Novel SACS mutations identified by whole exome sequencing in a norwegian family with autosomal recessive spastic ataxia of Charlevoix-Saguenay

Documenting manifestations and impacts of autosomal recessive spastic ataxia of Charlevoix-Saguenay to develop patient-reported outcome

BACKGROUND

Autosomal recessive cerebellar ataxias (ARCA) are a group of rare inherited disorders characterized by degeneration or abnormal development of the cerebellum. Autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS) is one of the most prevalent in Europe.

OBJECTIVES

The aim of this study is to provide a better understanding of the manifestations and impacts of ARSACS.

METHODS

A systematic review of the literature was conducted, followed by a qualitative study using semistructured interviews and discussion groups to obtain the experience of people affected.

RESULTS

According to the PROMIS framework, the results show manifestations and impacts in three components of health: physical, mental, and social. Fatigue and struggles with balance and dexterity are the physical manifestations of the disease most often cited by participants. Negative affects such as frustration and depression are among the mental health impacts with some loss in cognitive abilities. Social health is the least documented component; nonetheless, people with the disease report significant impacts in terms of social relationships, activities and work.

CONCLUSIONS

These findings shed new light on the experience of people with recessive ataxia and identify key aspects to assess to improve their overall health.

Genetics of Autosomal Recessive Spastic Ataxia of Charlevoix-Saguenay (ARSACS) and Role of Sacsin in Neurodegeneration

Autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS) is an early-onset neurodegenerative disease that was originally discovered in the population from the Charlevoix-Saguenay-Lac-Saint-Jean (CSLSJ) region in Quebec. Although the disease progression of ARSACS may start in early childhood, cases with later onset have also been observed. Spasticity and ataxia could be common phenotypes, and retinal optic nerve hypermyelination is detected in the majority of patients. Other symptoms, such as pes cavus, ataxia and limb deformities, are also frequently observed in affected individuals. More than 200 mutations have been discovered in the SACS gene around the world. Besides French Canadians, SACS genetics have been extensively studied in Tunisia or Japan. Recently, emerging studies discovered SACS mutations in several other countries. SACS mutations could be associated with pathogenicity either in the homozygous or compound heterozygous stages. Sacsin has been confirmed to be involved in chaperon activities, controlling the microtubule balance or cell migration. Additionally, sacsin may also play a crucial role in regulating the mitochondrial functions. Through these mechanisms, it may share common mechanisms with other neurodegenerative diseases. Further studies are needed to define the exact functions of sacsin. This review introduces the genetic mutations discovered in the SACS gene and discusses its pathomechanisms and its possible involvement in other neurodegenerative diseases.

Novel frameshift mutation in the SACS gene causing spastic ataxia of charlevoix-saguenay in a consanguineous family from the Arabian Peninsula: A case report and review of literature

BACKGROUND

Familial cases of autosomal recessive spastic ataxia of charlevoix-saguenay have not been reported in the Arabian Peninsula, although the consanguineous marriage rate is very high. We report the first family from the Arabian Peninsula harboring a novel frameshift mutation in the SACS gene.

CASE SUMMARY

A 33-year-old man presented to our neurology clinic with balance problems and weakness of distal upper and lower limbs. He was previously clinically diagnosed with Friedreich's ataxia. However, the severity of polyneuropathy and the electrodiagnostic studies (EDX) findings are atypical features of Friedreich’s ataxia, and the deterioration was attributed to diabetic neuropathy. Close examination of other family members identified cerebellar ataxia, lower-limb pyramidal signs, peripheral neuropathy, and magnetic resonance imaging findings characterized by pontine linear hypointensities. Genetic testing for Friedreich’s ataxia did not yield a diagnosis. Whole exome sequencing identified a novel frameshift germline mutation in the SACS gene termed c.5824_5827delTACT using the transcript NM_014363.5, which is predicted to cause premature termination of the sacsin protein at amino acid position 1942 (p.Tyr1942Metfs*9) and disrupts the sacsin SRR3 and domains downstream from it. The mutation segregated with the disease in the family.

CONCLUSION

Our data add to the spectrum of mutations in the SACS gene and argues for a need to implement suitably integrated clinical and diagnostic services, including next generation sequencing technology, to better classify ataxia in this area of the world.

