Autophagy and Neurodegeneration: Pathogenic Mechanisms and Therapeutic Opportunities

Autophagy is a conserved pathway that delivers cytoplasmic contents to the lysosome for degradation. Here we consider its roles in neuronal health and disease. We review evidence from mouse knockout studies demonstrating the normal functions of autophagy as a protective factor against neurodegeneration associated with intracytoplasmic aggregate-prone protein accumulation as well as other roles, including in neuronal stem cell differentiation. We then describe how autophagy may be affected in a range of neurodegenerative diseases. Finally, we describe how autophagy upregulation may be a therapeutic strategy in a wide range of neurodegenerative conditions and consider possible pathways and druggable targets that may be suitable for this objective. Autophagy is a conserved pathway that delivers cytoplasmic contents to the lysosome for degradation. Here we consider its roles in neuronal health and disease. We review evidence from mouse knockout studies demonstrating the normal functions of autophagy as a protective factor against neurodegeneration associated with intracytoplasmic aggregate-prone protein accumulation as well as other roles, including in neuronal stem cell differentiation. We then describe how autophagy may be affected in a range of neurodegenerative diseases. Finally, we describe how autophagy upregulation may be a therapeutic strategy in a wide range of neurodegenerative conditions and consider possible pathways and druggable targets that may be suitable for this objective. Macroautophagy (henceforth called autophagy) is a major intracytoplasmic protein degradation pathway whereby cytoplasmic contents are delivered, by double-membraned vesicles called autophagosomes, to the lysosome for degradation. It should be differentiated from other pathways that will not be considered in this review, like chaperone-mediated autophagy and microautophagy, where substrates are directly translocated into the lysosome without vesicular transport. The first morphologically characteristic structure in autophagy is the double-membraned, cup-shaped autophagosome precursor, called the phagophore, that engulfs substrates as its edges extend. After the phagophore edges close to form a vesicle, the completed autophagosomes traffic along microtubules to enable autophagosome-lysosome fusion, which leads to the degradation of the autophagic contents (Figure 1). Autophagy is regulated by a series of proteins defined as autophagy-related (ATG) proteins. Autophagy was initially characterized as a bulk and non-selective degradation pathway induced by nutrient deprivation. However, more recent studies made clear that autophagy also contributes to intracellular homeostasis in non-starved cells by degrading cargo material such as aggregate-prone proteins, including those causing many neurodegenerative conditions (aggrephagy), damaged mitochondria (mitophagy), excess peroxisomes (pexophagy), and invading pathogens (xenophagy) (Stolz et al., 2014Stolz A. Ernst A. Dikic I. Cargo recognition and trafficking in selective autophagy.Nat. Cell Biol. 2014; 16: 495-501Crossref PubMed Scopus (226) Google Scholar). In the classic example, aggregates of aberrantly folded proteins are tagged with ubiquitin chains that are recognized by ubiquitin-binding domain-containing receptors such as Sequestosome 1 (SQSTM1)/p62 (Bjørkøy et al., 2005Bjørkøy G. Lamark T. Brech A. Outzen H. Perander M. Overvatn A. Stenmark H. Johansen T. p62/SQSTM1 forms protein aggregates degraded by autophagy and has a protective effect on huntingtin-induced cell death.J. 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To date, receptors identified in this class come from the tripartite motif-containing (TRIM) family, a diverse group of proteins associated with the degradation of targets such as innate immunity signaling molecules (reviewed by Kimura et al., 2016Kimura T. Mandell M. Deretic V. Precision autophagy directed by receptor regulators - emerging examples within the TRIM family.J. Cell Sci. 2016; 129: 881-891Crossref PubMed Google Scholar). It seems likely that there are many other molecules that play such roles in autophagy, and identifying them will be key for our understanding of autophagy in non-starved cells. Autophagy activation in response to the primordial stimuli of nutrient deprivation and/or low cellular energy levels is mediated by signaling pathways that converge on ULK1/2 (mammalian homologs of the C. elegans uncoordinated-51 kinase) (Figure 2). ULK1/2 forms a complex with ATG13, ATG101, and focal adhesion kinase family-interacting protein of 200 kDa (FIP200). Nutrients and growth factor availability and levels of AMP/ATP (which reflect the energetic status of the cell) are sensed by mammalian target of rapamycin complex 1 (mTORC1) and AMP-dependent protein kinase (AMPK), respectively, which, in turn, oppositely regulate the ULK1/2 complex through a series of phosphorylation events. For instance, activation of AMPK by allosteric binding of AMP and phosphorylation of Thr172 promotes autophagy by directly activating ULK1 through phosphorylation of Ser317 and Ser77 under glucose deprivation (Kim et al., 2011Kim J. Kundu M. Viollet B. Guan K.L. AMPK and mTOR regulate autophagy through direct phosphorylation of Ulk1.Nat. Cell Biol. 2011; 13: 132-141Crossref PubMed Scopus (1619) Google Scholar) or Ser555 under amino acid starvation and mitophagy (Egan et al., 2011Egan D. Kim J. Shaw R.J. Guan K.L. 