Biology subjects

Tyrrell, V.

Publications and source records attributed to Tyrrell, V..

13 recordsLinked to original sources

bioRxiv2025

Single-cell RNA-sequencing of cerebral spinal fluid identifies circulating tumour cells in children with brain cancer

Paediatric central nervous system (CNS) tumours are the leading cause of cancer-related death in children, yet disease monitoring remains challenging. Conventional approaches, including imaging and cytology, lack sensitivity, delaying intervention. Liquid biopsy offers a minimally invasive alternative, but the utility of circulating tumour cells (CTCs) in paediatric CNS tumours as biomarkers is poorly defined. We developed a CTC detection and characterisation workflow from cerebrospinal fluid (CSF) utilising single-cell RNA-sequencing (scRNA-seq) and applied this to ten CNS tumour subtypes in 16 patients. CTCs were identified in all cases, with higher burdens in pineoblastoma, medulloblastoma and atypical teratoid rhabdoid tumours. Longitudinal profiling revealed CTC dynamics correlated with clinical disease course and anticipated relapse. Critically, scRNA-seq uncovered a sub-clonal canonical driver alteration at diagnosis that only became detectable by bulk RNA-seq at progression, underscoring its potential to resolve clonal dynamics. This workflow enables real-time molecular profiling, offering a transformative strategy for disease monitoring and personalised therapy in paediatric brain tumours.

cancer biology↗

bioRxiv2025

The coronavirus envelope is conserved, contains bioactive lipids needed for replication, and is modulated in response to host inflammation

How inflammation or disease regulates coronavirus lipid membranes is currently unknown, while patient-derived viral envelopes have never been structurally characterized. Here, we show that four cultured SARS-CoV-2 strains (England2, Alpha, Beta, and Delta) possess conserved, phospholipid- and cholesterol-rich envelopes, with pro-thrombotic and infection-promoting aminophospholipids (aPL) displayed predominantly on the outer leaflet (approximately 70-80%). Exposure to interleukin-4 (IL-4) markedly altered envelope fatty acyl composition, whereas interleukin-6 (with or without its soluble receptor IL-6R) and dexamethasone had no detectable effect. Viral envelopes were susceptible to hydrolysis by secretory phospholipase A2 (sPLA2), an enzyme associated with adverse clinical outcomes. SARS-CoV-2 isolated directly from patient saliva exhibited cholesterol-enriched envelopes that were highly conserved across clinical isolates. In addition, clinical samples contained pro-coagulant oxidized phospholipids and bioactive lipoxygenase (LOX)-derived oxylipins. The dominance of external facing pro-coagulant aPL and eoxPL may support known thrombotic complications of severe COVID19 viremia. Last, gene-silencing experiments demonstrated that 15-LOX2 is required for replication of related coronaviruses. Together, these findings reposition the coronavirus envelope as an active, dynamic structure rather than a passive scaffold, and challenge the protein-centric view of viral function. The lipid envelope is proposed as a potential therapeutic target through modulation of host innate immunity, and dampening thrombotic potential. Significance statementViruses such as SARS-CoV-2 are surrounded by a host-derived lipid envelope. Little is known about how this changes during infection/inflammation. We determined the lipid composition of the SARS-CoV-2 envelope using both laboratory-grown viruses and patient isolates. Across several pandemic strains, the envelope was rich in cholesterol and phospholipids and showed a consistent structure. Lipids linked to thrombosis and infection were mainly exposed on the outer virus surface. The inflammatory cytokine interleukin-4 altered the envelopes fatty acid composition, while other treatments did not. Patient-derived viruses contained additional bioactive lipids, and blocking an enzyme that generates these lipids reduced coronavirus replication. In summary, the envelope is an active component of infection and potential target for new treatments to dampen infectivity and thrombosis.

immunology↗

bioRxiv2025

Pro-coagulant lipids in physiological ratios found in the activated platelet membrane do not impact clot structure or fibrinolysis in purified assays.

