VPS13A Mutation Research Articles

Physiological and Pathogenesis Significance of Chorein in Health and Disease

This comprehensive review explores the physiological and pathophysiological significance of VPS13A, a protein encoded by the VPS13A gene. The VPS13A gene is associated with Chorea-acanthocytosis (ChAc), a rare hereditary neurodegenerative disorder. The review covers essential aspects, beginning with the genetics of VPS13A, highlighting its role in the pathogenesis of ChAc, and addressing the spectrum of genetic variants involved. It delves into the structure and function of the VPS13A protein, emphasizing its presence in various tissues and its potential involvement in protein trafficking and lipid homeostasis. Molecular functions of VPS13A in the brain tissue and other cell types or tissues with respect to their role in cytoskeletal regulation and autophagy are explored. Finally, it explores the intriguing link between VPS13A mutations, lipid imbalances, and neurodegeneration, shedding light on future research directions. Overall, this review serves as a comprehensive resource for understanding the pivotal role of VPS13A in health and disease, particularly in the context of ChAc. Key words: Chorein • Tumor • Actin • Microfilament • Gene expression • Chorea-acanthocytosis

Exome sequencing of choreoacanthocytosis reveals novel mutations in VPS13A and co-mutation in modifier gene(s)

Choreoacanthocytosis, one of the forms of neuroacanthocytosis, is caused by mutations in vacuolar protein sorting-associated protein A (VPS13A), and is often misdiagnosed with other form of neuroacanthocytosis with discrete genetic defects. The phenotypic variations among the patients with VPS13A mutations significantly obfuscates the understanding of the disease and treatment strategies. In this study, two unrelated cases were identified, exhibiting the core phenotype of neuroacanthocytosis but with considerable clinical heterogeneity. Case 1 presented with an additional Parkinsonism phenotype, whereas seizures were evident in case 2. To decipher the genetic basis, whole exome sequencing followed by validation with Sanger sequencing was performed. A known homozygous pathogenic nonsense mutation (c.799C > T; p.R267X) in exon 11 of the VPS13A gene was identified in case 1 that resulted in a truncated protein. A novel missense mutation (c.9263T > G; p.M3088R) in exon 69 of VPS13A identified in case 2 was predicted as pathogenic. In silico analysis of the p.M3088R mutation at the C-terminus of VPS13A suggests a loss of interaction with TOMM40 and may disrupt mitochondrial localization. We also observed an increase in mitochondrial DNA copy numbers in case 2. Mutation analysis revealed benign heterozygous variants in interacting partners of VPS13A such as VAPA in case 1. Our study confirmed the cases as ChAc and identified the novel homozygous variant of VPS13A (c.9263T > G; p.M3088R) within the mutation spectrum of VPS13A-associated ChAc. Furthermore, mutations in VPS13A and co-mutations in its potential interacting partner(s) might contribute to the diverse clinical manifestations of ChAc, which requires further study.

VPS13 Forum Proceedings: XK, XK-Related and VPS13 Proteins in Membrane Lipid Dynamics.

In 2020, the pandemic interrupted the series of biannual International Neuroacanthocytosis Meetings that brought together clinicians, scientists, and patient groups to share research into a small group of devastating genetic diseases that combine both acanthocytosis (deformed red blood cells) and neurodegeneration with movement disorders. This Meeting Report describes talks at the 5th VPS13 Forum in January 2022, one of a series of online meetings held to fill the gap. The meeting addressed the basic biology of two key proteins implicated in chorea-acanthocytosis (mutations in VPS13A) and McLeod syndrome (mutations in XK). In a remarkable confluence of ideas, the speakers described different aspects of a single functional unit that comprises of VPS13A and XK proteins working together. Conditions caused by VPS13 (A-D) gene family mutations and related genes, such as XK, previously footnote knowledge, seem to turn central for a novel disease paradigm: bulk lipid transfer disorders.

Interaction between VPS13A and the XK scramblase is important for VPS13A function in humans.

