Biology subjects

Schneider, N.

Publications and source records attributed to Schneider, N..

14 recordsLinked to original sources

bioRxiv2026

Transcript-Specific Site-Directed RNA Editing Reveals Principles for Splice-aware guide RNA Design

Site-directed RNA editing (SDRE) utilizing the adenosine deaminase acting on RNA (ADAR) enzymes is commonly facilitated by guide RNAs (gRNAs) optimized to enhance on-target editing and minimize bystander effects. However, the impact of gRNA binding and ADAR-mediated SDRE on canonical pre-mRNA splicing remains poorly understood. Here, we developed an in vitro transcript-specific editing strategy that enables selective targeting and direct comparison of SDRE in pre-mRNA and mature mRNA. Using splice-relevant variants associated with inherited retinal diseases, we investigated the effects of SDRE on exonic, near-canonical intronic, and deep intronic splice variants. We identified gRNA-induced splice perturbation at exonic and intronic targets and observed that higher editing levels could be associated with increased splice disruption. Conversely, SDRE of two exonic splice variants and a deep intronic variant resulted in increased production of correctly spliced transcripts, demonstrating the potential of SDRE for splice modulation. Finally, by dissecting the effects of ADAR expression and gRNA design on editing and splicing outcomes, we established a system for identifying design principles that reduce splice interference and enhance the generation of correctly spliced, edited transcripts. These findings highlight the importance of considering transcript context and splicing consequences in the development of SDRE-based therapeutic strategies. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=92 SRC="FIGDIR/small/741163v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@55e0cforg.highwire.dtl.DTLVardef@1a5c29org.highwire.dtl.DTLVardef@98aec7org.highwire.dtl.DTLVardef@1fab73b_HPS_FORMAT_FIGEXP M_FIG Created in BioRender. Schneider, N. (2026) https://BioRender.com/59i0tiy C_FIG

molecular biology↗

bioRxiv2026

From anti-fungal to potential neurotherapeutic: Posaconazole as an effective inhibitor of cellular TDP-43 pathology

Recently, we showed that ketoconazole, a known anti-fungal inhibitor of CYP51, stabilized TAR DNA-binding protein 43 (TDP-43) native self-interactions, reduced TDP-43 pathology and rescued TDP-43-induced SREBP2 downregulation. Despite its promising effects, ketoconazole is not viable for repurposing for ALS due to liver toxicity side effects that occur when orally delivered. To address this, we tested the activities of seven additional known azole-based CYP51 inhibitors in order identify a viable alternative to ketoconazole. Using our established TDP-43 mislocalization and aggregation assay in HEK293T cells, we identified posaconazole, an FDA-approved, CNS-penetrant and orally delivered anti-fungal, as the strongest inhibitor of TDP-43 pathology. Posaconazole was able to reduce insoluble TDP-43 and restore SREBP2 levels, outperforming ketoconazole. Mechanism of action (MOA) experiments suggest posaconazole is able to outperform ketoconazole by inducing a significantly stronger activation of autophagy and upregulation of heat shock proteins known to clear TDP-43. Further MOA experiments show that the effects of posaconazole on TDP-43 are dependent on its known ability to lower cellular cholesterol levels. By correlating our experimental results on the eight CYP51 inhibitors tested, we show that predicted affinity towards human CYP51 strongly correlates with the inhibitors ability to lower TDP-43 aggregation and mislocalization. Finally, we tested posaconazole in a low dose sodium arsenite ALS model in iPSC-derived motor neurons, showing that it is efficacious at inhibiting TDP-43 pathology in the nanomolar range. Altogether, these results support the repurposing of posaconazole for ALS/FTD as a means to prevent TDP-43 pathology.

cell biology↗

bioRxiv2026

miR-495-3p inhibition in mice rescues mTORC1 hyperactivation-driven autistic-like behaviors

