One hallmark of neurodegenerative diseases is the abnormal accumulation of certain neuroproteins. Because autophagy is critical for the degradation of protein aggregates and maintaining cellular homeostasis, it is not surprising to see that autophagy has a close connection with neurodegeneration: autophagy is responsible for the clearance of accumulated proteins, and this role is particularly important in non-dividing cells. In this section, we will discuss the role of autophagy in Parkinson, Alzheimer, and Huntington diseases.
3.1. Parkinson Disease
PD is characterized by the progressive loss of dopaminergic neurons of the substantia nigra, which is accompanied by the accumulation of SNCA/α-synuclein in the form of Lewy bodies and Lewy neurites 
. From genome-wide association studies (GWAS), great advances have been made in recent decades with the identification of monogenetic causes of PD, including mutations in SNCA
, and PINK1 
SNCA is a substrate of CMA 
, and, consistent with this fact, boosting CMA decreases SNCA levels and protects cells from wild-type SNCA-induced neurotoxicity 
. The SNCA accumulation and neurotoxicity in PD patients may result from two factors related to CMA. First, PD-associated mutant SNCA, A53T and A30P, are degraded by CMA less efficiently because they bind to the lysosome but cannot be translocated into the lysosomal lumen, which, at the same time, inhibits the degradation of other CMA cargos and increases cell toxicity 
. Second, the expression level of essential CMA proteins, such as LAMP2A and HSPA8, decreases significantly in PD patient brains 
. In addition, the PD-associated UCHL1I93M
mutation facilitates interaction with LAMP2A, thus inhibiting CMA 
Besides CMA, SNCA is degraded through macroautophagy in neuronal cells 
and particularly, via selective-autophagy mediated by SQSTM1 as the receptor in microglia 
. At the same time, SNCA regulates autophagy. Overexpression of SNCA inhibits autophagy via RAB1, which further leads to the mislocalization of ATG9 
. Overexpression of PD-associated mutant SNCAE46K
impairs autophagosome formation through the inactivation of the MAPK8/JNK1-BCL2 pathway 
. One recent study, expressing human SNCA in Drosophila, found that SNCA impairs macroautophagy through stabilizing the actin cytoskeleton, which inhibits the fusion between lysosomes and autophagosomes 
. Even though SNCA is a target of autophagy, SNCA aggregates are not easily degraded by autophagy and inhibit this process by impairing autophagosome clearance 
. Autophagy is not only responsible for the degradation of SNCA, but also affects its cell-to-cell transmission 
. Several studies indicate that the blockage of autophagy induces SNCA secretion through exosomes 
, which reduces cell death, but creates a microenvironment with an inflammatory and neurotoxic response 
. Additionally, the secreted SNCA will be taken up by other neurons and act as a seed for aggregation in the recipient cells 
LRRK2 mutations are one of the most common causes of PD. In most cases of LRRK2-associated PD, the protein has the G2019S mutation and the cells display the SNCA aggregates as Lewy bodies and undergo cell death 
. Similar to SNCA, LRRK2 is another substrate of CMA, but the LRRK2G2019S
mutant is again difficult to degrade and inhibits CMA, which underlies the toxicity in PD by compromising the CMA-mediated degradation of SNCA 
. Besides, LRRK2R1441G
, which leads to age-dependent SNCA accumulation, also inhibits CMA 
. LRRK2 regulates macroautophagy as well, but the role remains undetermined. Many studies, involving LRRK2 kinase inhibitor and LRRK2G2019S
, which has higher kinase activity, demonstrate that LRRK2 inhibits autophagy 
. In contrast, some studies indicate that LRRK2 may promote autophagy through the activation of the MAP2K/MEK-MAPK/JNK-MAPK/ERK pathway 
and it is reported that age-dependent dopaminergic neurodegeneration and autophagy impairment occur in lrrk1 lrrk2
double-knockout mice 
. Further studies should integrate these relevant findings and draw a more complete model of how LRRK2 affects autophagy, which will be of great significance in designing autophagy-targeting PD therapy.