VPS13 family proteins form conduits between the membranes of different organelles through which lipids are transferred. In humans, there are four VPS13 paralogs, and mutations in the genes encoding each of them are associated with different inherited disorders. VPS13 proteins contain multiple conserved domains. The Vps13 adaptor-binding (VAB) domain binds to adaptor proteins that recruit VPS13 to specific membrane contact sites. This work demonstrates the importance of a different domain in VPS13A function. The pleckstrin homology (PH) domain at the C-terminal region of VPS13A is required to form a complex with the XK scramblase and for the co-localization of VPS13A with XK within the cell. Alphafold modeling was used to predict an interaction surface between VPS13A and XK. Mutations in this region disrupt both complex formation and co-localization of the two proteins. Mutant VPS13A alleles found in patients with VPS13A disease truncate the PH domain. The phenotypic similarities between VPS13A disease and McLeod syndrome caused by mutations in VPS13A and XK, respectively, argue that loss of the VPS13A-XK complex is the basis of both diseases.

A partnership between the lipid scramblase XK and the lipid transfer protein VPS13A at the plasma membrane

Chorea-acanthocytosis (ChAc) and McLeod syndrome are diseases with shared clinical manifestations caused by mutations in VPS13A and XK, respectively. Key features of these conditions are the degeneration of caudate neurons and the presence of abnormally shaped erythrocytes. XK belongs to a family of plasma membrane (PM) lipid scramblases whose action results in exposure of PtdSer at the cell surface. VPS13A is an endoplasmic reticulum (ER)-anchored lipid transfer protein with a putative role in the transport of lipids at contacts of the ER with other membranes. Recently VPS13A and XK were reported to interact by still unknown mechanisms. So far, however, there is no evidence for a colocalization of the two proteins at contacts of the ER with the PM, where XK resides, as VPS13A was shown to be localized at contacts between the ER and either mitochondria or lipid droplets. Here we show that VPS13A can also localize at ER-PM contacts via the binding of its PH domain to a cytosolic loop of XK, that such interaction is regulated by an intramolecular interaction within XK, and that both VPS13A and XK are highly expressed in the caudate neurons. Binding of the PH domain of VPS13A to XK is competitive with its binding to intracellular membranes that mediate other tethering functions of VPS13A. Our findings support a model according to which VPS13A-dependent lipid transfer between the ER and the PM is coupled to lipid scrambling within the PM. They raise the possibility that defective cell surface exposure of PtdSer may be responsible for neurodegeneration.

VPS13A and VPS13C Influence Lipid Droplet Abundance.

Lipid transfer proteins mediate the exchange of lipids between closely apposed membranes at organelle contact sites and play key roles in lipid metabolism, membrane homeostasis, and cellular signaling. A recently discovered novel family of lipid transfer proteins, which includes the VPS13 proteins (VPS13A-D), adopt a rod-like bridge conformation with an extended hydrophobic groove that enables the bulk transfer of membrane lipids for membrane growth. Loss of function mutations in VPS13A and VPS13C cause chorea acanthocytosis and Parkinson’s disease, respectively. VPS13A and VPS13C localize to multiple organelle contact sites, including endoplasmic reticulum (ER) – lipid droplet (LD) contact sites, but the functional roles of these proteins in LD regulation remains mostly unexplored. Here we employ CRISPR-Cas9 genome editing to generate VPS13A and VPS13C knockout cell lines in U-2 OS cells via deletion of exon 2 and introduction of an early frameshift. Analysis of LD content in these cell lines revealed that loss of either VPS13A or VPS13C results in reduced LD abundance under oleate-stimulated conditions. These data implicate two lipid transfer proteins, VPS13A and VPS13C, in LD regulation.

