Biology subjects

Bailey, S.

Publications and source records attributed to Bailey, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Biophytometallurgy: biomining metals from plant resources

The physicochemical controls governing metal acquisition, release, and redistribution across biological interfaces remain poorly understood. Biophytometallurgy--the microbially assisted release and recovery of plant-associated metals--was used to probe the directionality of the mechanisms controlling nickel and rare earth element (REE) release from Phytolacca during solid-liquid extraction. Bulk characterization did not support a dominant crystalline REE-phosphate-like host in hydroponically enriched shoots. Dissolution and rebinding experiments instead revealed chemically accessible nickel and REE pools, the latter of which had behaviors consistent with apparent equilibrium-like partitioning under mildly acidic conditions. During sulfur biooxidation, Acidithiobacillus ferrooxidans promoted REE release while providing a competing cell-associated REE sink. Consequently, aqueous REE concentrations reflected net redistribution among the separable plant, solution, and microbial phases instead of dissolution alone. These results establish a framework for studying metal partitioning across complex and coupled biological systems and support a route for aqueous REE recovery from plants without thermochemical conversion to ash.

bioengineering↗

bioRxiv2026

Cellular Morphology and Motility Defects are Conserved Phenotypes of Trisomy 21 Despite Heterogeneous Adhesion Mechanisms

Down syndrome is a neurodevelopmental disorder caused by the trisomy of human chromosome 21 (T21). Down syndrome is associated with a wide range of variable clinical features, including congenital heart defects and slow wound healing; however, intellectual disability is ubiquitous and results, in part, from altered neuronal connectivity. Here, we used three sets of control and T21 human fibroblasts, and one set of human induced pluripotent stem cell (hiPSC)-derived cortical neurons, to examine whether changes in cellular morphology and motility are consistent across cell types in Down syndrome and to elucidate the underlying mechanisms. We found that fibroblast morphology is dysregulated in all T21 fibroblast lines. Using a transwell migration assay, cellular migration is decreased in two of the three T21 fibroblast lines. T21 hiPSC-derived cortical neurons also exhibit morphological defects, including a decrease in the length of the longest neurite and growth cone area. Because of these significant changes in morphology and motility in T21 cells, we examined proteins in the focal adhesion complex, which links the intracellular cytoskeleton to the extracellular matrix and directly controls these processes. Multiple proteins in the adhesion complex, including paxillin, vinculin, talin, and RACK1, are dysregulated in T21 fibroblasts and hiPSC-derived neurons, but these changes have high inter-individual variability. Taken together, these findings suggest that altered cellular morphology and motility are conserved features of Down syndrome that arise through heterogeneous alterations in adhesion networks. Thus, this work significantly contributes to the recent literature highlighting the need for personalized medicine in Down syndrome.

cell biology↗

bioRxiv2026

Palliative Irradiation Affects Temporal Degradation of Rodent Vertebral Bone Mechanics, Architecture, and Composition

