In Silico Prediction of Potential Inhibitors for Targeting RNA CAG Repeats via Molecular Docking and Dynamics Simulation: A Drug Discovery Approach

Spinocerebellar ataxia (SCA) is a rare neurological illness inherited dominantly that causes severe impairment and premature mortality. While each rare disease may affect individuals infrequently, collectively they pose a significant healthcare challenge. It is mainly carried out due to the expansion of RNA triplet (CAG) repeats, although missense or point mutations can also be induced. Unfortunately, there is no cure; only symptomatic treatments are available. To date, SCA has about 48 subtypes, the most common of these being SCA 1, 2, 3, 6, 7, 12, and 17 having CAG repeats. Using molecular docking and molecular dynamics (MD) simulation, this study seeks to investigate effective natural herbal neuroprotective compounds against CAG repeats, which are therapeutically significant in treating SCA. Initially, virtual screening followed by molecular docking was used to estimate the binding affinity of neuroprotective natural compounds toward CAG repeats. The compound with the highest binding affinity, somniferine, was then chosen for MD simulation. The structural stability, interaction mechanism, and conformational dynamics of CAG repeats and somniferine were investigated via MD simulation. The MD study revealed that during the simulation period, the interaction between CAG repeats and somniferine stabilizes and results in fewer conformational variations. This in silico study suggests that Somniferine can be used as a therapeutic medication against RNA CAG repeats in SCA.

Hereditary Ataxias: From Bench to Clinic, Where Do We Stand?

Cerebellar ataxias are a wide heterogeneous group of movement disorders. Within this broad umbrella of diseases, there are both genetics and sporadic forms. The clinical presentation of these conditions can exhibit a diverse range of symptoms across different age groups, spanning from pure cerebellar manifestations to sensory ataxia and multisystemic diseases. Over the last few decades, advancements in our understanding of genetics and molecular pathophysiology related to both dominant and recessive ataxias have propelled the field forward, paving the way for innovative therapeutic strategies aimed at preventing and arresting the progression of these diseases. Nevertheless, the rarity of certain forms of ataxia continues to pose challenges, leading to limited insights into the etiology of the disease and the identification of target pathways. Additionally, the lack of suitable models hampers efforts to comprehensively understand the molecular foundations of disease's pathophysiology and test novel therapeutic interventions. In the following review, we describe the epidemiology, symptomatology, and pathological progression of hereditary ataxia, including both the prevalent and less common forms of these diseases. Furthermore, we illustrate the diverse molecular pathways and therapeutic approaches currently undergoing investigation in both pre-clinical studies and clinical trials. Finally, we address the existing and anticipated challenges within this field, encompassing both basic research and clinical endeavors.

On the Cut-Off Value of the Anteroposterior Diameter of the Midbrain Atrophy in Spinocerebellar Ataxia Type 2 Patients

(1) Background: Spinocerebellar ataxias (SCA) is a term that refers to a group of hereditary ataxias, which are neurological diseases characterized by degeneration of the cells that constitute the cerebellum. Studies suggest that magnetic resonance imaging (MRI) supports diagnoses of ataxias, and linear measurements of the aneteroposterior diameter of the midbrain (ADM) have been investigated using MRI. These measurements correspond to studies in spinocerebellar ataxia type 2 (SCA2) patients and in healthy subjects. Our goal was to obtain the cut-off value for ADM atrophy in SCA2 patients. (2) Methods: This study evaluated 99 participants (66 SCA2 patients and 33 healthy controls). The sample was divided into estimations (80%) and validation (20%) samples. Using the estimation sample, we fitted a logistic model using the ADM and obtained the cut-off value through the inverse of regression. (3) Results: The optimal cut-off value of ADM was found to be 18.21 mm. The area under the curve (AUC) of the atrophy risk score was 0.957 (95% CI: 0.895-0.991). Using this cut-off on the validation sample, we found a sensitivity of 100.00% (95% CI: 76.84%-100.00%) and a specificity of 85.71% (95% CI: 42.13%-99.64%). (4) Conclusions: We obtained a cut-off value that has an excellent discriminatory capacity to identify SCA2 patients.