Mitochondria dysfunction has long been recognized as the initiating factor in dopaminergic neuronal loss 
. Of note, mutations in PINK1 and PRKN, two critical proteins in mitophagy, are highly associated with PD 
. Interestingly, PD-associated PINK1 mutations are clustered in the kinase domain 
and several mutations such as G309D, L347P and W437X have a compromised interaction with PRKN, thus inhibiting mitophagy execution 
. In addition to the mutations in these two proteins, studies focused on other PD-associated proteins also shed light on the importance of mitophagy in PD. Pathogenic SNCA impairs mitochondrial function via binding to OMM proteins such as TOMM20, which impairs protein import to mitochondria 
, or decreasing the mitochondrial SIRT3 level 
. As mentioned above, mitophagy is responsible for impaired mitochondria degradation and a study expressing SNCA in yeast shows that Sir2-mediated mitophagy is induced and the selective degradation of mitochondria is responsible for the SNCA toxicity 
. However, in neurons or in in vivo models, how SNCA-mediated mitochondrial damage is related to or affects mitophagy is unknown. Compared with SNCA, there are more studies about LRRK2 and mitophagy. It is found that the PD-associated LRRK2G2019S
mutation inhibits mitophagy by affecting mitochondria motility 
, inhibiting mitochondrial fission 
, and phosphorylating RAB10 to inhibit its mitochondrial accumulation and interaction with OPTN 
Here, we focus on SNCA, LRRK2, PINK1 and PRKN, summarizing how they interact with autophagy. Other proteins with PD-associated mutations, such as VPS35, VPS13C and FBXO7, have been suggested to play a role in autophagy (Table 1).
Table 1. PD-associated genes from GWAS and their connection with autophagy (except SNCA, LRKK2, PINK1 and PRKN).
||Loss of GBA function impairs autophagy via PPP2/PP2A inactivation.
PD-associated mutation L444P heterozygote impairs autophagy, mitochondria priming and autophagy-lysosome degradation.
||Deletion of VPS13C is correlated with impaired mitochondrial morphology and upregulate PINK1-PRKN-dependent mitophagy, but the study does not show the connection between PD-associated mutations with mitophagy.
||VPS35D620N causes autosomal-dominant Parkinson disease.
VPS35D620N has a reduced affinity for WASH and impairs ATG9A trafficking and localization, thus compromising autophagosome formation.
|VPS35D620N impairs endosome-to-Golgi retrieval of LAMP2A and accelerates LAMP2A degradation, thus inhibiting SNCA degradation through CMA.
|VPS35D620N hampers PINK1 and PRKN recruitment to mitochondria thus impairing mitophagy.
||PARK7 knockdown impairs autophagy and the SNCA uptake and degradation in microglia.
|PARK7 deficiency downregulates HSPA8 expression level and accelerates the degradation of LAMP2A, inhibiting SNCA degradation through CMA.
|Park7 may function in mitophagy because it is important for proper mitochondria function and Park7 upregulation can rescue the phenotype in pink1 mutant Drosophila.
||SREBF1 knockdown inhibits PRKN translocation to mitochondria, thus inhibiting mitophagy.
||FBXO7T22M inhibits its interaction with PRKN and impairs PRKN translocation to mitochondria.
|FBXO7R378G mutation impairs ubiquitination of MFN1.
|FBXO7R498X truncation inhibits PRKN recruitment to mitochondria.
|T22M, R378G and R498X mutations aggravate aggregation of FBXO7 in mitochondria, which may inhibit mitophagy.
||TMEM175 deficiency leads to the impaired autophagosome degradation in the lysosome.
|TMEM175M393T shows similar autophagosome clearance phenotype as a knockout.
GWAS provides us with invaluable information to study the connection between PD and autophagy and identify therapeutic targets. However, with 90 variants nominated as PD-related factors 
, how to study them, particularly how they are related to autophagy, needs further consideration. First, some PD-associated genes are only studied by knockout instead of using the PD-associated mutated form (such as VPS13C 
). Even though studies of mutant proteins may lead to the concern that the point mutation may not be sufficient to result in either an autophagy or pathological phenotype, further studies focusing on the mutation may shed light on a more detailed mechanism of PD and autophagy. Second, some PD-associated genes discovered through GWAS studies may affect autophagy, but few studies delve into them with regard to mechanism. For instance, several genes, such as CHCHD2 
and ATP13A2 
, are critical for mitochondrial quality, but whether they have any connection with mitophagy remains unclear. Third, controversial data exist, which may have resulted from the use of different cells lines, and the phenotype at the cellular level is sometimes different from that at the behavioral level 
. Therefore, based on the goal of specific studies, the model used to study these genes and what marker(s)/phenotype(s) should be used as an indication of PD need consideration as well.