Therapeutic targeting of Lyn kinase to treat chorea-acanthocytosis

Chorea-Acanthocytosis (ChAc) is a devastating, little understood, and currently untreatable neurodegenerative disease caused by VPS13A mutations. Based on our recent demonstration that accumulation of activated Lyn tyrosine kinase is a key pathophysiological event in human ChAc cells, we took advantage of Vps13a−/− mice, which phenocopied human ChAc. Using proteomic approach, we found accumulation of active Lyn, γ-synuclein and phospho-tau proteins in Vps13a−/− basal ganglia secondary to impaired autophagy leading to neuroinflammation. Mice double knockout Vps13a−/− Lyn−/− showed normalization of red cell morphology and improvement of autophagy in basal ganglia. We then in vivo tested pharmacologic inhibitors of Lyn: dasatinib and nilotinib. Dasatinib failed to cross the mouse brain blood barrier (BBB), but the more specific Lyn kinase inhibitor nilotinib, crosses the BBB. Nilotinib ameliorates both Vps13a−/− hematological and neurological phenotypes, improving autophagy and preventing neuroinflammation. Our data support the proposal to repurpose nilotinib as new therapeutic option for ChAc patients.

Targeting Copper Homeostasis Improves Functioning of vps13Δ Yeast Mutant Cells, a Model of VPS13-Related Diseases.

Ion homeostasis is crucial for organism functioning, and its alterations may cause diseases. For example, copper insufficiency and overload are associated with Menkes and Wilson’s diseases, respectively, and iron imbalance is observed in Parkinson’s and Alzheimer’s diseases. To better understand human diseases, Saccharomyces cerevisiae yeast are used as a model organism. In our studies, we used the vps13Δ yeast strain as a model of rare neurological diseases caused by mutations in VPS13A–D genes. In this work, we show that overexpression of genes encoding copper transporters, CTR1, CTR3, and CCC2, or the addition of copper salt to the medium, improved functioning of the vps13Δ mutant. We show that their mechanism of action, at least partially, depends on increasing iron content in the cells by the copper-dependent iron uptake system. Finally, we present that treatment with copper ionophores, disulfiram, elesclomol, and sodium pyrithione, also resulted in alleviation of the defects observed in vps13Δ cells. Our study points at copper and iron homeostasis as a potential therapeutic target for further investigation in higher eukaryotic models of VPS13-related diseases.

Phenotypic variability in chorea-acanthocytosis associated with novel VPS13A mutations.

ObjectiveTo perform a comprehensive characterization of a cohort of patients with chorea-acanthocytosis (ChAc) in Sweden.MethodsClinical assessments, targeted genetic studies, neuroimaging with MRI, [18F]-fluorodeoxyglucose (FDG) PET, and dopamine transporter with 123I FP-CIT (DaTscan) SPECT. One patient underwent magnetic resonance spectroscopy (MRS).ResultsFour patients living in Sweden but with different ethnical backgrounds were included. Their clinical features were variable. Biallelic VPS13A mutations were confirmed in all patients, including 3 novel mutations. All tested patients had either low or absent chorein levels. One patient had progressive caudate atrophy. Investigation using FDG-PET revealed severe bilateral striatal hypometabolism, and DaTscan SPECT displayed presynaptic dopaminergic deficiency in 3 patients. MRS demonstrated reduced N-acetylaspartate/creatine (Cr) ratio and mild elevation of both choline/Cr and combined glutamate and glutamine/Cr in the striatum in 1 case. One patient died during sleep, and another was treated with deep brain stimulation, which transiently attenuated feeding dystonia but not his gait disorder or chorea.ConclusionsLarger longitudinal neuroimaging studies with different modalities, particularly MRS, are needed to determine their potential role as biomarkers for ChAc.

