Biology subjects

Vogt, A.

Publications and source records attributed to Vogt, A..

14 recordsLinked to original sources

bioRxiv2026

Unscheduled DNA synthesis reveals a DNA repair hotspot and biomarker of somatic instability at the expanded-CAG repeat tract in the huntingtin gene

Somatic instability (SI) of expanded DNA repeats is a hallmark of repeat expansion disorder (REDs) and drives onset and progression in Huntingtons disease (HD) yet the absence of target engagement (TE) biomarkers for SI-modulating therapies represents a critical gap to clinical development. Here, we describe the development of the unscheduled repair synthesis assay (URSA)--combining 5-ethynyl-2-deoxyuridine (EdU) pulse-labeling with digital PCR or sequencing--and show that the CAG-expanded huntingtin (HTT) exon 1 allele is a highly active DNA repair hotspot in cells from people with HD (PwHD). Repair activity increases with repeat length, is allele-specific, and depends strongly on MSH3, a central driver of somatic expansion. URSA robustly quantifies MSH3 modulation in preclinical models within days compared to weeks or months required by conventional repeat-length measurements. Critically, substantial repair activity is detectable in peripheral blood mononuclear cells (PBMCs) from PwHD, where signal correlates with CAG length and improves predictive models of somatic expansion (SE) beyond age and CAG length alone. Unlike repeat-length changes, which require years to accumulate in blood, URSA signal is measurable within days. These findings establish DNA repair activity at the mutant HTT locus as a mechanistically grounded pharmacodynamic biomarker, enabling TE monitoring on a clinically actionable timescale, and with broad applicability to REDs and other diseases where modulation of the DNA damage response is therapeutically targeted.

neuroscience↗

bioRxiv2026

Preclinical efficacy of a systemically-administered, second-generation STING agonist that promotes antitumour immunity in combination with radiotherapy

As potent triggers of innate immunity, STING agonists hold promise as active immunotherapeutic agents for cancer treatment. Second-generation STING agonists, suitable for systemic delivery, are being investigated in preclinical research and have entered clinical trials. Here, the novel synthetic STING agonist, BI-1703880 (STINGa), which was designed for intravenous delivery, was investigated for anti-tumour and immunological effects. We show that STINGa activates the STING pathway and results in a transient and dose-dependent upregulation and secretion of interferons and proinflammatory cytokines in vitro and in vivo. We show that intravenous administration of repeated dosing with low-dose STINGa is well tolerated. We report that radiotherapy (RT) and STING agonism synergizes to generate innate immune cell and CD8+ T cell responses that control tumour growth. Anti-tumour activity induced by combined RT / STINGa was reduced in mice lacking a functional immune system. RT / STINGa combination treatment also initiated development of protective immune memory. RT / STINGa upregulated PD-L1, PD-1 and CTLA-4 in the tumour microenvironment. Our findings show that combining RT / STINGa with immune checkpoint inhibitors further increases therapeutic benefit. Our data confirm STING as a therapeutic target in cancer and support the clinical development of BI-1703880 STING agonist, thereby suggesting radiotherapy as a potential combination for enhancing anti-tumour efficacy.

cancer biology↗

bioRxiv2025

Change in motor state equilibrium explains prokinetic effect of apomorphine on locomotion in experimental Parkinsonism

Gait impairments remain a major therapeutic challenge in Parkinsons disease (PD). Apomorphine is gaining renewed clinical attention with the expanding use of pump infusion systems. Yet, the specific role of apomorphine on the neural regulation of gait has remained poorly characterized, limiting its targeted use for symptom-specific therapy in PD. Here, we examined the neurobehavioral effects of apomorphine on runway locomotion in the unilateral 6-hydroxydopamine (6-OHDA) rat model. Therapeutic drug doses significantly increased total walking distance, related to reduced akinesia and prolonged gait episodes. Conversely, 3D kinematic analysis revealed reduced limb velocities under medication. At the neural level, therapy doses selectively enhanced cortical high-gamma rhythms without substantially altering beta or low-gamma activity. Instead, beta and low-gamma oscillations were consistently suppressed during motor activity in both medication ON and OFF conditions. Neurobehavioral correlations showed that transitions into gait were facilitated by reductions in beta and low-gamma activity, whereas transitions to akinesia were primarily suppressed when high-gamma activity was elevated. Our findings suggest that modulating cortical activity can aid ameliorating gait deficits in PD. We further propose that the complex therapy effects of apomorphine are best explained by a shift in motor-state equilibrium that is defined by the transitions of akinesia, stationary movements and gait. Together, these insights establish a mechanistic framework to guide the development of targeted gait therapies in PD.

