Biology subjects

Schuetz, A.

Publications and source records attributed to Schuetz, A..

13 recordsLinked to original sources

bioRxiv2026

HIV lymphoid tissue fibrosis occurs in the earliest stages of acute HIV infection and is associated with macrophage-derived TGF-β

HIV infection is associated with lymphatic tissue damage caused by collagen deposition in the fibroblastic reticular cell network (FRCn) of the parafollicular T cell zone (TZ), which leads to impaired antigen presentation, T cell depletion, and reduced antibody formation. In treated chronic HIV infection, damage persists despite antiretroviral therapy (ART), but it is not known if very early initiation of ART could limit damage and preserve immune function. We studied participants in the Thai RV254 acute infection cohort and found significant collagen deposition in the FRCn even in the earliest Fiebig stage 1 acute infection. The amount of TZ collagen correlates with the frequency of TGF-{beta}+ macrophages which, in turn, correlates with the frequency of HIV RNA-producing cells. We conclude that immediate initiation of ART may have limited impact in preventing or reversing collagen accumulation in LNs.

microbiology↗

bioRxiv2025

Hepatitis B virus HBx protein masks epigenetic reader Spindlin1 via an inter-molecular zinc finger to subvert transcriptional control

The HBx protein from Hepatitis B virus (HBV) is essential for replication and promotes pathogenicity during chronic infection. HBx hijacks host proteins, reprogramming them to evade antiviral defence. However, the structural basis of recruitment remains largely unknown. The HBx1-120 isoform derives from integration of viral DNA into the host genome and is linked to hepatocellular carcinoma. We present an NMR-based setup to characterize HBx-host protein interactions at residue-level resolution. HBx1-120 is disordered in isolation but undergoes local folding upon binding apoptosis regulator Bcl-xL and epigenetic reader Spindlin1. The HBx-Spindlin1 complex is bivalent: a hydrophobic interaction combines with a sticky patch realized via a rare inter-molecular zinc finger. HBx thus conceals the region responsible for recruiting Spindlin1 to histone tails, promoting transcription of extrachromosomal viral DNA. This mechanism exemplifies the capacity of HBx to engage diverse host factors into dynamic complexes.

biophysics↗

bioRxiv2024

TENM4 is an essential transduction component for touch and pain

Gentle touch is conveyed to the brain by fast-conducting sensory fibers. Mechanosensitive ion channels at the terminals of these neurons are thought to be gated by extracellular tethers that transmit force from the surrounding matrix to the channel complex, but the molecular identity of such tethers has remained unknown. Here, we identify Teneurin-4 (TENM4) as an essential extracellular linker protein for mechanotransduction in mechanoreceptors. Sensory neuron-specific deletion of Tenm4 in mice caused profound touch insensitivity, while acute and reversible proteolytic disassembly of TENM4 at sensory endings confirmed its direct role in force transduction. Ultrastructural analyses revealed TENM4 localization to filamentous structures at the neurite-laminin interface, defining it as a structural component of the mechanosensory tether. These findings identify TENM4 as a core element of fast somatic sensation and provide molecular insight into how extracellular forces are coupled to ion channel activation.

neuroscience↗

bioRxiv2023

Multiunit frontal eye field activity codes the visuomotor transformation, but not gaze prediction or target memory, in a delayed saccade task

