The endo-lysosomal pathway and ALS/FTD

Abstract

Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are considered part of a disease spectrum associated with causative mutations and risk variants in a wide range of genes. Mounting evidence indicates that several of these genes are linked to the endo-lysosomal system, highlighting the importance of this pathway in ALS/FTD. While many studies have focused on how the disruption of this pathway impacts autophagy, recent findings reveal that this may not the whole picture: specifically disrupting autophagy may not be sufficient to induce disease, while disrupting the endo-lysosomal system could represent a crucial pathogenic driver. In this review, we discuss the connections between ALS/FTD and the endo-lysosomal system, including a breakdown of how disease-associated genes are implicated in this pathway. We also explore the potential downstream consequences of disrupting endo-lysosomal activity in the brain, outside of an effect on autophagy.

The endo-lysosomal system is disrupted in neurodegenerative disease

Amyotrophic sclerosis (ALS) and frontotemporal dementia (FTD) are part of a single disease spectrum (ALS/FTD): specific genetic lesions can induce either or both conditions in patients, and both disorders are associated with the formation of protein inclusions containing TAR DNA-binding protein 43 (TDP-43) [1, 2]. Despite decades of research, the mechanisms underlying pathogenesis in ALS/FTD remain elusive – but studies have highlighted cellular pathways that are repeatedly disrupted in patient samples and disease models. One such pathway is the endo-lysosomal system: a dynamic interconnected series of vesicles and organelles that facilitate the internalization, modulation, and eventual degradation of various cargo molecules. In the simplest sense, the endo-lysosomal pathway involves the internalization of cargo from the cellular plasma membrane to early endosomes; these organelles can then be converted to recycling endosomes to bring material back to the plasma membrane or undergo endosome maturation to become late endosomes and eventually fuse with lysosomes (Figure 1). Trafficking through the endo-lysosomal pathway is regulated by the Rab family of GTPases (Box 1) and a shifting population of phosphoinositides (Box 2). The surface of early endosomes is populated by Rab5, early endosome antigen 1 (EEA1), and the phosphoinositide PI3P. A switch to Rab4 or Rab11 will direct the vesicle to the recycling endosome pathways, while maturation to a late endosome involves a switch from Rab5 to Rab7 and a conversion from PI3P to PI(3,5)P₂ [3–5]. Throughout the maturation process, the endosome takes in vesicles containing cargo from the trans-Golgi network (TGN), including newly synthesized acid hydrolases that are targeted to late endosomes via their interaction with mannose-6-phosphate receptors (MPRs) [6]. Intraluminal vesicles (ILVs) accumulate inside the endosome through an invagination process regulated by endosomal sorting complex required for transport (ESCRT) protein complexes, resulting in the formation of multivesicular bodies (MVBs, see Glossary) [5]. MPRs and other factors are later recycled back to the TGN through a process mediated by the retromer complex or by Rab9 [6]. The late endosome then fuses with a lysosome, forming an endolysosome, to degrade remaining cargo before condensing down to become a lysosome itself [5]. Finally, the pathway can intersect with autophagy, as autophagosomes can fuse with endosomes to form amphisomes, or with lysosomes to form autophagolysosomes, both of which eventually become degradative autolysosomes [7].

Figure 1: A brief overview of the endo-lysosomal pathway.

After endocytosis, cargo is shuttled into the early endosome, which is marked by Rab5 and EEA1. From here, vesicles can be recycled back to the plasma membrane or can undergo maturation to become a late endosome, as marked by Rab7 and PI(3,5)P₂. During this maturation process, the endosome accumulates intraluminal vesicles (ILVs) through a process regulated by ESCRT complexes. It also takes in vesicles from the trans-Golgi network which can contain MPR-linked lysosomal enzymes and hydrolases. The resultant structure is called a multivesicular body (MVB). After depositing their cargo, MPRs are shuttled backed to the trans-Golgi network through a retrograde transport pathway mediated by the retromer. Late endosomes can fuse with lysosomes to become endolysosomes and degrade cargo. Both MVBs and endolysosomes can also fuse with autophagosomes en route to the autophagic degradation of cargo. Finally, endolysosomes can condense down to become lysosomes. LAMPs, like LAMP1 and LAMP2, are transmembrane glycoproteins that populate both late endosomes and lysosomes.

Box 1: Rab GTPases as effectors of the endo-lysosomal pathway.

Trafficking through the endo-lysosomal pathway is regulated by a network of Rab GTPases (for a recent review, see [3]). GTPases function by catalyzing the hydrolysis of guanine triphosphate (GTP) to guanine diphosphate (GDP), releasing inorganic phosphate in the process. This chemical reaction allows GTPases to act as molecular switches: they are active when bound to GTP and become inactive once the reaction is complete and they remain bound to GDP. These proteins are regulated by interactors that help speed up or slow down this reaction. Guanine exchange factors (GEFs) help release the bound GDP, allowing the GTPases to reactivate by binding a new GTP. GTPase-activating proteins (GAPs) speed up the hydrolysis reaction, pushing the GTPase into an inactive state sooner. Thus, by stimulating the GTPase activity of the enzymes, these factors act as negative regulators of GTPase function. A third class of regulators is also associated with Rab and Rho GTPases: guanine dissociation inhibitors (GDIs). GDIs interact with the GDP-bound form of the GTPase and prevent the dissociation of the nucleotide, preventing the protein from re-activating. Rab GTPases only interact with vesicles when in their active state, so GDIs also prevent the enzymes from localizing to endosomal membranes [3].

Rab GTPases localize to specific compartments along the endocytic pathway: for instance, Rab5 localizes to early endosomes while Rab7 localizes to late endosomes and Rab4 and Rab11 populate fast and slow recycling endosomes, respectively [3]. As vesicles travel through the endo-lysosomal pathway, each Rab GTPase helps mediate a switch to the next Rab, forming what is known as a Rab cascade. Rab GTPases also regulate the functions of the endosome at each stage by recruiting specific effector molecules – including tethering, fusion, and motor proteins [3]. A disruption in the activity of any Rab GTPases, or their specific regulators, can therefore inhibit the function of their native endosomes and disrupt the next chain in the Rab cascade, stalling the pathway and contributing to the development of aberrant or enlarged endosomes.

Box 2: Shifting populations of phosphoinositides build the endo-lysosomal landscape.

