Under starvation or stress, TFEB translocates to the nucleus and binds the CRE element to promote expression of macroautophagy and lysosomal genes [88].
Protein clearance in animal models has been successfully demonstrated using several small molecules and drugs that enhance induction of macroautophagy reduces AD-relevant pathology, including rapamycin in 3xTGAD mice [32] and temsirolimus in P301S transgenic mice [156] and trehalose in APP/PS1 and P301S MAPT transgenic mice [157,158].
For instance, while accumulation of Aβ activates the mTOR signaling pathway and subsequently blocks macroautophagy, rapamycin reduces the Aβ load by enhancing macroautophagy [32]
This inhibition of Aβ secretion during macroautophagy deficiency results in aberrant cytosolic accumulation of Aβ, which ultimately evokes neurodegeneration accompanied with memory loss.
Although exact relations remain unknown, it was reported that Aβ can induce a cascade that results in phosphorylation and subsequent deposition of TDP-43 in the cytosol [70]
Overexpression of PICALM in APP/PS1 mice substantially elevates Aβ levels, whereas knockdown reduces the Aβ plaque load, respectively [98]
Identified as a candidate susceptibility gene for AD by GWAS [116], reduced level of SORL1 has been consistently correlated with brain Aβ levels [118,119].
Furthermore, presenilin-1, the most common mutation associated with early-onset familial AD (FAD), plays an essential role in calcium homeostasis and maintaining acidic lysosomal pH, with FAD-associated mutations disrupting calcium-dependent vATPase function in lysosomes [7,18–20]
Methylene blue, a contrast agent that can reduce tau misfolding, has also been shown to induce macroautophagy, as indicated by elevated Beclin 1 and LC3-II levels and reduced tau and p62 levels in organotypic neuronal cultures and a mouse model of FTD [159]
Sphingolipids are also strongly implicated in AD pathology, with upregulated levels of ceramide, a key component in sphingolipid metabolism, detected in the early phase of AD [80].
Cellular cholesterol can directly impact the level of Aβ, as decreases in cholesterol levels inhibit the generation of Aβ peptides through direct modulation of γ-secretase activity [78,79].
Paclitaxel reversed Aβ-induced microtubule disruption and restored autophagosomal transport in neurons [161], while a similar compound, epothilone D/BMS-241027, reduced tauopathy and improved cognition in P301S transgenic mice [162] although the compound did not progress beyond Phase I clinical testing
In addition to their structural role in membranes, lipids are essential in the maintenance of cellular energy homeostasis as well as regulation of intracellular signaling pathways
Decreased triglyceride breakdown upon macroautophagy inhibition and impairment in macroautophagy by lipid supplementation demonstrates reciprocally interrelated regulation of autophagy and lipids [72]
Lipid biology can also impact proteinopathy, with strong evidence that Aβ metabolism is modulated by lipids
In addition to the direct modulation of protein generation, lipids can also influence the levels of proteins through autophagic clearance; for instance, increasing lipid contents has been shown to impair autophagy [72].
For instance, rapamycin, an inhibitor of the Ser/Thr protein kinase mammalian target of rapamycin (mTOR), improves cognitive function and reduces Aβ in AD mouse model by enhancing autophagic flux [23].
Modulation of mTOR can influence the levels of tau, with upregulation increasing tau phosphorylation and accumulation by reducing autophagic clearance [87], and conversely, pharmacological treatment with rapamycin reducing tau levels and rescuing motor deficits in the Tau P301S mice [53]
The finding of reduced Aβ generation when conversion of sphingomyelin to ceramide is blocked further substantiates the crucial involvement of sphingolipids in Aβ metabolism through modulation of γ-secretase [81,82]
For example, levels of Beclin 1, a key component of the class III type phosphoinositide 3-kinase/VPS34 complex essential to the pre-autophagosomal structure (PAS), has been suggested to be reduced in AD brains [16,17], with Rohn et al. demonstrating the cleavage of Beclin 1 by caspase-3 in the AD brain and colocalization of the cleaved product with NFTs [16].
Other studies have also demonstrated the accumulation of autolysosomes in the AD brain and experimentally when lysosomal proteolysis is compromised via genetic knockdown of specific cathepsins or use of pharmacological inhibition of lysosomes [2,3,15]
Mitochondria are instrumental in the regulation of energy metabolism, and impairment in mitochondrial function has been implicated in the pathogenesis of AD, leading to the mitochondrial cascade hypothesis of AD [121].
Tau aggregates can be targeted by two protein clearance pathways, the UPS and the A-LS, with the latter pathway encompassing microautophagy,CMA and macroautophagy.
