Biology subjects

Mueller, P.

Publications and source records attributed to Mueller, P..

17 recordsLinked to original sources

bioRxiv2026

Systemic stress states are reversed by NPBWR1 inhibition

Chronic stress is widely studied as a brain-centered driver of depression, yet its effects across the body remain unclear. Here, we define chronic stress as a coordinated molecular state across tissues in mice. Using a whole-body proteomic atlas of 13 tissues, we find that stress effects are strongest in peripheral metabolic and endocrine organs, whereas classical stress-associated brain regions show comparatively modest changes. Cross-organ analyses reveal structured, tissue-specific responses rather than uniform shifts. Inhibition of the stress-regulated receptor NPBWR1 reverses both behavioral deficits and proteomic alterations across organs in both sexes, indicating that this state is dynamically modifiable. Integration with human serum proteomics identifies shared, sex-specific signatures. Across tissues, lipid metabolism emerges as a common stress-responsive pathway, confirmed by hepatic lipid remodeling that is normalized by NPBWR1 inhibition. To facilitate exploration of these data, we provide an interactive cross-organ web-based resource. Together, these findings challenge the brain-centric view of stress pathology and define chronic stress as an organism-wide molecular state.

systems biology↗

bioRxiv2025

Decades-long elevation of interferon-alpha drives a Sjogren disease endotype: an interdisciplinary study

BACKGROUNDMechanistic heterogeneity is a major obstacle to the development of effective treatment for Sjogren disease (SjD) and there is a pressing need to stratify SjD according to precision medicine principles. Aberrant activation of the type I interferon (IFN) pathway represents a leading candidate pathway, but a causal role of elevated IFN- in driving a Sjogren disease endotype remains to be established. METHODSWe used ultrasensitive single molecule ELISA, and an oligoprotein interferon signature score (derived from broad capture proteomics), to study the role of IFN- in Sjogren disease. We analysed samples from the UK Primary Sjogren Syndrome Registry (UKPSSR, n=177) and UK Biobank Plasma Proteomics Project (n=47606 without Sjogren, n=257 with Sjogren, including 137 individuals sampled prior to diagnosis) to determine the timecourse and immune endotype associated with elevated IFN-. To address causality we created a new transgenic mouse model of IFN- overexpression to establish whether chronically elevated IFN- drives this immune endotype. FINDINGSOligoprotein interferon signatures can be detected at least 14 years prior to diagnosis of Sjogren disease in the UK Biobank-PPP. IFN- concentrations are elevated in 60% of Sjogren disease patients in the UKPSSR. Individuals with elevated IFN- display a distinct immunological endotype characterised by cytopenias, hypergammaglobulinaemia, multiple autoantibodies and autoimmunity against the Sjogren autoantigen TRIM21/Ro52. To address the key question of causal direction, we created a new mouse model of systemic chronic IFN- elevation, in which Ifn4 is overexpressed by conventional dendritic cells. This model recapitulates key features of the endotype and can be partially reversed by IFNAR1 blockade. INTERPRETATIONElevation of IFN- drives an immune endotype of Sjogren disease, originating over a decade prior to diagnosis. SjD patients with elevated IFN- concentrations are broadly clinically similar to those with normal IFN- concentrations, yet are immunologically distinct. This highlights the mechanistic heterogeneity of SjD and the need for immunological stratification along precision medicine principles, using high resolution biomarkers. As well as demonstrating causal direction, biological modelling shows that chronic IFN- elevation over the lifecourse has the potential to establish persistent immune dysregulation which responds only partially to interferon receptor blockade. These findings provide insights into SjD and other "interferonopathic" rheumatological disorders. Research in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched MEDLINE for "Sjogrens Syndrome/Disease" and "interferon", including the terms "subsets", "sub-groups", "phenotypes", and "endotypes", filtering by "clinical trial", "stratification", and "immune-mediated inflammatory". We also included major review articles from noted experts. We identified reports of associations between IFN- and SjD, usually using indirect or imprecise measures of IFN-. None of these studies included prediagnostic samples and causal inference was limited. Added value of this studyThis study shows that IFN-, when measured directly using ultrasensitive single molecule ELISA approaches (uniquely optimised to determine healthy control concentrations), is elevated in a subset of people with SjD with a specific immunological endotype. Analysis of prediagnostic proteomics shows this elevation can be detected up to 14 years before diagnosis. We show that IFN- drives this endotype (as opposed to vice versa) by recapitulating key endotype features in a novel and unambiguous experimental mouse model of chronic IFN- elevation. We also show that the pathogenic consequences of IFN- elevation over long periods of time can only be partially reversed using IFNAR blockade. Implications of all the available evidenceThese data have important implications for future research, clinical practice, trial design, and therapeutic development. First, our findings provide clinical evidence, supported by unambiguous preclinical evidence, that decades-long elevated IFN can cause and drive a SjD endotype - and accurately defines the level of heterogeneity. Secondly, we provide biomarkers which may be of use in stratifying clinical trial design and also for early identification of at-risk individuals. Thirdly we provide biological proof of principle that longstanding and potentially undiagnosed elevation of IFN- can establish persistent immune dysregulation which may respond only partially to IFNAR blockade. Together these findings inform precision medicine approaches and future trial design.

