Biology subjects

Simon, A.

Publications and source records attributed to Simon, A..

At least 19 recordsLinked to original sources

bioRxiv2026

LNP Delivery of Prime Editors Enables Durable Correction of PAH R408W in Phenylketonuria Models

Phenylketonuria (PKU) is a monogenic metabolic disorder caused by mutations in the phenylalanine hydroxylase (PAH) gene, the most common of which is c.1222C>T (p.R408W). Current treatment options, including dietary restriction and enzyme substitution, can be effective but are often challenging for patients to maintain and do not address the underlying genetic defect. Gene editing represents a compelling one-time treatment approach for PKU. Herein, we demonstrate mRNA:LNP-mediated delivery of prime editors that enable therapeutically-relevant levels of correction of the R408W mutation in both in vitro and in vivo model systems. Further, we found that co-delivery of the DNA repair modulator RAD18 and engineering of the prime editor protein, enabled 2-fold and 3-fold increases in prime editing relative to PE3 respectively, resulting in ~50% correction efficiency in a humanized PKU mouse model. Collectively, this work identifies novel potential approaches to enhancing prime editing and establishes LNP-delivered prime editing as a mutation-specific, non-viral therapeutic strategy for PKU, as well as providing a framework for extending prime editing to other inherited liver diseases.

pharmacology and toxicology↗

bioRxiv2026

Coordinated immune, chloroplast and chemical defences underpin multilayered resistance to barley yellow dwarf virus and its aphid vector associated with the Hordeum bulbosum-derived Ryd4 introgression in barley

Barley yellow dwarf virus (BYDV), transmitted by the bird cherry-oat aphid (Rhopalosiphum padi L.), is among the most damaging viral diseases of barley, but the mechanisms underlying resistance to both the virus and its vector remain poorly understood. Here, we investigated resistance associated with the Hordeum bulbosum-derived Ryd4 introgression in the barley hybrid SY Kestrel by integrating behavioural, electrophysiological, physiological and multi-omics analyses with functional validation of defence metabolites. SY Kestrel exhibited constitutive volatile-mediated antixenosis together with strong post-settlement antibiosis characterised by impaired phloem feeding, reduced aphid fitness and suppression of BYDV gene expression 10 days after transmission. Integrated transcriptomic, metabolomic and small RNA analyses revealed coordinated immune activation, chloroplast remodelling and defence metabolism associated with the resistance introgression. Candidate immune regulators were identified both within the refined Ryd4 interval and the surrounding introgressed region. Maintenance of photosystem II function was accompanied by reprogramming of -linolenic acid-derived oxylipin metabolism, while phenylpropanoid and branched-chain amino acid/lysine pathways generated metabolites that directly reduced aphid survival. We demonstrate that the Ryd4 introgression coordinates constitutive vector deterrence with host defence reprogramming to restrict aphid colonisation and suppress BYDV establishment. These results provide a mechanistic framework for improving durable resistance to aphid-transmitted viruses in cereals.

systems biology↗

bioRxiv2026

Role of transposons in the specialization of Botrytis cinerea to grapevine: Insights into small RNAs and a new Starship