BackgroundPalliative radiation therapy (RT) for metastatic spine disease significantly increases the risk of vertebral fractures. However, the temporal mechanisms underlying radiation-induced vertebral bone fragility remain poorly understood. ObjectiveTo evaluate the longitudinal effects of a single high-dose irradiation, simulating palliative RT, on vertebral bone mechanical, architectural, and compositional properties in a healthy, skeletally mature rat model. MethodsThirty-one male Sprague Dawley rats received a single 15 Gy lumbar spine irradiation (IR). L4 vertebrae were assessed across all groups (irradiation: 7, 14, and 28 days post-IR, controls: at 0 and 28 days post-IR) for compressive strength and stiffness, micro-CT-derived bone composition and trabecular indices, serum bone turnover markers (NTX and BAP) and advanced glycation endproducts (AGEs). ResultsIrradiation induced progressive deterioration of vertebral bone mechanical properties, with strength decreasing up to 44% and stiffness up to 38% by 28 days post-IR, compared to 0- day controls. Trabecular bone exhibited reduced BMD, BV/TV, and Tb.N with increased Tb.Sp, a shift toward a more rod-like structure. Early post-IR changes suggested disrupted bone remodeling, characterized by elevated NTX and AGEs, but decreased BAP. Multivariable regression demonstrated that Tb.Th and AGEs were independent predictors of stiffness, collectively explaining 61% of its variance. DiscussionHigh-dose irradiation induces sustained temporal degradation of vertebral mechanical properties driven by both trabecular architectural deterioration and alterations in bone matrix quality. Measures of bone composition and non-enzymatic bone turnover suggest this early damage was driven by disruption of bone cellular homeostasis, favoring increased resorption over formation. These findings support that radiation impairs both structural integrity and pre-yield mechanical behavior, providing mechanistic insight into the elevated fracture risk observed clinically after irradiation for metastatic spine disease. Lay summaryThis study used a rat model to mimic palliative radiation therapy for cancer that has spread to the spine and evaluated the changes in bone quality up to 28 days post-therapy. We found that irradiation progressively weakened the structural integrity and composition of the bones in the spine and disrupted the normal balance of bone breakdown and repair, leading to greater bone loss and fragility. Our findings provide insight into the increased risk of fractures observed in patients receiving radiation therapy to the spine and may support efforts to better protect bone health during treatment.

bioengineering↗

bioRxiv2026

Integrative Clinical-Molecular Modeling Identifies LRRN4CL as a Determinant of Structural and Functional Myocardial Improvement

BackgroundMechanical ventricular unloading and systemic circulatory support with left ventricular assist devices (LVADs) enable myocardial recovery in a subset of advanced heart failure (HF) patients, but predictors and mechanisms of recovery are not well understood. Integrating clinical and molecular data may improve identification of patients most likely to recover and uncover biologically relevant targets in HF. MethodsWe collected and analyzed left ventricular apical myocardial tissue and clinical data from 208 patients undergoing LVAD implantation across five centers. Pre-implant transcriptomic profiles (22,373 mRNA transcripts) were integrated with 59 clinical variables using supervised machine learning with repeated cross-validation to identify and prioritize features associated with myocardial recovery, defined as a binary outcome based on improvement in left ventricular ejection fraction (LVEF [≥]40%) and left ventricular end-diastolic diameter (LVEDD [≤]5.9 cm). We also modeled functional (LVEF) and structural (LVEDD) improvement as a continuous outcome without any predefined LVEF and LVEDD pathological thresholds. Feature prioritization was followed by validation in human myocardial tissue and mechanistic interrogation in human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs). ResultsIntegrative models achieved modest discrimination for myocardial recovery as a binary categorical outcome (maximum mean cross-validated area under the curve 0.73{+/-}0.15), identifying clinical features such as HF duration, LVEDD, HF pharmacologic therapy, and device configuration. Leucine-rich repeat neuronal 4C-like (LRRN4CL), measured in human myocardium, consistently emerged as a top transcriptomic predictor across both binary and continuous metric models (functional and structural). Higher pre-LVAD LRRN4CL expression was associated with reduced likelihood of myocardial recovery and localized primarily to cardiomyocytes. In iPSC-CMs, LRRN4CL overexpression localized to the sarcoplasmic reticulum, induced transcriptional remodeling characterized by suppression of contractile pathways and activation of stress programs, impaired calcium handling, impaired contraction-relaxation kinetics, and diminished mitochondrial respiratory reserve capacity. ConclusionsIntegration of clinical and myocardial transcriptomic data identifies LRRN4CL as a novel marker associated with impaired myocardial recovery following LVAD-mediated ventricular unloading and systemic circulatory support. These findings move beyond predictive modeling, linking integrative computational discovery to cardiomyocyte dysfunction and providing a translational framework for biologically informed risk stratification and therapeutic targeting for myocardial recovery. CLINICAL PERSPECTIVEO_ST_ABSWhat Is New?C_ST_ABSO_LIIntegrative clinical and myocardial transcriptomic modeling identifies LRRN4CL as a novel molecular determinant of structural and functional changes after LVAD-mediated ventricular unloading and enhanced systemic circulatory support. C_LIO_LIElevated LRRN4CL expression is associated with adverse remodeling signatures, impaired calcium handling, and stress responses in human iPSC-derived cardiomyocytes. C_LIO_LIExperimental overexpression of LRRN4CL directly disrupts calcium cycling, contractile performance, and mitochondrial respiration linking molecular signature to functional phenotype. C_LI What Are the Clinical Implications?O_LIIdentification of LRRN4CL as a marker associated with impaired myocardial recovery supports future efforts toward biologically informed risk stratification for patients undergoing LVAD therapy. C_LIO_LILRRN4CL as a marker of cardiac improvement potential may extend beyond advanced HF to earlier stage disease patients and inform prognosis, risk stratification, and response to medical therapies. C_LIO_LIThese findings highlight LRRN4CL-associated pathways as potential therapeutic targets and demonstrate how integrative clinical-transcriptomic approaches can move beyond clinical prediction toward identification of new biologically precise therapeutic targets in HF following a bedside to bench and back approach. C_LI

