Biology subjects

Grant, S. G. N.

Publications and source records attributed to Grant, S. G. N..

At least 19 recordsLinked to original sources

bioRxiv2026

Stage-specific proteomic signatures of synaptopathy in Alzheimers disease

Synapse loss is the strongest pathological correlate of cognitive decline in Alzheimers disease, yet the molecular basis of synaptic vulnerability across disease progression remains poorly understood. We performed proteomic profiling of isolated synaptoneurosomes from post-mortem middle temporal gyrus tissue from 67 individuals, comprising 40 individuals spanning all Alzheimers disease Braak stages and 27 non-diseased controls. Differential abundance and weighted gene co-expression network analyses were combined with pathway, cell-type and gene set variation analyses to characterise stage-associated changes in the synaptic proteome. Brain-derived candidate proteins were subsequently evaluated using receiver operating characteristic and regression analyses against cognitive examination scores in two independent plasma proteomics datasets. We identified six distinct stage-associated synaptic proteomic signatures. Mitochondrial function and synaptic signalling declined by mid-stage Alzheimers disease, while clathrin-mediated endocytosis increased at mid-stage without further change at later stages. By contrast, proteostasis and perisynaptic astrocytic processes increased progressively throughout the disease course. Global excitatory and inhibitory protein signals also showed a progressive shift in their relative balance (P = 7.80 x 10-3; adjusted R{superscript 2} = 0.072). These findings guided targeted investigation of candidate plasma markers linked to distinct synaptic processes in two independent proteomic datasets. We nominated 42 plasma proteins mapping to synaptic signatures of progression, which showed associations with disease stage and cognitive measures including Mini-Mental State Examination, Montreal Cognitive Assessment and Clinical Dementia Rating. PHGDH was prioritised across analyses through associations with cognitive impairment from early disease stages (Clinical Dementia Rating transition 0 to 0.5, false discovery rate = 8.87 x 10-18), neuropathological progression (P = 6.85 x 10-7) and excitatory-inhibitory protein imbalance (P = 5.56 x 10-3). Together, our findings define the stage-associated molecular changes at the AD synapse and connect distinct brain pathways to accessible plasma candidates, establishing a mechanistically anchored framework for future patient stratification and evaluation of synapse-directed therapies.

neuroscience↗

bioRxiv2026

Discovery of the Honeycomb Synapse in Spinal Motor Circuits

The structural and molecular diversity of synapses in the nervous system contributes to the specialisation of neural circuits underlying diverse behaviours. We have discovered a morphologically distinct postsynaptic specialisation in the mammalian spinal cord. We have named this the Honeycomb Synapse based on its elaborate postsynaptic nanostructure, comprising rings formed of ~6 scaffolding protein domains that create multiple perforations throughout the large postsynaptic domain. Analysis of the organisation of other synaptic proteins reveals that Honeycomb Synapses harbour mixed signalling properties structurally facilitated by a postsynaptic scaffold matrix supporting chemical transmission, with gap junction proteins occupying some of the perforations. We reveal anatomical diversity in the presence of Honeycomb Synapses on populations of -motoneurons across the lumbar spinal cord in mice from approximately 2 weeks of age through to adulthood. The Honeycomb Synapse was found to be a subtype of synapse within the Ia afferent monosynaptic stretch reflex circuit. Finally, we have identified that Honeycomb Synapses are highly vulnerable to degeneration in two different genetically engineered mouse models of Amyotrophic Lateral Sclerosis (ALS), contributing to monosynaptic stretch reflex circuit dysfunction. These findings suggest that synaptic diversity within circuits may confer selective vulnerability to distinct synaptic subclasses.

neuroscience↗

bioRxiv2026

A Brainwide Atlas of Synaptic Nanoarchitecture Across the Mouse Lifespan

How biological complexity emerges from the ordered assembly of molecular building blocks into supramolecular systems remains a central question, particularly in the mammalian brain with its vast synaptic diversity. We introduce NanoSYNMAP, a genetic, optical, and computational platform that integrates FRET with synaptome mapping to quantify nanoscale proximity of proteins in individual synapses brain-wide. We generate the first brain atlas of synaptic nanoarchitecture, based on the proximity of postsynaptic MAGUK supercomplexes. This reveals a molecular logic in which spacing of supramolecular assemblies specifies nanoscale architecture that organizes the global synaptome architecture. Nanoarchitecture varies across brain regions, differentiates during postnatal development, and remodels with aging. Supercomplex proximity reflects scaffold abundance, nanodomain organization, and competitive interactions among MAGUK assemblies. Deletion of a neuropsychiatric risk gene triggers widespread reorganization of nanoscale architecture. These findings establish molecular proximity as a fundamental scalable dimension of synapse diversity in health and disease.