In addition to the Rab GTPases, trafficking through the endo-lysosomal pathway is also regulated by a network of kinases and phosphatases that maintain local pools of specific phosphoinositide species. There are seven main forms of phosphoinositides, all generated from the modification of the ubiquitous membrane phospholipid phosphatidylinositol [4]. In concert with Rab GTPases, these molecules undergo a conversion process as a vesicle moves along the endo-lysosomal pathway. Thus, the compartmental identity of a vesicle is coded by its specific population of membrane phosphoinositides, Rab GTPases, and other proteins – and converting between different species of membrane markers provides a level of spatiotemporal control. For example, PI3P marks the membranes of early endosomes, while PI(3,5)P₂ marks late endosome membranes. The FYVE-type zinc finger containing phosphoinositide kinase PIKfyve converts PI3P to PI(3,5)P₂ as endosomes mature – mirroring the Rab5 to Rab7 conversion. Other phosphoinositides populate other compartments: PI4P marks vesicles in the trans-Golgi secretory pathway, while PI(4,5)P₂ enriches the plasma membrane and both PI(3,5)P₂ and PI5P have been detected on lysosomes [4]. Individual phosphoinositides are also recognized by specific protein interactors, allowing them to act as signaling molecules. They help recruit other proteins essential for compartmental identity and function, as well as mediate membrane contact sites between different vesicles and organelles [4].

Analyses of ALS/FTD patient samples suggest disruption at multiple stages of the endo-lysosomal pathway. For example, sporadic ALS patients show a reduction in the expression of retromer components [8], suggesting altered retrograde trafficking, as well as a reduction in Rab11 [9], suggesting disrupted endosomal recycling. Aberrant and enlarged endosomes and lysosomes are observed in models of ALS/FTD [10–14], as well as in familial FTD samples [14–16] and sporadic ALS tissue [12]. Recently, aberrant filaments composed of lysosomal transmembrane protein 106B (TMEM106B) were detected in multiple neurodegenerative diseases, including ALS/FTD [17–20]. This finding, together with the fact that TMEM106B genetic variants are associated with increased risk for frontotemporal lobar degeneration with TDP-43 inclusions (FTLD-TDP) [21], points toward a role for impaired lysosomal function in ALS/FTD. In this review, we will discuss lines of evidence pointing towards a causative role for impaired endo-lysosomal activity in disease pathogenesis, including an in-depth discussion of the various connections between ALS/FTD-associated genes and the different steps of the endo-lysosomal pathway. Disruption of any stage in this pathway could impact autophagy and aggrephagy, but protein clearance is not the only function of this dynamic cellular system. We aim to explore the diverse downstream consequences of endo-lysosomal disruption in the brain and its implications in ALS/FTD pathogenesis.

Disruption of the endo-lysosomal pathway could be causative in ALS/FTD

Disruption of the endo-lysosomal system is detrimental to neurons in vivo. A prime example comes from a classic model of ALS: the wobbler mouse. Wobbler mice were identified in 1956 as a spontaneous mouse mutant that develops behavioral defects and muscle atrophy associated with motor neuron degeneration. This phenotype prompted researchers to use the model as a proxy for ALS, but it was not until 2005 that the causative mutation was identified: a partial loss of function mutation in vacuolar protein sorting factor 54 (Vps54) [22]. Vps54 is a component of the Golgi-associated retrograde protein (GARP) complex, a tethering complex that receives vesicles that are recycling cargo (including MPRs) from late endosomes back to the TGN [23]. The wobbler mutation destabilizes the complex and reduces its expression [24], impairing retrograde transport [25]. As a result, wobbler mice show enlarged Rab7-positive late endosomes that resemble the enlarged vesicles seen in sporadic ALS tissue [12].

A major pathogenic step in ALS/FTD is the mislocalization and aggregation of TDP-43. How TDP-43 inclusions form is an important unanswered question in the field, but, excitingly, recent studies have suggested that the disruption of the endo-lysosomal pathway could be a key event upstream of TDP-43 proteinopathy. TDP-43 levels can be regulated by the endo-lysosomal pathway [26–28], and a recent pre-print study found that the protein accumulates into enlarged MVBs when overexpressed in cells [28]. Our group has shown that disrupting endosome maturation, either by inhibiting PIKfyve (Box 2) or overexpressing a constitutively active Rab5, can induce endogenous (and ectopic) TDP-43 aggregation in cells [13]. We also observed enhanced TDP-43 inclusion formation in mice that co-harbored two separate ALS/FTD-associated defects: the chromosome 9 open reading frame 72 (C9orf72)-associated protein poly(GA) and a mutation in tank-binding kinase 1 (TBK1) [13]. TDP-43 inclusions occurred in neurons with aberrantly enlarged early endosomes in this model, suggesting a mechanistic link between these phenomena [13]. Separately, it has been shown that disrupting lysosome acidification and fusion can also induce TDP-43 proteinopathy in human motor neurons [29]. The endo-lysosomal system is also intrinsically connected to autophagy, and it has been speculated that a decline in protein clearance with age contributes to the formation of protein aggregates in neurodegenerative disease [30]. ALS/FTD is associated with mutations in autophagy-related genes, further implicating autophagy in pathogenesis [30].

Despite evidence suggesting a connection between the endo-lysosomal and autophagy systems and TDP-43 proteinopathy, few studies have directly examined the effects of disrupting elements of this pathway on TDP-43 homeostasis. Furthermore, although inhibiting autophagy exacerbates TDP-43 accumulation in cells with existing aggregates [31, 32], specifically disrupting early selective autophagy was not sufficient to initiate TDP-43 aggregation in human neurons, according to a pre-print study [29]. This finding suggests that the disruption of the endo-lysosomal system may not induce aggregation simply by preventing autophagic protein clearance. Rather, another function of the endo-lysosomal system is likely at play. ALS/FTD-associated genes and their respective roles in the endo-lysosomal system may provide important clues to candidate pathomechanisms. In the following sections, we will summarize how some of the main ALS/FTD-associated genes have been linked to the endo-lysosomal pathway (Figure 2), focusing on their autophagy-independent functions.

Figure 2: Several ALS/FTD-related genes and risk factors have been implicated in the endo-lysosomal pathway.

