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Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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bioRxiv2026

A conserved serotonin receptor pathway is a druggable modifier of Tau pathology, neural circuit formation and neurodegeneration

Tauopathies are devastating neurodegenerative disorders characterized by Tau hyperphosphorylation, neurofibrillary tangle (NFT) formation, neuronal dysfunction, and cognitive decline. Here, we establish a new Drosophila tauopathy model expressing eGFP-tagged human TauWT or the disease-associated TauP301L variant in the nervous system. TauP301L expression recapitulates key pathological and behavioral hallmarks of tauopathy, including elevated Tau hyperphosphorylation, accumulation of NFT-like, pTau-positive assemblies in vivo, reduced lifespan, hyperactivity, sleep loss, progressive locomotor decline, and age-dependent brain degeneration. Strikingly, TauP301L also disrupts the architecture of the mushroom body, a learning- and memory-related circuit in Drosophila, revealing an early disruption of neural circuit formation that is distinct from adult neurodegenerative phenotypes. We further show that suppression of serotonin 5-HT7R-CDK5 signaling pathway, either by genetic knockdown or pharmacological inhibition with inverse agonist, rescues Tau-induced behavioral and anatomical phenotypes. These findings identify 5-HT7R signaling as a conserved and druggable modifier of Tau toxicity and establish this model as a powerful in vivo platform for mechanistic studies and therapeutic discovery in tauopathies.

neuroscience↗

bioRxiv2026

Cryo-ET and Sub-Volume Analysis of Fibrillar Pathology in the Neurodegenerative Human Brain

Structural studies of amyloid fibrils extracted from brain tissue have identified disease-specific fibril polymorphs. However, the mechanisms driving distinct polymorphs remain unclear because no method currently links the cellular context, composition and ultrastructure of individual aggregates to their constituent fibril polymorphs. Here, we present a workflow for in situ cryo-electron tomography (cryo-ET) to study amyloids within individual aggregates in the human neurodegenerative postmortem brain. Using chemically fixed tissue, we studied in situ tau fibrils in the hippocampus of an Alzheimer's disease (AD) donor and -synuclein fibrils within a glial nuclear inclusion in the cingulate gyrus of a multiple systems atrophy (MSA) donor. Subtomogram averaging and helical reconstruction of fibril subvolumes yielded low-resolution (~30-35A) density maps, which were compared to existing ex vivo structures. Preserved ultrastructure enabled detailed observations of pathology, including an alpha-synuclein fibril penetrating the nuclear envelope, providing mechanistic insight into intranuclear aggregate formation. Combined with existing high-resolution fibril structures lacking spatial context, cryo-ET offers a powerful approach to understanding amyloid polymorphism in neurodegenerative diseases, advancing anti-amyloid therapies and diagnostic tools.

neuroscience↗

bioRxiv2026

Two functionally distinct amyloid-β intermediates link aggregation pathways to pathology in Alzheimer's disease

Neurotoxic intermediates formed during amyloid-{beta}(A{beta}) aggregation are thought to drive Alzheimer's disease, yet their rarity and transient nature have obscured their identity and formation pathways in the human brain. Here, we combine super-resolution microscopy and single-molecule functional imaging with kinetic modelling to classify A{beta} intermediates according to their membrane-disrupting activity and connect their damaging effects to the aggregation pathways that generate them. Applying this framework to recombinant A{beta}42, an Alzheimer's knock-in mouse model and human Alzheimer's brain tissue, we find two functionally distinct intermediate populations present across all systems. They form through separate aggregation routes and differ in their neurotoxicity, abundance and susceptibility to inhibition. Both damage neurons and glia, but only one converts into plaques. Suppressing these intermediates pharmacologically in mice reduces plaque burden, attenuates astrogliosis and improves cognition. Our findings connect model systems with human pathology and identify intermediate formation pathways as actionable therapeutic targets across protein-misfolding disorders.

biophysics↗

bioRxiv2026

Alignment with sex-typical brain architecture: Links to mood pathology, sex hormones and transcriptomics of neurodegenerative conditions

