Whole Exome Sequencing Indicating GGCCTG Hexanucleotide Repeat in Patients with Spinocerebellar Ataxia Type 36.

INTRODUCTION: Spinocerebellar ataxia type 36 (SCA36) is caused by large GGCCTG repeat expansion in the NOP56 gene. The genetic diagnosis based on Southern blot is expensive and time-consuming. This study aimed to evaluate the reliability and effectiveness of whole exome sequencing (WES) for routine genetic diagnosis of suspected SCA36 patients. METHODS: Pathogenic repeat expansions for SCAs including SCA36 were first analyzed based on WES data using ExpansionHunter in five probands from SCA families, then the results were confirmed by triplet repeat primed polymerase chain reaction (TP-PCR) and Southern blot. RESULTS: GGCCTG repeat expansion in NOP56 was indicated in all five probands by WES, then it was found in 11 SCA patients and three asymptomatic individuals by TP-PCR. The sizes of GGCCTG repeat expansions were confirmed to be 1,390-1,556 by Southern blot. The mean age at onset of the patients was 51.0 ± 9.3 (ranging from 41 to 71), and they presented slowly progressive cerebellar ataxia, atrophy and fasciculation in tongue or limb muscles. CONCLUSION: The patients were clinically and genetically diagnosed as SCA36. This study proposed that WES could be a rapid, reliable, and cost-effective routine test for the preliminarily detection of SCA36 and other ataxia diseases.

Long-read sequencing identified intronic (GGCCTG)n expansion in NOP56 in one SCA36 family and literature review.

BACKGROUND: Spinocerebellar ataxias (SCA) are often caused by expansions of short tandem repeats. Recent methodological advances have made repeat expansion detection with long-read sequencing (LRS) feasible. Our study investigated one family with SCA 36 and further summarized the genetic and clinical characteristics of the total of 161 patients across different ethnic groups reported worldwide. METHODS: We enrolled a pedigree of 4 patients. The proband was a 55-year-old male. And he was screened for dynamic mutations of SCA subtypes by Tri-prime PCR (TP-PCR) and capillary electrophoresis, showing NOP56 as the candidate gene. The cosegregation was conducted by screening the NOP56 gene in his daughter and further confirmed by low-coverage (∼15 ×) LRS on the Oxford Nanopore platform. RESULTS: The SCA36 pedigree included a total of 4 patients. The proband showed the initial manifestation at the age of 45 years old, which was characterized by truncal ataxia. Genetic test results showed the (GGCCTG)n expansion in NOP56 gene (3/>15 and 6/>15 times respectively). To clarify the diagnosis genetically, LRS was performed in his daughter showing a large intronic insertion (chr20: 2633004 INS 7603 bp) containing (GGCCTG)n expansion of 782 units in NOP56 as the causative mutation. CONCLUSIONS: We identified one SCA36 pedigree by combining TP-PCR with LRS. Our study suggested LRS as an effective tool for molecular diagnosis. LRS also worked as a supplementary but necessary diagnostic tool for dynamic mutation-related SCA on the basis of repeat-primed PCR as well as capillary electrophoresis.

NMR solution structures of d(GGCCTG)n repeats associated with spinocerebellar ataxia type 36.

Expansion of d(GGCCTG)n hexanucleotide repeats in the NOP56 gene is the genetic cause of spinocerebellar ataxia type 36 (SCA36) which is an inheritable neurodegenerative disease. Non-B DNA is known to be the structural intermediate causing repeat expansions. Yet, the structure and mechanism of genetic instability of d(GGCCTG)n repeats remain elusive. In this work, we investigated the solution structures of sequences containing two to eight GGCCTG repeats using nuclear magnetic resonance (NMR) spectroscopy. They were found to form diverse secondary structures, including hairpin, duplex and G-quadruplex (G4). Intriguingly, the hairpin structure was present in all the investigated sequences. The NMR solution structure of the hairpin formed by d(GGCCTG)2 was determined, disclosing an unprecedented CCTGGG hexanucleotide loop in which the first and sixth loop residues formed a Watson-Crick loop-closing base pair, the second and third loop residues stacked in the major groove, whereas the fourth and fifth loop residues formed a G·G mismatch. Apart from the hairpin, antiparallel G4 and palindromic duplex structures were found to form in d(GGCCTG)2 and d(GGCCTG)3-8, respectively. Results of this work provide new insights into the genetic instability of d(GGCCTG)n repeats and structure-based drug design for SCA36.

Porphyrins ameliorate spinocerebellar ataxia type 36 GGCCTG repeat expansion-mediated cytotoxicity.