VCP and alsin are implicated in endocytosis and the conversion of recycling endosomes into early endosomes, respectively. Alsin is also a regulator of Rab5 at the early endosome, where C9ORF72 and VCP also localize. TBK1 regulates Rab7 and endosome maturation, a process that is also dependent upon phosphoinositide conversions governed by FIG4 in complex with PIKfyve. Several factors are associated with late endosomes and MVBs, including proteins involved in the sorting of cargo into ILVs, like VCP and the ESCRT factor CHMP2B, and proteins linked to retromer function and retrograde transport, like C9ORF72, TBK1, and VAPB. At lysosomes, UBQLN2 regulates vacuolar ATPase (V-ATPase) levels, PGRN regulates lysosomal function and hydrolase activity, and C9ORF72 regulates mTOR and TFEB signaling. TMEM106B, an FTD risk factor, forms fibrils in diseased and aged brains, potentially inside the lysosome. TBK1, VCP and spatacsin are implicated in endosome and lysosome clearance and renewal. Under disease conditions (right), some factors are lost to haploinsufficiency and others are mutated, often resulting in impaired activity. TDP-43 often aggregates. In c9ALS/FTD, TBK1 is sequestered by poly(GA). These diverse defects can disrupt endo-lysosomal flux, stalling the pathway and resulting in the accumulation of enlarged endosomes and changes in lysosomal morphology and number. Of note, specific mutations and types of protein loss are unique to different familial conditions.

Multiple ALS/FTD-associated genes impact the endo-lysosomal pathway

TBK1

TBK1 was first associated with ALS in 2015 [33, 34] and accounts for ~1–2% of ALS/FTD cases in reported cohorts [35]. While overexpression of TBK1 causes glaucoma, ALS-associated mutations typically confer a loss of function or haploinsufficiency, often by introducing deletions or null alleles [34]. Disease-associated point mutations in TBK1 impact its kinase activity and reduce its autophosphorylation and activation [36]. Studies in mice, however, indicate that loss of TBK1 function is not sufficient to induce disease in vivo, and second hits (or an additional ALS/FTD-associated lesion) are required [13, 36, 37]. TBK1 sits at a crossroads between autophagy and innate immunity – two pathways that are both heavily implicated in neurodegenerative diseases. Recently, however, the role of TBK1 in the endo-lysosomal pathway has emerged as a topic of interest in ALS/FTD research.

TBK1 can target specific cargo to MVBs for eventual degradation by the lysosome [38], and also helps maintain the integrity of the endo-lysosomal pathway by recognizing stalled and damaged endosomes and lysosomes and mediating their autophagosomal degradation [39, 40]. TBK1 can also directly impact the endo-lysosomal system by phosphorylating Rab7; this modification prevents Rab7 from localizing to endosomes and inhibits late endosomal activity [41, 42]. Recently, TBK1 was found to regulate endosomal maturation in human motor neurons, as reported in a pre-print study [29]; whether this also relates to TBK1-mediated regulation of Rab7 remains to be seen. Importantly, this study linked TBK1-mediated inhibition of endosome maturation to the development of TDP-43 proteinopathy [29]. Finally, TBK1 also works with the retromer complex in the regulation of ferratin levels through an autophagy-independent lysosomal degradation pathway, and ALS-associated mutations in TBK1 inhibit this process [43], representing a putative mechanism for the elevated ferratin levels observed in patient biofluids [44, 45] and the iron deposits observed in patient brains [46]. Disrupted retromer function could negatively impact lysosome maturation and it will be interesting to see if this also influences TDP-43 proteinopathy in TBK1-depleted cells.

C9orf72

A hexanucleotide repeat expansion in C9orf72 is the most common genetic cause of ALS/FTD (c9ALS/FTD) [47, 48], particularly in individuals of European descent [49]. It accounts for ~16% of familial ALS and ~20% of familial FTD, and is associated with ~6–8% of sporadic cases – but can reach a prevalence of 30–40% or more in certain populations [49, 50]. This intronic expansion results in haploinsufficiency, but also causes transcripts to accumulate into RNA foci and undergoes repeat associated non-ATG translation to produce five different dipeptide repeat (DPR) proteins that aggregate in neurons [49]. Expression of the C9orf72 hexanucleotide repeat in Drosophila resulted in the accumulation of enlarged and dysfunctional late endosomes and lysosomes in motor neurons, coupled with a decrease in the nuclear localization of the fly orthologue of transcription factor EB (TFEB) [51], a master regulator of lysosome biogenesis. Vesicles marked by lysosome-associated membrane proteins (LAMP1 or LAMP2) were also increased in the brains of a c9ALS/FTD mouse model [52], suggesting an influx in late endosomes or lysosomes, and the nuclear localization of TFEB is reduced in the motor cortex of c9ALS patients, as well as in HeLa cells expressing either the repeat expansion or the DPR poly(GA) [51]. In accordance with these observations, recent work has shown that poly(GA) also induced the formation of abnormal enlarged endosomes in mouse brains [13]. Poly(GA) sequestered TBK1, inhibiting its function in endosome maturation. When a mutation was introduced into TBK1 in this context, the observed endosomal defects were enhanced, TDP-43 inclusion pathology was heightened, and neurodegeneration exacerbated [13]. These findings are consistent with rare reports of patients co-harboring both C9orf72 and TBK1 mutations: compared to other c9ALS/FTD cases, these individuals show an earlier age of onset and a more rapid disease course [53]. Interestingly, this disease mechanism appears to be unique to poly(GA), as neither poly(GR) nor poly(PR) were able to sequester TBK1 [13] or influence TFEB localization in cells [51].

While c9ALS/FTD is thought to be driven by gain of function mechanisms, the loss of endogenous C9ORF72 can modulate disease [54, 55]. C9ORF72 has homology to the differentially expressed in normal and neoplasia (DENN) module, suggesting it could act as a guanine exchange factor (GEF) for Rab GTPases (Box 2) [56]. C9ORF72 primarily exists as part of a complex with Smith-Magenis syndrome chromosomal region 8 (SMCR8) and WD repeat containing protein 41 (WDR41) [57–60], but the exact function of this complex is unclear: while some studies suggest that it can act as a GEF [58, 61], more recent studies suggest that the complex instead acts as a GTPase activating protein (GAP) [62–64].

Immunocytochemical studies suggest that C9ORF72 localizes to Rab-positive vesicles [65, 66], and although multiple groups have performed co-labeling studies to identify these vesicles, perhaps the most disease-relevant data come from human spinal motor neurons, where C9ORF72 colocalized with Rab5, Rab7 and Rab11 [65]. Interaction with Rab5 would suggest a role in early endosomes, and this is consistent with data from induced pluripotent stem cell-derived neurons (iPSNs), where C9ORF72 primarily colocalized with Rab5, interacted with EEA1, and co-segregated with EEA1-positive fractions [67]. Interaction with Rab7, on the other hand, would suggest a role in late endosomes. MVBs were decreased in c9ALS/FTD patient fibroblasts [68], and the retrograde trafficking of MPRs was impaired in these cells and iPSNs [67, 68]. C9ORF72 has also been reported to colocalize with LAMP-positive vesicles in cultured cells, mouse models, iPSNs, and human motor neurons [57, 65–67], and similar vesicles are enlarged in C9orf72 deficient cells [57]. Finally, interaction with Rab11 would indicate a role in endosome recycling, but other studies have failed to see this colocalization [66].

