Biology subjects

Bauer, M.

Publications and source records attributed to Bauer, M..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

eQTL in diseased colon tissue identifies novel target genes associated with IBD

Genome-wide association studies (GWAS) have identified over 300 loci associated with the inflammatory bowel diseases (IBD), but putative causal genes for most are unknown. We conducted the largest disease-focused expression quantitative trait loci (eQTL) analysis using colon tissue from 252 IBD patients to determine genetic effects on gene expression and potential contribution to IBD. Combined with two non-IBD colon eQTL studies, we identified 194 potential target genes for 108 GWAS loci. eQTL in IBD tissue were enriched for IBD GWAS loci colocalizations, provided novel evidence for IBD-associated genes such as ABO and TNFRSF14, and identified additional target genes compared to non-IBD tissue eQTL. IBD-associated eQTL unique to diseased tissue had distinct regulatory and functional characteristics with increased effect sizes. Together, these highlight the importance of eQTL studies in diseased tissue for understanding functional consequences of genetic variants, and elucidating molecular mechanisms and regulation of key genes involved in IBD.

genomics↗

bioRxiv2024

Phylogenomics and metabolic engineering reveal a conserved gene cluster in Solanaceae plants for withanolide biosynthesis

Withanolides are steroidal lactones from nightshade (Solanaceae) plants. Of the over 1,200 known representatives, many possess potent biological activities, but their drug potential has not been fully realised up until now. A central obstacle is the limited availability of minor withanolides, caused by a lack of knowledge about the underlying biosynthetic pathways. Here, we combine phylogenomics with metabolic engineering to overcome this limitation. By sequencing the genome of the medicinal plant and archetypical withanolide producer ashwagandha (Withania somnifera) and comparing the genome sequences of nine Solanaceae species, we discovered a conserved gene cluster for withanolide biosynthesis, consisting of two sub-gene clusters which differ in their expression patterns. To investigate the functions of the encoded enzymes, we established metabolic engineering platforms in yeast (Saccharomyces cerevisiae) and the model plant Nicotiana benthamiana. This allowed us to reconstitute the first three oxidative steps of withanolide biosynthesis, catalysed by the cytochrome P450 monooxygenases CYP87G1, CYP88C7, and CYP749B2, leading to the aglycone of the known compound withanoside V. Our work sets the basis for the biotechnological production of withanolides in heterologous hosts and will therefore help to fully harness the drug potential of these plant steroids in the future.

plant biology↗

bioRxiv2024

Identification of a novel myosin antigen activating CD8+ T cells in C57BL/6 mice

Heart-specific T cells play important roles in myocardial diseases, including myocarditis, myocardial infarction, and heart failure. However, only few cardiac antigens and their respective specific T cell receptors (TCRs) have been validated so far. Therefore, we sought to identify new cardiac T cell epitopes in C57BL/6 mice and to characterize the specific TCRs. Antigen mapping of myosin heavy chain alpha (MYHCA) led to the identification of a 9-mer epitope (MYHCA724-732) recognized by CD8+ T cells. Single-cell TCR sequencing (scTCR-seq) analysis of MYHCA-stimulated CD8+ T cells enabled the identification of distinct TCRs enriched on specific T cells. Selected TCRs inferred from scTCR-seq data were then expressed on reporter cell lines and functionally validated. Our study expands the toolkit required to study heart-directed immune responses by revealing a new cardiac antigen and specific TCRs. These tools will enable in vivo characterization of myosin-specific CD8+ T cells in murine models of myocardial diseases.

immunology↗

bioRxiv2024

Enhanced Visualization of Influenza A Virus Entry Using Virus-View Atomic Force Microscopy

Virus entry begins with attachment of virions to the cell surface, multivalent binding of viral proteins to receptors, signaling, and endocytosis. Using ViViD-AFM (Virus-View Dual confocal and Atomic Force Microscopy), we visualized the nanoscale morphology of influenza A virus (IAV) virions interacting with the cell membrane during virus entry. Following attachment to the cell surface, spherical IAV (90-100 nm in diameter) diffused in a sialic acid- and neuraminidase-dependent manner. Reduced diffusion signified the onset of clathrin coat assembly, followed by formation of actin-rich ruffles that promoted pit closure and IAV endocytosis. Cell surface ruffles sheared filamentous IAV (>1{micro}m in length) into shorter fragments that became internalized. ViViD-AFM is a powerful tool that provides nanoscale morphological insights of virus-cell membrane interplay in living cells.

