Synaptic pathology in ALS-FTD
Lead Research Organisation:
UNIVERSITY OF EDINBURGH
Department Name: Centre for Clinical Brain Sciences
Abstract
Dementia will affect 1 in 3 people in their lifetime. The inexorable decline in mental function, mood and movement ability comes about because of damage to synapses - the connections between nerve cells. Synapses come in many varieties and particular types are affected as dementia progresses. By finding and tracking these damaged synapses we can understand how the brain is damaged in dementia and help to bring on improvements in the diagnosis and treatment of these diseases.
We have recently developed ground-breaking technology that enables us to examine billions of individual synapses in the human brain and discover how the are damaged. We will now drive this technology forward to discover the synapses that are damaged in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). ALS, or motor neuron disease, is a rapidly progressive, fatal condition which overlaps clinically, genetically and pathologically with frontotemporal dementia (FTD). ALS-FTD are the commonest forms of neurodegenerative disease in people under 65 years of age.
Our team of scientists from the UK and Japan will use several state-of-the-art microscopy methods to examine synapses in post-mortem brain tissue obtained from individuals who have had their behavioural features examined during life. This will potentially enable us to identify the synapses that when damaged cause speech and language impairments, deterioration in mood and emotions, and movement disorders.
The tools and knowledge from our program will inform on the use of brain imaging methods in the clinic and trials of therapies aimed at preventing the progression of ALS-FTD and other dementias. Our findings will also provide valuable data resources that can be exploited by the international scientific community to advance our understanding of the brain and its diseases,
We have recently developed ground-breaking technology that enables us to examine billions of individual synapses in the human brain and discover how the are damaged. We will now drive this technology forward to discover the synapses that are damaged in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). ALS, or motor neuron disease, is a rapidly progressive, fatal condition which overlaps clinically, genetically and pathologically with frontotemporal dementia (FTD). ALS-FTD are the commonest forms of neurodegenerative disease in people under 65 years of age.
Our team of scientists from the UK and Japan will use several state-of-the-art microscopy methods to examine synapses in post-mortem brain tissue obtained from individuals who have had their behavioural features examined during life. This will potentially enable us to identify the synapses that when damaged cause speech and language impairments, deterioration in mood and emotions, and movement disorders.
The tools and knowledge from our program will inform on the use of brain imaging methods in the clinic and trials of therapies aimed at preventing the progression of ALS-FTD and other dementias. Our findings will also provide valuable data resources that can be exploited by the international scientific community to advance our understanding of the brain and its diseases,
Technical Summary
Synapse loss and damage is a hallmark of neurodegenerative disease. New molecular imaging methods reveal that there is a far greater diversity of synapse types than previously known, and that these are spatially distributed across nerve cells, brain regions and the whole brain into a remarkable spatial organisation. This 'synaptome architecture' provides a roadmap for understanding how molecular perturbations, such as genetic disorders, pathogenic proteins and drug interactions, can impact on specific synapses, circuits and brain regions. Crucially, we know that specific types of synapses - some are vulnerable, whereas others are resistant - are targeted in neurological disease. Although synapse loss in neurodegenerative disorders is well documented, very little is known about the nature of vulnerable and resilient synapses and how they are involved in the behavioural features of dementia. To address this, we will study the synaptome architecture of Amyotrophic Lateral Sclerosis (ALS) and Fronto-Temporal Dementia (FTD), which share clinical, genetic and pathological features.
We will use a collection of samples from ALS-FTD cases that were characterised in life with the Edinburgh Cognitive and Behavioural ALS Screen. Four brain regions aligned to executive and language functions have been selected, allowing the synaptic pathology of specific brain areas to be correlated with behavioural phenotypes. The molecular and morphological properties of synapses from 75 ALS-FTD cases and 10 age-matched controls will be examined with multiple complementary microscopy platforms (high throughput spinning disk confocal microscopy, expansion microscopy, super-resolution microscopy, and electron microscopy), which together are capable of characterising billions of individual synapses and resolving their architecture at nanoscale resolution. The protocols and tools developed can be applied to the study of synapse pathology in any brain disease.
