Biology subjects

Grant-Peters, M.

Publications and source records attributed to Grant-Peters, M..

18 recordsLinked to original sources

bioRxiv2025

APOE E4 Alzheimer's Risk Converges on an Oligodendrocyte Subtype in the Human Entorhinal Cortex

The entorhinal cortex (ERC) is implicated in early progression of Alzheimers disease (AD). Here we investigated the impact of established biological risk factors for AD, including APOE genotype (E2 versus E4 alleles), sex, and ancestry, on gene expression in the human ERC. We generated paired spatially-resolved transcriptomics (SRT) and single-nucleus RNA sequencing data (snRNA-seq) in postmortem human ERC tissue from middle aged brain donors with no history of AD. APOE-dependent changes in gene expression predominantly mapped to a transcriptionally-defined oligodendrocyte subtype, which varied substantially with ancestry, and suggested differences in oligodendrocyte differentiation and myelination. Integration of SRT and snRNA-seq data identified a common gene expression signature associated with APOE genotype, which we localized to the same oligodendrocyte subtype and a white matter spatial domain. This suggests that AD risk in ERC may be associated with disrupted oligodendrocyte function, potentially contributing to future neurodegeneration. Lay SummaryAlzheimers disease (AD) is a neurodegenerative disorder that accounts for 60-80% dementia cases. Apolipoprotein E (APOE) genotype is the strongest genetic risk factor for AD, and the entorhinal cortex (ERC) is a brain region implicated in its earliest progression. Our study investigated how APOE genotype impacts gene expression in the ERC. We identified genotype-dependent effects on oligodendrocytes with different transcriptional profiles related to maturation that may help explain how APOE genotype mediates its effects on AD risk.

neuroscience↗

bioRxiv2025

Long-Read epigenetic clocks identify improved brain aging predictions

Epigenetic clocks are widely used to estimate biological aging, yet most are built from array-based data from peripheral tissues of predominantly European-ancestry individuals, limiting their generalizability. Here, we present aging clocks on DNA methylation from Oxford Nanopore long-read sequencing (LRS), leveraging over 28 million CpG sites from prefrontal cortex samples across individuals of African and European ancestry. These models were developed using GenoML, an automated machine learning platform for multi-omics data that leverages a diverse catalog of existing model architectures. Our long-read-informed clocks were developed using promoter-based and whole-genome window-based features, yielding models for each individual cohort as well as a combined-cohort clock. Each of these models demonstrated favorable performance compared to existing methylation clocks and was externally validated in a cohort of Colombian individuals. We further performed enrichment analyses and nominated both shared and cohort-specific pathways, cell types, and transcription factor binding motifs which may be implicated in aging and were not fully explained by cell type proportions or postmortem interval. Altogether, our findings highlight the power of long-read methylation data for constructing accurate, ancestry-aware aging clocks and emphasize the importance of inclusive training datasets.

bioinformatics↗

bioRxiv2025

Alternate Splicing Directs PMCA2 to Lysosomes and is Linked to Neurodegeneration

Plasma membrane calcium ATPases (PMCAs) are believed to function exclusively at the plasma membrane where they expel calcium from the cytosol. We have unexpectedly identified a splice variant-dependent localisation of the PMCA isoform PMCA2 to the lysosome, where it forms an evolutionarily conserved complex with NPC1, the lysosomal membrane protein defective in the rare lysosomal storage disease Niemann-Pick disease type C (NPC). This interaction is required for lysosomal Ca2+ homeostasis and implicates PMCA2 as a mediator of Ca2+ uptake into lysosomes. Disruption of the NPC1-PMCA2 complex contributes to the pathophysiology of both Niemann-Pick disease type C and Parkinsons disease, revealing an unrecognised intracellular function for PMCA2 and a shared mechanism linking lysosomal Ca2+ and lipid regulation in neurodegeneration.

cell biology↗

bioRxiv2025

Mapping the molecular landscape of the living brain: integrating spatial transcriptomics and qMRI

Profiling dynamic molecular processes in neurodegeneration in vivo remains a major clinical challenge. Limited brain tissue accessibility especially limits the development and effective deployment of emerging disease modifying therapies, highlighting the need for non-invasive methods for profiling molecular disease processes. We introduce a non-invasive imaging framework that integrates ultra-high-resolution 7T quantitative MRI (qMRI) with spatially-resolved transcriptomics (SRT) to infer cell-type and pathway-specific molecular features within the cortical grey matter. This proof-of-concept establishes the integration of qMRI and SRT as a scalable, non-invasive platform for molecular profiling in neurodegeneration, with significant potential for precision therapeutic monitoring, drug development and clinical trials.