cell biology↗

bioRxiv2024

Diffusing protein binders to intrinsically disordered proteins

Proteins which bind intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) with high affinity and specificity could have considerable utility for therapeutic and diagnostic applications. However, a general methodology for targeting IDPs/IDRs has yet to be developed. Here, we show that starting only from the target sequence of the input, and freely sampling both target and binding protein conformation, RFdiffusion can generate binders to IDPs and IDRs in a wide range of conformations. We use this approach to generate binders to the IDPs Amylin, C-peptide and VP48 in a range of conformations with Kds in the 3 -100nM range. The Amylin binder inhibits amyloid fibril formation and dissociates existing fibers, and enables enrichment of amylin for mass spectrometry-based detection. For the IDRs G3bp1, common gamma chain (IL2RG) and prion, we diffused binders to beta strand conformations of the targets, obtaining 10 to 100 nM affinity. The IL2RG binder colocalizes with the receptor in cells, enabling new approaches to modulating IL2 signaling. Our approach should be widely useful for creating binders to flexible IDPs/IDRs spanning a wide range of intrinsic conformational preferences.

biochemistry↗

bioRxiv2024

Information on Oral Temperature is More Robustly Encoded Than Taste in Neurons of the Mouse Gustatory Cortex

Eating behaviors are influenced by the integration of gustatory, olfactory, and somatosensory signals, which all contribute to the perception of flavor. Although extensive research has explored the neural correlates of taste in the gustatory cortex (GC), less is known about its role in encoding thermal information. This study investigates the encoding of oral thermal and chemosensory signals by GC neurons compared to the oral somatosensory cortex. In this study, we recorded the spiking activity of more than 900 GC neurons and 500 neurons from the oral somatosensory cortex in mice allowed to freely lick small drops of gustatory stimuli or deionized water at varying non-nociceptive temperatures. We then developed and used a Bayesian-based analysis technique to assess neural classification scores based on spike rate and phase timing within the lick cycle. Our results indicate that GC neurons rely predominantly on rate information, although phase information is needed to achieve maximum accuracy, to effectively encode both chemosensory and thermosensory signals. GC neurons can effectively differentiate between thermal stimuli, excelling in distinguishing both large contrasts (14{degrees}C vs. 36{degrees}C) and, although less effectively, more subtle temperature differences. Finally, a direct comparison of the decoding accuracy of thermosensory signals between the two cortices reveals that while the somatosensory cortex showed higher overall accuracy, the GC still encodes significant thermosensory information. These findings highlight the GCs dual role in processing taste and temperature, emphasizing the importance of considering temperature in future studies of taste processing. Key PointsO_LIFlavor perception relies on gustatory, olfactory, and somatosensory integration, with the gustatory cortex (GC) central to taste processing. C_LIO_LIGC neurons also respond to temperature, but the specifics of how the GC processes taste and oral thermal stimuli remain unclear. C_LIO_LIThe focus of this study is on the role of GC neurons in the encoding of oral thermal information, particularly compared to the coding functions of the oral somatosensory cortex. C_LIO_LIWe found that while the somatosensory cortex shows a higher classification accuracy for distinguishing water temperature, the GC still encodes a substantial amount of thermosensory information. C_LIO_LIThese results emphasize the importance of including temperature as a key factor in future studies of cortical taste coding. C_LI

neuroscience↗

bioRxiv2024

Dissecting translation elongation dynamics through ultra-long tracking of single ribosomes