Single-unit (SU) activity - action potentials isolated from one neuron -- has traditionally been employed to relate neuronal activity to behavior. However, recent investigations have shown that multi-unit (MU) activity - ensemble neural activity recorded within the vicinity of one microelectrode - may also contain accurate estimations of task-related neural population dynamics. Here, using a well-established model-fitting approach, we compared the spatial codes of SU response fields with corresponding MU response fields recorded from the frontal eye fields (FEF) in head-unrestrained monkeys (Macaca mulatta) during a memory-guided saccade task. We focused on characterizing the visuomotor transformation from Target-in-Eye coordinates to future Gaze-in-Eye coordinates (Sajad et al., 2015). Most SU visual response fields coded targets (with some predicting Gaze), whereas the MU population only coded targets. Most SU motor responses coded Gaze, but many still retained a target code. In contrast, MU motor activity predominantly coded Gaze with very little target coding. Finally, both SU and MU populations showed a progressive transition through intermediate Target-to-Gaze codes during the delay period, but the MU activity showed a smoother transition. These results confirm the theoretical and practical potential of MU activity recordings as a biomarker for fundamental sensorimotor transformations (e.g., Target-to-Gaze coding in the oculomotor system), while also highlighting the importance of SU activity for coding more cognitive (e.g., predictive / memory) aspects of sensorimotor behavior. SIGNIFICANCE STATEMENTMulti-unit recordings (undifferentiated signals from several neurons) are relatively easy to record and provide a simplified estimate of neural dynamics, but it is not clear which single-unit signals are retained, amplified, or lost. Here, we compared single-/multi-unit activity from a well-defined structure (the frontal eye fields) and behavior (memory-delay saccade task), tracking their spatial codes through time. The progressive transformation from target to gaze coding observed in single-unit activity was retained in multi-unit activity, but gaze prediction (in the visual response) and target memory (in the motor response) were lost. This suggests that multi-unit activity provides an excellent biomarker for healthy sensorimotor transformations, at the cost of missing more subtle cognitive signals.

neuroscience↗

bioRxiv2023

Unravelling ATP processing by the AAA+ protein p97 at the atomic level

The human enzyme p97 regulates various cellular pathways by unfolding hundreds of protein substrates in an ATP-dependent manner, making it an essential component of homeostasis and impactful pharmacological target. The hexameric complex undergoes substantial conformational changes in the course of its catalytic cycle. Here, we elucidate the molecular motions that occur at the active site in the temporal window immediately before and after ATP hydrolysis by merging cryo-EM, NMR spectroscopy and MD simulations. p97 populates a metastable reaction intermediate, the ADP.Pi state, which is poised between hydrolysis and product release. Detailed snapshots reveal that the active site is finely tuned to trap and eventually discharge the cleaved phosphate. Signalling pathways originating at the active site coordinate the action of the hexamer subunits and couple hydrolysis with allosteric conformational changes. Our multidisciplinary approach enables a glimpse into the sophisticated spatial and temporal orchestration of ATP handling by a prototype AAA+ protein.

biophysics↗

bioRxiv2023

AI-guided pipeline for protein-protein interaction drug discovery identifies a SARS-CoV-2 inhibitor

Protein-protein interactions (PPIs) offer great opportunities to expand the druggable proteome and therapeutically tackle various diseases, but remain challenging targets for drug discovery. Here, we provide a comprehensive pipeline that combines experimental and computational tools to identify and validate PPI targets and perform early-stage drug discovery. We have developed a machine learning approach that prioritizes interactions by analyzing quantitative data from binary PPI assays and AlphaFold-Multimer predictions. Using the quantitative assay LuTHy together with our machine learning algorithm, we identified high-confidence interactions among SARS-CoV-2 proteins for which we predicted three-dimensional structures using AlphaFold Multimer. We employed VirtualFlow to target the contact interface of the NSP10-NSP16 SARS-CoV-2 methyltransferase complex by ultra-large virtual drug screening. Thereby, we identified a compound that binds to NSP10 and inhibits its interaction with NSP16, while also disrupting the methyltransferase activity of the complex, and SARS-CoV-2 replication. Overall, this pipeline will help to prioritize PPI targets to accelerate the discovery of early-stage drug candidates targeting protein complexes and pathways.

systems biology↗

bioRxiv2023

Parallelized Acquisition of Orbitrap and Astral Analyzers Enables High-Throughput Quantitative Analysis.

The growing trend towards high-throughput proteomics demands rapid liquid chromatography-mass spectrometry (LC-MS) cycles that limit the available time to gather the large numbers of MS/MS fragmentation spectra required for identification. Orbitrap analyzers scale performance with acquisition time, and necessarily sacrifice sensitivity and resolving power to deliver higher acquisition rates. We developed a new mass spectrometer that combines a mass resolving quadrupole, the Orbitrap and the novel Asymmetric Track Lossless (Astral) analyzer. The new hybrid instrument enables faster acquisition of high-resolution accurate mass (HRAM) MS/MS spectra compared to state-of-the-art mass spectrometers. Accordingly, new proteomics methods were developed that leverage the strengths of each HRAM analyzer, whereby the Orbitrap analyzer performs full scans with high dynamic range and resolution, synchronized with Astral analyzers acquisition of fast and sensitive HRAM MS/MS scans. Substantial improvements are demonstrated over previous methods using current state-of-the-art mass spectrometers. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=100 SRC="FIGDIR/small/543408v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@1eedfdeorg.highwire.dtl.DTLVardef@1ab7939org.highwire.dtl.DTLVardef@a3b2f8org.highwire.dtl.DTLVardef@13ac46b_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2023

