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Biology subjects

Koch, M.

Publications and source records attributed to Koch, M..

At least 19 recordsLinked to original sources

B cell response to HCMV gH/UL116 elicits neutralizing and FcγR-activating antibodies

Humoral immune mechanisms that can contribute to limiting HCMV disease include neutralizing antibodies that block viral entry and Fc-mediated effector functions that promote elimination of infected cells. Here, we identify the gH/UL116 envelope complex as a naturally immunogenic target that elicits antibodies capable of mediating both of these immune mechanisms. Using single-cell sorting of antigen-specific memory B cells, we isolated gH/UL116-reactive monoclonal antibodies from HCMV-seropositive donors. Epitope mapping showed that gH binding was required for virus neutralization, whereas UL116 targeting was associated with potent and broad Fc{gamma} receptor (Fc{gamma}R) activation. Furthermore, cryo-electron microscopy provided high-resolution structures revealing how UL116-specific antibodies bind gH/UL116. In mice, gH/UL116 immunization elicited serum IgG responses whose binding titers strongly correlated with both neutralization and mouse Fc{gamma}R activation. Together, these findings provide an epitope-level map linking antibody specificity to neutralization and Fc{gamma}R activation across HCMV gH-associated complexes and position gH/UL116 as a promising HCMV vaccine candidate.

immunology↗

Chemically-induced Jamming and 3D printing of Granular Hydrogels: Microgels as Reservoirs of Volume

Granular hydrogels, made of jammed soft microparticles, are of great interest for 3D (bio)printing, as they combine ideal rheological properties and extensive modularity, yielding favorable microstructures for tissue engineering. Typically, the yield-stress properties of these materials, which facilitate printability, are defined by the preparation state and the initial particle content of the hydrogel. Here, we propose a granular hydrogel whose yield-stress and, consequently, printability and printed scaffolds shape retention can be controlled not only by the initial weight fraction of particles but also by their stimuli-responsive swelling. The responsive microgels are prepared from poly(N-isopropylacrylamide) crosslinked by dynamic covalent disulfide bonds. The particles swelling is triggered by reduction-induced cleavage of the disulfide bonds into two pendant thiol groups, enabling printing of multilayer scaffolds with high shape fidelity. Without chemically induced swelling, the same formulation requires higher particle concentrations to be printable. Importantly, the printed structures can be annealed by oxidizing the thiol units back into disulfide inter-particle bonds. The printed scaffolds are compatible with human dermal fibroblasts (HDF) and support cell-material interactions. This system offers a unique opportunity for on-demand modulation of both printability and scaffold microstructure, enabling unique control over local stiffness, packing density, and porosity in granular scaffolds.

bioengineering↗

Pil-Chp orchestrates a multi-level regulatory system to control type IV pilus dynamics in Pseudomonas aeruginosa

The cyclical extension and retraction dynamics of type IV pili (T4P) mediate critical virulence traits in many bacterial species, yet how these dynamics are regulated remain poorly understood. Here, by analyzing individual pilus dynamics across mutants covering the entire T4P system of Pseudomonas aeruginosa, we identified active pili in several mutants previously classified as non-piliated. Correlating these dynamics with intracellular cAMP levels, transcriptional profiles, and T4P protein abundances reveals how the chemosensory Pil-Chp system controls T4P fiber length, count, extension rate, and polarity in surface-naive cells by modulating cAMP levels. Specifically, fiber length is tuned by modulating the effective association and dissociation rates of the extension ATPase PilB; fiber count is regulated by controlling machine abundance; and extension rate is limited by the abundance of the major pilin (PilA). Furthermore, we demonstrate that these regulatory mechanisms of T4P length and count differentially impact T4P-dependent functions: phage infection efficiency increases continuously with fiber count or length, whereas twitching motility exhibits step-like activation thresholding. This indicates that the functional output of T4P dynamics is strictly context dependent. Because the Pil-Chp system is conserved across diverse human and plant pathogens, this multi-level regulatory logic may represent a widespread mechanism controlling T4P-mediated virulence.

microbiology↗

Identification of a pan-orthoebolavirus-reactive antibody from an rVSV-EBOV vaccinated individual