We will use a collection of samples from ALS-FTD cases that were characterised in life with the Edinburgh Cognitive and Behavioural ALS Screen. Four brain regions aligned to executive and language functions have been selected, allowing the synaptic pathology of specific brain areas to be correlated with behavioural phenotypes. The molecular and morphological properties of synapses from 75 ALS-FTD cases and 10 age-matched controls will be examined with multiple complementary microscopy platforms (high throughput spinning disk confocal microscopy, expansion microscopy, super-resolution microscopy, and electron microscopy), which together are capable of characterising billions of individual synapses and resolving their architecture at nanoscale resolution. The protocols and tools developed can be applied to the study of synapse pathology in any brain disease.
Organisations
- UNIVERSITY OF EDINBURGH (Collaboration, Lead Research Organisation)
- University of Tokyo (Collaboration)
- Columbia University (Collaboration)
- UK Dementia Research Institute (Collaboration)
- Nikon (Collaboration)
- New York Genome Center (Collaboration)
- University of Strathclyde (Collaboration)
- Niigata University (Collaboration)
- Nikon (International) (Project Partner)
| Description | The loss and malfunction of synapses - the billions of connections between nerve cells (neurons) in the brain - underlies many neurological conditions, including dementias such as ALS-FTD. To fully understand the impact of ALS-FTD on the human brain we need to be able to compare the number and types of synapses (collectively, the 'synaptome') between ALS-FTD cases and healthy individuals. This is challenging for a number of reasons, not least the large size of the human brain. In this and parallel projects we have successfully developed 'human synaptome mapping', a method to describe and compare brain synaptomes at both single-synapse resolution and large scale. Human synaptome mapping uses antibodies to label different synapse proteins (e.g. PSD95), which are present in different synapse types, in sections of tissue obtained from Edinburgh Brain Bank. The sections are observed by confocal microscopy and the images obtained are processed through a computational pipeline that reports the number, type and location of each synapse labelled, producing a comprehensive brain synaptome map. Using an ever expanding toolbox of tried-and-tested synaptic protein antibodies, we have mapped an area of the primary motor cortex, a known ALS-FTD target region, in 20 ALS cases and 24 age-matched controls. This first-ever synaptome-level analysis has uncovered a distinct synaptic pathology focussed on PSD95-positive excitatory synapse subtypes. The ALS impact signature nonetheless shares underlying features with those of Alzheimer's disease and schizophrenia, as revealed by our parallel human synaptome mapping studies, including a tendency to reduce synapse diversity across cortical layers. This is likely to reflect a loss of disease-specific vulnerable synapse types and a reduction in cortical computational capacity. Synapse loss is a prominent neuropathological feature of ALS-FTD that correlates with symptom severity, and these findings are uncovering for the first time the characteristics and potential mechanisms of that synapse impairment. |
| Exploitation Route | Development of human synaptome mapping provides the research community with a new discovery tool applicable to any neurological condition at resolution and scale. The highly systematic testing and optimisation undertaken, including tissue sourcing and choice/application of commercial antibodies across synaptic compartments and synapse types, will save researchers substantial time and effort. A partnership with IPI, a supplier of synaptic protein antibodies, has also emerged from this work. Take-up of this technology by other researchers across neurodegeneration and dementias will likely identify underlying commonalities and distinctions in mechanisms of synapse pathology and new biomarkers and potential targets for therapeutic or pharmacological intervention. This project's data will be shared as the ALS-FTD human synaptome atlas, with a complementary database of ALS and control samples used across our lab and collaborators. This will maximize opportunities for integration of ALS-FTD synaptomic data with multi-omic (e.g. transcriptomic) and multi-scale (e.g. nanoarchitecture) data from other groups, and with neuropsychiatric and behavioural impacts recorded for each case analysed. All of this expands our knowledge of brain function in health and dysfunction. The research data management systems, computational, statistical and software tools developed in this project (collectively, the Grant lab neuroscience research computing platform) will find broader application among the imaging data community. |
| Sectors | Education Healthcare Pharmaceuticals and Medical Biotechnology |
| Description | Perspective article Murray et al (2025): guidelines and recommendations for neuropathology research |
| Geographic Reach | Multiple continents/international |
