Biology subjects

Kaufmann, J.

Publications and source records attributed to Kaufmann, J..

11 recordsLinked to original sources

bioRxiv2026

Translational Pharmacokinetics and Pharmacodynamics of a Cationic mRNA-Lipid Nanoparticle from Mice to Non-Human Primates

Cationic lipid nanoparticles have demonstrated unique potential for extrahepatic mRNA delivery, particularly enabling selective targeting of the pulmonary endothelium. However, their translational development has been hampered by reports of infusion-related immune reactions and innate immune system activation, most notably transient complement activation. Here, we present a case study illustrating the discovery and translational advancement of a selected cationic LNP into non-human primates (NHPs) for initial pharmacokinetic assessment and evaluation of potential immunostimulatory side effects. We show surface charge dependent organ-selective expression of reporter mRNAs from different LNPs in vivo. An mRNA encoding the Tie2 agonist COMP-Angl, was formulated with LNP002, and respective pharmacokinetic and pharmacodynamic readouts were analyzed in two independent non-human primate studies. Notably, dose-dependent transient complement activation could be abrogated by extending the infusion time. Finally, we identified the blood-borne pharmacodynamic biomarker PDGFB for LNP002/mRNA-76 treatment reflecting activated Tie2-signalling in healthy pulmonary endothelium in vivo supported by single cell sequencing and cluster-alignment of downstream effector genes with the same spatial profile as the delivered mRNA.

pharmacology and toxicology↗

bioRxiv2026

A targetable dependency on nonsense-mediated decay for proteostasis and immune control in small cell lung cancer

Small cell lung cancer (SCLC) is among the deadliest cancers with excessive somatic alterations, expectedly resulting in immunogenic epitopes. However, patient benefit from immunotherapy is limited. We found abundant frameshift mutations in SCLC, regarded as highly immunogenic, counterbalanced by a hyperactive nonsense-mediated decay (NMD) pathway, responsible for frameshift-mRNA degradation. NMD activity correlated with tumor mutational burden (TMB) across cancers, suggesting that SCLC depends on NMD for cellular homeostasis and immune evasion. NMD inhibition impaired SCLC proliferation and induced ER stress-dependent apoptosis in a TMB-dependent manner, thereby enabling pharmacological inhibition in vivo which effectively controlled tumor growth. By integrating genome and transcriptome sequencing with MHC-I immunopeptidomics and functional in vitro and in vivo assays, we identified that NMD inhibition boosted neoantigen expression and presentation by tumor cells and increased T cell recognition, thus enhancing overall tumor immunogenicity and further improving immunotherapy efficacy in vivo. Our work shows that SCLC - as a TMBhigh cancer - relies on NMD for survival and immune escape, uncovering a novel TMB-dependent tractable vulnerability for this devastating disease.

cancer biology↗

bioRxiv2026

Wash-Free Multi-Target Super-Resolution Microscopy with Photocaged DNA Labels

Super-resolution microscopy with DNA-fluorophore labels is primed for multi-target imaging of cell biological samples. However, direct interaction with the sample is required to exchange or add DNA-fluorophore labels in each imaging round, which can impair the accuracy of the imaging data at the nanometer scale. To bypass this requirement, we introduce a wash-free method that employs DNA oligonucleotides equipped with photocaging groups. Irradiation with light removes these photo-modulatable groups and changes the hybridization properties of DNA labels, enabling light-modulated targeting. We demonstrate this concept by imaging various cellular targets with confocal microscopy, single-molecule localization microscopy, and stimulated emission depletion (STED) microscopy.

biophysics↗

bioRxiv2025

Comparative Analysis of Pathology Foundation Models for Automated Detection of Tertiary Lymphoid Structures in H&E-Stained Digital Pathology Images