While transposable elements (TEs) are recognized as major drivers of fungal genome structure, evidence of their direct involvement in the interaction with host plants and the environment is only beginning to emerge. Retrotransposons can generate small RNA (sRNA) that act through cross-kingdom RNA interference, while giant DNA TEs called Starships carry dozens of cargo genes that enrich the accessory gene compartment of fungal genomes. In the polyphagous pathogen Botrytis cinerea, the Vv3 strain and other strains specialized on grapevine display a specific repertoire of TEs, including the retrotransposons BcCopia4, BcGypsy6, and BcGypsy7. This study first explored the putative role of sRNA generated from these retrotransposons in the interaction between the Vv3 strain and its host of origin, grapevine. Putative targets were identified among the host mRNAs, but predicted cleavage sites could not be experimentally validated. Moreover, Dicer mutants unable to produce retrotransposons-derived sRNA remained fully pathogenic on grapevine, indicating that these sRNAs do not act as virulence factors on this host. In parallel, this study provides an updated RNA-seq-based annotation of the accessory genes of the Vv3 strain, which revealed a new 93 kb-Starship harboring 43 cargo genes, some of which are related to arsenic resistance. A formal genetic approach confirmed that this locus confers resistance to this metalloid. This giant TE, named Ariane, was also detected in additional grapevine-specialized strains resistant to arsenic but not in strains isolated from other hosts such as tomato. In conclusion, this study highlights how a Starship giant transposon shaped the accessory genes compartment of the polyphagous fungus B. cinerea and may have contributed to its adaptation to vine cultivation by conferring resistance to arsenic, a compound widely used in vineyards during the last century. IMPACT STATEMENTFungal genomes contain many families of transposons whose functional role in adaptation to the environment and in biotic interactions remained hidden for a long time. In the grey mold fungus Botrytis cinerea, strains specialized on grapevine, such as Vv3, carry a specific repertoire of transposons which provides a valuable opportunity to investigate their role in niche adaptation. In this study, we first investigated retrotransposon-derived small RNA, previously described as effectors capable of manipulating the immunity of the model plant Arabidopsis thaliana. Although in silico analysis of the specific repertoire of small RNAs of the Vv3 strain suggested that some could target the expression of grapevine genes, a genetic approach demonstrated that they do not play a significant role in virulence on this host. In contrast, this study identified a new transposon, named Ariane, that carries 43 cargo genes and confers a selective advantage to the Vv3 strain. Ariane belongs to a family of giant transposons called Starships, recently discovered in fungi and considered to be responsible for horizontal genes transfers between unrelated species. Ariane was detected only in some B. cinerea strains isolated from grapevine, and a genetic cross showed that it provides these strains with the ability to grow in presence of arsenic. Arsenic was used in vineyards until the beginning of the 21st century to control fungal trunk diseases and insect pests. Therefore, Ariane appears to have played an important role in the adaptation of B. cinerea strains to cultivated grapevine. Overall, these results underline the importance of considering Starships when predicting emergence of resistance to antifungal compounds. DATA SUMMARYThe novel data described in this study, i.e., RNA-Seq data and the Starship element are accessible under NCBI GEO accession GSE327899 and at https://doi.org/10.57745/HYWRNM, respectively. All information related to Botrytis cinerea genomes used in this study are centralized and kept up to date at the Bioinfo Bioger genomic web portal: https://bioinfo.bioger.inrae.fr/portal/genome-portal/. Direct links to individual portals are respectively https://bioinfo.bioger.inrae.fr/portal/genome-portal/3/ for B. cinerea Vv3 genome, https://bioinfo.bioger.inrae.fr/portal/genome-portal/2/ for B. cinerea Sl3 genome, and https://bioinfo.bioger.inrae.fr/portal/genome-portal/4/ for B. cinerea populations isolated on tomato or grapevine. Each portal provides: (i) a centralized access to public genomic resources, including the genome, transposon, and RNA repositories; (ii) a data browser to download the genomic files; (iii) a genome browser that enables visualization of features within their genomic context, along with associated expression data. As a summary, the prior main public B. cinerea genomic accessions and resources used in this study are: GCA_039644125 for VV3 genome, GCA_022560135 for Sl3 genome, GCA_000143535 for B05.10 genome, PRJNA624742 for populations, https://doi.org/10.57745/HYWRNM for transposons, and GSE181592 for small RNAs. Furthermore, table S1 summarizes the list and characteristics of the 64 B. cinerea genomes publicly available to date. The genomic data for Vitis vinifera genome PN40024.v4 used in this study are available at: https://integrape.eu/resources/genes-genomes/genome-accessions/.

genomics↗

bioRxiv2026

Adaptive immunity is dispensable for salamander appendage regeneration

Complex multi-tissue regeneration capacity varies across vertebrates. Mammals are amongst the least regenerative species, while salamanders can regenerate complex tissues such as limbs and tails throughout life. Previous studies have shown that innate and adaptive immune cells are present during salamander limb regeneration. While innate immune cells have been shown to promote limb regeneration, it is unknown whether adaptive immunity is responsive to amputation or plays a role in appendage regeneration. Here we show that during limb regeneration in axolotls, the immune response is characterized by a coordinated immunoregulatory signature including the downregulation of antigen presentation, cytokine secretion, and T cell activation. We corroborate this transcriptomic data in vivo using skin allografts in newts and define the blastema as an immunosuppressed niche. To test the role of adaptive immune cells in regeneration, we generated Recombination activating gene 1 deficient (Rag1-/-) newts. Rag1-/- newts lack antigen receptor recombination and show a marked reduction of adaptive immune cells. We find that Rag1-/- newts do not reject allografts, confirming their functional immunodeficiency. Finally, we demonstrate that both larval and adult newts regenerate appendages in the absence of adaptive immunity. Our work demonstrates that the adaptive arm of the immune system is not required for appendage regeneration and establishes an important model for novel experimental approaches in comparative immunology and regenerative biology.

