Biology subjects

Walter, M.

Publications and source records attributed to Walter, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Dissociating Resting-State Networks of Pedohebephilic Preference and Child Sexual Offending Using Network-Based Prediction

Background: Pedohebephilia (P+), the sexual preference for prepubescent and early pubertal minors, regularly causes distress in those affected. While associated with child sexual offending (CSO), P+ is not a prerequisite for CSO. Limited neuroimaging studies have identified alterations associated with P+, while these may primarily reflect offending history. The correlates of P+ independent of CSO therefore remain unclear. We examined this distinction using intrinsic functional networks within a multivariate predictive framework. Methods: Using resting-state functional connectivity (rsFC) and network-based prediction (NBS-Predict), we performed pairwise classifications among non-offending pedohebephilic men (P+CSO-, n=35), pedohebephilic men with CSO (P+CSO+, n=38), and non-pedohebephilic controls without CSO (P-CSO-, n=63). Classification-relevant subnetwork nodal strength was associated post hoc with trait impulsivity within P+ groups. Results: P+CSO- were significantly distinguished from P-CSO- (balanced accuracy [BAC]=0.621, pFDR=.041), and showed reductions between default-mode hubs and temporoparietal somatomotor and ventral attention regions. P+CSO+ were also significantly distinguished from P+CSO- (BAC=0.645, pFDR=.032) and yielded a smaller subnetwork centered on the substantia nigra. Against P-CSO-, P+CSO+ showed widespread reductions, particularly across subcortical, default mode, visual, limbic, and somatomotor regions (BAC=0.640, pFDR=0.032). Right precentral gyrus nodal strength correlated with impulsivity in P+CSO+ only (r=0.57, pFDR=0.024). Conclusions: Whole-brain rsFC contains information distinguishing pedohebephilic preference in the absence of known CSO, while P+CSO+ show additional and more widespread network alterations involving systems implicated in action selection and behavioral regulation. These findings open new avenues for integrating pedohebephilia into broader neurobiological research frameworks.

neuroscience↗

bioRxiv2026

Sex-Dependent Proteomic Remodelling During ex vivo Degeneration of Young and Aged Murine Peripheral Nerves

