Biology subjects

Quaegebeur, A.

Publications and source records attributed to Quaegebeur, A..

14 recordsLinked to original sources

bioRxiv2026

mRNA-LNP therapy restores systemic nucleoside imbalance in a mitochon-drial DNA depletion syndrome

Mitochondrial DNA depletion syndromes (MDS) are inherited conditions caused by pathogenic variants in mitochondrial DNA maintenance genes. Most MDS are severe, fatal and incurable conditions. Mitochondrial neurogastrointestinal encephalomyopathy (MNGIE) is an MDS resulting from loss-of-function mutations in the TYMP gene, encoding Thymidine Phosphorylase (TP). Systemic nucleoside accumulation caused by TP deficiency disrupts mitochondrial nucleotide homeostasis, which underlies disease progression and mortality. Current treatments, including liver and hematopoietic stem cell transplantation, partially restore TP activity but are invasive, carry substantial risk and are limited by donor availability. Here, we establish TYMP-mRNA in lipid nanoparticles (hTYMP-mRNA-LNPs) as a safe non-viral protein-replacement therapy for MNGIE. Intravenous administration of hTYMP-mRNA-LNPs induced robust hepatic TP expression in a mouse model of MNGIE, was well tolerated and restored circulating nucleosides to wild-type levels within hours, lasting up to three weeks, at a preclinical minimally effective dose of 0.25mg/kg. To facilitate repeat administration and patient access, we demonstrate enhanced efficiency of subcutaneous mRNA-LNP delivery by co-administration of recombinant or mRNA-encoded (SPAM1-mRNA-LNPs) hyaluronidase, achieving effective hepatic TP expression and systemic nucleoside clearance. These findings establish mRNA-LNP-mediated protein replacement as a therapeutic strategy for a primary mitochondrial disease where transient liver-targeted expression is sufficient to correct a systemic metabolic defect. More broadly, our results support the development of mRNA-LNP therapeutics and their subcutaneous delivery as a generalizable platform for treating monogenic diseases, through repeatable, non-viral protein replacement.

pharmacology and toxicology↗

bioRxiv2026

Tau aggregate replication occurs at the pre-synapse of cultured human neurons and increases with application of TNFa

Tau aggregation at synapses is a key process driving Alzheimers disease but the mechanism(s) that cause this have not been established. We used a model system of forward-programming induced glutamatergic neurons (iNeurons) with three independent cell lines treated with TNF[a]. Using aggregate-specific SIMOA, STED microscopy, and SynPull to detect nanoscopic tau aggregates in bulk samples and at individual synapses, we found that TNF[a]-driven tau aggregation occurs preferentially at the pre-synapse, forming predominantly non-fibrillar aggregates that are larger than ones in the extra- and post-synaptic regions. Using mathematical models of aggregate formation, we fitted the frequency of AT8-positive tau aggregates in synaptosomes, which showed that aggregate replication is the dominant process and is much faster than de-novo aggregate formation, leading to rapid local amplification once one aggregate is formed. Our results provide direct evidence for tau aggregate replication at the pre-synapse, linking inflammation induced tau aggregation with synaptic pathology. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=134 SRC="FIGDIR/small/728997v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@169dacorg.highwire.dtl.DTLVardef@c9894corg.highwire.dtl.DTLVardef@1551253org.highwire.dtl.DTLVardef@260ae7_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2026

TEsingle enables locus-specific transposable element expression analysis at single-cell resolution