immunology↗

bioRxiv2026

A scalable approach to inoculate plant viral vectors into plant tissue using non-pathogenic, transgenic galls

Vascular plant pathogens transmitted by insects inflict devastating economic losses on crops worldwide. By obstructing and usurping the natural flow of nutrients, plant infection by these pathogens drastically reduces yields, vigor and productivity. Treating fruit-bearing trees against persistent vascular pathogens poses a unique challenge, as systemic delivery of therapeutics must navigate the compartmentalized architecture of the trees vascular system under changing environmental conditions without disrupting fruit production or long-term tree health. Plant viruses have gained traction as a novel approach to deliver therapies to crop plants, including fruit trees, but delivery of viral vectors to orchards at scale remains a significant challenge. We tested whether transgenic galls can be used to systemically infect plants with a plant virus infectious clone. We combined the plant growth regulator gene cassette from Agrobacterium tumefaciens strain C58 with the wild-type strain of citrus yellow vein associated virus-1 (CY1) on a single plasmid within the T-DNA for plant cell transformation. Using EHA105, a disarmed strain of A. tumefaciens, we inoculated stems with these gall-forming plasmids and initiated systemic CY1 infection in citrus and Arabidopsis thaliana over three independent experiments. We provide proof-of-concept that transgenic galls, referred to as symbionts, can launch the systemic infection of CY1 in economically important and model plants. Symbiont delivery of therapeutic viral vectors is theoretically scalable from inoculation of mother trees within the nursery to millions of trees in the field and may be a valuable tool for the commercial delivery of therapeutic plant viral vectors.

plant biology↗

bioRxiv2026

An adaptive gain model for predicting auditory brain activity in mice outperforms standard methods for predicting cortical speech tracking in human EEG

Human brain activity tracks slow fluctuations in continuous sound, including speech, and modelling this relationship provides insight into how the brain encodes naturalistic auditory input. Traditional approaches to modelling brain tracking of speech with linear regression often use the amplitude envelope of the stimulus as a regressor, implicitly assuming that neural responses scale linearly with sound intensity. However, previous studies of central auditory processing in both animals and humans have shown that adaptive mechanisms adjust auditory responses based on recent sound history. Here, we find that a simple nonlinear transformation of the stimulus envelope, derived from studies of mouse auditory thalamic responses to temporally varying sounds, significantly improves modelling of human cortical speech tracking. This Adaptive Gain transformation essentially normalizes sound level by its recent context. Improvements in modelling of cortical speech tracking using the Adaptive Gain stimulus representation are robust across experiments, participant groups, and languages, indicating that short-timescale adaptation to recent sound level is a general feature of auditory processing. We further show that the optimal adaptation time constant for human cortical responses to continuous speech is approximately 50-100 ms, longer than previously observed for auditory thalamic responses to temporally varying sounds in mice. In summary, the Adaptive Gain transformation is a mathematically simple alternative to the standard envelope representation that captures dynamic adaptation in auditory processing and reliably improves prediction of human cortical EEG signals during listening to continuous speech. Significance StatementStandard models of human brain responses to continuous speech use the raw stimulus envelope as a predictor of EEG responses, implicitly assuming stationary sensitivity to sound intensity. Here, we use instead a simple nonlinear transformation of the stimulus envelope, Adaptive Gain, which normalizes sound level based on recent sound history over tens to hundreds of milliseconds. Originally derived from studies of auditory processing in mice, the Adaptive Gain transformation robustly improves prediction of EEG responses to continuous speech in humans across experiments, participant groups, and languages. Results demonstrate that dynamic adaptation to sound level is a core feature of auditory processing, and can be approximated in a mathematically simple form to improve prediction of cortical speech tracking.

neuroscience↗

bioRxiv2026

Single-cell profiling of synchronous multi-organ metastasis reveals a systemic CD74+ lipid-associated macrophage niche driving polymetastatic breast cancer