Understanding the mechanisms that underpin the pervasive sex bias in risk for specific psychiatric and neurodegenerative conditions could substantially advance efforts promoting personalized medicine. As a first step towards addressing this issue, we applied imaging transcriptomics and multivariate analysis techniques to data from an adolescent sample enriched in anxiety/depression cases, a child sample enriched in attention deficit hyperactivity disorder (ADHD) cases, and adult patients with treatment resistant major depressive disorder (MDD). We tested whether, across sexes, alignment with female-typical, rather than male-typical, patterns of neural functional connectivity (FC) would relate to a diagnosis (adolescent sample) or severity of symptoms (adult sample) associated with internalizing disorders, which tend to be more often diagnosed in females. To provide preliminary evidence on its functional specificity, we compared the sex-aligned FC profile that distinguished neurotypical adolescents from those diagnosed with depression/anxiety against the sex-aligned FC patterns that distinguished neurotypical children from those diagnosed with ADHD. All the analyses controlled for age within each sample and sex. Finally, we examined the spatial overlap between the sex-aligned FC profile linked to an internalizing diagnosis in adolescence and the transcriptomic maps of genes that show sex-dependent dysregulation in neurodegenerative conditions. Across sexes, increasing alignment with female-typical FC patterns, from sensory-perceptual to default mode regions, discriminated between typically developing and anxious/depressed teens and tracked longitudinal fluctuations in depressive symptoms within adult MDD patients. The identified internalizing-related gradient showed a negative correlation with risk for ADHD in the child sample. The brain regions most strongly aligned with female-, rather than male-, typical FC in depression/anxiety overlapped the spatial expression profiles of genes linked to gonadal hormone synthesis, as well as genes dysregulated in female autism spectrum disorder (ASD) and male neurodegenerative conditions, specifically, Alzheimer's Disease (AD), Huntington's Disease (HD) and Multiple Sclerosis (MS). The brain areas most strongly aligned with male-typical, rather than female-typical, FC patterns overlapped the transcriptomic maps of genes related to androgen and estrogen receptors, as well as of genes dysregulated in male ASD and female neurodegenerative conditions (i.e., AD, HD, MS). Our results raise the possibility that the link between mood pathology and neurodegeneration could reflect a partial, regional reversal of sex-normative functional brain profiles.

neuroscience↗

bioRxiv2026

Large-scale cerebrospinal fluid proteomics identifies diagnostic biomarker candidates across the clinico-pathological continuum of frontotemporal lobar degeneration

Frontotemporal lobar degeneration (FTLD), predominantly comprised of tau and TDP-43 proteinopathies, is a common cause of early-onset dementia. Biomarkers that reliably classify FTLD subtypes are limited, thereby hindering in-vivo diagnosis and clinical trial stratification. We conducted large-scale, multi-platform cerebrospinal fluid proteomics in 566 individuals, including 274 FTLD-spectrum (48 autopsy-confirmed FTLD-TDP, 90 autopsy-confirmed FTLD-tau), 171 Alzheimers disease, and 95 controls. In neuropathological subtype contrasts, elevated matrix metalloproteinase MMP10 classified Picks disease (PiD) versus other subtypes with near-perfect accuracy across proteomic platforms. We further validated CSF MMP10 as a potential PiD diagnostic biomarker via a targeted immunoassay in an independent, autopsy-confirmed FTLD cohort. Post-synaptic proteins HOMER1 and DLG4 exhibited elevations across FTLD-TDP subtypes (A, B, and C) versus FTLD-tau. Network analysis identified RNA metabolism and pro-inflammatory signatures in FTLD-TDP, and cytoskeletal and heat shock signatures in progressive supranuclear palsy. These findings reveal candidate diagnostic biomarkers and proteomic pathways underlying FTLD clinico-pathological heterogeneity.

neuroscience↗

bioRxiv2026

RAPTOR-targeted Antisense Oligonucleotides Restrict Pathological mTORC1 Activity in GATOR1-dependent Disease