PurposeA central role for the pro-coagulant membrane comprising aminophospholipids (aPL) and enzymatically oxidized phospholipids (eoxPL) in promoting hemostasis via interaction with coagulation factor Gla domains is well established. However, little is known about their interactions with the fibrinolytic pathway, their ability to alter clot structure or to support the activated protein C (APC) pathway. Previous studies used membrane liposome compositions that differ from those expected physiologically and/or generated inconsistent findings. To address this, pro-coagulant membranes comprising physiological proportions of aPL and eoxPL will be tested for their ability to support fibrinolysis using standard assays. MethodsThe impact of phospholipids on clot structure and clot lysis was tested using absorbance-based assays. To investigate the impact of PS or eoxPL on fibrinolysis, plasmin was monitored chromogenically, and clot dissolution measured in a purified lysis system activated by tissue plasminogen activator or urokinase. To determine the impact of eoxPL on APC/protein S, FVa was incubated with APC (+/-protein S) in a purified prothrombinase assay. ResultsAt the concentrations of lipids tested in our study, PS did not significantly impact clot structure or fibrinolysis. Similarly, eoxPL did not impact either fibrinolysis or activity of APC/Protein S. ConclusionUsing liposome compositions that approximate activated blood cells, we found that the pro-coagulant membrane is unlikely to influence either clot structure or fibrinolytic activity directly, beyond its well characterized role in supporting Gla dependent coagulation factors and the actions of platelet associated proteins/receptors.

pharmacology and toxicology↗

bioRxiv2025

Expanding the utility of transcriptome analysis for mutation detection in high-risk childhood precision oncology

In precision oncology, whole transcriptome sequencing (RNA-seq) excels at identifying oncogenic fusions. Here, using a cohort of 477 high-risk paediatric tumours, we demonstrate that RNA-seq can identify all mutation classes found previously using whole genome sequencing (WGS) and provides additional functional insights into their pathogenicity. By incorporating reference-guided fusion, and reference-free structural variant (SV) detection algorithms with RNA abundance assessment, RNA-seq identified 96% of SVs and resolved 33 complex SVs that WGS failed to identify. Furthermore, RNA-seq identified 92% of all single nucleotide variants and small insertions and deletions. Importantly RNA-seq informed the pathogenicity assessment in 22% of variants through identification of allele specific expression or the functional consequence of splice-altering variants. The utility of RNA-seq extends beyond fusion identification to the interpretation of mutation pathogenicity and the discovery of important mutations that would otherwise go undetected. We propose that RNA-seq is an indispensable companion to WGS in precision medicine.

genomics↗

bioRxiv2025

Interleukin-6 elevates thrombosis via pro-coagulant phospholipids from platelet 12-lipoxygenase in rheumatoid arthritis.

BackgroundRheumatoid arthritis (RA) is associated with significantly higher thrombotic risk, which is not yet mechanistically understood. Here, the role of pro-coagulant membranes of platelets and blood cells in driving thrombosis, and their regulation by inflammation was determined using human cohorts and genetically-modified mice. MethodsAntigen-induced arthritis (AIA) was induced in WT, Il27ra-/-, Il6ra-/-, Alox12-/- and Alox15-/- mice. Coagulation and inflammatory markers were measured in plasma. Lipidomics was performed on blood cells and synovium analyzing pro-coagulant enzymatically-oxidized phospholipids (eoxPL) and oxylipins. Two human RA patient cohorts were characterized for eoxPL generation in blood cells, and chronic immune response to eoxPL in vivo. ResultsAIA induction significantly elevated plasma thrombin-antithrombin (TAT) complexes, serum amyloid A (SAA), and eoxPL in blood cells and platelets. Elevations in TATs, SAA and eoxPL were suppressed by genetic deletion of IL-6Ra, while platelet Alox12 deletion prevented TAT and eoxPL increases. This indicates a direct role for IL-6 in elevating thrombosis via upregulation of platelet eoxPL. In contrast, leukocyte Alox15 deletion did not impact TATs or eoxPL. Deletion of either LOX isoform worsened AIA joint pathology. Synovial tissue demonstrated raised eoxPL, but exclusively from Alox15, indicating leukocyte origin. Thus, both LOX isoforms contribute to AIA, but through different mechanisms. In human RA, platelet counts, and plasma TATs were elevated, and plasma had significantly elevated IgG against eoxPL, indicating patients experience chronic exposure to the lipids in vivo. ConclusionsPlatelet-derived pro-coagulant eoxPL are elevated in human and murine arthritis along with higher coagulation markers. In mice, this was mediated by the IL-6/Alox12 axis and directly responsible for the higher thrombotic risk. IL-6 plays a central role in driving platelet activation in RA, with the pro-coagulant lipid membrane representing a novel target. Reducing inflammation using DMARDs, particularly targeting IL-6 may reduce platelet pro-coagulant activity and thrombosis risk in RA.