Systemic, multi-organ metastasis is the primary cause of breast cancer mortality, yet the biological mechanisms that allow disseminated tumor cells to simultaneously colonize physiologically diverse tissues remain poorly understood. Current paradigms focus on organ-specific tropism, largely overlooking the potential for systemic, conserved and synchronized programs that facilitate widespread colonization. Here, we present a high-resolution, multi-organ atlas of metastatic ecosystems and their niches using a synchronous model of brain, lung, liver, and bone metastasis combined with in vivo proximal niche labeling and single-cell RNA sequencing. We identify a remarkably conserved proximal niche program defined by the accumulation of CD74+ lipid-associated, metastasis-associated macrophages (LA-MAMs) across all metastatic sites. CD74+ LA-MAMs are characterized by a unique metabolic-immune signature and drive T cell suppression. We show that the cytokine Macrophage Migration Inhibitory Factor (MIF), secreted by metastatic cells, acts as the universal paracrine mediator that instructs the LA-MAM phenotype via the CD74 receptor. Interference of the MIF-CD74 axis effectively disrupts the LA-MAM niche, mitigates T cell exhaustion, and reduces metastatic burden across all organs. Analysis of a 100-patient cohort of metastasis samples from different sites confirms that the MIF-CD74 axis is a hallmark of human multi-organ colonization and independently predicts poor post-metastasis survival. Our findings define a synchronized and systemic metastatic niche that can be targeted, providing a mechanistic rationale for neutralizing the MIF-CD74 axis to treat polymetastatic breast cancer.

cancer biology↗

bioRxiv2025

A novel mechanism for centrosome expulsion ensures metabolic activity in polyploid cells

Programmed polyploidy is often linked to increase cell size to support enhanced metabolism, barrier function or regeneration. In certain polyploid cells, the cytoskeleton is drastically remodeled-most notably by eliminating centrosomes. However, the purpose and mechanisms underlying centrosome elimination have remained unclear. We investigated this question in Drosophila acentrosomal salivary glands (SGs), a physiological polyploid model where cells reach high chromosome content through endoreplication. Using genetic tools, live imaging approaches, super-resolution microscopy combined with tissue clearing and electron microscopy, our study uncovers a novel centrosome elimination pathway in vivo. This process requires non-muscle myosin II (MyoII) activity and the macroautophagic machinery to drive centrosome release into the lumen of the salivary glands via autolysosomal exocytosis. Failure to eliminate centrosomes disrupts the mitochondria network, impairing respiration and ATP production. Our findings reveal a previously unknown mechanism that removes centrosomes through the secretory autophagy pathway to protect mitochondrial function and support the high metabolic demands of polyploid cells.

cell biology↗

bioRxiv2025

Role of oligodendroglial ADAM10 in oligodendrocyte maturation, myelination and myelin maintenance

In the central nervous system, oligodendrocytes extend their processes to wrap axons to form myelin sheaths, ensuring saltatory conduction of action potentials and providing trophic support for the axon. Our previous work demonstrated that pharmacological activation of -secretase promotes myelin protection and remyelination after both ex vivo and in vivo demyelination. Based on these findings, the present study aims to investigate the role of oligodendroglial ADAM10 (OLA10; a member of the a-secretase family) in myelin development and maintenance. Using an inducible knockout mouse model for OLA10 (KOOL-A10), we demonstrated that OLA10 deficiency results in delayed maturation of OPC in primary culture, and altered myelination in primary neuron/glia co-culture. Furthermore, an induction of OLA10 deficiency in adult mice was associated with an alteration of myelin sheath thickness and long-term motor and cognitive deficit in males but not in females. Overall, our study highlights the subtle but significant role of ADAM10 expressed by oligodendrocytes in the formation and maintenance of the myelin over time, while emphasizing a sexual dimorphism that carries important relevance for current research.

neuroscience↗

bioRxiv2025

Distinctive neurophysiological correlates of sound onset and offset perception in humans