Defective social behavior and cognitive functions are hallmarks of Autism spectrum disorders (ASD). The molecular mechanisms keeping social behavior in a physiological range are largely unknown. We recently found that conditional knockout (cKO) of tmiRNA cluster miR-379-410 in mouse hippocampal neurons leads to hypersocial behavior. Therefore, inhibiting miR-379-410 members might represent a strategy to promote sociability in ASD. As an ASD model, we chose knockdown (KD) of the ASD risk gene Tsc1, a key negative regulator of mTORC1. Acute Tsc1 knockdown (KD) in hippocampal neurons was sufficient to induce hyposociability and memory deficits in adult wild-type mice. In contrast, Tsc1 KD had no effect on sociability in miR-379-410 cKO mice, indicating a requirement of miR-379-410. Furthermore, Tsc1 KD led to upregulation of tmiR-495-3p, and inhibition of this miRNA by antisense oligonucleotides was sufficient to prevent hyposociability and memory impairments. Our findings suggest that miR-495-3p is a key downstream effector of the Tsc1/mTORC1 pathway in sociability, and that targeting miR-495-3p represents a therapeutic avenue for restoring social and cognitive impairments in ASD without affecting mTORC1 homeostasis.

neuroscience↗

bioRxiv2026

Single-cell characterization of skin response to a bite by West Nile virus-infected mosquito reveals fibroblast-mediated barrier to transmission

Cutaneous events at the mosquito bite site that determine orthoflavivirus transmission efficiency remain largely uncharacterized. Here, we report single-cell RNA-sequencing of skin from immunocompetent mice bitten by West Nile virus-infected mosquitoes, capturing early response at a critical transmission bottleneck. Fibroblasts were the dominant cells exposed to infectious saliva. While neutrophils and Folr2+ macrophages diminished, monocyte-derived and antigen-presenting macrophages, and lymphocytes became more abundant. Cell-cell communication analysis revealed the central roles of fibroblasts and myeloid cells in induced immune-related signaling. Transcriptional profiling defined cell type-specific responses to infectious bite integrating immune modulation, skin repair and metabolic remodeling. Using in vivo gene silencing, we demonstrated that fibroblast-expressed LRRC15 (leucine rich repeat-containing 15) functions as a cutaneous restriction factor, limiting viral replication in skin, viral dissemination to draining lymph nodes, and disease severity. Collectively, our analyses provide cellular and molecular understanding of bite-initiated arboviral transmission, establishing skin-resident fibroblasts as frontline defender cells. HIGHLIGHTSO_LISingle-cell profiling captures early cutaneous response to West Nile virus-infected mosquito bites with cell type resolution. C_LIO_LISkin-resident fibroblasts are the dominant frontline cells exposed to infectious mosquito saliva. C_LIO_LIInfectious bite reconfigures cutaneous immune cells, and activates multi-directional signaling between immune and structural skin cell types. C_LIO_LIBite-induced fibroblast-expressed LRRC15 restricts viral transmission and attenuates disease severity. C_LI

zoology↗

bioRxiv2025

Dengue virus harnesses mosquito Syntenin to load and secrete viral RNA into salivary exosomes

