A quantitative high-throughput screen identifies compounds that lower expression of the SCA2-and ALS-associated gene ATXN2

ATXN2L primarily interacts with NUFIP2, the absence of ATXN2L results in NUFIP2 depletion, and the ATXN2-polyQ expansion triggers NUFIP2 accumulation

The cytoplasmic Ataxin-2 (ATXN2) protein associates with TDP-43 in stress granules (SG) where RNA quality control occurs. Mutations in this pathway underlie Spinocerebellar Ataxia type 2 (SCA2) and Amyotrophic Lateral Sclerosis. In contrast, Ataxin-2-like (ATXN2L) is predominantly perinuclear, more abundant, and essential for embryonic life. Its sequestration into ATXN2 aggregates may contribute to disease. In this study, we utilized two approaches to clarify the roles of ATXN2L. First, we identified interactors through co-immunoprecipitation in both wild-type and ATXN2L-null murine embryonic fibroblasts. Second, we assessed the proteome profile effects using mass spectrometry in these cells. Additionally, we examined the accumulation of ATXN2L interactors in the SCA2 mouse model, Atxn2-CAG100-KnockIn (KIN). We observed that RNA-binding proteins, including PABPN1, NUFIP2, MCRIP2, RBMS1, LARP1, PTBP1, FMR1, RPS20, FUBP3, MBNL2, ZMAT3, SFPQ, CSDE1, HNRNPK, and HNRNPDL, exhibit a stronger association with ATXN2L compared to established interactors like ATXN2, PABPC1, LSM12, and G3BP2. Additionally, ATXN2L interacted with components of the actin complex, such as SYNE2, LMOD1, ACTA2, FYB, and GOLGA3. We noted that oxidative stress increased HNRNPK but decreased SYNE2 association, which likely reflects the relocalization of SG. Proteome profiling revealed that NUFIP2 and SYNE2 are depleted in ATXN2L-null fibroblasts. Furthermore, NUFIP2 homodimers and SYNE1 accumulate during the ATXN2 aggregation process in KIN 14-month-old spinal cord tissues. The functions of ATXN2L and its interactors are therefore critical in RNA granule trafficking and surveillance, particularly for the maintenance of differentiated neurons.

Identifying Molecular Properties of Ataxin-2 Inhibitors for Spinocerebellar Ataxia Type 2 Utilizing High-Throughput Screening and Machine Learning

Spinocerebellar ataxia type 2 (SCA2) is an autosomal dominant neurodegenerative disorder marked by cerebellar dysfunction, ataxic gait, and progressive motor impairments. SCA2 is caused by the pathologic expansion of CAG repeats in the ataxin-2 (ATXN2) gene, leading to a toxic gain-of-function mutation of the ataxin-2 protein. Currently, SCA2 therapeutic efforts are expanding beyond symptomatic relief to include disease-modifying approaches such as antisense oligonucleotides (ASOs), high-throughput screening (HTS) for small molecule inhibitors, and gene therapy aimed at reducing ATXN2 expression. In the present study, data mining and machine learning techniques were employed to analyze HTS data and identify robust molecular properties of potential inhibitors of ATXN2. Three HTS datasets were selected for analysis: ATXN2 gene expression, CMV promoter expression, and biochemical control (luciferase) gene expression. Compounds displaying significant ATXN2 inhibition with minimal impact on control assays were deciphered based on effectiveness (E) values (n = 1321). Molecular descriptors associated with these compounds were calculated using MarvinSketch (n = 82). The molecular descriptor data (MD model) was analyzed separately from the experimentally determined screening data (S model) as well as together (MD-S model). Compounds were clustered based on structural similarity independently for the three models using the SimpleKMeans algorithm into the optimal number of clusters (n = 26). For each model, the maximum response assay values were analyzed, and E values and total rank values were applied. The S clusters were further subclustered, and the molecular properties of compounds in the top candidate subcluster were compared to those from the bottom candidate subcluster. Six compounds with high ATXN2 inhibiting potential and 16 molecular descriptors were identified as significantly unique to those compounds (p < 0.05). These results are consistent with a quantitative HTS study that identified and validated similar small-molecule compounds, like cardiac glycosides, that reduce endogenous ATXN2 in a dose-dependent manner. Overall, these findings demonstrate that the integration of HTS analysis with data mining and machine learning is a promising approach for discovering chemical properties of candidate drugs for SCA2.