IntroductionPeripheral nerve ageing leads to profound proteomic remodelling, with shifts in metabolic and inflammatory signalling pathways resembling changes that occur during nerve degeneration and regeneration following injury. Moreover, aged nerves exhibit impaired degeneration and regeneration, contributing to age-related peripheral neuropathies that show sex-specific differences in prevalence. However, it remains unclear whether these alterations arise from intrinsic nerve changes or an altered systemic environment. Therefore, we investigated the impact of sex on age-related proteome changes and nerve-intrinsic proteomic responses in young and aged male and female nerves using an ex vivo degeneration model. MethodsMass spectrometry-based proteomics were performed on young and old nerves from male and female animals, as well as on contralateral nerves after seven days of ex vivo nerve degeneration. A comparative bioinformatic analysis was then used to identify changes during ageing and ex vivo nerve degeneration that were independent of sex, as well as changes that were sex-specific. ResultsEx vivo nerve degeneration induced extensive proteome remodelling in mouse sciatic nerves that was largely independent of age and sex. Principal component and clustering analyses clearly separated intact from degenerated nerves, while revealing only subtle age- and sex-related effects, with more pronounced ageing-associated changes in males. Approximately 20% of age-regulated proteins and 7-10% of degeneration-regulated proteins exhibited sex-specific expression patterns. Degeneration was characterised by increased abundance of lysosomal and repair-associated proteins alongside reduced myelin and axonal proteins, consistent with active tissue remodelling. In aged nerves, impaired protein clearance and partial pre-activation of degeneration-associated pathways suggested altered injury responses. Comparative analyses demonstrated positive correlations of protein abundance changes between ex vivo and in vivo degeneration datasets, although the temporal dynamics were altered in aged nerves. Pathway enrichment analyses identified coordinated regulation of metabolic, RNA-processing and vesicular transport pathways, while ageing was associated with enhanced immune signalling and reduced lipid metabolism. Sex-specific analyses revealed stronger inflammatory signatures in males, whereas females exhibited enrichment of metabolic pathways, including folate biosynthesis. ConclusionThese findings reveal distinct sex-specific molecular features of peripheral nerve ageing, characterised by enhanced inflammatory signalling in males and metabolic adaptations that may confer resilience in females. Our datasets provide a comprehensive molecular resource of sex-dependent changes in peripheral nerve ageing and nerve-intrinsic injury responses, offering a foundation for identifying therapeutic strategies to promote healthy peripheral nerve ageing. Plain English summaryAge-related peripheral neuropathies are common disorders that can cause pain, numbness, weakness and reduced mobility, affecting millions of people worldwide. They become more common from around the age of 50 and affect men and women differently. These conditions are thought to result from age-related changes in the structure and function of peripheral nerves, which reduce their ability to repair themselves after injury. In this study, we used advanced protein analysis (proteomics) to investigate how ageing affects peripheral nerves in male and female mice. We also used an ex vivo model, in which nerves are studied outside the body, to examine how age and sex influence the molecular changes that occur during nerve degeneration. We found that degeneration caused widespread changes in the proteins present in the sciatic nerve in both young and old mice. Most of these changes were similar in males and females, but some important differences emerged. Male nerves showed stronger signs of inflammation, whereas female nerves showed increased activity of metabolic pathways, including those involved in folate metabolism. Ageing nerves also appeared less able to remove damaged material and showed signs of activating degeneration-related processes even before injury. Overall, the ex vivo model reproduced many of the molecular changes seen after nerve injury in living animals, although it did not fully capture the inflammatory response, suggesting that signals from the rest of the body, including factors carried in the blood, also contribute to nerve degeneration. HighlightsO_LIEx vivo nerve degeneration caused major protein changes in young and old mouse sciatic nerves. C_LIO_LIMost degeneration-related protein changes were shared between males and females. C_LIO_LIAgeing altered the nerve proteome, with stronger ageing-related shifts in males. C_LIO_LIMale nerves showed stronger inflammatory and immune-related signatures. C_LIO_LIFemale nerves showed enrichment of metabolic pathways, including folate biosynthesis, and ex vivo degeneration did not fully reproduce the inflammatory response seen after injury in vivo. C_LI

neuroscience↗

bioRxiv2026

No Evidence for a Wakeful Rest Benefit on Associative Memory: A Within-Participant EEG Study

Wakeful rest after learning has been proposed to facilitate memory consolidation compared to engaging in a distraction task, with prior EEG studies linking slow oscillation power during rest to better memory performance. However, replication attempts have yielded mixed results. We investigated whether 10 minutes of wakeful rest would enhance associative memory performance relative to 10 minutes of a hippocampus-dependent auditory short-term memory distraction task, using a within-participant design with continuous EEG recording. We employed both a replication-inspired analytical approach, closely modeled on prior work, and a data-specific approach adapted to our dataset. Contrary to our hypotheses, we found no advantage of rest over distraction on associative memory performance. We did, however, observe an order effect: performance was better for the second learning than the first, and this improvement was more pronounced when rest was performed second compared to first. At the neurophysiological level, neither slow oscillation nor alpha power during the post-learning period correlated with memory performance, regardless of analytical pipeline, although cross-over analyses revealed that the choice of EEG reference influenced the direction of some correlations. At the phenomenological level, self-reported mental activity during rest and distraction, as well as trait daydreaming frequency, were not related to memory outcomes, despite the two conditions inducing distinct subjective cognitive states. Together, these findings do not support a robust benefit of post-learning wakeful rest over a hippocampus-dependent distraction task for associative memory, nor do they replicate prior EEG correlates of consolidation. We discuss methodological factors, including task-learning effects in within-participant designs, the coarseness of averaged spectral power measures, and variability in EEG preprocessing pipelines, that may contribute to inconsistencies across the literature, and we call for greater standardization and transparency in future studies.