Loss-of-function mutations in the GATOR1 complex (NPRL2, NPRL3, and DEPDC5) are among the most common genetic causes of epilepsy. These mutations impair amino acid-dependent regulation of mTORC1 and cause hyperactive signaling, neuronal hyperexcitability, astrocytic metabolic remodeling, seizures, and early mortality. Here, we report the development of antisense oligonucleotides (ASOs) targeting RAPTOR, an mTORC1 scaffolding subunit, to correct pathological mTORC1 hyperactivity caused by defective upstream regulation. RAPTOR-targeted ASO treatment reduced RAPTOR expression in mouse and human systems and dampened mTORC1 signaling in GATOR1-deficient models. ASO-mediated RAPTOR reduction rescued neuronal hyperexcitability, corrected astrocytic mitochondrial dysfunction, and suppressed spontaneous seizures in vivo. A single treatment significantly extended longevity across neuronal and astrocytic models of GATOR1 deficiency. Collectively, these findings establish RAPTOR-targeted ASOs as a mechanism-based therapeutic approach that durably corrects cellular and circuit-level consequences of GATOR1 deficiency. By tuning RAPTOR abundance, this strategy provides a therapeutic framework for mTORC1-driven epilepsies and related diseases.

neuroscience↗

bioRxiv2026

Decomposing scanner batch effects and their impact on pathology foundation models

Pathology foundation models (PFMs) are expected to represent the same tissue in the same way on any scanner, but their embeddings still carry scanner signals. Scanner-related image differences and the scanner sensitivity of PFMs have each been described. How tissue-dependent changes in color and spatial frequency relate to shifts in PFM representations, and what this means for correction, is less understood. We imaged 103 slides from 37 normal tissue types on six scanners (PanNormal; 95,780 matched locations) and used the real paired images as targets. We used the public PLISM dataset for external validation. First, we decomposed scanner differences into image properties. Color and spatial frequency changed together, by amounts that depended on tissue type. Second, corrections that matched these measured properties brought images closer to the target more reliably than representations. Pix2Pix reduced the image residual by 69% but increased UNI distance to the target by 27%. The same frequency matching helped one scanner and hurt another. Probes still distinguished corrected from real target embeddings after every correction. Third, changing one frequency band at a time showed that PFMs differ in how strongly each band moves them and whether it moves them toward the target. Across eight PFMs pretrained on whole-slide image tiles, the models that moved least under these small changes were the most robust to real scanner differences (Spearman {rho}=-0.90). Aligning images and aligning representations are therefore different goals. The gap between them depends on scanner, tissue, and model.

bioinformatics↗

bioRxiv2026

Fine-tuning genomic models on rare splicing events identifies a novel biomarker of TDP-43 pathology

Genomic foundation models (GFMs) are pretrained on large genomic datasets, but their ability to predict rare disease-associated events after fine-tuning remains unclear. We tested this using TDP-43 cryptic exons, well characterized splicing events linked to neurodegenerative disease that are poorly represented in standard annotations. We compared the state-of-the-art GFM AlphaGenome with OpenSpliceAI, a specialized splice site prediction model. Fine-tuned OpenSpliceAI detected held-out cryptic exons in human and mouse and captured allele-specific splicing effects at the disease-associated UNC13A locus. In contrast, a splicing prediction head trained on AlphaGenome's frozen pretrained backbone failed to predict cryptic exons. Unfreezing and fine-tuning all model weights, however, enabled AlphaGenome to generalize to held-out data. To investigate cryptic splicing in cell types that are difficult to study experimentally, we applied fine-tuned OpenSpliceAI across the genome to study cell type-specific genes. This led to the identification of new cryptic splicing events in CLDN11 and ARHGAP23, which were subsequently validated in FTLD-TDP brain tissue. Notably, the cryptic exon in CLDN11 is predicted to generate a neoepitope that could serve as an oligodendrocyte-specific biomarker of TDP-43 pathology. Our results show that even a state-of-the-art GFM can fail to generalize to rare splicing events, even with substantial pretraining. However, both foundation and specialized models that learn to generalize to rare biological events can have broad applications in biological discovery and medicine.

