Alan J Thomas’s research while affiliated with The Queen Elizabeth Hospital and other places

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Publications (407)


Fig. 2: SuStaIn identified a two-subtype model as being the best representation of brain atrophy progression in patients. (a) CVIC across 10-fold cross-validation of left-out individuals; lower CVIC represents better model fit. (b) Distribution of subtypes across SuStaIn stages. (c) The assignability of disease subtype, operationalised as the distance from the top or bottom axis, which represents the maximum probability (100%) of that subtype. (d) SuStaIn identified two unique subtypes of brain atrophy progression. At each stage, the colour in each region indicates the level of severity of atrophy, with grey representing unaffected regions, red mildly affected regions (z-score of −1), magenta moderately affected regions (z-score of −2), and blue severely affected regions (z-score of −3 or more). Brainstem atrophy begins at approximately stage 6 in the subcortical-first subtype (not shown). CVIC = cross-validation information criterion; CVS = cross-validation similarity; iRBD = idiopathic/isolated REM sleep behaviour disorder; SuStaIn = Subtype and Staging Inference.
Fig. 3: Progression of cortical and subcortical atrophy by subtype and stage in iRBD. The progression of atrophy in cortical regions (a) and subcortical regions (b) used in the SuStaIn modelling in classifiable patients with iRBD. iRBD = idiopathic/isolated REM sleep behaviour disorder; SuStaIn = Subtype and Staging Inference.
Fig. 4: Progression of clinical variables by SuStaIn stage. Higher SuStaIn stages was associated with worse clinical scores on MDS-UPDRS-III and MoCA in patients. MoCA = Montreal Cognitive Assessment; MDS-UPDRS-III = Movement Disorders Society -Unified Parkinson's Disease Rating Scale, Part III; SuStaIn = Subtype and Staging Inference.
Fig. 5: Phenoconversion risk (calculated from the logistic regression predicting phenoconversion) differs in patients with iRBD based on classifiability and stage. Patients with iRBD classified in the cortical-first subtype had a stronger likelihood of DLB compared to PD as disease severity (atrophy) increases. iRBD = idiopathic/isolated REM sleep behaviour disorder; SuStaIn = Subtype and Staging Inference.
Fig. 6: Hypothetical schematic representing the pathways of evolution of brain atrophy progression in iRBD, as simulated by SuStaIn. In this model, the subcortical-first subtype is associated with increased phenoconversion compared to non-classified patients, possibly due to initial involvement of the basal ganglia structures. By contrast, the cortical-first subtype is associated with specific phenoconversion to DLB compared to PD as disease severity (atrophy) progresses. This model suggests that the cortical-first subtype is more closely related to what is classically known as DLB (i.e., initial cortical involvement followed by subcortical involvement, with a long-term risk of dementia), whereas the subcortical-first subtype is more closely related to PD (i.e., initial subcortical involvement followed by cortical involvement, with earlier phenoconversion to PD and an increased long-term risk of dementia under the label of PD dementia). DLB = dementia with Lewy bodies; iRBD = idiopathic/isolated REM sleep behaviour disorder; PD = Parkinson's disease.
Distinct brain atrophy progression subtypes underlie phenoconversion in isolated REM sleep behaviour disorder
  • Article
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May 2025

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62 Reads

EBioMedicine

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Aline Delva

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Alpha-synuclein aggregation induces prominent cellular lipid changes as revealed by Raman spectroscopy and machine learning analysis