neuroscience↗

bioRxiv2025

TDP-43 loss of function drives aberrant splicing in Parkinson's disease

Introductory paragraphWhile mRNA splicing dysregulation is a well-established contributor to neurodegeneration in disorders such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), its role in Parkinsons disease (PD) remains underexplored. Here, we analyse transcriptomic data from >500 post-mortem human brain samples from individuals with and without PD to show that splicing alterations are frequently detected. Differentially spliced genes were significantly more enriched for those causally-implicated in both PD and ALS than genes that were differentially expressed. Furthermore, we observed a strong association between these splicing alterations and dysfunction of the RNA-binding protein (RBP), TAR DNA-binding protein 43 (TDP-43). Strikingly, genes and exon junctions affected by TDP-43 knockdown overlapped significantly with those dysregulated across brain regions in PD. In brains from individuals with the LRRK2 c.6055G>A (p.G2019S) mutation, the most common genetic cause of PD, we also observed significant enrichment of TDP-43-dependent splicing changes. This finding was corroborated in human pluripotent stem cell-derived midbrain dopaminergic neurons and a LRRK2 p.G2019S knock-in mouse model, where reduced nuclear TDP-43 levels evidenced the well-recognised loss-of-function mechanism contributing to splicing dysregulation. By leveraging our RNA-based analyses we predicted TDP-43-dependent novel peptide sequences and validated their existence within human LRRK2 mutation mDNs, while also demonstrating an overall loss of protein and mRNA expression in mis-spliced genes. Collectively, our findings reveal that PD is marked by extensive splicing dysregulation dependent on TDP-43, making TDP-43 a promising new therapeutic target in PD.

neuroscience↗

bioRxiv2025

Microglial activation and alpha-synuclein oligomers drive the early inflammatory phase of Parkinson's disease

Parkinsons disease (PD) is characterised by insoluble -synuclein (Syn) aggregates in Lewy bodies (LBs) within the substantia nigra, with cortical pathology appearing as the disease progresses. Late-stage LB deposition, cellular stress, and neuronal loss obscure disease-driving events, we therefore performed multi-regional transcriptomic and aggregate profiling in early-midstage PD brains (Braak 3-4), where cortical regions are pathologically unaffected. We report neuroimmune activation as an early PD feature, characterised by the expansion of a high-SNCA-expressing microglial state. This robust immune signature occurs prior to LB formation, but is associated with oligomeric Syn within cortical microglia. In hiPSC-derived microglia, both endogenous Syn oligomerisation, and exogenous oligomer uptake, trigger transcriptional reprogramming, characterised by interferon-driven inflammation, antigen presentation, and mitochondrial suppression, closely mirroring the early PD brain. These findings describe mechanisms by which Syn oligomerisation potently initiates early neuroinflammation, highlighting a critical interplay between proteinopathy and immune activation at the earliest stages of disease.

neuroscience↗

bioRxiv2025

Evidence for divergent cortical organisation in Parkinsons disease and Lewy Body Dementia

Dementia is a defining feature of Lewy body disease: its timing and onset distinguish different clinical diagnoses, and its effect on quality of life is profound. However, it remains unclear whether processes leading to cognitive and motor symptoms in Lewy body disease differ. To clarify this, we used in-vivo neuroimaging to assess spatial gradients of inter-regional differences in structural and functional connectivity in 108 people across the Lewy body disease spectrum (46 Parkinsons with normal cognition (PD-NC), 62 Lewy body dementia (LBD)) and 23 controls. We found divergent structural gradient differences with cognitive impairment: PD-NC showed increased inter-regional differentiation, whilst LBD showed overall gradient distribution similar to controls despite widespread organisational differences at the regional level. We then assessed cellular and molecular underpinnings of these organisational changes. We reveal similarities and also important differences in the drivers of cortical organisation between LBD and PD-NC, particularly in layer 4 excitatory neurons.

neuroscience↗

bioRxiv2025

17q21.31 locus regulates Parkinson's disease relevant pathways through KANSL1 activity