Viruses exploit extracellular vesicles (EVs) to transfer infection-enhancing viral RNAs. However, mechanisms underlying viral RNA loading remain elusive. We leveraged our previous discovery that dengue virus secretes transmission-enhancing subgenomic flaviviral RNA (sfRNA) into mosquito salivary EVs to investigate viral RNA loading mechanism. We demonstrate that sfRNA alone promotes the secretion of sfRNA-containing EVs marked by the mosquito EV biogenesis protein AeSyntenin, by applying microscopy and viral genetic editing in in vitro and in vivo models. SfRNA via its stem loop structures interacts intracellularly with mosquito AeSyntenin and this interaction is selectively maintained within EVs as shown by complementary RNA-affinity chromatography and RNA immunoprecipitation, and AI-based prediction. Finally, we used systemic and salivary gland-specific protein depletion to establish a functional role for mosquito AeSyntenin in exosome production and salivary secretion of sfRNA. We propose that sfRNA binds AeSyntenin to drive its selective packaging and release into exosomes, elucidating a mechanism for viral RNA incorporation into EVs. Significance statementViruses hijack extracellular vesicles (EVs) to enhance viral dissemination, but the mechanisms enabling selective viral RNA packaging into EVs remain unclear. Specifically, dengue virus transmission by mosquitoes relies on EV-based delivery of an immune-inhibitory subgenomic flaviviral RNA (sfRNA). Here, we uncover how dengue virus sfRNA is actively sorted into EVs from mosquito saliva. We show that sfRNA alone induces its secretion via EVs. We discover that sfRNA directly interacts with AeSyntenin intracellularly, and that this interaction persists in secreted EVs. Functional depletion studies reveal AeSyntenins role in salivary EV formation and sfRNA secretion. These findings establish a novel paradigm by which viral RNAs exploit vector EV pathways for dissemination.

microbiology↗

bioRxiv2025

RetiGene, a comprehensive gene atlas for inherited retinal diseases (IRDs)

Inherited retinal diseases (IRDs) are rare disorders, typically presenting as Mendelian traits, that result in stationary or progressive visual impairment. They are characterized by extensive genetic heterogeneity, possibly the highest among all human genetic diseases, as well as diverse inheritance patterns. Despite advances in gene discovery, limited understanding of gene function and challenges in accurately interpreting variants continue to hinder both molecular diagnosis and genetic research in IRDs. One key problem is the absence of a comprehensive and widely accepted catalogue of disease genes, which would ensure consistent genetic testing and reliable molecular diagnoses. With the rapid pace of IRD gene discovery, gene catalogues require frequent validation and updates to remain clinically and scientifically useful. To address these gaps, we developed RetiGene, an expert-curated gene atlas that integrates variant data, bulk and single-cell RNA sequencing, and functional annotations. Through the integration of diverse data sources, RetiGene supports candidate gene prioritization, functional studies, and therapeutic development in IRDs.

genetics↗

bioRxiv2025

Computationally Designed RNA Aptamers Enable Selective Detection of FUS Pathology in ALS

FUS is an RNA/DNA-binding protein whose mislocalization and aggregation are defining pathological features of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). Detecting pathological FUS assemblies remains challenging, as antibody-based approaches are frequently limited by epitope masking, conformational heterogeneity, and cross-reactivity with physiological FUS pools. Here we apply rationally designed RNA aptamers to selectively recognize FUS across soluble and aggregated states. The aptamers bind solvent-exposed RNA-binding regions of FUS with low-nanomolar affinity and adopt stable hairpin conformations that support high specificity. In cultured cells expressing the ALS-associated p.P525L FUS mutation, the aptamers detect cytoplasmic and nuclear FUS assemblies that are frequently missed by commercial antibodies and show reduced recognition of FUS-containing protein complexes. Using super-resolution imaging, the aptamers enable visualization of early FUS aggregation intermediates that are inaccessible to conventional amyloid dyes. In post-mortem brain tissue from individuals with FUS-ALS, aptamer staining selectively labels pathological FUS while sparing normal nuclear FUS, revealing prominent nuclear and nucleolar pathology that is poorly resolved by antibody-based methods. Together, these findings establish RNA aptamers as sensitive and selective probes for pathological FUS and uncover previously underappreciated features of FUS aggregation in ALS. This work highlights the value of nucleic-acid-based recognition tools for interrogating protein misfolding and neurodegenerative disease pathology.

biochemistry↗

bioRxiv2023

Four-Core Genotypes mice harbour a 3.2MB X-Y translocation that perturbs Tlr7 dosage

