared to a simple gel infusion model. The result shows different diffusion profiles at each location and between the simple and complex models. This model can better represent the interference the complex shape of the brain has on particle movement compared to simple gel models.

bioengineering↗

bioRxiv2022

In Silico, Brain Mesh Platform for Computing Topographic Dependent Internal Facets

Individualized and anatomically correct computational models of the brain can be leveraged to improve knowledge of drug dispersal following simulation of drug delivery. Using a patients magnetic resonance image (MRI) scans, we were able to reconstruct the pial surface of the brain of the left hemisphere with strong anatomic accuracy. We then established the major internal features, including the lateral ventricle, a tumor, and drug delivery catheters. These were able to include relevant tissue characteristics such as porosity and permeability in the Multiphysics platform COMSOL to create a platform for brain modeling. To test the performance of this platform, we simulated direct drug infusion in both a healthy patient brain and a diseased patient model, focusing on glioblastoma (GBM). Using this platform, we simulated perturbed convection enhanced delivery of a cancer medication (similar to temozolomide (TMZ) but modeled using methylene blue) to the tumor. Consequently, with our patient derived model, we are able to simulate solute dispersal and fluid flow representative of in vivo conditions.

bioengineering↗

bioRxiv2022

Convection-enhanced diffusion and directed withdrawal of methylene blue in agarose hydrogel using finite element analyses

Precision drug delivery for optimized therapeutic targeting requires knowledge of momentum transport and molecular diffusion of molecules within the patients interstitial tissue, especially for tumor treatment within the brain. Dispersion in the interstitial space is impacted by delivery method, tissue material properties, individual-specific fluid flow, and particle size of the input solute. Knowledge of a drugs dispersion allows for optimizing solute delivery, concentration, and flow rates to maximize drug distribution and biomarker recovery. For delivering drugs, increased knowledge of drug location after delivery can improve therapeutic treatment by optimizing the dosing of healthy and unhealthy tissue. Finite element methods (FEM) tools, such as COMSOL Multiphysics, can simulate molecular distribution inside-individual specific shapes and porous material properties. Furthermore, an additional unmet need is delivery methods that can be adjusted to manipulate diffusion regions through tissue via techniques such as directed flow. This would be especially valuable in targeted drug delivery within tumors to increase the cancerous surface area covered while limiting damage to surrounding tissues. In this project, the directed flow was induced by perfusing the injected solution at an input probe while withdrawing fluid at an output probe, enabling targeted flow through the desired region. FEM computation faithfully replicated these conditions and could be used to determine the effective concentrations perfused over the region of interest. We leveraged COMSOL Multiphysics to perform a computational study simulating convection-enhanced delivery (CED) with an output probe pulling the concentration profile over the region of interest. This simulation system can be applied to therapeutics targeting, vaccine subcutaneous injection, and waste and media diffusion in tissue engineering.

bioengineering↗

bioRxiv2020

Selective Vulnerability of Senescent Glioblastoma Cells to Bcl-XL Inhibition

Despite decades of research and numerous basic science advances, there have only marginal gains in improving glioblastoma multiforme survival. Therefore, new ideas and approaches for treating this aggressive disease are essential to drive progress forward. Conventional therapies, such as radiation and Temozolomide (TMZ), function to cause oxidative stress and DNA damage yielding a senescent-like state of replicative arrest in susceptible cells. However, increasing evidence demonstrates malignant cells can escape senescence leading to tumor recurrence. Ablation of non-replicating senescent tumor cells after radiation and chemotherapy may be an avenue to reduce the rates of tumor recurrence. Senolytic agents have been developed that selectively target senescent cells, but it remains unknown whether senolytics might be utilized against senescent-like glioma cells. We employed radiation or TMZ to induce a functionally senescent state in human glioblastoma cells. Viable cells that survive these treatments were then utilized to screen candidate senolytic drugs, to identify those selectively effective at ablating senescent-like cells over naive non-tumor and proliferative cells. Among 10 candidate senolytic drugs evaluated, only Bcl-XL inhibitors demonstrated reproducible senolytic activity in radiated or TMZ-treated glioma across the majority of GBM cell lines evaluated. Conversely, Bcl-2 inhibitors and other established senolytic drugs failed to show any consistent senolytic activity. In agreement with these data, Bcl-XL knockdown selectively reduced the viability of senescent-like GBM cells, whereas knockdown of Bcl-2 or Bcl-W yielded no senolytic effect. These findings demonstrate the potential to harness radiation-induced biology to ablate latent surviving cells and highlight Bcl-XL dependency as a potential vulnerability of surviving GBM cells after exposure to radiation or TMZ.

cancer biology↗

bioRxiv2020

Radiation Induced Metabolic Alterations Associate with Tumor Aggressiveness and Poor Outcome in Glioblastoma

Glioblastoma (GBM) is uniformly fatal with a one year median survival rate, despite the best available treatment, including radiotherapy (RT). Impacts of prior RT on tumor recurrence are poorly understood but may increase tumor aggressiveness. Metabolic changes have been investigated in radiation-induced brain injury; however, the tumor-promoting effect following prior radiation is lacking. Since RT is vital to GBM management, we quantified the tumor-promoting effects of prior radiotherapy (RT) on patient-derived intracranial GBM xenografts and characterized the metabolic alterations associated with the protumorigenic microenvironment. Human xenografts (GBM143) were implanted into nude mice 24h following 20Gy cranial radiation vs. sham animals. Tumors in pre-radiated mice were more proliferative and more infiltrative, yielding faster mortality (p<0.0001). Histologic evaluation of tumor associated macrophage/microglia (TAMs) revealed cells with a more fully activated ameboid morphology in pre-radiated animals. Microdialyzates from the radiated brain at the margin of tumor infiltration contralateral to the site of implantation were analyzed by unsupervised liquid chromatography-mass spectrometry (LC-MS). In pre-radiated animals, metabolites known to be associated with tumor progression (like, modified nucleotides and polyols) were identified. Whole-tissue metabolomic analysis of the pre-radiated brain microenvironment for metabolic alterations in a separate cohort of nude mice using 1H-NMR revealed significant decrease in levels of antioxidants (glutathione (GSH) and ascorbate (ASC)), NAD+, TCA intermediates, and increased ATP and GTP. Glutathione and ASC showed highest VIPpred (1.65) in OPLS-DA analysis. Involvement of ASC catabolism was further confirmed by GC-MS. To assess longevity of radiation effects, we compared survival with implantation occuring 2 months vs. 24h following radiation, finding worse survival in animals implanted at 2 months. These radiation-induced alterations are consistent with a chronic disease-like microenvironment characterized by reduced levels of antioxidants and NAD+, as well as elevated extracellular ATP and GTP serving as chemoattractants, promoting cell motility and vesicular secretion with decreased levels of GSH and ASC exacerbating oxidative stress. Taken together, these data suggest that IR induces tumor-permissive changes in the microenvironment with metabolomic alterations that may facilitate tumor aggressiveness with important implications for recurrent glioblastoma. Harnessing these metabolomic insights may provide opportunities to attenuate RT-associated aggressiveness of recurrent GBM.

cancer biology↗