Fig 1 - available via license: Creative Commons Attribution 4.0 International
Content may be subject to copyright.
Brain MRI demonstrated white matter abnormality suggesting leukoencephalopathy in a patient homozygous for VPS11: c.2536T>G (p.C846G). In patient B at nine months of age, thin corpus callosum (A), T2 diffuse hyperintensity in the peri-Rolandic white matter (B) and posterior occipital white matter region (C) were seen; FLAIR diffuse hyperintensity in the white matter region was also seen (D). At five years of age, diminutive corpus callosum (E), T2 diffuse hyperintensity signal in peri-Rolandic areas (F) and supratentorial white matter, most pronounced within the bilateral parieto-occipital regions (G) were seen; FLAIR diffuse hyperintensity in the white matter region with a mild increase of myelination was seen(H).
Source publication
Genetic leukoencephalopathies (gLEs) are a group of heterogeneous disorders with white matter abnormalities affecting the central nervous system (CNS). The causative mutation in ~50% of gLEs is unknown. Using whole exome sequencing (WES), we identified homozygosity for a missense variant, VPS11: c.2536T>G (p.C846G), as the genetic cause of a leukoe...
Citations
... This complex regulates membrane fusion in the endolysosomal compartment and has been shown to drive membrane fusion between autophagosomes and lysosomes 49 . Additionally, mutations in the VPS11 and VPS33A subunits of the complex have been found in patients with neurodegenerative diseases 50,51 . ...
... Under this hypothesis, defects in the complex would result in increased STING signaling. Interestingly, mutations in both VPS11 and VPS33A have been found in patients with neurodegenerative disease 50,51 . Exacerbated activation of STING via dysregulation of its trafficking has been associated with neurodegeneration in multiple diseases such as Niemann-Pick Disease and ALS 20,21,64 . ...
STING is an innate immune sensor that traffics across many cellular compartments to carry out its function of detecting cyclic di-nucleotides and triggering defense processes. Mutations in factors that regulate this process are often linked to STING-dependent human inflammatory disorders. To systematically identify factors involved in STING trafficking, we performed a genome-wide optical pooled screen and examined the impact of genetic perturbations on intracellular STING localization. Based on subcellular imaging of STING protein and trafficking markers in 45 million cells perturbed with sgRNAs, we defined 464 clusters of gene perturbations with similar cellular phenotypes. A higher-dimensional focused optical pooled screen on 262 perturbed genes which assayed 11 imaging channels identified 73 finer phenotypic clusters. In a cluster containing USE1, a protein that mediates Golgi to ER transport, we found a gene of unknown function, C19orf25. Consistent with the known role of USE1, loss of C19orf25 enhanced STING signaling. Other clusters contained subunits of the HOPS, GARP and RIC1-RGP1 complexes. We show that HOPS deficiency delayed STING degradation and consequently increased signaling. Similarly, GARP/RIC1-RGP1 loss increased STING signaling by delaying STING exit from the Golgi. Our findings demonstrate that genome-wide genotype-phenotype maps based on high-content cell imaging outperform other screening approaches, and provide a community resource for mining for factors that impact STING trafficking as well as other cellular processes observable in our dataset.
... Vps11 and Vps18 complexes are E3 ubiquitin ligases that control several signaling factors and pathways, including Wnt, estrogen receptor alpha (ERalpha), and NFκB. Because the mutation in Vps11 promotes ubiquitination-mediated protein degradation and impaired autophagy, the events result in oligodendrocyte cell death, the suppression of myelination, and possibly hypomyelination [63]. Another report demonstrated that the mutant inhibits oligodendrocyte differentiation via the downregulation of p70S6K signaling that controls the expression of myelin genes such as myelin regulatory factor (MyRF), MBP, and PLP1 [64]. ...
Hypomyelinating leukodystrophies (HLDs) represent a group of congenital rare diseases for which the responsible genes have been identified in recent studies. In this review, we briefly describe the genetic/molecular mechanisms underlying the pathogenesis of HLD and the normal cellular functions of the related genes and proteins. An increasing number of studies have reported genetic mutations that cause protein misfolding, protein dysfunction, and/or mislocalization associated with HLD. Insight into the mechanisms of these pathways can provide new findings for the clinical treatments of HLD.