[Spastic ataxia of Charlevoix-Saguenay: the first Russian case report and literature review]

Spastic ataxia of Charlevoix-Saguenay (ARSACS) is a rare autosomal recessive neurodegenerative disease related to SACS gene and characterized by cerebellar, pyramidal and some other signs. The disease was delineated in Quebec, where it cumulates due to founder effect and has similar phenotype with very early onset. ARSACS in other populations is more variable. The first Russian case of ARSACS in a 37-year-old woman, an only patient in a Lak (one of Dagestan ethnicities) family, is presented. Along with main typical features, she had atypical late disease onset (in 32 years) and moderate cognitive decline. MPS-panel 'hereditary paraplegias' detected an earlier reported homo- or hemizygous mutation c.72276C>T (p.Arg2426Stop) in SACS exon 10.

Complicated paroxysmal kinesigenic dyskinesia associated with SACS mutations

Background

Autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS) is caused by pathogenic variants in the SACS gene and is characterized by ataxia, peripheral neuropathy, pyramidal impairment and episodic conditions such as epilepsy. Paroxysmal kinesigenic dyskinesia (PKD) had not been previously described in ARSACS.

Methods

We analyzed clinical manifestations and performed whole-exome sequencing (WES) in two independent patients with ARSACS and PKD. Both patients' parents were unaffected. Genetic data were filtered for potential pathogenic variants, searching for de novo mutations suggestive of a dominant disease model or homozygous and compound heterozygous variants of a recessive model. Potential mutations that existed in both patients were generated and subjected to Sanger sequencing. The WES results of 163 PKD patients without additional symptoms from previous experiments were also reviewed.

Results

Novel compound heterozygous mutations in the SACS gene were identified in Patient 1 (p.P3007S and p.H3392fs), and a novel homozygous truncating mutation (p.W1376X) was identified in Patient 2. In both patients, each mutant allele was inherited from one of his or her unaffected parents. All 3 mutations were absent in 196 ethnic-matched control chromosomes or in data from the 1000 Genomes Project. No pathogenic variants associated with paroxysmal diseases, especially PKD and episodic ataxia, were identified. In PKD patients without additional symptoms, no homozygous or compound heterozygous variants in the SACS gene were detected.

Conclusions

This study expands the clinical phenotype of ARSACS and suggests the inclusion of SACS screening in patients with PKD plus ARSACS.

A novel homozygous SACS mutation identified by whole exome sequencing-genotype phenotype correlations of all published cases

ARSACS is an autosomal recessive disorder characterized by ataxia, spasticity, and polyneuropathy. A plethora of worldwide distributed mutations have been described so far. Here, we report two brothers, born to non-consanguineous parents, presenting with cerebellar ataxia and peripheral neuropathy. Whole-exome sequencing revealed the presence of a novel homozygous variant in the SACS gene. The variant was confirmed by Sanger sequencing and found at heterozygous state in both parents. This is the first reported mutation in this gene, in Greek population. This case report further highlights the growing trend of identifying genetic diseases previously restricted to single, ethnically isolated regions in many different ethnic groups worldwide. Additionally, we performed a systematic review of all published cases with SACs mutations. ARSACS seems to be an important cause of ataxia and many different types of mutations have been identified, mainly located in exon 10. We evaluated the mutation pathogenicity in all previously reported cases to investigate possible phenotype-genotype correlations. We managed to find a correlation between the pathogenicity of mutations, severity of the phenotype, and age of onset of ARSACS. Greater mutation numbers in different populations will be important and mutation-specific functional studies will be essential to identify the pathogenicity of the various ARSACS variants.

Short Review: Investigating ARSACS: models for understanding cerebellar degeneration

Autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS) is an early-onset neurodegenerative disease that includes progressive cerebellar dysfunction. ARSACS is caused by an autosomal recessive loss-of-function mutation in the SACS gene, which encodes for SACSIN. Although animal models are still necessary to investigate the role of SACSIN in the pathology of this disease, more reliable human cellular models need to be generated to better understand the cerebellar pathophysiology of ARSACS. The discovery of human induced pluripotent stem cells (hiPSC) has permitted the derivation of patient-specific cells. These cells have an unlimited self-renewing capacity and the ability to differentiate into different neural cell types, allowing studies of disease mechanism, drug discovery and cell replacement therapies. In this study, we discuss how the hiPSC-derived cerebellar organoid culture offers novel strategies for targeting the pathogenic mutations related to ARSACS. We also highlight the advantages and challenges of this 3D cellular model, as well as the questions that still remain unanswered.

