Biology subjects

Weber, A.

Publications and source records attributed to Weber, A..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

The proximity-based protein interaction landscape of the transcription factor p65 NF-kappaB/RELA and its gene-regulatory logics

The protein interactome of p65 / RELA, the most active subunit of the transcription factor (TF) NF-{kappa}B, has not been previously determined in living cells. Using p65-miniTurbo fusion proteins, we identified by biotin tagging > 350 RELA interactors from untreated and IL-1-stimulated cells, including many TFs (47 % of all interactors) and > 50 epigenetic regulators belonging to different classes of chromatin remodeling complexes. According to point mutants of p65, the interactions primarily require intact dimerization rather than DNA binding properties. A targeted RNAi screen for 38 interactors and subsequent functional transcriptome and bioinformatics studies identified gene regulatory (sub)networks, each controlled by RELA in combination with one of the TFs ZBTB5, GLIS2, TFE3 / TFEB or S100A8 / A9. The remarkably large, dynamic and versatile high resolution interactome of RELA and its gene-regulatory logics provides a rich resource and a new framework for explaining how RELA cooperativity determines gene expression patterns. HighlightsO_LIIdentification of > 350 largely dimerization-dependent interactors of p65 / RELA by miniTurboID C_LIO_LIThe interactome is dominated by transcription factors and epigenetic regulator complexes C_LIO_LIFunctional validation of 38 high confidence interactors by targeted siRNA screen C_LIO_LIIdentification of genetic networks regulated by RELA and six of its interactors in the IL-1 response C_LI

molecular biology↗

bioRxiv2023

Benchmarking sample pooling for epigenomics of natural populations

Interest in the role of DNA methylation (DNAm) has grown in ecological and evolutionary research of natural populations. While researchers are typically interested in comparing population-level variation, individual sequencing is the current standard. Natural populations have low effect sizes and thus need large sample sizes to detect differences. The cost of sequencing the necessary samples can be prohibitive in DNAm work. Pooling DNA before library preparation is a powerful tool to reduce costs but no recommendations exist for DNAm pooling in ecology-epigenetics research. We test if pooled and individual libraries provide similar global and region-specific DNA methylation signals in a natural system of response to pollution. We generated whole-epigenome data for two freshwater invasive molluscs (Corbicula flumina and Dreissena polymorpha) collected from a polluted and unpolluted locality, Lake Maggiore, Italy. Our results support that pooling effectively captures the same genome-wide and global treatment-level signals as individual libraries but we note that pooled libraries yielded orders of magnitude more input data and differentially-methylated regions (DMRs) detected compared with individual libraries. We estimated greatly lower power for regions from individual libraries compared with pooled libraries. The post-hoc process of computationally pooling data from individual libraries produced results comparable to pooled libraries in volumes but had discrepancies between DMRs. We discuss the possible causes for the discrepancies and put our results in the context of the benefits and drawbacks of sample pooling for epigenomics of natural populations.

genomics↗

bioRxiv2023

Predmoter - Cross-species prediction of plant promoter and enhancer regions

MotivationThe identification of cis-regulatory elements (CREs) is crucial for the analysis of gene regulatory networks in plants. Several next generation sequencing (NGS)-based methods were developed to identify CREs. However, these methods can be time-consuming and costly. They also involve creating sequencing libraries for the entire genome. Since many research efforts only focus on specific genomic loci, this presents a considerable expenditure. Computational prediction of the outputs of specialized NGS methods to analyze CREs, like Assay for Transposase Accessible Chromatin using sequencing (ATAC-seq), would significantly cut costs and time investment. Yet, no such method is available to date. ResultsWe present Predmoter, a deep neural network able to predict base-wise ATAC-seq and histone Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) read coverage for plant genomes. Predmoter uses only the DNA sequence as input. We evaluated our model on two plant genomes, the genome of the dicot Arabidopsis thaliana and of the monocot Oryza sativa. We trained our models on 10 species with publicly available ATAC-seq data and 15 species with ChIP-seq data. Our best models showed accurate predictions in peak positions and the overall pattern of peaks for ATAC- and Histone H3 trimethylated at lysine 4 (H3K4me3) ChIP-seq. Annotating putatively accessible chromatin regions provides valuable input for the identification of CREs. In conjunction with other in silico data, such as predicted binding affinities for transcription factors (TFs), this can significantly narrow down the search space to a manageable number of experimentally verifiable DNA-protein interaction pairs. Availability and ImplementationThe source code for Predmoter is available at: https://github.com/weberlab-hhu/Predmoter along with documentation for installation and usage. Predmoter uses a single-command inference, Predmoter.py, for both training and prediction. Predmoter takes a fasta file as input and outputs an h5 file and optionally bigWig and bedGraph files. HighlightPredmoter will help identifying CREs and so gaining further insight into gene regulatory networks in plants.