Orthoebolaviruses such as Ebola virus (EBOV), Sudan virus (SUDV) and Bundibugyo virus (BDBV) can cause severe disease with high case-fatality rates. While licensed EBOV vaccines and therapeutic antibodies protect against EBOV infection, no single monoclonal antibody currently provides broad protection across multiple orthoebolaviruses. Here, we analyzed the humoral immune response of an rVSV-EBOV vaccinee to identify pan-orthoebolavirus-neutralizing antibodies. Using BDBV- and SUDV-glycoproteins for single B cell-sorting, we identified B10, which neutralized authentic EBOV and SUDV, with potent activity against SUDV compared with established cross-reactive antibodies. Structural analysis mapped antibody B10 binding to the pan-orthoebolavirus conserved GP2-stalk/HR2 region, associated with asymmetric trimer destabilization and spike opening. In vivo, B10 showed significant prophylactic efficacy in an EBOV mouse model and partial protection with antiviral activity in a SUDV mouse model. Together, these findings demonstrate that rVSV-EBOV vaccination induced the development of a broadly orthoebolavirus-neutralizing antibody that holds exeptional therapeutic potential.

immunology↗

Structural characterization of antibodies for synergistic HCMV neutralization

The limited mechanistic understanding of Human Cytomegalovirus (HCMV) infection and neutralization has hindered the effective application of antibodies for HCMV prevention and therapy. To address this, we conducted high-resolution cryo-EM analysis of 17 human monoclonal antibodies targeting HCMV glycoproteins gH and gL. This analysis revealed a landscape of vulnerable epitopes, including detailed binding modes, spatial orientations, and structural features associated with distinct neutralization phenotypes. By comprehensively characterizing the neutralizing properties of these antibodies and their combinations, we identified synergistic antibody cocktails that enhance the neutralization capacity of individual antibodies. Notably, while single antibodies only partially neutralized HCMV, their synergistic combinations achieved substantially more complete inhibition. Together, these findings delineate structural correlates of HCMV neutralization and establish functional principles for antibody-based combinatorial targeting of HCMV.

immunology↗

Multimodal characterization of variation in neuronal types in the mouse basal ganglia

AbstractThe basal ganglia (BG) are a set of topographically organized, interconnected structures that are pivotal for regulating volitional movement and other aspects of cognitive, motivational, and affective behavior. Recently generated taxonomies of transcriptomically-defined cell types (T-types) have revealed both fine-grained distinctions in gene expression between neurons in these structures as well as continuous transcriptomic variation across similar T-types1-9, which are both related to location within a structure. However, it remains unclear to what extent these and other cellular properties co-vary with each other. Therefore, we performed Patch-seq experiments10,11 on over 900 neurons in mouse brain slices from BG to provide an integrated view of the co-variation between gene expression, location, physiology, and morphology measured from the same neurons. Medium spiny neurons (MSNs) from both the direct and indirect pathways across the dorsal and ventral striatum follow a gene expression gradient that varies in a dorsolateral to ventromedial direction; we find that this gradient also corresponds with systematic differences in action potential kinetics and dendritic arborization. Our analysis also characterizes additional multimodal dimensions of MSN variation, such as those between direct and indirect pathway neurons and between matrix and striosome neurons. Furthermore, through comparison with Patch-seq data from macaque, we demonstrate that the relationship between the transcriptomic/spatial gradient and electrophysiological and morphological properties is conserved across these two species. We also find that properties of striatal interneurons, such as action potential kinetics, vary across the striatum in a manner consistent with the MSN gradient. Outside the striatum, our multimodal Patch-seq dataset from the globus pallidus, subthalamic nucleus, and substantia nigra enabled us to characterize transcriptomically-defined types and link them to prior descriptions of cell types in these structures. Finally, we examined to what extent the MSN transcriptomic/spatial gradient persisted across different stages of the BG circuit by comparing Patch-seq neurons to reconstructed whole-neuron morphologies and the topography of their interareal projections, finding that the gradient is better preserved in GPe and GPi compared to SNr. Our study links transcriptomic variation across T-types in mouse BG to spatial localization and phenotypic differences at the level of individual cells, improving our understanding of cell type architecture in topographically organized circuits of the brain.