Spinocerebellar ataxia type 36 (SCA36) is a noncoding repeat expansion disorder caused by an expanded GGCCTG hexanucleotide repeat (HNR) in the first intron of the nucleolar protein 56 (NOP56) gene. Another disease-causing HNR expansion derived from C9orf72-linked GGGGCC repeats that form G-quadruplexes (GQs) affects genetic stability, RNA splicing, and mRNA localization within neurites. The porphyrin derivative TMPyP4 was shown to ameliorate RNA toxicity caused by GGGGCC HNR expansion by binding and distorting RNA GQ structures. SCA36 GGCCTG HNRs can potentially form RNA GQs; therefore, we investigated whether several porphyrin derivatives could reduce RNA toxicity in SCA36 cell models. Among these, sodium copper chlorophyllin and hemin chloride, which have already been used in clinical practice, reduced SCA36 GGCCTG expansion-mediated cytotoxicity and improved cell viability. These data suggest that porphyrins are potential therapeutic candidates against SCA36 pathogenesis.

Suppression of the yeast elongation factor Spt4 ortholog reduces expanded SCA36 GGCCUG repeat aggregation and cytotoxicity.

A hexanucleotide GGCCTG repeat expansion in intron 1 of the nucleolar protein 56 gene causes spinocerebellar ataxia type 36 (SCA36), which is a relatively pure cerebellar ataxia with progressive motor neuron involvement. In this study SCA36 cell models were generated by introducing expanded GGCCTG/CAGGCC repeats into cultured Neuro2A cells. Sense (GGCCUG)exp but not antisense (CAGGCC)exp RNA foci were detected in the cells, consistent with observations in autopsied brains of patients with SCA36. Glycine-proline dipeptide repeat (DPR) formation due to repeat-associated non-ATG translation rarely occurred in cells expressing expanded GGCCTG repeats; in contrast, cells harboring expanded c9orf72 GGGGCC/GGCCCC repeats robustly expressed DPR proteins. There are currently no effective treatments for microsatellite repeat expansion diseases including SCA36. In order to identify potentially useful therapies, we screened five candidate chemical compounds for their ability to diminish the toxicity of expanded SCA36 repeats and evaluated whether small interfering RNA-mediated silencing of Supt4a/Supt5, the murine ortholog of the yeast transcriptional elongation factor Spt4/Spt5, has therapeutic potential based on RNA foci quantification and cytotoxicity assays. Supt4a knockdown and erythromycin treatment suppressed the formation of (GGCCUG)exp RNA foci and DPR protein formation via regulation of (GGCCUG)exp mRNA, thereby ameliorating the cytotoxicity in SCA36 cell models. These data provide a basis for developing effective therapeutic strategies for the treatment of SCA36 and other repeat expansion disorders.

Spinocerebellar ataxia 36 (SCA36): «Costa da Morte ataxia¼. / La ataxia espinocerebelosa 36 (SCA36): «Ataxia da Costa da Morte¼.

INTRODUCTION-OBJECTIVE: To describe the history of the discovery of SCA36 and review knowledge of this entity, which is currently the most prevalent hereditary ataxia in Galicia (Spain) owing to a founder effect. DEVELOPMENT: SCA36 is an autosomal dominant hereditary ataxia with late onset and slow progression. It presents with cerebellar ataxia, sensorineural hearing loss, and discrete motor neuron impairment (tongue atrophy with denervation, discrete pyramidal signs). SCA36 was first described in Japan (Asida River ataxia) and in Galicia(Costa da Morte ataxia). The condition is caused by a genetic mutation (intronic hexanucleotide repeat expansion) in the NOP56 gene on the short arm of chromosome 20 (20p13). Magnetic resonance image study initially shows cerebellar vermian atrophy that subsequently extends to the rest of the cerebellum and finally to the pontomedullary region of the brainstem without producing white matter lesions. Peripheral nerve conduction velocities are normal, and sensorimotor evoked potential studies show delayed conduction of stimuli to lower limbs. In patients with hearing loss, audiometric studies show a drop of >40dB in frequencies exceeding 2,500Hz. Auditory evoked potential studies may also show lack of waves I and II. CONCLUSIONS: Costa da Morte ataxia or SCA36 is the most prevalent SCA in the Spanish region of Galicia. Given the region's history of high rates of emigration, new cases may be diagnosed in numerous countries, especially in Latin America. Genetic studies are now available to patients and asymptomatic carriers. Since many people are at risk for this disease, we will continue our investigations aimed at elucidating the underlying pathogenic molecular mechanisms and discovering effective treatment.