Biology subjects

Gillingwater, T. H.

Publications and source records attributed to Gillingwater, T. H..

10 recordsLinked to original sources

bioRxiv2026

Breakdown in the synaptic vesicle cycle defines early and reversible cortical pathogenesis in ALS

Synaptic failure is considered an early driver of Amyotrophic Lateral Sclerosis (ALS), yet identifying the molecular events initiating synaptic decline remains challenging in end-stage human tissue. Here, we exploit the late involvement of the primary visual cortex (Brodmann Area 17 (BA17)) to investigate early disease-associated changes in human ALS. Structural analyses revealed neuropil compaction, presynaptic terminal shrinkage, and synaptic degeneration despite preservation of local neuronal populations. Deep synaptoneurosome proteomics identified a regional signature characterised by disruption of presynaptic vesicle cycling, which closely resembles early pathological changes observed in the inducible human TDP-43 rNLS8 mouse model. Importantly, suppression of TDP-43 expression in vivo restored these proteomic alterations, highlighting recovery of presynaptic vesicle machinery within preserved synaptic structures. Together, these findings reveal early synaptic pathology as a distinct and potentially reversible stage of ALS neurodegeneration.

neuroscience↗

bioRxiv2025

Translation-specific disruption of Col1a1 expression in multiple models of Spinal Muscular Atrophy can be rescued by Risdiplam.

Spinal muscular atrophy (SMA) is a monogenic neurodegenerative disorder caused by decreased levels of Survival of Motor Neuron (SMN) protein. If left untreated, SMA patients have a poor prognosis, marked by the degeneration of motor neurons, progressive muscle weakness and atrophy. The approval of SMN-restoring therapies that improve symptoms and lifespan in patients with SMA has created emerging, non-neuronal phenotypes and an urgent need for deepening our understanding of disease pathogenesis. Leveraging the knowledge that SMN loss drives alterations in translation, we used multiple tissues from a mouse model of SMA to uncover early translational alterations in key mRNAs and proteins, which act as contributors to pathogenesis and hallmarks of the disease. Among hundreds of differentially translated mRNAs, Col1a1 emerged as a translation-specific manifestation of early defects in the mouse model. These findings were confirmed in fibroblasts derived from patients with varying levels of disease severity. Notably, treatment with SMN-restoring therapies rescued COL1A1 protein levels, particularly in fibroblasts from patients with the most severe forms of the disease. Overall, our study identifies COL1A1 as an indicator of disease severity in SMA, which captures early molecular alterations and respond to SMN-modifying therapies.

molecular biology↗

bioRxiv2025

Mifepristone alone and in combination with scAAV9-SMN1 gene therapy improves disease phenotypes in Smn2B/- spinal muscular atrophy mice

Spinal muscular atrophy (SMA) is a neuromuscular disease caused by deletions or mutations in the survival motor neuron 1 (SMN1) gene. SMA is characterised by alpha motor neuron loss in the spinal cord and subsequent muscle atrophy. There are currently three approved SMN-directed therapies for SMA patients. While these therapies have transformed what was once a life-limiting condition into one that can be managed and even improved, they are unfortunately not cures, highlighting the need for additional supporting second-generation therapies. These should not only target the neuromuscular system but also peripheral and metabolic perturbations that are present in both SMA models and patients. Kruppel-like factor 15 (Klf15) is a transcription factor that maintains metabolic homeostasis and is involved in the glucocorticoid-glucocorticoid receptor (GR) signalling pathway, in several peripheral and metabolic tissues in SMA mice. Here, we used murine and human cellular models as well as SMA mice and Caenorhabditis Elegans (C. elegans) to assess the therapeutic potential of reducing Klf15 activity with mifepristone, a glucocorticoid antagonist, combined with SMN-targeted gene therapy. We report that mifepristone reduces Klf15 expression across several in vitro models, ameliorates neuromuscular pathology in SMA smn-1(ok355) C. elegans and improves survival of SMA Smn2B/- mice. Furthermore, we show that combining mifepristone with an approved SMN-directed gene therapy (scAAV9-SMN1) results in improved tissue- and sex-specific responses to treatment. Our study demonstrates that a multi-tissue targeting SMN-independent drug, alone and in combination with an approved SMN-dependent therapy, has the potential to improve SMA disease pathology.

pharmacology and toxicology↗

bioRxiv2024

Patient-specific responses to SMN2 splice-modifying treatments in spinal muscular atrophy fibroblasts