pharmacology and toxicology↗

bioRxiv2025

12/15-Lipoxygenase orchestrates murine wound healing via PPARg-activating oxylipins acting holistically to dampen inflammation.

12/15-lipoxygenase (12/15-LOX, Alox15) generates bioactive oxygenated lipids during inflammation, however its homeostatic role(s) in normal healing are unclear. Here, the role of 12/15-LOX in resolving skin wounds was elucidated, focusing on how its lipids act together in physiologically relevant amounts. In mice, wounding caused acute appearance of 12/15-LOX-expressing macrophages and stem cells, coupled to early generation of [~]12 monohydroxy-oxylipins and enzymatically oxygenated phospholipids (eoxPL). Alox15 deletion increased -smooth muscle actin, collagen deposition, stem cell/fibroblast proliferation, IL6/pSTAT3, pSMAD3, and IFN-{gamma} levels. Conversely, CD206 expression, F480+ cells, MMP9 and MMP2 activities were reduced. Alox15-/- skin was deficient in PPAR{gamma}/adiponectin activity. Furthermore, while pro-inflammatory genes were upregulated as normal during wounding, many including Il6, Il1b, ccl4, Cd14, Cd274, Clec4d, Clec4e, Csf3, and Cxcl2 failed to revert to baseline during healing, indicating disruption of an anti-inflammatory brake. Reconstituting Alox15-/- wounds with a physiological mixture of Alox15-derived primary oxylipins generated by healing wounds restored MMP and dampened collagen deposition. The oxylipin mixture activated PPAR{gamma} in vitro, while in vivo, the PPAR{gamma} co-activator, Helz2, was significantly upregulated. Additional inflammatory and proliferative gene networks impacted by Alox15-/-included Elf4, Cebpb and Tcf3, with many of their associated genes significantly dysregulated. In summary, the impact of 12/15-LOX is ascribed to the deficiency of abundantly generated monohydroxy oxylipins acting together via PPAR{gamma}/adiponectin. The identification of multiple gene alterations reveals several new targets for treatment of non-healing wounds. Our studies demonstrate that abundant 12/15-LOX oxylipins act together, dampening inflammation in vivo, revealing a need to consider lipid signaling holistically. Significance statementDefective wound healing is a significant global clinical problem. Macrophage 12/15-lipoxygenase (12/15-LOX, Alox15) generates abundant lipid mediators termed oxylipins during inflammation. However, its physiological role during resolving wound healing is unclear, with studies so far assessing the bioactivity of individual lipids pharmacologically, rather than holistically in physiological amounts. Here, we report that Alox15 deficiency in mice caused a fibrotic response with failure to dampen inflammation, due to a dysregulated PPAR{gamma}/adiponectin axis. Treatment of Alox15-/- wounds with physiological mixtures of PPAR{gamma}-activating 12/15-LOX primary monohydroxy products restored the phenotype. Several transcriptional networks (Elf4, Cebpb and Tcf3) controlled by Alox15 were uncovered, identifying new targets for promoting physiological wound healing.

