Case Report: Chorea-Acanthocytosis Presents as Epilepsy in a Consanguineous Family With a Nonsense Mutation of in VPS13A

A novel cryptic splice donor due to synonymous variant in VPS13A as an underlying cause of a chorea-acanthocytosis in a large family

Chorea-acanthocytosis (ChAc) is a rare inherited disease of the nervous system. In this disease the neurological manifestations are associated with acanthocytosis of the red blood cells. The clinical features appear in the third to fourth decades of life. Generalized weakness, choreiform movement disorder, decline in cognition, and psychiatric symptoms are the characteristic features of the disease. The differential diagnosis between Huntington's disease and ChAc is difficult because both the diseases share similar neurological features. Herein, we recruited a large family with multiple individuals initially diagnosed as having Huntington's disease. Analysis of the DNA samples of affected individuals by exome sequencing detected a synonymous variant (NM_001018037.2; c.5040C > T) in the VPS13A. Multiple splice site detection tools were used to predict the potential pathogenicity of the novel synonymous variant. The variant, identified in this study, was predicted to be a cryptic splice donor site that may lead to aberrant pre-mRNA splicing. Reverse transcriptase PCR analyses of patient blood-derived RNA showed activation of a cryptic mid-exon splice donor, leading to frameshift. The variant was confirmed in all other affected and unaffected individuals using Sanger sequencing. This is the first report of synonymous variants of VPS13A as an underlying cause of ChAc. Our results provide the first direct evidence of the involvement of a synonymous variant of VPS13A in ChAc. Additionally, this study emphasized the importance of considering VPS13A gene mutations in the screening of Huntington's patients.

Identification of pivotal genes and pathways in Chorea-acanthocytosis using comprehensive bioinformatic analysis

Chorea-acanthocytosis (ChAc), an autosomal recessive disorder, is associated with cognitive and behavioral abnormalities. Previous studies were focused around exploring the functional annotation of VPS13A gene in ChAc, whereas the genetic labyrinth underlying this disease and plausible drug targets were underexplored. In the present study, we have identified the pivotal genes and molecular pathways implicated in ChAc using comprehensive bioinformatics analysis. In our analysis we found 27 distinct genes in Homo sapiens linked to ChAc, out of which 15 were selected as candidate genes for enrichment analysis based on their Gene Ontology (GO) annotations and involvement in relevant molecular pathways. By constructing a Protein-Protein Interaction (PPI) network consisting of 26 nodes and 62 edges, we identified two gene modules. Subsequently, using the MCODE algorithm, we identified 6 hub genes-ATN1, JPH3, TBP, VPS13A, DMD, and HTT-as core candidates. These hub genes are primarily associated with processes such as neuron development and differentiation, the CAMKK-AMPK signaling cascade, ion transmembrane transport systems, and protein localization. Furthermore, using drug gene databank we identified 23 FDA-approved drugs that possess the propensity to target 3 out of the 6 identified hub genes. We believe that our findings could open promising avenues for potential therapeutic interventions in ChAc.

Identification of four novel mutations in VSP13A in Iranian patients with Chorea-acanthocytosis (ChAc)

Chorea-acanthocytosis (ChAc) is a rare autosomal recessive neurodegenerative disorder characterized by a variety of involuntary movements, predominantly chorea, and the presence of acanthocytosis in peripheral blood smears. ChAc is caused by mutations in the vacuolar protein sorting-associated protein 13A (VPS13A) gene. The aim of the present study was to conduct a clinical and genetic analysis of five patients with suspected ChAc in Iran. This study included five patients who were referred to the genetic department of the Endocrinology and Metabolism Research Institute between 2020 and 2022, with a suspicion of ChAc. Clinical features and the presence of characteristic MRI findings were evaluated in the patients. Whole-exome sequencing (WES) followed by Sanger sequencing was employed to identify the disease-causing variants. The functional effects of novel mutations were analyzed by specific bioinformatics prediction tools. WES and data analysis revealed the presence of five distinct VPS13A mutations in the patients, four of which were novel. These included one nonsense mutation (p.L984X), and three splice site mutations (c.755-1G>A, c.144+1 G>C, c.2512+1G>A). All mutations were validated by Sanger sequencing, and in silico analysis predicted that all mutations were pathogenic. This study provides the first molecular genetic characteristics of Iranian patients with ChAc, identifying four novel mutations in the VPS13A gene. These findings expand the VPS13A variants spectrum and confirm the clinical variability in ChAc patients.

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.

Striking a balance: PIP2 and PIP3 signaling in neuronal health and disease

Phosphoinositides are membrane phospholipids involved in a variety of cellular processes like growth, development, metabolism, and transport. This review focuses on the maintenance of cellular homeostasis of phosphatidylinositol 4,5-bisphosphate (PIP₂), and phosphatidylinositol 3,4,5-trisphosphate (PIP₃). The critical balance of these PIPs is crucial for regulation of neuronal form and function. The activity of PIP₂ and PIP₃ can be regulated through kinases, phosphatases, phospholipases and cholesterol microdomains. PIP₂ and PIP₃ carry out their functions either indirectly through their effectors activating integral signaling pathways, or through direct regulation of membrane channels, transporters, and cytoskeletal proteins. Any perturbations to the balance between PIP₂ and PIP₃ signaling result in neurodevelopmental and neurodegenerative disorders. This review will discuss the upstream modulators and downstream effectors of the PIP₂ and PIP₃ signaling, in the context of neuronal health and disease.

Case Report: Exome Sequencing Identified a Novel Frameshift Mutation of α-Actin 1 in a Chinese Family With Macrothrombocytopenia and Mild Bleeding

Inherited macrothrombocytopenia (IMTP) is a rare disorder characterized by a reduced platelet count and abnormally large platelets. The main clinical symptom of IMTP is mild bleeding in some patients. At present, more than 30 genes have been identified in patients with syndromic and non-syndromic IMTP. In this study, a 3-year-old boy and his mother who presented with mild epistaxis and/or gingival bleeding were diagnosed as having IMTP. Wen then selected whole sequencing to explore the genetic lesion of the patients. After data filtering and mutation validation, a novel frameshift mutation (NM_001130004: c.398_399insTGCG, p.F134AfsX60) of α-actin 1 (ACTN1) was identified in the proband and his mother but absent in other unaffected individuals. Previous studies have proven that mutations in ACTN1 may lead to IMTP with mild to absent bleeding phenotype. The novel mutation, resulting in a truncated protein in exon 4 of the ACTN1 gene, was absent in the public database, such as 1000G and genomAD. Further Western blot revealed that the expression of α-actin 1 in the proband was decreased overtly, which indicated that the novel frameshift mutation may induce non-sense-mediated mRNA decay. In summary, this study not only broadened the variants spectrum of ACTN1 gene, which may contribute to the genetic counseling of IMTP, but also confirmed the diagnosis of IMTP, which may help the management and prognosis for the family members.