immunology↗

bioRxiv2025

Spatially aligned random partition models on spatially resolved transcriptomics data

We propose spatially aligned random partition (SARP) models for clustering multiple types of experimental units, incorporating dependence in a subvector of the cluster-specific parameters, e.g., a subvector of spatial information, as in the motivating application. The approach is developed for inference about co-localization of immune, stromal, and tumor cell sub-populations. The aim is to understand the recruitment of immune and stromal cell subtypes by tumor cells, formalized as spatial dependence of the corresponding homogeneous cell subpopulations. This is achieved by constructing Bayesian nonparametric random partition models for the different types of cells, with a hierarchically structured prior introducing the desired dependence. Specifically, we use Pitman-Yor priors and add dependence in the base measure for spatial features, while leaving the base measure corresponding to gene expression features a priori independent across different types of cells. Details of the model construction are designed to lead to a convenient MCMC algorithm for posterior inference. Simulation studies show favorable performance in identifying co-localization between types of cells. We apply the proposed approach with colorectal cancer (CRC) data and discover subtypes of immune and stromal cells that are spatially aligned with specific tumor regions.

bioinformatics↗

bioRxiv2025

Cytochrome P450 inhibition impedes pyrethroid effects on insects through Nav channel regulation

Insecticides used in various formulations are inevitable in agricultural pest control and prevention of vector-borne diseases. Piperonyl butoxide (PBO) is a synergist widely used to enhance the effectiveness of insecticides, notably pyrethroids, by inhibiting the detoxifying cytochrome P450 enzymes, thus reducing the capacity of insects to metabolize and resist insecticides. Recent studies, however, reveal an unexpectedly weak restoration of pyrethroid efficacy by PBO, but the underlying mechanism is unknown. Here, we demonstrate that the PBO-induced inhibition of cytochrome P450 impedes the effect of deltamethrin by mainly affecting its interaction with the inactivated state of voltage-gated sodium channels (Nav). We describe a new octopamine-dependent regulatory mechanism involving Gs, PKA, DARPP-32, and PP1-2A, which affect the cytochrome P450 conformation, thus limiting the effect of PBO and modulating the Nav gating. As a result, deltamethrin cannot reach its final binding site in the fenestration to exert its full effect. We confirmed in vivo that under chemical stressor, the level of octopamine is elevated, which decreases the deltamethrin efficacy. Our findings reveal a novel adaptation mechanism that increases insect survival by reducing insecticide efficacy, thus emphasizing the necessity of developing more effective formulations and technologies for pest and vector control.

pharmacology and toxicology↗

bioRxiv2024

Proton-pump inhibitors increase C. difficile infection risk by altering pH rather than by affecting the gut microbiome based on a bioreactor model