3.2. Alzheimer Disease
Alzheimer disease (AD) is a progressive neurodegenerative disease characterized by cognitive impairment and loss of memory. AD patients usually show the accumulation of misfolded proteins such as amyloid-β (Aβ) and hyperphosphorylated MAPT (microtubule associated protein tau) 
Several lines of evidence indicate deficient autophagy in AD patients, which include the decreased level of autophagy-related genes, including BECN1 
and LC3B 
, and the accumulation of autophagosomes 
. More importantly, the accumulation of autophagosomes correlates with AD pathology 
, which further indicates the importance of understanding the connections between autophagy and AD. Besides these direct lines of evidence, AD-associated mutation in PSEN1 disrupt autophagy 
. A decreasing level of PICALM, which occurs in AD, inhibits autophagy and exacerbates AD pathology 
. However, some studies report an increase in autophagy when cells are treated with Aβ 
. This discrepancy could at least in part be a consequence of the AD stage. In 2016, Bordi et al. carried out a comprehensive analysis at different stages of AD, finding an upregulation of autophagy-related genes at the early stage, but an impeded autophagy flux at the late stage 
. The mechanism of this change is not clear, possibly because autophagy is induced at the early stage to degrade the protein aggregates. However, at the later stage, autophagy or lysosome clearance ability becomes inhibited by the accumulation of abnormal proteins.
The relationship between Aβ and autophagy is complicated. First, Aβ is degraded through autophagy, and several studies show a decreased Aβ level in cells and improved cognitive ability in an AD mouse model when autophagy is induced 
. Second, Aβ may also be generated inside autophagosomes because both APP (amyloid beta precursor protein) and PSEN1, an enzyme involved in the cleavage of APP to form Aβ, are found within the autophagosome 
. Third, one study reported that the secretion of Aβ to the extracellular space, where plaque forms, depends on autophagy in neurons 
. On the contrary, a recent study indicates that MTORC1 inhibition reduces amyloid secretion due to the upregulation of autophagy 
. Interestingly, the activation of AMPK does not induce autophagy in neurons, and different AMPK activators results in differential regulation of Aβ secretion, either increasing or reducing, which indicates a complex role of AMPK in Aβ secretion independent from autophagy 
APP has a KFERQ motif, which is typically associated with CMA. However, the deletion of this motif in APP does not abolish its interaction with HSPA8, but conversely, increases the interaction 
. The authors raise the possibility that the KFERQ motif may be used to bind to AP2, which is an autophagy adaptor, because the AP2 recognition sequence is part of KFERQ; deletion of the KFERQ motif impairs AP2-dependent targeting to the lysosome. Further studies should investigate the binding partner of the KFERQ motif other than HSPA8; this may lead to the identification of new functions of this motif other than acting as the CMA signal and shed more light on AD pathology.
The other hallmark protein in AD, MAPT, is a substrate of macroautophagy, CMA and microautophagy, but some AD-associated MAPT mutations cannot be cleared efficiently by autophagy 
. Consistently, activation of autophagy through inhibiting MTORC1 helps with prolonged clearance of MAPT 
. CMA is downregulated in AD patient brains 
; CMA upregulation improves the disease phenotype that results from MAPT or combined MAPT and Aβ pathologies, and inhibition of CMA accelerates the AD pathology in a mouse model 
Together with Aβ and MAPT, compromised mitochondria accumulation is another hallmark of AD. Although it is unclear whether the mitochondrial dysfunction is a cause or a consequence of Aβ and phosphorylated MAPT accumulation 
, it indicates that quality control of mitochondria is impaired in AD neurons. Deficient mitophagy has been discovered in AD patient brain and patient stem-cell derived neurons 
. The compromised mitophagy in AD may resulted from the following. First, in AD patient brains, PINK1-PRKN-dependent mitophagy is enhanced with Aβ accumulation, but it is followed by a progressively depleted PRKN 
, suggesting that mitophagy is induced at the early stage of AD, but finally shows an inadequate capacity compared with the huge number of damaged mitochondria. Additionally, higher levels of Δ1 PINK1, the main cleaved product of PINK1, is found in AD patient brain, which inhibits PRKN translocation to mitochondria and impairs mitophagy 
. Second, emerging data are showing that Aβ and phosphorylated MAPT interfere in the mitophagy pathway and MAPT impairs PRKN translocation to mitochondria 
. Overall, these studies demonstrate that compromised mitophagy and abnormal mitochondrial dynamics contribute to AD pathogenesis.