mRNA translation by ribosomes is a highly dynamic and heterogeneous process. However, current approaches cannot readily resolve individual ribosomes during translation, limiting our understanding of translation dynamics. Here, we develop an imaging approach based on Stopless-ORF circular RNAs (socRNAs) to monitor individual translating ribosomes for hours. Using the socRNA imaging technology we obtained accurate measurements of ribosome pausing on various problematic RNA sequences or induced by ribosome-targeting drugs. In addition, we identified a novel translation factor involved in translation elongation, and revealed that translocation rates of ribosomes vary, indicative of intracellular ribosomal heterogeneity. Finally, socRNAs allow very sensitive measurements of translation elongation fidelity, revealing widespread frameshifting during translation. In summary, our single-ribosome imaging approach provides a detailed view of ribosome translocation kinetics and a powerful new tool to study the translation elongation phase.

molecular biology↗

bioRxiv2024

Unravelling differential Hes1 dynamics during axis elongation of mouse embryos through single-cell tracking

The intricate dynamics of Hes expression across diverse cell types in the developing vertebrate embryonic tail have remained elusive. To address this, we developed an endogenously tagged Hes1-Achilles mouse line, enabling precise quantification of dynamics at the single-cell resolution across various tissues. Our findings reveal striking disparities in Hes1 dynamics between presomitic mesoderm (PSM) and preneural tube (pre-NT) cells. While pre-NT cells display variable, low-amplitude oscillations, PSM cells exhibit synchronized, high-amplitude oscillations. Upon the induction of differentiation, the oscillation amplitude increases in pre-NT cells. Additionally, our study of Notch inhibition on Hes1 oscillations unveiled distinct responses in PSM and pre-NT cells, corresponding to differential Notch ligand expression dynamics. These findings suggest the involvement of separate mechanisms driving Hes1 oscillations. Thus, Hes1 demonstrates dynamic behaviour across adjacent tissues of the embryonic tail, yet the varying oscillation parameters give rise to differences in the information that can be conveyed by these dynamics.

developmental biology↗

bioRxiv2024

Dorsomedial Striatal Glutamatergic Transmission Inhibits Binge Drinking in Selectively Bred Crossed High Alcohol Preferring Mice

Crossed high alcohol preferring (cHAP) mice have been selectively bred to consume considerable amounts of alcohol resulting in binge drinking. The dorsal striatum (DS) is a brain region involved in action selection where the dorsomedial striatum (DMS) is involved in goal-directed action selection and dorsolateral striatum (DLS) is involved in habitual action selection. Alcohol use disorder (AUD) may involve a disruption in the balance between the DMS and DLS. While the DLS is involved in binge drinking, the reliance on the DMS and DLS in binge drinking has not been investigated in cHAP mice. We have previously demonstrated that glutamatergic activity in the DLS is necessary for binge-like alcohol drinking in C57BL/6J mice, another high drinking mouse. Because of this, we hypothesized that DLS glutamatergic activity would gate binge-like alcohol drinking in cHAP mice. cHAP mice underwent bilateral cannulation into the DMS or DLS and were allowed free-access to 20% alcohol for two-hours each day for 11 days. Mice were microinjected with the AMPA receptor (AMPAR) antagonist, NBQX, into the DMS or DLS immediately prior to alcohol access. AMPAR protein expression was also assessed in a separate group of animals in DS subregions following an 11-day drinking history. We found that intra-DMS (but not intra-DLS) NBQX, alters binge alcohol drinking, with intra-DMS NBQX increasing alcohol consumption. We also found that the ratio of GluA1 to GluA2 differs across DS subregions. Together, these findings suggest that glutamatergic activity in the DMS may serve to limit binge drinking in cHAP mice.

neuroscience↗

bioRxiv2024

A Genome-Wide Arrayed CRISPR Screen Reveals PLSCR1 as an Intrinsic Barrier to SARS-CoV-2 Entry