genomics↗

bioRxiv2026

Reverse engineering Lewy bodies suggests alpha-synuclein pathology as condensatopathy

Understanding how soluble monomeric alpha-synuclein transitions into pathological alpha-synuclein (Lewy bodies) has remained a central challenge in neurodegeneration. Existing models, largely based on treating cells and animals with pre-formed alpha-synuclein fibrils cannot account for the emergence of the first inclusion without pre-existing seeds. Here, we combine in vitro reconstitutions, computational modeling and a minimal cellular system to show that phase separation of alpha-synuclein with an interacting scaffold can recapitulate Lewy body-like structures. An unbiased proteomics screen, live-cell imaging, correlative light-electron microscopy, and soft X-ray tomography show that Lewy body-like structures are associated with redistribution of actin and membrane-bound organelles, with mitochondria accumulating at their periphery in an actin-dependent manner. Structural analyses further indicate that alpha-synuclein condensates provide local environments in which the insoluble beta-sheets can form. Together, these findings support a seed-independent trajectory from soluble alpha-synuclein through condensation and progressive immobilization to Lewy body-like assemblies and, subsequently, insoluble beta-sheet fibrils. This framework offers a new mechanistic route for understanding the disease progression and promises to guide the design of innovative therapeutic interventions.

neuroscience↗

bioRxiv2026

Insulin fails to mitigate amyloid pathology but modulates intestinal morphology in the 5xFAD model revealed by synchrotron-based XPCT

Intranasal insulin has been investigated as a metabolic intervention in Alzheimers disease (AD), but its effects across the brain-gut axis remain unclear. We combined multiscale synchrotron X-ray phase-contrast tomography (XPCT), amyloid-{beta} immunofluorescence, and fecal metaproteomics to examine structural and molecular responses in 5xFAD mice. Twenty-four mice representing wild-type and 5xFAD genotypes, saline and insulin conditions, and terminal ages of 2 and 6 months received insulin at 1 U/mouse/day for 5 weeks. Micro-XPCT visualized plaque-like deposits, nanoXPCT revealed their heterogeneous internal organization, and MOAB-2 labeling provided qualitative support for amyloid pathology. Detectable plaque burden was not lower after treatment: deposits occurred in two of three treated versus none of three untreated 5xFAD mice at 2 months, and treated animals had higher descriptive regional means at 6 months. In the ileum, insulin was associated with lower villus length and crypt depth in 6-month-old 5xFAD mice, whereas no significant differences were detected at 2 months. Fecal profiles retained broad taxonomic overlap but differed in functional annotations, with hydrolase-associated fractions of 81%, 92%, 96%, and 93% across untreated wild-type, treated wild-type, untreated 5xFAD, and treated 5xFAD conditions, respectively, within the selected peptide subset. Thus, lower ileal dimensions coexisted with non-reduced detectable brain plaque burden and a fecal protein profile distinct from untreated wild type. Together, these findings reveal contrasting central and peripheral patterns following intranasal insulin treatment in 5xFAD mice: no detectable reduction in cerebral plaque burden, alongside attenuation of selected ileal structural alterations and distinct fecal metaproteomic profiles. Although exploratory, the findings raise the possibility that intranasal insulin alters amyloid compartmentalization or plaque detectability rather than promoting amyloid clearance, while producing distinct peripheral remodeling.

biophysics↗

bioRxiv2026

Beyond Segmentation Accuracy: Evaluating Biological Fidelity in Spatial Pathology

