Dysfunctional Ubiquitination: A Critical Signaling Process in Neurodegenerative Diseases and a Protac Target
Introduction
Neurodegenerative diseases are characterized by the progressive deterioration of the nervous system, a phenomenon marked by the selective loss of vulnerable neuronal populations. Aging is the most prominent risk factor for numerous neurodegenerative disorders, including Alzheimer's and Parkinson's diseases (AD and PD, respectively)1. A hallmark feature of neurodegeneration is the accumulation of misfolded proteins within the brain. These protein aggregates can arise from disease-associated gene mutations or disruptions in protein homeostasis2. Cells employ two major protein degradation pathways, the ubiquitin-proteasome system (UPS)3 and the autophagy-lysosome pathway (ALP)4 to eliminate unnecessary or misfolded proteins and maintain cellular integrity. Both pathways involve ubiquitination, a process that utilizes ubiquitin (Ub) to tag proteins for degradation. Beyond its role in protein degradation, ubiquitin signaling plays a critical role in maintaining cellular homeostasis, a process essential for neuronal function and survival. With advancing age, there is a decline in the efficiency of both UPS and ALP, leading to the accumulation of potentially neurotoxic protein aggregates such as Amyloid β (Aβ), tau, α-synuclein, SOD1, and TDP-43, where Ub is frequently observed5. This Newsletter will discuss current knowledge about ubiquitination in neurodegenerative diseases, including underlying mechanisms and potential therapeutic targets.
Dysfunctional Ubiquitination in AD and PD
The intricate balance of UPS is crucial for maintaining cellular homeostasis, especially in long-lived neuronal cells. Impaired proteasomal degradation emerges as a hallmark in neurodegenerative diseases such as AD and PD, as observed in the brains of patients and mouse models6,7. In AD, this reduction in proteasome activity leads to the aggregation of proteins such as neurotoxic Aβ42 and tau, ultimately leading to neuronal cell death8. Aβ42 is derived from the amyloid precursor, a glycoprotein with pivotal roles in neuronal homeostasis, including signaling, development, and transport. The other mis-regulated protein, tau, is a substrate for UPS and, under normal conditions, maintains microtubule assembly and stabilization, which are fundamental for normal neuronal structure and function9. The abnormal accumulation of tau leads to increased levels of ubiquitinated tau, which, in turn, directly inhibits proteasome function10.
PD is characterized by the degeneration of dopaminergic neurons and the accumulation of protein aggregates, known as Lewy Bodies, which primarily contain α-synuclein and Ub. While most cases of PD are sporadic, mutations in genes related to UPS contribute to familial cases of the disease11. Furthermore, studies have shown that prolonged dysfunction of the proteasome in PD leads to downregulation of autophagy components. This finding suggests a link between defective mitophagy, responsible for clearing damaged mitochondria, and the buildup of mitochondrial proteins, potentially driving neurodegeneration12.
Figure Legend: A1 - Hippocampal neurons stain for 10 min with 20 nM MemGlow-590 (Cat. # MG03). A2,3,4 – Astrocytes show multiple filopodia. Reproduced from Collot et al. 2019. https://doi.org/10.1016/j.chembiol.2019.01.009
Ubiquitin-Related Proteins Affect Neuronal Cell Death and Neuroinflammation
Apoptosis is regarded as the primary pathway leading to neuronal death in various neurodegenerative diseases13. E3 ubiquitin ligases like XIAP and Parkin modulate apoptotic pathways, influencing neuronal survival by targeting key proteins like caspases and BCL-2 family members14. Ubiquitination regulates death receptor signaling, diverting it from cell death to pro-survival pathways15. Moreover, ubiquitin signaling is implicated in necroptosis, where it influences the activation of key proteins like RIPK1, RIPK3, and MLKL16. Pyroptosis, another inflammatory mode of cell death, also involves ubiquitin signaling, although its precise role remains uncertain17. Emerging evidence suggests that ubiquitin signaling may regulate ferroptosis, a process involving iron-dependent lipid peroxidation implicated in neurodegenerative diseases18.