bioinformatics↗

bioRxiv2025

Cooperative and antagonistic interactions between sub-clones favour the co-existence of multiple resistance mechanisms in melanoma

Intra-tumour heterogeneity is a major obstacle to durable responses to targeted cancer therapy, yet how different resistant cell states interact within the same tumour remains poorly understood. In this study, we demonstrate cooperativity between co-occurring resistant states in a single tumour. Using BRAF mutant melanoma as a paradigm, we generate three different resistant states within a single model and demonstrate that they exhibit varying differentiation states and migratory capacities and share few common therapeutic vulnerabilities. Through a combination of experiments, including using Cre-mediated recombination to generate heterogeneity in existing tumours, and in silico modelling, we show that intra-tumour heterogeneity is the most favoured state for therapy resistant tumours. This is underpinned by signalling between different melanoma states, with YAP1 active cells providing supporting signals for other cells but inhibiting their own proliferation. Optimal disease control requires targeting both the YAP1 active cell state and the inter- cellular communication networks. We identify the histone demethylase inhibitor GSK-J4 as being particularly effective in targeting both features of resistant tumours and demonstrate its ability to control melanoma with multiple concurrent resistance mechanisms.

cancer biology↗

bioRxiv2025

Splenic granulopoiesis and S100A9 drive resistance to checkpoint inhibitors conferred by liver metastases

Here, we investigate why liver metastases reduce the efficacy of immune checkpoint inhibitors (CPI). The poor prognosis of patients with liver metastases is associated with a systemic increase in neutrophils. Using experimental models, we confirm that mice with liver metastases respond poorly to CPI, have elevated neutrophils and suppress the response of subcutaneous lesions to CPI. We demonstrate that liver metastases, acting partly via IL-6, boost granulopoiesis in the spleen and promote the generation of immature S100A9hi neutrophils that suppress T-cell proliferation. Human liver metastases exhibit a similar increase in S100A9hi neutrophils. Neutrophil depletion attenuates the growth of liver metastases, but not subcutaneous metastases. Moreover, genetic deletion of S100A9 enables liver metastases to be effectively treated with CPI, and prevents liver metastases from suppressing the response in subcutaneous metastases. Thus, we document how liver metastases specifically change splenic granulopoiesis leading to changes in the microenvironment of non-hepatic lesions, and how targeting a key neutrophil protein restores the efficacy of CPI.

immunology↗

bioRxiv2025

Cell migration sculpts evolutionary dynamics favouring therapy resistance in lung cancer

