Biology subjects

Fuchs, D.

Publications and source records attributed to Fuchs, D..

6 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

Multiomic profiling of human and canine soft-tissue sarcomas reveals extensive molecular homology across species and identifies clinically relevant subgroups

Soft-tissue sarcoma (STS) are rare and heterogeneous mesenchymal tumours with over 100 recognized human subtypes. Despite advances in cytogenetic and molecular characterization, diagnostic precision and therapeutic options remain limited for most subtypes. Spontaneously occurring canine STS could represent valuable translational models, due to their higher incidence and clinical similarity to human counterparts. However, molecular cross-species comparisons of specific subtypes are largely missing. Here, we performed a tissue-resolved, cross-species analysis of tumour and matched adjacent normal tissue (NT) in human and canine fibrosarcoma (FSA) and myxofibrosarcoma (MFS) by laser-capture microdissection of FFPE specimens combined with RNAseq and LC-MS/MS. Multimodal profiling revealed FSA and MFS to represent a molecular continuum rather than distinct entities in both species, resulted in identification of clinically relevant subgroups based on immune activation, proliferative activity and copy number alterations, and identified a novel canine STS subtype associated with a gene fusion. Moreover, our analyses revealed cross-species conserved transcriptomic and proteomic alterations distinguishing tumour from NT, including pathways linked to extracellular matrix remodelling, immune modulation, and cell proliferation. These data establish the first comprehensive molecular comparison of canine and human FSA and MFS, highlight the translational relevance of canine models, and identify candidate biomarkers for diagnostic refinement and development of targeted therapeutic modalities.

cancer biology↗

bioRxiv2025

Non-Invasive Photoacoustic Imaging of Cerebral Oxygenation and Hemoglobin Content in Awake Mice

IntroductionInvestigating cerebral oxygen saturation dynamics in awake animal models remains technically challenging due to motion artifacts and anesthesia-related biases. Here, we introduce a novel high-resolution ultrasound-photoacoustic (PA) imaging approach enabling real-time, non-invasive monitoring of deep cerebrovascular oxygenation dynamics in awake mice with intact skulls. Materials and MethodsSwiss male and female mice (n = 5-6) were head-fixed using a customized holder adapted to the Neurotar Mobile HomeCage floating platform. High-resolution ultrasound combined with PA imaging (VevoLAZR-X, VisualSonics) was used to discriminate oxyhemoglobin, deoxyhemoglobin, and total hemoglobin in multiple brain regions. Cerebrovascular responses were assessed under three paradigms: (i) baseline awake state vs. 2% isoflurane anesthesia, and (ii) right whisker stimulation to probe sensory-driven hemodynamics. ResultsPA imaging successfully resolved deep-brain oxygenation in awake, intact-skull mice. Under isoflurane anesthesia, we observed a rapid and transient increase in cerebrovascular sO{square} (p < 0.01). During whisker stimulation, we detected robust, region-specific increases in total hemoglobin, reflecting localized neurovascular coupling in awake mice. ConclusionsThis study establishes high-resolution PA imaging as a powerful, non-invasive tool to monitor cerebrovascular oxygenation dynamics in awake mice. By integrating baseline, anesthetic, and sensory paradigms, we demonstrate its potential to dissect neurovascular physiology without the confounding effects of anesthesia. These findings provide new opportunities for preclinical neuroscience research and translational applications investigating cerebral oxygen metabolism.

neuroscience↗

bioRxiv2024

Changes in Cerebrospinal Fluid Proteins across the Spectrum of Untreated and Treated Chronic HIV-1 Infection

Using the Olink Explore 1536 platform, we measured 1,463 unique proteins in 303 cerebrospinal fluid (CSF) specimens from four clinical centers that included uninfected controls and 12 groups of people living with HIV-1 infection representing the spectrum of progressive untreated and treated chronic infection. We present three initial analyses of these measurements: an overview of the CSF protein features of the sample; correlations of the CSF proteins with CSF HIV-1 RNA and neurofilament light chain protein (NfL) concentrations; and comparison of the CSF proteins in HIV-associated dementia (HAD) and neurosymptomatic CSF escape (NSE). These reveal a complex but coherent picture of CSF protein changes that includes highest concentrations of many proteins during CNS injury in the HAD and NSE groups and variable protein changes across the course of neuroasymptomatic systemic HIV-1 progression, including two common patterns, designated as lymphoid and myeloid patterns, related to the principal involvement of their underlying inflammatory cell lineages. Antiretroviral therapy reduced CSF protein perturbations, though not always to control levels. The dataset of these CSF protein measurements, along with background clinical information, is posted online. Extended studies of this unique dataset will provide more detailed characterization of the dynamic impact of HIV-1 infection on the CSF proteome across the spectrum of HIV-1 infection, and further the mechanistic understanding of HIV-1-related CNS pathobiology.

microbiology↗

bioRxiv2020

Herpes zoster in HIV-1 infection: the role of CSF pleocytosis in secondary CSF escape and discordance