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Activation of the ULK complex is required for the recruitment of the class III PI3K VPS34 to the phagophore initiation sites where VPS34 generates phosphatidylinositol 3-phosphate (PI3P) while in a complex with VPS15, ATG14, and Beclin 1. The exact functions of PI3P in autophagy are still unclear. However, it appears to aid the recruitment of tryptophan-aspartic acid (WD) repeat domain phosphoinositide-interacting (WIPI) proteins to the phagophore membrane, which, in turn, controls the recruitment of crucial downstream autophagic proteins (e.g., ATG16L1 by WIPI2) that dictate where the phagophores form (Dooley et al., 2014Dooley H.C. Razi M. Polson H.E. Girardin S.E. Wilson M.I. Tooze S.A. WIPI2 links LC3 conjugation with PI3P, autophagosome formation, and pathogen clearance by recruiting Atg12-5-16L1.Mol. Cell. 2014; 55: 238-252Abstract Full Text Full Text PDF PubMed Scopus (105) Google Scholar). The ATG12 and ATG8/LC3 ubiquitin-like conjugation systems are then required for sustaining the expansion of the phagophore. In the first system, ATG12 is conjugated to ATG5 in a reaction that involves ATG7 and ATG10 (E1-like and E2-like enzymes, respectively), and the resulting complex binds non-covalently to ATG16L1. ATG12-ATG5-ATG16L1 associates with pre-autophagosomal membranes, enabling their elongation by assisting in the recruitment of LC3. However, before this can happen, LC3 has to be processed by the cysteine protease ATG4, which cleaves the C terminus of LC3, exposing a glycine residue (LC3-I form). This cleavage is crucial for LC3-I conjugation to phosphatidylethanolamine (PE) by a mechanism dependent on ATG7, ATG3, and ATG12-ATG5-ATG16L1 (E1-like, E2-like, and E3-like enzymes, respectively), leading to the formation of LC3-II, which is tightly associated with autophagosomal membranes. This cascade of reactions then sustains extension of the phagophore edges and its closure to form mature autophagosomes (Bento et al., 2016bBento C.F. Renna M. Ghislat G. Puri C. Ashkenazi A. Vicinanza M. Menzies F.M. Rubinsztein D.C. Mammalian Autophagy: How Does It Work?.Annu. Rev. Biochem. 2016; 85: 685-713Crossref PubMed Scopus (32) Google Scholar). Extension of the phagophore is also assisted by mATG9, the only identified multi-pass transmembrane protein among the core ATG proteins. This protein appears to localize to the trans-Golgi network and the endocytic compartment, including early endosomes, late endosomes, and recycling endosomes, and is postulated to aid in the supply of lipid bilayers to the nascent phagophore, enabling its further elongation prior to closure of the fully formed autophagosome (Bento et al., 2016bBento C.F. Renna M. Ghislat G. Puri C. Ashkenazi A. Vicinanza M. Menzies F.M. Rubinsztein D.C. Mammalian Autophagy: How Does It Work?.Annu. Rev. 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The source of autophagosome membranes is an area of active investigation. The endoplasmic reticulum (ER), Golgi and trans-Golgi network, mitochondria, plasma membrane, and endosomal compartments have all been suggested as possible sources of phagophore membranes (Bento et al., 2016bBento C.F. Renna M. Ghislat G. Puri C. Ashkenazi A. Vicinanza M. Menzies F.M. Rubinsztein D.C. Mammalian Autophagy: How Does It Work?.Annu. Rev. Biochem. 2016; 85: 685-713Crossref PubMed Scopus (32) Google Scholar). The ER emerged as one of the possible sources of membranes for pre-autophagosomes, not only because isolation membranes were observed cradled within a subdomain of the ER and interconnected with it (Axe et al., 2008Axe E.L. Walker S.A. Manifava M. Chandra P. Roderick H.L. Habermann A. Griffiths G. Ktistakis N.T. Autophagosome formation from membrane compartments enriched in phosphatidylinositol 3-phosphate and dynamically connected to the endoplasmic reticulum.J. 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Among these genes, many are directly related to the lysosome and autophagy (e.g., lysosomal hydrolases, vacuolar-type H+-ATPase (v-ATPase) subunits, and ATG proteins), and, thus, TFEB appears to co-ordinately regulate the expression of many of the key genes required for autophagy/lysosome function (Sardiello et al., 2009Sardiello M. Palmieri M. di Ronza A. Medina D.L. Valenza M. Gennarino V.A. Di Malta C. Donaudy F. Embrione V. Polishchuk R.S. et al.A gene network regulating lysosomal biogenesis and function.Science. 2009; 325: 473-477Crossref PubMed Scopus (579) Google Scholar, Settembre et al., 2011Settembre C. Di Malta C. Polito V.A. Garcia Arencibia M. Vetrini F. Erdin S. Erdin S.U. Huynh T. Medina D. Colella P. et al.TFEB links autophagy to lysosomal biogenesis.Science. 2011; 332: 1429-1433Crossref PubMed Scopus (663) Google Scholar). Zinc-finger protein with KRAB and SCAN domains 3 (ZKSCAN3) is a transcriptional repressor of autophagy that appears to oppose TFEB. 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