| Policy Influence Type | Contribution to new or improved professional practice |
| URL | https://doi.org/10.1016/j.neuron.2025.06.014 |
| Description | Perspective article: Neuroscience needs single-synapse studies |
| Geographic Reach | Multiple continents/international |
| Policy Influence Type | Contribution to new or improved professional practice |
| URL | https://www.thetransmitter.org/molecular-neuroscience/neuroscience-needs-single-synapse-studies/?swc... |
| Description | UK DRI Affiliate Membership |
| Geographic Reach | National |
| Policy Influence Type | Participation in a guidance/advisory committee |
| URL | https://www.ukdri.ac.uk/our-people/researchers/member-directory |
| Description | Synaptome alterations associated with ageing |
| Amount | $300,000 (USD) |
| Funding ID | 2024-351071 |
| Organisation | Chan Zuckerberg Initiative |
| Sector | Private |
| Country | United States |
| Start | 12/2024 |
| End | 11/2026 |
| Description | The synaptome architecture of the mammalian brain |
| Amount | £4,899,878 (GBP) |
| Funding ID | 302077/Z/23/Z |
| Organisation | Wellcome Trust |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 06/2024 |
| End | 06/2032 |
| Title | CortiBin (cortical binning tool) |
| Description | This tool is a spatial discretization utility designed to reveal intra-regional heterogeneity within delineated human cortical cores. By systematically splitting segmented ROIs into configurable sub-bins - either parallel to the cortical surface or via custom grids - the tool transforms static anatomical zones into dynamic spatial profiles. This granular approach allows for the quantification of marker intensity and cell density as a function of distance or depth, capturing subtle gradients that are lost in whole-ROI averages. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2025 |
| Provided To Others? | No |
| Impact | Traditional ROI analysis often obscures localized pathological trends by averaging signals across large tissue areas. CortiBin unlocks the spatial dimension of human brain pathology, allowing researchers to map the precise trajectory of disease progression across cortical layers. By enabling the visualization of protein or gene expression gradients, this tool provides the resolution necessary to detect 'transition zones' in neurodegeneration, ultimately offering a more nuanced understanding of how pathology spreads through the human cortex. Collaborator Dr Hidefumi Suzuki has been using CortiBin to look at areas of synapse pathology associated with TDP-43 pathology in ALS cases. |
| URL | https://github.com/nic506/binning_tool |
| Title | Cross-modal cortical delineation automation for human cores |
| Description | We present a novel automated framework that leverages the cytoarchitectural clarity of Nissl staining to define cortical boundaries in corresponding cross-modal pairs. The pipeline initiates delineation on high-contrast Nissl images, establishing a structural ground truth. It then learns a linear spatial transformation to register the Nissl modality to the target genetic/antibody modality. Finally, the learned transformation parameters are applied to the segmentation masks, seamlessly projecting precise anatomical boundaries onto the molecular data. This approach eliminates the need for difficult manual re-delineation on functional markers, ensuring spatially consistent analysis across multi-modal datasets. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2025 |
| Provided To Others? | No |
| Impact | This tool eliminates the ambiguity of segmenting low-contrast genetic markers in the human cortex. By decoupling structural definition from molecular detection, it allows researchers to achieve layer-specific precision without manual re-annotation. This significantly accelerates multi-modal analysis workflows while ensuring that gene expression profiles are mapped to their exact cytoarchitectural coordinates. |
| URL | https://git.ecdf.ed.ac.uk/kyuan3/automatic_delineation_hbsp |
| Title | Grant Lab Image Processing Cluster |
| Description | A Docker Swarm-based distributed computing platform for processing large-scale microscopy images in neuroscience research. The system provides a web interface for managing image processing workflows across a compute cluster, combining CPU and GPU workers for parallel processing. Key capabilities include: (a) Conversion of proprietary microscope formats (IMS, CZI, ND2) to standard TIFF with automated tile stitching and sub-pixel alignment. (b) Synaptome mapping pipelines for human (as well as other species') brain tissue, covering a diversity of synaptic proteins. (c) Automated brain region delineation using deep learning (nnUNet). (d) ROI-based analysis and statistical workflows. The platform enables researchers to process datasets by distributing computation across multiple nodes, with real-time job monitoring and email notifications on completion. |
| Type Of Material | Improvements to research infrastructure |
| Year Produced | 2025 |
| Provided To Others? | No |