The availability of three therapies for the neuromuscular disease spinal muscular atrophy (SMA) highlights the need to match patients to the optimal treatment. Two of these treatments (nusinersen and risdiplam) target splicing of SMN2, but treatment outcomes vary from patient to patient. An incomplete understanding of the complex interactions between SMA genetics, SMN protein and mRNA levels, and gene-targeting treatments, limits our ability to explain this variability and identify optimal treatment strategies for individual patients. To address this, we analyzed responses to nusinersen and risdiplam in 45 primary fibroblast cell lines. Pre-treatment SMN2-FL, SMN2{Delta}7 mRNA, and SMN protein levels were influenced by SMN2 copy number, age, and sex. After treatment, SMN and mRNA levels were more heterogeneous. In 43% of patients, response to both therapies was similar, but in 57% one treatment led to a significantly higher SMN increase than the other treatment. Younger age, higher SMN2 copy number, and higher SMN levels before treatment predicted better in vitro efficacy. These findings showcase patient-derived fibroblasts as a tool for identifying molecular predictors for personalized treatment.

molecular biology↗

bioRxiv2020

Phospho-RNA sequencing with CircAID-p-seq

Accurate positional information concerning ribosomes and RNA binding proteins with respect to their transcripts is important to understand the global regulatory network underlying protein and RNA fate in living cells. Most footprinting approaches generate RNA fragments bearing a phosphate or cyclic phosphate groups at their 3' end. Unfortunately, all current protocols for library preparation rely only on the presence of a 3' hydroxyl group. Here, we developed circAID-p-seq, a PCR-free library preparation for 3' phospho-RNA sequencing. We applied circAID-p-seq to ribosome profiling, which produces fragments protected by ribosomes after endonuclease digestion. CircAID-p-seq, combined with the dedicated computational pipeline circAidMe, facilitates accurate, fast, highly efficient and low-cost sequencing of phospho-RNA fragments from eukaryotic cells and tissues. While assessing circAID-p-seq to portray ribosomes engaged with transcripts, we provide a versatile tool to unravel any 3'-phospho RNA molecules.

molecular biology↗

bioRxiv2020

A mouse model for spinal muscular atrophy provides insights into non-alcoholic fatty liver disease pathogenesis

Background & aims Spinal muscular atrophy (SMA) is an inherited neuromuscular disorder leading to paralysis and death in children. SMA patients are more susceptible to dyslipidemia as well as liver steatosis, features reproduced in SMA mouse models. As current pre-clinical models of NAFLD are invariably imperfect and generally take a long time to develop, the rapid development of liver steatosis in SMA mice provides a means to identify molecular markers of non-alcoholic fatty liver disease (NAFLD). Here, we investigated whether Smn2B/- mice, a model of severe SMA, display typical features of NAFLD/non-alcoholic steatohepatitis (NASH).Methods Biochemical, histological, electron microscopy, proteomic, and high-resolution respirometry were used.Results The Smn2B/- mice develop steatohepatitis early in life. The consequent liver damage arises from mitochondrial reactive oxygen species production and results in impaired hepatic function including alterations in protein output, complement, coagulation, iron homeostasis, and IGF-1 metabolism. The steatohepatitis is reversible by AAV9-SMN gene therapy. The NAFLD phenotype is likely due to non-esterified fatty acid (NEFA) overload from peripheral lipolysis, subsequent to hyperglucagonemia compounded by reduced muscle use. Mitochondrial β-oxidation contributed to hepatic damage as we observed enhanced hepatic mitochondrial β-oxidation and reactive oxygen species production. Hepatic mitochondrial content, however, was decreased. In contrast to typical NAFLD/NASH, the Smn2B/- mice lose weight due to their neurological condition, develop hypoglycemia and do not develop hepatic fibrosis.Conclusion The Smn2B/- mice represent a good model of microvesicular steatohepatitis. Like other models, it is not representative of the complete NAFLD/NASH spectrum. Nevertheless, it offers a reliable, low-cost, early onset model that is not dependent on diet to identify molecular players in NAFLD pathogenesis and can serve as one of the very few models of microvesicular steatohepatitis for both adult and pediatric populations.Competing Interest StatementMarc-Olivier Deguise received honoraria and travel accommodations from Biogen for speaking engagements at the SMA Summit 2018 held in Montreal, Canada and SMA Academy 2019 held in Toronto, Canada. Rashmi Kothary received honoraria and travel accommodations from Roche as an invited speaker at their global and national board meetings in 2019. RK and the Ottawa Hospital Research Institute have a licensing agreement with Biogen for the Smn2B/- mouse model. Thomas H. Gillingwater has served on global and UK advisory boards for Roche. These COI are outside the scope of this study. All other authors have no competing interests to declare.List of abbreviationsAGCautomatic gain controlALPalkaline phosphataseALTalanine aminotransferaseASTaspartate aminotransferaseBaxBCL2 associated X proteinDAVIDThe Database for Annotation, Visualization and Integrated DiscoveryESEnrichment ScoreFasRFas receptorH&EHematoxylin & eosinHFDhigh fat dietIGF-1insulin-like growth factor 1IGFbp1insulin like growth factor binding protein 1IGF1Rinsulin like growth factor 1 receptorigfalsinsulin like growth factor binding protein acid labile subunitIPAingenuity pathway analysisMCDmethionine and choline deficient dietMCLMarkov Clustering AlgorithmNAFLDnon-alcoholic fatty liver diseaseNASHnon-alcoholic steatohepatitisNEFAnon-esterified fatty acidPpostnatal dayp21cyclin dependent kinase inhibitor 1Ap53tumor protein p53PASPeriodic acid-SchiffSMAspinal muscular atrophySMN1Survival motor neuron 1TMTTandem Mass TaggingTNFR1TNF receptor superfamily member 1AView Full Text