Interferons (IFNs) play a crucial role in the regulation and evolution of host-virus interactions. Here, we conducted a genome-wide arrayed CRISPR knockout screen in the presence and absence of IFN to identify human genes that influence SARS-CoV-2 infection. We then performed an integrated analysis of genes interacting with SARS-CoV-2, drawing from a selection of 67 large-scale studies, including our own. We identified 28 genes of high relevance in both human genetic studies of COVID-19 patients and functional genetic screens in cell culture, with many related to the IFN pathway. Among these was the IFN-stimulated gene PLSCR1. PLSCR1 did not require IFN induction to restrict SARS-CoV-2 and did not contribute to IFN signaling. Instead, PLSCR1 specifically restricted spike-mediated SARS-CoV-2 entry. The PLSCR1-mediated restriction was alleviated by TMPRSS2 over-expression, suggesting that PLSCR1 primarily restricts the endocytic entry route. In addition, recent SARS-CoV-2 variants have adapted to circumvent the PLSCR1 barrier via currently undetermined mechanisms. Finally, we investigate the functional effects of PLSCR1 variants present in humans and discuss an association between PLSCR1 and severe COVID-19 reported recently.

immunology↗

bioRxiv2024

Spatiotemporal visualization of DNA replication by click chemistry reveals bubbling of viral DNA in virion formation

The organisation of human chromosomes reversibly changes in cell division, and irreversibly in apoptosis or erythropoiesis by DNA condensation and fragmentation processes. Yet, how viral replication in the nucleus affects host and viral chromatin organisation remains poorly understood. Here we used dual-color click chemistry to image human adenovirus DNA replication, demonstrating host chromatin compaction during active expansion of the viral replication compartment (VRC). Early-replicated viral DNA (vDNA) segregated from VRC and lost phospho-serine5-RNA Pol-II and viral DNA-binding protein (DBP), while late-replicated vDNA retained active RNA Pol-II, besides viral RNA-splicing and DNA-packaging proteins. Depending on replication and the assembly protein 52K, the late-stage VRCs gave rise to progeny by droplet formation of vDNA with GFP-tagged virion protein V into 52K biomolecular condensates. The study reveals distinct functions of early and late-replicated vDNA and provides insight into active and passive liquid phase separated zones conducive to selective genome packaging of nascent virions.

microbiology↗

bioRxiv2023

The Interferon gamma Pathway Enhances Pluripotency and X-Chromosome Reactivation in iPSC Reprogramming

Reprogramming somatic cells into induced pluripotent stem cells (iPSCs) requires activation of the pluripotency network and resetting of the epigenome by erasing the epigenetic memory of the somatic state. In female mouse cells, a critical epigenetic reprogramming step is the reactivation of the inactive X chromosome. Despite its importance, a systematic understanding of the regulatory networks linking pluripotency and X-reactivation is missing. Here we reveal the pathways important for iPSC reprogramming and X-reactivation using a genome-wide CRISPR screen. In particular, we discover that activation of the interferon {gamma} (IFN{gamma}) pathway early during reprogramming accelerates pluripotency acquisition and X-reactivation. IFN{gamma} stimulates STAT3 signaling and the pluripotency network and leads to enhanced TET-mediated DNA demethylation, which consequently boosts X-reactivation. We therefore gain a mechanistic understanding of the role of IFN{gamma} in reprogramming and X-reactivation and provide a comprehensive resource of the molecular networks involved in these processes.

genetics↗

bioRxiv2023

Multiple myeloma long-term survivors display sustained immune alterations decades after first line therapy

The long-term consequences of cancer or cancer therapy on the patients immune system years after cancer-free survival remain poorly understood. Here, we have performed an in-depth characterization of the bone marrow ecosystem of multiple myeloma long-term survivors at initial diagnosis and up to 17 years following cancer-free survival. Using comparative single-cell analyses in combination with molecular, genomic and functional approaches, we demonstrate that multiple myeloma long-term survivors display pronounced alterations in their bone marrow microenvironment associated with impaired immunity. These immunological alterations were frequently driven by an inflammatory immune circuit fueled by the long-term persistence or resurgence of residual myeloma cells. Notably, even in the complete absence of any detectable residual disease for decades, sustained changes in the immune system were observed, suggesting an irreversible immunological scarring caused by the initial exposure to the cancer and therapy. Collectively, our study provides key insights into the molecular and cellular bone marrow ecosystem of multiple myeloma long-term survivors, revealing reversible and irreversible alterations of the immune compartment, which can serve as diagnostic and predictive tools. Statement of significanceLarge-scale single-cell profiling of a unique cohort of multiple myeloma long-term survivors uncovered that exposure to cancer and its treatment causes both reversible and irreversible immune alterations associated with impaired immunity. These findings have far-reaching implications for the understanding of long-term immune alterations in cancer, which need to be considered also in the context of immune therapeutic approaches. Furthermore, our study demonstrates how cancer-associated immune trafficking can be used to predict disease re-initiation in the bone marrow, opening new avenues for minimally invasive disease monitoring.