| Impact | (a) Throughput and scale: Enables processing of large microscopy datasets (current samples up to 50 GB, with capacity for larger files through memory-efficient chunked processing). Parallel processing across the cluster reduces analysis time from days to hours. (b) Accessibility: Provides a web-based interface that allows researchers without programming expertise to run complex image processing and analysis pipelines, lowering the barrier to advanced computational methods. (c) Standardisation: Automates previously manual workflows for tile stitching, format conversion, and region delineation, improving reproducibility and reducing human error across studies. (d) Research support: Currently supports multiple synaptome mapping projects investigating synaptic protein distributions in human and mouse brain tissue, contributing to ongoing studies of brain connectivity and neurodegenerative disease. |
| Title | Synaptome mapping in human postmortem brain tissue |
| Description | In this project we have developed, in parallel with Wellcome-funded Human Brain Synaptome Project (218293/Z/19/Z) and a UK DRI grant looking at Alzheimers disease (XCPD2019-01), the capacity to analyse synaptome architecture in human brain tissue. The approach enables large-scale, single-synapse resolution synaptome maps to be generated that can reveal the impact of natural ageing or disease on the brain. Importantly, this research method employs antibodies to detect synaptic proteins, whereas that previously used in mice employed transgenic lines with endogenously labelled proteins. We have optimised the methodology for high throughput (e.g. using tissue cores, ten per slide) and generated an ever-expanding toolbox of antibodies that work reliably, with high signal-to-noise ratio (high background labelling is a well-known problem in immunolabelling of human tissue), including PSD95, PSD93, GluN1, GluA2, VGAT, GPHN and VGLUT1, and specific marker combinations. These antibodies detect a range of pre- and postsynaptic proteins associated with particular neuron types and are being employed across brain regions in ALS-FTD and control samples. We are also harmonising the synapse markers that we use across human and other animals in order to facilitate species comparisons. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2025 |
| Provided To Others? | Yes |
| Impact | By developing a method for the direct analysis of synaptome architecture in human brain tissue, this removes any need for analysis in mouse models of the disease under study. Alternatively, by comparing synaptome architecture in human and mouse brain tissue, this may inform on the validity of the mouse model, or indeed of other models such as organoids. Development of the research method has required very stringent, systematic optimisation, including testing of material from a number of UK human brain banks with a range of commercial antibodies against synaptic proteins individually and in combination. This knowledge will save other researchers substantial time and money when planning their research strategy in terms of source material and neuropathological marker selection, and has been shared (e.g. at UK DRI meetings) and has informed ongoing Grant lab projects investigating the impacts of ageing (CZI Neuropathology Collaboration Network) and schizophrenia (Medical Research Scotland PhD project) on the human brain synaptome, as well as collaborative ALS-FTD work with JSPS Overseas Research Fellow Dr Hidefumi Suzuki. |
| Title | Computational analysis of human brain synaptome imaging data |
| Description | The development of laboratory methods for high-throughput collection of synaptome imaging data from human brain samples has been matched by the development, refinement and acceleration of the downstream computational pipeline for the analysis of these data, which was originally developed and published for the mouse brain. Components of this coding pipeline include delineation of human brain regions and subregions, the detection, segmentation and classification of synaptic puncta according to a set of parameters using deep-learning algorithms and statistical analyses, and their mapping across single-synapse resolution images. The datasets, which are output as synaptome maps, compare ALS-FTD cases with controls across brain regions. Once fully developed, they will be made available online as the ALS-FTD Human Synaptome Atlas resource (similar to e.g. https://brain-synaptome.org/ for the mouse). |
| Type Of Material | Data analysis technique |
| Year Produced | 2025 |
| Provided To Others? | Yes |
| Impact | The computational pipeline for the analysis, presentation and sharing of human brain synaptome imaging data has been developed as part of this and a number of other human brain health-focussed projects in the Grant lab, all of which have benefitted from this collaborative effort (e.g. bioRxiv https://doi.org/10.1101/2025.01.23.634408; Wong et al. (2025) Wellcome Open Res. 10, 415). The synaptome dataset from ALS-FTD is being compared with those that we have generated from schizophrenia and Alzheimer's disease cases to identify distinctions and commonalities that might inform on mechanism. We aim to develop a Cloud-based synaptome mapping pipeline, supported by guidance hosted as a Wiki resource, that would allow users to run data through a user-friendly webpage interface, negating the need for any special hardware, software or coding knowledge at their end, and thereby enhancing the accessibility and potential impact of this data analysis approach. |