Recent research highlights the pivotal role of glial cells, particularly microglia and astrocytes, in neurodegenerative diseases, challenging the traditional neuron-centric perspective19. These cells, fundamental to brain homeostasis and neuronal support, undergo significant functional changes in neurodegenerative states, transitioning to a phenotype characterized by impaired debris clearance and a shift towards a pro-inflammatory, neurotoxic profile20,21. This transformation is crucial in the progression of neurodegeneration and responds to pathological stimuli, including mitochondrial DNA fragments and misfolded proteins that accumulate in the spaces between neural cells22,23. In particular, NLRP3 and caspase-1, modulated by ubiquitin ligases, are key players in neuroinflammation and microglial function impairment during AD24. The activation of the NLRP3 inflammasome by Aβ promotes the production of interleukin-1 beta (IL-1β) through the action of caspase-1. This process is linked to neurotoxicity by altering the microglial phagocytosis response and promoting Aβ deposition. As a result, both NLRP3 and caspase-1 have emerged as promising therapeutic targets24,25. On the other hand, the immunoproteasome, an alternative form of the proteasome upregulated in response to inflammatory signals, plays a crucial role in degrading ubiquitinated proteins. The immunoproteasome participates in the regulation of the cerebral inflammatory milieu during neurodegeneration and may aid in clearing misfolded proteins; thus, it could represent another avenue for therapeutic targeting26. Modulating the activity of the immunoproteasome could help alleviate the burden of damaged proteins and mitigate the inflammatory responses characteristic of AD and PD26.
Potential Therapeutic Targets in Ubiquitin Signaling
Targeting ubiquitin signaling holds significant promise as a therapeutic approach for neurodegenerative diseases, especially since few viable treatments currently exist. While clinical trials for ubiquitin-targeting drugs are mainly focused on cancer27, preclinical studies demonstrate their potential in treating neurodegenerative conditions. Deubiquitinase USP14 has emerged as a key target due to its role in the regulation of protein degradation17. Inhibiting USP14 enhances proteasomal degradation, offering a strategy to clear toxic protein aggregates associated with diseases like AD and PD. Similarly, UCHL1 modulation shows neuroprotective potential, although its utility remains uncertain due to conflicting findings and its involvement in PD28.
Moreover, exploiting targeted degradation technologies, such as proteolysis targeting chimeras (PROTACs) and autophagy-targeting chimeras (AUTACs), offers a novel avenue for protein clearance29. PROTACs recruit E3 ligases to induce ubiquitination and subsequent degradation of target proteins, including tau and α-synuclein aggregates, presenting a promising approach for combating neurodegeneration. Efforts are underway to create degraders, with dozens of investigational drugs in active clinical trials, such as TH006, QC-01-175, and C004019, which induce the degradation of tau30,31. Moreover, Lu et al. introduced a Keap1-dependent peptide PROTAC that effectively promoted the poly-ubiquitination and proteasome-dependent degradation of tau. This PROTAC demonstrated potential in the treatment of neurodegenerative diseases and represents and advancement towards previously "undruggable" proteins32. AUTACs, which induce autophagic degradation of proteins and organelles, represent another innovative strategy, although their efficacy in compromised neurodegenerative environments warrants further investigation.
Summary and future perspectives
Neurodegenerative diseases involve progressive nervous system deterioration, affecting millions globally. Protein misfolding and impaired degradation pathways contribute to the accumulation of toxic aggregates, exacerbating neuronal loss. Given the chronic nature of neurodegenerative diseases and the irreversible neuronal loss they entail, interventions targeting ubiquitin signaling offer hope for slowing or halting disease progression. Inhibiting USP14 and modulating UCHL1 show promise, alongside innovative degradation technologies like PROTACs and AUTACs. Long-term safety and efficacy assessments, along with global collaboration, will be crucial for realizing the full potential of ubiquitin-targeting therapies in combating neurodegeneration.
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