April 2025

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36 Reads

Brain Communications

The aggregation of α-synuclein is a central neuropathological hallmark in neurodegenerative disorders known as Lewy body diseases, including Parkinson's disease and dementia with Lewy bodies. In the aggregation process, α-synuclein transitions from its native disordered/α-helical form to a β-sheet-rich structure, forming oligomers and protofibrils that accumulate into Lewy bodies, in a process that is thought to underlie neurodegeneration. Lipids are thought to play a critical role in this process by facilitating α-synuclein aggregation and contributing to cell toxicity, possibly through ceramide production. This study aimed to investigate biochemical changes associated with α-synuclein aggregation, focusing on lipid changes, using Raman spectroscopy coupled with machine learning. HEK293, Neuro2a and SH-SY5Y expressing increased levels of α-synuclein were treated with sonicated α-synuclein pre-formed fibrils, to model seeded aggregation. Raman spectroscopy, complemented by an in-house lipid spectral library, was used to monitor the aggregation process and its effects on cellular viability over 14 days. We detected α-synuclein aggregation by assessing β-sheet peaks at 1045 cm⁻1, in cells treated with α-synuclein pre-formed fibrils, using machine learning (principal component analysis and uniform manifold approximation and projection) analysis based on Raman spectral features. Changes in lipid profiles, and especially sphingolipids, including a decrease in sphingomyelin and increase in ceramides, were observed, consistent with oxidative stress and apoptosis. Altogether, our study informs on biochemical alterations that can be considered for the design of therapeutic strategies for Parkinson's disease and related synucleinopathies.



Plasma Biomarkers and Disease Prognosis in Mild Cognitive Impairment with Lewy Bodies

March 2025

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23 Reads

Movement Disorders

Background Little is known about the prognostic value of plasma biomarkers in mild cognitive impairment with Lewy bodies (MCI‐LB). Objectives To investigate the association of four plasma biomarkers with disease progression in MCI. Methods Plasma amyloid‐beta (Aβ) 42/40 , glial fibrillary acidic protein (GFAP), neurofilament light (NfL), and phosphorylated tau 181 (pTau181) were measured at baseline in a longitudinal MCI cohort (n = 131). Results Baseline plasma NfL was associated with increased risk of dementia/death in the entire cohort. In MCI‐LB, baseline plasma NfL, GFAP, and pTau181 were associated with increased risk of dementia/death and increased cognitive decline measured by the Addenbrooke's Cognitive Examination‐Revised. Conclusions pTau181, GFAP, and NfL are associated with more rapid disease progression in MCI‐LB and, with further validation, could be useful to support prognosis and stratification for clinical practice and treatment trials. Further work, including clinicopathological studies, is needed to understand the biological correlates of these markers in MCI‐LB. © 2025 The Author(s). Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.


Dopaminergic changes in the subgenual cingulate cortex in dementia with lewy bodies associates with presence of depression

March 2025

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13 Reads

Translational Psychiatry

In addition to the core clinical features of fluctuating cognition, visual hallucinations, and parkinsonism, individuals with dementia with Lewy bodies (DLB) frequently experience chronic and debilitating major depression. Treatment of depression in DLB is hampered by a lack of available effective therapies and standard serotonergic medication for major depressive disorder (MDD) is typically ineffective. Dysfunction of dopaminergic neurotransmission contributing to anhedonia and loss of motivation has been described in MDD. The subgenual anterior cingulate cortex (sgACC) is important in mood regulation and in the symptomatic expression of depression, displaying structural, functional and metabolic abnormalities in MDD. To assess dopaminergic and serotonergic synaptic changes in DLB, post mortem sgACC tissue from DLB donors with and without depression was investigated using high-resolution stimulated emission depletion (STED) microscopy, as well as Western and dot blotting techniques. STED imaging demonstrated the presence of α-synuclein within individual dopaminergic terminals in the sgACC, α-synuclein presence showing a significant positive correlation with increased synaptosomal associated protein 25 kDa (SNAP25) volumes in depressed DLB cases. A reduction in dopaminergic innervation in the sgACC was observed in DLB cases with depression compared to controls (p < 0.001), but not in non-depressed DLB donors, along with reduced levels of multiple dopaminergic markers and receptors. Limited alterations were observed in serotonergic markers. Our work demonstrates a role for dopaminergic neurotransmission in the aetiology of depression in DLB. Careful and selective targeting of dopaminergic systems in the sgACC may be a therapeutic option for treatment of depression in DLB.