The Four Core Genotypes (FCG) is a mouse model system heavily used to disentangle the function of sex chromosomes and hormones. We report that a copy of a 3.2 MB region of the X chromosome has translocated to the YSry- chromosome and thus increased the expression of multiple genes including the auto-immune master regulator Tlr7. This previously-unreported X-Y translocation complicates the interpretation of studies reliant on FCG mice.

genetics↗

bioRxiv2023

Superovulation and aging perturb oocyte-granulosa cell communication

In vitro fertilization has been developed to overcome reduced fertility, which is increasingly due to a decline in reproductive cell quality during aging. Here, we quantitatively investigated the interplay between superovulation and aging in mouse oocytes and their paired granulosa cells using newly adapted isolation techniques. We tested the hypothesis that superovulation disrupts oocyte maturation, revealing the key intercellular communication pathways dysregulated by forced hormonal stimulation. We further demonstrated that granulosa cell transcriptional markers can prospectively predict an associated oocytes early developmental potential. By using naturally ovulated old mice as a non-stimulated reference, we showed that aging and superovulation dysregulate similar genes and interact with each other. By comparing mice and human transcriptional responses of granulosa cells, we found that age-related dysregulation of hormonal responses and cell cycle pathways was shared, though substantial divergence exists in other pathways. HighlightsO_LISuperovulation perturbs cumulus-oocyte communication C_LIO_LIGranulosa cell transcription predicts superovulated oocyte quality C_LIO_LISuperovulation and aging non-additively perturb similar sets of genes C_LI

developmental biology↗

bioRxiv2023

ADBP-1 regulates ADR-2 nuclear localization to control editing substrate selection

Adenosine-to-inosine (A-to-I) RNA editing, catalyzed by ADAR enzymes, is a prevalent and conserved RNA modification. While A-to-I RNA editing is essential in mammals, in Caenorhabditis elegans, it is not, making them invaluable for RNA editing research. In C. elegans, ADR-2 is the sole catalytic A-to-I editing enzyme, and ADR-1 is an RNA editing regulator. ADAR localization is well-studied in humans but not well-established in C. elegans. In this study, we examine the cellular and tissue-specific localization of ADR-2. We show that while ADR-2 is present in most cells in the embryo, at later developmental stages, its expression is both tissue- and cell-type-specific. Additionally, both ADARs are mainly in the nucleus. ADR-2 is adjacent to the chromosomes during the cell cycle. We show that the nuclear localization of endogenous ADR-2 depends on ADBP-1, not ADR-1. In adbp-1 mutant worms, ADR-2 is mislocalized, while ADR-1 is not, leading to decreased editing levels and de-novo editing, mostly in exons, suggesting that ADR-2 is also functional in the cytoplasm. Besides, mutated ADBP-1 affects gene expression. Furthermore, we show that ADR-2 targets adenosines with different surrounding nucleotides in exons and introns. Our findings indicate that ADR-2 cellular localization is highly regulated and affects its function.

cell biology↗

bioRxiv2022

The function and decline of the female reproductive tract at single-cell resolution

The female reproductive tract (FRT) undergoes extensive remodeling during each reproductive cycle, regulated by systemic changes in sex hormones. Whether this recurrent remodeling influences a specific organs aging trajectory is unknown. To address this, we systematically characterized at single-cell resolution the morphological and transcriptional changes that occur in ovary, oviduct, uterus, cervix, and vagina at each phase of the mouse estrus cycle, during decidualization, and into aging. Transcriptional and cell-to-cell communication networks in estrus cycle and aging are enriched for ECM reorganization and inflammation, two essential components of FRT remodeling. We directly link the organ-specific level of these two processes over reproductive lifespan with the gradual, age-related development of fibrosis and chronic inflammation. Our data represent a comprehensive atlas of the FRT lifespan, revealing pathological consequences of incomplete resolution of recurrent inflammation and tissue repair.

genomics↗

bioRxiv2022

A scalable screening platform for phenotypic subtyping of ALS patient-derived fibroblasts