pathology↗

bioRxiv2019

SMN-primed ribosomes modulate the translation of transcripts related to Spinal Muscular Atrophy

The contribution of ribosome heterogeneity and ribosome-associated factors to the molecular control of proteomes in health and disease remains enigmatic. We demonstrate that Survival Motor Neuron (SMN) protein, loss of which causes the neuromuscular disease spinal muscular atrophy (SMA), binds to ribosomes and that this interaction is tissue-dependent. SMN-primed ribosomes are positioned within the first five codons of a set of mRNAs which are enriched in IRES-like sequences in the 5UTR and rare codons at the beginning of their coding sequence. Loss of SMN at early-stages of SMA induces translational defects in vivo, characterized by ribosome depletion in rare codons at the third and fifth position of the coding sequence. These positional defects cause ribosome depletion from mRNAs bound by SMN-primed ribosomes and translational impairment of proteins involved in motor neuron function and stability, including acetylcholinesterase. Thus, SMN plays a crucial role in the regulation of ribosome fluxes along mRNAs which encode proteins relevant to SMA pathogenesis.

neuroscience↗

bioRxiv2017

Active ribosome profiling with RiboLace

Ribosome profiling, or Ribo-Seq, is based around large-scale sequencing of RNA fragments protected from nuclease digestion by ribosomes. Thanks to its unique ability to provide positional information concerning ribosomes flowing along transcripts, this method can be used to shed light on mechanistic aspects of translation. However, current Ribo-Seq approaches lack the ability to distinguish between fragments protected by ribosomes in active translation or by inactive ribosomes. To overcome these significant limitation, we developed RiboLace: a novel method based on an original puromycin-containing molecule capable of isolating active ribosomes by means of an antibody-free and tag-free pull-down approach. RiboLace is fast, works reliably with low amounts of input material, and can be easily and rapidly applied both in vitro and in vivo, thereby generating a global snapshot of active ribosome footprints at single nucleotide resolution.

molecular biology↗

bioRxiv2017

riboWaltz: optimization of ribosome P-site positioning in ribosome profiling data

Ribosome profiling is a powerful technique used to study translation at the genome-wide level, generating unique information concerning ribosome positions along RNAs. Optimal localization of ribosomes requires the proper identification of the ribosome P-site in each ribosome protected fragment, a crucial step to determine trinucleotide periodicity of translating ribosomes, and draw correct conclusions concerning where ribosomes are located. To determine the P-site within ribosome footprints at nucleotide resolution, the precise estimation of its offset with respect to the protected fragment is necessary. Here we present riboWaltz, an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of data. Compared to existing tools, riboWaltz shows improved accuracies for P-site estimation and neat ribosome positioning in multiple case studies.\n\nAvailability and ImplementationriboWaltz was implemented in R and is available at https://github.com/LabTranslationalArchitectomics/RiboWaltz\n\nContactgabriella.viero@cnr.it or fabio.lauria@unitn.it

bioinformatics↗

bioRxiv2017

In vivo translatome profiling reveals early defects in ribosome biology underlying SMA pathogenesis

BackgroundGenetic alterations impacting on ubiquitously expressed proteins involved in mRNA metabolism often result in neurodegenerative conditions, with increasing evidence suggesting that translational defects can contribute to disease. Spinal Muscular Atrophy (SMA) is a neuromuscular disease caused by low levels of SMN protein, whose role in disease pathogenesis remains unclear.\n\nResultsBy determining in parallel the in vivo transcriptome and translatome in SMA mice we identified a robust decrease in translational efficiency, arising during early stages of disease. Translational defects affected translation-related transcripts, were cell autonomous, and were fully rescued after treatment with antisense oligonucleotides to restore SMN levels. Defects in translation were accompanied by a decrease in the number of ribosomes in motor neurons in vivo.\n\nConclusionOur findings suggest that neuronal tissues and cells are particularly sensitive to perturbations in translation during SMA, and identify ribosome biology as an important, yet largely neglected, factor in motor neuron degeneration.

neuroscience↗