... Autophagic deficiency may be one of the important pathological features underlying many neurodegenerative diseases in patients (1). In recent years, findings from a large number of studies have demonstrated a strong link between disruptions in autophagic pathways and various neurodegenerative diseases such as Parkinson's disease, Alzheimer's disease, Huntington's disease, and even some leukoencephalopathies (2)(3)(4)(5)(6). ...
Objectives
X-linked adrenoleukodystrophy (ALD) is a peroxisomal disease caused by mutations in the ABCD1 gene. Childhood cerebral ALD (CCALD) is characterized by inflammatory demyelination, rapidly progressing, often fatal. Hematopoietic stem cell transplant only delays disease progression in patients with early-stage cerebral ALD. Based on emergency humanitarianism, this study aims to investigate the safety and efficacy of sirolimus in the treatment of patients with CCALD.
Methods
This was a prospective, single-center, one-arm clinical trial. We enrolled patients with CCALD, and all enrolled patients received sirolimus treatment for three months. Adverse events were monitored and recorded to evaluate the safety. The efficacy was evaluated using the neurologic function scale (NFS), Loes score, and white matter hyperintensities.
Results
A total of 12 patients were included and all presented with CCALD. Four patients dropped out and a total of eight patients in the advanced stage completed a 3-month follow-up. There were no serious adverse events, and the common adverse events were hypertonia and oral ulcers. After sirolimus treatment, three of the four patients with an initial NFS > 10 showed improvements in their clinical symptoms. Loes scores decreased by 0.5–1 point in two of eight patients and remained unchanged in one patient. Analysis of white matter hyperintensities revealed a significant decrease in signal intensity ( n = 7, p = 0.0156).
Conclusions
Our study suggested that autophagy inducer sirolimus is safe for CCALD. Sirolimus did not improve clinical symptoms of patients with advanced CCALD significantly. Further study with larger sample size and longer follow-up is needed to confirm the drug efficacy.
Clinical Trial registration: https://www.chictr.org.cn/historyversionpuben.aspx , identifier ChiCTR1900021288.
... VPS11 is a core component of both the CORVET (class C core vacuole/endosome tethering) and HOPS (homotypic fusion and protein sorting) complexes, involved in membrane trafficking in the endosomal-lysosomal pathway, as well as in autophagy (HOPS). The VPS11-C846G mutation is a founder mutation in the AJs, and is known to cause autosomal recessive hypomyelination and leukoencephalopathy linked to endosomal and autophagic network defects [49,50]. Zhang et al. showed that the mutant allele remarkably reduced the expression level of the protein, with half-life time of five-fold lower than the wild-type, and significant decreased interaction with VPS18, suggesting reduction of the VPS-C core assembly. ...
Objectives:
VPS35 and VPS13 have been associated with Parkinson's disease (PD), and their shared phenotype in yeast when reduced in function is abnormal vacuolar transport. We aim to test if additional potentially deleterious variants in other genes that share this phenotype can modify the risk for PD.
Methods:
77 VPS and VPS-related genes were analyzed using whole-genome-sequencing data from 202 PD patients of Ashkenazi Jewish (AJ) ancestry. Filtering was done based on quality and functionality scores. Ten variants in nine genes were further genotyped in 1200 consecutively recruited unrelated AJ-PD patients, and allele frequencies and odds ratio calculated compared to gnomAD-AJ-non-neuro database, in un-stratified (n = 1200) and stratified manner (LRRK2-G2019S-PD patients (n = 145), GBA-PD patients (n = 235), and non-carriers of these mutations (NC, n = 787)).