neuroscience↗

Topographic structure and function of locus coeruleus norepinephrine neurons

Norepinephrine (NE) is released throughout most of the central nervous system by neurons in the locus coeruleus (LC). We found a relationship between the morphologies, gene expression, and activity of LC-NE neurons in mice. Axonal projections of individual neurons were extensive but largely confined to subsets of brain regions. Axonal projections and graded gene expression correlated with locations of cell bodies in LC. In a behavioral task requiring ongoing learning from actions, neurons in dorsal LC projecting to the cerebral cortex were excited when mice made a different choice from the previous one and by reward prediction errors, a signal driving learning. Background activity of neurons in ventral LC was higher when mice ignored stimuli indicating potential reward availability. These observations reveal a topographically organized structure and function of a neurotransmitter system and show that it contains learning signals for flexible behavior.

neuroscience↗

Morphoelectric Diversity and Specialization of Neuronal Cell Types in the Primate Striatum

The basal ganglia are evolutionary ancient subcortical nuclei that form interconnected loops with the neocortex and limbic system to regulate movement, learning, habit formation, emotion, and motivation. Their dysfunction contributes to major neurological and psychiatric disorders, yet most cellular-level insights derive from rodent studies, leaving knowledge gaps in humans and translationally relevant primate species. To address this, we generated multi-modal Patch-seq data linking transcriptomic identity with morphological and electrophysiological properties in macaque striatum, the input nucleus of the basal ganglia. We found underappreciated diversity among medium spiny neurons, including non-canonical types, and variation aligned with functional gradients. Interneurons also exhibited spatial variation and even greater morphoelectric diversity, highlighting their functional modularity. Despite broad evolutionary conservation, we identified primate-specific features and key differences from rodent striatal neurons. By integrating molecular classification with cellular properties that shape network function, our findings provide insights into the functional organization of the primate striatum.

neuroscience↗

A ligand/receptor trafficking clock governs self-renewal and abscission dynamics in pluripotent stem cells

Summary/AbstractHow extracellular cues are temporally integrated to regulate self-renewal and differentiation propensities across the cell cycle remains largely unresolved. We identify a ligand/receptor trafficking clock in rodent and human pluripotent stem cells (PSCs) in which the cyclic turnover of Netrin-1 and its receptors Neo1 and Unc5b (NNU) governs self-renewal capacity and abscission dynamics. In G1, NNU complexes undergo Clathrin-mediated internalization and lysosomal degradation, a process required for timely post-mitotic bridge abscission. At later stages of the cycle, NNU activate Src within early endosomes, inducing a genome-wide redistribution of the transcriptional co-activator Yap1. This reshapes gene regulatory networks by activating stemness- and ectoderm-associated transcriptional programs enriched for Sox2/Nanog binding and by repressing mesodermal- and cell cycle-related targets enriched for Sox2 and Tcf3. Functionally, recombinant Netrin-1 reduces functional heterogeneity and enhances clonogenicity in G1, uncovering a tractable strategy to canalize stem cell behavior. Collectively, our results reveal cell cycle-dependent ligand/receptor trafficking as a temporal clock that directly links membrane dynamics to epigenetic regulation and stem cell fate, opening new avenues for regenerative medicine.

cell biology↗

Reduced CSF1R expression in myeloid cells has limited impact on chronic lymphocytic leukemia progression

Targeting the colony-stimulating factor 1 receptor (CSF1R) to remove tumor-associated macrophages is being explored as cancer therapy. This strategy may be relevant for chronic lymphocytic leukemia (CLL), which strongly depends on support from myeloid cells. However, it is unclear how CSF1R expression affects the CLL microenvironment and leukemic progression. To examine this question, we created CLL mice with Csf1r haploinsufficiency to investigate changes in myeloid cells, Csf1r expression, and leukemia progression. Reducing Csf1r expression on circulating monocytes did not change the overall numbers of monocytes or macrophages in blood and lymphoid tissues. Mice with lower Csf1r levels had less leukemia during early disease, but this effect faded with disease progression, and their overall survival was similar to controls. Furthermore, reduced Csf1r expression on macrophages did not affect the survival or migration of patient-derived CLL cells. In summary, our results show that while the CSF1R pathway is important for maintaining the myeloid cells that support CLL, simply reducing CSF1R expression has only a limited effect on disease progression. Attempts to target the CSF1R for leukemic therapy might benefit from a stronger depletion of macrophages or the combination with other agents.