Transposable elements (TEs) are mobile genetic sequences that can generate new copies of themselves via insertional mutations. These viral-like sequences comprise nearly half the human genome and are present in most genome wide sequencing assays. While only a small fraction of genomic TEs have retained their ability to transpose, TE sequences are often transcribed from their own promoters or as part of larger gene transcripts. Accurately assessing TE expression from each individual genomic TE locus remains an open problem in the field, due to the highly repetitive nature of these multi-copy sequences. These issues are compounded in single-cell and single-nucleus transcriptome experiments, where additional complications arise due to sparse read coverage and unprocessed mRNA introns. Here we present our tool for single-cell TE and gene expression analysis, TEsingle. Using synthetic datasets, we show the problems that arise when not properly accounting for intron retention events, failing to address uncertainty in alignment scoring, and failing to make use of unique molecular identifiers for transcript resolution. Addressing these challenges has enabled an accurate TE analysis suite that simultaneously tracks gene expression as well as locus-specific resolution of expressed TEs. We showcase the performance of TEsingle using single-nucleus profiles from substantia nigra (SN) tissues of Parkinsons Disease (PD) patients. We find examples of young and intact TEs that mark dopaminergic neurons (DA) as well as many young TEs from the LINE and ERV families that are elevated in PD neurons and glia. These results demonstrate that TE expression is highly cell-type and cellular-state specific and elevated in particular subsets of neurons, astrocytes, and microglia from PD patients.

genomics↗

bioRxiv2025

Uncertainty-Aware Tau Detection in Progressive Supranuclear Palsy Using Object Detection Models

Abnormal tau accumulation is a hallmark of neurodegenerative tauopathies such as Progressive Supranuclear Palsy (PSP). Traditional post-mortem assessments rely on manual lesion annotation, which is time-consuming and subjective. Existing machine learning methods typically involve multi-stage, feature-based pipelines, resulting in limited scalability and reliance on handcrafted features. This work evaluates deep learning-based object detection (OD) as a unified, end-to-end alternative for automating tau lesion identification and classification. We fine-tuned YOLO and Faster R-CNN models on a dataset of 29,852 tau lesions from 16 PSP brain slides, achieving mAP@50 of 0.702. To address the limitations of conventional OD models, which assume overconfident spatial predictions, we integrated Monte Carlo Dropout into both architectures to estimate spatial and label uncertainty. We evaluated detection uncertainty using Probability-based Detection Quality. Our results demonstrate that incorporating uncertainty offers a more comprehensive evaluation of detection reliability, complementing traditional metrics like mAP. For clinical application, we integrate a non-stochastic YOLO model into QuPath for whole-slide inference. Downstream clinical validation was conducted, including SHAP-based saliency analysis and correlation between model-predicted tau densities and PSP Rating Scale scores, a clinical disease severity measure. The alignment of detection outputs with pathological features and clinical severity underscores the clinical utility of OD models. Overall, this work highlights the complementary strengths of deep object detectors and uncertainty quantification, offering a path toward scalable, interpretable, and clinically meaningful tau pathology analysis. Code is available at https://github.com/Pidongg/dl_histopathology.

bioinformatics↗

bioRxiv2025

Early synaptic pathology is associated with small tau aggregates in Alzheimer's disease

Alzheimers disease (AD) is phenotypically characterised by progressive memory loss, which involves tau aggregation and synaptic pathology. Here we characterised the tau aggregates in individual synaptosomes from AD cases and controls measuring their number and size using single molecule fluorescence microscopy. A total of 7,888 synaptosomes from pre-frontal cortex samples were studied, showing the presence of AT8-positive tau aggregates in a small fraction of synaptosomes ([~]3%) from control brains, reaching [~]20% by Braak stage 6 with more larger aggregates. We then investigated the multi-phosphorylation of synaptic tau aggregates for AT8 and T181 and quantified the co-localisation of phosphatidylserine and CD47, synaptic "eat me" and "dont eat me" signals respectively, along with synaptogyrin-3, which contributes to tau mediated synaptic dysfunction. T181, phosphatidylserine, and synaptogyrin-3 co-localisation with AT8-positive tau were increased during stage 3 and CD47 was decreased, indicating early synaptic pathology is associated with the formation of small tau aggregates, contributing to microglia-driven synaptic loss.

neuroscience↗

bioRxiv2025

Super-resolution microscopy of alpha-synuclein aggregates in brain samples indicates a subset of cells have disrupted protein homeostasis