Accurate detection of sound onsets and offsets is vital for speech perception. Sound-onset event-related potentials (ERPs) have been well-characterised in electroencephalography (EEG) studies, but the characteristics of sound-offset ERPs have often been obscured by temporal confounds in experimental design. Here, two EEG studies were conducted in human listeners performing an interval duration discrimination task with (i) noise intervals in silence or (ii) silent intervals (gaps) in noise. Stimuli used in the active task were also presented under passive listening conditions. This design enabled us to investigate whether features of the offset ERP could be masked by task demands, and whether the usual temporal precedence of the onset cue in a sound influences the relative magnitude and shape of onset and offset ERPs. The morphology of the offset ERP was distinct from that of the onset ERP in both noise and silent interval duration discrimination tasks, even though the roles of onset and offset cues as initial versus final markers of interval duration were reversed. This observation corroborates evidence from animal studies that there are fundamental differences in brain mechanisms of onset and offset perception. In all experimental conditions, the amplitude of the offset ERP was one-third to one-half that of the onset ERP. Differences between active and passive listening conditions were largely explained by enhancement of ERPs for whichever cue (onset or offset) marked the end of the intervals compared in the duration discrimination task. However, this context dependence emerged in earlier ERP waves for offset than onset responses. Key points summaryO_LIOnset and offset event-related potentials (ERPs) differ in morphology and amplitude C_LIO_LIFor both onset and offset ERPs, P200 and later waves depend on behavioural context C_LIO_LIFor offset ERPs only, P100/N100 waves also depend on behavioural context C_LIO_LIEngagement in duration discrimination alters ERPs primarily for end-interval cues C_LI

neuroscience↗

bioRxiv2025

Mitotic slippage causes nuclear instability in polyploid cells

Whole-genome duplication (WGD), leading to polyploidy can arise in physiological and pathological contexts1-5. WGD can occur via non-canonical cell cycles such as mitotic slippage, cytokinesis failure or endoreplication1,3. Whether the routes to WGD influence the behaviour of the resulting polyploid cells remains unclear. Here, we compared these routes under both physiological and non-physiological conditions. Remarkably, only mitotic slippage led to widespread nuclear abnormalities defined by highly variable nuclear deformations that we termed nuclear instability. Mechanistically, we found that these nuclei were softer - due to high levels of histone 3 phosphorylation in G1 altering chromatin compaction - and thus more vulnerable to microtubule-driven deformations. The resulting nuclear instability leads to local nuclear reorganisation and changes in 3D genome organisation impacting ultimately gene expression. Importantly, we observed similar nuclear instability in megakaryocytes, which are physiological polyploid cells that we show here to be generated by mitotic slippage, providing a molecular mechanism for their atypical nuclear architecture6,7. In striking contrast, nuclear shape was stable in different physiological polyploid cells generated by cytokinesis failure and endoreplication. Overall, our findings highlight that the route towards WGD matters and that mitotic slippage uniquely destabilizes nuclear architecture, with implications for both physiology and disease.

cell biology↗

bioRxiv2025

Open-science discovery of DNDI-6510, a compound that addresses genotoxic and metabolic liabilities of the COVID Moonshot SARS-CoV-2 Mpro lead inhibitor

The 2020 SARS-CoV-2 coronavirus pandemic highlighted the urgent need for novel small molecule antiviral drugs. (S)-x38 DNDI-6510 is a non-covalent SARS-CoV-2 main protease inhibitor developed by the open science collaboration COVID Moonshot. Here, we report on the metabolic and toxicologic optimization of the lead series previously disclosed by the COVID Moonshot Initiative, leading up to the selection of (S)-x38 DNDI-6510 as the preclinical candidate. We describe the thorough profiling of the series, identifying key risks such as formation of genotoxic metabolites and high clearance, which were successfully addressed during lead optimization. In addition, we disclose the in vitro and in vivo evaluation of (S)-x38 DNDI-6510 in pharmacokinetic and pharmacodynamic models, exploring multiple approaches to ameliorate rodent-specific metabolic clearance, and show that both co-dosing of (S)-x38 DNDI-6510 with an ABT inhibitor and utilizing a metabolically humanized mouse model (8HUM) achieve significant improvements in exposure. Through comparisons of ABT co-dosing and humanized mouse models in efficacy experiments, we demonstrate that continuous exposure over cellular EC90 is required for SARS-CoV-2 antiviral efficacy in vivo in an antiviral model using a mouse-adapted SARS-CoV-2 strain. Finally, (S)-x38 DNDI-6510 was assessed in maximum tolerated dose experiments in two species, demonstrating significant in vivo PXR-linked auto-induction of metabolism, leading to the discontinuation of this compound. In summary, we report the successful effort to overcome series-specific AMES liabilities in a lead development program. Downstream optimization of existing series will require in-depth optimization of rodent-specific liabilities and metabolic induction profile.

pharmacology and toxicology↗

bioRxiv2025

Differentiating unirradiated mice from those exposed to conventional or FLASH radiotherapy using MRI