bioinformatics↗

bioRxiv2023

Do Domain-Specific Protein Language Models Outperform General Models on Immunology-Related Tasks?

Deciphering the antigen recognition capabilities by T cell and B cell receptors (antibodies) is essential for advancing our understanding of adaptive immune system responses. In recent years, the development of protein language models (PLMs) has facilitated the development of bioinformatic pipelines where complex amino acid sequences are transformed into vectorized embeddings, which are then applied to a range of downstream analytical tasks. With their success, we have witnessed the emergence of domain-specific PLMs tailored to specific proteins, such as immune receptors. Domain-specific models are often assumed to possess enhanced representation capabilities for targeted applications, however, this assumption has not been thoroughly evaluated. In this manuscript, we assess the efficacy of both generalist and domain-specific transformer-based embeddings in characterizing B and T cell receptors. Specifically, we assess the accuracy of models that leverage these embeddings to predict antigen specificity and elucidate the evolutionary changes that B cells undergo during an immune response. We demonstrate that the prevailing notion of domain-specific models outperforming general models requires a more nuanced examination. We also observe remarkable differences between generalist and domain-specific PLMs, not only in terms of performance but also in the manner they encode information. Finally, we observe that the choice of the size and the embedding layer in PLMs are essential model hyperparameters in different tasks. Overall, our analyzes reveal the promising potential of PLMs in modeling protein function while providing insights into their information-handling capabilities. We also discuss the crucial factors that should be taken into account when selecting a PLM tailored to a particular task.

bioinformatics↗

bioRxiv2023

Simulated complexes formed from a set of postsynaptic proteins suggest a localised effect of a hypomorphic Shank mutation

The postsynaptic density is an elaborate protein network beneath the postsynaptic membrane built up from the same major proteins but differing between synapses in exact composition and organization. Mutations perturbing generally occurring protein:protein interactions in this network can lead to specific effects, and the translation of biochemical effects to the system level can be especially challenging. In this work we use systems biology-based modeling of protein complex distributions in a set of major postsynaptic proteins including either a wild-type or a hypomorphic PDZ mutant Shank protein. Our results suggest that the effect of such mutations is heavily dependent on the overall availability of the protein components of the whole network. We simulated protein complex formation based on experimental data of various cell types with diverse protein abundances. The simulations revealed that mutations interfering with a single protein interaction can lead to protein complex changes only in specific cell types and in specific complexes. Although our system is currently far from a comprehensive description of the PSD, the results suggest a way to interpret specific mutations within a complex framework. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=69 SRC="FIGDIR/small/562557v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@fdf273org.highwire.dtl.DTLVardef@3891deorg.highwire.dtl.DTLVardef@1f0c37borg.highwire.dtl.DTLVardef@1b1e629_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIEffect of mutations affecting protein:protein interactions can be modeled in context C_LIO_LIChanges in emerging protein complexes upon mutations are dependent on the availability of the individual proteins C_LIO_LIOur model provides conceptual explanation of confided phenotypic effects of a mutation C_LI

systems biology↗

bioRxiv2023

A HEV ORF2 protein-mediated mechanism of hepatitis E associated kidney disease.