neuroscience↗

bioRxiv2026

Shared Pain, Shared Decisions: How Empathy Shapes Social Conformity Through Physiology and Visual Attention

Empathy enables individuals to attune to others experiences through shared affective, sensorimotor, and neural representations, but its influence on higher-level decision-making and social alignment remains unknown. We examined whether empathy promotes social conformity and whether this effect depends on physiological arousal, visual attention, and socio-emotional traits. Seventy-three participants completed an empathy-for-pain task followed by a modified random-dot task in which they interacted with previously seen empathy targets, while physiological signals and eye movements were recorded. Drift-diffusion modeling showed that feedback from empathy targets increased conformity, reflected in stronger decision bias toward targets, faster evidence accumulation, and reduced decision conservatism. Visual attention to the eyes or mouth was linked to greater conformity depending on the context. Heart rate variability was unrelated to conformity, whereas phasic skin conductance was associated with smaller bias changes and greater conservatism. Alexithymia and autistic traits further shaped the empathy-conformity relationships. These findings suggest that empathic shared representation extends beyond affective resonance to influence social alignment in decision-making.

neuroscience↗

bioRxiv2026

Transposon end recognition and excision mechanisms of type I-F CRISPR-associated transposases

CRISPR-associated transposons (CASTs) are Tn7-like elements that have co-opted RNA-guided CRISPR effectors for targeted DNA insertion. CASTs have been adapted as genome editing tools for programmable, site-specific integration. Among them, the type I-F system from Pseudoalteromonas (PseCAST) shows uniquely robust activity in human cells, yet its mechanistic basis remains poorly understood. Here, we present structural and biochemical analysis of the PseCAST transposase TnsAB. Biochemical reconstitution of transposon DNA excision defines key characteristics of the transposition mechanism. Cryogenic electron microscopy (cryo-EM) structures of PseTnsAB paired-end complexes reveal molecular determinants of transpososome assembly, transposon end recognition and cleavage. We validate these findings using biochemical and in vivo assays of structure-based transposase mutants, and provide mechanistic insights into the enhanced activity of a laboratory-evolved TnsAB variant. Together, our studies highlight molecular features underlying the efficiency of natural and engineered type I-F transposases and establish a mechanistic framework for their continued rational optimization.

biochemistry↗

bioRxiv2026

A normative reference for large-scale human brain dynamics across the lifespan

Human brain function emerges from dynamic reconfigurations of large-scale neural networks. While population-level reference charts have transformed the study of static brain structure and connectivity, an equivalent normative framework for intrinsic brain dynamics has been lacking. This gap has limited our ability to characterize individual variability, development, ageing, and mental health conditions at scale. Here, we establish a population-level normative reference for large-scale human brain dynamics using resting-state fMRI data from more than 10,000 individuals spanning the lifespan and 91 scanning sites. We derive a compact set of recurring brain-state configurations that are reproducible across scanners and acquisition paradigms and that generalize to previously unseen cohorts. Anchoring these dynamic states to normative lifespan models enables the quantification of individual deviations relative to population reference distributions. We show that intrinsic brain dynamics undergo systematic reorganization across development and ageing, with pronounced changes before early adulthood and more gradual modulation thereafter. Applying this framework across multiple mental health conditions reveals disorder-specific and highly heterogeneous deviations in brain dynamics that are not captured by static neuroimaging measures. Robust transfer to independent cohorts and longitudinal analyses demonstrate that normative brain dynamics can be reliably assessed out of distribution. These results delineate a population-scale dynamic architecture of the human brain and extend normative brain mapping from static phenotypes to the temporal domain, providing a reference framework for studying brain function across the lifespan in health and disease.

neuroscience↗

bioRxiv2026

Convergent molecular signatures of ageing and injury in the peripheral nervous system