Clostridioides difficile infections often occur after antibiotic use, but they have also been linked to proton-pump inhibitor (PPI) therapy. The underlying mechanism--whether infection risk is due to a direct effect of PPIs on the gut microbiome or changes in gastrointestinal pH--has remained unclear. To disentangle both possibilities, we studied the impact of the proton-pump inhibitor omeprazole and pH changes on key members of the human gut microbiome and stool-derived microbial communities from different donors in vitro. We then developed a custom multiple-bioreactor system to grow a model human microbiome community in chemostat mode and tested the effects of omeprazole exposure, pH changes, and their combination on C. difficile growth within this community. Our findings show that changes in pH significantly affect the gut microbial communitys biomass and the abundances of different strains, leading to increased C. difficile growth within the community. However, omeprazole treatment alone did not result in such effects. These findings imply that the higher risk of C. difficile infection following proton-pump inhibitor therapy is probably because of alterations in gastrointestinal pH rather than a direct interaction between the drug and the microbiome. This understanding paves the way for reducing infection risks in proton-pump inhibitor therapy.

microbiology↗

bioRxiv2024

Optical quantification of molecular interaction strength in protein condensates

Biomolecular condensates have been identified as a ubiquitous means of intracellular organization, exhibiting very diverse material properties. However, techniques to characterize these material properties and their underlying molecular interactions are scarce. Here, we introduce two optical techniques - Brillouin microscopy and quantitative phase imaging (QPI) - to address this scarcity. We establish Brillouin shift and linewidth as measures for average molecular interaction and dissipation strength, respectively, and we used QPI to obtain the protein concentration within the condensates. We monitored the response of condensates formed by FUS and by the low-complexity domain of hnRNPA1 (A1-LCD) to altering temperature and ion concentration. Conditions favoring phase separation increased Brillouin shift, linewidth, and protein concentration. In comparison to solidification by chemical crosslinking, the ion-dependent aging of FUS condensates had a small effect on the molecular interaction strength inside. Finally, we investigated how sequence variations of A1-LCD, that change the driving force for phase separation, alter the physical properties of the respective condensates. Our results provide a new experimental perspective on the material properties of protein condensates. Robust and quantitative experimental approaches such as the presented ones will be crucial for understanding how the physical properties of biological condensates determine their function and dysfunction.

biophysics↗

bioRxiv2024

Environmental controls of dark CO2 fixation in wetland microbiomes

Rising atmospheric concentration of CO2 is a major concern to society due to its global warming potential. In soils, CO2 fixing microorganisms are preventing a part of the CO2 from entering the atmosphere. Yet, the pathways behind dark CO2 fixation are rarely studied in situ. Here we examined the environmental controls on the abundance and expression of key genes involved in microbial CO2 fixation in estuarine wetlands. A combined multi-omics approach incorporating metabarcoding, deep metagenomic and metatranscriptomic analyses confirmed that wetland microbiota harbor all six known CO2 fixation pathways and that these pathways are transcribed at high frequencies along several environmental gradients, albeit at different levels depending on the environmental niche. Notably, the transcription of the key genes for the reductive tricarboxylic acid cycle (rTCA) and the Calvin cycle were favored by low salinity and O2 rich niches high in organic matter, while the transcription of the key genes for the Wood-Ljungdahl pathway (WLP) and dicarboxylate/4-hydroxybutyrate cycle (DC/4-HB cycle) were favored by low O2 niches poor in organic matter. Taxonomic assignment of transcripts implied that dark CO2 fixation was mainly linked to few bacterial phyla, namely, Desulfobacterota, Gemmatimonadota, Methylomirabilota, Nitrospirota and Pseudomonadota.

microbiology↗

bioRxiv2023

Non-antibiotic drugs break colonization resistance against pathogenic Gammaproteobacteria

Non-antibiotic drugs can alter the composition of the gut microbiome, with largely undefined implications for human health. Here we compared the susceptibility of commensal and pathogenic bacteria to non-antibiotic drugs and found that pathogens show higher drug resistance, which could favor their expansion after treatment. We then developed a model system to screen for drug-microbiome interactions that increase the risk of enteropathogenic infections. Approximately 35% of the >50 drugs we tested increased the abundance of Salmonella Typhimurium in synthetic and human stool-derived microbial communities. This was due to direct effects of non-antibiotics on individual commensals, altered microbial interactions within communities and the potential of Salmonella to exploit different metabolic niches. Non-antibiotic drugs that favored Salmonella expansion in vitro also promoted other enteric pathogens and increased Salmonella loads in gnotobiotic and conventional mice. These findings may inform future strategies to control pathogen proliferation and to assess individual microbiota-drug-pathogen risks for infection.