neuroscience↗

bioRxiv2025

Shapes of synaptic protein distributions distinguish brain architectures

Neuronal activity is the result of the orchestrated actions of multitudes of synapses, acting and evolving not as individuals, but as populations. We therefore collected, for millions of synapses, a functionally relevant proxy for their strengths. Namely, we measured postsynaptic protein content by deploying a fluorescent PSD95 variant. Then we summarized, by statistical moments, the shapes of the distributions of protein contents, over local synaptic populations. In this way we explored the hypothesis that such collective properties inform on brain architectures. Our measurements cover complete parasagittal sections of the mouse brain, in animals one week to 18 months old. We identified a hierarchical organization of regions along the anterior-posterior axis, with three main clusters of divergent synaptic population shapes. One includes telencephalic regions, one is centered in the midbrain and hindbrain, and one comprises mainly the thalamus and the cerebellum. The structure emerging from our approach aligns with discoveries in studies of regional patterns of cellular gene expressions. Our results suggest that synaptic populations are dynamically regulated over the lifespan. Regions which at three months of age have thinner tails largely conserve their distribution shapes later in life, whereas heavy tails in other regions strikingly grow ever more so.

neuroscience↗

bioRxiv2025

Distributed disruption and remodelling of synaptome architecture following traumatic brain injury

A single cortical impact in mice altered the number and molecular composition of excitatory synapses across 222 brain regions. Early effects targeted synapses with rapid protein turnover, followed by changes in slow-turnover synapses. This injury-induced remodelling of synaptome architecture mirrors responses to genetic mutation, ageing, sleep deprivation and experience, suggesting that reorganisation of excitatory synapse populations is a shared mechanism underlying brain plasticity across diverse conditions.

neuroscience↗

bioRxiv2025

The Overlap Area as a Novel Measure of Effect Size in Neuroscience Research

In experimental biomedical research, a common concern is whether a manipulation produces a biologically meaningful effect. Another concern is whether effect sizes are reliable, statistically significant, and generalizable. Traditional effect size measures, such as Cohens d, quantify mean differences but ignore variance heterogeneity between groups. This can result in biased effect size estimates and a lack of thresholds for statistical significance testing. Motivated by this, we introduce a novel effect size measure, termed overlap area (OA), which quantifies the difference between the population distributions of the experimental and control groups. A robust Bayesian method estimated OA, and random resampling determined OA thresholds for statistical significance in single and replicated experiments. Simulations confirmed the approachs sensitivity and robustness. Applied to a real-world dataset, OA revealed that environmental enrichment affects the mouse brain synaptome. Moreover, we developed an open-source toolbox supporting OA as a powerful new measurement for conducting robust, reliable, and reproducible analyses of manipulation effects in neuroscience and related fields.

neuroscience↗

bioRxiv2025

Experiences are encoded by brainwide reprogramming of synaptome architecture

Synaptome architecture describes the spatiotemporal distribution of highly diverse excitatory synapses throughout the brain. Whether and how this architecture is impacted by experience is key to understanding its role in learning and memory. We found that environmental enrichment and monocular visual deprivation drive large-scale, type-and subtype-specific reorganisation of excitatory synapses in more than one hundred brain regions. Each experience modifies distinct subsets of synapses, with patterns aligned with protein turnover rates and connectome architecture. These reorganisations occur during development and adulthood, revealing a conserved mechanism of synaptome plasticity across the lifespan. Our findings support a population-selection model in which experience drives adaptation by selectively modifying synapse varieties, generating a distributed trace of past experiences. Our results also point to synaptome architecture as a shared framework integrating experience, lifespan changes, sleep, genetic variation and disease.

neuroscience↗

bioRxiv2025

Developmental plasticity facilitates the structural maturation of cochlear inner hair cell ribbon synapses