Peripheral nervous system (PNS) ageing is marked by structural and functional decline, yet it remains unclear whether ageing constitutes a distinct biological programme or reflects a chronic injury-like state. To address this, we performed an unbiased, comparative molecular analysis of PNS ageing, neuroprotective dietary restriction (DR), and nerve injury. We conducted transcriptomic and proteomic profiling of peripheral nerves from young, old and geriatric mice fed ad libitum or subjected to long-term DR, and proteomics of nerves collected at multiple time points following injury. Age-associated molecular changes followed both linear and non-linear trajectories, and DR partially attenuated these ageing-related alterations. Notably, ageing-and injury-induced proteomic signatures showed considerable similarities, supporting the concept that an aged nerve resembles an injured nerve. Together, our study provides the most comprehensive molecular resource of PNS changes during ageing, DR, and injury, enabling the definition of key molecular signatures underlying PNS physiology. All datasets are integrated into the "PNS-omics Viewer", a Shiny web application designed to facilitate data mining of the herein presented datasets (tba).

neuroscience↗

bioRxiv2025

From stomach to striatum: Ghrelin infusions increase work for rewards

Preclinical evidence demonstrates that gut signals influence motivated behavior through the dopaminergic system. However, translational research in humans is scarce, and it is not known if surges of the stomach-derived hormone ghrelin acutely boost motivation via dopamine transmission. To close this gap, we investigated the effects of acyl ghrelin infusions (vs. saline) on instrumental work for rewards, brain responses, and dopamine transmission in healthy adults in a double-blind, randomized and placebo-controlled crossover study with [11C]raclopride PET-fMRI. In line with preclinical findings, ghrelin enhanced hunger sensations (p = .007), and effort for food and small rewards. Crucially, ghrelin enhanced functional connectivity between the hypothalamus and the striatum (NAcc: pSVC = .016), as well as within the striatum (NAcc<>Putamen: pSVC = .001), pointing to an enhanced coupling between homeostatic and motivational circuits. However, ghrelin did not alter dopamine binding potential (reflecting changes in endogenous tone), but boosted task-free phasic pulses of the NAcc BOLD signal (p = .020), which were negatively associated with binding potential (p = .034). During the task, ghrelin increased cue- (precentral gyrus: pFWE = .003) and effort-evoked brain responses (e.g., VTA/SN: psvc = .002) in accordance with increases in motivation. Together, these findings recapitulate preclinical work that ghrelin primarily boosts phasic dopamine release, reflecting enhanced incentive salience of food and smaller rewards. This highlights the potential of targeting gut-brain interactions to improve motivational symptoms, such as loss of appetite or anhedonia. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=131 SRC="FIGDIR/small/691596v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@4321e6org.highwire.dtl.DTLVardef@166bda5org.highwire.dtl.DTLVardef@2ca69dorg.highwire.dtl.DTLVardef@16e93a9_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2025