microbiology↗

bioRxiv2023

Immune Profiling among Colorectal Cancer Subtypes using Dependent Mixture Models

Comparison of transcriptomic data across different conditions is of interest in many biomedical studies. In this paper, we consider comparative immune cell profiling for early-onset (EO) versus late-onset (LO) colorectal cancer (CRC). EOCRC, diagnosed between ages 18-45, is a rising public health concern that needs to be urgently addressed. However, its etiology remains to be poorly understood. We work towards filling this gap by identifying homogeneous T cell subpopulations that show significantly distinct characteristics across the two tumor types, and to identify others that are shared between EOCRC and LOCRC. Such inference may reveal underlying determinants of clinically observed differences in the two disease subpopulations. We develop dependent finite mixture models where immune subtypes enriched under a specific condition are characterized by terms in the mixture model with common atoms but distinct weights across conditions, whereas common subtypes are characterized by sharing both atoms and relative weights. The proposed model defines a variation of mixtures of finite mixture models, facilitating the desired comparison by introducing highly structured multi-layer Dirichlet priors. The model allows us to explicitly compare features across conditions. We illustrate inference with simulation studies and data examples. Results identify EO-enriched and LO-enriched T cells subtypes whose biomarkers are found to be linked to mechanisms of tumor progression. The findings reveal distinct characteristics of the immune profiles in EOCRC and LOCRC, and potentially motivate insights into treatment and management of CRC.

bioinformatics↗

bioRxiv2022

Analysis of SMAD1/5 target genes in a sea anemone reveals ZSWIM4-6 as a novel BMP signaling modulator

BMP signaling has a conserved function in patterning the dorsal-ventral body axis in Bilateria and the directive axis in anthozoan cnidarians. So far, cnidarian studies have focused on the role of different BMP signaling network components in regulating pSMAD1/5 gradient formation. Much less is known about the target genes downstream of BMP signaling. To address this, we generated a genome-wide list of direct pSMAD1/5 target genes in the anthozoan Nematostella vectensis, several of which were conserved in Drosophila and Xenopus. Our ChIP-Seq analysis revealed that many of the regulatory molecules with documented bilaterally symmetric expression in Nematostella are directly controlled by BMP signaling. Among the so far uncharacterized BMP-dependent transcription factors and signaling molecules we identified several, whose bilaterally symmetric expression may be indicative of their involvement in secondary axis patterning. One of these molecules, zswim4-6, encodes a novel nuclear modulator of the pSMAD1/5 gradient potentially promoting BMP-dependent gene repression. Strikingly, overexpression of the zebrafish homologue zswim5 suggests that its effect on the pSMAD1/5 gradient is conserved between anthozoan Cnidaria and Bilateria.

developmental biology↗

bioRxiv2022

Single-molecule tracking of Nodal and Lefty in live zebrafish embryos supports hindered diffusion model

The influential hindered diffusion model postulates that the global movement of a signaling molecule through an embryo is affected by local tissue geometry and binding-mediated hindrance, but these effects have not been directly demonstrated in vivo for any signaling molecule. Nodal and Lefty are a prime example of an activator-inhibitor signaling pair whose different global diffusivities are thought to arise from differential hindrance. Here, we used single-molecule tracking of Nodal and Lefty to directly probe the tenets of the hindered diffusion model on the nanoscale. We visualized individual fluorescently-tagged Nodal and Lefty molecules in developing zebrafish embryos using reflected light-sheet microscopy. Single-particle tracking revealed molecules in three states: molecules diffusing in extracellular cavities, molecules diffusing within cell-cell interfaces, and molecules bound to cell membranes. While the diffusion coefficients of molecules were high in extracellular cavities, mobility was reduced and bound fractions were higher within cell-cell interfaces; counterintuitively, molecules nevertheless accumulated in cavities. Using agent-based simulations, we identified the geometry of the extracellular space as a key factor influencing the accumulation of molecules in cavities. For Nodal, the fraction of molecules in the bound state was larger than for Lefty, and individual Nodal molecules had binding times of tens of seconds. Together, our single-molecule measurements and simulations provide direct support for the hindered diffusion model in a developing embryo and yield unprecedented insights into the nanometer to micrometer scale transport mechanisms that together lead to macroscopic signal dispersal and gradient formation.