Novel pathogenic VPS13A mutation in Moroccan family with Choreoacanthocytosis: a case report

BackgroundChoreoacanthocytosis (ChAc), is a rare neurodegenerative disease, characterized by movement disorders and acanthocytosis in the peripheral blood smears, and various neurological, neuropsychiatric and neuromuscular signs. It is caused by mutations in VPS13A gene with autosomal recessive pattern of inheritance.Case presentationHere we report two patients belonging to a consanguineous Moroccan family who present with movement disorder pathology. They were suspected to have choreoacanthocytosis according to biological, clinical and radiological finding. Thus, whole-exome sequencing was performed for precise diagnosis and identified a homozygous novel nonsense mutation c.337C > T (p.Gln113*) in exon 5 of VPS13A in the two affected siblings.ConclusionHere, we report a novel nonsense p.Gln113* mutation in VPS13A identified by whole-exome sequencing, which caused ChAc in a Moroccan family. This is the first description of ChAc in Morocco with genetic confirmation, that expands the mutation diversity of VPS13A and provide clinical, neuroimaging and deep brain stimulation findings.

Progress in the Diagnosis and Management of Chorea-acanthocytosis.

Chorea-acanthocytosis (ChAc) is the most common subtype of neuroacanthocytosis syndrome, characterized by the presence of acanthocytes and neurological disorders. It is thought to be caused by VPS13A mutations. Characteristic movement disorders in ChAc is choreiform movements affecting both trunk and extremities and prominent orolingual dyskinesia is pathognomonic. Acanthocytosis in peripheral blood smear, elevated serum creatine kinase and atrophy of heads of caudate nuclei and dilation of the anterior horn of the lateral ventricles in magnetic resonance imaging could assist the diagnosis of ChAc. Botulinum toxin injection is a possible treatment for the typical orofacial dystonia. Deep brain stimulation is a novel surgical treatment modality. Most cases chose globus pallidus internus as target. Patients with dystonia as a major manifestation will benefit more from high-frequency stimulation and those with major findings of chorea and dysarthria are suitable for low-frequency stimulation. More evidence of long-term outcomes is warranted.

Deficiency in the expression of Vps13C is associated with altered retinal and lens development in mice

SummaryWhile performing genotyping screening in the German Mouse Clinic we identified the Vps13C mouse mutant with eye phenotype where the homozygous mutant mice show signs of neurodegeneration, indicated by a reduction in the total retinal thickness, additionally the retinal blood vessels showed a pattern with structural alteration. Eye histology revealed the display of lipid‐like droplets in the retinal layers and in the anterior lens matrix. VPS 13C is a member of the VPS13 family of vacuolar protein sorting‐associated proteins highly conserved throughout eukaryotic evolution. While mutations in VPS13A and VPS13B cause the genetic diseases chorea‐acanthocytosis (ChAc) and Cohen syndrome, respectively, VSP13C is reported to be associated with Parkinsons disease and late onset Alzheimer's disease (LOAD). Moreover VPS13C has recently been found to be involved in the protein degradation through the ubiquitin being closely associated with lipid droplets and lysosomes. Human diseases are caused by the dysregulated accumulation of ubiquitinated protein aggregates, including neurodegenerative disorders. We believe Vps13c could open novel avenues for uncovering new treatments of metabolic and neurodegenerative disorders.

Axial Sensory Tricks in Chorea-Acanthocytosis: Insights into Phenomenology.

BackgroundTrunk flexion and axial extension are characteristic symptoms of chorea–acanthocytosis (ChAc).Phenomenology ShownA 41-year-old male with ChAc (confirmed by VPS13A mutations) reported that his involuntary axial movements were significantly ameliorated by either folding his arms over his chest or putting his hands behind his head.Educational ValueThese apparent “sensory tricks” suggest a dystonic pathophysiology, and also merit further study to analyze their potential for symptom control in ChAc.

Axial Sensory Tricks in Chorea–Acanthocytosis: Insights into Phenomenology

<strong>Background:</strong> Trunk flexion and axial extension are characteristic symptoms of chorea–acanthocytosis (ChAc). <strong>Phenomenology Shown:</strong> A 41-year-old male with ChAc (confirmed by VPS13A mutations) reported that his involuntary axial movements were significantly ameliorated by either folding his arms over his chest or putting his hands behind his head. <strong>Educational Value:</strong> These apparent ‘‘sensory tricks’’ suggest a dystonic pathophysiology, and also merit further study to analyze their potential for symptom control in ChAc.