Hepatitis E virus (HEV) infection, one of the most common forms of hepatitis worldwide, is often associated with extrahepatic, particularly renal, manifestations. However, the underlying mechanisms are incompletely understood. Here, we report the development of a de novo immune complex-mediated glomerulonephritis (GN) in a kidney transplant recipient with chronic hepatitis E. Applying immunostaining, electron microscopy, and mass spectrometry after laser-capture microdissection, we show that GN developed in parallel with increasing glomerular deposition of a noninfectious form of HEV open reading frame 2 (ORF2, capsid) protein secreted in excess. HEV particles or RNA, however, were not detectable. Patients with acute hepatitis E displayed similar but less pronounced deposits. Our results elucidate an immunologic mechanism by which this hepatotropic virus causes variable renal manifestations and establish a link between the HEV ORF2 protein and hepatitis E-associated GN. They directly provide a tool for etiology-based diagnosis of HEV-associated GN as a distinct entity and suggest therapeutic implications.

pathology↗

bioRxiv2023

Successful regeneration of the adult zebrafish retina is dependent on inflammatory signaling

Inflammation can lead to persistent and irreversible loss of retinal neurons and photoreceptors in mammalian vertebrates. In contrast, in the adult zebrafish brain, acute neural inflammation is both necessary and sufficient to stimulate regeneration of neurons. Here, we report on the critical, positive role of the immune system to support retina regeneration in adult zebrafish. After sterile, ablation of photoreceptors by phototoxicity, we find rapid response of tissue-resident microglia and neutrophils, which returns to homeostatic levels within 14 days post lesion. Pharmacological or genetic impairment of immune cell reactivity results in a reduced Muller glia stem cell response, seen as decreased reactive proliferation, and a strikingly reduced number of regenerated cells from them, including photoreceptors. Conversely, injection of the immune stimulators flagellin, zymosan, or M-CSF into the vitreous of the eye, in spite of the absence of a retinal lesion, leads to a robust proliferation response and the up-regulation of regeneration-associated marker genes in Muller glia. Our results suggest that neuroinflammation is a necessary and sufficient driver for retinal regeneration in the adult zebrafish retina.

developmental biology↗

bioRxiv2023

A common gene signature of the right ventricle in failing rat and human hearts

The molecular mechanisms of progressive right heart failure are incompletely understood. We systematically compared rat models of pulmonary artery or aortic banding to identify the transcriptomic changes that occur over months in the failing right versus left ventricle. Detailed bioinformatics analyses of 181 RNAseq datasets from cardiomyocytes or whole heart samples from these models, led to the identification of gene signatures, protein, and transcription factor networks specific to ventricles, compensated or decompensated disease states and type of heart failure. RNA-FISH approaches confirmed PAB-mediated regulation of key genes and revealed striking, spatially heterogeneous mRNA expression in the heart. Intersection of rat PAB-specific gene sets with 95 transcriptome data sets from human patients with chronic thromboembolic pulmonary hypertension led to the identification of more than 50 genes whose expression levels strongly correlated with the severity of right heart disease. Together, these data define a conserved, differentially regulated genetic network that coordinates progressive right heart failure in rats and humans. HighlightsO_LISide-by-side comparisons of RV or LV transcriptomes in the slowly failing rat heart C_LIO_LIIdentification of RV-specific gene sets in heart hypertrophy versus heart failure C_LIO_LIIdentification of RV gene sets correlating with severity of human CTEPH C_LIO_LIDevelopment of a core gene signature characteristic for RV failure C_LI

genomics↗

bioRxiv2023

scRNAseq unravels the transcriptional network underlying zebrafish retina regeneration

In the lesioned zebrafish retina, Muller glia produce multipotent retinal progenitors that generate all retinal neurons, replacing lost cell types. To study the molecular mechanisms linking Muller glia reactivity to progenitor production and neuronal differentiation, we used single cell RNA sequencing of Muller glia, progenitors and regenerated progeny from uninjured and light-lesioned retinae. We discover an injury-induced Muller glia differentiation trajectory that leads into a cell population with a hybrid identity expressing marker genes of Muller glia and progenitors. A glial self-renewal and a neurogenic trajectory depart from the hybrid cell population. We further observe that neurogenic progenitors progressively differentiate to generate retinal ganglion cells first and bipolar cells last, similar to the events observed during retinal development. Our work provides a comprehensive description of Muller glia and progenitor transcriptional changes and fate decisions in the regenerating retina, which are key to tailor cell differentiation and replacement therapies for retinal dystrophies in humans.