cancer biology↗

Axon guidance deficits in a human sensory neuron model of Fabry disease

Fabry disease (FD) is a rare genetic galactosidase alpha (GLA) gene associated lysosomal disorder caused by alpha-galactosidase A (AGAL) deficiency, leading to sphingolipid (globotriaosylceramide, Gb3) accumulation in multiple tissues. Burning pain due to small fiber neuropathy is an early symptom with great impact on health- related quality of life. The pathophysiological role of Gb3 accumulations in sensory neurons of the dorsal root ganglia is incompletely understood. We have differentiated induced pluripotent stem cells of an isogenic GLA knockout line (p.S364del, hemizygous) and its healthy control into sensory neurons to model FD in vitro. We have compared both lines on transcriptional and proteomic level and investigated the effects of AGAL enzyme supplementation. FD sensory neurons showed dysregulation of disease-related pathways, including axon guidance at both RNA and protein level and microfluidic assays revealed shorter neurite length. While AGAL did not restore the transcriptomic state, it reduced Gb3 accumulation and lowered protein ephrin 5A and glycoprotein M6A level. These findings highlight axon guidance alterations in an isogenic human FD sensory model, with potential implications for early central and peripheral innervation in small fiber neuropathy. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=173 SRC="FIGDIR/small/673441v1_ufig1.gif" ALT="Figure 1"> View larger version (71K): org.highwire.dtl.DTLVardef@199cd19org.highwire.dtl.DTLVardef@682521org.highwire.dtl.DTLVardef@15da60borg.highwire.dtl.DTLVardef@1404c10_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

Extracellular vesicles and their RNA cargo facilitate bidirectional cross-kingdom communication between human and bacterial cells

While extracellular vesicles (EVs) are established mediators of intra-species signaling, their role as active participants in cross-kingdom communication remains incompletely understood. Here, we reveal that human colon cells and both Gram-positive and Gram-negative gut bacteria engage in species-specific, EV-mediated molecular dialogue, driven in part by RNA cargo. We show that bacterial EVs (BEVs) induce distinct transcriptomic responses in human cells, and that BEV-RNA independently causes similar effects. Conversely, we demonstrate that human EVs and highly abundant miR-192-5p are differentially internalized by bacteria, affecting their physiology. Our findings support a conceptual model in which EVs function as directional messengers that shape host-microbiome interactions. This study introduces a framework for understanding EVs as cross-kingdom regulators and underscores the importance of tailored, context-specific analyses for understanding the scope of EV-mediated interactions in microbiome-host homeostasis and disease. Highlights[1] L. casei, E. faecalis and P. mirabilis produce BEVs that are internalized by Caco-2 cells at different rates. BEVs produced by L. casei have a positive influence on the viability of Caco-2 cells. Incubation of Caco-2 cells with BEVs leads to changes in the gene expression of immune-response-related genes. [2] BEVs carry RNAs and the type of RNA cargo varies significantly between the BEVs from the different bacteria. Comparison of Caco-2 gene deregulation between BEVs and transfection of RNA isolated from BEV highlights component-specific effects. [3] Caco-2 EVs are taken up by E. faecalis and influence their growth. MiRNA-192-5p can be frequently detected in EVs from Caco-2 cells. Synthetic miR-192-5p is internalized by P. mirabilis and the ability to take up human miRNAs by L. casei and E. faecalis can be increased by packaging of the miRNA in artificial liposomes.

molecular biology↗

SVEP1 enables efficient binding of Angiopoietin-2 to the TIE1 receptor, allowing receptor phosphorylation and downstream signaling