Furthermore, the membrane bilayer lipid can influence protein aggregation and subsequent tau pathology, with recent studies showing that tau binds to the membrane, which has subsequent effects on the formation of fibrillary tau aggregates [85,86].
While AD is generally considered a disorder with two proteinopathies, other protein aggregates are also seen in AD, like α-synuclein
First identified as a nonamyloid component of Aβ plaques in the AD brain, α-synuclein aggregates are detected in the majority of the brains of patients with AD [56,57].
Misfolded α-synuclein proteins form insoluble oligomers, which in turn lead to the cascade of pathogenic neurotoxicity-induced responses such as neuroinflammation and cell death [55]
The presence of aberrant protein aggregates is common to neurodegenerative diseases
Defective chaperone-mediated autophagy (CMA), a type of autophagy that targets proteins with a specific KFERQ-like motif recognizable to its chaperones, plays a significant role in aggregate formation of disease-related proteins [28].
Evidence suggests that CMA can degrade tau via the chaperone heat shock cognate of 70 kDa (Hsc70), which recognizes KFERQ-like motifs and transfers its substrates via LAMP-2 into the lysosome [47]
Cuervo et al. have revealed a distinct interaction of wild-type and mutant α-synuclein proteins with CMA [64]
While wild-type α-synuclein protein efficiently clears via CMA, the pathogenic A53T and A30P variants remain bound to LAMP-2, blocking lysosomal degradation by preventing binding of other substrate complexes to the receptor [64].
Such evidence of lysosomal proteolytic failure in AD brain further strengthens the concept that impaired macroautophagy in AD is a critical event
Even early autophagic activation may become impaired due to progressively diminishing lysosomal clearance of substrates.
With neurons profoundly relying on macroautophagy for clearance of toxic protein aggregates, impairment in the proteolytic systems ultimately results in progressive neuronal death, a common feature in several neurodegenerative diseases [27].
Impairment in the UPS is cardinal to the development of neurodegeneration, in part because of its reciprocal interplay with protein aggregation
For instance, phosphorylated insoluble tau proteins dampen 26S proteasome activity, while activation of the UPS attenuates tauopathy [27]
These experimental differences may be attributed to the intricate interplay between the UPS and autophagy, as α-synuclein is degraded by both proteolytic systems [62,63].
Robust AV accumulation in dystrophic neurites from biopsy tissues from patients with AD implicate a compromised state of autophagic flux
Although the UPS is accountable for the degradation of up to 80–90% of proteins, misfolded proteins and aggregates are too large to be processed through the proteasome barrel and can impede UPS function by physical occlusion, leaving autophagic-lysosomal breakdown as the only effective pathway to clear these proteins [25,26]
Abnormal phosphorylation and truncation of tau are hallmarks of AD pathology and are targets of proteasome and autophagy pathways [27,44,45].
TFEB has been shown to effectively clear phosphorylated tau proteins through A-LS, resulting in ameliorated neuronal loss and neuroinflammation, as well as improved cognitive performance [89].
Decreased autophagy in the diseased brain may contribute to aberrant lipid accumulation that occurs along with an increased incidence of the metabolic syndrome in aged humans [76]
While autophagic-lysosomal degradation is more commonly associated with protein degradation, it serves to degrade all cellular material including carbohydrates and lipids.
A recent study has demonstrated that activation of AMPKα1 enhances tau phosphorylation, while inhibition reduces tau phosphorylation at Ser-262, an epitope that is increased in early stages of AD, which promotes the autophagic degradation of tau [87]
These results may be attributed to coincidental evidence of the involvement of Beclin 1 in VPS34-mediated trafficking pathways including macroautophagy and endocytosis [37], both of which are pronouncedly affected in AD pathology [38]
Since Nixon and colleagues first reported the pathological evidence of defective macroautophagy in EM images in the AD brain, similar observations have been made in cellular and animal models of AD [2,3,7,14]
Defects in macroautophagy in AD are supported by additional lines of evidence
Maintenance of neuronal macroautophagy can counteract AD pathology [22,23].
Lastly, macroautophagy, but not UPS or CMA can clear protein aggregates.
Increased Aβ generation and accumulation in lysosomes suggest that Aβ metabolism, at least partially, is regulated by macroautophagy [3,14,32–34].
In line with this, reduced Beclin 1 levels, as seen in AD models [16], increase the levels of intracellular and extracellular Aβ peptides, supporting the role of macroautophagy in the generation and degradation of Aβ [33,35].