The evolution of cancer undermines the long-term efficacy of therapy. In this study, we combine experimental, computational, and clinical data analysis to investigate factors influencing the competition of subclones in lung cancer. Lineage tracing reveals unexpected variation in the long-term fate of neutral subclones, with subclones arising near the edge of tumours being favoured. Low levels of cell migration and cell mixing lead to high cell densities in the interior of the tumour that suppress proliferation. Using agent-based modelling and in silico analysis we inferred the extent of cell mixing in human tumours from the TRACERx lung cancer study. This reveals correlations between Epithelial to Mesenchymal Transition (EMT), stromal fibroblasts and levels of cell mixing. Experimental analysis confirms that both TGF{beta}-driven EMT and stromal fibroblasts reduce the variability in subclone fate and promote subclone mixing. Moreover, mixing favours clonal sweeps by subclones resistant to therapy-induced cell killing. Together, these analyses demonstrate that EMT and stromal fibroblasts sculpt tumour evolution by promoting cell mixing and thereby favour the rapid dominance of therapy resistant subclones.

cancer biology↗

bioRxiv2025

Optimized large-scale longitudinal biorepository of gastroesophageal adenocarcinoma patient-derived organoids: High-fidelity models for personalized treatment to overcome resistance.

A major limitation in studying gastroesophageal adenocarcinoma (GEA) has been the lack of reliable models that represent the diseases complexity. We present lessons learned from a comprehensive large-scale biobanking effort combining traditional sample collection with several in vitro models including 3-dimensional patient-derived organoids (PDOs), 2-dimensional cancer-associated fibroblasts (CAFs), tumor-infiltrating lymphocytes (TILs) and/or in vivo xenografts. This initiative started in 2018, integrating multiple advanced ex-vivo models such as PDOs, patient-derived xenografts (PDXs) and organoids (PDXOs). This unique resource now includes tumor avatars from over 380 consented patients, making it the largest living GEA biobank in the world. We achieved > 90% success rate in creating per-patient models, including 227 tumor-derived and 203 neighboring normal PDOs. These organoids accurately mirror key features of the original tumors, such as their histology (e.g. microsatellite instability), mutations, and drug response, across treatment points. Notably, PDOs can predict individual patient responses to chemotherapy within five weeks, underscoring their clinical relevance. Furthermore, high-throughput drug screening on PDO subsets generates personalized chemosensitivity profiles for 22 drugs. Through a process of continued refinement of culture techniques and tumor sampling approach, our large-scale comprehensive collection of GEA avatars represents a unique and valuable preclinical experimental resource for precision oncology. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=76 SRC="FIGDIR/small/663874v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@f8a032org.highwire.dtl.DTLVardef@dd6fa3org.highwire.dtl.DTLVardef@1cc558corg.highwire.dtl.DTLVardef@492a5_HPS_FORMAT_FIGEXP M_FIG Schematic depiction of GEA live-banking workflow C_FIG

cancer biology↗

bioRxiv2025

Discovery of a VHL molecular glue degrader of GEMIN3 by Picowell RNA-seq

Targeted protein degradation (TPD) is an emerging therapeutic modality in which small molecules are used to recruit targets to the natural protein degradation machinery of the cell. Molecular glue degraders (MGD) are monovalent small molecules that accomplish this by redirecting E3 ubiquitin ligases to target proteins, offering the potential to degrade previously unliganded and "undruggable" proteins in cancer, neurodegenerative, and other diseases. While attractive due to their drug-like properties, MGDs are exceptionally hard to discover and have largely been identified serendipitously. The Von Hippel-Lindau (VHL) E3 ligase is the second most widely used effector for TPD, though current VHL-based degraders are primarily large heterobifunctional PROTACs (proteolysis-targeting chimeras) designed using target-based ligands. Here, we have instead pursued target-agnostic discovery of VHL MGDs leveraging proprietary ultra-miniaturized microfluidics devices (Picowells) to facilitate unbiased RNA-seq screening of a biased E3-focused library. This resulted in dGEM3, a novel VHL molecular glue that targets the survival of motor neuron (SMN) complex member GEMIN3 for degradation. Through a combination of cellular, biochemical, and biophysical assays, we have characterized the GEMIN3 degron within its helicase ATP-binding domain, and how the kinetics of ternary complex formation impact degradation. These findings provide insights on the re-programmability of VHL for novel targets using drug-like molecular glues.