Multiplex immunofluorescence (MxIF) resolves cellular identity, state, and spatial organization within tumor tissue, enabling higher-order representations of cancer ecosystems including immune infiltration, multicellular neighborhoods, and tissue niches. Yet these analyses depend on a deceptively simple first step: accurately identifying individual cells. Segmentation errors can alter marker quantification, cellular phenotypes, cell-cell relationships, and ultimately the spatial organization inferred from an image. Consequently, improvements in conventional segmentation benchmarks matter biologically only if they propagate to more faithful representations of the tumor microenvironment. We test this relationship directly using an expert-curated benchmark of 31,924 expert-reviewed cells on three slides under a leave-slide-out protocol. We compare a domain-specific self-supervised encoder, adapted to multiplex tissue imaging, with supervised, microscopy-specific, prompted generalist, and general-purpose vision models, and pass every method's predicted cells through an identical downstream pipeline. We evaluate fidelity across four levels: cell segmentation, phenotype assignment, spatial neighborhood structure, and tissue organization, comprising niches and tumor-immune interactions. The resulting hierarchy reveals that these levels do not improve in lockstep. Cellular phenotype assignment is comparatively robust to segmentation differences, whereas missed cells increasingly disrupt neighborhood structure and tumor-immune interactions. As a stringent spatial-interaction test, tumor-CD8+ contact recovery is poorly predicted by conventional segmentation quality (Panoptic Quality: {rho} = 0.18), while errors specifically at tumor-immune interfaces are strongly associated with contact fidelity ({rho} = -0.80). Methods with nearly identical segmentation accuracy can therefore produce substantially different biological representations. These results argue that cell segmentation for spatial pathology should be evaluated not only by boundary and instance accuracy, but also by preservation of the biological relationships that downstream analyses are intended to measure.

bioinformatics↗

bioRxiv2026

Alpha-synuclein and neuromelanin converge to promote Parkinsons disease pathology

Parkinsons disease (PD) is defined by the preferential degeneration of neuromelanin (NM)-containing dopamine-producing neurons in the substantia nigra (SN), accompanied by intraneuronal inclusions rich in alpha-synuclein (aSYN). However, the mechanistic relationship between NM accumulation and aSYN pathology remains unclear. Here, we reveal a bidirectional pathogenic relationship between aSYN and NM. In human post-mortem midbrain tissue, ventral nigral neurons with high NM content display increased aSYN mRNA expression and are preferentially lost in PD. In a rat model that recapitulates age-dependent, human-like NM accumulation via targeted tyrosinase (TYR) expression, co-expression of aSYN accelerates NM buildup, enhances aSYN oligomerization, and aggravates nigrostriatal degeneration. Mechanistically, aSYN oligomerization in NM-producing rats decreases vesicular dopamine storage and impairs vesicle fusion with the plasma membrane, increasing cytosolic dopamine availability for oxidation into NM. Together, these findings support a pathogenic feedback loop in which elevated aSYN accelerates NM synthesis through disrupted dopamine compartmentalization, while NM accumulation further promotes aSYN aggregation and neuronal loss. This aSYN-NM axis may underlie the preferential vulnerability of pigmented nigral neurons in PD and provide a mechanistic framework for the development of future targeted therapeutics.

neuroscience↗

bioRxiv2026

Hydrogel confinement of the secreted nascent matrix imposes solid stress and mediates pathology of chondrocytes

Mechanical confinement of cells in 3D hydrogel scaffolds mediates cell fate and activity across a wide range of biological processes. Many cells secrete a nascent matrix within the hydrogel niche, which provides important biological signals to the cells but also obstructs direct cell-hydrogel interactions, making it unclear how the cells sense hydrogel confinement and carry out mechanotransduction. Here, we show that chondrocytes sense the solid stress arising from the accumulation of the nascent matrix in the hydrogel niche, which is mediated by hydrogel viscoelasticity and plasticity. We show that solid stresses elicit a wide range of pathophysiological responses, most notably an inflammatory response associated with cartilage osteoarthritis and injury, alongside a striking progenitor-like migratory response where the chondrocytes leverage mitosis to breach their nascent matrix and migrate to escape confinement. Our findings establish the role of the nascent matrix as an important transducer of mechanical confinement and illustrate how emergent solid stresses can drive chondrocyte pathology.

bioengineering↗

bioRxiv2026

Brain mitovesicles undergo stage-specific remodelling during the progression of amyloid-β pathology