An inversion polymorphism at the 17q21.31 locus defines the H1 and H2 haplotypes, with the former linked to multiple neurodegenerative disorders, including an increased risk of Parkinsons disease (PD). Although the high linkage disequilibrium at this locus has made it difficult to decipher which gene(s) drive the PD association, there is increasing evidence to support the role of KANSL1 as a risk gene. KANSL1 has been shown to regulate the expression of some PD-associated genes and pathways, likely as part of the histone acetylating non-specific lethal (NSL) complex. Here for the first time, we studied the global effects of 17q21.31 haplotype variation using bulk and single-nuclear RNA-sequencing data from control and PD patient brain. We first analysed differential gene expression across haplotype groups, and then assessed the contribution of KANSL1 by comparing with the results of an siRNA knockdown in neuronal and glial human cell lines. We demonstrated that the PD risk-associated H1 haplotype downregulates autophagy, lysosomal and mitochondrial processes, all of which have already been implicated in PD aetiology. Furthermore, these effects were apparent in both neuronal and glial cell types, and in the case of the latter, appear to be associated with the modulation of innate and adaptive immune responses. Thus, we identify important links between NSL complex activity and PD pathophysiology that can be leveraged for novel therapeutic interventions.

neuroscience↗

bioRxiv2025

Molecular and cellular signatures differentiate Parkinson's disease from Parkinson's disease with dementia

Parkinsons disease (PD) affects millions of people worldwide, and up to 40% of these patients develop dementia, profoundly affecting their quality of life. Whether Parkinsons disease dementia (PDD) simply represents a late stage of PD or constitutes a distinct neurodegenerative process remains unresolved. To clarify this, we generated the largest single nuclear transcriptomic atlas of PD and PDD to date--almost one million nuclei derived from the anterior cingulate cortex and inferior parietal lobule of 64 post-mortem donors. By integrating these data with long-read RNA-seq, we found that the cellular compositions, biological pathways, and molecular profiles diverge substantially between PD and PDD, with limited overlap in differentially expressed genes and pathways. While PD was characterised by widespread upregulation of gene expression programs and robust regional signatures, PDD showed extensive pathway downregulation, loss of cortical regional identity, and significant shifts in transcript usage, including alterations in APP isoforms that may influence pathological amyloid beta accumulation. These findings reveal that PD and PDD represent fundamentally distinct disease states, offering important insights for understanding their underlying mechanisms and will guide the development of targeted therapies and more effective clinical trials.

neuroscience↗

bioRxiv2025

Transcriptomic analysis of repeat expansion-ataxias uncovers distinct non-neuronal cell type-specific signatures of disease across the human brain

Hereditary ataxias are a heterogeneous group of neurogenetic conditions characterised by the clinical syndrome of progressive loss of coordination from neurodegeneration of the cerebellum. A commonality across the most prevalent ataxias is the underlying disease mechanism secondary to expansions of short tandem DNA repeats. There is currently an incomplete understanding of the pathogenic mechanisms of these repeat expansion disorders, a core feature of which revolves around RNA-dysregulation. In this study, we used both bulk and single nuclear RNA-sequencing to study post-mortem brain tissue of human donors with a range of repeat-expansion ataxias to reveal further mechanistic insights. We compared post-mortem paired cerebellar and frontal cortex tissue bulk RNA-sequencing data from 23 ataxia patients and 22 sex-, age-matched controls from two brain banks (spinocerebellar ataxia (SCA)1, SCA2, SCA6, SCA7, SCA17, Friedreichs ataxia (FRDA), and 7 cases with unknown molecular diagnoses). We analysed bulk RNA-sequencing data for transcript usage, differential and cell-type-specific expression to transcriptomically profile these diseases. We also generated single nuclear RNA-sequencing data of the cerebellum from donors with SCA1, SCA2, SCA6 and FRDA to decipher changes in cell type proportions in the disease state. Using this approach, we found that: (i) despite the commonalities in the genetics of ataxia, there were components of their transcriptional signatures which were distinct; (ii) there were extensive transcriptional changes evident not only in the cerebellum but also the frontal cortex in ataxia cases; (iii) activation of immune and inflammatory pathways, as well as involvement of non-neuronal cell types was a feature of all ataxias to a lesser or greater extent. This study provides a novel resource to understand the mechanisms of disease in ataxia. Furthermore, taken together, these results highlight immune pathways and the role of non-neuronal cell types as early and potentially important therapeutic targets. These findings provide a map of transcriptomic changes in ataxia to further understanding of the underlying pathogenesis.