neuroscience↗

bioRxiv2025

End Processing in NHEJ by Polymerase {lambda} and PNKP is coordinated during short-range synapsis

Non-homologous end joining (NHEJ) is a major pathway of DNA double strand break (DSB) repair, capable of directly joining both damaged strands of DNA through the coordinated activities of repair factors that detect the termini, physically bridge them together, and perform the chemistry necessary to complete repair. NHEJ is capable of repairing a variety of damaged DNA, employing various accessory end-processing factors to resolve chemically blocked ends, trim overhangs, and fill gaps in order to achieve directly ligatable DNA ends. To investigate the molecular mechanisms underlying end-processing, we determined the cryo-EM structure of the NHEJ specific polymerase Pol {lambda} bound to the short-range synaptic complex, uncovering the mode of its recruitment to the complex as well as a putative model for its activity. Furthermore, the coordinated end-processing activities of the short-range (SR) synaptic complex simultaneously bound by both Pol {lambda} and PNKP, another accessory factor, demonstrates the ability of NHEJ to form large, multifunctional repair complexes capable of processing a variety of different DNA end structures to effect repair.

biophysics↗

bioRxiv2025

Uncovering the Neural Fingerprint of Akinetic States in a Parkinsons Disease Rodent Model

Gait deficits present an unresolved therapeutic challenge in Parkinsons Disease. At the behavioral level, symptoms exhibit heterogeneity, including bradykinesia and hypokinesia during cyclical limb movement, as well as sudden interruptions in the gait sequence, also known as freezing of gait. The neural activities that drive these various deficits remain largely unknown. Here, we investigated the neural correlates of gait sequence interruptions with deep neurobehavioral phenotyping. For this, we transformed kinematic trajectories and cortical oscillations into continuous time series of multimodal feature vectors. Next, we applied machine learning, combining low-dimensional embedding with supervised classification, to identify cortical oscillation features that drive gait deficits. In a rodent Parkinsons disease model, our approach revealed that gait, akinesia, and stationary movements occupy prominently different regions in the low-dimensional embedding space. Among the predominant features separating the states, we found Hjorth complexity and mobility to modulate with the onset of akinetic episodes. Additionally, we validated our analysis approach in two Parkinson patients with freezing of gait, where neural features in STN recordings partially reflected the findings from ECoG measurements in rodents. The presented neurobehavioral phenotyping approach is translational and can easily generalize to the analysis of other complex movement disorders. Together, our results highlight specific features of neural oscillations as potential biomarkers that may support the development of adaptive closed-loop algorithms for gait therapy in PD.

neuroscience↗

bioRxiv2024

The dorsal fan-shaped body is a neurochemically heterogeneous sleep-regulating center in Drosophila

Sleep is a behavior that is conserved throughout the animal kingdom. Yet, despite extensive studies in humans and animal models, the exact function or functions of sleep remain(s) unknown. A complicating factor in trying to elucidate the function of sleep is the complexity and multiplicity of neuronal circuits that are involved in sleep regulation. It is conceivable that distinct sleep-regulating circuits are only involved in specific aspects of sleep and may underlie different sleep functions. Thus, it would be beneficial to assess the contribution of individual circuits in sleeps putative functions. The intricacy of the mammalian brain makes this task extremely difficult. However, the fruit fly Drosophila melanogaster, with its simpler brain organization, available connectomics, and unparalleled genetics offers the opportunity to interrogate individual sleep-regulating centers. In Drosophila, neurons projecting to the dorsal Fan-Shaped Body (dFB) have been proposed to be key regulators of sleep, particularly sleep homeostasis. We recently demonstrated that the most widely used genetic tool to manipulate dFB neurons, the 23E10-GAL4 driver, expresses in two sleep-regulating neurons (VNC-SP neurons) located in the Ventral Nerve Cord (VNC), the fly analog of the vertebrate spinal cord. Since most data supporting a role for the dFB in sleep regulation have been obtained using 23E10-GAL4, it is unclear whether the sleep phenotypes reported in these studies are caused by dFB neurons or VNC-SP cells. A recent publication replicated our finding that 23E10-GAL4 contains sleep-promoting neurons in the VNC. However, it also proposed that the dFB is not involved in sleep regulation at all, but this suggestion was made using genetic tools that are not dFB-specific and a very mild sleep deprivation protocol. In this study, using a newly created dFB-specific genetic driver line, we demonstrate that the majority of 23E10-GAL4 dFB neurons can promote sleep when activated and that these neurons are involved in sleep homeostasis. We also show that dFB neurons require stronger stimulation than VNC-SP cells to promote sleep. In addition, we demonstrate that dFB-induced sleep can consolidate Short-Term Memory (STM) into Long-Term Memory (LTM), suggesting that the benefit of sleep on memory is not circuit-specific. Finally, we show that dFB neurons are neurochemically heterogeneous and can be divided in 3 populations. Most dFB neurons express both glutamate and acetylcholine, while a minority of cells express only one of these two neurotransmitters. Importantly, dFB neurons do not express GABA, as previously suggested. Using neurotransmitter-specific dFB tools, our data also points at cholinergic dFB neurons as particularly potent at regulating sleep and sleep homeostasis.