cancer biology↗

bioRxiv2023

Neural Correlates and Reinstatement of Recent and Remote Memory: A Comparison Between Children and Young Adults

Memory consolidation tends to be less robust in childhood than adulthood. However, little is known about the corresponding functional differences in the developing brain that may underlie age-related differences in retention of memories over time. This study examined system-level memory consolidation of object-scene associations after learning (immediate delay), one night of sleep (short delay), as well as two weeks (long delay) in 5-to-7-year-old children (n = 49) and in young adults (n = 39), as a reference group with mature consolidation systems. Particularly, we characterized how functional neural activation and reinstatement of neural patterns change over time, assessed by functional magnetic resonance imaging combined with representational similarity analysis (RSA). Our results showed that memory consolidation in children was less robust and strong (i.e., more forgetting) compared to young adults. Contrasting correctly retained remote versus recent memories across time delay, children showed less upregulation in posterior parahippocampal gyrus, lateral occipital cortex, and cerebellum than adults. In addition, both children and adults showed decrease in scene-specific neural reinstatement over time, indicating time-related decay of detailed differentiated memories. At the same time, we observed the emergence of generic gist-like neural representations in prefrontal brain regions uniquely in children, indicating qualitative difference in memory trace in children. Taken together, 5-to-7- year-old children, compared to young adults, show less robust memory consolidation, possibly due to difficulties in engaging in differentiated neural representations in neocortical mnemonic regions during retrieval of remote memories, coupled with relying more on gist-like generic neural representations. RESEARCH HIGHLIGHTSChildren showed less robust memory consolidation across short and long delay compared to young adults. From short to long delay, children show differential neural upregulation for remote versus recent memory compared to young adults. Over time, both children and young adults showed reduced scene-specific reinstatement of neural patterns. Children relied more on gist-like neural representations in medial and ventrolateral prefrontal brain regions.

neuroscience↗

bioRxiv2023

Fit by design: Developing substrate-specific seed mixtures for functional dike grasslands

O_LISowing is a well-established restoration technique to overcome dispersal limitation. Site-specific seed mixtures are most effective to achieve functional communities. This is especially important if the restored vegetation has to protect critical infrastructure like roadsides and dikes. Here, an improved seed-substrate combination will secure slope stability, reduce mowing efforts, and generate species-rich grasslands. C_LIO_LIA factorial field experiment addressed this topic on a dike at River Danube in SE Germany in 2018-2021. Within 288 plots, we tested three sand admixtures, two substrate depths, two seed densities and two seed mixture types (mesic hay meadow, semi-dry calcareous grassland) in north and south exposition, and measured the recovery completeness by calculating the successional distance to reference sites, the persistence of sown species, and the Favourable Conservation Status (FCS) of target species. C_LIO_LIOverall, the sown vegetation developed in the desired direction, but a recovery debt remained after four years, and some plots still showed similarities to negative references from ruderal sites. In north exposition, hay meadow-seed mixtures developed closer to the respective reference communities than dry-grassland mixtures. C_LIO_LIIn south exposition, the sown communities developed poorly which might be due to a severe drought during establishment. This initial negative effect remained over the entire observation period. C_LIO_LISand admixture had a slightly positive effect on target variables, while substrate depth, seed density and mixture type had no effects on species persistence or FCS. C_LIO_LISynthesis and applications: Site-adapted seed mixtures make restoration more effective. However, applying several seed-substrate combinations might foster beta diversity. Furthermore, additional management efforts are recommended, as they might be necessary to reduce the recovery debt, as well as re-sowing after unfavourable conditions. C_LI

ecology↗

bioRxiv2023

A multi-omics integrative approach unravels novel genes and pathways associated with senescence escape after targeted therapy in NRAS mutant melanoma