biophysics↗

bioRxiv2021

Experimental platform for the functional investigation of membrane proteins in giant unilamellar vesicles

Giant unilamellar vesicles (GUVs) are micrometer-sized model membrane systems that can be viewed directly under the microscope. They serve as scaffolds for the bottom-up creation of synthetic cells, targeted drug delivery and have been used in many in vitro studies of membrane related phenomena. GUVs are also of interest for the functional investigation of membrane proteins that carry out many key cellular functions. A major hurdle to a wider application of GUVs in this field is the diversity of existing protocols that are optimized for individual proteins. Here, we compare PVA assisted and electroformation techniques for GUV formation under physiologically relevant conditions, and analyze the effect of immobilization on vesicle structure and membrane tightness towards small substrates and protons. There, differences in terms of yield, size, and leakage of GUVs produced by PVA assisted swelling and electroformation were found, dependent on salt and buffer composition. Using fusion of oppositely charged membranes to reconstitute a model membrane protein, we find that empty vesicles and proteoliposomes show similar fusion behavior, which allows for a rapid estimation of protein incorporation using fluorescent lipids.

synthetic biology↗

bioRxiv2019

Comprehensive identification of HSP70/HSC70 Chaperone Clients in Human Cells

The HSP70 family of chaperones are the front-line of protection from stress-induced misfolding and aggregation of polypeptides in most organisms and are responsible for promoting the stability, folding, and degradation of clients to maintain cellular protein homeostasis. Here we demonstrate quantitative identification of HSP70 and HSC70 clients using an ubiquitin-mediated proximity tagging strategy and show that, despite their high degree of similarity, these enzymes have largely non-overlapping specificities. Both proteins show a preference for association with newly synthesized polypeptides but each responds differently to changes in the stoichiometry of proteins in obligate multi-subunit complexes. In addition, expression of an ALS-associated SOD1 mutant protein induces changes in HSP70 and HSC70 client association and aggregation toward polypeptides with predicted disorder, indicating that there are global effects from a single misfolded protein that extend to many clients within chaperone networks. Together these findings show that the ubiquitin-mediated UBAIT fusion system can efficiently isolate the complex interactome of HSP chaperone family proteins under normal and stress conditions.

molecular biology↗

bioRxiv2018

Standardized microgel beads as elastic cell mechanical probes

Cell mechanical measurements are gaining increasing interest in biological and biomedical studies. However, there are no standardized calibration particles available that permit the cross-comparison of different measurement techniques operating at different stresses and time-scales. Here we present the rational design, production, and comprehensive characterization of poly-acylamide (PAAm) microgel beads mimicking biological cells. We produced mono-disperse beads at rates of 20 - 60 kHz by means of a microfluidic droplet generator, where the pre-gel composition was adjusted to tune the beads elasticity in the range of cell and tissue relevant mechanical properties. We verified bead homogeneity by optical diffraction tomography and Brillouin microscopy. Consistent elastic behavior of microgel beads at different shear rates was confirmed by AFM-enabled nanoindentation and real-time deformability cytometry (RT-DC). The remaining inherent variability in elastic modulus was rationalized using polymer theory and effectively reduced by sorting based on forward-scattering using conventional flow cytometry. Our results show that PAAm microgel beads can be standardized as mechanical probes, to serve not only for validation and calibration of cell mechanical measurements, but also as cell-scale stress sensors.\n\nSignificance StatementOften vastly different cell mechanical properties are reported even for the same cell type when employing different measurement techniques. This discrepancy shows the urgent need for standardized calibration particles to cross-compare and validate techniques. Microgel beads can serve this purpose, but they have to fulfil specific requirements such as homogeneity, sizes and elasticities in the range of the cells, and they have to provide comparable results independent of the method applied. Here we demonstrate the standardized production of polyacrylamide microgel beads with all the features an elastic cell-mimic should have. These can not only be used as method calibration particles, but can also serve as cell-scale sensors to quantify normal and shear stresses exerted by other cells and inside tissues, enabling many new applications.

