Abstract
The majority of the clinico-pathological variability observed in patients harboring a repeat expansion in the C9orf72-SMCR8 complex subunit (C9orf72) remains unexplained. This expansion, which represents the most common genetic cause of frontotemporal lobar degeneration (FTLD) and motor neuron disease (MND), results in a loss of C9orf72 expression and the generation of RNA foci and dipeptide repeat (DPR) proteins. The C9orf72 protein itself plays a role in vesicular transport, serving as a guanine nucleotide exchange factor that regulates GTPases. To further elucidate the mechanisms underlying C9orf72-related diseases and to identify potential disease modifiers, we performed an extensive RNA sequencing study. We included individuals for whom frontal cortex tissue was available: FTLD and FTLD/MND patients with (n = 34) or without (n = 44) an expanded C9orf72 repeat as well as control subjects (n = 24). In total, 6706 genes were differentially expressed between these groups (false discovery rate [FDR] < 0.05). The top gene was C9orf72 (FDR = 1.41E-14), which was roughly two-fold lower in C9orf72 expansion carriers than in (disease) controls. Co-expression analysis revealed groups of correlated genes (modules) that were enriched for processes such as protein folding, RNA splicing, synaptic signaling, metabolism, and Golgi vesicle transport. Within our cohort of C9orf72 expansion carriers, machine learning uncovered interesting candidates associated with clinico-pathological features, including age at onset (vascular endothelial growth factor A [VEGFA]), C9orf72 expansion size (cyclin dependent kinase like 1 [CDKL1]), DPR protein levels (eukaryotic elongation factor 2 kinase [EEF2K]), and survival after onset (small G protein signaling modulator 3 [SGSM3]). Given the fact that we detected a module involved in vesicular transport in addition to a GTPase activator (SGSM3) as a potential modifier, our findings seem to suggest that the presence of a C9orf72 repeat expansion might hamper vesicular transport and that genes affecting this process may modify the phenotype of C9orf72-linked diseases.
Highlights
Substantial clinical and pathological variability has been reported in patients carrying an expanded repeat in the C9orf72-SMCR8 complex subunit (C9orf72) [58], which leads to frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS) [14, 50]
Top differentially expressed gene is C9orf72 We performed RNA sequencing on carriers of a C9orf72 repeat expansion (n = 34), frontotemporal lobar degeneration (FTLD) and FTLD/motor neuron disease (MND) patients without this expansion (n = 44), and control subjects without any neurological disease (n = 24; Table 1)
We have discovered promising candidate modifiers that were consistently associated with relevant disease features and that may serve as urgently needed biomarkers and/or point to new treatment strategies
Summary
Substantial clinical and pathological variability has been reported in patients carrying an expanded repeat in the C9orf72-SMCR8 complex subunit (C9orf72) [58], which leads to frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS) [14, 50]. While FTD is the second most frequent cause of dementia in the presenile group, ALS is the most common form of motor neuron disease (MND). TAR DNA-binding protein 43 (TDP-43) inclusions can be observed in approximately 50% of FTD patients and more than 90% of ALS patients [43, 44]. Given this overlap, FTD and ALS are thought to represent a disease spectrum
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