Mitochondrial dysfunction is an early feature of Alzheimer's disease that shows nonlinear changes as the disease progresses. However, how these changes are reflected in the mitochondrial material released by brain cells remains poorly understood. Mitovesicles are a recently described extracellular vesicle subpopulation of mitochondrial origin that provide a unique insight into mitochondrial alterations in the brain and could potentially show how nonlinear changes evolve across disease stages of amyloid-beta pathology. Here, we isolated forebrain-derived small extracellular vesicles and mitovesicles from wild-type and Amyloid precursor protein (App) knock-in (AppKI) mice, carrying familial AD mutations and progressively accumulating amyloid-beta plaques, at presymptomatic (2-month) and symptomatic (12-month) stages using high-resolution density gradient fractionation. Vesicle identity and composition were assessed by morphological, biophysical and quantitative proteomic analyses, and mitovesicle respiratory function was measured by extracellular flux analysis. We show that mitovesicles carry a distinct, predominantly mitochondrial inner membrane proteome that is remodelled by age and disease in a stage-specific manner. Compared with small extracellular vesicles, mitovesicle proteomic profiles captured disease progression more clearly, with symptomatic AppKI mice forming the most molecularly distinct group. At the presymptomatic stage, AppKI mitovesicles showed reduced mitochondrial protein representation, most notably of fatty acid {beta}-oxidation and lipid-metabolism proteins associated with astroglial and vascular signatures, preceding any detectable respiratory impairment. At the symptomatic stage this reversed: AppKI mitovesicles were enriched for oxidative phosphorylation, mitochondrial membrane and transporter proteins, yet showed reduced Complex IV-linked respiration, revealing a dissociation between mitochondrial cargo abundance and respiratory function. Selected cargo changes were not mirrored in whole-brain tissue, indicating selective remodelling of mitovesicle content. Comparison with mitovesicles from post-mortem human Alzheimer's disease frontotemporal cortex and hippocampus identified a conserved 62-protein mitovesicle core, dominated by oxidative phosphorylation subunits and mitochondrial carriers. In addition, 25 of these proteins were enriched in mitovesicles derived from Alzheimer's and AppKI forebrains, defining a conserved mitovesicular disease signature. Together, these findings establish forebrain-derived mitovesicles as a dynamically remodelled vesicle population that reflects progressive mitochondrial dysfunction in the Alzheimer's disease brain and provides a cross-species resource for future biomarker and mechanistic studies.

neuroscience↗

bioRxiv2026

NTAD: A longitudinal neuroimaging dataset of Alzheimer's disease pathology

We introduce the New Therapeutics in Alzheimer's Disease (NTAD) dataset, a multi-modal and longitudinal imaging dataset from 70 biomarker-positive people with early dementia or Mild Cognitive Impairment (MCI) due to Alzheimer's Disease (AD), assessed over 2.5 years, and 35 healthy controls assessed at baseline. The data include simultaneous magneto- and electro-encephalography (M/EEG), 3-Tesla structural and functional magnetic resonance imaging (MRI), Amyloid-beta; positron emission tomography (PET), fluid proteomic biomarkers in cerebrospinal fluid and blood, and a battery of clinical and neuropsychological assessments. 11C UCB-J PET was undertaken for a subset of participants. For people with AD, assessments were repeated at approximately three weeks, 15 months, and 28 months after baseline. The data can be accessed through the Dementias Platform UK (DPUK), including pre-processed M/EEG and T1 MRI in pseudonymised BIDS format. With the pressing need to develop treatments for slowing, reversing, and preventing AD, these data provide an opportunity for identifying and validating novel biomarkers of Alzheimer's disease neurophysiology, as well as understanding its treatable pathology.

neuroscience↗

bioRxiv2026

ROCK inhibitor Ripasudil reduces Alzheimer pathological proteins and enhances cellular bioenergetics