Tertiary lymphoid structures (TLS) have been observed in solid tumors and have been associated with better outcomes in patients treated with immunotherapy, but their dynamic nature makes identifying TLS in clinical samples challenging. Recently, pathology foundation models have emerged as powerful tools in computational pathology. In this study, we aimed to develop a computational tool capable of identifying TLS across different cancer types. To this end, we utilized multiple pathology foundation models, along with the ImageNet-pretrained ResNet50 as a baseline, to identify TLS in pancreatic ductal adenocarcinoma (PDAC) and head and neck squamous cell carcinoma (HNSCC) using hematoxylin and eosin (H&E) stained images from The Cancer Genome Atlas (TCGA) and a licensed Real-World Evidence (RWE) cohort. Both pathologist-annotated and transcriptomic signature-based TLS outcomes were employed for performance assessment. Pathologist-identified TLS-positive tumors showed higher expression of TLS signatures in both diseases. Among the models tested, PLIP and CTransPath exhibited strong performance in identifying TLS within PDAC samples (AUC = 0.94 and 0.89, respectively). However, all models struggled in the analysis of HNSCC, likely due to the increased heterogeneity of the tumor microenvironment (TME). Despite their overall utility in detecting TLS in PDAC, all foundation models demonstrated poor performance in predicting transcriptomic signature-based outcomes in both PDAC and HNSCC. This suggests that TLS signatures may reflect broader or more transient aspects of TLS biology, whereas pathology-based assessment anchors on visible morphological features, more closely aligned with the focus of foundation model training. These findings highlight the potential of advanced pathology foundation models for TLS detection and broader tumor immune profiling tasks. These models can also be utilized on routinely collected patient biosamples with nominal costs. However, further refinement is needed to enhance their utility in tumors with more complex TME. Additionally, the identification of transcriptomics-based biomarkers from H&E images remains a significant challenge, despite advancements in digital pathology.

bioinformatics↗

bioRxiv2025

Noradrenaline and Acetylcholine shape Functional Connectivity organization of NREM substages: an empirical and simulation study

Sleep onset is characterized by a departure from arousal, and can be separated into well-differentiated stages: NREM (which encompasses three substages: N1, N2 and N3) and REM (Rapid Eye Movement). Awake brain dynamics are maintained by various wake-promoting mechanisms, particularly the neuromodulators Acetylcholine (ACh) and Noradrenaline (NA), whose levels naturally decrease during the transition to sleep. The combined influence of these neurotransmitters on brain connectivity during sleep remains unclear, as previous models have examined them mostly in isolation or only in deep sleep. In this study, we employ a Whole Brain model to investigate how changes in brain neurochemistry during NREM sleep, specifically involving ACh and NA, affect the Functional Connectivity (FC) of the brain. Using a Wilson-Cowan whole brain model informed by an empirical connectome and a heterogeneous receptivity map of neuromodulators, we explore these dynamics. Initial FC analysis reveals distinct connectivity changes: a decrease in Locus Coeruleus (LC) connectivity with the cortex during N2 and N3, and a decrease in Basal Forebrain (BF) connectivity with the cortex during N3. Additionally, compared to Wakefulness (W), there is a transition to a more integrated state in N1 and a more segregated state in N3. We adjust the coupling and input-output slope of the Whole Brain model for ACh and NA, based on BF or LC priors, to show that region-specific neurotransmitter distribution is key to explaining their effects on FC. This work enhances our understanding of neurotransmitters roles in modulating sleep stages and their significant contribution to brain state transitions between different states of consciousness, both in health and disease.

neuroscience↗

bioRxiv2022

Spatial expression of an mRNA encoding Tie2-agonist in the capillary endothelium of the lung prevents pulmonary vascular leakage

