Genetic topography and cortical cell loss in Huntington's disease link development and neurodegeneration

Abstract

Cortical cell loss is a core feature of Huntington's disease (HD), beginning many years before clinical motor diagnosis, during the premanifest stage. However, it is unclear how genetic topography relates to cortical cell loss. Here, we explore the biological processes and cell types underlying this relationship and validate these using cell-specific post-mortem data. Eighty premanifest participants on average 15 years from disease onset and 71 controls were included. Using volumetric and diffusion MRI we extracted HD-specific whole brain maps where lower grey matter volume and higher grey matter mean diffusivity, relative to controls, were used as proxies of cortical cell loss. These maps were combined with gene expression data from the Allen Human Brain Atlas (AHBA) to investigate the biological processes relating genetic topography and cortical cell loss. Cortical cell loss was positively correlated with the expression of developmental genes (i.e. higher expression correlated with greater atrophy and increased diffusivity) and negatively correlated with the expression of synaptic and metabolic genes that have been implicated in neurodegeneration. These findings were consistent for diffusion MRI and volumetric HD-specific brain maps. As wild-type huntingtin is known to play a role in neurodevelopment, we explored the association between wild-type huntingtin (HTT) expression and developmental gene expression across the AHBA. Co-expression network analyses in 134 human brains free of neurodegenerative disorders were also performed. HTT expression was correlated with the expression of genes involved in neurodevelopment while co-expression network analyses also revealed that HTT expression was associated with developmental biological processes. Expression weighted cell-type enrichment (EWCE) analyses were used to explore which specific cell types were associated with HD cortical cell loss and these associations were validated using cell specific single nucleus RNAseq (snRNAseq) data from post-mortem HD brains. The developmental transcriptomic profile of cortical cell loss in preHD was enriched in astrocytes and endothelial cells, while the neurodegenerative transcriptomic profile was enriched for neuronal and microglial cells. Astrocyte-specific genes differentially expressed in HD post-mortem brains relative to controls using snRNAseq were enriched in the developmental transcriptomic profile, while neuronal and microglial-specific genes were enriched in the neurodegenerative transcriptomic profile. Our findings suggest that cortical cell loss in preHD may arise from dual pathological processes, emerging as a consequence of neurodevelopmental changes, at the beginning of life, followed by neurodegeneration in adulthood, targeting areas with reduced expression of synaptic and metabolic genes. These events result in age-related cell death across multiple brain cell types.

Keywords: Huntington’s disease; atrophy; diffusivity; gene expression; imaging transcriptomics.

Figure 1

Summary of analysis pipeline and main results. T-maps examining areas with lower cortical volume and higher mean diffusivity (cortical cell loss) in premanifest Huntington’s disease (preHD) compared to healthy controls were obtained and correlated with Allen Human Brain Atlas (AHBA) data at the voxel-level. Gene lists positively and negatively associated with cortical cell loss in preHD were provided. Genes positively associated with cortical cell loss were involved in development and enriched in transcriptomic profiles from astrocytes. The expression of HTT in the healthy human brain was associated with developmental biological processes and correlated with the expression of developmental genes. Genes negatively associated with cortical cell loss were involved in neurodegenerative (synaptic and metabolic) biological processes, being enriched in transcriptional profiles from neurons and microglial cells. The cell-specific transcriptional profiles from post-mortem Huntington’s disease (HD) brains using single-nucleus RNA sequencing (snRNAseq) were enriched within gene lists associated with cortical cell loss, affecting the same cell types and in the same directions as the ones found in the EWCE analyses. wt = wild-type.

Figure 2

Results of the imaging analyses comparing preHD and healthy controls. T-maps showing the volumetric (A) and mean diffusivity (B) differences between premanifest Huntington’s disease (preHD) and controls, used in the transcriptomic analyses. Statistically significant differences in volume (C) and mean diffusivity (D) between preHD and controls, thresholded at P < 0.05 (family-wise error cluster-corrected, cluster forming threshold P = 0.001), overlaid onto the grey matter map of a representative participant. The colour bar represents T-scores. In E the associations between T-values for mean diffusivity and for cortical volume from A and B are represented in the voxels selected for the transcriptomic analysis.

Figure 3

Scatterplot representing the genes associated with cortical cell loss. The y axis represents the logarithmic of the P value while the x axis shows the T value. The horizontal line represents the threshold for significance while the vertical lines show the T = 2 threshold for gene expression positively (right side) or negatively (left side) correlated with cortical volume loss (A) and increases in cortical diffusivity (B). The “ggrepel” package in Rstudio was used to avoid label overlap.

Figure 4

Total number of GO biological process terms positively associated with cortical cell loss in premanifest Huntington’s disease. Each row represents the number of GO terms involved within the module. GO = gene ontology.

Figure 5

Total number of GO biological process terms negatively associated with cortical cell loss in premanifest Huntington’s disease. Each row represents the number of GO terms involved within the module. GO = gene ontology.

Figure 6

Association between HTT expression and developmental genes. Average expression of the HTT in the Allen Human Brain Atlas (AHBA), left hemisphere only (n = 6). Expression normalized with the Abagen toolbox and depicted in the Desikan (cortical and subcortical) and Diedrichesen (cerebellar) atlases using BrainNet Viewer (A). The genes involved in early brain development obtained from Kang et al. and also present in the AHBA dataset were: CYP26A1, FBXW7, MCHR2, OSTN, PART1, RORB, SATB2, SSX2IP, TMS6SF1 and TSHZ3. The correlation between HTT expression from the AHBA and the first component of the expression of developmental genes is shown in B. In C, the distribution of the correlations between HTT expression and the first principal components component of the expression of random sets of 10 genes from the AHBA through bootstrapping (resampling 10 000 times) is represented. The red circle illustrates the association between HTT expression and correlation with the first principal components analysis component of developmental genes from Kang et al. The y-axis represents the number of permutations of random genes from the AHBA list. The x-axis represents the correlation coefficients.

Figure 7

EWCE analysis examining cell types enriched within the developmental and neurodegenerative profiles using the AHBA single-cell transcription dataset. Data are presented as standard deviations from the mean. *Statistically significant. AHBA = Allen Human Brain Atlas; EWCE = expression weighted cell type enrichment; OPC = oligodendrocyte precursor cells; VLMC = vascular leptomeningeal cell.