Figure 1. Cohort summary of samples used in DNA methylation association meta-analysis of Lewy bodies. A) Brain regions and analysis protocol for meta-analyses. Brain regions include two cortical regions, the prefrontal cortex (PFC, BA9) and the anterior cingulate cortex (ACC, BA24). Analysis plan outlining steps in data generation, harmonization, within cohort linear association analyses and fixed effects meta-analysis. B) Summary of sample numbers in the UK Brain Bank Network (UKBBN), Netherlands Brain Bank (NBB) and Brains for Dementia Research (BDR) cohorts. Left hand bar plots show number of samples per Braak LB Stage, right hand plots show number of samples with coinciding AD pathology as measured by the Braak NFT stage. Components of figure created in https://BioRender.com
Figure 3. A) Gene ontology (GO) analysis of primary full cohort Lewy body pathology meta-analysis. The nine FDR-significant terms identified in the ontological analysis are shown, with -log10 transformed raw p-value shown on the x-axis. REVIGO prioritized gene parent terms are shown on the y-axis. B) Mini-Manhattan plots of the LTF gene region, C) NDRG4 gene region and D) MYO16 gene region. Y-axis shows -log10 transformed p-
Interrogating DNA methylation associated with Lewy body pathology in a cross brain-region and multi-cohort study

March 2025

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26 Reads

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1 Citation

Lewy body (LB) diseases are an umbrella term encompassing a range of neurodegenerative conditions all characterized by the hallmark of intra-neuronal α-synuclein associated with the development of motor and cognitive dysfunction. In this study, we have conducted a large meta-analysis of DNA methylation across multiple cortical brain regions, in relation to increasing burden of LB pathology. Utilizing a combined dataset of 1239 samples across 855 unique donors, we identified a set of 30 false discovery rate (FDR) significant loci that are differentially methylated in association with LB pathology, the most significant of which were located in UBASH3B and PTAFR, as well as an intergenic locus. Ontological enrichment analysis of our meta-analysis results highlights several neurologically relevant traits, including synaptic, inflammatory and vascular alterations. We leverage our summary statistics to compare DNA methylation signatures between different neurodegenerative pathologies and highlight a shared epigenetic profile across LB diseases, Alzheimer's disease and Huntington's disease, although the top-ranked loci show disease specificity. Finally, utilizing summary statistics from previous large-scale genome-wide association studies we report FDR significant enrichment of DNA methylation differences with respect to increasing LB pathology in the SNCA genomic region, a gene previously associated with Parkinson's disease and dementia with Lewy bodies.



Dementia with Lewy Bodies

February 2025

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9 Reads

A comprehensive and multidisciplinary guide to understanding and treating a wide range of movement disorders, including parkinsonisms, tremor, tics, dystonia, chorea, ballism and myoclonus. Split into five sections, the first is a basic introduction to the subject, covering the principles of human motor behavior and functional anatomy. The next three sections discuss movement disorders in depth, grouped into hypokinetic, hyperkinetic, and dyscoordinative and otherwise inappropriate motor behaviours, covering clinical manifestations, diagnostic features and therapeutic strategies. The last section explores the different ways of objectifying selected behavioral movement disorders. 90 videos, hosted online, and over 200 figures illustrate the concepts covered in the book, offering a visual reference for the disorders discussed. This compendium offers an essential tool to recognize, interpret and understand the clinical manifestations and underlying disorders of neurological movement disorders, and to select the best therapeutic strategies.


Lord et al. [16]’s model of gait for older adults. Gait domains include pace, rhythm, variability, asymmetry, and postural control.
Flowchart of search strategy and extraction of eligible studies.
Heat map detailing number of studies comparing groups. AD, Alzheimer’s disease; VaD, vascular dementia; DLB, dementia with Lewy bodies; PDD, Parkinson’s disease with dementia, LBD, Lewy body dementia; OD, unspecified non-AD dementias; MCI, mild cognitive impairment; PD, Parkinson’s disease.
Associations between dementia subtypes and gait implied by the current literature, using Lord et al. [16]’s as a framework to interpret results.
What Can Quantitative Gait Analysis Tell Us about Dementia and Its Subtypes? A Structured Review