Angiopoietin ligands Ang1 and Ang2 and the Tie2 receptor tyrosine kinases form an endothelial signaling pathway regulating vascular homeostasis and controlling vessel permeability, inflammation and angiogenic responses. Whereas Ang1-mediated Tie2 activation reduces inflammation and endothelial permeability, its antagonist, Ang2 increases it. Increased plasma Ang2 levels are associated with poor outcomes in patients with acute lung injury (ALI), as well as in acute respiratory distress syndrome (ARDS). In the study presented here we tested the effect of a novel synthetic, nucleoside-modified mRNA-76 encoding for a hyperactive Ang1 derived fusion protein (COMP-Ang1) on attenuating post-inflammation vascular leakage. COMP-Ang1 mRNA was formulated into a cationic lipid nanoparticle (cLNP) using an optimized mixture of three different lipids and a microfluidic mixing technology. After intravenous injection, the respective mRNA-loaded LNPs were found to be delivered predominantly to the endothelial cells of the lung, while sparing other vascular beds. Also, the specific multimeric folding of the COMP-Ang1 protein complex appeared to be pivotal for its activity in preventing vascular leakage and in restoring the alveolar-endothelial barrier function in the inflamed and injured pulmonary vasculature. The mode of action of mRNA-76, such as its activation of the Tie2 signal transduction pathway, was tested by pharmacological studies in vitro and in vivo by systemic administration in respective mouse models. mRNA-76 was found to prevent lung vascular leakage/lung edema as well as neutrophil infiltration in an LPS-challenging model.

molecular biology↗

bioRxiv2022

A bead-based GPCR phosphorylation immunoassay for high-throughput ligand profiling and GRK inhibitor screening

Analysis of agonist-driven phosphorylation of G protein-coupled receptors (GPCRs) can provide valuable insights into the receptor activation state and ligand pharmacology. However, to date, assessment of GPCR phosphorylation using high-throughput applications has been challenging. We have developed and validated a bead-based immunoassay for the quantitative assessment of agonist-induced GPCR phosphorylation that can be performed entirely in multiwell cell culture plates. The assay involves immunoprecipitation of affinity-tagged receptors using magnetic beads followed by protein detection using phosphorylation-state-specific and phosphorylation state-independent anti-GPCR antibodies. As proof of concept, five prototypical GPCRs (MOP, C5a1, D1, SST2, CB2) were treated with different agonists and antagonists, and concentration-response curves were generated. We then extended our approach to establish selective cellular GPCR kinase (GRK) inhibitor assays, which led to the rapid identification of a selective GRK5/6 inhibitor (LDC8988) and a highly potent pan-GRK inhibitor (LDC9728). In conclusion, this versatile GPCR phosphorylation assay can be used extensively for ligand profiling and inhibitor screening.

pharmacology and toxicology↗

bioRxiv2020

In-situ non-lethal rapid test to accurately detect the presence of the nematode parasite, Anguillicoloides crassus, in European eel, Anguilla anguilla.

Anguillicoloides crassus is an invasive nematode parasite of the European eel, Anguilla anguilla, and one of the primary drivers of eel population collapse. The presence of the parasite has been shown to impact many features of eel physiology and life history. Early detection of the parasite is vital to limit the spread of A. crassus. However, until recently, accurate diagnosis of infection could only be achieved via terminal dissection. To support A. anguilla fisheries management in the context of A. crassus we developed a rapid non-lethal and non-invasive environmental DNA method to detect the presence of the parasite in the swim bladder. Screening of 131 wild eels was undertaken between 2017 and 2019 Ireland and UK to validate the procedure. DNA extractions and PCR were conducted using both a Qiagen Stool kit at Glasgow University and in situ using Whatman qualitative filter paper No. 1 and a miniPCR DNA Discovery System. Primers were specifically designed from the cytochrome oxidase mtDNA gene region. In situ extraction and amplification takes approx. 3h for up to 16 individuals with higher specificity and sensitivity compare to the laboratory Qiagen kit extraction. The local diagnostic procedure demonstrated Positive Predictive Values at 96% and Negative Predictive Values at 87%. Our method will be a powerful tool in the hands of fisheries managers to help protect this iconic but critically endangered species. It will allow a non-invasive monitoring of the A. crassus dispersion across the European waters.