C9orf72 knockout mice develop enlarged spleens and compromised immune responses attributed to defects in endo-lysosomal function in glial cells, which accumulate LAMP1-positive vesicles but show no change in Rab5- or Rab7-positive vesicles [59, 60, 69]. C9orf72 deficient macrophages also show upregulation of lysosomal and autophagy proteins [59], a finding consistent with studies showing that lysosomal C9ORF72 mediates mammalian target of rapamycin (mTOR) activity [57, 60, 64], which in turn phosphorylates TFEB, suppressing its nuclear localization and signaling [60, 64]. Notably, the effects of C9orf72 deficiency appear to vary between glial cells and neurons: as opposed to the lysosome accumulation seen in macrophages, C9orf72-deficient motor neurons show a decrease in lysosomal number [67] and a pre-print study reported that C9orf72-deficient mouse hippocampal neurons showed a decrease in early endosomes [70]. Lysosome number is also decreased in c9ALS/FTD iPSNs and patient samples, perhaps due to defects in MPR trafficking [67]. Interestingly, C9orf72 haploinsufficient and c9ALS/FTD iPSNs were more sensitive to exogenous DPR expression, as the reduction in functional lysosomes delayed the degradation of these toxic proteins [67]. This finding prompted researchers to explore methods of therapeutically increasing lysosome production in c9ALS/FTD, with particular attention being paid to PIKfyve inhibitors [67, 70, 71]. PIKfyve is the kinase responsible for converting PI3P to PI(3,5)P₂, and inhibiting its function both stalls endosome maturation and promotes lysosome biogenesis (Box 3). Clinical trials focused on a PIKfyve inhibitor are already underway for ALSⁱ. Based on our recent study [13] and other emerging concepts, however, we would argue that the use of such inhibitors as therapeutic agents should be explored with caution (Box 3).

Box 3: PIKfyve inhibitors and ALS/FTD: protective or pathogenic?

Reducing PIKfyve activity decreased DPR and TDP-43 pathology and increased neuronal survival in c9ALS/FTD iPSNs and mice [67, 70, 71]. Similar treatments were neuroprotective in C9orf72 deficient neurons [67, 70], poly(GR) Drosophila and mouse models [71], and iPSNs from patients with sporadic or familial ALS [71]. Inhibiting PIKfyve also reduced pathology and improved or delayed degenerative phenotypes in Drosophila, C. elegans, and mouse models of TDP-43 proteinopathy [71]. Together, these findings suggest that inhibiting PIKfyve could be of therapeutic value, but the effects of this inhibition in ALS/FTD may not be so clear-cut. PIKfyve inhibition increases the pool of PI3P in the cell [181], which promotes the association of EEA1 with early endosomes and stabilizes Rab5, preventing the Rab5 to Rab7 conversion: this may explain why early endosomes increased in c9ALS/FTD and C9orf72 deficient mice upon apilimod treatment [70]. PI3P also drives autophagosome formation [7] and promotes lysosomal degradation by mediating the sorting of cargo into ILVs [4]. These effects, coupled with an increase in TFEB activation upon PIKfyve inhibition [4, 182], could explain why apilimod reduced inclusion levels in ALS/FTD neurons [67, 70]. Alternatively, in lieu of any effects on TFEB activity, a recent study uncovered a different mechanism: secretory autophagy [71]. PIKfyve inhibition impairs autolysosome formation, and cells respond by targeting MVBs to the plasma membrane to secrete their contents via exosome release [183]. Aggregation-prone proteins like DPRs and pTDP-43 were thus ejected from the cell, providing protection against neuronal death and dysfunction [71]. Unfortunately, the packaging of neuropathological proteins into exosomes is believed to contribute to their propagation during disease progression [174]. Furthermore, while either inhibiting PIKfyve or disrupting endosome maturation through the use of a constitutively active Rab5 improved survival in c9ALS/FTD iPSNs, these same methods also triggered the accumulation of enlarged early endosomes [184] and induced TDP-43 pathology in cells [13]. The protective effects of PIKfyve inhibitors could therefore be short-lived, and the promotion of TDP-43 proteinopathy and propagation could ultimately outweigh initial inclusion-clearing benefits. Longitudinal studies could address these concerns. The impact of PIKfyve inhibition in ALS/FTD may also hinge upon the dosage used, as a fifty percent reduction in PIKfyve activity or expression was beneficial in ALS/FTD models [71], while a more substantial decrease in PIKfyve expression is associated with degeneration in prion diseases [185]. Nevertheless, alternative means of promoting aggregate clearance without disrupting endosome maturation or potentially impacting propagation should also be sought.

FIG4

While PIKfyve is responsible for converting PI3P to PI(3,5)P₂, FIG4 is responsible for the opposite: it dephosphorylates PI(3,5)P₂ and converts it back to PI3P. Yet the role of FIG4 in cells is not as straightforward. FIG4 exists in a complex with PIKfyve and its regulator ArPIKfyve at the late endosome [72], and within this complex, FIG4 and PIKfyve regulate each other’s activity [73]. In this way, FIG4 plays a role in both increasing and decreasing PI(3,5)P₂ levels [74]. As a result, knocking down FIG4 increased PI(3,5)P₂ levels in cells [72], but mutating FIG4 in mice actually results in a reduction in PI(3,5)P₂ [10]. This complexity is among the reasons for caution when considering therapeutic use of PIKfyve inhibitors (Box 3): the degeneration observed in pale tremor mice suggests that a loss of FIG4, and thus a reduction in PI(3,5)P₂, could negatively impact neuronal health and survival in vivo [10].

A mutation in FIG4 is responsible for the phenotypes observed in a spontaneous mouse mutant known as “pale tremor” [10]. Pale tremor mice develop diluted pigmentation and a severe tremor, along with locomotor defects and neurodegeneration reminiscent of both Charcot-Marie-Tooth (CMT) disease and ALS [10]. Both diseases were later linked to mutations in human FIG4 [10, 11], while complete loss of FIG4 is associated with the congenital disorder Yunis-Varón syndrome [75]. Currently, mutations in FIG4 remain a rare cause of ALS: while some studies found mutations in ~2–3% of the populations examined [11, 76], others observed a prevalence around 0.4% or less [77, 78]

Mutations in FIG4 impair its function in the PIKfyve-ArPIKfyve complex, resulting in a reduction of PI(3,5)P₂ without any apparent change in PI3P or other phosphoinositides [10]. This reduction in PI(3,5)P₂ disrupts endosomal trafficking, and fibroblasts and degenerating neurons from pale tremor mice accumulate enlarged LAMP2-positive vacuoles [10]. Similar enlarged vacuoles are observed in Yunis-Varón syndrome patient tissues [75] and fibroblasts from FIG4-associated CMT patients, where it was further noted that some vacuoles, although derived from late endosomes/lysosomes, did not contain any cargo [79]. This observation could reflect defects in the sorting of cargo into MVBs – another process that requires PI(3,5)P₂ [80]. Interestingly, studies in flies and mice indicate that the formation of enlarged late endosomes/lysosomes [81] and the degeneration of cortical neurons [82] can both be rescued by the expression of a catalytically inactive FIG4. Thus, the principal disease-inducing outcome of FIG4 loss of function could be endo-lysosomal disruption, and this effect may not require the phosphatase activity of FIG4, but perhaps only its ability to stabilize the PIKfyve complex.