February 2025

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1,550 Reads

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80 Citations

Distinguishing dementia subtypes can be difficult due to similarities in clinical presentation. There is increasing interest in discrete gait characteristics as markers to aid diagnostic algorithms in dementia. This structured review explores the differences in quantitative gait characteristics between dementia and healthy controls, and between four dementia subtypes under single-task conditions: Alzheimer’s disease (AD), dementia with Lewy bodies and Parkinson’s disease dementia, and vascular dementia. Twenty-six papers out of an initial 5,211 were reviewed and interpreted using a validated model of gait. Dementia was associated with gait characteristics grouped by slower pace, impaired rhythm, and increased variability compared to normal aging. Only four studies compared two or more dementia subtypes. People with AD are less impaired in pace, rhythm, and variability domains of gait compared to non-AD dementias. Results demonstrate the potential of gait as a clinical marker to discriminate between dementia subtypes. Larger studies using a more comprehensive battery of gait characteristics and better characterized dementia sub-types are required.


Molecular Insights into α-Synuclein Fibrillation: A Raman Spectroscopy and Machine Learning Approach

January 2025

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27 Reads

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2 Citations

ACS Chemical Neuroscience

The aggregation of α-synuclein is crucial to the development of Lewy body diseases, including Parkinson’s disease and dementia with Lewy bodies. The aggregation pathway of α-synuclein typically involves a defined sequence of nucleation, elongation, and secondary nucleation, exhibiting prion-like spreading. This study employed Raman spectroscopy and machine learning analysis, alongside complementary techniques, to characterize the biomolecular changes during the fibrillation of purified recombinant wild-type α-synuclein protein. Monomeric α-synuclein was produced, purified, and subjected to a 7-day fibrillation assay to generate preformed fibrils. Stages of α-synuclein fibrillation were analyzed using Raman spectroscopy, with aggregation confirmed through negative staining transmission electron microscopy, mass spectrometry, and light scattering analyses. A machine learning pipeline incorporating principal component analysis and uniform manifold approximation and projection was used to analyze the Raman spectral data and identify significant peaks, resulting in differentiation between sample groups. Notable spectral shifts in α-synuclein were found in various stages of aggregation. Early changes (D1) included increases in α-helical structures (1303, 1330 cm–1) and β-sheet formation (1045 cm–1), with reductions in COO– and CH2 bond regions (1406, 1445 cm–1). By D4, these structural shifts persist with additional β-sheet features. At D7, a decrease in β-sheet H-bonding (1625 cm–1) and tyrosine ring breathing (830 cm–1) indicates further structural stabilization, suggesting a shift from initial helical structures to stabilized β-sheets and aggregated fibrils. Additionally, alterations in peaks related to tyrosine, alanine, proline, and glutamic acid were identified, emphasizing the role of these amino acids in intramolecular interactions during the transition from α-helical to β-sheet conformational states in α-synuclein fibrillation. This approach offers insight into α-synuclein aggregation, enhancing the understanding of its role in Lewy body disease pathophysiology and potential diagnostic relevance.


Citations (59)


... Accordingly, neurotoxic agent exposures, alcohol consumption, smoking habits, or brain injuries can significantly raise the risk of AD and FTD by interfering with neurodegenerative genes through DNA methylation. Alterations in DNA methylation have been identified as key factors in the pathogenesis of these disorders [27][28][29][30][31][32][33][34][35][36]. ...

Reference:

Evaluation of Illumina and Oxford Nanopore Sequencing for the Study of DNA Methylation in Alzheimer’s Disease and Frontotemporal Dementia
Interrogating DNA methylation associated with Lewy body pathology in a cross brain-region and multi-cohort study

... Tawhid et al. [23] introduced a Convolutional Neural Network (CNN)-based framework to pinpoint precise frequency band biomarkers for MCI diagnosis. Hasoon et al. [24] explored EEG functional connectivity to differentiate stable MCI from converting MCI. Patients who progress to dementia show altered EEG connectivity in alpha and beta bands, making these measures valuable for early prediction. ...