neuroscience↗

bioRxiv2023

Refined movement analysis in the Staircase test reveals differential motor deficits in mouse models of stroke

Accurate assessment of post-stroke deficits is vital in translational research. Recent advances in machine learning provide unprecedented precision in quantifying rodent motor behavior post-stroke. However, the extent to which these tools can detect lesion-specific upper extremity deficits remains unclear. Using proximal middle cerebral artery occlusion (MCAO) and cortical photothrombosis (PT), we assessed post-stroke impairments in mice through the Staircase test. Lesion locations were identified using 7T-MRI. Machine learning was applied to reconstruct kinematic trajectories using MouseReach, a data-processing toolbox. This yielded 30 refined outcome parameters effectively capturing motor deficits. Lesion reconstructions located ischemic centers in the striatum (MCAO) and sensorimotor cortex (PT). Pellet retrieval was altered in both cases but did not correlate with stroke volume or ischemia extent. Instead, cortical ischemia was characterized by increased hand slips and modified reaching success. Striatal ischemia led to progressively prolonged reach durations, mirroring delayed symptom onset in basal ganglia strokes. In summary, refined machine learning-based movement analysis revealed specific deficits in mice after cortical and striatal ischemia. These findings emphasize the importance of thorough behavioral profiling in preclinical stroke research to increase translational validity of behavioral assessments.

neuroscience↗

bioRxiv2023

Dynamic control of gene expression by ISGF3 and IRF1 duringIFNbeta and IFNgamma signaling

Type I interferons (IFN-I, including IFN{beta}) and IFN{gamma} produce overlapping, yet clearly distinct immunological activities. Recent data show that distinctness of global transcriptional responses to the two IFN types is not apparent when comparing their immediate effects. By analyzing nascent transcripts induced by IFN-I or IFN{gamma} over a period of 48hrs we now show that the distinctiveness of the transcriptomes emerges over time and is based on a different employment of the ISGF3 complex as well as the second-tier transcription factor IRF1. The distinct transcriptional properties of ISGF3 and IRF1 correspond with a largely diverse nuclear protein interactome. Mechanistically, we describe specific input of ISGF3 and IRF1 into enhancer activation and the regulation of chromatin accessibility at interferon-induced genes (ISG). We further report differences between the IFN types in altering RNA polymerase II pausing at ISG 5 ends. Our data provide insight how transcriptional regulators create immunological identities of IFN-I and IFN{gamma}.

immunology↗

bioRxiv2023

Transcriptional landscape of DTP-DTEP transition reveals DUSP6 as a driver of HER2 inhibitor tolerance via Neuregulin/HER3 axis

