Mitochondrial function-associated genes underlie cortical atrophy in prodromal synucleinopathies

Abstract

Isolated rapid eye movement sleep behaviour disorder (iRBD) is a sleep disorder characterized by the loss of rapid eye movement sleep muscle atonia and the appearance of abnormal movements and vocalizations during rapid eye movement sleep. It is a strong marker of incipient synucleinopathy such as dementia with Lewy bodies and Parkinson's disease. Patients with iRBD already show brain changes that are reminiscent of manifest synucleinopathies including brain atrophy. However, the mechanisms underlying the development of this atrophy remain poorly understood. In this study, we performed cutting-edge imaging transcriptomics and comprehensive spatial mapping analyses in a multicentric cohort of 171 polysomnography-confirmed iRBD patients [67.7 ± 6.6 (49-87) years; 83% men] and 238 healthy controls [66.6 ± 7.9 (41-88) years; 77% men] with T1-weighted MRI to investigate the gene expression and connectivity patterns associated with changes in cortical thickness and surface area in iRBD. Partial least squares regression was performed to identify the gene expression patterns underlying cortical changes in iRBD. Gene set enrichment analysis and virtual histology were then done to assess the biological processes, cellular components, human disease gene terms, and cell types enriched in these gene expression patterns. We then used structural and functional neighbourhood analyses to assess whether the atrophy patterns in iRBD were constrained by the brain's structural and functional connectome. Moreover, we used comprehensive spatial mapping analyses to assess the specific neurotransmitter systems, functional networks, cytoarchitectonic classes, and cognitive brain systems associated with cortical changes in iRBD. All comparisons were tested against null models that preserved spatial autocorrelation between brain regions and compared to Alzheimer's disease to assess the specificity of findings to synucleinopathies. We found that genes involved in mitochondrial function and macroautophagy were the strongest contributors to the cortical thinning occurring in iRBD. Moreover, we demonstrated that cortical thinning was constrained by the brain's structural and functional connectome and that it mapped onto specific networks involved in motor and planning functions. In contrast with cortical thickness, changes in cortical surface area were related to distinct genes, namely genes involved in the inflammatory response, and to different spatial mapping patterns. The gene expression and connectivity patterns associated with iRBD were all distinct from those observed in Alzheimer's disease. In summary, this study demonstrates that the development of brain atrophy in synucleinopathies is constrained by specific genes and networks.

Keywords: MRI; Parkinson’s disease; REM sleep behaviour disorder; dementia with Lewy bodies; network analysis; transcriptomics.

Figure 1

Patterns of gene expression underlying cortical thinning in iRBD. (A) Vertex-wise patterns showing the significant changes in cortical thickness in iRBD patients compared to controls. (B) Violin plots showing the percentage of variance in cortical thickness W-scores explained by gene expression; the dot represents the empirical variance, and the asterisk indicates the components that were significant against random and spatial null models. (C) Scatterplot of the association between thickness W-scores and the regional weights of the first component. (D) Brain renderings of the thickness W-scores and the regional weights of the first component. (E) Density plots of each gene’s bootstrapped weight on the first component; gene set enrichment analysis was performed on all genes, whereas over-representation analysis was performed on genes with bootstrap ratios ± 5.0. C = component; RM = random null models; SM = spatial null models.

Figure 2

Enrichment analyses of the genes associated with cortical thinning in iRBD. (A) The top 10 biological process terms from the Gene Ontology Consortium knowledge base that are enriched in the positively and negatively weighted gene sets predicting cortical thinning in iRBD. Terms are ranked based on the normalized enrichment score; darker coloured bars present significantly enriched terms after FDR correction. (B) Volcano plot of the over-representation analysis showing the biological process terms enriched in the genes most strongly associated with cortical thinning in iRBD (bootstrap ratio < −5.0). The colour bar represents the number of overlapping edges for each gene category and the size of the dot represents the size of the gene category. (C) Additional gene enrichment analyses performed on different subsets of post-mortem brains (different gene expression matrices) showed that the enriched patterns in association with cortical thinning in iRBD were stable and different from Alzheimer’s disease. The upper grid represents the different post-mortem brains selected for each analysis, with post-mortem brain #15496 being a female donor. The lower grid represents the top 10 biological process terms obtained in each analysis, with numbers representing the respective ranking of the term based on the normalized enrichment score. GO = Gene Ontology.

Figure 3

The connectome constrains cortical thinning in iRBD. Brain renderings showing the associations between the deviation in cortical thickness W-scores in iRBD and (A) structural and (B) functional connectivity. The edge thickness on the brain plots represents the interregional connection strength, whereas the node size and colour represent the local deviation in the W-score in iRBD compared to controls (i.e. the larger and redder, the greater the change in thickness). The scatterplots show the associations, for connected regions and non-connected regions, between the deviations in W-scores and the average W-scores observed in structural or functional neighbours. The violin plots show the empirical correlation against sets of 10 000 correlations generated from spatial and random null models. The asterisk indicates associations that were significant against null models.

Figure 4

Cortical thinning in iRBD map onto specific regional tracer density, resting-state networks, and cytoarchitectonic classes. (A) Brain renderings and scatterplots showing the tracer density maps of the receptors, transporters, and binding sites associated with cortical thickness W-scores in iRBD. The violin plots show the empirical correlations tested against distributions of correlations from sets of spatial and random null models. The asterisk indicates the significant associations after Bonferroni correction. Radar charts showing the correlation between cortical thickness W-scores in iRBD and (B) resting-state networks and (C) cytoarchitectonic classes. The regular line represents the empirical correlations, and the dashed line represents the average correlation observed in sets of 10 000 spatial null models. The asterisk indicates the networks and classes where the observed spatial correlation was significantly different from the null correlation.