ALS2

ALS2 is a rare recessive, juvenile form of ALS that arises from mutations in ALS2 [83, 84], which encodes alsin, a protein with three different GEF-like domains [85, 86]. ALS2-causing mutations often result in a truncation of the protein, which removes the region responsible for targeting alsin to early endosomes and deletes or disrupts the GEF domains that are responsible for regulating Rac1 and Rab5 [85, 86]. Thus, ALS2 likely arises from an inability to effectively regulate these GTPases. While Rab5 plays a key role in endosome maturation, Rac1 plays a role in endocytosis and macropinocytosis. Work in cell lines suggests that alsin interacts with Rac1 at membrane ruffles, where it is transferred to macropinosomes to later catalyze the Rab5-mediated fusion of these vesicles with early endosomes [87]. Rac1 activity also recruits recycling endosomes to membrane ruffles, and alsin helps convert these endosomes to EEA1-positive early endosomes [88].

In accordance with its GEF activities, alsin-deficient primary neurons showed impaired endosome maturation and enlarged Rab5-positive endosomes [89], as well as defective Rab5-dependent early endosome fusion [90] and reduced macropinocytosis [91]. In contrast, knocking down ALS2 in rat motor neurons resulted in a Rac1-dependent increase in endocytosis and smaller EEA1-positive endosomes [92]. Nevertheless, the clear association between alsin and the endo-lysosomal system adds support to the notion that this pathway is implicated in ALS.

VAPB

Vesicle-associated membrane protein (VAMP)-associated protein B (VAPB) and the related protein VAPA are endoplasmic reticulum (ER) proteins that can act as tethers between the ER and other membranes and organelles – including endosomes and lysosomes [93]. A point mutation in VAPB induces ALS [94], likely through a reduction of its endogenous functions [95, 96]. VAP proteins regulate PI4P production on endosomes, which is important for retromer function [97]. Loss of VAP proteins increased PI4P levels in cells, resulting in an accumulation of Golgi-derived endosomes harboring TGN proteins [97, 98]. These endosomes then fused with lysosomes, producing lysosomes with aberrant acidity and morphology, as well as abnormal contents [98]. Thus, in addition to its defined roles in the unfolded protein response, autophagy, and other processes [93], loss of VAPB also affects endosomal trafficking and lysosome biogenesis which could impact ALS.

VCP

Mutations in valosin-containing protein (VCP) are associated with multisystem proteinopathy (MSP), a condition formerly known as inclusion body myopathy associated with Paget disease of bone and FTD [99, 100]. Mutations in VCP are also associated with other diseases, including ALS/FTD [101, 102], with MSP being the more prevalent outcome: amongst individuals with VCP mutations, ~30% have FTD, but only ~3% have FTD alone and ~9% have ALS [103]. VCP mutations account for ~1–2% of cases in ALS cohorts [77, 102]. VCP is an AAA+ ATPase capable of segregating ubiquitin-tagged protein complexes, and through this function, it plays a role in several cellular processes, including diverse protein clearance pathways [104]. Disease-associated mutations in VCP span the length of the protein and can have various detrimental effects on its activity [101]. Interestingly, enlarged late endosomes/lysosomes are observed in the cells of patients harboring VCP mutations [15] and VCP activity is important for endo-lysosomal-mediated degradation of cargo [105, 106]. VCP appears to impact the endo-lysosomal system at multiple steps: it interacts with clathrin, suggesting a role in receptor-mediated endocytosis [107]. VCP also interacts with EEA1 and can regulate its oligomerization, affecting its ability to regulate early endosome size and sorting [106]. At later stages, VCP regulates the sorting of cargo into MVBs, using its segregase activity to deconstruct oligomers and enable their loading into ILVs [105]. When VCP was mutated or inhibited, its targets accumulated on the surface of enlarged late endosomes and the overall number of functional MVBs was reduced [105]. VCP also regulates lysosomal homeostasis by mediating the clearance of defective lysosomes [108].

CHMP2B

Although rarely a cause of sporadic FTD, a missplicing mutation in charged multivesicular body protein 2B (CHMP2B) is associated with a form of familial FTD (CHMP2B-FTD) [109]. This mutation results in the expression of truncated isoforms with a defective C-terminal regulatory region [109]; this region autoinhibits the protein’s lipid binding domain [110] and its deletion causes the truncated isoforms to act as dominant-negative mutants. Expression of mutant CHMP2B in mice results in the formation of enlarged late endosomes [14], and similar structures were detected in CHMP2B-FTD patient brains, fibroblasts, and iPSNs [14, 16, 111]. CHMP2B is part of the ESCRT-III complex responsible for altering membrane shape during several cellular processes. As part of the endo-lysosomal system, ESCRT-III acts at the membrane of MVBs, facilitating the sorting of cargo into ILVs [5]. Expression of mutant CHMP2B impairs the dissociation of ESCRT-III from MVBs and reduces Rab7 recruitment, resulting in reduced late endosome-lysosome fusion, aberrant endosomal trafficking, and inefficient endosomal-mediated degradation [16, 112]. Importantly, although CHMP2B regulates autophagy, inhibiting autophagy in cultured neurons delayed but did not completely prevent mutant CHMP2B-induced toxicity [113]. As TBK1 and other factors that influence early endosome trafficking can modulate mutant CHMP2B-induced toxicity in flies [114], it is possible that neuronal loss in CHMP2B-FTD also depends upon non-autophagy-associated functions of the endo-lysosomal system.