neuroscience↗

bioRxiv2024

Network nature of ligand-receptor interactions underlies disease comorbidity in the brain

Neurodegenerative disorders have overlapping symptoms and have high comorbidity rates, but this is not reflected in overlaps of risk genes. We have investigated whether ligand-receptor interactions (LRIs) are a mechanism by which distinct genes associated with disease risk can impact overlapping outcomes. We found that LRIs are likely disrupted in neurological disease and that the ligand-receptor networks associated with neurological diseases have substantial overlaps. Specifically, 96.8% of LRIs associated with disease risk are interconnected in a single LR network. These ligands and receptors are enriched for roles in inflammatory pathways and highlight the role of glia in cross-disease risk. Disruption to this LR network due to disease-associated processes (e.g. differential transcript use, protein misfolding) is likely to contribute to disease progression and risk of comorbidity. Our findings have implications for drug development, as they highlight the potential benefits and risks of pursuing cross-disease drug targets.

neuroscience↗

bioRxiv2024

Alpha-synuclein aggregates trigger anti-viral immune pathways and RNA editing in human astrocytes

RNA editing is a post transcriptional mechanism that targets changes in RNA transcripts to modulate innate immune responses. We report the role of astrocyte specific, ADAR1 mediated RNA editing in neuroinflammation in Parkinsons disease. We generated hiPSC-derived astrocytes, neurons and co-cultures and exposed them to small soluble alpha-synuclein aggregates. Oligomeric alpha-synuclein triggered an inflammatory glial state associated with TLR activation, viral responses, and cytokine secretion. This reactive state resulted in loss of neurosupportive functions, and the induction of neuronal toxicity. Notably, interferon response pathways were activated leading to upregulation, and isoform switching of the RNA deaminase enzyme, ADAR1. ADAR1 mediates A-to-I RNA editing, and increases in RNA editing were observed in inflammatory pathways in cells, as well as in post-mortem human PD brain. Aberrant, or dysregulated, ADAR1 responses and RNA editing may lead to sustained inflammatory reactive states in astrocytes triggered by alpha-synuclein aggregation, and this may drive the neuroinflammatory cascade in Parkinsons.

neuroscience↗

bioRxiv2023

hadge: a comprehensive pipeline for donor deconvolution in single cell

Single cell multiplexing techniques (cell hashing and genetic multiplexing) allow to combine multiple samples, thereby optimizing sample processing and reducing batch effects. Cell hashing conjugates antibody-tags or chemical-oligonucleotides to cell membranes, while genetic multiplexing allows to mix genetically diverse samples and relies on aggregation of RNA reads at known genomic coordinates. We developed hadge (hashing deconvolution combined with genotype information), a Nextflow pipeline that combines 12 methods to perform both hashing- and genotype-based deconvolution. We propose a joint deconvolution strategy combining the best performing methods and we demonstrate how this approach leads to recovery of previously discarded cells in a nuclei hashing of fresh-frozen brain tissue.

bioinformatics↗

bioRxiv2023

Splicing accuracy varies across human introns, tissues and age

Alternative splicing impacts most multi-exonic human genes. Inaccuracies during this process may have an important role in ageing and disease. Here, we investigated mis-splicing using RNA-sequencing data from ~14K control samples and 42 human body sites, focusing on split reads partially mapping to known transcripts in annotation. We show that mis-splicing occurs at different rates across introns and tissues and that these splicing inaccuracies are primarily affected by the abundance of core components of the spliceosome assembly and its regulators. Using publicly available data on short-hairpin RNA-knockdowns of numerous spliceosomal components and related regulators, we found support for the importance of RNA-binding proteins in mis-splicing. We also demonstrated that age is positively correlated with mis-splicing, and it affects genes implicated in neurodegenerative diseases. This in-depth characterisation of mis-splicing can have important implications for our understanding of the role of splicing inaccuracies in human disease and the interpretation of long-read RNA-sequencing data.

genetics↗

bioRxiv2023

Integrated single cell and unsupervised spatial transcriptomic analysis defines molecular anatomy of the human dorsolateral prefrontal cortex