Results:
Five variants in PIK3C3, VPS11, AP1G2, HGS and VPS13D were significantly associated with PD-risk. PIK3C3-R768W showed a significant association in an un-stratified (all PDs) analysis, as well as in stratified (LRRK2, GBA, and NC) analyses (Odds ratios = 2.71, 5.32, 3.26. and 2.19 with p = 0.0015, 0.002, 0.0287, and 0.0447, respectively). AP1G2-R563W was significantly associated in LRRK2-carriers (OR = 3.69, p = 0.006) while VPS13D-D2932N was significantly associated in GBA-carriers (OR = 5.45, p = 0.0027). VPS11-C846G and HGS-S243Y were significantly associated in NC (OR = 2.48 and 2.06, with p = 0.022 and 0.0163, respectively).
Conclusions:
Variants in genes involved in vesicle-mediated protein transport and recycling pathways, including autophagy and mitophagy, may differentially modify PD-risk in LRRK2-carriers, GBA carriers, or NC. Specifically, PIK3C3-R768W is a PD-risk allele, with the highest effect size in LRRK2-G2019S carriers. These results suggest oligogenic effect that may depends on the genetic background of the patient. An unbiased burden of mutations approach in these genes should be evaluated in additional PD and control groups. The mechanisms by which these novel variants interact and increase PD-risk should be researched in depth for better tailoring therapeutic intervention for PD prevention or slowing disease progression.
... The putative proteins may be specifically involved in autolysosome formation since the vesicle transport system around the lysosome plays a key role in morphological differentiation in oligodendroglial cells [24,25]. Actually, a loss-of-function mutation of vacuolar protein sorting 11 (VPS11), as the core subunit of complexes of class C core vacuole/endosome tethering (CORVET) and homotypic fusion and vacuole protein sorting (HOPS), specifically causes hypomyelinating leukodystrophy 11 (HLD11), which is a genetic oligodendroglial cell disease [26]. It may be important to clarify the specific organelle role of Rab2a in oligodendroglial cells, judging by the relationship between Rab2a and morphological differentiation in oligodendroglial cells. ...
Autism spectrum disorder (ASD) is a central nervous system (CNS) neurodevelopmental disorder that includes autism, pervasive developmental disorder, and Asperger’s syndrome. ASD is characterized by repetitive behaviors and social communication deficits. ASD is thought to be a multifactorial disorder with a range of genetic and environmental factors/candidates. Among such factors is the rab2b gene, although it remains unclear how Rab2b itself is related to the CNS neuronal and glial developmental disorganization observed in ASD patients. Rab2 subfamily members regulate intracellular vesicle transport between the endoplasmic reticulum and the Golgi body. To the best of our knowledge, we are the first to report that Rab2b positively regulates neuronal and glial cell morphological differentiation. Knockdown of Rab2b inhibited morphological changes in N1E-115 cells, which are often used as the neuronal cell differentiation model. These changes were accomplished with decreased expression levels of marker proteins in neuronal cells. Similar results were obtained for FBD-102b cells, which are used as the model of oligodendroglial cell morphological differentiation. In contrast, knockdown of Rab2a, which is another Rab2 family member not known to be associated with ASD, affected only oligodendroglial and not neuronal morphological changes. In contrast, treatment with hesperetin, a citrus flavonoid with various cellular protective effects, in cells recovered the defective morphological changes induced by Rab2b knockdown. These results suggest that knockdown of Rab2b inhibits differentiation in neuronal and glial cells and may be associated with pathological cellular phenotypes in ASD and that hesperetin can recover their phenotypes at the in vitro level at least.
... Vps16 shares a large interface with the coiled-coil motif formed by Vps18 and Vps41 and the N-terminus of Vps18, which is stabilized through interactions between hydrophobic and charged residues ( Figure 2C). Vps33 is in immediate contact with the structured loop of Vps18 (residues 824-831) that connects the elongated helix with the RING finger domain ( Figure 2C) Robinson et al., 1991;van der Welle et al., 2021;Zhang et al., 2016) and cause failure of correct HOPS assembly ( Figure 2-figure supplement 2). Overall, the SNARE binding module appears to be stably connected to the central core, while only the short C-terminal section of Vps16 α-solenoid (residues 739-798) displays high variability and is not resolved in our structure. ...