The molecular mechanisms that drive (lymph-)angiogenesis are crucial to understand diseases, such as lymphedema, that are caused due to malformations of the lymphatic vasculature. Recently, an interaction between the secreted protein Svep1, a key regulator in lymphangiogenesis, and the transmembrane receptor Tie1 was shown in zebrafish, human, and mice. Here, guided by in silico AlphaFold-multimer structure predictions of SVEP1 complexes, we assert with protein binding studies that the human CCP20 domain is the primary binding site for TIE1. We further demonstrate that SVEP1 mediates strong binding of ANG2 and TIE1, and that combined stimulation of hdLECs with SVEP1 and ANG2 leads to phosphorylation of TIE1. TIE1 activation by SVEP1 and ANG2 enables downstream signaling and, in turn, potentiates nuclear exclusion of FOXO1 and phosphorylation of AKT compared to SVEP1 or ANG2 alone. We present a model in which ANG1/2 dimers bind to both SVEP1 and TIE1, resulting in the recruitment of multiple TIE1 receptor molecules to a multimeric complex at the cell membrane, potentially amplifying its signaling capacity.

developmental biology↗

Neuropathic pain and distinct CASPR2 autoantibody IgG subclasses drive neuronal hyperexcitability

Patients with autoantibodies (aAbs) against the contactin-associated protein-like 2 (CASPR2) suffer from a variety of clinical syndromes including neuropathic pain, in some patients even as the only symptom. CASPR2 is an adhesion protein of the neurexin IV family and part of the voltage-gated potassium channel complex (VGKC) in neurons of dorsal root ganglia (DRG). The subsequent pathological mechanisms following the binding of CASPR2 aAbs and their association with pain are only partially understood. CASPR2 aAbs are mainly of the IgG4 subclass. Previous studies have neglected subclass-dependent effects. Here we investigated 49 subclassified patient serum samples positive for CASPR2 aAbs. To unravel underlying molecular mechanisms, we used a combination of super-resolution lattice structural illumination microscopy (SIM2) and functional readouts by calcium imaging and electrophysiological recordings. CASPR2-positive patient sera subclassified in IgG4 together with at least one other IgG subclass (IgGX) and patients with only IgG4 were further subdivided into the pain and no pain group. Patient subclassification shed further light on the pathological mechanisms of CASPR2 aAbs. A decrease of CASPR2 expression after long-term exposure to CASPR2 aAbs was only observed for the patient group without pain. Upon withdrawal of the CASPR2 aAbs, CASPR2 expression returned to normal level. Structural alterations were obtained by increased distances between CASPR2 and associated potassium channels along DRG axons using high-resolution lattice SIM2 microscopy but only following binding of CASPR2 aAbs from patients with pain. Similarly, CASPR2 aAbs of patients with pain significantly increased overall neuronal excitability of cultured DRG neurons as measured by calcium imaging. Patch-clamp recordings revealed significantly decreased current amplitudes of voltage-gated potassium (Kv) channels after incubation with all four CASPR2 aAbs subclassifications with the most prominent effect of serum samples harboring IgG4 aAbs. Notably, a patient serum sample lacking IgG4 did not alter Kv channel function. Withdrawal of aAbs rescued Kv channel function to normal levels suggesting that the affected potassium channel function is rather due to a functional block of the VGKC rather than altered structural integrity of the VGKC. Taken together, we found IgG4 aAbs to be a major modifier of potassium channel function. The increase in DRG excitability is primarily due to impaired Kv channel conductance as a consequence of CASPR2 aAbs binding but additional and so far unidentified signal pathways contribute to this process in patients with neuropathic pain.

neuroscience↗

Fibre type differences in the organisation of mononuclear cells and myonuclei at the tips of human myofibres

The myotendinous junction (MTJ) is a weak link in the musculoskeletal system. Here, we isolated the tips of single myofibres from healthy human hamstring muscles for confocal microscopy (n=6) and RNAscope in situ hybridization (n=6) to gain insight into the profiles of cells and myonuclei in this region. A marked presence of mononuclear cells was observed coating the fibre tips, with a median of 29 (range 16-63) and 16 (9-23) cells per fibre for type I and II myofibres, respectively (p<0.05). The number and density of myonuclei gradually increased from the myofibre proper towards the tip (p<0.05), similarly for both fibre types, and a greater number of COL22A1-expressing nuclei was seen in type II vs type I myofibres (p<0.05). These divergent fibre type-specific characteristics of the MTJ reflect the respective demands for remodelling of the tendon and myofibre sides of the junction according to loading patterns. This insight refines our fundamental understanding of the human MTJ at the cell and structural levels. Summary statementAt the site of attachment to tendon, type I and II human myofibre tips display divergent numbers of mononuclear cells and COL22A1+ nuclei, changing our understanding of myotendinous junction biology.