Chorea-acanthocytosis:Report of 1 case

Abstract: To report 1 case of chorea-acanthocytosis (ChAc). The case was studied with clinical symptoms,signs, biochemical,red blood cell morphology and gene sequencing observation.The patient’s main symptoms and signs were mouth-tongue dystonia, tongue bite, walking instability, seizures,abated gag reflex,decreased muscle tone,abated tendon reflex.Blood lactate dehydrogenase (LDH, 459 U/L) ,creatine kinase (CK, 2806 U/L), prolactin (PRL, 38.35 ng/ml)were increased.There were large number of acanthocyte in blood smear(50% of the red blood cell),and there were lot acanthocyte in blood smear of her parents(30% of father and 25% of mother).Electromyography showed peripheral nerve damage. Brain MRI scans showed caudate nucleus atrophy.Gene sequencing detected mutations in VPS13A. According to the clinical features of patients, blood LDH, CK, PRL,blood smear, brain MRI imaging characteristics, gene sequencing result, the patient diagnosed ChAc.The disease treatment is limited, need clinical tracking,and explore effective methods of diagnosis and treatment. Keywords: chorea;acanthocyteosis

Yeast Vps13 promotes mitochondrial function and is localized at membrane contact sites.

The Vps13 protein family is highly conserved in eukaryotic cells. Mutations in human VPS13 genes result in a variety of diseases, such as chorea acanthocytosis (ChAc), but the cellular functions of Vps13 proteins are not well defined. In yeast, there is a single VPS13 orthologue, which is required for at least two different processes: protein sorting to the vacuole and sporulation. This study demonstrates that VPS13 is also important for mitochondrial integrity. In addition to preventing transfer of DNA from the mitochondrion to the nucleus, VPS13 suppresses mitophagy and functions in parallel with the endoplasmic reticulum-mitochondrion encounter structure (ERMES). In different growth conditions, Vps13 localizes to endosome-mitochondrion contacts and to the nuclear-vacuole junctions, indicating that Vps13 may function at membrane contact sites. The ability of VPS13 to compensate for the absence of ERMES correlates with its intracellular distribution. We propose that Vps13 is present at multiple membrane contact sites and that separation-of-function mutants are due to loss of Vps13 at specific junctions. Introduction of VPS13A mutations identified in ChAc patients at cognate sites in yeast VPS13 are specifically defective in compensating for the lack of ERMES, suggesting that mitochondrial dysfunction might be the basis for ChAc.

Autosomal recessive transmission of chorea-acanthocytosis confirmed

We would like to draw attention to new genetic data recently reported [8] on a patient previously described as suffering from chorea-acanthocytosis (ChAc) with autosomal dominant transmission [7] and for whom neuropathological findings were published in this journal in 2009 [4]. At that time we questioned the apparent inheritance, given the limitations of the molecular methodology employed, and the lack of support for this mode of transmission otherwise found [2]. A correction concerning the original publication by Saiki et al. [7] has recently been published [1] stating: “an error in sequencing occurred and the inheritance pattern should have been reported as autosomal recessive (pseudodominant)”. This erratum reflects the findings reported by Tomiyasu et al. [8] whose patient no. 22 was identified with III-3 from the pedigree originally published and is identical with the patient in whom autopsy findings had been described in this journal [4]. This subject was also reported as case 1 of a further clinical study [6]. The new molecular findings describe compound heterozygous VPS13A mutations in him and also in his affected sister: 1305G>A in exon 15 and 8035G>A in exon 57. The nomenclature of the latter mutation was corrected from 8295G>A in the original report [4, 7]. The patients’ mother (II-4) was shown to be an asymptomatic carrier of a single heterozygous 1305G>A mutation. The father of the postmortem case of Ishida et al. [4], by conclusion a carrier of the 8035G>A mutation, was said to be suffering from early onset hyperkinesia as did other family members [5]. Unfortunately, no further analyses on DNA were feasible and the presence of mutations in other genes, e.g., IT15, responsible for the supposedly dominant features observed in this man, his father, his two sisters and a sister’s son could not be investigated [7]. In addition, there is still a possibility of subclinical involvement in subjects who carry a single heterozygous VPS13A mutation although, so far, no convincing evidence has yet been put forward to support that claim [3, 9]. In summary, the suggestion of dominant transmission of a condition recognized as an autosomal recessive trait (OMIM 200150) has eventually been put to rest in the autopsy case reported in this journal in 2009 and one source of confusion has been removed.

