Investigating the molecular etiologies of sporadic ALS (sALS) using RNA-Sequencing

ALS is an often lethal disease involving degeneration of motor neurons in the brain and spinal cord. Current treatments only extend life by several months, and novel therapies are needed. We combined RNA-Sequencing, systems biology analyses, and molecular biology assays to elucidate sporadic ALS group-specific differences in postmortem cervical spinal sections (7 sALS and 8 control samples) that may be relevant to disease pathology. \u3e55 million 2X150 RNA-sequencing reads per sample were generated and processed. In Chapter 2, we used bioinformatics tools to identify nuclear differentially expressed genes (DEGs) between our two groups. Further, we used Weighted Gene Co-Expression Network Analysis to identify gene co-expression networks associated with disease status. Qiagen’s Ingenuity Pathway Analysis revealed our sALS group-specific DEGs and a sALS group-specific gene co-expression network were associated with inflammatory processes and TNF-α signaling. Further, TNFAIP2 was identified as a sALS group-specific upregulated DEG and a network hub gene within that network. We hypothesized TNFAIP2’s upregulation in our ALS samples reflected increased TNF-α signaling and that TNFAIP2 promoted motor neuron death via TNF superfamily apoptotic pathways. Transient overexpression of TNFAIP2 decreased cell viability in both neural stem cells and induced pluripotent stem cell-derived motor neurons. Further, inhibition of activated caspase 9 (a protein necessary for TNF superfamily mitochondrial-mediated apoptosis) reversed this effect in neural stem cells. In Chapters 3 and 4, we used bioinformatics tools to identify sALS group-specifc mitochondrial DEGs and differentially used exons (DUEs). Qiagen’s Ingenuity Pathway Analysis revealed our sALS group-specific DUEs were associated with cholesterol biosynthesis