Therapy Induced Senescence (TIS) leads to sustained growth arrest of cancer cells. The associated cytostasis has been shown to be reversible and cells escaping senescence further enhance the aggressiveness of cancers. Together with targeted therapeutics, senolytics, specifically targeting senescent cancer cells, constitute a promising avenue for improved cancer treatments. Understanding how cancer cells evade senescence is needed to optimise the clinical benefits of this therapeutic approach. Here we characterised the response of three different NRAS mutant melanoma cell lines to a combination of CDK4/6 and MEK inhibitors over 33 days. Transcriptomic data show that all cell lines trigger a senescence programme coupled with strong induction of interferons. Kinome profiling revealed the activation of Receptor Tyrosine Kinases (RTKs) and enriched downstream signaling of neurotrophin, ErbB and insulin pathways. Characterisation of the miRNA interactome associates miR-211-5p with resistant phenotypes. Finally, iCELL-based integration of bulk and single-cell RNA-seq data identified biological processes perturbed during senescence, and predicts new genes involved in its escape. Overall, our data associate insulin signaling with persistence of a senescent phenotype and suggest a new role for interferon gamma in senescence escape through the induction of EMT and the activation of ERK5 signaling.

cancer biology↗

bioRxiv2023

H2A.X mutants exhibit enhanced DNA demethylation in Arabidopsis thaliana

H2A.X is an H2A variant histone in eukaryotes, unique for its ability to respond to DNA damage, initiating the DNA repair pathway. H2A.X replacement within the histone octamer is mediated by the FAcilitates Chromatin Transactions (FACT) complex, a key chromatin remodeler. FACT is required for DEMETER (DME)-mediated DNA demethylation at certain loci in Arabidopsis thaliana female gametophytes during reproduction, though it is not known how FACT targets DME sites. Here, we investigated whether H2AX is involved in DME- and FACT-mediated DNA demethylation during Arabidopsis reproduction. We show that h2a.x mutants are more sensitive to genotoxic stress, consistent with previous reports. H2A.X fused to the Green Fluorescent Protein (GFP) gene under the H2A.X promoter was highly expressed in newly developing Arabidopsis tissues, including in male and female gametophytes. We examined DNA methylation in h2a.x developing seeds using whole genome bisulfite sequencing, and found that CG DNA methylation in the developing endosperm, but not the embryo, is decreased genome-wide in h2a.x mutants, predominately in transposons and intergenic DNA. Hypomethylated sites overlapped 62 % with canonical DME loci. These data indicate that H2A.X is not required for DME function, but is important for DNA methylation homeostasis in the unique chromatin environment of Arabidopsis endosperm.

plant biology↗

bioRxiv2022

Clonally resolved single-cell multi-omics identifies routes of cellular differentiation in acute myeloid leukemia

Inter-patient variability and the similarity of healthy and leukemic stem cells have impeded the characterization of leukemic stem cells (LSCs) in acute myeloid leukemia (AML), and their differentiation landscape. Here, we introduce CloneTracer, a novel method that adds clonal resolution to single-cell RNA-seq datasets. Applied to samples from 19 AML patients, CloneTracer revealed routes of leukemic differentiation. While residual healthy cells dominated the dormant stem cell compartment, active leukemic stem cells resembled their healthy counterpart and retained erythroid capacity. By contrast, downstream myeloid progenitors were highly aberrant and constituted the disease-defining compartment: Their gene expression and differentiation state determined both chemotherapy response and the leukemias ability to differentiate to transcriptomically normal monocytes. Finally, we demonstrated the potential of CloneTracer to identify surface markers mis-regulated specifically in leukemic cells by intra-patient comparisons. Taken together, CloneTracer revealed a differentiation landscape that mimics its healthy counterpart and determines biology and therapy response in AML.

cancer biology↗