Rapid genetic diagnosis in single‐gene movement disorders

Rapid genetic diagnosis in single‐gene movement disorders

Chorea-acanthocytosis with upper motor neuron degeneration and 3419_3420 delCA and 3970_3973 delAGTC VPS13A mutations

Chorea-acanthocytosis (ChAc) is caused by loss of function mutations of VPS13A gene encoding the large disease protein named chorein [8, 10]. However, McLeod syndrome, Huntington’s disease-like 2, and pantothenate kinase-associated neurodegeneration also present with choreic movements and acanthocytosis. To our knowledge, only five autopsy cases of genetically proven ChAc have been reported [1, 6, 7, 9, 11]. Here, we report an autopsy case of ChAc with upper motor neuron degeneration and with novel VPS13A mutations. A Japanese man developed generalized tonic-clonic seizure at age of 35. At age of 37, he presented with postural instability due to lapse of knees, self-mutilation, orofacial dyskinesia with tongue-biting, involuntary vocalization, and pill-rolling tremor in the left hand. Blood smear showed that 30% of erythrocytes were acanthocytes after 5 min of incubation in normal saline (normal, less than 1%) [5]. Neurological examination showed that deep tendon reflexes in all limbs were absent. Brain CT and MRI revealed mild atrophy of the bilateral caudate nuclei. Genetic analysis revealed no expansion of CAG repeats in the genes of Huntington’s disease and dentatorubral-pallidoluysian atrophy. Expression of Kell antigen of erythrocytes was normal. At age of 42, he was bound to a wheelchair and gradually unable to move his left upper and lower extremities. At age of 47, congestive heart failure became apparent and he died suddenly. Postmortem examination revealed severe degeneration of the neostriatum (Fig. 1a, b). Moderate neuronal loss was found in the substantia nigra pars reticulata and mild in the spinal anterior horn. These findings were consistent with histopathological features of ChAc [12]. Furthermore, neuronal loss in the motor cortex with pyramidal tract degeneration, more severe on the right side, was evident (Fig. 1c–i). No Bunina bodies or TDP-43-positive inclusions were noted in the upper and lower motor neurons. Genetic analysis revealed two novel heterozygous mutations in exon 32 (c.3419_3420 delCA) and exon 35 (c.3970_3973 delAGTC) of the VPS13A gene (Fig. 2). Both mutations, which lead to premature stop codon further downstream resulting in truncated chorein, are considered to be pathogenic. Although epilepsy has been well recognized in patients with ChAc [2], the cortical degeneration in our case is not due to epilepsy, because of the absence of neuronal loss or gliosis in the medial temporal lobe. Moreover, no Bunina bodies or TDP-43-immunoreactive inclusions were noted in our case. Therefore, complication of neurodegenerative diseases causing bilateral pyramidal tract degeneration, such as amyotrophic lateral sclerosis and frontotemporal lobar degeneration with motor neuron disease, appeared to be excluded. Although the inheritance of ChAc is widely known as autosomal recessive, single heterozygous VPS13A Y. Miki (&) F. Mori K. Wakabayashi Department of Neuropathology, Institute of Brain Science, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki 036-8562, Japan e-mail: yasuomiki@hotmail.com

Dominant transmission of chorea-acanthocytosis with VPS13A mutations remains speculative

Dominant transmission of chorea-acanthocytosis with VPS13A mutations remains speculative