Compromised macroautophagy, via the genetic suppression of Atg7, leads to the blockade of Aβ secretion and contributes to the subsequent diminution in extracellular Aβ plaque load
Wang et al., using an N2a neuroblastoma cell line that expresses the repeat domain of tau with an FTD-17 mutation (TauRDΔK280), has demonstrated that tau aggregates can be degraded by macroautophagy [48]
Finally, numerous studies using iPSC models have implicated changes in macroautophagy pathways in Parkinson’s disease [137–144], Gaucher disease [145], Niemann-Pick Type C1 disease [146–148] and diseases affecting motor neurons, including ALS [149,150], spinal and bulbar muscular atrophy (SBMA) [151], Brown- Vialetto disease [152], Charcot-Marie-Tooth 2A [153] and hereditary spastic paraplegia [154]
However, recent work provides direct evidence that PICALM can also modulate macroautophagy, via its role in SNARE endocytosis to clear tau aggregates [102].
Aβ peptides originate from the transmembrane protein amyloid precursor protein (APP) which undergoes sequential cleavage via two distinct pathways by the enzyme complexes β- and γ-secretase [31]
Since the initial finding of proteasome-dependent degradation of α-synuclein [58], significant efforts have been made to clarify the modes of α-synuclein metabolism
Cytosolic tau is highest in density in membrane-rich axons and growth cones where lipid interaction with cytosolic tau may contribute to fibrillary tau aggregation [84].
Tau serves an important function by enabling microtubules to connect with cytoskeletal components and facilitates anterograde and retrograde axonal transport of vesicles and organelles [39].
Dysregulation of tau proteins can produce a spectrum of neurodegenerative diseases or tauopathies characterized by dementia and tau deposition, including AD, frontotemporal dementia (FTD), Niemann- Pick disease, corticobasal degeneration (CBD), tangle-only dementia (TOD) and progressive supranuclear palsy (PSP).
NBR1 colocalizes with tau and has primary sequence domains for binding [52].
In a more recent GWAS investigation, TREM2 (triggering receptor expressed on myeloid cells 2) was identified as one of the markers strongly associated with increased levels of tau and phosphorylated tau in cerebrospinal fluid from AD patients [91].
While misfolding of Aβ peptide and hyperphosphorylation of tau are recognized as pathogenic mechanisms of AD, accumulation of α-synuclein, which is recognized more as a risk factor for Parkinson’s disease (PD), also plays a pathological role in AD [29].
Recent clinical and immunohistochemistry studies demonstrate the contribution of α-synuclein in the development of AD pathology
One intriguing molecule that interacts with VPS35 is SORL1, a VPS10P-domain receptor protein that has been linked to autosomal dominant early-onset AD [116,117].
VPS35, one of the retromer-related genes identified from GWAS datasets on AD [110], regulates TREM2’s function in microglia [111].
Another modulator of A-LS implicated in AD pathology is transcription factor EB (TFEB), a master regulator of lysosome biogenesis
Activation of PTEN, another inducer of macroautophagy, by TFEB is indispensable for this TFEB-mediated increase in macroautophagy [89]
However, in another study, iPSC-derived tau A152T and MAPT IVS 10+16 (a tau splice mutant) cortical neurons had increased cell death in response to rapamycin treatment, although basal cell death was ∼10 times higher in these tau mutants relative to controls, making interpretation of the work difficult [134].
For example, in tau A152T iPSC-derived cortical neurons, total and phosphorylated Tau levels are elevated, particularly the insoluble forms [133], which is associated with decreases in UPS function as measured by total polyubiquitinated proteins and an upregulation of macroautophagy markers.
For instance, adenosine monophosphate- activated protein kinase (AMPK) phosphorylates ULK1 and inactivates mTOR through the raptor and tuberous sclerosis complex (TSC2).
For instance, ApoE4–an important determinant of cholesterol metabolism and the strongest genetic risk factor for sporadic AD – regulates Aβ degradation [77].
Tau phosphorylation, the major disease-related post-translational modification, is highly regulated by glycogen synthase kinase-3β (GSK-3β), cyclin-dependent kinase 5 (CDK5), mitogen-activated protein kinase (MAPK) and other kinases.
For example, Beclin 1 suppression results in impaired microglial phagocytosis of Aβ and reduced recycling of TREM2 [108].
BIN1 is involved in the endocytosis and the endosomal sorting of membrane proteins
Similar to PICALM, BIN1, due to its role in endocytosis and trafficking, is implicated in APP metabolism [103].
Suppression of BIN1 disrupts cellular trafficking of BACE1 and reduces BACE1 lysosomal degradation, leading to increased Aβ production [103].