Nanoscopic aggregates of alpha-synuclein have been observed in Parkinsons disease (PD). However, the processes that occur in-vivo leading to the formation of these small aggregates are not well understood. We used ultra-sensitive single-molecule methods including SIMOA and super-resolution microscopy to quantify and characterise alpha-synuclein aggregates harvested from human brain samples alongside the Line 61 mouse model using different tissue processing methods. While aggregate numbers did not differ between PD and control samples, larger aggregates were detected in PD brain samples. Moreover, different sub-populations of aggregates were obtained by different extraction methods, with diffusible and membrane-bound aggregates producing a more pronounced difference between disease and control samples. Our data suggests that alpha-synuclein aggregates slowly in the brain, leading to formation of larger aggregates in a sub-set of cells.

neuroscience↗

bioRxiv2025

A molecular atlas of cell-type specific signatures in the parkinsonian striatum.

The progressive degeneration of dopaminergic projections to the striatum is a key disease mechanism in Parkinsons disease (PD). To define the cellular landscape in the parkinsonian striatum, we mapped the cell-type specific transcriptional landscape in early and progressive PD mouse models and in human PD stages. Our analyses revealed substantial transcriptomic changes across both neuronal and glial populations, with astrocytes and oligodendrocytes exhibiting distinct disease-associated gene expression profiles. Notably, progressive dopamine depletion uncovered differential neuronal vulnerability, identifying eccentric striatal projection neurons (SPNs) and Chst9-expressing direct-pathway SPNs as among the most resilient subtypes in both species. This cross-species resource establishes a comprehensive framework for investigating cell-state dynamics in the parkinsonian striatum and uncovers selectively vulnerable and resistant cell types that can inspire new therapeutic strategies.

neuroscience↗

bioRxiv2025

Activation of transposable elements is linked to a region- and cell-type-specific interferon response in Parkinson's disease

Parkinsons disease (PD) is a neurodegenerative disorder involving a neuroinflammatory response, the cause of which remains unclear. Transposable elements (TE) have been linked to inflammation, but their potential role in PD remains unexplored. Using bulk- and single-nuclei RNAseq of postmortem brain tissue from four brain regions, we studied TE transcription and its correlation with PD neuroinflammation. Over a thousand TEs, including LINE-1s and ERVs, were expressed in a cell-type and region-specific manner in the human brain. Increased TE expression was found in microglia and neurons in the substantia nigra and putamen of PD brains, but not amygdala or prefrontal cortex, compared to controls. This TE activation correlated with an innate immune response in the same brain regions. The link between an interferon response and TE activation was mechanistically confirmed using human pluripotent stem cell-derived microglia and neurons. Our findings provide insights into TE transcription in the PD brain and suggest TEs may contribute to neuroinflammation and pathological progression in PD. Teaser: Transposable elements are linked to a cell type specific inflammatory state in Parkinsons Disease.

neuroscience↗

bioRxiv2025

Nanoscopic tau aggregates in Parkinson's disease

Post-mortem tau pathology is frequently observed in Parkinsons disease (PD) using immunohistochemistry (IHC) to measure large inclusions, however, small protein aggregates that precede inclusions are considered a major driver of toxicity in neurodegenerative disease. We aimed to uncover the distribution of nanoscopic aggregates across six brain regions in post-mortem tissue from 14 PD and 15 controls using the single-molecule pull-down assay (SiMPull). In the hippocampus and amygdala, tau IHC and SiMPull were associated with advanced age in controls and dementia status in PD. Despite negligible tau IHC-labelled aggregates in the putamen, we identified a unique population of high-intensity nanoscopic tau aggregates for a subset of PD cases using SiMPull, ranging from 10-1,000 epitopes per aggregate and 30-1,000 nm in length. Previous evidence linking nigrostriatal tau pathology and motor deficits indicates that the nanoscopic tau aggregates identified in this study may contribute to striatal dysfunction in PD.