developmental biology↗

bioRxiv2022

Application of self-organizing maps to AFM-based viscoelastic characterization of breast cancer cell mechanics

Cell mechanical properties have been proposed as label free markers for diagnostic purposes in diseases such as cancer. Cancer cells show altered mechanical phenotypes compared to their healthy counterparts. Atomic Force Microscopy (AFM) is a widely utilized tool to study cell mechanics. These measurements often need skilful users, physical modelling of mechanical properties and expertise in data interpretation. Together with the need to perform many measurements for statistical significance and to probe wide enough areas in tissue structures, the application of machine learning and artificial neural network techniques to automatically classify AFM datasets has received interest recently. We propose the use of self-organizing maps (SOMs) as unsupervised artificial neural network applied to mechanical measurements performed via AFM on epithelial breast cancer cells treated with different substances that affect estrogen receptor signalling. We show changes in mechanical properties due to treatments, as estrogen softened the cells, while resveratrol led to an increase in cell stiffness and viscosity. These data were then used as input for SOMs. Our approach was able to distinguish between estrogen treated, control and resveratrol treated cells in an unsupervised manner. In addition, the maps enabled investigation of the relationship of the input variables.

biophysics↗

bioRxiv2022

Benchmarking solutions to the T-cell receptor epitope prediction problem: IMMREP22 workshop report

Many different solutions to predicting the cognate epitope target of a T-cell receptor (TCR) have been proposed. However several questions on the advantages and disadvantages of these different approaches remain unresolved, as most methods have only been evaluated within the context of their initial publications and data sets. Here, we report the findings of the first public TCR-epitope prediction benchmark performed on 23 prediction models in the context of the ImmRep 2022 TCR-epitope specificity workshop. This benchmark revealed that the use of paired-chain alpha-beta, as well as CDR1/2 or V/J information, when available, improves classification obtained with CDR3 data, independent of the underlying approach. In addition, we found that straight-forward distance-based approaches can achieve a respectable performance when compared to more complex machine-learning models. Finally, we highlight the need for a truly independent follow-up benchmark and provide recommendations for the design of such a next benchmark.

bioinformatics↗

bioRxiv2022

Light-dependent Control of Bacterial Expression at the mRNA Level

Sensory photoreceptors mediate numerous light-dependent adaptations across organisms. In optogenetics, photoreceptors achieve the reversible, non-invasive, and spatiotemporally precise control by light of gene expression and other cellular processes. The light-oxygen-voltage receptor PAL binds to small RNA aptamers with sequence specificity upon blue-light illumination. By embedding the responsive aptamer in the ribosome-binding sequence of genes of interest, their expression can be downregulated by light. We developed the pCrepusculo and pAurora optogenetic systems that are based on PAL and allow to down- and upregulate, respectively, bacterial gene expression using blue light. Both systems are realized as compact, single plasmids that exhibit stringent blue-light responses with low basal activity and up to several ten-fold dynamic range. As PAL exerts light-dependent control at the RNA level, it can be combined with other optogenetic circuits that generally control transcription initiation. By integrating regulatory mechanisms operating at the DNA and mRNA levels, optogenetic circuits with emergent properties can thus be devised. As a case in point, the pEnumbra setup permits to upregulate gene expression under moderate blue light whereas strong blue light shuts off expression again. Beyond providing novel signal-responsive expression systems for diverse applications in biotechnology and synthetic biology, our work also illustrates how the light-dependent PAL-aptamer interaction can be harnessed for the control and interrogation of RNA-based processes.

biochemistry↗

bioRxiv2022

Lactational delivery of Triclosan promotes non-alcoholic fatty liver disease in newborn mice

