Amyotrophic lateral sclerosis (ALS) is a neurodegenerative motor disorder, which results in death within a few years of diagnosis. While the cause of most cases of ALS is unknown, 10% of cases are familial (fALS), and associated with mutations in one of over 25 genes (Renton et al., 2014). Several lines of evidence suggest alterations of neuroinflammatory factors in both ALS patients and animal models (Henkel et al., 2006; Kuhle et al., 2009; Mishra et al., 2016). Among these altered factors are the nuclear factor kappa-light-chain enhancer of activated B cells (NF-kappaB) proteins, which becomes progressively activated in cells such as astrocytes and microglia (Crosio et al., 2011; Frakes et al., 2014). This thesis describes the generation of novel genome engineered fALS animal models and utilization of these models to interrogate the connection between the NF-kappaB pathway and ALS pathogenesis. We generate gene replacement 'humanized' fALS Drosophila melanogaster models by introducing either human TAR DNA-binding protein 43 (hTDP-43) or human Fused in Sarcoma (hFUS), with or without ALS-associated mutations, into the Drosophila genome, removing and replacing the respective Drosophila homologous coding regions while maintaining host regulatory sequences. We find that gene replacement with hFUS wild-type or TDP-43 wild-type sequences can fully rescue development deficits of orthologous Drosophila gene knockouts, and allows longevity, motor behavior, and synapse morphology similar to controls. Surprisingly, we also observe no or very modest motor phenotypes in models where hFUS and hTDP-43 sequences including ALS mutations. We speculate that these ALS-associated mutations create a predisposition to disease that requires additional environmental factors to develop ALS pathology. To identify these factors, we utilized loss-of-function alleles of Drosophila TDP-43 or FUS to examine potential interactions between FUS, TDP-43 and NF-kappaB signaling. We observe a significant rescue of adult survival of TDP-43-/- and FUS-/- mutant Drosophila by reducing the gene dosage of NF-kappaB components. Building on the hypothesis that excessive activation of the NF-kappaB pathway in ALS-associated mutants could induce disease pathology, we investigated if bacterial infection, which activates the NF-kappaB pathway, could trigger disease in our models. However, we observed that hTDP-43 and hFUS ALS mutant longevity and motor behavior were not more susceptible to infection than controls. We conclude that peripheral bacterial infection is not sufficient to induce ALS-like symptoms in our humanized models. To interrogate the potential of NF-kappaB as a therapeutic target in rodent ALS models, we expressed NF-kappaB inhibitors using viral vectors in the SOD1G93A ALS mouse model. Unfortunately, we observed no improvements in motor behavior or electromyographical measurements by this treatment. However, we did observe increased CNS resident macrophages in ALS mouse models compared to controls, which we speculate may be necessary to target. In sum, our results identify a potent interaction between FUS, TDP-43 and NF-kappaB signaling, that support the potential of this pathway as an ALS therapeutic target, but also caution that the relationship is complex and involves the intersection of several CNS cell types.