biochemistry↗

bioRxiv2025

Gut Competition Dynamics of Live Bacterial Therapeutics Are Shaped by Microbiome Complexity, Diet, and Therapeutic Transgenes

Competitive exclusion is conventionally believed to prevent the establishment of a secondary strain of the same bacterial species in the gut microbiome, raising concerns for the deployment of live bacterial therapeutics (LBTs), especially if the bacterial chassis is a strain native to the gut. In this study, we investigated factors influencing competition dynamics in the murine gut using isogenic native Escherichia coli strains. We found that competition outcomes are context-dependent, modulated by microbiome complexity, LBT transgene expression, intestinal inflammation, and host diet. Furthermore, we demonstrated that native LBTs can establish long-term engraftment in the gut alongside a parental strain, with transgene-associated fitness effects influencing competition. We identified various interventions, including strategic dosing and dietary modulation, that significantly enhanced LBT colonization levels by 2 to 3 orders of magnitude. These insights provide a framework for optimizing LBT engraftment and efficacy, supporting their potential translation for human therapeutic applications.

microbiology↗

bioRxiv2024

Low-pass nanopore sequencing for measurement of global methylation levels in plants

Nanopore sequencing enables detection of DNA methylation at the same time as identification of canonical sequence. A recent study validated low pass nanopore sequencing to accurately estimate global methylation levels in vertebrates with sequencing coverage as low as 0.01x. We investigated the applicability of this approach to plants by testing three plant species and analysed the effect of technical and biological parameters on estimate precision and accuracy. Our results indicate that a higher coverage (0.1x) is required to assess plant global methylation at an equivalent accuracy to vertebrates. Shorter read length and a closer sequence match between sample and reference genome improved measurement accuracy. Application of this method in Vitis vinifera showed consistent global methylation levels across different leaf sizes, and different sample preservation and DNA extraction methods, whereas different varieties and tissue types did exhibit methylation differences. Similarly, distinct methylation patterns could be observed in different genomic features. Our findings suggest the suitability of this method as a low-cost screening tool for validation of experimental parameters, developmental time courses and to assess methylation status for different modification types and sequence contexts at the level of whole genome or for abundant genomic features such as transposable elements.

genomics↗

bioRxiv2024

Imaging of MAP kinase dynamics reveals endocytic regulation of pulsatile signalling and network re-wiring in response to targeted therapy in EGFR-mutant non-small cell lung cancer

A better understanding of the signalling mechanisms underlying transitions from drug-sensitive to drug-tolerant states is required to overcome therapy failure. We combined single-cell biosensor imaging with functional perturbations to investigate the regulation of oncogenic signalling in EGFR-mutant lung adenocarcinoma. We find that despite the constant presence of the mutant oncogene, ERK signalling exhibits pulsatile dynamics, with pulse characteristics determined by the endocytic machinery. Analysis of drug-tolerant persisters (DTPs) revealed that, after an initial phase of complete pathway shut-down, signalling was rewired leading to renewed ERK pulses that drive cell cycle progression. FAK- and SRC-regulated adhesion complexes replace mutant EGFR as the driver of reactivated ERK pulses in DTPs, yet they remain controlled by the membrane trafficking machinery. We show that DTPs rely on additional survival pathways including YAP signalling, and that the phosphatase PTPRS represents a key node in therapy resistant cells, coordinating regulation of ERK, the cytoskeleton, and YAP.

cancer biology↗

bioRxiv2024

Repix: reliable, reusable, versatile chronic Neuropixels implants using minimal components