Impact of specialist ataxia centres on health service resource utilisation and costs across Europe: cross-sectional survey

BACKGROUND

Little is known about the costs of treating ataxia and whether treatment at a specialist ataxia centre affects the cost of care. The aim of this study was to investigate whether patients who attended specialist ataxia centres in three European countries reported differences in their health care use and costs compared with patients who did not attend a specialist ataxia centre. We compared mean resource use and health service costs per patient affected by ataxia in the United Kingdom, Italy and Germany over a 12-month period. Data were obtained from a survey distributed to people with ataxia in the three countries. We compared mean resource use for each contact type and costs, stratifying patients by whether they were currently attending a specialist ataxia centre or had never attended one.

RESULTS

Responses were received from 181 patients from the United Kingdom, 96 from Italy and 43 from Germany. Differences in the numbers of contacts for most types of health service use between the specialist ataxia centre and non-specialist ataxia centre groups were non-significant. In the United Kingdom the mean total cost per patient was €2209 for non-specialist ataxia centre patients and €1813 for specialist ataxia centre patients (P = 0.59). In Italy these figures were €2126 and €1971, respectively (P = 0.84). In Germany they were €2431 and €4087, respectively (P = 0.19). Inpatient stays made the largest contribution to total costs.

CONCLUSIONS

Within each country, resource use and costs were broadly similar for specialist ataxia centre and non-specialist ataxia centre groups. There were differences between countries in terms of health care contacts and costs.

Patient pathways for rare diseases in Europe: ataxia as an example

BACKGROUND

Progressive ataxias are rare and complex neurological disorders that represent a challenge for the clinicians to diagnose and manage them. This study explored the patient pathways of individuals attending specialist ataxia centres (SAC) compared with non-specialist settings. We investigated specifically how diagnosis was reached, the access to healthcare services, treatments, and care satisfaction. The focus of this study was on early intervention, coordination of treatment to understand the care provision in different countries.

METHODS

A patient survey was done in the UK, Germany and Italy to gather information about diagnosis and management of the ataxias in specialist (SAC) and non-specialist settings, utilisation of other primary and secondary health care services, and patients' satisfaction of received treatment.

RESULTS

Patients gave positive feedback about the role of SAC in understanding their condition, ways to manage their ataxia (p < 0.001; UK) and delivering care adapted to their needs (p < 0.001; UK), in coordinating referrals to other healthcare specialists, and in offering opportunities to take part in research studies. Similar barriers for patients were identified in accessing the SACs among the selected countries, UK, Germany, and Italy.

CONCLUSIONS

This study provides crucial information about the ataxia patients care pathways in three European countries. Overall, the results showed a trend in patients' satisfaction being better in SAC compared to non-SAC. The outcomes can be used now for policy recommendations on how to improve treatment and care for people with these very rare and complex neurological diseases across Europe.

A novel biallelic variant further delineates PRDX3-related autosomal recessive cerebellar ataxia

Cerebellar ataxias (CAs) comprise a rare group of neurological disorders characterized by extensive phenotypic and genetic heterogeneity. In the last several years, our understanding of the CA etiology has increased significantly and resulted in the discoveries of numerous ataxia-associated genes. Herein, we describe a single affected individual from a consanguineous family segregating a recessive neurodevelopmental disorder. The proband showed features such as global developmental delay, cerebellar atrophy, hypotonia, speech issues, dystonia, and profound hearing impairment. Whole-exome sequencing and Sanger sequencing revealed a biallelic nonsense variant (c.496A > T; p.Lys166*) in the exon 5 of the PRDX3 gene that segregated perfectly within the family. This is the third report that associates the PRDX3 gene variant with cerebellar ataxia. In addition, associated hearing impairment further delineates the PRDX3 associated gene phenotypes.

Prevalence of neurodegenerative/demyelinating disorders in patients with achalasia

Introduction

Esophageal achalasia is a primary motility disorder. Although the exact pathogenesis is unknown, autoimmune, and neurodegenerative processes seem to be involved similarly to neurodegenerative and/or demyelinating disorders (NDDs). We hypothesized that the prevalence of NDD may be higher among patients with achalasia and vice versa as the background pathogenetic mechanisms are similar.