Grey matter embedding of the cholinergic system

Integrity of acetylcholine-producing basal forebrain nuclei Ch1-4 is crucial for neurocognitive functioning and grey matter decline represents a hallmark of neuropsychiatric disorders, including Alzheimers disease, Parkinsons disease and schizophrenia. Approaches that link brain-wide grey matter atrophy with diminished cholinergic innervation from Ch1-4 projections are required for neuroimaging of disease stages and pharmacological decisions addressing cholinergic deficits. The current study assessed human magnetic resonance imaging-based markers for cholinergic nucleus subregions and synaptic targets in healthy exploration (HCP, n = 1113) and replication (IXI, n = 587) cohorts. Ch1-3 and Ch4 were delineated at 50% cytoarchitectonic probability to determine their grey matter coupling patterns using structural covariance analyses. Spatial colocalization with vesicular acetylcholine transporter, M1-muscarinic and 4{beta}2-nicotinic receptor density quantified the correspondence with synaptic cholinergic markers. All individual-level cholinergic nucleus and target region indices showed good test-retest reliability (R [≥] 0.80) when restricted to voxels with at least 10% grey matter probability. Spatial colocalization with presynaptic acetylcholine transporters emphasized a cholinergic nature of Ch1-4 grey matter and its coupling with corticopetal projections such as amygdala, insula and cingulate cortices. Subcortical gradients of M1-muscarinic receptor density and the Ch1-3 structural covariance map, however, dominated in locations of striatal cholinergic interneurons, such as nucleus accumbens, caudate nucleus and putamen. Ch4 covaried with medial thalamus and hippocampus, while both subregions structural covariance networks converged in a posterolateral Ch4 extensions, potentially resembling subputaminal nucleus of Ayala. The results emphasize Ch1-4 morphometry as marker for acetylcholine-driven brain regions and describe neuroimaging strategies to indicate synaptic cholinergic involvement. Significance StatementPrevious studies have suggested that grey matter alterations in basal forebrain Ch1-4 nuclei indicate cholinergic deficits in neurodegenerative and psychiatric pathologies. However, the use of Ch1-4 volume as a marker of cholinergic system integrity has yet to be validated. Additionally, there is a lack of non-invasive procedures to quantify integrity of regions innervated by its cholinergic projections. Our results suggest that grey matter coupling with Ch1-4 is a sensitive cholinergic system marker, mimicking the density distribution of synaptic cholinergic innervation. Furthermore, we introduce grey matter-based target region indices, evaluate their robustness in individual participants and describe regional contributions to M1-muscarinic, 4{beta}2-nicotinic and vesicular acetylcholine transporter gradients. The study advances our understanding of cholinergic circuits in vivo using magnetic resonance imaging.

neuroscience↗

bioRxiv2025

SLFN11 restricts escape from telomere crisis to prevent alternative lengthening of telomeres

The tRNA nuclease SLFN11 is epigenetically silenced in [~]50% of treatment-naive tumours and is the strongest predictor of chemoresistance but why it is frequently inactivated in cancer is unknown. To acquire immortality, cancer cells can activate alternative lengthening of telomeres (ALT), typically accompanied by ATRX loss. Here, we implicate SLFN11 in sensing telomere replication stress, triggering eradication of ATRX deficient cells prior to ALT establishment. Whereas progressive telomere shortening of cells lacking telomerase and ATRX leads to telomere crisis and cell death, SLFN11 loss confers tolerance to PML-BLM dependent ALT intermediates, permitting emergence of ALT survivors. We propose that during tumorigenesis SLFN11 inactivation is selected as means to tolerate endogenous replication stress following telomere crisis, leading to the development of therapy resistant tumours before treatment.

molecular biology↗

bioRxiv2025

Tracing colorectal malignancy transformation from cell to tissue scale

The transformation of normal intestinal epithelium into colorectal cancer (CRC) involves coordinated changes across molecular, cellular, and architectural scales; yet, how these layers integrate remains poorly resolved. Here, we survey colorectal tumorigenesis by combining whole-transcriptome spatial molecular imaging (WTx CosMx SMI) with single-nucleus RNA-sequencing (snPATHO-seq) and digital histopathology on colon samples containing reference mucosa, adenomas and carcinomas, as well as a metastatic lymph node. Leveraging (discrete) histological annotations and (continuous) data-driven trajectories, we quantify the dynamics of cellular density, heterogeneity, function and signaling along the reference-adenoma-carcinoma axis, which is concordant in its spatial and molecular definition. This combination of analytical approaches across different data views let us chart tissue transformation across dimensions (physical/transcriptional) and scales (cell/tissue). We resolve [~]3.5 million cells into 43 epithelial, immune, and stromal subpopulations that exhibit a bi-furcating tumor evolution: On the one hand, LGR5+ stem-like epithelial cells are enriched in highly homogeneous proliferative tumor cores. On the other hand, MMP7+ fetal-like states are restricted to immunosuppressive invasive fronts, rich in cancer-associated fibroblasts (CAFs) and tumor-associated macrophages. These subpopulations form concentric spatial layers that organize transformed regions, and their compound aligns with histological malignancy. We further define transition crypts - single colonic crypts with divided histological and transcriptional makeup - that arise from rare crypt fusion or abrupt transformation events. Finally, we trace MMP7+ fetal-like tumor cell states and concomitant myofibroblast-like FAP+ CAFs to lymphovascular invasion sites and matched lymph node metastases, thereby recapitulating invasive programs at single-cell resolution and across sites. In all, we present single cell- and WTx-resolved spatial data that are among the first of their kind. These open up spatial-centric, out-of-the-box analytical avenues to resolve the molecular, cellular and architectural dynamics that attend tissue transformation during CRC onset, progression and dissemination.