Lysosomes are essential for cellular recycling, nutrient signaling, autophagy, and pathogenic bacteria and viruses invasion. Lysosomal fusion is fundamental to cell survival and requires HOPS, a conserved heterohexameric tethering complex. On the membranes to be fused, HOPS binds small membrane-associated GTPases and assembles SNAREs for fusion, but how the complex fulfills its function remained speculative. Here, we used cryo-electron microscopy to reveal the structure of HOPS. Unlike previously reported, significant flexibility of HOPS is confined to its extremities, where GTPase binding occurs. The SNARE-binding module is firmly attached to the core, therefore, ideally positioned between the membranes to catalyze fusion. Our data suggest a model for how HOPS fulfills its dual functionality of tethering and fusion and indicate why it is an essential part of the membrane fusion machinery.
... Functional annotation analysis shows that these proteins are mostly involved in protein or nucleotide binding (Table 1). Furthermore, seven proteins (PSL3 (52), ABHD12 (53), VPS11 (54,55), AFG3L2 (56), GK (57), ROGDI (58), and ATX10 (59)) have established causal links to other diseases (supplemental Table S6). Of these, ABHD12, VPS11, ATX10, AFG3L2, and ROGDI are all associated with neurological disorders (respectively, PHARC syndrome (53), hypomyelinating leukodystrophy 12 (54), spinocerebellar ataxia type 10 (59) and 28 (56,60), and Kohlschutter's syndrome (58)) (supplemental Table S6). ...
... Furthermore, seven proteins (PSL3 (52), ABHD12 (53), VPS11 (54,55), AFG3L2 (56), GK (57), ROGDI (58), and ATX10 (59)) have established causal links to other diseases (supplemental Table S6). Of these, ABHD12, VPS11, ATX10, AFG3L2, and ROGDI are all associated with neurological disorders (respectively, PHARC syndrome (53), hypomyelinating leukodystrophy 12 (54), spinocerebellar ataxia type 10 (59) and 28 (56,60), and Kohlschutter's syndrome (58)) (supplemental Table S6). ...
Mouse models of Alzheimer’s Disease (AD) show progression through stages reflective of human pathology. Proteomics identification of temporal and sex-linked factors driving AD related pathways can be used to dissect initiating and propagating events of AD stages to develop biomarkers or design interventions. In the present study we conducted label-free proteome measurements of mouse hippocampus tissue with variables of time (three, six, and nine months), genetic background (5XFAD vs. WT), and sex (equal males and females). These time points are associated with well-defined phenotypes with respect to: Aβ42 plaque deposition, memory deficits, and neuronal loss, allowing correlation of proteome based molecular signatures with the mouse model stages. Our data show 5XFAD mice exhibit increases in known human AD biomarkers as amyloid-beta peptide (Aβ), APOE, GFAP, and ITM2B are upregulated across all time points/stages. At the same time, 23 proteins are here newly associated with Alzheimer’s pathology as they are also dysregulated in 5XFAD mice. At a pathways level the 5XFAD specific upregulated proteins are significantly enriched for DNA damage and stress-induced senescence at 3-months only, while at 6-months the AD-specific proteome signature is altered and significantly enriched for membrane trafficking and vesicle-mediated transport protein annotations. By 9-months AD-specific dysregulation is also characterized by significant neuro-inflammation with innate immune system, platelet activation and hyper-reactive astrocyte related enrichments. Aside from these temporal changes, analysis of sex-linked differences in proteome signatures uncovered novel sex and AD-associated proteins. Pathway analysis revealed sex-linked differences in the 5XFAD model to be involved in regulation of well-known human AD related processes of amyloid fibril formation, wound healing, lysosome biogenesis, and DNA damage. Verification of the discovery results by Western blot and parallel reaction monitoring confirm the fundamental conclusions of the study and poise the 5XFAD model for further use as a molecular tool for understanding AD.
... Vps33 is in immediate contact with the structured loop of Vps18 (residues 824-831) that connects the elongated helix with the RING finger domain (Fig. 2c). This, as well as the role of RING finger domains in the interlocking of other subunits, explains, why mutations at RING domains result in devastating human diseases 5,19,30,31 and cause failure of correct HOPS assembly (Extended Data 140 Fig. 6). Overall, the SNARE binding module appears to be rigidly connected to the central core, while only the short C-terminal section of Vps16 a-solenoid (residues 739-798) displays high variability and is not resolved in our structure. ...