Studies on CHMP2B add evidence to the notion that disrupting the endo-lysosomal pathway could contribute to FTD. At the same time, these studies raise an interesting question in relation to the endo-lysosomal pathway and TDP-43 aggregation. Given emerging evidence that disruption of the endo-lysosomal pathway could be a key factor in the formation of TDP-43 proteinopathy, why do CHMP2B-FTD patients lack TDP-43 inclusions [115]? TDP-43 can be degraded by the endo-lysosomal system [26, 27], and a recent pre-print study suggests that disrupting the activity of ESCRT proteins could modulate this process, leading to an increase in TDP-43 levels and toxicity [28]. Simply increasing TDP-43 levels appears insufficient to induce inclusion formation, however, as many TDP-43 overexpressing rodent models fail to replicate this proteinopathy [116]. Rare CHMP2B point mutations have also been detected in a handful of ALS cases, which are positive for TDP-43 inclusions, but the rarity of these point mutations has precluded confirmation of their pathogenicity [117]. As CHMP2B acts at MVBs, perhaps the lack of TDP-43 inclusions in CHMP2B-FTD indicates that a disruption of early endosome function and/or more downstream lysosome activity is necessary for aggregate formation.

SPG11

Although more commonly associated with hereditary spastic paraplegia (HSP), mutations in spastic paraplegia 11 (SPG11) have also been linked to juvenile ALS [118]. Patients with SPG11-associated HSP can also develop pathology that is reminiscent of ALS [119], and the same genetic lesions are associated with either disease [120]. Mutations in SPG11 result in a loss of the encoded spatacsin protein, which is important for the autophagic lysosome renewal pathway [121–123]. Accordingly, loss of spatacsin results in a reduction in lysosomal number [122] and aberrant lipid clearance [123].

UBQLN2

Point mutations in ubiquilin 2 (UBQLN2) are causative in X-linked familial ALS and rare sporadic cases [124, 125]. UBQLN2 also co-localizes with TDP-43 and accumulates in inclusions in non-UBQLN2-associated ALS/FTD [124, 125]. There are four mammalian ubiquilins, but most disease-associated mutations localize to a proline-rich repeat domain that is unique to UBQLN2 [124, 125]. This domain resembles Src homology 3 ligand binding sites [126], suggesting that disease may arise from a disruption of UBQLN2 protein-protein interactions. Ubiquilins are ubiquitin-binding proteins responsible for shuttling specific cargoes to the ubiquitin proteasome system for degradation [125]. Ubiquilins also regulate the levels of vacuolar-ATPase, and their disruption leads to impaired lysosomal acidification and decreased autophagic flux [127, 128]. While restoring wildtype UBQLN2 to knockout cells can restore these autophagy-lysosomal defects, expression of disease-associated UBQLN2 mutants cannot – presumably due to weakened interactions with vacuolar-ATPase subunits [128]. Furthermore, both rat and iPSN models of UBQLN2-associated ALS accumulate large LAMP1-positive vesicles that partially overlap with UBQLN2 aggregates [129, 130] and in Drosophila, Rab5 was shown to be a genetic modifier of UBQLN2 [130].

GRN

Loss of function heterozygous mutations in GRN, which result in a reduction in progranulin (PGRN), are associated with FTLD-TDP [131, 132], while homozygous mutations are associated with neuronal ceroid lipofuscinosis (NCL) [133], a lysosomal storage disorder. Mutations in GRN account for ~5% of all FTD cases and ~20% of familial cases [134]. PGRN is processed by cysteine proteases to generate granulin fragments with additional downstream functions [135], and these granulins are also reduced in GRN-associated FTLD-TDP [136]. This processing primarily occurs in the lysosome and requires proper lysosome acidification [136]. Consequently, loss of PGRN processing could be a downstream effect of endo-lysosomal dysfunction in disease. At the same time, its association with NCL suggests that PGRN itself also directly regulates lysosomal activity. Even the heterozygous loss of PGRN associated with FTLD-TDP can impact lysosome activity, as NCL storage components and lysosomal proteins are elevated in FTLD-TDP tissue [137, 138] and NCL-like pathology is observed in FTD iPSNs [139].

Homozygous Grn knockout mice show features of NCL [140], as well as decreased mTOR signaling and enhanced lysosome accumulation in activated microglia in response to injury and aging [141, 142]. Heterozygous Grn knockout mice, a model for GRN-associated FTLD-TDP, also show an increase in lysosomal number in neurons [140]. This accumulation could suggest that lysosome generation is altered in these mice: PGRN is a putative TFEB target [141] and its levels are increased during normal lysosome biogenesis [142]. The accumulated lysosomes are unable to mature [143], however, and proteins involved in lysosomal lipid metabolism are decreased in Grn knockout mouse brains [144]. GRN-associated FTLD-TDP patients also show altered brain lipid profiles [140]. PGRN regulates lysosome acidification [142], and acts as a chaperone for multiple lysosomal proteases. For example, PGRN and its cleavage products bind the lysosomal protease cathepsin D and facilitate its maturation under acidic conditions [145]. Accordingly, cathepsin D activity is decreased in Grn knockout mice and GRN-associated FTLD-TDP cells [138, 139, 146]. Further loss of cathepsin D exacerbates PGRN-mediated defects, as mice deficient in both Grn and Ctsd (the gene encoding cathepsin D) showed enhanced accumulation of myelin debris in microglial lysosomes and increased TDP-43 pathology in white matter regions [147]. In addition to cathepsin D, PGRN influences the neuronal uptake and lysosomal targeting of prosaposin [148], which regulates sphingolipid hydrolases, as well as its cleavage into saposin C [149], which activates β-glucocerebrosidase (GCase). PGRN also interacts with GCase [150], and loss of PGRN causes GCase to dissociate from lysosomes and aggregate in the cytoplasm [151]. GCase activity is reduced in GRN-associated FTD iPSNs [149] and Grn deficient mice [150], and the latter recapitulate some features of Gaucher disease, a lysosomal storage disorder caused by mutations in GCase [152].

TMEM106B

Genetic variation at the TMEM106B locus is associated with increased risk for FTLD-TDP [21], specifically in GRN and C9orf72 carriers, and reduced cognition in ALS [153]. Recently, amyloid fibrils composed of a C-terminal fragment of TMEM106B were detected in several neurodegenerative diseases – including tauopathies, amyloid-β amyloidoses, synucleinopathies, and TDP-43 proteinopathies [17–20] – suggesting that the dysregulation of TMEM106B may be a common feature in disease, regardless of genetic lesion. The severity of this pathology appears to weakly correlate with TMEM106B risk haplotypes and may be particularly relevant to FTLD-TDP [154], but TMEM106B fibrils have also been detected in the brains of elderly non-demented individuals, suggesting that fibrillization is also driven by aging [19, 20, 154]. So, what are these fibrils, how do they form, and do they play a role in pathogenesis? These questions have sparked a renewed interest in understanding how TMEM106B influences endo-lysosomal function – and how it could become aggregated in the brain.