cancer biology↗

bioRxiv2025

Herpes simplex virus 1 strain 17+ with R2 mutation in UL37 has residual retrograde transport

Herpes simplex virus 1 (HSV-1) causes lifelong recurrent infections. Following primary infection of the oral or genital mucosa, HSV-1 travels retrogradely through axons and establishes latency in the cell body of ganglionic neurons of the peripheral nervous system. Periodic reactivation in neurons and anterograde transport of virions back to peripheral regions causes oral or genital ulcerations. Many host and viral factors implicated in retrograde and anterograde transport of HSV-1 have been identified. In particular, studies reported that introducing five amino acid substitutions in the R2 region of the viral tegument protein UL37 was sufficient to completely eliminate retrograde transport of HSV-1 strain F. Here, we introduced the same R2 mutations in the highly neurovirulent HSV-1 strain 17+. We report that this R217 virus has residual retrograde travel. We show that R217 can establish latency in mouse models of ocular and vaginal infection and reactivate. These results contradict published evidence and show that the R2 mutation is not sufficient to fully prevent retrograde transport of HSV-1.

microbiology↗

bioRxiv2025

Intracellular and extracellular dynamics of herpes simplex virus 1 DNA and infectious particles in epithelial and neuronal cells

Herpes simplex virus 1 (HSV-1) infection of epithelial cells is lytic, while infection of neurons typically results in long-term latency. However, the rates at which HSV-1 replicates and spreads in epithelial cells versus neurons under low and high multiplicity of infection (MOI) conditions remain undefined. Identifying these rates requires the application of mathematical models to carefully designed viral kinetic experiments. It is also critical to differentiate the dynamics of infectious viral particles versus viral DNA, as both quantities are routinely measured in in vitro experiments and human studies using plaque assays and polymerase chain reactions, respectively. Here, we developed mechanistic mathematical models to describe HSV-1 dynamics after infection of epithelial Vero cells and neuronal N2A cells, at high (3) and low (0.01) MOI. Our model recapitulates the dynamics of cell-free and cell-associated viral DNA and plaque-forming units (PFU). In epithelial cells, the model describes a pre-productive eclipse phase with a mean duration of 10.9 and 12.8 hours prior to HSV DNA replication and PFU production, respectively. Cells exited the eclipse phase as early and late as 2.5 and 32 hours, respectively. Infected cells produced a single PFU for every 224 HSV DNA genomes. PFU egressed at a constant rate, whereas the HSV DNA egress rate increased over time, before saturating at a 15 times higher rate. Under low relative to high MOI conditions, Vero cells spent 7 hours longer in the eclipse phase, had a 12-hour delay prior to egress, and had a longer mean duration of productive infection (14 versus 3.5-hour half-life). Secondary epithelial cell infection in low MOI experiments was overwhelmingly due to cell-to-cell viral spread and originated from a small number of early-producer cells. Neuronal cells produced viruses at a 5-fold lower rate and had a longer (mean: 42 hours) and more variable eclipse phase, with some neurons remaining in eclipse for more than a week. Our results highlighted large differences in HSV egress rates, as well as infected cell eclipse phase duration and death rates, in epithelial cells versus neurons during low and high MOI infection. The observed viral dynamics in neurons reflect a balance between active replication and latency.

