Valosin-containing protein (VCP) is a AAA+ protein that uses ATP hydrolysis to remove proteins from membranes and complexes. VCP variants cause multisystem proteinopathy (MSP), a disease characterized by multiple clinical phenotypes consisting of inclusion body myopathy, Paget’s disease of the bone, and frontotemporal dementia. In Chapter 2, we explore how VCP variants associated with MSP may lead to a paradoxical loss of VCP function that can cause defects in nuclear proteostasis. We provide evidence that the different clinical phenotypes of MSP are unified via the presence of ubiquitinated intranuclear inclusions and that cells expressing MSP variants of VCP show a reduction in nuclear VCP. We also generate a nuclear model of TDP-43 aggregation using an RNA-binding deficient TDP-43 construct that forms insoluble intranuclear inclusions with proteasomal inhibition. Clearance of these inclusions is decreased in MSP variant cell lines or with specific inhibition of VCP. Furthermore, we identify four novel activators of VCP that increase VCP’s ATPase activity primarily through the D2 ATPase domain by different mechanisms of action. Clearance of TDP-43 aggregates is enhanced in all cell lines when treated with the most potent activator.Ultrastructure of human brain tissue has traditionally been examined using electron microscopy (EM) following fixation, staining, and sectioning, which limit resolution and introduce artifacts. Alternatively, cryo-electron tomography (cryo-ET) allows for higher resolution imaging of unfixed cellular samples while preserving architecture, but it requires samples to be vitreous and thin enough for transmission EM. Due to these requirements, cryo-ET had not previously been employed to describe unfixed, never previously frozen human brain tissue. In Chapter 3, we present a method for generating thin lamellae in human brain tissue obtained at time of autopsy that can be imaged via cryo-ET. We vitrify the tissue via plunge-freezing and use xenon plasma focused ion beam milling to generate lamellae directly on-grid in Alzheimer’s disease brain tissue. Cryo-ET reveals intact subcellular structures including components of autophagy, pathologic tau fibrils, and myelination to provide a framework for nanoscale description of relatively unperturbed human brain tissue. These studies together provide a framework for studying and targeting potential mechanisms of neurodegenerative disease.