pharmacology and toxicology↗

bioRxiv2023

Comprehensive multi-platform tyrosine kinase profiling reveals novel actionable FGFR aberrations across pediatric and AYA sarcomas

No targeted agents are approved for pediatric sarcomas. Tyrosine kinase (TK) inhibitors represent attractive therapeutic candidates, however, beyond rare TK-activating fusions or mutations, predictive biomarkers are lacking. RNA overexpression of TKs is more commonly observed in pediatric sarcomas, however, an unresolved question is when upregulated TK expression is associated with kinase activation and signaling dependence. We explored the TK molecular landscape of 107 sarcoma patients from the ZERO Childhood Cancer precision medicine program using whole genomic and transcriptomic sequencing. Phosphoproteomic analyses of tyrosine phosphorylation (pY) and functional in vitro and in vivo assays were also performed in cell lines and patient-derived xenografts (PDXs). Our integrated analysis shows that although novel genomic driver lesions are rare, they are present and therapeutically actionable in selected patients as exemplified by a novel LSM1-FGFR1 fusion identified in an osteosarcoma patient. We further show that in certain contexts, TK expression data can be used to indicate TK pathway activity and predict TK-inhibitor sensitivity. We exemplify the utility of FGFR-inhibitors in PAX3-FOXO1 fusion-positive rhabdomyosarcomas (FP-RMS) mediated by high FGFR4 and FGF8 RNA expression levels, and overt activation of FGFR4 (FGFR4_pY). We demonstrate marked tumor growth inhibition in all FP-RMS PDXs treated with single agent FGF401 (FGFR4-specific inhibitor) and single agent lenvatinib (multi-kinase FGFR-inhibitor). Clinical benefit of lenvatinib in a relapsed metastatic FP-RMS patient further exemplifies that FGFR-inhibitors deserve additional investigation in FP-RMS patients. Statement of significanceOur multi-omic interrogation of sarcomas in the ZERO Childhood Cancer program illustrates how an RNA-expression biomarker signature (FGFR4+/FGF8+) in association with FGFR4 activation identifies that PAX3-FOXO1-positive rhabdomyosarcoma patients could benefit from FGFR-inhibitors.

cancer biology↗

bioRxiv2023

Upregulated NF-κB pathway proteins may underlie APOE4 associated astrocyte phenotypes in sporadic Alzheimer's disease

The Apolipoprotein-E4 allele (APOE) is the strongest genetic risk factor for sporadic Alzheimers disease but its role in disease pathogenesis is incompletely understood. The APOE gene encodes Apolipoprotein E (ApoE). Astrocytes are the main source of ApoE in the central nervous system (CNS) and are essential for homeostasis in health and disease. In response to CNS insult, a coordinated multicellular inflammatory response is triggered causing reactive astrogliosis with changes in astrocytic gene expression, cellular structure and function. Human embryonic stem-cells with the neutral APOE33 genotype were edited using CRISPR Cas-9 gene-editing to create isogenic APOE lines with an APOE44 genotype. Quiescent astrocytes were differentiated then stimulated with TNF-, IL1 and C1q inducing an astrogliotic A1 phenotype. Several potentially pathological APOE44-related phenotypes were identified in both quiescent cells and reactive A1 astrocytes including significantly decreased phagocytosis, impaired glutamate and a defective immunomodulatory response. In quiescent APOE44 astrocytes there was significantly decreased secretion of IL6, IL8 and several oxylipins. In A1 astrocytes there was a pro-inflammatory phenotype in APOE44 astrocytes with increases in GRO, ENA78, IL6 and IL8, a decrease in IL10 as well as significant differences in oxylipin expression. As TNF- induced signaling in astrocytes is driven by Nuclear factor kappa B (NF-{kappa}B) proteins of this pathway were measured. Significantly higher levels of the p50, p65 and I{kappa}B sub-units were found in both quiescent and A1 APOE44 astrocytes. This suggests that perturbation of NF-{kappa}B signaling may contribute to the damaging APOE44 cell phenotypes observed providing a new direction for targeted disease therapeutics.