Background and purposeThe FLASH effect expands the therapeutic ratio of tumor control to normal tissue toxicity observed after delivery of ultra-high (>100 Gy/s FLASH-RT) vs. conventional dose rate radiation (CONV-RT). In this first exploratory study, we assessed whether ex-vivo Magnetic Resonance Imaging (MRI) could reveal long-term differences after FLASH-RT and CONV-RT whole-brain irradiation. Materials and methodsFemale C57BL/6 mice were divided into three groups: control (non-irradiated), conventional (CONV-RT 0.1 Gy/s), and ultra-high dose rates (FLASH-RT 1 pulse, 5.5 x 106 Gy/s), and received 10 Gy of whole-brain irradiation in a single fraction at 10 weeks of age. Mice were evaluated by Novel Object Recognition cognitive testing at 10 months post-irradiation and were sampled at 13 months post-irradiation. Ex-vivo brains were imaged with a 14.1 Tesla/26 cm magnet with a multimodal MRI protocol, including T2-weighted TurboRare (T2W) and diffusion-weighted imaging (DWI) sequences. ResultsIn accordance with previous results, cognitive tests indicated that animals receiving CONV-RT exhibited a decline in cognitive function, while FLASH-RT performed similarly to the controls. MRI showed decreased hippocampal mean intensity in the CONV-RT mice compared to controls but not in the FLASH-RT group. Comparing CONV-RT to control, we found significant changes in multiple whole-brain diffusion metrics, including the mean Apparent Diffusion Coefficient (ADC) and Mean Apparent Propagator (MAP) metrics. By contrast, no significant diffusion changes were found between the FLASH-RT and control groups. In an exploratory analysis compared to controls, regional diffusion metrics were primarily altered in the basal forebrain and the insular cortex after CONV-RT, and after FLASH-RT, a trend reduction was also observed. ConclusionThis study presents initial evidence that MRI can uncover clear changes in the brain after CONV-RT but not after FLASH-RT. The MRI results aligned with the observed cognitive protection after FLASH-RT, indicating the potential use of MRI to analyze the FLASH response.

neuroscience↗

bioRxiv2025

A novel DNA repair-independent role for Gen nuclease in promoting unscheduled polyploidy cell proliferation

Unscheduled whole genome duplication (WGD), also described as unscheduled or non-physiological polyploidy, can lead to genetic instability and is commonly observed in human cancers. WGD generates DNA damage due to scaling defects between replication factors and DNA content. As a result, DNA damage repair mechanisms are thought to be critical for ensuring cell viability and proliferation under these conditions. In this study, we explored the role of homologous recombination and Holliday junction resolution in non-physiological polyploidy in vivo. Using Drosophila genetics and high-resolution imaging, we identified a key and surprising role for Gen/Gen1 nuclease. Our findings revealed that loss-of-function and overexpression of Gen have opposing effects, delaying or accelerating the proliferation of polyploid cells, respectively. These changes ultimately impact cell proliferation, nuclear asynchrony and mitotic DNA damage levels. Surprisingly, our findings show that this effect is unrelated with the expected Gens function in DNA damage repair. Instead, Gen seems to influence polyploid DNA replication rates. This work identifies a novel function for Gen nuclease and provides new insights into the cellular and molecular requirements of non-physiological polyploidy.

cell biology↗

bioRxiv2025

Spatial profiling of central nervous system cellular markers in murine breast cancer to brain metastases

BackgroundBrain metastasis occurs in approximately 16% of metastatic breast cancer patients, and incidence is increasing. Patients with breast cancer brain metastases frequently develop neurological problems including cognitive impairments and seizures. We previously demonstrated accumulation of activated microglia around the tumour site in a breast cancer brain metastasis model, which co-localised with spontaneously occurring local field potential events that resembled interictal epileptic discharges. However, the mechanisms underlying these spatially restricted effects on neuronal excitability are poorly understood. MethodsTo better understand the underlying cellular changes and potential mechanisms, we used digital spatial profiling of brain cell subtype-specific markers to chart the spatial organisation of neurons, oligodendrocytes, astrocytes, and microglia in relation to metastatic lesion site. We developed a novel chordline-based approach to analyse these spatial changes in biomarker distribution. ResultsSeveral protein markers associated with proliferation (Ki67), astrocytes (GFAP) and microglia (CD11b, IBA1, CD45, MSR1) were upregulated in the tumour compared to healthy contralateral brain parenchyma. In contrast, some neuroglial markers (MAP2, Neurofilament light, NeuN, S100B and TMEM119) were lower in the lesion compared to normal tissue. ConclusionsOverall, the protein marker changes in the lesion are indicative of neuronal cell loss and changes in the immune microenvironment of the metastatic lesion involving activated microglia, astrocytes and recruitment of peripheral immune cells. Such cellular changes may contribute to the changes in electrical activity resulting from brain metastases observed in mice and patients.