EEG Functional Connectivity Differences Predict Future Conversion to Dementia in Mild Cognitive Impairment With Lewy Body or Alzheimer Disease
  • Citing Article
  • September 2024

International Journal of Geriatric Psychiatry

... 45,4 It also aligns with specific clinical features shown to predict specific phenoconversion trajectories in iRBD. 46 Previous studies by our group show, using in silico models, 47,48 that neurodegenerative changes found in iRBD, namely brain atrophy, can be recreated based on the spread of alpha-synuclein proteins in the brain as a function of deafferentation and the accumulation of toxic proteins in specific regions. 48 Although only connection strength and local gene expression were used as spreading and vulnerability factors in these simulations, our study suggests that altered glymphatic function may be an additional player in such models. ...

Distinct brain atrophy progression subtypes underlie phenoconversion in isolated REM sleep behaviour disorder

... DNA methylation changes in the cortex are closely associated with neurodegenerative diseases such as Alzheimer's and Parkinson's [107,108]. To address the limitations of earlier clocks-which were often not rigorously calibrated for specific tissues and were prone to age-related phenotypic influences leading to false positives-recent efforts have focused on developing clocks specifically for the human cerebral cortex [109,110]. These cortical clocks weigh the DNA methylation levels at specific sites, distinguishing themselves from clocks developed from multi-tissue or blood samples. ...

Genetic architecture of epigenetic cortical clock age in brain tissue from older individuals: alterations in CD46 and other loci

... Alzheimer's disease (AD) represents one of the most significant social, economic, and medical challenges of our time due to its insidious onset, prolonged progression, and unclear pathogenesis [1]. Substantial evidence demonstrates that the irreversible decline in cognitive abilities in AD patients is closely associated with the deterioration and degeneration of neurons in the AD brain [2,3]. Current therapeutic approaches offer limited effectiveness and fail to compensate for the neuronal loss in the cortex and hippocampus. ...

Outcomes of Patients With Mild Cognitive Impairment With Lewy Bodies or Alzheimer Disease at 3 and 5 Years After Diagnosis

Neurology

... 12 A recent large consortium-based study of 338 patients with pathologicallyconfirmed PiD reported CBS as a presenting feature in 15 cases (4.4%). 13 Therefore, in larger datasets CBS appears to be a more frequent presentation of PiD than smaller single-center series had hitherto indicated. ...

MAPT H2 haplotype and risk of Pick's disease in the Pick's disease International Consortium: a genetic association study

The Lancet Neurology

... Collectively, the association between PLAUR and the development of AD observed in this study might be bridged by the pro-inflammatory effects (potentially associated with microglial activation) of it in the central nervous system (CNS). Notably, despite two SNPs located in the PLAUR gene were indicative of a trend toward association, Cetinsoy et al. (2024) Forest plot of the MR results in discovery (A) and validation (B) stage. SNP, single nucleotide polymorphism; IVW, inverse-variance weighted; OR, odds ratio; AD, Alzheimer's disease. ...

Gene Association Study of the Urokinase Plasminogen Activator and Its Receptor Gene in Alzheimer’s Disease

... Further details can be found in Supplementary Table 2 and in the main trial paper. 34 At 12 months, complete cost and utility data were available for 109 (65%) participants in the adapted PATH arm and 106 (63%) in the TAU arm. The Consolidated Standards of Reporting Trials (CONSORT) diagram is reported in Supplementary Fig. 1. ...

Adapted problem adaptation therapy for depression in mild to moderate Alzheimer's disease dementia: A randomized controlled trial

... MPS are progressive and linked to significant functional impairments, including a marked decline in autonomy in daily living activities [81,85]. The presence of MPS has also been associated with an increased risk of cognitive impairment (ranging from mild cognitive impairment to dementia), PD, and mortality [86][87][88]. While the underlying neurophysiological mechanisms are not well understood, they are believed to involve multifactorial processes, including age-related declines in dopaminergic activity, vascular pathologies, and neurodegenerative conditions such as PD and AD [5,6,80]. ...

Identifying parkinsonism in mild cognitive impairment

Journal of the Neurological Sciences

... The prevalence of CAA has been reported in 70% of DLB patients ex-vivo (5) and the prevalence of cerebral microbleeds has been identified in 30% of DLB patients (6). ...

Prevalence, distribution, and severity of cerebral amyloid angiopathy differ between Lewy body diseases and Alzheimer’s disease

Acta Neuropathologica Communications