| Description | Collaboration with Dr Hemali Phatnani research group |
| Organisation | Columbia University |
| Department | Department of Neurology |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | The technical approaches developed by our research team in the analysis of human postmortem tissue and the impacts of disease upon the brain synaptome have contributed to the development of collaborative grant applications (NIH COMBINE RFA-NS-23-027: Identifying the basis of selective synaptic vulnerability in ALS-FTD; Target ALS Basic Biology Consortia: TDP-43 and selective synaptic vulnerability in ALS-FTD) and the publication of a collaborative Perspective article with the potential to influence research policy worldwide (Murray et al., 2025), each led by Dr Hemali Phatnani. |
| Collaborator Contribution | This collaboration has provided us with access to potential new funding routes via NIH and to the administrative support in making those applications, direct introduction to a new network of US researchers in the human brain disease field who contribute complementary omics that raise the overall health discovery value of our data, and the opportunity to contribute to collaborative research publications and reviews. Furthermore, the Phatnani group can provide spatial transcriptomics data to complement the project's ALS-FTD synaptome mapping outputs. In fact, they have already generated spatial transcriptomics data for a subset of our Alzheimer's disease cohort and integrating this dataset with our synaptome mapping will inform our approach to the ALS cohort. |
| Impact | Murray M.E., Smith C., Menon V., Keene C.D., Lein E., Hawrylycz M., Aguzzi A., Benedetti B., Brose K., Caetano-Anolles K., Sillero M.I.C., Crary J.F., De Jager P.L., Faustin A., Flanagan M.E., Gokce O., Grant S.G.N., Grinberg L.T., Gutman D.A., Hillman E.M.C., Huang Z., Irwin D.J., Jones D.T., Kapasi A., Karch C.M., Kukull W.T., Lashley T., Lee E.B., Lehner T., Parkkinen L., Pedersen M., Pritchett D., Rutledge M.H., Schneider J.A., Seeley W.W., Shepherd C.E., Spires-Jones T.L., Steen J.A., Sutherland M., Vickovic S., Zhang B., Stewart D.J., Keiser M.J., Vogel J.W., Dugger B.N., Phatnani H. (2025). Accelerating biomedical discoveries in brain health through transformative neuropathology of aging and neurodegeneration. Neuron 113, 3703-3721. |
| Start Year | 2023 |
| Description | Collaboration with Dr Hemali Phatnani research group |
| Organisation | New York Genome Center |
| Country | United States |
| Sector | Charity/Non Profit |
| PI Contribution | The technical approaches developed by our research team in the analysis of human postmortem tissue and the impacts of disease upon the brain synaptome have contributed to the development of collaborative grant applications (NIH COMBINE RFA-NS-23-027: Identifying the basis of selective synaptic vulnerability in ALS-FTD; Target ALS Basic Biology Consortia: TDP-43 and selective synaptic vulnerability in ALS-FTD) and the publication of a collaborative Perspective article with the potential to influence research policy worldwide (Murray et al., 2025), each led by Dr Hemali Phatnani. |
| Collaborator Contribution | This collaboration has provided us with access to potential new funding routes via NIH and to the administrative support in making those applications, direct introduction to a new network of US researchers in the human brain disease field who contribute complementary omics that raise the overall health discovery value of our data, and the opportunity to contribute to collaborative research publications and reviews. Furthermore, the Phatnani group can provide spatial transcriptomics data to complement the project's ALS-FTD synaptome mapping outputs. In fact, they have already generated spatial transcriptomics data for a subset of our Alzheimer's disease cohort and integrating this dataset with our synaptome mapping will inform our approach to the ALS cohort. |
| Impact | Murray M.E., Smith C., Menon V., Keene C.D., Lein E., Hawrylycz M., Aguzzi A., Benedetti B., Brose K., Caetano-Anolles K., Sillero M.I.C., Crary J.F., De Jager P.L., Faustin A., Flanagan M.E., Gokce O., Grant S.G.N., Grinberg L.T., Gutman D.A., Hillman E.M.C., Huang Z., Irwin D.J., Jones D.T., Kapasi A., Karch C.M., Kukull W.T., Lashley T., Lee E.B., Lehner T., Parkkinen L., Pedersen M., Pritchett D., Rutledge M.H., Schneider J.A., Seeley W.W., Shepherd C.E., Spires-Jones T.L., Steen J.A., Sutherland M., Vickovic S., Zhang B., Stewart D.J., Keiser M.J., Vogel J.W., Dugger B.N., Phatnani H. (2025). Accelerating biomedical discoveries in brain health through transformative neuropathology of aging and neurodegeneration. Neuron 113, 3703-3721. |
| Start Year | 2023 |
| Description | Collaboration with Dr Hidefumi Suzuki |