neuroscience↗

bioRxiv2025

Elucidating the molecular landscape of centronuclear myopathies in mouse models: an integrative multi-omics and network analysis

Centronuclear myopathies (CNM) are rare inherited muscle disorders characterized by muscle atrophy, weakness, and altered muscle fiber structure, primarily due to mutations in genes like MTM1, DNM2, and BIN1. The pathomechanisms implicated in CNM are only partially understood, and no curative therapies are available for patients. This study exploits a unique multi-omics dataset and network-based analyses to elucidate the molecular pathways involved in CNM. First, we performed Weighted Gene Co-expression Network Analysis (WGCNA) to identify gene modules correlated with CNM phenotypes. We find that modules correlated to a positive muscular phenotype were enriched for genes involved in muscle contraction, RNA processes and oxidative phosphorylation, while modules associated with impaired muscle structure and function were enriched in immune response, innervation, vascularization processes, and fatty acid oxidation. Next, we integrated transcriptomic, proteomic, and metabolomic data from the Mtm1-/y mouse model with public knowledge bases using a multilayer network approach and explored the network using a random walk with restart approach. This study revealed novel metabolites that could be targeted through dietary supplementation as potential therapeutic strategies. Our findings demonstrate how multi-omics network analyses can reveal new aspects of CNM pathomechanisms and identify avenues for intervention.

bioinformatics↗

bioRxiv2024

Reversible and reusable compartmentalized microfluidic chip for coculture of dorsal root ganglion neurons

Compartmentalized microfluidic chips play an important role in understanding the cellular mechanisms involved in neurodegenerative disorders. Dorsal root ganglia are a well-established model for modelling the peripheral nervous system (PNS), but their development on a chip remains limited. Furthermore, it would be beneficial for the devices to be openable in order to access the biological material inside for analyses. Easy to prototype and biocompatible, styrenic block copolymers (SBC) are an alternative to polydimethylsiloxane (PDMS) that offer both reversible and permanent bonding properties. This paper presents a fast and straightforward method to produce compartmentalized SBC chips. The study validates the culture of murine dorsal root ganglia explants, comparing it to the standard methods, to obtain a model of the PNS. Moreover, the reversible bonding properties of the SBC permit the reuse of the chip with a quick and easy cleaning protocol. It provides direct access to the cells, opening the way for imaging and molecular biology analysis. The comparison of the resources required to produce PDMS and SBC chips highlights the importance of moving to reusable devices. These detachable, easy-to-manufacture and sustainable all-thermoplastic platforms provide an alternative way of prototyping compartmentalized devices for in vitro PNS modeling.

biophysics↗

bioRxiv2024

Cortical layer-specific and cell type-specific dendritic expression of Arc (Arg 3.1) in an in vitro model of slow-wave sleep

An abundance of evidence shows sleep homeostatically regulates synaptic plasticity and memory consolidation but the underlying molecular regulators of this important function of sleep have been difficult to directly elucidate. Arc is an immediate early gene that has a fundamental role in several aspects of synaptic plasticity including regulation and maintenance. Using a physiological brain slice model of slow-wave sleep, here we show that Arc protein has a characteristic spatial and cell-type specific distribution during persistent sleep-related delta oscillations in neocortical slices, which may correlate with aspects of sleep-dependent regulation of synaptic plasticity in cortical regions. In delta oscillating slices, Arc is highly expressed in layer 2/3 dendrites of the primary and secondary association cortex and this dendritic localisation is specific to intrinsically bursting cells (IB) whose cell bodies are in layer 5. Moreover, Arc immunopositive dendrites are clustered together arranged in a quasi hexagonal arrangement with a spacing of [~] 50 {micro}m between clusters. The cytoarchitectural distribution of Arc across the association cortex has implications for the mechanisms of sleep and for the synaptic homeostasis hypothesis regarding the function of sleep.

neuroscience↗