Pediatric non-alcoholic fatty liver disease (NAFLD) is escalating in the United States, with a limited mechanistic understanding. Triclosan (TCS) is a high-volume antimicrobial additive that has been detected in human breastmilk and shown in adult mice to cause hepatosteatosis. To examine the effect of TCS presented to neonatal mice through lactation, we exposed pregnant females to TCS in their diet and evaluated its impact on nursing neonates. TCS is efficiently transferred by lactation to newborn mice, causing significant fatty liver (FL) during the suckling period. Lactational delivery stimulated hepatosteatosis, triglyceride accumulation, endoplasmic reticulum (ER) stress, inflammation, and liver fibrosis. These events were mirrored by inhibition of key metabolic regulators, FGF21 and AMPK. De novo lipogenesis (DNL) induced by lactational TCS exposure was blocked in mice deficient in hepatic ATF4 . In primary hepatocytes, siRNA specific inhibition of PERK, an ATF4 upstream activator and initiator of ER stress, blocked TCS induced DNL. Also, in the absence of PPAR, which targets regulation of ATF4, TCS induced triglyceride accumulation and the induction of DNL was blocked. The administration of obeticholic acid (OCA), a potent FXR agonist, as well as activation of intestinal mucosal-regenerative gp130 signaling, led to reduced liver ATF4 expression, PPAR signaling, and DNL when neonates were exposed to TCS. In summary, TCS exposure via lactation leads to early indicators of NAFLD development accompanied by hepatosteatosis that were mediated in a PERK-eIF2-ATF4-PPAR cascade. These studies indicate that mother to child transmission of environmental toxicants such as TCS may underlie the recent increases in pediatric NAFLD.

pharmacology and toxicology↗

bioRxiv2022

Natural and human-mediated drivers of microevolution in Neotropical palms: a historical genomics approach

O_LIMicroevolution in Amazonia has been far less documented than in temperate regions and still constitutes a major knowledge gap. Moreover, the actual influence of pre-Columbian societies through the Holocene remains unclear, although it could provide interesting insights on the relationship between natural and human-mediated evolutionary processes in driving microevolution. C_LIO_LIBecause they are widespread and traditionally managed since pre-Columbian times, Neotropical palms are choice models to investigate the drivers of microevolution in Amazonia. In this study, we carried out a preliminary exploration of the genomic diversity in two pairs of congeneric palm species in French Guiana (Astrocaryum spp. and Oenocarpus spp.). C_LIO_LIWe built upon an original sampling design, taking into account both regional climate variations and local-scale pre-Columbian occupation, and designed a new target capture kit of 20,000 molecular probes scattered across exonic regions of more than 5,000 nuclear genes in Arecoideae ("ARECO5000+"). Hundreds of palm libraries were sequenced through Illumina sequencing, providing a unique - high-coverage - genomic dataset in these non-model species. C_LIO_LIWe explored patterns of genomic diversity and differentiation within and across populations, bringing state-of-the-art knowledge about the roles of climate adaptation and pre-Columbian domestication. By documenting original cases of "incipient" domestication, these pioneer results open new avenues toward a better understanding of microevolution in Amazonia and of the impact of pre-Columbian societies on present-day biodiversity patterns. C_LI

evolutionary biology↗

bioRxiv2021

miRNA mediated downregulation of non-muscle Cyclase associated protein 1 is required for myogenic differentiation

Myoblast fusion is crucial for the formation, growth and regeneration of healthy skeletal muscle, but the molecular mechanisms that govern fusion and myofiber formation remain poorly understood. Here we report that Cyclase-associated protein 1 (Cap1), a regulator of actin dynamics, plays a critical role in cytoskeletal remodeling during myoblast fusion and formation of myotubes. Cap1 mRNA and protein are expressed in murine C2C12 and human LHCN-M2 myoblasts, but its abundance decreases during myogenic differentiation. Perturbing the temporally controlled expression of Cap1 by overexpression or Crispr-Cas9 mediated knockout impaired actin rearrangement, myoblast alignment, expression of profusion molecules, differentiation into multinucleated myotubes and myosin heavy chain expression. Endogenous Cap1 expression is posttranscriptionally downregulated during differentiation by canonical myomiRs miR-1, miR-133 and miR-206, which have conserved binding sites in the 3 UTR of the Cap1 mRNA. Deletion of the endogenous 3 UTR in C2C12 cells phenocopies overexpression of Cap1 by inhibiting myotube formation. Our findings implicate Cap1 and its myomiR-mediated downregulation in the myoblast fusion process and the generation of skeletal muscle.