The molecular organization of the human neocortex has been historically studied in the context of its histological layers. However, emerging spatial transcriptomic technologies have enabled unbiased identification of transcriptionally-defined spatial domains that move beyond classic cytoarchitecture. Here we used the Visium spatial gene expression platform to generate a data-driven molecular neuroanatomical atlas across the anterior-posterior axis of the human dorsolateral prefrontal cortex (DLPFC). Integration with paired single nucleus RNA-sequencing data revealed distinct cell type compositions and cell-cell interactions across spatial domains. Using PsychENCODE and publicly available data, we map the enrichment of cell types and genes associated with neuropsychiatric disorders to discrete spatial domains. Finally, we provide resources for the scientific community to explore these integrated spatial and single cell datasets at research.libd.org/spatialDLPFC/. SummaryGeneration of a molecular neuroanatomical map of the human prefrontal cortex reveals novel spatial domains and cell-cell interactions relevant for psychiatric disease.

neuroscience↗

bioRxiv2022

Pseudogenes limit the identification of novel common transcripts generated by their parent genes

The human genome contains numerous duplicated regions, such as parent-pseudogene pairs, causing sequencing reads to align equally well to either gene. The extent to which this ambiguity complicates transcriptomic analyses is currently unknown. This is concerning as many parent genes have been linked to disease, including GBA1, causally linked to both Parkinsons and Gaucher disease. We find that most of the short sequencing reads that map to GBA1, also map to its pseudogene, GBAP1. Using long-read RNA-sequencing in human brain, where all reads mapped uniquely, we demonstrate significant differences in expression compared to short-read data. We identify novel transcripts from both GBA1 and GBAP1, including protein-coding transcripts that are translated in vitro and detected in proteomic data, but that lack GCase activity. By combining long-read with single-nuclear RNA-sequencing to analyse brain-relevant cell types we demonstrate that transcript expression varies by brain region with cell-type-selectivity. Taken together, these results suggest a non-lysosomal function for both GBA1 and GBAP1 in brain. Finally, we demonstrate that inaccuracies in annotation are widespread among parent genes, with implications for many human diseases.

genetics↗

bioRxiv2022

Biochemical and metabolic maladaption defines pathological niches in progressive multiple sclerosis

Progressive multiple sclerosis (MS) is driven by demyelination, neuroaxonal loss, and mitochondrial damage occurring behind a closed blood-brain barrier (BBB).1,2 Patients with progressive MS typically fail to respond to available immunomodulatory drugs that reduce relapses in early disease.2 This indicates a dire need to identify non-canonical therapeutic avenues to limit neurodegeneration and promote protection and repair.3 Here, we have employed high-resolution multiomic profiling to characterise the biochemical and metabolic adaptations underpinning MS pathology, as these have been incompletely described but critically, may be amenable to BBB-permeable drug targeting. Using synchrotron radiation (SR)- and focal plane array (FPA)-based Fourier transform infrared microspectroscopy (FTIR), we spatially mapped the biochemical features present in human progressive MS and control post-mortem brain and rare spinal cord tissue. By employing single-nuclear RNA sequencing (snRNA-seq), 10x Genomics Visium spatial transcriptomics and spatial proteomics to resolve their cellular context, we found that these biochemical features provide a uniquely and highly disease-specific barcode for distinct pathological niches within the tissue. Characterisation of the metabolic processes underpinning these niches revealed an associated re-organisation of the astrocytic landscape in the grey and white matter, with implications for the treatment of progressive MS.

neuroscience↗

bioRxiv2022

Photizo: an open-source library for cross-sample analysis of FTIR spectroscopy data

With continually improved instrumentation, Fourier transform infrared (FTIR) microspectroscopy can now be used to capture thousands of high-resolution spectra for chemical characterisation of a sample. The spatially resolved nature of this method lends itself well to histological characterisation of complex biological specimens. However, commercial software currently available can make joint analysis of multiple samples challenging and, for large datasets, computationally infeasible. In order to overcome these limitations, we have developed Photizo - an open-source Python library for spectral analysis which includes functions for pre-processing, visualisation and downstream analysis, including principal component analysis, clustering, macromolecular quantification and biochemical mapping. This library can be used for analysis of spectroscopy data without a spatial component, as well as spatially-resolved data, such as data obtained via infrared (IR) microspectroscopy in scanning mode and IR imaging by focal plane array (FPA) detector. Contactcdendrou@well.ox.ac.uk

bioinformatics↗