| Organisation | University of Edinburgh |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We provide Dr Suzuki with access to human brain postmortem samples gathered for the project and to the human synaptome mapping pipeline that the project helped to develop. |
| Collaborator Contribution | Dr Suzuki (supported by an Overseas Postdoctoral Fellowship from Japan Society for the Promotion of Science) has carried out characterisation of the human cortical synaptome, identifying distinct impacts of ALS-FTD and Alzheimer's disease on BA4 and BA20/21, making a direct contribution to project aims and outcomes. |
| Impact | This work has been presented as a conference poster co-authored with ALS project staff Jessica Griffiths, Beverley Notman, Colin Smith and Seth Grant and presented at the Tribute to Euan MacDonald Symposium 8/9 Oct 2025. |
| Start Year | 2025 |
| Description | Collaboration with Dr Zhen Qiu |
| Organisation | University of Strathclyde |
| Department | Department of Biomedical Engineering |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We provide access to imaging research data and to the challenges that the collection, analysis, integration and sharing of these data present, which drive computational advances contributed by Dr Qiu. |
| Collaborator Contribution | Dr Qiu provides coding expertise and advice that helps to support the maintenance, development and refinement of the computational data analysis pipeline of synaptome mapping, which he was instrumental in developing for mice and then migrating to application on human brain. |
| Impact | Dr Qiu continues to develop code for the improvement and refinement of the human synaptome mapping pipeline. Dr Qiu is currently developing a deep-learning approach that will greatly reduce the need for manual intervention in generating ground-truth training datasets for synapse cataloguing. By introducing a degree of automation, this will increase consistency, speed and cost-effectiveness of synaptome mapping, especially in the analysis of human brain imaging data and as the number of synaptic proteins analysed increases. |
| Start Year | 2024 |
| Description | Collaboration with Nikon Healthcare UK |
| Organisation | Nikon |
| Department | Nikon UK |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | We provide feedback to Nikon on the functioning of the microscope and its associated software and illustrate its use in cutting-edge brain research in promotional material. |
| Collaborator Contribution | Nikon provided to the project the loan of a SoRa spinning disk microscope as well as technical advice from one of their advanced imaging specialists. Nikon continue to work closely with the research team to support project needs from spinning disc confocal microscopy. |
| Impact | As a publicly available output: Tackling a vast number of synapses to uncover brain disease, Nikon UK Healthcare (Sep 2024), https://www.healthcare.nikon.com/en/well-being/detail18.html |
| Start Year | 2023 |
| Description | Collaboration with UK DRI |
| Organisation | UK Dementia Research Institute |
| Country | United Kingdom |
| Sector | Charity/Non Profit |
| PI Contribution | We have applied synaptome mapping to analyse cortical organoids provided by researchers at the UK Dementia Research Institute, University of Edinburgh. A key focus related to this project has been assessing synapse pathology in TDP43-knockout cortical organoids, a model for studying ALS pathology. We have shared the brain tissue coring technique and staining protocols that we developed for human synaptome mapping with teams from UK DRI. |
| Collaborator Contribution | We have collaborated with the labs of Dr Bhuvaneish T. Selvaraj and Prof. Siddharthan Chandran's at the UK Dementia Research Institute, University of Edinburgh (https://www.ukdri.ac.uk/centres/edinburgh), who have provided expertise and advice on organoid studies. Dr Vidya Ramesh, a postdoc in Prof. Chandran's lab, has generated cortical organoids for us to analyse by synaptome mapping. |
| Impact | No public outcome as yet, as the organoids are still being analysed; this work will inform on the value of TDP43-knockout cortical organoids as a model for studying synapse pathology in ALS. Discussions are ongoing to create a shared database to track ALS-FTD human postmortem case and tissue usage across collaborating groups and projects, particularly with the Selvaraj group and with the Phatnani group in the USA, enabling harmonisation and identifying opportunities for data integration using omic tools and specialist assays. The Selvaraj group has generated an imaging mass cytometry dataset on a subset of ALS cases prepared by project staff Beverley Notman, and these will be processed and analysed for complementary synaptome mapping by Dr Suzuki and project staff. |
| Start Year | 2023 |
| Description | Collaboration with project partners Prof. Shigeo Okabe and Prof. Akiyoshi Kakita |
| Organisation | Niigata University |
| Department | Brain Research Institute (Niigata University) |
| Country | Japan |
| Sector | Academic/University |