HIV cerebrospinal fluid (CSF) escape is defined by a concentration of HIV-1 RNA in CSF above the lower limit of quantification of the employed assay and equal to or greater than the plasma HIV-1 RNA level in the presence of treatment-related plasma viral suppression, while CSF discordance is similarly defined by equal or higher CSF than plasma HIV-1 RNA in untreated individuals. During secondary CSF escape or discordance disproportionate CSF HIV-1 RNA develops in relation to another infection in addition to HIV-1. We performed a retrospective review of people living with HIV receiving clinical care at Sahlgrenska Infectious Diseases Clinic in Gothenburg, Sweden who developed uncomplicated herpes zoster (HZ) and underwent a research lumbar puncture (LP) within the ensuing 150 days. Based on treatment status and the relationship between CSF and plasma HIV-1 RNA concentrations, they were divided into 4 groups: i) antiretroviral treated with CSF escape (N=4), ii) treated without CSF escape (N=5), iii) untreated with CSF discordance (N=8), and iv) untreated without CSF discordance (N=8). We augmented these with two additional cases of secondary CSF escape related to neuroborreliosis and HSV-2 encephalitis and analyzed these two non-HZ cases for factors contributing to CSF HIV-1 RNA concentrations. HIV-1 CSF escape and discordance were associated with higher CSF white blood cell (WBC) counts than their non-escape (P=0.0087) and non-discordant (P=0.0017) counterparts, and the CSF WBC counts correlated with the CSF HIV-1 RNA levels in both the treated (P=0.0047) and untreated (P=0.002) group pairs. Moreover, the CSF WBC counts correlated with the CSF:plasma HIV-1 RNA ratios of the entire group of 27 subjects (P=<0.0001) indicating a strong effect of the CSF WBC count on the relation of the CSF to plasma HIV-1 RNA concentrations across the entire sample set. The inflammatory response to HZ and its augmenting effect on CSF HIV-1 RNA was found up to 5 months after the HZ outbreak in the cross-sectional sample and, was present for one year after HZ in one individual followed longitudinally. We find that HZ provides a model of secondary CSF escape and discordance. Likely, the inflammatory response to HZ pathology within the CNS provoked local HIV-1 production by enhanced trafficking or activation of HIV-1-infected CD4+ T lymphocytes. Whereas treatment and other systemic factors determined the plasma HIV-1 RNA concentrations, in this setting the CSF WBC counts established the relation of the CSF HIV-1 RNA levels to this plasma set-point. Author summaryHerpes zoster is a neurotropic infection common in people living with HIV. We studied if herpes zoster caused alterations in the cerebrospinal fluid viral (CSF) load when compared with blood levels in patients with and without antiretroviral treatment by studies of the cerebrospinal fluid. HIV-1 CSF escape and discordance were associated with higher CSF white blood cell counts than their non-escape (P=0.0087) and non-discordant (P=0.0017) counterparts, and the CSF white blood cell counts correlated with the CSF HIV-1 RNA levels in both the treated (P=0.0047) and untreated (P=0.002) group pairs. We found that the inflammatory response to herpes zoster pathology within the CSF provoked local HIV-1 production by enhanced trafficking or activation of HIV-1-infected CD4+ T lymphocytes. We suggest that herpes zoster provides a model of secondary HIV CSF escape and HIV CSF/blood discordance, which increase the understanding of HIV central nervous system infection and might be of importance for eradication trials in sanctuary sites such as the central nervous system.

neuroscience↗

bioRxiv2019

Does training method matter?: Evidence for the negative impact of aversive-based methods on companion dog welfare

There is a growing number of dogs kept as companion animals, and the methods by which they are trained range broadly from those using mostly positive punishment and negative reinforcement (aversive-based methods) to those using primarily positive reinforcement (reward-based methods). Although the use of aversive-based methods has been strongly criticized for negatively affecting dog welfare, these claims do not find support in solid scientific evidence. Previous research on the subject lacks companion dog-focused research, investigation of the entire range of aversive-based techniques (beyond shock-collars), objective measures of welfare, and long-term welfare studies. The aim of the present study was to perform a comprehensive evaluation of the short- and long-term effects of aversive- and reward-based training methods on companion dog welfare. Ninety-two companion dogs were recruited from three reward-based (Group Reward, n=42) and four aversive-based (Group Aversive, n=50) dog training schools. For the short-term welfare assessment, dogs were video recorded for three training sessions and six saliva samples were collected, three at home (baseline levels) and three after the training sessions (post-training levels). Video recordings were then used to examine the frequency of stress-related behaviors (e.g., lip lick, yawn) and the overall behavioral state of the dog (e.g., tense, relaxed), and saliva samples were analyzed for cortisol concentration. For the long-term welfare assessment, dogs performed a cognitive bias task. Dogs from Group Aversive displayed more stress-related behaviors, spent more time in tense and low behavioral states and more time panting during the training sessions, showed higher elevations in cortisol levels after training and were more pessimistic in the cognitive bias task than dogs from Group Reward. These findings indicate that the use of aversive-based methods compromises the welfare of companion dogs in both the short- and the long-term.

animal behavior and cognition↗