Lysosomes are of central importance in cellular recycling, nutrient signaling and endocytosis, are tightly connected to autophagy and the invasion of pathogenic bacteria and viruses. Lysosomal fusion events are fundamental to cell survival and require HOPS, a conserved heterohexameric tethering complex. HOPS recognizes and binds small membrane-associated GTPases on lysosomes and organelles, and assembles membrane bound SNAREs for fusion. Through tethering, HOPS brings membranes in close proximity to each other and significantly increases fusion efficacy by catalysing SNARE assembly. Consequently, different HOPS mutations are causative for severe diseases. Despite its fundamental cellular duties, it remained speculative how HOPS fulfils its function as high-resolution structural data were unavailable. Here, we used cryo-electron microscopy to reveal the structure of HOPS. In the complex, two central subunits form the backbone and an assembly hub for the functional domains. Two GTPase binding units extend to opposing ends, while the SNARE binding module points to the side, resulting in a triangular shape of the complex. Unlike previously reported, HOPS is surprisingly rigid and extensive flexibility is confined to its extremities. We show that HOPS complex variants with mutations proximal to the backbone can still tether membranes but fail to efficiently promote fusion indicating, that the observed integrity of HOPS is essential to its function. In our model, the core of HOPS acts as a counter bearing between the flexible GTPase binding domains. This positions the SNARE binding module exactly between the GTPase anchored membranes to promote fusion. Our structural and functional analysis reveals the link between the spectacular architecture of HOPS and its mechanism that couples membrane tethering and SNARE assembly, to catalyse lysosomal fusion.
... Recent advances in whole exome sequencing (WES) now permit more definite diagnoses for gLE and for the discovery of novel genetic mutations that result in gLE 3,4 . WES was recently used to identify a novel mutation in Vacuolar Protein Sorting 11 (VPS11) in patients with gLE 5,6 . The autosomal recessive mutation VPS11:C846G results in infantile onset of gLE characterized by hypomyelination and developmental delay, along with classic gLE hallmarks of progressive motor and sensory system deficiencies 6 . ...
... WES was recently used to identify a novel mutation in Vacuolar Protein Sorting 11 (VPS11) in patients with gLE 5,6 . The autosomal recessive mutation VPS11:C846G results in infantile onset of gLE characterized by hypomyelination and developmental delay, along with classic gLE hallmarks of progressive motor and sensory system deficiencies 6 . With a high carrier frequency of 1:250 in Ashkenazi Jewish (AJ) families, this missense mutation was hypothesized to arise from a founder effect 6 . ...
... The autosomal recessive mutation VPS11:C846G results in infantile onset of gLE characterized by hypomyelination and developmental delay, along with classic gLE hallmarks of progressive motor and sensory system deficiencies 6 . With a high carrier frequency of 1:250 in Ashkenazi Jewish (AJ) families, this missense mutation was hypothesized to arise from a founder effect 6 . Biochemical in vitro analysis revealed that the truncated mutant protein has lower expression, faster turnover, and impairments in autophagy flux 6 ; however, the exact mechanism that leads to hypomyelination and disease pathology is unclear. ...