An unconventional gatekeeper mutation sensitizes inositol hexakisphosphate kinases to an allosteric inhibitor

Inositol hexakisphosphate kinases (IP6Ks) are emerging as relevant pharmacological targets because a multitude of disease-related phenotypes has been associated with their function. While the development of potent IP6K inhibitors is gaining momentum, a pharmacological tool to distinguish the mammalian isozymes is still lacking. Here, we implemented an analog-sensitive approach for IP6Ks and performed a high-throughput screen to identify suitable lead compounds. The most promising hit, FMP-201300, exhibited high potency and selectivity towards the unique valine gatekeeper mutants of IP6K1 and IP6K2, compared to the respective wild-type kinases. Biochemical validation experiments revealed an allosteric mechanism of action that was corroborated by HDX-MS measurements. The latter analysis suggested that displacement of the C helix, caused by the gatekeeper mutation, facilitates the binding of FMP-201300 to an allosteric pocket adjacent to the ATP binding site. FMP-201300 therefore serves as a valuable springboard for the further development of compounds that can selectively target the three mammalian IP6Ks; either as analog-sensitive kinase inhibitors or as an allosteric lead compound for the wild-type kinases.

biochemistry↗

bioRxiv2022

Productive and latent HIV infections originate in resting CD4+ T cells

Productively and latently HIV-infected cells are the source of virus that respectively establishes and sustains systemic infections and the reservoir in which HIV persists and rebounds when anti-retroviral therapy (ART) is interrupted. While infected activated CD4+ T cells are thought to be the principal source of HIV production, and reversion of activated infected cells to a resting state as the major pathway to establishment of the latently infected cell reservoir, we now show that in the earliest stages of detectable HIV infection in the lymphoid tissue reservoir, infection of resting CD4+ T cells establishes the first populations of both productively and latently infected cells. We further show that the early infection of resting T cells reflects their predominance in lymphoid tissues and the expression of pTEFb in vivo in resting T cells to support their infection. The immediate establishment of productively and latently infected cell populations enable HIV to propagate and persist, and generates reservoirs from which infection can rebound despite instituting ART at the earliest stage of detectable infection.

immunology↗

bioRxiv2021

Integration of allocentric and egocentric visual information in a convolutional / multilayer perceptron network model of goal-directed gaze shifts

Allocentric (landmark-centered) and egocentric (eye-centered) visual codes are fundamental for spatial cognition, navigation, and goal-directed movement. Neuroimaging and neurophysiology suggest these codes are segregated initially, but then reintegrated in frontal cortex for movement control. We created and validated a theoretical framework for this process using physiologically constrained inputs and outputs. To implement a general framework, we integrated a Convolutional Neural Network (CNN) of the visual system with a Multilayer Perceptron (MLP) model of the sensorimotor transformation. The network was trained on a task where a landmark shifted relative to the saccade target. These visual parameters were input to the CNN, the CNN output and initial gaze position to the MLP, and a decoder transformed MLP output into saccade vectors. Decoded saccade output replicated idealized training sets with various allocentric weightings, and actual monkey data where the landmark shift had a partial influence (R2 = 0.8). Furthermore, MLP output units accurately simulated prefrontal response field shifts recorded from monkeys during the same paradigm. In summary, our model replicated both the general properties of the visuomotor transformations for gaze and specific experimental results obtained during allocentric-egocentric integration, suggesting it can provide a general framework for understanding these and other complex visuomotor behaviors.

neuroscience↗

bioRxiv2021

Gaze-Related Activity in Primate Frontal Cortex Predicts and Mitigates Spatial Uncertainty