TMEM106B is a type II integral transmembrane receptor with a complex N-glycosylated luminal domain [155]. It predominantly localizes to Rab7-, Rab9-, and LAMP1-positive late endosomes/lysosomes and appears to be trafficked there from both the TGN and the plasma membrane [155, 156]. Overexpressing TMEM106B in cells resulted in the nuclear translocation of TFEB [157], suggesting an activation of lysosome biogenesis – but these cells accumulated enlarged endolysosomes and suffered from impaired lysosome acidification and degradation, as well as defects in MPR trafficking [156–159]. Knocking down TMEM106B induced the opposite effect, resulting in fewer, smaller lysosomes [157]. In mice, loss of Tmem106b results in impaired lysosomal acidification due to a loss of its stabilizing effect on vacuolar-ATPase [160]. Finally, TMEM106B can be processed by lysosomal enzymes, generating a luminal fragment that is released and a membrane-bound N-terminal fragment that can be further processed [161, 162]. The role of these cleavage products is largely unknown, although the TMEM106B fibrils identified in human brains correspond to the luminal domain of the protein [17–20], implicating this fragment in aging and disease.

The observation that TMEM106B variants specifically increase FTD disease risk in GRN and C9orf72 carriers is intriguing, as all three proteins have been implicated in the endo-lysosomal pathway. The proteins may also interact: TMEM106B colocalizes with PGRN in late endosomes [158, 163] and TMEM106B is increased in Grn knockout mouse brain [164]. TMEM106B risk variants could sensitize cells to lysosomal disruption mediated by the impact of Grn and C9orf72 loss on endo-lysosomal activity, while protective alleles of TMEM106B could help suppress disease-associated lysosome dysfunction. Accordingly, in Grn knockout mice, overexpression of TMEM106B exacerbated lysosomal defects [164], while loss of Tmem106b failed to rescue defects in heterozygous knockout mice [165], but did improve behavioral abnormalities and dampen the overactive lysosomal activity seen young homozygous animals [160]. Studies in c9ALS/FTD are less clear: In mice expressing the C9orf72 repeat, complete loss of Tmem106b increased astrogliosis in the brain with no change in repeat-dependent neuronal loss, while a heterozygous Tmem106b reduction improved neuronal loss but had no effect on neuroinflammation [166]. There was no change in lysosomal activity in these animals, however, regardless of Tmem106b expression levels [166]. In contrast to these studies, recent work in cells and c9ALS/FTD iAstrocytes indicates that knocking down TMEM106B can increase DPR deposition by impairing autophagy and lysosome acidification [167]. The discrepancy between these studies could relate to the fact that the mouse models only recapitulate c9ALS/FTD gain of function defects; given their similar functions, it is more likely that TMEM106B influences the effects of C9ORF72 loss of function. In fact, one study found that knocking down C9orf72 could alleviate lysosomal defects induced by TMEM106B overexpression in cells, pointing towards a functional interplay between these proteins [159].

Interestingly, unlike what is reported for young animals, Tmem106b deficiency enhanced defects in aged Grn knockout mice [168–170]. Intriguingly, the TDP-43 pathological burden was increased in these animals – even though Grn knockout models alone often lack this pathology. Indeed, the minor allele of TMEM106B variants – which is associated with lower TMEM106B levels – associated with increased TDP-43 burden in ALS patients, and partial loss of TMEM106B increased TDP-43 aggregation in a cellular model [171]. These findings support the emerging hypothesis that the disruption of the endo-lysosomal system could be a key determinant in the eventual development of TDP-43 proteinopathy, and further suggest that the disruption of this pathway may need to reach a certain threshold of severity before this age-dependent phenotype can be observed in vivo. Why the minor allele of TMEM106B, often considered protective, becomes detrimental in aged animals is still unclear, but these findings further highlight the importance of aging as a factor in disease. TMEM106B fibrils may also form in an age-dependent manner [19, 20, 154].

Downstream effects of disrupting the endo-lysosomal pathway

As discussed in the previous sections, accumulating evidence suggests that disruption of the endo-lysosomal pathway contributes to toxicity in ALS/FTD. Accordingly, mapping the mechanisms by which these impairments drive pathogenesis will be essential for better understanding of these diseases and developing new therapeutics. Unfortunately, disruption of this pathway can have diverse cell type-specific downstream consequences. One of the most well-defined functions of the endo-lysosomal system is to facilitate the lysosomal degradation of cargo, and a disruption of this process could result in an overabundance of target molecules, enhancing their activity and putting strain on other degradation pathways. Furthermore, recent work suggests that proteins that mediate the clearance of compromised endosomes and lysosomes – like TBK1 [39, 40] or VCP [108] – could regulate the propagation of aggregation-prone proteins like TDP-43 or tau [172, 173]. If defective vesicles harboring these proteins are not efficiently cleared from the cell, pathogenic seeds could escape degradation and be released [172, 173]. Pathological propagation is also linked to exosome biogenesis, an offshoot of the endo-lysosomal pathway [174].

In addition to protein clearance, the endosomal system is also important for membrane trafficking, and the disruption of this process, particularly of the generation of recycling endosomes, can impact neuronal spine formation [175] and synaptic growth [176]. The endo-lysosomal system also acts as a signaling platform. In neurons, receptors are internalized by endocytosis and then either recycled or degraded by the lysosome [177]; disruption of this process could lead to neuronal dysfunction and neurotoxicity. Neurotrophic and cell survival factors like tropomyosin receptor kinases also utilize the endo-lysosomal system to regulate long-distance signaling in neurons [177]. Signaling from the endo-lysosomal pathway is particularly important for immunity, and neuroinflammation and hyperactive immune responses are known to be factors in neurodegeneration. The initiation of various signaling pathways depends upon the sensing of specific triggers inside of endosomes and lysosomes, and these pathways can remain active until relevant receptors and signaling factors are processed or degraded within the lysosome [178]. The endo-lysosomal system thus regulates the timing and duration of specific signaling and immune responses within the cell [178] and the disruption of lysosomal function could have adverse effects on this process. For example, some toll-like receptors reside in the lumen of endolysosomes, and the disruption of lysosomal activity could prolong contact between these receptors and their ligands, hyperactivating the downstream pathway. This could explain the increases in inflammatory signaling and cytokine production observed in C9orf72 deficient cells and related mouse models [69, 179, 180].