Genetic Leukoencephalopathies (gLEs) are heritable white matter disorders that cause progressive neurological abnormalities. A founder mutation in the human endolysosomal trafficking protein VPS11 has been identified in Ashkenazi Jewish patients manifesting classic gLE symptoms of hypomyelination, developmental delay, motor and systemic deficits. In this study, we characterized the visual and sensorimotor function of two zebrafish vps11 mutant lines: the previously reported vps11(plt), and a new vps11(−/−) null mutant line, using behavioral analysis to track larval motor responses to visual and acoustic stimuli. We found that mutant larvae from both vps11(plt) and vps11(−/−) lines were able to visually distinguish light and dark, but showed a progressive loss of a normal sensorimotor response to visual stimuli from 5 days post fertilization (dpf) to 7dpf. Additionally, optokinetic response analysis performed at 5dpf indicated that the mutants were significantly visually impaired. Both mutant lines also displayed a progressively lower sensorimotor response to a singular acoustic stimulus from 5-7dpf. Next, we tested the habituation response of the mutant lines to series of acoustic taps. We found both mutant lines habituated faster than their siblings, and that vps11(plt) mutants habituated faster than the vps11(−/−) mutants. Together, these data suggest that loss of Vps11 function results in progressive visual and sensorimotor abnormalities in the zebrafish vps11(plt) and vps11(−/−) mutant lines. This is the first study to characterize behavioral deficits in a vertebrate model of Vps11-dependent gLE. The mutants and behavioral assays described here could be a valuable model system in which to test potential pharmacological interventions for gLE.
... 7 The CORVET complex comprises 6 subunits (VPS3, VPS8, VPS11, VPS16, VPS18, and VPS33A) and regulates early endosome fusion and endosomal maturation. 8,9 The HOPS complex also consists of 6 subunits (VPS11, VPS16, VPS18, VPS39, VPS41, and VPS33A) and plays an essential role in facilitating the fusion of lysosomes with late endosomes and autophagosomes. 10 One homozygous missense variant in VPS16 has been associated with adolescent-onset primary dystonia in a consanguineous family. ...
... Biallelic variants in VPS11, VPS33A, and VPS41 have been associated with hypomyelinating leukodystrophy type 12, mucopolysaccharidosis-plus syndrome, and early-onset dystonia with ataxia, respectively. 8,9,12,14,15 Here, we provide data on rare VPS16 variants observed in patients with dystonia and patients without dystonia and elaborate on our interpretation of VPS16 pLoFs affecting different transcripts. In addition, we describe detailed disease course of the 4 identified patients with dystonia and compared their clinical presentations with previously published cases. ...
Background and Objectives
Our objective was to improve rare variant interpretation using statistical measures as well as publicly accessible annotation of expression levels and tissue specificity of different splice isoforms. We describe rare VPS16 variants observed in patients with dystonia and patients without dystonia, elaborate on our interpretation of VPS16 variants affecting different transcripts, and provide detailed clinical description of the movement disorder caused by VPS16 variants.
Methods
In-house exome and genome data sets (n = 11,539) were screened for rare heterozygous missense and putative loss-of-function (pLoF) variants in VPS16 . Using pext (proportion expressed across transcripts) values from the Genome Aggregation Database (gnomAD), we differentiated variants affecting weakly and highly expressed exons/transcripts and applied statistical measures to systematically identify disease-associated genetic variation among patients with dystonia (n = 280).
Results
Six different heterozygous pLoFs in VPS16 transcripts were identified in 13 individuals. Three of these pLoFs occurred in 9 individuals with different phenotypes, and 3 pLoFs were identified in 4 unrelated individuals with early-onset dystonia. Although pLoFs were enriched in the dystonia cohort (n = 280; p = 2.04 × 10 ⁻⁴ ; 4/280 cases vs 9/11,259 controls; Fisher exact test), it was not exome-wide significant. According to the pext values in gnomAD, all 3 pLoFs observed in the patients with dystonia were located in the highly expressed canonical transcript ENST00000380445.3, whereas 2 of 3 pLoFs detected in 8 individuals without dystonia were located in the first exon of the noncanonical transcript ENST00000380443.3 that is weakly expressed across all tissues. Taking these biological implications into account, pLoFs involving the canonical transcript were exome-wide significantly enriched in patients with dystonia ( p = 1.67 × 10 ⁻⁶ ; 4/280 cases vs 1/11,259 controls; Fisher exact test). All VPS16 patients showed mild progressive dystonia with writer's cramp as the presenting symptom between age 7 and 34 years (mean 20 years) that often progressed to generalized dystonia and was even accompanied by hyperkinetic movements and myoclonus in 1 patient.
Discussion
Our data provide strong evidence for VPS16 pLoFs to be implicated in dystonia and knowledge on exon resolution expression levels as well as statistical measures proved to be useful for variant interpretation.