The mechanisms promoting re-growth of dormant cancer cells under continuous tyrosine kinase inhibitor (TKI) therapy are poorly understood. Here we present transcriptional profiling of HER2+ breast cancer cells treated continuously with HER2 TKI (HER2i) therapy for 9 months. The data reveals specific gene regulatory programs associated with transition from dormant drug tolerant persister cells (DTPs) to proliferating DTEP (drug tolerant expanding persister) cells and eventually long-term resistance. Focusing on yet poorly understood phosphatases as determinants of therapy tolerance, expression of dual-specificity phosphatase DUSP6 was found inhibited in DTPs, but strongly induced upon re-growth of DTEPs. DUSP6 overexpression conferred apoptosis resistance whereas its pharmacological blockade prevented DTEP development under HER2i therapy. The DUSP6-driven HER2i tolerance was mediated by activation of neuregulin-HER3 axis, and consistent with the role of HER3 in widespread therapy tolerance, DUSP6 targeting also synergized with clinically used HER2i combination therapies. In vivo, pharmacological DUSP6 targeting induced synthetic lethal effect with HER2i in independent tumor models, and its genetic targeting reduced tumor growth in orthotopic brain metastasis model. Collectively this work provides first transcriptional landscape of DTP-DTEP transition under TKI therapy, and identify DUSP6 as a novel candidate therapy target to overcome widespread HER3-driven therapy resistance.

cancer biology↗

bioRxiv2023

YidC from Escherichia coli forms an ion-conducting pore upon activation by ribosomes.

The universally conserved protein YidC aids the insertion and folding of transmembrane polypeptides independently or as a part of the SecYEG translocon complex. In the former scenario, the lipid-exposed YidC surface equipped with a highly conserved positively charged arginine is thought to facilitate membrane insertion of the nascent chain by providing a countercharge for the acidic residues at the polypeptides N-terminal region. Here we show that the purified and reconstituted E. coli YidC forms an ion-conducting transmembrane pore upon binding a ribosome or ribosome-nascent chain complex (RNC). This pore is closed in the absence of ribosomes. As this pore is not visible in the published monomeric YidC structure, we used AlphaFold to construct the model of a parallel YidC dimer. Experimental evidence for a dimeric assembly comes from our BN-PAGE analysis of native vesicles, fluorescence correlation spectroscopy studies, and single-molecule fluorescence microscopy. In the dimeric model, the conserved positively charged arginine and many residues interacting with nascent chains point into the putative pore. This result suggests the possibility of an alternative mode of YidC-assisted membrane protein insertion.

biophysics↗

bioRxiv2022

CeGAL: revisiting a widespread fungal-specific TF family using an in silico error-aware approach to identify missing zinc cluster domains

Transcription factors (TF) regulate gene activity in eukaryotic cells by binding specific regions of genomic DNA. In fungi, the most abundant TF class contains a fungal-specific GAL4-like Zn2C6 DNA binding domain (DBD), while the second class contains another fungal-specific domain, known as fungal_trans or Middle Homology Domain (MHD), whose function remains largely uncharacterized. Remarkably, almost a third of MHD-containing TF in public sequence databases apparently lack DNA binding activity, since they are not predicted to contain a DBD. Here, we reassess the domain organization of these MHD-only proteins using an in silico error-aware approach. Our large-scale analysis of ~17000 MHD-only TF sequences showed that the vast majority (>90%) result from gene annotation errors, thus contradicting previous findings that the MHD-only TF are widespread in fungi. We show that they are in fact exceptional cases, and that the Zn2C6-MHD domain pair represents the canonical domain signature defining a new TF family composed of two fungal-specific domains. We call this family CeGAL, after the most characterized members: Cep3, whose 3D structure has been determined and GAL4, an archetypal eukaryotic TF. This definition should improve the classification of the Zn2C6 TF and provide critical insights into fungal gene regulatory networks. IMPORTANCEIn fungi, extensive efforts focus on genome-wide characterization of potential Transcription Factors (TFs) and their targets genes to provide a better understanding of fungal processes and a rational for transcriptional manipulation. The second most abundant families of fungal-specific TFs, characterized by a Middle Homology Domain, are major regulators of primary and secondary metabolisms, multidrug resistance and virulence. Remarkably, one third of these TFs do not have a DNA Binding Domain (DBD-orphan) and thus are excluded from genome-wide studies. This particularity has been the subject of debate for many years. By computationally inspecting the close genomic environment of about 20,000 DBD-orphan TFs from a wide range of fungal species, we reveal that more than 90% contained sequences encoding a zinc-finger DBD. This analysis implies that the arrays of DBD containing TFs and their control DNA-sequences in target genes need to be reconsidered and expands the combinatorial regulation degree of the crucial fungal processes controlled by this TF family.

bioinformatics↗

bioRxiv2022

A Split-GAL4 screen identifies novel sleep-promoting neurons in the Ventral Nerve Cord of Drosophila