A remarkable feature of primate behavior is the ability to predict future events based on past experience and current sensory cues. To understand how the brain plans movements in the presence of unstable cues, we recorded gaze-related activity in the frontal cortex of two monkeys engaged in a quasi-predictable cue-conflict task. Animals were trained to look toward remembered visual targets in the presence of a landmark that shifted with fixed amplitude but randomized direction. As simulated by a probabilistic model based on known physiology/behavior, gaze end points assumed a circular distribution around the target, mirroring the possible directions of the landmark shift. This predictive strategy was reflected in frontal cortex activity (especially supplementary eye fields), which anticipated future gaze distributions before the actual landmark shift. In general, these results implicate prefrontal cortex in the predictive integration of environmental cues and their learned statistical properties to mitigate spatial uncertainty.

neuroscience↗

bioRxiv2020

Landmark-Centered Coding in Frontal Cortex Visual Responses

Visual landmarks influence spatial cognition [1-3], navigation [4,5] and goal-directed behavior [6-8], but their influence on visual coding in sensorimotor systems is poorly understood [6,9-11]. We hypothesized that visual responses in frontal cortex control gaze areas encode potential targets in an intermediate gaze-centered / landmark-centered reference frame that might depend on specific target-landmark configurations rather than a global mechanism. We tested this hypothesis by recording neural activity in the frontal eye fields (FEF) and supplementary eye fields (SEF) while head-unrestrained macaques engaged in a memory-delay gaze task. Visual response fields (the area of visual space where targets modulate activity) were tested for each neuron in the presence of a background landmark placed at one of four oblique configurations relative to the target stimulus. 102 of 312 FEF and 43 of 256 SEF neurons showed spatially tuned response fields in this task. We then fit these data against a mathematical continuum between a gaze-centered model and a landmark-centered model. When we pooled data across the entire dataset for each neuron, our response field fits did not deviate significantly from the gaze-centered model. However, when we fit response fields separately for each target-landmark configuration, the best fits shifted (mean 37% / 40%) toward landmark-centered coding in FEF / SEF respectively. This confirmed an intermediate gaze / landmark-centered mechanism dependent on local (configuration-dependent) interactions. Overall, these data show that external landmarks influence prefrontal visual responses, likely helping to stabilize gaze goals in the presence of variable eye and head orientations. HighlightsO_LIPrefrontal visual responses recorded in the presence of visual landmarks C_LIO_LIResponse fields showed intermediate gaze / landmark-centered organization C_LIO_LIThis influence depended on specific target-landmark configurations C_LI

neuroscience↗

bioRxiv2018

Monocyte Infection Dynamics Shape HIV-1 Phyloanatomy in the Peripheral Blood

Human immunodeficiency virus (HIV) RNA and DNA have been isolated from patient monocytes, an immune cell population that is quite different in several aspects from the canonical T-cell viral target. Because monocytes are migratory and resilient to both natural and synthetic antiviral defenses, knowledge of the contribution of monocyte infection to ongoing viral evolution and spread in vivo is of significant interest for drug development and treatment strategies. Using single viral genome sequencing from different peripheral blood compartments and phyloanatomic statistical inference, we demonstrate that productively infected monocytes follow an evolutionary trajectory that is distinct from peripheral T cells during multiple stages of disease progression. Gene flow and selection analysis reveal plasticity in the source of monocyte infection and in the region of the HIV envelope glycoprotein that experiences selection pressure across individuals. The findings, thus, point to a potential reservoir showing a range of infection and transmission dynamics, for which the current universal, T cell-targeted treatment strategies would be inadequate.\n\nAuthor summaryHuman immunodeficiency virus is a rapidly evolving virus, allowing its genetic material to act as a fingerprint for epidemiological processes among, as well as within, individual infected hosts. In this study, sampling of viral RNA from plasma and differing infected immune cell populations from the peripheral blood was undertaken for three separate individuals in order to infer such processes. The results revealed a productively infected monocyte cell population, for which distinct selection pressures were linked to differing spatiotemporal origins of infection. In light of previous evidence of the migratory nature of these cells and resilience to both natural and synthetic antiviral defenses, this study underscores the importance of further investigation into the role of monocytes, and monocyte-rich tissues, as viral reservoirs during treatment of HIV with antiretroviral therapy.

evolutionary biology↗