Methods

This was a prospective, comparative questionnaire-based study. Patients with achalasia and patients with NDD were enrolled. Selected patients with achalasia were thoroughly examined by a neurologist and selected patients with NDD were examined by a gastroenterologist to confirm or rule out NDD or achalasia. We assessed the prevalence of both achalasia and NDD and compared them with their prevalence in general population.

Results

A total of 150 patients with achalasia and 112 patients with NDD were enrolled. We observed an increased prevalence of NDD among patients with achalasia (6.0% (9/150); 95% CI (confidence interval): 3.1–11.2%) as compared to the estimated 2.0% prevalence in general population (p = 0.003). Although 32 out of 112 patients (28.6%) with NDD reported dysphagia, we did not observe significantly increased prevalence of achalasia in these patients (1.8% (2/112) vs 0.8% in general population, p = 0.226).

Conclusion

The prevalence of NDD was significantly higher among patients with achalasia (6.0%) compared to general population (2.0%), suggesting an association of these disorders. Large-volume studies are necessary to confirm this finding.

A resting-state fMRI pattern of spinocerebellar ataxia type 3 and comparison with 18F-FDG PET

•

This is the first study identifying a resting-state fMRI pattern in SCA3.

•

This pattern was closely associated with a metabolic (¹⁸F-FDG PET) counterpart.

•

Pattern subject scores were highly correlated with ataxia severity.

Spinocerebellar ataxia type 3 (SCA3) is a rare genetic neurodegenerative disease. The neurobiological basis of SCA3 is still poorly understood, and up until now resting-state fMRI (rs-fMRI) has not been used to study this disease. In the current study we investigated (multi-echo) rs-fMRI data from patients with genetically confirmed SCA3 (n = 17) and matched healthy subjects (n = 16). Using independent component analysis (ICA) and subsequent regression with bootstrap resampling, we identified a pattern of differences between patients and healthy subjects, which we coined the fMRI SCA3 related pattern (fSCA3-RP) comprising cerebellum, anterior striatum and various cortical regions. Individual fSCA3-RP scores were highly correlated with a previously published ¹⁸F-FDG PET pattern found in the same sample (rho = 0.78, P = 0.0003). Also, a high correlation was found with the Scale for Assessment and Rating of Ataxia scores (r = 0.63, P = 0.007). No correlations were found with neuropsychological test scores, nor with levels of grey matter atrophy. Compared with the ¹⁸F-FDG PET pattern, the fSCA3-RP included a more extensive contribution of the mediofrontal cortex, putatively representing changes in default network activity. This rs-fMRI identification of additional regions is proposed to reflect a consequence of the nature of the BOLD technique, enabling measurement of dynamic network activity, compared to the more static ¹⁸F-FDG PET methodology. Altogether, our findings shed new light on the neural substrate of SCA3, and encourage further validation of the fSCA3-RP to assess its potential contribution as imaging biomarker for future research and clinical use.

Genetics of Ataxias in Indian Population: A Collative Insight from a Common Genetic Screening Tool

Cerebellar ataxias (CAs) represent a group of autosomal dominant and recessive neurodegenerative disorders affecting cerebellum with or without spinal cord. Overall, CAs have preponderance for tandem nucleotide repeat expansions as an etiological factor (10 TREs explain nearly 30-40% of ataxia cohort globally). The experience of 10 years of common genetic ataxia subtypes for ≈5600 patients' referrals (Pan-India) received at a single center is shared herein. Frequencies (in %, n) of SCA types and FRDA in the sample cohort are observed as follows: SCA12 (8.6%, 490); SCA2 (8.5%, 482); SCA1 (4.8%, 272); SCA3 (2%, 113); SCA7 (0.5%, 28); SCA6 (0.1%, 05); SCA17 (0.1%, 05), and FRDA (2.2%, 127). A significant amount of variability in TRE lengths at each locus is observed, we noted presence of biallelic expansion, co-occurrence of SCA-subtypes, and the presence of premutable normal alleles. The frequency of mutated GAA-FRDA allele in healthy controls is 1/158 (0.63%), thus an expected FRDA prevalence of 1:100 000 persons. The data of this study are relevant not only for clinical decision making but also for guidance in direction of genetic investigations, transancestral comparison of genotypes, and lastly provide insight for policy decision for the consideration of SCAs under rare disease category.