physiology↗

mTOR controls growth and internal architecture of human breast cancer spheroids

mTOR is a serine/threonine kinase participating in two distinct functional complexes: mTORC1 and mTORC2. mTORC1 regulates protein translation, cell cycle progression and autophagy. mTORC2 controls cell survival, proliferation and actin cytoskeleton reorganization. mTOR signaling is often deregulated during breast cancer. We investigated how mTOR and its downstream process autophagy determine the inner architecture of solid tumor aggregates at multiple levels. We focused on structures, which are morphologically altered during progression of cancer, including: nuclei number and volume, cell density, number, shape and volume of polarized structures. We developed a breast cancer spheroid model, in which the effects of mTOR and autophagy modulation were investigated by pharmacological inhibition mTOR signaling and induction autophagy, as well as using ATG7 KO spheroids. Spheroids were imaged with light sheet-based fluorescence microscopy and data were quantitatively analyzed. Our data suggest that mTORC1 regulates the spheroid volume, cell number and size. mTORC2 controls nuclei volume and determines growth and elongation of polarized acini inside a spheroid.

cell biology↗

Genome-wide SNP data reveal recent population structure of Huidobria fruticosa (Loasaceae), a paleo-endemic lineage from the Atacama Desert

The Atacama Desert is a biodiversity hotspot of neo-endemic radiation, where long-term aridity and complex physiographic processes create a unique environmental setting. Current species assemblages are mainly concentrated in highly patchy loma formations, and plant populations occurring in these are often geographically isolated from each other. Despite a general consensus on long-term aridity in the Atacama, climatological and geological evidence points to repeated climate change, making the Atacama Desert an ideal system for studying population genetic processes in highly unstable habitats. We are analyzing the genetic structure within and between populations of Huidobria fruticosa, a paleo-endemic lineage of the Atacama Desert, to shed new light on its biogeographic history and broaden our understanding of the evolution of life in extreme aridity, as well as plant evolution in response to a changing environment. To do this, we analyzed SNP data from genotyping-by-sequencing of 354 individuals from 21 populations. Our results suggest that, despite being an ancient lineage, the current population structure of Huidobria fruticosa only reflects changing abiotic conditions over the last 2 million years. We therefore conclude that the present distribution, together with the evolutionary processes documented here, is the result of climatic fluctuations and prolonged periods of hyperaridity during the Pleistocene. Building on this understanding, our findings contribute to a global narrative that highlights the complex interplay between climate change and evolutionary dynamics, and emphasize the importance of deserts as living laboratories for deciphering how species have historically adapted to some of the most extreme habitats on Earth.

evolutionary biology↗

Structure and dynamics of human cardiac fibroblast nanotubes

Efficient and dynamic interactions between cardiac fibroblasts and their environment are essential for the maintenance of tissue homeostasis in healthy hearts and play an important role during pathological remodelling. Here, we investigate a relatively obscure mechanism through which human atrial fibroblasts communicate with each other, with other cells, and with the extracellular matrix (ECM) - nanotubes (NT). We investigated NT structure and dynamics in primary right atrial fibroblasts isolated from patients in sinus rhythm (SR) and atrial fibrillation (AF), in an immortalised human atrial fibroblasts cell line, and in intact human tissue, using a wide range of imaging approaches (including confocal microscopy, label-free reflection microscopy, rotating coherent scattering microscopy, and cryo-electron tomography). We show that fibroblasts maintain continuous NT activity in vitro, with numerous protrusions constantly probing the surrounding environment. NT structure and activity change during AF and following pharmacological (transforming growth factor-{beta}, latrunculin B) and environmental (hypoxia) interventions. We also show that cardiac fibroblast NT mediate intercellular organelle exchange and dynamically interact with ECM. Finally, we present evidence for the presence of fibroblast-borne NT in human atrial tissue. Our results advance our understanding of how cardiac fibroblasts interact with their environment. NT are versatile structures capable of both sensory and actuating functions, and offer a dynamic and rapid communication conduit that facilitates cell-cell and cell-extracellular matrix interactions.

cell biology↗