A major challenge for understanding and treating Amyotrophic Lateral Sclerosis (ALS) is that most patients have no known genetic cause. Even within defined genetic subtypes, patients display considerable clinical heterogeneity. It is unclear how to identify subsets of ALS patients that share common molecular dysregulation or could respond similarly to treatment. Here, we developed a scalable microscopy and machine learning platform to phenotypically subtype readily available, primary patient-derived fibroblasts. Application of our platform identified robust signatures for the genetic subtype FUS-ALS, allowing cell lines to be scored along a spectrum from FUS-ALS to non-ALS. Our FUS-ALS phenotypic score negatively correlates with age of diagnosis and provides information that is distinct from transcript profiling. Interestingly, the FUS-ALS phenotypic score can be used to identify sporadic patient fibroblasts that have consistent pathway dysregulation with FUS-ALS. Further, we showcase how the score can be used to evaluate the effects of ASO treatment on patient fibroblasts. Our platform provides an approach to move from genetic to phenotypic subtyping and a first step towards rational selection of patient subpopulations for targeted therapies.

systems biology↗

bioRxiv2020

Single-dose ethanol intoxication causes acute and lasting neuronal changes in the brain

Alcohol intoxication at early ages is a risk factor for development of addictive behavior. To uncover neuronal molecular correlates of acute ethanol intoxication, we used stable-isotope labeled mice combined with quantitative mass spectrometry to screen over 2000 hippocampal proteins of which 72 changed synaptic abundance up to two-fold after ethanol exposure. Among those were mitochondrial proteins and proteins important for neuronal morphology, including MAP6 and Ankyrin-G. Based on these candidate proteins, we found acute and lasting molecular, cellular, and behavioral changes following a single intoxication in alcohol-naive mice. Immunofluorescence analysis revealed a shortening of axon initial segments. Longitudinal two-photon in vivo imaging showed increased synaptic dynamics and mitochondrial trafficking in axons. Knockdown of mitochondrial trafficking in dopaminergic neurons abolished conditioned alcohol preference in Drosophila. This introduces mitochondrial trafficking as a process implicated in reward learning, and highlights the potential of high-resolution proteomics to identify cellular mechanisms relevant for addictive behavior.

neuroscience↗

bioRxiv2019

Mice optimize switching decisions through cost-benefit evaluation

In the classical view of economic choices, subjects make rational decisions evaluating the costs and benefits of options in order to maximize their overall income. Nonetheless, subjects often fail to reach optimal outcomes. The overt value of an option drives the direction of decisions, but covert factors such as emotion and sunk cost are thought to drive the observed deviations from optimality. Many questions remain to be answered as to 1) which contexts contribute the most to deviation from an optimal solution; and 2) the extent of these effects. In order to tackle these questions, we devised a decision-making task for mice, in which cost and benefit parameters could be independently and flexibly adjusted and for which a tractable optimal solution was known. Comparing mouse behavior with this optimal solution across parameter settings revealed that the factor most strongly contributing to suboptimality was the cost parameter. The quantification of sunk cost, a covert factor implicated in our task design, revealed it as another contributor to suboptimality. In one condition where the large reward option was particularly unattractive and the small reward cost was low, the sunk cost effect and the cost-led suboptimality almost vanished. In this regime and this regime only, mice could be viewed as close to rational. Taken together, our findings support a model whereby parallel neural circuits independently activate and modulate multiple valuation algorithms, and suggest that "rationality" is a task-specific construct even in mice. Significant StatementIrrational factors in economic decision-making often cause significant deviation from optimal outcomes. By devising a flexible economic choice behavior for mice and comparing their behavior with an optimal solution, we investigated overt and covert factors that contributed to suboptimal outcomes and quantified the deviation from optimality. This investigation identified regimes where mice could be viewed as rational or irrational depending upon the parameters in the same task. These findings may provide a platform to investigate biological substrates underlying rational and irrational decision factors.

neuroscience↗