ecology↗

bioRxiv2019

Triple visual hemifield maps in optic chiasm hypoplasia

In humans, each hemisphere comprises an overlay of two visuotopic maps of the contralateral visual field, one from each eye. Is the capacity of the visual cortex limited to these two maps or are plastic mechanisms available to host more maps? Using an integrative approach of submillimeter fMRI, diffusion-weighted imaging and population receptive field mapping, we found three hemiretinal inputs to converge onto the left hemisphere in a rare individual with chiasma hypoplasia. This generates extremely atypical responses in striate and extrastriate cortices, specifically an overlay of three hemifield representations. Unexpectedly, the effects of this large abnormality on visual function in daily life are not easily detected. We conclude that developmental plasticity including the re-wiring of local intra- and cortico-cortical connections is pivotal to support the coexistence and functioning of three hemifield maps within one hemisphere.

neuroscience↗

bioRxiv2019

Quantifying nerve decussation abnormalities in the optic chiasm

ObjectiveThe human optic chiasm comprises partially crossing optic nerve fibres. Here we used diffusion MRI (dMRI) for the in-vivo identification of the abnormally high proportion of crossing fibres found in the optic chiasm of people with albinism.\n\nMethodsIn 9 individuals with albinism and 8 controls high-resolution 3T dMRI data was acquired and analyzed with a set of methods for signal modeling [Diffusion Tensor (DT) and Constrained Spherical Deconvolution (CSD)], tractography, and streamline filtering (LiFE, COMMIT, and SIFT2). The number of crossing and non-crossing streamlines and their weights after filtering entered ROC-analyses to compare the discriminative power of the methods based on the area under the curve (AUC). The dMRI results were cross-validated with fMRI estimates of misrouting in a subset of 6 albinotic individuals.\n\nResultsWe detected significant group differences in chiasmal crossing for both unfiltered DT (p=0.014) and CSD tractograms (p=0.0009) also reflected by AUC measures (for DT and CSD: 0.61 and 0.75, respectively), underlining the discriminative power of the approach. Estimates of crossing strengths obtained with dMRI and fMRI were significantly correlated for CSD (R2=0.83, p=0.012). The results show that streamline filtering methods in combination with probabilistic tracking, both optimized for the data at hand, can improve the detection of crossing in the human optic chiasm.\n\nConclusionsEspecially CSD-based tractography provides an efficient approach to detect structural abnormalities in the optic chiasm. The most realistic results were obtained with filtering methods with parameters optimized for the data at hand.\n\nSignificanceOur findings demonstrate a novel anatomy-driven approach for the individualized diagnostics of optic chiasm abnormalities.\n\nHighlightsO_LIDiffusion MRI is capable of detecting structural abnormalities of the optic chiasm.\nC_LIO_LIQuantification of crossing strength in optic chiasm is of promise for albinism diagnostics.\nC_LIO_LIOptic chiasm is a powerful test model for neuroimaging methods resolving crossing fibers.\nC_LI

neuroscience↗

bioRxiv2019

MerMAIDs: A novel family of metagenomically discovered, marine, anion-conducting and intensely desensitizing channelrhodopsins.

Channelrhodopsins (ChRs) are algal light-gated ion channels widely used as optogenetic tools for manipulating neuronal activity. ChRs desensitize under continuous bright-light illumination, resulting in a significant decline of photocurrents. We describe a novel, metagenomically identified family of phylogenetically distinct anion-conducting ChRs (designated MerMAIDs). MerMAIDs almost completely desensitize during continuous illumination due to accumulation of a late non-conducting photointermediate that disrupts the ion permeation pathway. MerMAID desensitization can be fully explained by a single photocycle in which a long-lived desensitized state follows the short-lived conducting state. A conserved cysteine is the critical factor in desensitization, as its mutation results in recovery of large stationary photocurrents. The rapid desensitization of MerMAIDs enables their use as optogenetic silencers for transient suppression of individual action potentials without affecting subsequent spiking during continuous illumination. Our results could facilitate the development of further novel optogenetic tools from metagenomic databases and enhance general understanding of ChR function.

biophysics↗