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Head of Queen Square Brain Bank Professor Thomas Warner 
Director of Research Professor Tammaryn Lashley 
Clinical Lecturer and Honorary Consultant Neuropathologist Dr Zane Jaunmuktane 
Emeritus Professor of Neuropathology Janice Holton “QSBB is an invaluable resource for clinicians and scientists worldwide. For 30 years we have built a unique collection of tissue focussing on neurodegenerative diseases. Our own research programme, and that of groups to whom we have supplied tissue for research, has resulted in a greater understanding of the underlying processes that lead to the death of specific brain cells, improvements in diagnostic precision, and opened new avenues for more effective treatments.”
Transcriptomic analysis of frontotemporal lobar degeneration with TDP‑43 pathology reveals cellular alterations across multiple brain regions
Rahat Hasan, Jack Humphrey, Conceição Bettencourt, Jia Newcombe, NYGC ALS Consortium , Tammaryn Lashley, Pietro Fratta, Towfique Raj
Abstract:Frontotemporal lobar degeneration (FTLD) is a group of heterogeneous neurodegenerative disorders affecting the frontal and temporal lobes of the brain. Nuclear loss and cytoplasmic aggregation of the RNA-binding protein TDP-43 represents the major FTLD pathology, known as FTLD-TDP. To date, there is no effective treatment for FTLD-TDP due to an incomplete understanding of the molecular mechanisms underlying disease development. Here we compared postmortem tissue RNA-seq transcriptomes from the frontal cortex, temporal cortex, and cerebellum between 28 controls and 30 FTLD-TDP patients to profile changes in cell-type composition, gene expression and transcript usage. We observed downregulation of neuronal markers in all three regions of the brain, accompanied by upregulation of microglia, astrocytes, and oligodendrocytes, as well as endothelial cells and pericytes, suggesting shifts in both immune activation and within the vasculature. We validate our estimates of neuronal loss using neuropathological atrophy scores and show that neuronal loss in the cortex can be mainly attributed to excitatory neurons, and that increases in microglial and endothelial cell expression are highly correlated with neuronal loss. All our analyses identified a strong involvement of the cerebellum in the neurodegenerative process of FTLD-TDP. Altogether, our data provides a detailed landscape of gene expression alterations to help unravel relevant disease mechanisms in FTLD.
Fig. 1 Overview of differential expression analyses. a Principal
component analysis of the RNA-seq expression matrix, following
TMM-normalisation and covariate adjustment. Colour corresponds
to disease status and shape corresponds to brain region. Distinct
clusters can be seen between the cortical and cerebellar samples. b
Upset plot showing the number of distinct and overlapping differentially
expressed genes in each brain region. c. Volcano plots comparing
FTLD-TDP samples with controls. Red and blue dots represent
genes that are upregulated and downregulated, respectively (FDR
adjusted P < 0.05), while gray dots are genes that are not differentially
expressed. Key genes related to FTLD or ALS are labelled. d Scatter
plots comparing log2-
fold changes of all genes tested between each
pair of brain regions. Each point is a gene, coloured by the density of
overlapping points. Log2-
fold changes are highly concordant between
the frontal and temporal cortex, but less so between the cerebellum
Fig. 2 Cellular and pathway-level enrichment analyses. a–c Heatmaps showing the GSEA results for cellular pathways, cell types, and glial activation states. Coloured tiles represent the normalisedenrichment score (NES) for each term. Grey tiles were not tested. d Boxplots comparing the log2- fold changes between the activation genes in c and standard marker genes in b for astrocytes and microglia. Comparisons were made using the Wilcoxon rank sum test. All P values from a–d are Bonferroni-corrected. ***P < 1e-4; **P < 1e-3; *P < 0.05; ns P > 0.05
Fig. 3 Cellular proportion changes and atrophy correlations. a Comparisons
of the cellular proportion estimates between control and
FTLD-TDP samples. Estimates were generated with dtangle using
single nuclear RNA-seq data from Mathys et al. b Hematoxylin and
eosin stained sections of select frontal cortex FTLD-TDP samples.
From left to right, the slides depict cases with mild, moderate, and
severe microscopic atrophy. Neurons are indicated by black arrows. c
Comparisons of the cellular proportion estimates of the frontal cortex
FTLD-TDP samples between each microscopic atrophy stage. Excitatory
neurons are associated with neuronal loss as the estimates show
significant decreases between all atrophy stages. Inhibitory neurons
show decreases between stages 2 and 3, but not 1 and 2, indicating a
partial negative association. Positive associations with neuronal loss
are observed for endothelial cells and microglia. Asterisks in a and
c represent Bonferroni-adjusted P values from Wilcoxon rank sum
tests. ***P < 1e-4; **P < 1e-3; * P < 0.05; ns P > 0.05
Fig. 4 Differential transcript usage analysis. a. Upset plots showing
overlaps between the gDTUs (adjusted P < 0.05) and DEGs (adjusted
P < 0.05) for each brain region. b, c Cell types, glial activation states,
and pathways enriched in gDTUs (b) and gDTUs + DEGs (c). Coloured
tiles represent the negative logarithm of the adjusted P value
for each term. Grey tiles were not tested. d Transcript usage of the
four UNC13B isoforms with significant effect sizes in at least one
brain region. e. Alignment chart of the UNC13B isoforms in d, showing
the region with greatest variation in transcript structure. Purple
rectangles correspond to protein-coding exons. Asterisks in b-d
refer to P values that meet the FDR threshold of 0.05. ***P < 1e-4;
**P < 1e-3; *P < 0.05; ns P > 0.05
Faster disease progression in Parkinson's disease with type 2 diabetes is not associated with increased α-synuclein, tau, amyloid-β or vascular pathology
Eduardo de Pablo-Fernández , Robert Courtney , Alice Rockliffe , Steve Gentleman , Janice L Holton , Thomas T Warner
"Neuropathol Appl Neurobiol" Dec 2021
Abstract
Aims: Growing evidence suggests a shared pathogenesis between Parkinson's disease and diabetes although the underlying mechanisms remain unknown. The aim of this study was to evaluate the effect of type 2 diabetes on Parkinson's disease progression and to correlate neuropathological findings to elucidate pathogenic mechanisms.
Methods: In this cohort study, medical records were retrospectively reviewed of cases with pathologically confirmed Parkinson's disease with and without pre-existing type 2 diabetes. Time to disability milestones (recurrent falls, wheelchair dependence, dementia and care home placement) and survival were compared to assess disease progression and their risk estimated using Cox hazard regression models. Correlation with pathological data was performed, including quantification of α-synuclein in key brain regions and staging of vascular, Lewy and Alzheimer's pathologies.
Results: Patients with PD and diabetes (male 76%; age at death 78.6 ± 6.2 years) developed earlier falls (p < 0.001), wheelchair dependence (p = 0.004), dementia (p < 0.001), care home admission (p < 0.001) and had reduced survival (p < 0.001). Predating diabetes was independently associated with a two to three-fold increase in the risk of disability and death. Neuropathological assessment did not show any differences in global or regional vascular pathology, α-synuclein load in key brain areas, staging of Lewy pathology or Alzheimer's disease pathology.
Conclusions: Pre-existing type 2 diabetes contributes to faster disease progression and reduced survival in Parkinson's disease which is not driven by increased vascular, Lewy or Alzheimer's pathologies. Additional non-specific neurodegeneration related to chronic brain insulin resistance may be involved.