Sound detection occurs in the cochlea, where sensory inner hair cells (IHC) accurately convert auditory stimuli into neurochemical signals. Presynaptically, IHCs harbor synaptic ribbons, specialized scaffolds that facilitate ultrafast and indefatigable exocytosis. During synapse assembly and subsequent maturation, IHC ribbons increase in volume and synaptic vesicle tethering capacity. This development is thought to result from progressive precursor aggregation. However, the underlying mechanisms of ribbon synapse formation have remained elusive thus far. In this study, we established a novel triple-color live-cell imaging approach to monitor IHC pre-synaptogenesis in situ. We found that ribbon precursors are highly dynamic and undergo bidirectional plasticity. The presynaptic active zone (AZ) forms a focal point for dramatic structural remodeling of precursors, which the AZ recruits, confines and redistributes. Furthermore, silencing spontaneous synaptic activity decreased precursor mobility and plasticity at the AZ. This suggests a fundamental role for activity-dependent Ca2+ influx in the plastic development shaping the unique properties of auditory ribbon synapses.

neuroscience↗

bioRxiv2025

PRMix: Primary Region Mix Augmentation and Benchmark Dataset for Precise Whole Mouse Brain Anatomical Delineation

The architecture of the mouse brain shares remarkable similarities with the human brain, making it an essential model for studying brain pathologies, synaptic diversity, and regional specialization. A key step in such studies involves registering molecular images to reference brain atlases, a process hindered by the difficulty of accurately delineating brain regions. Toward this, we have curated a collection of high-resolution, dual-fluorescence microscopy images, termed as dual-fluorescence mouse brain microscopy (DMBM) dataset, complemented by expert annotations of 118 subregions. This dataset provides unprecedented insights into the molecular and structural complexity of the mouse brain. However, its full potential for detailed whole-brain analysis is compromised by challenges such as boundary ambiguity and sample scarcity in existing automated segmentation methods, prompting the development of the primary region mix (PRMix) augmentation method. PRMix is specifically designed to expand these datasets, enhance the realism of synthetic data and minimize overlap between adjacent regions. Our approach, together with the curated dataset, achieves superior segmentation performance across the mouse brain compared with existing methods, setting a new benchmark in brain imaging research. Code and data are available at https://git-pages.ecdf.ed.ac.uk/dmbm-datasets-5c13cd/.

neuroscience↗

bioRxiv2025

Protein trafficking and synaptic demand configure complex and dynamic synaptome architectures of individual neurons

Excitatory synapses are the most abundant synapse type in the brain. Being essential for behaviour and are implicated in hundreds of brain disorders, these synapses exhibit striking structural and functional diversity. Synaptome mapping at single-synapse resolution reveals that synaptic protein diversity is spatially organised along the dendritic tree of individual neurons and varies with age and cell-type. However, the cell biological mechanisms underlying the generation of these complex spatial synaptic patterns remain poorly understood. Potential mechanisms include somatic and dendritic protein synthesis, protein trafficking, and local regulatory mechanisms such as activity-dependent degradation. Here we developed computational models to test how combinations of these processes account for empirical synaptome data. We found that a combination of molecular transport mechanisms and local synaptic demand for proteins was sufficient to explain very complex profiles of synaptic protein distributions observed in young, mature and old mice and in different cell types. Our findings suggest the highly complex and dynamic synaptome architecture of the brain is an emergent property of a minimal set of cell biological processes. Our model sets the stage for simulations of brain tissue incorporating molecularly diverse neuronal and synaptic types in a synaptome and connectome architecture.

neuroscience↗

bioRxiv2025

SynaptopathyDB: a resource for studying the genetic and synaptic basis of nervous system disorders

Synaptic dysfunction resulting from pathogenic variants in genes encoding synaptic proteins is a major contributor to brain and behavioural disorders, collectively termed synaptopathies. To facilitate research into the genetic basis and clinical manifestations of synaptopathy we have created SynaptopathyDB, an online resource that integrates data from 64 mammalian synapse proteomic studies and multiple genetic and phenotypic resources. We identified a consensus set of 3,437 mammalian synapse proteins from presynaptic and postsynaptic compartments, which have wide application in genetic and omic studies. Mutations in 954 genes encoding 28% of the consensus synapse proteome were associated with 1,266 OMIM diseases of the central and peripheral nervous system. We present findings that underscore the pervasive role of synaptic gene variants in the phenotypes of neurological, psychiatric, developmental, and systemic disorders highlighting the significant burden they impose on individuals and healthcare systems. SynaptopathyDB is a versatile platform and discovery tool for understanding the role of synapse proteins and genetic variants in human disease phenotypes.