SACS variants are a relevant cause of autosomal recessive hereditary motor and sensory neuropathy

Mutations in the SACS gene have been initially reported in a rare autosomal recessive cerebellar ataxia syndrome featuring prominent cerebellar atrophy, spasticity and peripheral neuropathy as well as retinal abnormalities in some cases (autosomal recessive spastic ataxia of Charlevoix-Saguenay, ARSACS). In the past few years, the phenotypic spectrum has broadened, mainly owing to the availability and application of high-throughput genetic testing methods. We identified nine patients (three sib pairs, three singleton cases) with isolated, non-syndromic hereditary motor and sensory neuropathy (HMSN) who carried pathogenic SACS mutations, either in the homozygous or compound heterozygous state. None of the patients displayed spasticity or pyramidal signs. Ataxia, which was noted in only three patients, was consistent with a sensory ataxia. Nerve conduction and nerve biopsy studies showed mixed demyelinating and axonal neuropathy. Brain MRI scans were either normal or revealed isolated upper vermis atrophy of the cerebellum. Our findings confirm the broad clinical spectrum associated with SACS mutations, including pure polyneuropathy without characteristic clinical and brain imaging manifestations of ARSACS.

Ataxia in children: early recognition and clinical evaluation

Background

Ataxia is a sign of different disorders involving any level of the nervous system and consisting of impaired coordination of movement and balance. It is mainly caused by dysfunction of the complex circuitry connecting the basal ganglia, cerebellum and cerebral cortex.

A careful history, physical examination and some characteristic maneuvers are useful for the diagnosis of ataxia. Some of the causes of ataxia point toward a benign course, but some cases of ataxia can be severe and particularly frightening.

Methods

Here, we describe the primary clinical ways of detecting ataxia, a sign not easily recognizable in children. We also report on the main disorders that cause ataxia in children.

Results

The causal events are distinguished and reported according to the course of the disorder: acute, intermittent, chronic-non-progressive and chronic-progressive.

Conclusions

Molecular research in the field of ataxia in children is rapidly expanding; on the contrary no similar results have been attained in the field of the treatment since most of the congenital forms remain fully untreatable. Rapid recognition and clinical evaluation of ataxia in children remains of great relevance for therapeutic results and prognostic counseling.

Novel SACS mutations associated with intellectual disability, epilepsy and widespread supratentorial abnormalities

We describe eight subjects from two consanguineous families segregating with autosomal recessive childhood onset spastic ataxia, peripheral neuropathy and intellectual disability. The degree of intellectual disability varied from mild to severe and all four affected individuals in one family developed aggressive behavior and epilepsy. Using exome sequencing, we identified two novel truncating mutations (c.2656C>T (p.Gln886*)) and (c.4756_4760delAATCA (p.Asn1586Tyrfs*3)) in the SACS gene responsible for autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS). MRI revealed typical cerebellar and pontine changes associated with ARSACS as well as multiple supratentorial changes in both families as likely contributing factors to the cognitive symptoms. Intellectual disability and behavioral abnormalities have been reported in some cases of ARSACS but are not a part of the characteristic triad of symptoms that includes cerebellar ataxia, spasticity and peripheral neuropathy. Our combined findings bring further knowledge to the phenotypic spectrum, neurodegenerative changes and genetic variability associated with the SACS gene of clinical and diagnostic importance.

Progressive myoclonus epilepsy associated with SACS gene mutations

Pathogenic variants in the SACS gene (OMIM #604490) cause autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS). ARSACS is a neurodegenerative early-onset progressive disorder, originally described in French Canadians, but later observed elsewhere.(1) Whole-exome sequencing of a large group of patients with unclassified progressive myoclonus epilepsies (PMEs) identified 2 patients bearing SACS gene mutations.(2) We detail the PME clinical features associated with SACS mutations and suggest the inclusion of the SACS gene in diagnostic screening of PMEs.

Novel SLC19A3 Promoter Deletion and Allelic Silencing in Biotin-Thiamine-Responsive Basal Ganglia Encephalopathy

Background

Biotin-thiamine responsive basal ganglia disease is a severe, but potentially treatable disorder caused by mutations in the SLC19A3 gene. Although the disease is inherited in an autosomal recessive manner, patients with typical phenotypes carrying single heterozygous mutations have been reported. This makes the diagnosis uncertain and may delay treatment.