Rho-associated kinase (ROCK) inhibitors have been explored as an Alzheimer Disease (AD) therapeutic agent. In this study, we aim to determine the efficacy of a potent ROCK inhibitor, ripasudil, in impacting AD pathological protein tau in mice. The time-course study showed that ripasudil rapidly penetrated mouse brains, reaching maximal concentration half an hour post-injection. To determine the efficacy of ripasudil, we injected AppNL-G-F knock-in mice with ripasudil at 30 mg/kg and sacrificed them after three hours. We used Tandem Mass Tag labels and compared the proteomic profiles of mouse brains exposed to ripasudil to those exposed to saline. We also treated AD-patient-derived Neural Stem Cells (NSCs) with ripasudil and performed a Seahorse Mito Stress Test to evaluate their impact on mitochondrial activity. Bioinformatics analysis of the proteomic profiles revealed differentially enriched components of chromosome. The Mito Stress Test of NSCs revealed significant increases in basal oxygen consumption, ATP-linked respiration, maximal respiration, and reserve capacity oxygen consumption compared to untreated NSCs. Importantly, we found a significant reduction of Tau and pTau 396 in brains of mice treated with ripasudil. Overall, our findings highlight the feasibility and promise of ROCK inhibitor ripasudil as an AD therapeutic agent.

neuroscience↗

bioRxiv2026

Lipidic α-synuclein fibrils catalyze the formation of pathological mature fibrils

The aggregation of -synuclein into amyloid fibrils is a hallmark of a collection of neurodegenerative diseases termed synucleinopathies, including Parkinson's disease (PD). Interactions between -synuclein and lipid membranes modulate -synuclein aggregation and can produce protofibril structures consisting of both protein and lipid, termed lipidic fibrils. These lipidic fibrils can mature into mature fibrils, which resemble ex vivo fibrils extracted from Lewy bodies found in post-mortem brain samples of PD patients. Here, through the combination of experiments and kinetic theory, we study the influence of lipids and lipidic fibrils on the formation of mature fibrils. We find that lipidic fibrils catalyze mature fibril formation via a heterogeneous primary nucleation mechanism, which lowers the activation energy barrier of mature fibril formation relative to lipid-independent primary nucleation. The final stage of the reaction is governed by mature fibril elongation becoming limited by the rate at which protein monomers dissociate from the metastable lipidic fibrils, confirming that fibrils form in order of stability following Ostwald's Rule of Stages. This mechanism is validated using the small molecule inhibitor ambroxol, which selectively suppresses the formation of lipidic fibrils and in this manner shifts the aggregation kinetics to the slow, lipid-independent pathway. Taken together, these findings reveal that lipidic fibrils act as on-pathway intermediates and accelerate the aggregation of mature fibrils, which could provide a quantitative framework to design novel therapeutic strategies to inhibit pathological -synuclein aggregation.

biophysics↗

bioRxiv2026

Quantitative Spatial Analysis of Matrix Remodelling in Wounds Using Digital Pathology and Fractal Analysis

Wound healing involves spatially heterogeneous changes in matrix composition and organisation that can be difficult to capture using qualitative histological assessment alone. We developed a reproducible digital pathology workflow to quantify matrix features in cutaneous wound sections, compare them with unwounded skin, and derive an exploratory Histological Wound Index (HWI). Four normal-skin and six wound sections were analysed using QuPath, ImageJ/FracLac and Python. Approximately 500 x 500 micrometer regions of interest (ROI) were assigned to normal skin, wound centre, proximal edge or distant edge. Collagen, mucin and necrotic tissue coverage were quantified using image classifiers and analysed with linear mixed-effects models. Collagen architecture was assessed from collagen-selective binary masks using fractal dimension and lacunarity. Collagen coverage, fractal dimension, mucin coverage, necrosis and lacunarity were z-standardised and integrated into the HWI. Unwounded skin showed high collagen coverage and fractal dimension, with low lacunarity, mucin and necrosis. In contrast, wound-centre tissue showed low collagen coverage and fractal dimension together with higher mucin and necrosis. Distant-edge regions retained comparatively normal-like characteristics, whereas proximal-edge regions showed intermediate values. HWI was highest in normal skin and lowest in the wound centre. A descriptive matched-ROI comparison of two wound sections reproduced this regional ordering when all component measures were derived from identical ROI boundaries. This workflow provides a reproducible framework for quantifying regional ECM features and collagen-mask architecture in wound histology. The HWI is an exploratory histological summary requiring validation in larger longitudinal datasets.

bioinformatics↗