neuroscience↗

bioRxiv2025

Small tau aggregates exhibit disease-specific molecular profiles across tauopathies

Tauopathies are neurodegenerative diseases marked by pathological tau aggregation. While disease-specific folds of insoluble tau filaments have been established, it remains unclear whether the smaller, earlier species also differ across tauopathies. Here, we characterise these small tau aggregates from post-mortem brain of individuals with Alzheimers disease (AD), progressive supranuclear palsy (PSP), corticobasal degeneration, Picks disease, and healthy controls. Using two complementary single-molecule assays, we confirm that small tau aggregates vary in abundance, morphology, and post-translational modifications. AD features specific long, fibrillar-shaped aggregates enriched in phospho-epitopes, while PSP aggregates are shorter, round, and selectively phosphorylated at serine-356, a site we identify as correlating with markers of inflammation and apoptosis. Aggregate properties co-vary with cellular stress signatures and align with disease-specific seeding profiles, suggesting distinct pathological mechanisms. These findings suggest that small tau aggregates are not a shared intermediate, but instead encode disease-specific mechanisms, with potential as both biomarkers and therapeutic targets. Key pointsSmall tau aggregates show disease-specific signatures across tauopathies, differing in abundance, morphology, and post-translational modifications. Tau aggregates in AD show enhanced phosphorylation density and structural heterogeneity, including a distinct population of long fibrillar species detectable in the soluble fraction. Alzheimers disease is characterised by specific long, fibrillar-shaped tau aggregates enriched in disease-relevant phospho-epitopes. PSP features round pSer356-positive aggregates that correlate with apoptotic and inflammatory markers, suggesting a distinct mechanism of toxicity. Isoform-specific biosensor assays reveal divergent seeding behaviour: CBD shows strong 4R seeding, while PSP lacks seeding activity. Features of small aggregates co-vary with distinct patterns of gliosis and cell stress, suggesting disease-specific mechanisms of tau-mediated toxicity.

neuroscience↗

bioRxiv2025

A spatiotemporal cancer cell trajectory underlies glioblastoma heterogeneity

Cancer cells display highly heterogeneous and plastic states in glioblastoma, an incurable brain tumour. However, how these malignant states arise and whether they follow defined cellular trajectories across tumours is poorly understood. Here, we generated a deep single cell and spatial multi-omic atlas of human glioblastoma that pairs transcriptomic, epigenomic and genomic profiling of 12 tumours across multiple regions. We identify that glioblastoma heterogeneity is driven by spatially-patterned transitions of cancer cells from developmental-like states towards those defined by a glial injury response and hypoxia. This cellular trajectory regionalises tumours into distinct tissue niches and manifests in a molecularly conserved manner across tumours as well as genetically distinct tumour subclones. Moreover, using a new deep learning framework to map cancer cell states jointly with clones in situ, we show that tumour subclones are finely spatially intermixed through glioblastoma tissue niches. Finally, we show that this cancer cell trajectory is intimately linked to myeloid heterogeneity and unfolds across regionalised myeloid signalling environments. Our findings define a stereotyped trajectory of cancer cells in glioblastoma and unify glioblastoma tumour heterogeneity into a tractable cellular and tissue framework.

cancer biology↗

bioRxiv2024

SynPull: a novel method for studying neurodegeneration-related aggregates in synaptosomes using super-resolution microscopy