microbiology↗

bioRxiv2025

An intercellular signaling pathway in the mouse retina connects Kv2.1, GLT-1, and nitric oxide synthase 1 to optic nerve regeneration

We report here that a multicellular signaling pathway in the mouse retina targeting glutamate homeostasis and nitric oxide production is activated upon optic nerve injury and modulates reti-nal ganglion cells (RGCs) ability to mount a robust regenerative response. A novel highly sen-sitive and specific NO sensor (FL2) revealed that optic nerve injury leads to a rapid, prolonged elevation of NO in the inner retina. Amacrine cell-specific genetic deletion of the neuron-specific isoform of nitric oxide synthase (NOS1, nNOS) or the NOS1 inhibitor N(w)-propyl-L-arginine (L-NPA) suppressed optic nerve regeneration. Steps leading to NOS1 activation are shown to in-clude Kv2.1 phosphorylation and activation, reversal of glutamate uptake by the glutamate transporter GLT-1 (EAAT2), and subsequent NMDA receptor activation. Conditional knockout of the glutamate transporter GLT-1 in bipolar cells, intraocular injection of the GLT-1 blockers dihydrokainate (DHK) or WAY213613, the N-methyl-D-aspartate (NMDA) receptor antagonist D-2-amino-5-phosphonovalerate (D-AP5), or the Kv2.1 blockers RY796 or stromatoxin all sup-pressed NO generation and strongly diminished RGCs ability to respond to Pten deletion and other factors. Thus, optic nerve injury activates a sequence of pathophysiological changes in retinal interneurons that gates RGCs ability to regenerate injured axons. Significance StatementCells use extracellular signals to coordinate responses to injury and to promote repair and re-generation. The NMDA receptor, which has a high affinity for glutamate and is functionally cou-pled to nitric oxide synthase, has the potential to mediate such responses by responding to changes in extracellular glutamate. In the mouse retina after optic nerve injury, potassium channels in retinal ganglion cells, glutamate transporters in neighboring cells, and NMDA recep-tors in amacrine cells, are all involved in a pathway that regulates the generation of nitric oxide, which we show promotes axon regeneration after injury.

neuroscience↗

bioRxiv2025

Molecular surface mimicry enables CRBN to target G3BP2 for degradation

Molecular glue degraders (MGDs) are small molecule compounds that repurpose the ubiquitin-proteasome system to induce degradation of challenging therapeutic targets. Clinically effective MGDs bind cereblon (CRBN), a substrate receptor of the Cullin-4/RING E3 ubiquitin ligase (CRL4CRBN), and impose a gain-of-function activity to recruit, ubiquitinate and degrade so-called neosubstrate proteins. Known neosubstrates bind the CRBN/MGD neosurface on the CRBN CULT domain through a structural G-loop recognition motif that mimics contacts of a natural CRBN degron. Here we report the binding mode of G3BP2, a CRBN neosubstrate that bypasses the G-loop requirement by engaging an unconventional binding site on the CRBN LON domain. The MGD-induced ternary complex interface does not resemble known protein-protein interactions (PPI) with CRBN. Instead, CRBN mimics an endogenous binding partner of G3BP2 and repurposes a preexisting PPI hotspot on the target protein. Our findings provide a novel generalizable concept for the rationalization of unconventional neosubstrate binding modes on CRBN, demonstrate unprecedented potential for the reprogrammability of this substrate receptor by MGDs, and offer opportunities for rational expansion of the target repertoire accessible to this modality.

molecular biology↗

bioRxiv2025

Minimization of gene editing off-target effects by tissue restriction of expression