cell biology↗

bioRxiv2021

Rapid, multianalyte detection of opioid metabolites in wastewater

By monitoring opioid metabolites, wastewater-based epidemiology (WBE) could be an excellent tool for real-time information on consumption of illicit drugs. A key limitation of WBE is the reliance on costly laboratory-based techniques that require substantial infrastructure and trained personnel, resulting in long turnaround times. Here, we present an aptamer-based graphene field effect transistor (AptG-FET) platform for simultaneous detection of three different opioid metabolites. This platform provides a reliable, rapid, and inexpensive method for quantitative analysis of opioid metabolites in wastewater (WW). The platform delivers a limit of detection (LOD) 2-3 orders of magnitude lower than previous reports, but in line with the concentrations range (pg/ml to ng/ml) of these opioid metabolites present in real samples. To enable multianalyte detection we developed a facile, reproducible, and high yield fabrication process producing twenty G-FETs with integrated side gate platinum (Pt) electrodes on a single chip. Our devices achieved the simultaneous and selective multianalyte detection of three different metabolites: Noroxycodone (NX), 2-ethylidene-1,5-dimethyl-3,3-diphenylpyrrolidine (EDDP), and Norfentanyl (NF) in wastewater.

biophysics↗

bioRxiv2021

Nuclei are mobile processors enabling specialization in a gigantic single-celled syncytium

In multicellular organisms, the specification, coordination, and compartmentalization of cell types enable the formation of complex body plans. However, some eukaryotic protists such as slime molds generate diverse and complex structures while remaining in a multinucleated syncytial state. It is unknown if different regions of these giant syncytial cells have distinct transcriptional responses to environmental encounters, and if nuclei within the cell diversify into heterogeneous states. Here we performed spatial transcriptome analysis of the slime mold Physarum polycephalum in the plasmodium state under different environmental conditions, and used single-nucleus RNA-sequencing to dissect gene expression heterogeneity among nuclei. Our data identifies transcriptome regionality in the organism that associates with proliferation, syncytial substructures, and localized environmental conditions. Further, we find that nuclei are heterogenous in their transcriptional profile, and may process local signals within the plasmodium to coordinate cell growth, metabolism, and reproduction. To understand how nuclei variation within the syncytium compares to heterogeneity in single-nucleated cells, we analyzed states in single Physarum amoebal cells. We observed amoebal cell states at different stages of mitosis and meiosis, and identified cytokinetic features that are specific to nuclei divisions within the syncytium. Notably, we do not find evidence for predefined transcriptomic states in the amoebae that are observed in the syncytium. Our data shows that a single-celled slime mold can control its gene expression in a region-specific manner while lacking cellular compartmentalization, and suggests that nuclei are mobile processors facilitating local specialized functions. More broadly, slime molds offer the extraordinary opportunity to explore how organisms can evolve regulatory mechanisms to divide labor, specialize, balance competition with cooperation, and perform other foundational principles that govern the logic of life.

cell biology↗

bioRxiv2021

NRF1 Association with AUTS2-Polycomb Mediates Specific Gene Activation in the Brain

The heterogeneous complexes comprising the family of Polycomb Repressive Complex 1 (PRC1) are instrumental to establishing facultative heterochromatin that is repressive to transcription. Yet, two PRC1 species, PRC1.3 and PRC1.5, are known to comprise novel components, AUTS2, P300, and CK2 that convert this repressive function to that of transcription activation. Here, we report that patients harboring mutations in the HX repeat domain of AUTS2 exhibit defects in AUTS2 and P300 interaction as well as a developmental disorder reflective of Rubinstein-Taybi syndrome, which is mostly associated with a heterozygous pathogenic variant in CREBBP/EP300. As well, the absence of AUTS2 gives rise to a mis-regulation of a subset of developmental genes and curtails motor neuron differentiation from embryonic stem cells in the context of a well-defined system. Moreover, the transcription factor, Nuclear Respiratory Factor 1 (NRF1) exhibits a novel and integral role in this aspect of the neurodevelopmental process, being required for PRC1.3 recruitment to chromatin.

biochemistry↗