Transcriptomics Analyses of ALS Post-mortem Motor Cortex highlight alteration and potential biomarkers in the Neuropeptide Signalling pathway

BackgroundAmyotrophic lateral sclerosis (ALS) is a fatal heterogeneous neurodegenerative disease that typically leads to death from respiratory failure within two to five years. Despite the identification of several genetic risk factors, the biological processes involved in ALS pathogenesis remain poorly understood. The motor cortex is an ideal region to study dysregulated pathological processes in ALS as it is affected from the earliest stages of the disease. In this study, we investigated motor-cortex gene expression of cases and controls to gain new insight into the molecular footprint of ALS. MethodsWe performed a large case-control differential expression analysis of two independent post-mortem motor cortex bulk RNA-sequencing (RNAseq) datasets from the Kings College London BrainBank (N = 171) and TargetALS (N = 132). Differentially expressed genes from both datasets were subjected to gene and pathway enrichment analysis. Genes common to both datasets were also reviewed for their involvement with known mechanisms of ALS pathogenesis to identify potential candidate genes. Finally, we performed a correlation analysis of genes implicated in pathways enriched in both datasets with clinical outcomes such as the age of onset and survival. ResultsDifferential expression analysis identified 2,290 and 402 differentially expressed genes in KCL BrainBank and TargetALS cases, respectively. Enrichment analysis revealed significant synapse-related processes in the KCL BrainBank dataset, while the TargetALS dataset carried an immune system-related signature. There were 44 differentially expressed genes which were common to both datasets, which represented previously recognised mechanisms of ALS pathogenesis, such as lipid metabolism, mitochondrial energy homeostasis and neurovascular unit dysfunction. Differentially expressed genes in both datasets were significantly enriched for the neuropeptide signalling pathway. By looking at the relationship between the expression of neuropeptides and their receptors with clinical measures, we found that in both datasets NPBWR1, TAC3 and SSTR1 correlated with age of onset, and GNRH1, TACR1 with survival. We provide access to gene-level expression results to the broader research community through a publicly available web application (https://alsgeexplorer.er.kcl.ac.uk). ConclusionThis study identified motor-cortex specific pathways altered in ALS patients, potential molecular targets for therapeutic disease intervention and a set of neuropeptides and receptors for investigation as potential biomarkers.