Concluding Remarks and Future Perspectives

Multiple lines of evidence have long established an association between the endo-lysosomal pathway and ALS/FTD. Given the intrinsic connections between this pathway and autophagy, however, many studies have focused on defective aggregate clearance as the driving mechanism in disease, and research efforts have often overlooked other downstream effects of a disrupted endo-lysosomal system (see Outstanding Questions). The endo-lysosomal pathway appears to be particularly important for the development of TDP-43 proteinopathy, for example, whereas disrupting early autophagy alone does not appear to induce inclusion formation [13, 29]. These observations, along with growing list of connections between ALS/FTD-associated genes and endo-lysosomal activity, call for a re-evaluation of the implications of endo-lysosomal pathway disruption in ALS/FTD. Moreover, mitigating the impact of TDP-43 pathology on neuronal function will be essential for ALS/FTD therapeutics, and developing methods of preserving endo-lysosomal activity in diseased cells could represent an intriguing avenue towards achieving this goal.

Outstanding Questions.

• How do the newly discovered TMEM106B fibrils form in the disease brain? Do they impact lysosome activity, and do they contribute to pathogenesis?

• Disruption of the endo-lysosomal system appears to be relevant to the development of TDP-43 proteinopathy, but what are the mechanisms underlying this observed effect? Does this only depend on changes in TDP-43 clearance, or are other factors at play? Does a disrupted endo-lysosomal system also contribute to the development of neurotoxic inclusions in other proteinopathies?

• TBK1 is sequestered into poly(GA) aggregates in models of c9ALS/FTD. This kinase is known to be activated in response to the oligomerization of upstream triggers as part of its function in immune response signaling pathways. Its interaction with poly(GA) also depends upon the aggregation of the DPR. Does TBK1 interact with other aggregation-prone disease proteins, and could its sequestration be a more common pathomechanism in ALS/FTD and other neurodegenerative diseases?

• What are the functions of C9ORF72 and its interactors in the endo-lysosomal pathway? C9ORF72, the loss of which could impact c9ALS/FTD, bears homology to GEF and GAP proteins, but it is unclear which class of regulator it represents. It is also unclear exactly what client GTPases C9ORF72-containing complexes regulate.

• Which stages of the endo-lysosomal pathway are most significantly affected in ALS/FTD and how do they contribute to pathology? Many models show enlarged or aberrant late endosomes and lysosomes, suggesting that more downstream functions of the pathway may be most critical for pathogenesis – but some models instead show disrupted early endosomes. In these cases, does toxicity arise from downstream effects on late endosomes, or are other functions of upstream early or recycling endosomes also critical?

• As the field uncovers more ways in which the disruption of the endo-lysosomal system contributes to ALS/FTD, could this knowledge be harnessed to develop new therapeutics?

Highlights.

• ALS/FTD patient cells and tissue show evidence of a disrupted endo-lysosomal system, including enlarged endosomes and changes in the expression of endo-lysosomal genes. The discovery of TMEM106B filaments in insoluble brain extracts from several neurodegenerative disorders further highlights the potential importance of the lysosome in aging and disease.

• Multiple disease-associated genes play a role in the endo-lysosomal system, and emerging evidence suggests these roles may be particularly important for pathogenesis.

• Although autophagy is intrinsically linked to the endo-lysosomal system, some studies suggest that inhibiting this clearance pathway alone is insufficient to induce TDP-43 proteinopathy in laboratory models. Yet, inhibiting the endo-lysosomal system does induce TDP-43 inclusion formation in cells. The non-autophagy-associated functions of this pathway in ALS/FTD should be further explored.

Glossary

Amyloid

an insoluble protein with a fibril-like morphology and cross-β-sheet secondary structure. The constitutive proteins in pathological inclusions in neurodegenerative diseases are assembled into amyloids

Cathepsin D

a lysosomal aspartyl endo-protease in the peptidase A1 family. Cathespin D is ubiquitously expressed in lysosomes, where it helps degrade protein cargo

Charcot-Marie-Tooth (CMT) disease

a hereditary degenerative disease affecting the peripheral nerves. Symptoms include loss of sensation and muscle weakness or atrophy

GCase

β-glucocerebrosidase, a lysosomal enzyme responsible for breaking down glucocerebroside, an intermediate glycolipid metabolite abundant in cell membranes

Macropinocytosis

the nonspecific endocytosis of extracellular fluid into “macropinosomes”, which can be shuttled into the endo-lysosomal pathway. Macropinocytosis is important for cell motility, as well as for immune response in glial cells

mTOR

mammalian target of rapamycin, a protein kinase complex regulated by multiple upstream triggers including insulin and growth factors. It responds to changes in energy, nutrient, oxygen, and amino acid levels in cells and regulates signaling pathways related to cell proliferation, cell growth, autophagy, and apoptosis

Multivesicular body

an endosome containing multiple intraluminal vesicles (ILVs). MVBs could represent endosomes on the way to becoming endolysosomes and lysosomes, or they could be involved in other vesicle trafficking functions including the sorting, recycling, transport, and storage of cargo

Propagation

In the context of neurodegenerative diseases, propagation often refers to a prion-like phenomenon observed in proteinopathies where neurotoxic inclusions appear to spread through the brain as the disease progresses. Propagation, or seeding, occurs when misfolded protein species transfer to neighboring cells and template the misfolding of their endogenous counterparts

Proteinopathy

a disease characterized by protein misfolding and/or protein aggregation. Misfolded proteins accumulate into insoluble aggregates referred to as inclusions

Retromer

a multi-protein complex responsible for the sorting and packaging of cargo at endosomes for retrograde trafficking to either the TGN or the plasma membrane. It contains two subcomplexes: a trimer of Vps35, Vps26 and Vps29 responsible for cargo selection and a dimer of sorting nexins with bin-amphiphysin-rvs domains (Snx-BAR) responsible for membrane tubule and vesicle formation. Yeast have two Snx-BAR proteins (Vps5p and Vps17p), while mammals have two orthologues for each dimer component (Snx1 and Snx2 correspond to Vps5p; Snx5 and Snx6 correspond to Vps17p)

Transcription factor EB (TFEB)

a master regulator of autophagy and lysosome biogenesis. When localized to the nucleus, it activates the transcription of lysosomal and autophagy genes. Phosphorylation of TFEB by mTOR prevents its nuclear translocation, inhibiting its transcription factor activity

Vacuolar-ATPase

an ATP-driven proton pump that acts to acidify the lumen of vesicles

Vacuole

a general term for a membrane-bound vesicle within a cell. This term can also refer to a specific lysosome-like structure in yeast

Yunis-Varón syndrome

a rare autosomal-recessive genetic disorder affecting the skeletal system, nervous system, heart, respiratory system, and ectodermal tissue. It is primarily associated with mutations in FIG4