Digital Polymerase Chain Reaction Paired with High-Speed Atomic Force Microscopy for Quantitation and Length Analysis of DNA Length Polymorphisms

DNA length polymorphisms are found in many serious diseases, and assessment of their length and abundance is often critical for accurate diagnosis. However, measuring their length and frequency in a mostly wild-type background, as occurs in many situations, remains challenging due to their variable and repetitive nature. To overcome these hurdles, we combined two powerful techniques, digital polymerase chain reaction (dPCR) and high-speed atomic force microscopy (HSAFM), to create a simple, rapid, and flexible method for quantifying both the size and proportion of DNA length polymorphisms. In our approach, individual amplicons from each dPCR partition are imaged and sized directly. We focused on internal tandem duplications (ITDs) located within the FLT3 gene, which are associated with acute myeloid leukemia and often indicative of a poor prognosis. In an analysis of over 1.5 million HSAFM-imaged amplicons from cell line and clinical samples containing FLT3-ITDs, dPCR-HSAFM returned the expected variant length and variant allele frequency, down to 5% variant samples. As a high-throughput method with single-molecule resolution, dPCR-HSAFM thus represents an advance in HSAFM analysis and a powerful tool for the diagnosis of length polymorphisms.

Objective Assessment of Cerebellar Ataxia: A Comprehensive and Refined Approach

Parametric analysis of Cerebellar Ataxia (CA) could be of immense value compared to its subjective clinical assessments. This study focuses on a comprehensive scheme for objective assessment of CA through the instrumented versions of 9 commonly used neurological tests in 5 domains- speech, upper limb, lower limb, gait and balance. Twenty-three individuals diagnosed with CA to varying degrees and eleven age-matched healthy controls were recruited. Wearable inertial sensors and Kinect camera were utilised for data acquisition. Binary and multilabel discrimination power and intra-domain relationships of the features extracted from the sensor measures and the clinical scores were compared using Graph Theory, Centrality Measures, Random Forest binary and multilabel classification approaches. An optimal subset of 13 most important Principal Component (PC) features were selected for CA-control classification. This classification model resulted in an impressive performance accuracy of 97% (F1 score = 95.2%) with Holmesian dimensions distributed as 47.7% Stability, 6.3% Timing, 38.75% Accuracy and 7.24% Rhythmicity. Another optimal subset of 11 PC features demonstrated an F1 score of 84.2% in mapping the total 27 PC across 5 domains during CA multilabel discrimination. In both cases, the balance (Romberg) test contributed the most (31.1% and 42% respectively), followed by the peripheral tests whereas gait (Walking) test contributed the least. These findings paved the way for a better understanding of the feasibility of an instrumented system to assist informed clinical decision-making.

Cerebellar Development and Circuit Maturation: A Common Framework for Spinocerebellar Ataxias

Spinocerebellar ataxias (SCAs) affect the cerebellum and its afferent and efferent systems that degenerate during disease progression. In the cerebellum, Purkinje cells (PCs) are the most vulnerable and their prominent loss in the late phase of the pathology is the main characteristic of these neurodegenerative diseases. Despite the constant advancement in the discovery of affected molecules and cellular pathways, a comprehensive description of the events leading to the development of motor impairment and degeneration is still lacking. However, in the last years the possible causal role for altered cerebellar development and neuronal circuit wiring in SCAs has been emerging. Not only wiring and synaptic transmission deficits are a common trait of SCAs, but also preventing the expression of the mutant protein during cerebellar development seems to exert a protective role. By discussing this tight relationship between cerebellar development and SCAs, in this review, we aim to highlight the importance of cerebellar circuitry for the investigation of SCAs.