As in the mammalian system, sleep in Drosophila is regulated by multiple brain regions. Among them, neurons projecting to the dorsal Fan-Shaped Body (dFB) have been intensively studied and the data suggest they play a critical role in sleep regulation. The 23E10-GAL4 driver is the most widely used tool to label and manipulate dFB neurons. Multiple studies have reported that activation of 23E10-GAL4 neurons promotes sleep. However, anatomical analyses revealed that 23E10-GAL4 labels 23-30 dFB neurons in the Drosophila brain and many non-dFB neurons in the brain and in the Ventral Nerve Cord (VNC), the fly equivalent of the spinal cord. To better understand the role of individual dFB neurons in sleep regulation, we undertook a Split-GAL4 screen to gain access to subsets of 23E10-GAL4 expressing cells. In this study, we report the discovery of two VNC cholinergic sleep-promoting neurons labeled by the 23E10-GAL4 driver.

neuroscience↗

bioRxiv2021

Interferons Reshape the 3D Conformation and Accessibility of Macrophage Chromatin

Engagement of macrophages in innate immune responses is directed and enhanced by type I and type II interferons. An essential component of IFN activity is the use of JAK-STAT signal transduction for the transcriptional control of interferon-stimulated genes (ISG). Here, we study the immediate early nuclear response to type I IFN and IFN-{gamma} in murine macrophages. Despite their distinct immunological activities, both IFN types triggered highly overlapping epigenomic and transcriptional changes. These changes included a rapid rearrangement of the 3D chromatin organization and an increase of DNA accessibility at ISG loci. ISGF3, the major transcriptional regulator of ISG, controlled homeostatic as well as induced-state DNA accessibility at a subset of ISG. Increases in DNA accessibility correlated with the appearance of activating histone marks at surrounding nucleosomes. Collectively our data emphasize changes in the three-dimensional nuclear space and epigenome as an important facet of transcriptional control by the IFN-induced JAK-STAT pathway.

immunology↗

bioRxiv2020

Signaling input from divergent pathways subverts malignant B-cell transformation

Malignant transformation typically involves multiple genetic lesions whose combined activity gives rise to cancer1. Our analysis of 1,148 patient-derived B-cell leukemia (B-ALL) samples revealed that individual mutations did not promote leukemogenesis unless they converged on one single oncogenic pathway characteristic for the differentiation status of these transformed B cells. Specifically, we show here the JAK/STAT5 signaling pathway supports the developmental stage-specific expansion of pro-B ALL whereas the ERK-pathway that of pre-B ALL. Mutations that were not aligned with the central oncogenic driver would activate divergent pathways and subvert malignant transformation. Oncogenic lesions in B-ALL frequently mimic survival and proliferation signals downstream of cytokine receptors (through activation of STAT5)2-7 or the pre-B cell receptor (through activation of ERK)8-13. STAT5- (372 cases) and ERK- (386 cases) activating lesions were frequently found but only co-occurred in [~]3% (37) of cases (P=2.2E-16). Single-cell mutation and phosphoprotein analyses revealed that even in these rare cases, oncogenic STAT5- or ERK-activation were mutually exclusive and segregated to competing clones. STAT5 and ERK engaged opposing biochemical and transcriptional programs orchestrated by MYC and BCL6, respectively. Genetic reactivation of the divergent (suppressed) pathway came at the expense of the principal oncogenic driver and reversed malignant transformation. Conversely, Cre-mediated deletion of divergent pathway components triggered leukemia-initiation and accelerated development of fatal disease. Thus, persistence of divergent signaling pathways represents a powerful barrier to malignant transformation while convergence on one principal driver defines a key event during leukemia-initiation. Proof-of-concept studies in patient-derived B-ALL cells revealed that pharmacological reactivation of suppressed divergent circuits strongly synergized with direct inhibition of the principal oncogenic driver. Hence, pharmacological reactivation of divergent pathways can be leveraged as a previously unrecognized strategy to deepen treatment responses and to overcome drug-resistance. Current treatment approaches for drug-resistant cancer are focused on drug-combinations to suppress the central oncogenic driver and multiple alternative pathways14-17. Here, we introduce a concept based on inhibition of the principal driver combined with pharmacological reactivation of divergent pathways.

cancer biology↗