Synaptic dysfunction is one of the primary hallmarks of both Alzheimers and Parkinsons disease, leading to cognitive and behavioural decline. While alpha-synuclein, beta-amyloid, and tau are involved in the physiological functioning of synapses, their pathological aggregation has been linked to synaptic dysfunction. However, the methodology for studying the small (sub-diffraction limit) and soluble aggregates -often called oligomers, formed by these proteins is limited. Here we describe SynPull, a novel method combining single-molecule pulldown, super-resolution microscopy, and advanced computational analyses, in order to reliably study the quantity and morphology of the oligomeric alpha-synuclein, beta-amyloid, and AT8-positive tau aggregates in synaptosomes harvested from post-mortem human brain samples and mouse models. Using SynPull, we show that AT8-positive tau is the predominant aggregate type in AD, with significantly more aggregates compared to the control samples, yet the aggregate size does not differ between disease and control samples. Meanwhile, the relatively smaller amount of alpha-synuclein and beta-amyloid aggregates found in the synapses are larger than the extra-synaptic ones. Collectively, these results show the utility of SynPull to study pathological aggregates in dementia, which can help further understand the disease mechanisms causing synaptic dysfunction. O_FIG O_LINKSMALLFIG WIDTH=140 HEIGHT=200 SRC="FIGDIR/small/609517v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@d53d06org.highwire.dtl.DTLVardef@1995971org.highwire.dtl.DTLVardef@bf3edaorg.highwire.dtl.DTLVardef@1b75ca5_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstract.C_FLOATNO Human post-mortem orbitofrontal cortex samples from subjects with neuropathological diagnosis of Alzheimers and Parkinsons disease, as well as age-matched controls cut into [~]300 mg sections, and MI2, APPNL-G-F, P301S, and C57Bl/6J mouse brains were first homogenised in synaptosome buffer using a Dounce homogeniser and then filtered and centrifuged to separate nuclei and organelles from the synaptic fragments. Then, the isolated synaptosomes were incubated on the SiMPull surface with anti-neurexin antibody overnight, followed by fixation and permeabilisation. Imaging antibodies against beta-amyloid, alpha-synuclein, and AT8-positive tau were added to the samples and dSTORM imaging was performed to super-resolve the aggregates. C_FIG

neuroscience↗

bioRxiv2023

L1 retrotransposons drive human neuronal transcriptome complexity and functional diversification

The genetic mechanisms underlying the expansion in size and complexity of the human brain remains poorly understood. L1 retrotransposons are a source of divergent genetic information in hominoid genomes, but their importance in physiological functions and their contribution to human brain evolution is largely unknown. Using multi-omic profiling we here demonstrate that L1-promoters are dynamically active in the developing and adult human brain. L1s generate hundreds of developmentally regulated and cell-type specific transcripts, many which are co-opted as chimeric transcripts or regulatory RNAs. One L1-derived lncRNA, LINC01876, is a human-specific transcript expressed exclusively during brain development. CRISPRi-silencing of LINC01876 results in reduced size of cerebral organoids and premature differentiation of neural progenitors, implicating L1s in human-specific developmental processes. In summary, our results demonstrate that L1-derived transcripts provide a previously undescribed layer of primate- and human-specific transcriptome complexity that contributes to the functional diversification of the human brain.

neuroscience↗

bioRxiv2022

Pseudogenes limit the identification of novel common transcripts generated by their parent genes

The human genome contains numerous duplicated regions, such as parent-pseudogene pairs, causing sequencing reads to align equally well to either gene. The extent to which this ambiguity complicates transcriptomic analyses is currently unknown. This is concerning as many parent genes have been linked to disease, including GBA1, causally linked to both Parkinsons and Gaucher disease. We find that most of the short sequencing reads that map to GBA1, also map to its pseudogene, GBAP1. Using long-read RNA-sequencing in human brain, where all reads mapped uniquely, we demonstrate significant differences in expression compared to short-read data. We identify novel transcripts from both GBA1 and GBAP1, including protein-coding transcripts that are translated in vitro and detected in proteomic data, but that lack GCase activity. By combining long-read with single-nuclear RNA-sequencing to analyse brain-relevant cell types we demonstrate that transcript expression varies by brain region with cell-type-selectivity. Taken together, these results suggest a non-lysosomal function for both GBA1 and GBAP1 in brain. Finally, we demonstrate that inaccuracies in annotation are widespread among parent genes, with implications for many human diseases.

genetics↗