biophysics↗

bioRxiv2018

A conserved regulatory program drives emergence of the lateral plate mesoderm

Cardiovascular lineages develop together with kidney, smooth muscle, and limb connective tissue progenitors from the lateral plate mesoderm (LPM). How the LPM initially emerges and how its downstream fates are molecularly interconnected remain unknown. Here, we isolated a pan-LPM enhancer in the zebrafish draculin (drl) gene that provides specific LPM reporter activity from early gastrulation. In toto live imaging and lineage tracing of drl-based reporters captured the dynamic LPM emergence as lineage-restricted mesendoderm field. The drl pan-LPM enhancer responds to the transcription factors EomesoderminA, FoxH1, and MixL1 that combined with Smad activity drive LPM emergence. We uncovered specific drl reporter activity in LPM-corresponding territories of several chordates including chicken, axolotl, lamprey, Ciona, and amphioxus, revealing a universal upstream LPM program. Altogether, our work provides a mechanistic framework for LPM emergence as defined progenitor field, possibly representing an ancient mesodermal cell state that predates the primordial vertebrate embryo.

developmental biology↗

bioRxiv2017

Paracrine Activin-A Signaling Promotes Melanoma Growth And Metastasis Through Immune Evasion

The secreted growth factor Activin-A of the TGF{beta} family and its receptors can promote or inhibit several cancer hallmarks including tumor cell proliferation and differentiation, vascularization, lymphangiogenesis and inflammation. However, a role in immune evasion and its relationship with tumor-induced muscle wasting and tumor vascularization, and the relative contributions of autocrine versus paracrine Activin signaling remain to be evaluated. To address this, we compared the effects of truncated soluble Activin receptor II B as a ligand trap, or constitutively active mutant type IB receptor versus secreted Activin-A or the related ligand Nodal in mouse and human melanoma cell lines and tumor grafts. We found that while cell-autonomous receptor activation arrested tumor cell proliferation, Activin-A secretion stimulated melanoma cell dedifferentiation and tumor vascularization by functional blood vessels, and it increased primary and metastatic tumor burden and muscle wasting. Importantly, in mice with impaired adaptive immunity, the tumor-promoting effect of Activin-A was lost despite sustained vascularization and cachexia, suggesting that Activin-A promotes melanoma progression by inhibiting anti-tumor immunity. Paracrine Activin-A signaling emerges as a potential target for personalized therapies, both to reduce cachexia and to enhance the efficacy of immunotherapies.

cancer biology↗

bioRxiv2017

Estimation of Pairwise Genetic Distances Under Independent Sampling of Segregating Sites vs. Haplotype Sampling

Genetic distance is a standard measure of variation in populations. When sequencing genomes individually, genetic distances are computed over all pairs of multilocus haplotypes in a sample. However, when next-generation sequencing methods obtain reads from heterogeneous assemblages of genomes (e.g. for microbial samples in a biofilm or cells from a tumor), individual reads are often drawn from different genomes. This means that pairwise genetic distances are calculated across independently sampled sites rather than across haplotype pairs. In this paper, we show that while the expected pairwise distance under whole haplotype sampling (WHS) is the same as with independent locus sampling (ILS), the sample variances of pairwise distance differ and depend on the direction and magnitude of linkage disequilibrium (LD) among polymorphic sites. We derive a weighted LD value that, when positive, predicts higher sample variance in estimated genetic distance for WHS. Weighted LD is positive when on average, the most common alleles at two loci are in positive LD. Using individual-based simulations of an infinite sites model under Fisher-Wright genetic drift, variances of estimated genetic distance are found to be almost always higher under WHS than under ILS, suggesting a reduction in estimation error when sites are sampled independently. We apply these results to haplotype frequencies from a lung cancer tumor to compute weighted LD and the variances in estimated genetic distance under ILS vs. WHS, and find that the the relative magnitudes of variances under WHS vs. ILS are sensitive to sampled allele frequencies.

genetics↗