Methods and Results

In two siblings with early-onset encephalopathy dystonia and epilepsy, whole-exome sequencing revealed a novel single heterozygous SLC19A3 mutation (c.337T>C). Although Sanger-sequencing and copy-number analysis revealed no other aberrations, RNA-sequencing in brain tissue suggested the second allele was silenced. Whole-genome sequencing resolved the genetic defect by revealing a novel 45,049 bp deletion in the 5’-UTR region of the gene abolishing the promoter. High dose thiamine and biotin therapy was started in the surviving sibling who remains stable. In another patient two novel compound heterozygous SLC19A3 mutations were found. He improved substantially on thiamine and biotin therapy.

Conclusions

We show that large genomic deletions occur in the regulatory region of SLC19A3 and should be considered in genetic testing. Moreover, our study highlights the power of whole-genome sequencing as a diagnostic tool for rare genetic disorders across a wide spectrum of mutations including non-coding large genomic rearrangements.

A novel hemizygous SACS mutation identified by whole exome sequencing and SNP array analysis in a Chinese ARSACS patient

The array of autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS) has expanded worldwide after the first description in the Charlevoix-Saguenay region of Québec. Here, we report a Chinese ARSACS patient presenting progressive peripheral neuropathy (CMTNS2=15) with horizontal gaze nystagmus and mild spastic gait. Genetic studies including whole exome sequencing (WES), Sanger sequencing and single nucleotide polymorphism (SNP) array analysis revealed a novel hemizygous nonsense mutation (c.11803C>T, p.Gln3935X) of SACS and a 1.33Mb deletion involved in SACS on chromosome 13q12.12 in the patient. Our findings highlight the necessity of SACS mutation screening in the gene panel of inherited peripheral neuropathies, and stress the need of testing copy number variation (CNV) in SACS mutation screening.

SNP Analysis and Whole Exome Sequencing: Their Application in the Analysis of a Consanguineous Pedigree Segregating Ataxia

Autosomal recessive cerebellar ataxia encompasses a large and heterogeneous group of neurodegenerative disorders. We employed single nucleotide polymorphism (SNP) analysis and whole exome sequencing to investigate a consanguineous Maori pedigree segregating ataxia. We identified a novel mutation in exon 10 of the SACS gene: c.7962T>G p.(Tyr2654*), establishing the diagnosis of autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS). Our findings expand both the genetic and phenotypic spectrum of this rare disorder, and highlight the value of high-density SNP analysis and whole exome sequencing as powerful and cost-effective tools in the diagnosis of genetically heterogeneous disorders such as the hereditary ataxias.

Ataxia

Ataxia is a disorder of balance and coordination resulted from dysfunctions involving cerebellum and its afferent and efferent connections. While a variety of disorders can cause secondary ataxias, the list of genetic causes of ataxias is growing longer. Genetic abnormalities may involve mitochondrial dysfunction, oxidative stress, abnormal mechanisms of DNA repair, possible protein misfolding, and abnormalities in cytoskeletal proteins. Few ataxias are fully treatable while hope for efficacious gene therapy and pharmacotherapy is emerging. A discussion of the ataxias is presented here with brief mention of acquired ataxias, and a greater focus on inherited ataxias.

Late-onset sacsinopathy diagnosed by exome sequencing and comparative genomic hybridization

The molecular diagnosis of adult-onset autosomal recessive cerebellar ataxias remains challenging because of genetic heterogeneity. However, recently developed molecular genetic techniques will potentially revolutionize the diagnostic approach. Here we set out to define the genetic basis of the ataxia in two brothers with no molecular diagnosis. Clinical evaluation was followed by whole-exome second-generation sequencing and comparative genomic hybridization to determine the diagnosis. Whole-exome sequencing identified a hemizygous novel spastic ataxia of Charlevoix-Saguenay (SACS) stop-codon mutation in both brothers (c.13048G→T, p.E4350*) that was present in the mother, but not the father. Comparative genomic hybridization revealed a 0.7-Mb deletion on chromosome 13q12.12 in both brothers, which included SACS and was heterozygous in the asymptomatic father. The milder phenotype, caused by a whole-gene deletion and a stop-codon mutation in SACS, indicates a loss-of-function mechanism in late-onset autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS), and illustrates the importance of chromosomal rearrangements in the investigation of adult-onset ataxia.