cell biology↗

bioRxiv2022

A novel transcriptional signature identifies T-cell infiltration in high-risk paediatric cancer

Molecular profiling of the tumour immune microenvironment (TIME) has enabled the rational choice of immunotherapies in some adult cancers. In contrast, the TIME of paediatric cancers is relatively unexplored. We speculated that a more refined appreciation of the TIME in childhood cancers, rather than a reliance on commonly used biomarkers such as tumour mutation burden (TMB), neoantigen load and PD-L1 expression, is an essential prerequisite for improved immunotherapies in childhood solid cancers. We combined immunohistochemistry (IHC) and molecular profiling to develop an alternative, expression-based signature associated with CD8+ T-cell infiltration of the TIME in high-risk paediatric tumours. Using this novel 15-gene immune signature, Immune Paediatric Signature Score (IPASS), we estimate up to 31% of high-risk cancers harbour infiltrating T-cells. Our data provides new insights into the variable immune-suppressive mechanisms dampening responses in paediatric solid cancers. Effective immune-based interventions in high-risk paediatric cancer will require individualised analysis of the TIME.

cancer biology↗

bioRxiv2022

Effector Th1 cells alter the transcriptional output of IL-6 in acute resolving inflammation

Cytokines that signal via STAT1 and STAT3 transcription factors instruct decisions affecting tissue homeostasis, anti-microbial host defense, and inflammation-induced tissue injury. To understand the coordination of these activities, we applied RNA-seq, ChIP-seq, and ATAC-seq to identify the transcriptional output of STAT1 and STAT3 in peritoneal tissues during acute resolving inflammation and inflammation primed to drive fibrosis. Bioinformatics focussed on the transcriptional signature of the immuno-modulatory cytokine IL-6 in both settings and examined how pro-fibrotic IFN{gamma}-secreting CD4+ T-cells altered the interpretation of STAT1 and STAT3 cytokine cues. In resolving inflammation, STAT1 and STAT3 cooperated to drive stromal gene expression affecting anti-microbial immunity and tissue homeostasis. The introduction of IFN{gamma}-secreting CD4+ T-cells altered this transcriptional program and channeled STAT1 and STAT3 to a previously latent GAS motif in Alu-like elements. STAT1 and STAT3 binding to this conserved sequence revealed evidence of reciprocal cross-regulation and gene signatures relevant to pathophysiology. Thus, we propose that effector T-cells re-tune the transcriptional output of IL-6 by shaping a regulatory interplay between STAT1 and STAT3 in inflammation.

immunology↗

bioRxiv2020

Oxylipin metabolism is controlled by mitochondrial b-oxidation during bacterial inflammation.

Oxylipins are potent biological mediators requiring strict control, but how they are removed en masse during infection and inflammation is unknown. Here we show that lipopolysaccharide (LPS) dynamically enhances oxylipin removal via mitochondrial {beta}-oxidation. Specifically, genetic or pharmacological targeting of carnitine palmitoyl transferase 1 (CPT1), a mitochondrial importer of fatty acids, reveal that many oxylipins are removed by this protein during inflammation in vitro and in vivo. Using stable isotope-tracing lipidomics, we find secretion-reuptake recycling for 12-HETE and its intermediate metabolites. Meanwhile, oxylipin {beta}-oxidation is uncoupled from oxidative phosphorylation, thus not contributing to energy generation. Testing for genetic control checkpoints, transcriptional interrogation of human neonatal sepsis finds upregulation of many genes involved in mitochondrial removal of long-chain fatty acyls, such as ACSL1,3,4, ACADVL, CPT1B, CPT2 and HADHB. Also, ACSL1/Acsl1 upregulation is consistently observed following the treatment of human/murine macrophages with LPS and IFN-{gamma}. Last, dampening oxylipin levels by {beta}-oxidation is suggested to impact on their regulation of leukocyte functions. In summary, we propose mitochondrial {beta}-oxidation as a regulatory metabolic checkpoint for oxylipins during inflammation.