Therapeutic in vivo gene editing with highly specific nucleases has the potential to revolutionize treatment for a wide range of human diseases, including genetic disorders and latent viral infections like herpes simplex virus (HSV). However, challenges regarding specificity, efficiency, delivery, and safety must be addressed before its clinical application. A key concern is the risk of off-target effects, which can cause unintended and potentially harmful genetic changes. We previously developed a curative in vivo gene editing approach to eliminate latent HSV using HSV-specific meganuclease delivered by an AAV vector. In this study, we investigate off-target effects of meganuclease by identifying potential off-target sites through GUIDE-tag analysis and assessing genetic alterations using amplicon deep sequencing in tissues from meganuclease treated mice. Our results show that meganuclease expression driven by a ubiquitous promoter leads to high off-target gene editing in the mouse liver, a non-relevant target tissue. However, restricting the meganuclease expression with a neuron-specific promoter and/or a liver-specific miRNA target sequence efficiently reduces off-target effects in both liver and trigeminal ganglia. These findings suggest that incorporation of regulatory DNA elements for tissue-specific expression in viral vectors can reduce off-target effects and improve the safety of therapeutic in vivo gene editing.

molecular biology↗

bioRxiv2024

In silico PK predictions in Drug Discovery: Benchmarking of Strategies to Integrate Machine Learning with Empiric and Mechanistic PK modelling

A successful drug needs to combine several properties including high potency and good pharmacokinetic (PK) properties to sustain efficacious plasma concentration over time. To estimate required doses for preclinical animal efficacy models or for the clinics, in vivo PK studies need to be conducted. While the prediction of ADME properties of compounds using Machine Learning (ML) models based on chemical structures is well established in drug discovery, the prediction of complete plasma concentration-time profiles has only recently gained attention. In this study, we systematically compare various approaches that integrate ML models with mechanistic PK models to predict PK profiles in rats after i.v. administration prior to synthesis. More specifically, we compare a standard noncompartmental analysis (NCA) based approach (prediction of CL and Vss), a pure ML approach (non-mechanistic PK description), a compartmental modeling approach, and a physiologically based pharmacokinetic (PBPK) approach. Our study based on internal preclinical data shows that the latter three approaches yield PK profile predictions of comparable accuracy (evaluated as geometric mean fold errors for each profile) across a large test set (>1000 small molecules). In summary, we demonstrate the improved ability to prioritize drug candidates with desirable PK properties prior to synthesis with ML predictions.

bioinformatics↗

bioRxiv2024

Connecting the Dots: Approaching a Standardized Nomenclature for Molecular Connectivity Combining Data and Literature

PET-based connectivity computation is a molecular approach that complements fMRI-derived functional connectivity. However, the diversity of methodologies and terms employed in PET connectivity analysis has resulted in ambiguities and confounded interpretations, highlighting the need for a standardized nomenclature. Drawing parallels from other imaging modalities, we propose "molecular connectivity" as an umbrella term to characterize statistical dependencies between PET signals across brain regions at the individual level (within-subject). Like fMRI resting-state functional connectivity, "molecular connectivity" leverages temporal associations in the PET signal to derive brain network associations. Another within-subject approach evaluates regional similarities of tracer kinetics, which are unique in PET imaging, thus referred to as "kinetic connectivity". On the other hand, "molecular covariance" denotes group-level computations of covariance matrices across-subject. Further specification of the terminology can be achieved by including the employed radioligand, such as "metabolic connectivity/covariance" for [18F]FDG as well as "tau/amyloid covariance" for [18F]flutemetamol / [18F]flortaucipir. To augment these distinctions, high-temporal resolution functional [18F]FDG PET scans from 17 healthy participants were analysed with common techniques of molecular connectivity and covariance, allowing for a data-driven support of the above terminology. Our findings demonstrate that temporal band-pass filtering yields structured network organization, whereas other techniques like 3rd order polynomial fitting, spatio-temporal filtering and baseline normalization require further methodological refinement for high-temporal resolution data. Conversely, molecular covariance from across-subject data provided a simple means to estimate brain region interactions through regularized or sparse inverse covariance estimation. A standardized nomenclature in PET-based connectivity research can reduce ambiguity, enhance reproducibility, and facilitate interpretability across radiotracers and imaging modalities. Via a data-driven approach, this work provides a transparent framework for categorizing and comparing PET-derived connectivity and covariance metrics, laying the foundation for future investigations in the field.

neuroscience↗