Autophagy Induction as a Therapeutic Strategy for Neurodegenerative Diseases.

Autophagy is a major, conserved cellular pathway by which cells deliver cytoplasmic contents to lysosomes for degradation. Genetic studies have revealed extensive links between autophagy and neurodegenerative disease, and disruptions to autophagy may contribute to pathology in some cases. Autophagy degrades many of the toxic, aggregate-prone proteins responsible for such diseases, including mutant huntingtin (mHTT), alpha-synuclein (α-syn), tau, and others, raising the possibility that autophagy upregulation may help to reduce levels of toxic protein species, and thereby alleviate disease. This review examines autophagy induction as a potential therapy in several neurodegenerative diseases-Alzheimer's disease, Parkinson's disease, polyglutamine diseases, and amyotrophic lateral sclerosis (ALS). Evidence in cells and in vivo demonstrates promising results in many disease models, in which autophagy upregulation is able to reduce the levels of toxic proteins, ameliorate signs of disease, and delay disease progression. However, the effective therapeutic use of autophagy induction requires detailed knowledge of how the disease affects the autophagy-lysosome pathway, as activating autophagy when the pathway cannot go to completion (e.g., when lysosomal degradation is impaired) may instead exacerbate disease in some cases. Investigating the interactions between autophagy and disease pathogenesis is thus a critical area for further research

Scalable methods for the discovery of autophagy and disease genes

Macroautophagy (henceforth referred to as autophagy) is a major and conserved cellular process in which cells deliver cytoplasmic contents to lysosomes for degradation. As autophagy has been linked to various human diseases, the discovery and characterisation of autophagy genes is of interest for both basic science and medical research. This thesis develops scalable experimental and computational methods for the discovery of autophagy genes and elucidation of their relationships to human disease. To enable scalable genetic screens for autophagy, we develop two high-throughput autophagy assays: (1) an autophagic flux assay, SRAI-LC3B; and (2) an assay for levels of the ATG12-ATG5 conjugate, an important early autophagy marker. SRAI-LC3B can be used to assess autophagic flux via flow cytometry or microscopy and responds robustly to established pharmacological and genetic controls. Additionally, we exploit the optical properties of SRAI-LC3B to develop a novel high-throughput autophagy assay in a human neuronal model. By conducting a targeted screen with the ATG12-ATG5 assay, we identify two chaperone proteins as novel autophagy regulators. These chaperones act together to regulate autophagy at multiple stages, by mechanisms likely to involve stabilising the VPS34 complex and enabling DNM2-mediated autophagosome scission. Computational techniques such as network propagation and machine learning can help to condense large, complex data into testable predictions. We exploit these tools to develop a model that predicts new autophagy genes by analysing systematic datasets. Top predictions were screened using the SRAI-LC3B assay, resulting in eighteen new candidate autophagy genes. Predicted genes were enriched >5-fold in significant screen hits compared to a randomly selected control set. Subsequently, we develop a systematic procedure for process-to-phenotype prediction, which analyses interaction networks to predict diseases that may be associated with autophagy. A targeted screen of top predictions identifies twenty-eight diseases in which disruption to one or more associated genes caused significant changes in autophagy, raising the prospect that dysfunctional autophagy may play a role in some of these diseases.Mr Charles Allen (and family), Cambridge Australia Scholarships, the Cambridge Trust, the Cambridge Philosophical Society, and the UK Dementia Research Institute (funded by the MRC, Alzheimer’s Research UK, and the Alzheimer’s Society

Microglial-to-neuronal CCR5 signaling regulates autophagy in neurodegeneration.

In neurodegenerative diseases, microglia switch to an activated state, which results in excessive secretion of pro-inflammatory factors. Our work aims to investigate how this paracrine signaling affects neuronal function. Here, we show that activated microglia mediate non-cell-autonomous inhibition of neuronal autophagy, a degradative pathway critical for the removal of toxic, aggregate-prone proteins accumulating in neurodegenerative diseases. We found that the microglial-derived CCL-3/-4/-5 bind and activate neuronal CCR5, which in turn promotes mTORC1 activation and disrupts autophagy and aggregate-prone protein clearance. CCR5 and its cognate chemokines are upregulated in the brains of pre-manifesting mouse models for Huntington's disease (HD) and tauopathy, suggesting a pathological role of this microglia-neuronal axis in the early phases of these diseases. CCR5 upregulation is self-sustaining, as CCL5-CCR5 autophagy inhibition impairs CCR5 degradation itself. Finally, pharmacological or genetic inhibition of CCR5 rescues mTORC1 hyperactivation and autophagy dysfunction, which ameliorates HD and tau pathologies in mouse models.We are grateful to Alzheimer’s Research UK, the UK Dementia Research Institute (funded by the MRC, Alzheimer’s Research UK and the Alzheimer’s Society) (to DCR), The Tau Consortium, an anonymous donation to the Cambridge Centre for Parkinson-Plus, the Wellcome Trust ((095317/Z/11/Z) and NIHR Cambridge Biomedical Research Centre (BRC-1215-20014), European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 860035 (D.C.R., M.R.), and Cambridge Australia Scholarships (to AD) for funding

Compounds activating VCP D1 ATPase enhance both autophagic and proteasomal neurotoxic protein clearance.

Enhancing the removal of aggregate-prone toxic proteins is a rational therapeutic strategy for a number of neurodegenerative diseases, especially Huntington's disease and various spinocerebellar ataxias. Ideally, such approaches should preferentially clear the mutant/misfolded species, while having minimal impact on the stability of wild-type/normally-folded proteins. Furthermore, activation of both ubiquitin-proteasome and autophagy-lysosome routes may be advantageous, as this would allow effective clearance of both monomeric and oligomeric species, the latter which are inaccessible to the proteasome. Here we find that compounds that activate the D1 ATPase activity of VCP/p97 fulfill these requirements. Such effects are seen with small molecule VCP activators like SMER28, which activate autophagosome biogenesis by enhancing interactions of PI3K complex components to increase PI(3)P production, and also accelerate VCP-dependent proteasomal clearance of such substrates. Thus, this mode of VCP activation may be a very attractive target for many neurodegenerative diseases.We are grateful for funding from the UK Dementia Research Institute (funded by the MRC, Alzheimer’s Research UK and the Alzheimer’s Society) (to DCR), The Tau Consortium, Alzheimer’s Research UK, an anonymous donation to the Cambridge Centre for Parkinson-Plus, AstraZeneca, the Swedish Natural Research Council (VR) (to S.M.H; reference 2016–06605) and from the European Molecular Biology Organisation (EMBO long-term fellowships to SMH and LW; ALTF 1024-2016 and ALTF 135-2016, respectively)