Neuropixels probes represent the state-of-the-art for high-yield electrophysiology in neuroscience: the simultaneous recording of hundreds of neurons is now routinely carried out in head-restrained animals. In contrast, neural recording in unrestrained animals, as well as recording and tracking neurons over days, remains challenging, though it is possible using chronic implants. A major challenge is the availability of simple methods that can be implemented with limited or no prior experience with Neuropixels probes, while achieving reliable, reusable, versatile high-density electrophysiology. Here we developed, deployed, and evaluated the real-world performance of Repix, a chronic implantation system that permits the repeated re-use of Neuropixels probes. The lightweight system allows implanted animals to express a full range of natural behaviors, including social behaviors. We show that Repix allows the recording of hundreds of neurons across many months, up to a year, with implants across cortical and subcortical brain regions. Probes can be reused repeatedly with stable yield. Repix has been used by 16 researchers in 10 laboratories to date, and we evaluated the real-world performance of Repix in a variety of chronic recording paradigms in both mice and rats with a combined 209 implantations. We found that the key advantage of Repix is robustness and simplicity. Adopters of Repix became proficient at five procedures on average, regardless of prior experience with in vivo electrophysiology. With the companion protocol alongside this article, the performance and user-friendliness of Repix should facilitate a wide uptake of chronic Neuropixels recordings.

neuroscience↗

bioRxiv2024

Integrating molecular and clinical variables to predict myocardial recovery

Mechanical unloading and circulatory support with left ventricular assist devices (LVADs) mediate significant myocardial improvement in a subset of advanced heart failure (HF) patients. The clinical and biological phenomena associated with cardiac recovery are under intensive investigation. Left ventricular (LV) apical tissue, alongside clinical data, were collected from HF patients at the time of LVAD implantation (n=208). RNA was isolated and mRNA transcripts were identified through RNA sequencing and confirmed with RT-qPCR. To our knowledge this is the first study to combine transcriptomic and clinical data to derive predictors of myocardial recovery. We used a bioinformatic approach to integrate 59 clinical variables and 22,373 mRNA transcripts at the time of LVAD implantation for the prediction of post-LVAD myocardial recovery defined as LV ejection fraction (LVEF) [≥]40% and LV end-diastolic diameter (LVEDD) [≤]5.9cm, as well as functional and structural LV improvement independently by using LVEF and LVEDD as continuous variables, respectively. To substantiate the predicted variables, we used a multi-model approach with logistic and linear regressions. Combining RNA and clinical data resulted in a gradient boosted model with 80 features achieving an AUC of 0.731{+/-}0.15 for predicting myocardial recovery. Variables associated with myocardial recovery from a clinical standpoint included HF duration, pre-LVAD LVEF, LVEDD, and HF pharmacologic therapy, and LRRN4CL (ligand binding and programmed cell death) from a biological standpoint. Our findings could have diagnostic, prognostic, and therapeutic implications for advanced HF patients, and inform the care of the broader HF population. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=170 HEIGHT=200 SRC="FIGDIR/small/589326v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@17f0503org.highwire.dtl.DTLVardef@2231c1org.highwire.dtl.DTLVardef@f0ac56org.highwire.dtl.DTLVardef@c278f3_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗

bioRxiv2023

Deep Learning Model Imputes Missing Stains in Multiplex Images

Multiplex staining enables simultaneous detection of multiple protein markers within a tissue sample. However, the increased marker count increased the likelihood of staining and imaging failure, leading to higher resource usage in multiplex staining and imaging. We address this by proposing a deep learning-based MArker imputation model for multipleX IMages (MAXIM) that accurately impute protein markers by leveraging latent biological relationships between markers. The models imputation ability is extensively evaluated at pixel and cell levels across various cancer types. Additionally, we present a comparison between imputed and actual marker images within the context of a downstream cell classification task. The MAXIM models interpretability is enhanced by gaining insights into the contribution of individual markers in the imputation process. In practice, MAXIM can reduce the cost and time of multiplex staining and image acquisition by accurately imputing protein markers affected by staining issues.

pathology↗

bioRxiv2022

Cannabidiol targets a modulatory system for excitatory-inhibitory synaptic coordination, contributing to its anti-seizure action