| PI Contribution | This collaboration is a core component of the AMED-MRC project, as described in the plan of work. At present, our contribution has been to online and in-person discussions of project progress, preliminary results, and opportunities for reagent and sample exchange, including the possibility of sharing Edinburgh Brain Bank tissue samples for complementary analyses. |
| Collaborator Contribution | This collaboration is a core component of the AMED-MRC project, as described in the plan of work. At present, the contribution of our partners in Japan has been to online and in-person discussions of project progress, preliminary results, and possibilities for reagent and sample exchange. |
| Impact | No public output as yet. |
| Start Year | 2023 |
| Description | Collaboration with project partners Prof. Shigeo Okabe and Prof. Akiyoshi Kakita |
| Organisation | University of Tokyo |
| Department | Graduate School of Medicine |
| Country | Japan |
| Sector | Academic/University |
| PI Contribution | This collaboration is a core component of the AMED-MRC project, as described in the plan of work. At present, our contribution has been to online and in-person discussions of project progress, preliminary results, and opportunities for reagent and sample exchange, including the possibility of sharing Edinburgh Brain Bank tissue samples for complementary analyses. |
| Collaborator Contribution | This collaboration is a core component of the AMED-MRC project, as described in the plan of work. At present, the contribution of our partners in Japan has been to online and in-person discussions of project progress, preliminary results, and possibilities for reagent and sample exchange. |
| Impact | No public output as yet. |
| Start Year | 2023 |
| Description | Participation in Euan MacDonald Centre for Motor Neuron Disease Research Network |
| Organisation | University of Edinburgh |
| Department | Euan Macdonald Centre for Motor Neurone Disease Research |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | The research team provides the Euan MacDonald Centre with new intellectual input, practical expertise and guidance with analysis of human postmortem brain tissue using state-of-the-art microscopy methods as a means to identify the impacts of MND - of which ALS is the most common form - on synapses in the human brain. The tools, knowledge and data resources from our project will furthermore inform on the application of brain imaging methods in the clinic and trials of therapies aimed at preventing the progression of MND, complementing the work of the Euan MacDonald Centre in advancing understanding of the brain and its diseases. In May 2025, project staff Beverley Notman was awarded a Hampton Award from the Euan MacDonald Centre (http://www.euanmacdonaldcentre.org/about/hampton-awards). In Oct 2025, project staff attended the Tribute to Euan MacDonald Symposium. |
| Collaborator Contribution | Aligning with the Euan MacDonald Centre has raised the profile and visibility of our project, helping to promote our ALS-FTD research among the MND research community and its supporters. It also provides access to complementary advice, expertise, tools and research materials. |
| Impact | No specific research outcomes as yet |
| Start Year | 2024 |
| Title | nd2 to TIFF converter |
| Description | In collaboration with the Wellcome Human Brain Synaptome Project we have developed an application that will automatically and rapidly convert nd2 files captured by the Nikon spinning disk confocal microscope to the widely used TIFF image format. |
| Type Of Technology | Webtool/Application |
| Year Produced | 2024 |
| Impact | By bypassing laborious manual intervention for file conversion and naming, as well as any obligatory use of commercial software, this application has sped up the generation of systematically named, TIFF image files for post-capture data processing in the computational pipeline of synaptome mapping. As nd2 files are widely generated in biological imaging applications, this application, once fully developed and shared, may find many uses with other researchers. |
| Description | Annual Summer School 'Neural Circuit Development and Plasticity' |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | The University of Utrecht, The Netherlands, summer school 'Neural Circuit Development and Plasticity' educates masters and early PhD students in recent advances in this field of neuroscience from a multidisciplinary perspective. Project PI Seth Grant contributed a talk and discussion in the area of synapse structure and function. By highlighting state-of-the-art methods developed in the Grant lab for high-resolution, large-scale synaptomic analyses of the brain, which can uncover synaptome architecture during development and ageing, as well as diversity in synapse dynamics, resilience and vulnerability in the face of diseases such as ALS-FTD, this provoked much interest and discussion among the students. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://utrechtsummerschool.nl/sites/default/files/2024-04/Day-to-day%20Program%20%20Summerschool%20... |
