Investigating the role of TANK-binding kinase 1 in autophagy and amyotrophic lateral sclerosis

Amyotrophic lateral sclerosis (ALS) is a progressive fatal neurodegenerative disease leading to death 3 to 5 years from symptom onset. Protein inclusions containing Tar DNA binding protein of MW 43 (TDP-43) within dying motor neurons are the pathological hallmark of ALS. Mutations in TANK-binding kinase 1 (TBK1) have been identified in ALS as well as in the related conditions, frontotemporal dementia (FTD), but the underlying mechanisms remain largely unknown. Autophagy is responsible for the degradation of damaged organelles and insoluble protein inclusions in mammalian cells. TBK1 is a ubiquitously expressed kinase with a central role in the control of autophagic elimination of mitochondria and bacteria as well as in innate immune response. However, the wider functions of TBK1 in authophagy remain to be elucidated. Therefore, this thesis questioned how TBK1 is involved in other types of autophagy; basal or non-selective autophagy; and aggrephagy, the elimination of protein aggregates. Furthermore, it was also examined whether ALS/FTD mutant TBK1 leads to dysfunctional autophagy. The role of TBK1 in the aggregation of TDP-43 and clearance of ubiquitin was also studied. Here it was shown that the kinase activity of TBK1 is involved in degradation of autophagosomes during the three types of autophagy examined, suggesting a fundamental role for TBK1 in a wide variety of autophagy subtypes. Furthermore, TBK1's kinase activity was required for the formation of autophagosomes during basal autophagy. These results imply that TBK1 is involved in different stages of autophagy and its functions are restricted to specific types of autophagy. Inhibition of the kinase activity of TBK1 led to the impaired formation of autophagosomes, which was linked to impaired binding of microtubule-associated proteins 1A/1B light chain 3B (LC3) and autophagy receptors mediated by TBK1. This implies that TBK1 may act as a platform protein to bring LC3 and autophagy receptors together. In contrast, complete knock-out of TBK1 did not alter autophagosome formation or degradation, suggesting that dysfunctional TBK1 may be more harmful than the lack of protein expression. The knock-out of TBK1 enhance the degradation of ubiquitin, while overexpression resulted in elevated ubiquitin levels, indicating that TBK1 may be involved ubiquitin degradation. Unexpectedly, ALS/FTD mutant TBK1 did not cause autophagy dysfunction, however it induced the aggregation of TDP-43. In summary, it was shown here for the first time that TBK1 is central regulator of basal autophagy and starvation-induced autophagy. However, disease mechanisms linked to ALS/FTD mutant TBK1 do not involve dysfunctional autophagy, but instead, mutant TBK1 induces aggregation of TDP-43 -- abstract.