Motor neuron disease (MND) is a horrific neurodegenerative disease leading to progressive paralysis and death within 2-5 years of symptom onset. Pathological confirmation of MND is only possible post-mortem. The hallmark disease pathology is TDP-43 protein aggregates present in motor neurons in one or more affected regions of the brain. The presence/absence and severity (burden) of TDP-43 pathology varies amongst brain regions as well as among MND patients.
In this study, we aimed to explore molecular alterations occurring across the MND patient brain. We obtained post-mortem brain tissue for a cohort of MND cases with TDP-43 pathology (n=22) and neurologically normal controls (n=11). For each individual, RNA was extracted using our optimised methods [1] and mRNA-seq was performed on 5 brain regions varying in their presentation of TDP-43 pathology (n=165 samples): motor cortex (pathology always present), prefrontal cortex and hippocampus (pathology sometimes present), and occipital cortex and cerebellum (no pathology). Using multiple bioinformatic tools, we performed differential gene expression, cell-type deconvolution, differential transcript usage and alternative splicing analyses in cases and controls.
Significant gene expression differences were detected between MND cases and controls across all five brain regions, suggesting wider impacts of the disease in the brain. Strikingly, despite not presenting with TDP-43 pathology, cerebellum demonstrated the greatest number of differentially expressed genes, an increased number of de novo splicing events, and altered cell-type composition. We identified a district cerebellar gene expression profile for MND patients with the greatest global burden of TDP-43 pathology.
Widespread transcriptome alterations are present in MND brain, yet our finding of increased transcriptome changes in cerebellum is counter-intuitive considering this brain region is typically spared from pathology (i.e. considered “unaffected”) in MND patients. We propose that cerebellar gene expression changes may provide insight into protective or compensatory mechanisms in MND neurodegeneration.