| Description | Edinburgh BioQuarter Summer Internship Programme |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | Project staff participated in Edinburgh BioQuarter Summer Internship Programme 2024, an in-person education event that provided a student from the local Castlebrae high school with inspiring, real-world work experience in a biomedical environment for 4 weeks in July 2024. The student gained experience and connections to support and encourage her in pursuing an education and career in medicine. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://edinburghbioquarter.com/summer-internship |
| Description | Killam Seminar Series |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Postgraduate students |
| Results and Impact | Project PI Seth Grant presented 'The Role of Synapse Diversity and Synaptome Architecture in Behaviour and Disease' as part of the Killam Seminar Series, Montreal Neurological Institute, Canada (1 Oct 2024), which contributes to the wider graduate student education and discussion program that also encompasses the Department of Neuroscience, Université de Montréal. This highlighted the discovery value of the human brain synaptomics approaches developed and leveraged in the project, stimulating much interest among this healthcare-focussed audience. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.mcgill.ca/neuro/channels/event/killam-seminar-series-role-synapse-diversity-and-synaptom... |
| Description | Medical Research Scotland Academy |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Schools |
| Results and Impact | As part of an online education event organised by Medical Research Scotland Academy (https://medicalresearchscotland.org.uk/events/medical-research-scotland-academy-2024), PI Seth Grant showcased our research and contributed to a Q&A session for the 'live from the lab' webinar 'Your Future in Medical Research', which was live-streamed 22 Mar 2024 into classrooms across the UK, inspiring senior school pupils (S4-S6) to consider a career in medical research or to study a STEM subject. |
| Year(s) Of Engagement Activity | 2024 |
| URL | https://www.youtube.com/watch?v=7fvQ_9AVRfk&list=PLEp90uhqZ6Bf1VHfq_1AUlDBEMUYj0WwV&t=7s |
| Description | The Game of Life: Who gets to be 100? |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Schools |
| Results and Impact | Project postdoc Jess Griffiths participated in the interactive workshop 'The Game of Life: Who gets to be 100?' on brain and cognitive health for pupils at Niddrie Mill Primary School on the 4th June 2024, run by the Lothian Birth Cohort Group. There were three sessions of ~25 primary-5 (8+) children each. The children created a DNA bracelet as they reviewed basic concepts from genetics, explored 3D-printed brain models based on real MRI data and played a boardgame that took them on a journey from birth to old age. They learned how our genetic make-up and lifestyle choices influence cognitive and brain ageing and what factors increase or decrease our risk of developing conditions such as dementia in later life. |
| Year(s) Of Engagement Activity | 2024 |
| Description | UK DRI Connectome 2023 networking event |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Prof. Grant gave a talk entitled 'Identifying synapse vulnerability using synaptome mapping', which highlighted a method developed in the Grant lab that can be used to uncover disease signatures at high resolution and large scale in the human brain, an approach that is leveraged in the AMED-MRC project to understand the impact of ALS-FTD. By raising awareness of the discovery potential of synaptome mapping in human brain disease, this provoked much interest and discussion of potential collaborations among a much wider group than we would otherwise reach. |
| Year(s) Of Engagement Activity | 2023 |
| Description | Undergraduate summer internship |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Undergraduate students |
| Results and Impact | An undergraduate from St Andrews University joined the lab in July and August 2024 to gain experience and understanding of neuroscience research, shadowing project postdoc Jess Griffiths and other researchers working on human brain conditions, but also talking with other members of the lab about their journeys in science and their research projects. She was very much encouraged in pursuing a research career. |
| Year(s) Of Engagement Activity | 2024 |
| Description | Visit to New York Genome Centre and Columbia University, New York, USA |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Prof. Grant gave a talk entitled 'Synaptome architecture in health and disease', which highlighted approaches taken by the lab in uncovering the molecular impact of human brain diseases at the single-synapse level, an approach that is leveraged in the AMED-MRC project to understand how ALS-FTD alters the human brain synaptome. By raising awareness of the discovery potential of synaptome mapping, this engagement provoked substantial interest among a much wider group than we would otherwise reach, including opportunities for collaborations, new funding avenues, and potential new routes to obtaining human postmortem brain tissue for disease analysis. |
| Year(s) Of Engagement Activity | 2024 |