Cannabidiol (CBD), a non-euphoric component of cannabis, reduces seizures in multiple forms of pediatric epilepsy, but the mechanism(s) of anti-seizure action remain unclear. In one leading model, CBD acts at glutamatergic axon terminals, blocking pro-excitatory actions of an endogenous membrane phospholipid, lysophosphatidylinositol (LPI), at the G protein-coupled receptor GPR55. However, the impact of LPI-GPR55 signaling at inhibitory synapses and in epileptogenesis remains underexplored. We found that LPI transiently increased hippocampal CA3[->]CA1 excitatory presynaptic release probability and evoked synaptic strength in WT mice, while attenuating inhibitory postsynaptic strength by decreasing GABAAR{gamma}2 and gephyrin puncta. Effects of LPI at both excitatory and inhibitory synapses were eliminated by CBD pretreatment and absent after GPR55 deletion. Acute pentylenetrazole-induced seizures elevated levels of GPR55 and LPI, and chronic lithium pilocarpine-induced epileptogenesis potentiated the pro-excitatory effects of LPI. We propose that CBD exerts potential therapeutic effect both by blocking synaptic effects of LPI and dampening hyperexcitability.

neuroscience↗

bioRxiv2022

Deletion of 12-lipoxygenase normalizes platelet function after storage and transfusion in thrombocytopenic mice

ObjectivePlatelets for transfusion are stored for 5-7 days. During storage, platelets undergo numerous detrimental functional changes. In the current study, we sought to understand how genetic deletion of 12 -lipoxygenase (12-LOX) affects platelets during storage, before, and after transfusion. Approach and ResultsWe obtained platelets from wild-type (WT) and 12-LOX-/-mice and performed storage studies for 24 and 48 hours. Using LC-MS/MS-MRM, we showed that {omega}-3 and {omega}-6 fatty acids increased significantly in stored platelets from 12-LOX-/-mice, while oxylipins were significantly lower than in WT platelets. The circulation time of fresh 12-LOX-/-platelets was significantly shorter than that of fresh WT platelets, but no differences were observed after storage. Baseline IIb{beta}3 integrin activation was significantly lower before and after 24 hours of storage in 12-LOX-/-platelets than in WT platelets. Surprisingly, after transfusion, we observed more baseline IIb{beta}3 integrin activation in 12-LOX-/-platelets than in WT platelets. In line with this, transfusion of stored 12-LOX-/-platelets led to more frequent and significantly faster vessel occlusions than transfusion of stored WT platelets in a FeCl3-induced carotid artery injury model in thrombocytopenic mice. ConclusionDeleting 12-LOX improves the post-transfusion function of stored murine platelets. Pharmacologic inhibition of 12-LOX or dietary alterations of {omega}-3 and {omega}-6 PUFAs could significantly enhance human platelet quality and function after storage. Future studies must determine the feasibility and safety of 12-LOX inhibition in stored and transfused human platelets.

physiology↗

bioRxiv2022

Medulloblastoma Group 3 and 4 Tumors Comprise a Clinically and Biologically Significant Expression Continuum Reflecting Human Cerebellar Development

Medulloblastoma is currently sub-classified into distinct DNA methylation subgroups/subtypes with particular clinico-molecular features. Using RNA-seq in large well annotated cohorts of medulloblastoma we show that transcriptionally Group3 and Group4 medulloblastomas exist not as discrete types but as intermediates on a bipolar continuum between archetypal Group3 and Group4 entities. Continuum position is prognostic, reflects propensity for specific DNA copy-number changes, key switches in isoform/enhancer usage and RNA-editing. Examining scRNA-seq profiles we show intra-tumoral transcriptional heterogeneity along the continuum is limited in a subtype-dependent manner. By integrating with a human scRNA-seq reference atlas we show this continuum is mirrored by an equivalent continuum of transcriptional cell types in early fetal cerebellar development. We identify unique developmental niches for all four major subgroups and link each to a common developmental antecedent. Our findings show a transcriptional continuum arising from oncogenic disruption of highly specific fetal cerebellar cell types, linked to almost every aspect of Group3/Group4 molecular biology and clinico-pathology.

cancer biology↗