neuroscience↗

bioRxiv2025

Synaptome architecture shapes regional dynamics in the mouse brain

Synapses are the connections that transform neurons from simple electrically charged cells into complex circuits that support perception, cognition and action. Recent advances in single-punctum synapse mapping in mice have made it possible to study the diversity of synapses and how these synapse types are differentially expressed across the brain. A salient question is how synapse diversity shapes the spatial patterning of whole-brain dynamics. Here we derive > 6 000 time-series features from fMRI recordings in awake mice to construct a comprehensive macroscale dynamical phenotype of each synapse type. We find that spatial variation in synapse types colocalizes with spatial variation in regional dynamics. Time-series in regions enriched for SAP102-expressing synapses display high-amplitude events while time-series in regions enriched for PSD95-expressing synapses display low stationarity. These regional variations in synapse types and dynamics are associated with patterns of structural and functional connectivity and the placement of hubs. Finally, using two additional fMRI datasets in anaesthetized mice, we show that synapses expressing short- and long-lifetime proteins are differentially engaged across behavioural states. Collectively, this work demonstrates that the spatial organization of microscale synapse types fundamentally shapes whole-brain dynamics.

neuroscience↗

bioRxiv2024

Non-ionotropic signaling through the NMDA receptor GluN2B carboxy terminal domain drives morphological plasticity of dendritic spines and reverses fragile X phenotypes in mouse hippocampus

It is well known that activation of NMDA receptors can trigger long-term synaptic depression (LTD) and that a morphological correlate of this functional plasticity is spine retraction and elimination. Recent studies have led to the surprising conclusion that NMDA-induced spine shrinkage proceeds independently of ion flux and requires the initiation of de novo protein synthesis, highlighting an unappreciated contribution of mRNA translation to non-ionotropic NMDAR signaling. Here we used NMDA-induced spine shrinkage in slices of mouse hippocampus as a readout to investigate this novel modality of synaptic transmission. By using selective pharmacological and genetic tools, we find that structural plasticity is dependent on the ligand binding domain (LBD) of GluN2B-containing NMDA receptors and that metabotropic signaling occurs via the GluN2B carboxyterminal domain (CTD). Disruption of signaling by replacing the GluN2B CTD with the GluN2A CTD leads to increased spine density, dysregulated basal protein synthesis, and epileptiform activity in area CA3 reminiscent of phenotypes observed in the Fmr1-/y model of fragile X syndrome. By crossing the Fmr1-/y mice with animals in which the GluN2A CTD has been replaced with the GluN2B CTD, we observe a correction of these core fragile X phenotypes. These findings suggest that non-ionotropic NMDAR signaling through GluN2B may represent a novel therapeutic target for treatment of fragile X and related causes of intellectual disability and autism.

neuroscience↗

bioRxiv2024

3D super-resolution imaging of PSD95 reveals an abundance of diffuse protein supercomplexes in the mouse brain

PSD95 is an abundant scaffolding protein that assembles multiprotein complexes controlling synaptic physiology and behavior. Confocal microscopy has previously shown that PSD95 is enriched in the postsynaptic terminals of excitatory synapses and 2D super-resolution microscopy further revealed that it forms nanoclusters. In this study, we utilized 3D super-resolution microscopy to examine the nanoarchitecture of PSD95 in the mouse brain, characterizing over 8 million molecules. While we were able to identify structural subtypes previously reported, imaging in 3D allowed us to classify these with higher accuracy. Furthermore, 3D super-resolution microscopy enabled the quantification of protein levels, revealing an abundance of PSD95 molecules existed outside of synapses as a diffuse population of supercomplexes, containing multiple copies of PSD95. Further analysis of the supercomplexes containing two units identified two populations: one that had PSD95 molecules separated by 39 {+/-} 2 nm, and a second with a separation of 94 {+/-} 27 nm. These results suggest that PSD95 supercomplexes containing multiple protein copies assemble outside the synapse and then integrate into the synapse to form a supramolecular nanocluster architecture.

biophysics↗

bioRxiv2024

SV2A is expressed in synapse subpopulations in mouse and human brain: implications for PET radiotracer studies