Higher expression of BIN1 has been reported in AD brains, and suppression of BIN1 reduces tau toxicity, suggesting BIN1 involvement in tau pathology, as well [104].
However, when tau becomes hyperphosphorylated, it detaches from microtubules and aggregates, resulting in depolymerization of microtubules and formation of insoluble tau deposits [40]
A recent line of work revealed Aβ-promoting function of PICALM by demonstrating that PICALM depletion decreased Aβ generation through disrupting clathrin-mediated endocytosis and internalization of γ-secretase [99,100].
PICALM may also promote amyloid clearance from the brain by internalizing Aβ into endothelial cells and ultimately into to the bloodstream [101]
Multiple large-scale GWAS demonstrate that variants of PICALM (phosphatidylinositol-L-binding clathrin assembly protein involved in endocytosis) are significantly associated with AD [90,93,94].
PSEN1 M146L and A246E mutant cortical neurons have been shown to possess decreased activation of the CLEAR (coordinated lysosomal expression and regulation) gene network, as measured by a TFEB-driven luciferase assay, consistent with a reduction in autophagic activity [131].
In a similar vein, PSEN1 A246E mutant cortical neurons have reduced mitophagy compared to control neurons, which is associated more with decreased lysosomal function rather than mitochondrial targeting [132].
Evidence that p62 facilitates tau degradation has been demonstrated in several studies where p62 colocalized with tau in NFTs from AD patients [53].
For example, Babu et al. has shown that p62−/− knockout mice have increased levels of hyperphosphorylated tau, reduction of synaptophysin and changes in short term memory compared to p62+/− [54]
Another common proteinopathy occurs from the misfolding of TARDNA binding protein 43 kDa (TDP-43), which is primarily seen in amyotrophic lateral sclerosis (ALS) and FTD [67]
TFEB at normal state is phosphorylated by mTOR complex 1, which inhibits its activity
Recent work by Ulland et al. has also discovered an additional function of TREM2 in the maintenance of microglial macroautophagy and metabolism
TREM2 deficiency in an AD mouse model results in suppressed metabolic function in microglia through the dampening of the mTOR signaling pathway, which subsequently elicits a compensatory autophagic response to address the metabolic defect [109].
Variants of TREM2 have been found to increase the risk of developing AD by approximately three times [105,106], further validating it as a risk factor for AD.
VPS35 mutations have been shown to disrupt macroautophagy [113] and mitochondrial function [114] and are associated with AD and PD [102,115].
Accumulation of misfolded proteins and damaged organelles is highly detrimental for neuronal homeostasis and survival.
Altogether, as with proteinopathy, accumulation of damaged or dysfunctional mitochondria is detrimental to the development of AD pathologies
Dysfunctional mitochondria are critically harmful to cells, as this leads to decreased synthesis of cellular ATP and accumulation of ROS, which further overburden and damage other functional mitochondria.
Previous studies demonstrate impaired mitochondrial function preceding the accumulation of hallmark proteins in AD, such as Aβ [123,124] and tau [125].
Thus, as a quality control mechanism, mitophagy − a form of selective macroautophagy that specifically targets mitochondria − occurs in response to damaged or dysfunctional mitochondria in order to prevent mitochondrial bioenergetic deficits.
Recently, a comprehensive investigation utilizing gene expression analysis of the hippocampal region (CA1) of patients with Alzheimer’s disease identified that autophagosome formation and lysosomal biogenesis genes were upregulated at early stages of AD [21]
A recent study reported that mitophagy is robustly induced in AD brains and in vitro models of mutant APP, accompanied with abnormal accumulation of depoloarized mitochondria [126]
Formation of amyloid β (Aβ) plaques is one of the most notable hallmarks in AD pathology [30]
Cytosolic lipids are stored as triglycerides in lipid droplets and are hydrolyzed into fatty acid for energy under nutrient starvation
BEL Commons is developed and maintained in an academic capacity by Charles Tapley Hoyt and Daniel Domingo-Fernández at the Fraunhofer SCAI Department of Bioinformatics with support from the IMI project, AETIONOMY. It is built on top of PyBEL, an open source project. Please feel free to contact us here to give us feedback or report any issues. Also, see our Publishing Notes and Data Protection information.
If you find BEL Commons useful in your work, please consider citing: Hoyt, C. T., Domingo-Fernández, D., & Hofmann-Apitius, M. (2018). BEL Commons: an environment for exploration and analysis of networks encoded in Biological Expression Language. Database, 2018(3), 1–11.