biochemistry↗

bioRxiv2019

Metabolic dysregulation of the lysophospholipid/autotaxin axis in the chromosome 9p21 gene SNP rs10757274

AimsCommon chromosome 9p21 SNPs increase coronary heart disease (CHD) risk, independent of \"traditional lipid risk factors\". However, lipids comprise large numbers of structurally-related molecules not measured in traditional risk measurements, and many have inflammatory bioactivities. Here we applied lipidomic and genomic approaches to three model systems, to characterize lipid metabolic changes in common Chr9p21 SNPs which confer [~]30% elevated CHD risk associated with altered expression of ANRIL, a long ncRNA.\n\nMethods and ResultsUntargeted and targeted lipidomics was applied to plasma samples from Northwick Park Heart Study II (NPHSII) homozygotes for AA or GG in rs10757274. Elevated risk GG correlated with reduced lysophosphospholipids (lysoPLs), lysophosphatidic acids (lysoPA) and autotaxin (ATX). Five other risk SNPs did not show this phenotype. Correlation and network analysis showed that lysoPL-lysoPA interconversion was uncoupled from ATX in GG, indicating metabolic dysregulation. To identify candidate genes, transcriptomic data from shRNA downregulation of ANRIL in HEK293 cells was mined. Significantly-altered expression of several lysoPL/lysoPA metabolising enzymes was found (MBOAT2, PLA2G4C, LPCAT2, ACSL6, PNPLA2, PLBD1, PLPP1, PLPP2 and PLPPR2). Next, vascular smooth muscle cells differentiated from iPSCs of individuals homozygous for Chr9p21 risk SNPs were examined. Here, the presence of risk alleles was associated with altered expression of several lysoPL/lysoPA enzymes. Importantly, for several, deletion of the risk locus fully or partially reversed their expression to non-risk haplotype levels: ACSL3, DGKA, PLA2G2A, LPCAT2, LPL, PLA2G3, PNPLA3, PLA2G12A LIPC, LCAT, PLA2G6, ACSL1, MBOAT2.\n\nConclusionA Chr9p21 risk SNP associates with complex alterations in immune-bioactive phospholipids and their enzymatic metabolism. Lipid metabolites and genomic pathways associated with CHD pathogenesis in Chr9p21 and ANRIL-associated disease are demonstrated.\n\nOne sentence summaryInflammatory phospholipid metabolism defines a cardiovascular disease SNP

physiology↗

bioRxiv2019

Genomic landscape of 261 childhood cancer patient-derived xenograft models

Accelerating cures for children with cancer remains an immediate challenge due to extensive oncogenic heterogeneity between and within histologies, distinct molecular mechanisms evolving between diagnosis and relapsed disease, and limited therapeutic options. To systematically prioritize and rationally test novel agents in preclinical murine models, researchers within the Pediatric Preclinical Testing Consortium are continuously developing patient-derived xenografts (PDXs) from high-risk childhood cancers, many refractory to current standard-of-care treatments. Here, we genomically characterize 261 PDX models from 29 unique pediatric cancer malignancies and demonstrate faithful recapitulation of histologies, subtypes, and refine our understanding of relapsed disease. Expression and mutational signatures are used to classify tumors for TP53 and NF1 inactivation, as well as impaired DNA repair. We anticipate that these data will serve as a resource for pediatric oncology drug development and guide rational clinical trial design for children with cancer.\n\nHighlightsO_LIMultiplatform genomic analysis defines landscape of 261 pediatric cancer patient derived xenograft (PDX) models\nC_LIO_LIPediatric patient derived xenografts faithfully recapitulate relapsed disease\nC_LIO_LIInferred TP53 pathway inactivation correlates with pediatric cancer copy number burden\nC_LIO_LISomatic mutational signatures predict impaired DNA repair across multiple histologies\nC_LI

genomics↗