Synapse pathology is a feature of most brain diseases and there is a pressing need to monitor the onset and progression of this pathology using brain imaging in living patients. A major step toward this goal has been the development of small-molecule radiotracers that bind to synaptic vesicle glycoprotein 2A (SV2A) for use in positron emission tomography (PET). Changes in SV2A radiotracer binding in PET are widely interpreted to report differences in the density of all synapses throughout brain regions. Here, we analyse the expression of SV2A at single-synapse resolution across regions of adult mouse and human brain. We find that SV2A is expressed in fewer than 50% of excitatory and inhibitory synapses and that the density of SV2A-positive synapses differs between brain regions. Furthermore, individual synapses differ in their amounts of SV2A. These findings have important implications for the interpretation of PET imaging studies in a clinical setting and point to the need for a detailed understanding of SV2A synaptome architecture in both healthy brain and disease cases where PET imaging is being applied.

neuroscience↗

bioRxiv2024

MINFLUX fluorescence nanoscopy in biological tissue

Optical imaging access to nanometer-level protein distributions in intact tissue is a highly sought-after goal, as it would provide visualization in physiologically relevant contexts. Under the unfavorable signal-to-background conditions of increased absorption and scattering of the excitation and fluorescence light in the complex tissue medium, super-resolution fluorescence microscopy methods are severely challenged in attaining precise localization of molecules. We reasoned that the typical use of a confocal detection pinhole in MINFLUX nanoscopy, suppressing background and providing optical sectioning, should facilitate the detection and resolution of single fluorophores even amid scattering and optically challenging tissue environments. Here, we investigated the performance of MINFLUX imaging for different synaptic targets and fluorescent labels in tissue sections of the mouse brain. Single fluorophores were localized with a precision of < 5 nm at up to 80 {micro}m sample depth. MINFLUX imaging in two color channels allowed to probe PSD95 localization relative to the spine head morphology, while also visualizing presynaptic VGlut clustering and AMPA receptor clustering at the post-synapse. Our two-dimensional (2D) and three-dimensional (3D) two-color MINFLUX results in tissue, with < 10 nm 3D fluorophore localization, open up new avenues to investigate protein distributions on the single-synapse level in fixed and living brain slices.

biophysics↗

bioRxiv2023

Sleep maintains excitatory synapse diversity in the cortex and hippocampus

How sleep deprivation affects cognition remains elusive. Synaptome mapping of excitatory synapses in 125 regions of the mouse brain revealed that sleep deprivation selectively reduces synapse diversity in the cortex and hippocampus. Sleep deprivation targeted specific types and subtypes of excitatory synapses while maintaining total synapse density. Altered synaptic responses to neural oscillations in a computational model suggest that sleep prevents cognitive impairments by maintaining normal brain synaptome architecture.

neuroscience↗

bioRxiv2023

The organisation and turnover of synaptic proteins within molecular supercomplexes.

The concept that dimeric protein complexes in synapses can sequentially replace their subunits has been a cornerstone of Francis Cricks 1984 hypothesis, explaining how long-term memories could be maintained in the face of short protein lifetimes. However, it is unknown whether the subunits of protein complexes that mediate memory are sequentially replaced in the brain and if this process is linked to protein lifetime. We address these issues by focusing on supercomplexes assembled by the abundant postsynaptic scaffolding protein PSD95, which plays a crucial role in memory. We used single-molecule detection, super-resolution microscopy and MINFLUX to probe the molecular composition of PSD95 supercomplexes in mice carrying genetically encoded HaloTags, eGFP and mEos2. We found a population of PSD95-containing supercomplexes comprised of two copies of PSD95, with a dominant 12.7 nm separation. Time-stamping of PSD95 subunits in vivo revealed that each PSD95 subunit was sequentially replaced over days and weeks. Comparison of brain regions showed subunit replacement was slowest in the cortex, where PSD95 protein lifetime is longest. Our findings reveal that protein supercomplexes within the postsynaptic density can be maintained by gradual replacement of individual subunits providing a mechanism for stable maintenance of their organization. Moreover, we extend Cricks model by suggesting that synapses with slow subunit replacement of protein supercomplexes and long protein lifetimes are specialized for long-term memory storage and that these synapses are highly enriched in superficial layers of the cortex where long-term memories are stored.

neuroscience↗