TDP-43 Aggregate Seeding Impairs Autoregulation and Causes TDP-43 Dysfunction

The aggregation, cellular mislocalization and dysfunction of TDP-43 are hallmarks of multiple neurodegenerative disorders. We find that inducing TDP-43 aggregation through prion-like seeding gradually diminishes normal TDP-43 nuclear localization and function. Aggregate-affected cells show signature features of TDP-43 loss of function, such as DNA damage and dysregulated TDP-43-target expression. We also observe strong activation of TDP-43-controlled cryptic exons in cells, including human neurons treated with proteopathic seeds. Furthermore, aggregate seeding impairs TDP-43 autoregulation, an essential mechanism controlling TDP-43 homeostasis. Interestingly, proteins that normally interact with TDP-43 are not recruited to aggregates, while other factors linked to TDP-43 pathology, including Ataxin 2, specifically colocalize to inclusions and modify seeding-induced aggregation. Our findings indicate that TDP-43 aggregation, mislocalization and loss of function are strongly linked and suggest that disruption of TDP-43 autoregulation establishes a toxic feed-forward mechanism that amplifies aggregation and may be central in mediating this pathological connection.

Targeting common disease pathomechanisms to treat amyotrophic lateral sclerosis

The motor neuron disease amyotrophic lateral sclerosis (ALS) is a devastating condition with limited treatment options. The past few years have witnessed a ramping up of translational ALS research, offering the prospect of disease-modifying therapies. Although breakthroughs using gene-targeted approaches have shown potential to treat patients with specific disease-causing mutations, the applicability of such therapies remains restricted to a minority of individuals. Therapies targeting more general mechanisms that underlie motor neuron pathology in ALS are therefore of considerable interest. ALS pathology is associated with disruption to a complex array of key cellular pathways, including RNA processing, proteostasis, metabolism and inflammation. This Review details attempts to restore cellular homeostasis by targeting these pathways in order to develop effective, broadly-applicable ALS therapeutics.

Spinocerebellar Ataxia Type 2: A Review and Personal Perspective

Spinocerebellar ataxias (SCAs) are dominantly inherited diseases that lead to neurodegeneration in the cerebellum and other parts of the nervous system. This review examines the progress that has been made in SCA2 from its initial clinical description to discovery of DNA CAG-repeat expansions in the ATXN2 gene. ATXN2 repeat alleles cover the range from recessive and dominant mendelian alleles to risk alleles for amyotrophic lateral sclerosis. We review studies aimed at defining the normal function of ATXN2 and mutant ATXN2 using cellular and mouse models. Progress in testing small compounds and antisense oligonucleotides in preclinical studies is described as well including our recent focus on staufen-1 (STAU1) and mRNA metabolism and control of autophagy.

Localization of Potential Energy in Hydrogen Bonds of the ATXN2 Gene

It is known that a number of neurodegenerative diseases, also called diseases of waiting, are associated with the expansion of the polyQ tract in the first exon of the ATXN2 gene. In the expanded polyQ tract, the probability of occurrence of non-canonical configurations (hairpins, G-quadruplexes, etc.) is significantly higher than in the normal one. Obviously, for their formation, the occurrence of open states (OSs) is necessary. Calculations were made for these processes using the angular mechanical model of DNA. It has been established that the probability of the large OS zones genesis in a DNA segment depends not only on the "strength" of the nucleotide sequence but also on the factors determining the dynamics of DNA; localization of the energy in the DNA molecule and the potential energy of interaction between pairs of nitrogenous bases also depend on environmental parameters. The potential energy of hydrogen bonds does not remain constant, and oscillatory movements lead to its redistribution and localization. In this case, OSs effectively dissipate the energy of oscillations. Thus, mathematical modeling makes it possible to calculate the localization of mechanical energy, which is necessary for the OSs formation, and to predict the places of their origin, taking into account the mechanical oscillations of the DNA molecule.

The Role of Protein Quantity Control in Polyglutamine Spinocerebellar Ataxias

Polyglutamine spinocerebellar ataxias (polyQ SCAs) represent the most prevalent subtype of SCAs. The primary pathogenic mechanism is believed to be the gain-of-function neurotoxicity of polyQ proteins. Strategies such as enhancing the degradation or inhibiting the accumulation of these mutant proteins are pivotal for reducing their toxicity and slowing disease progression. The protein quality control (PQC) system, comprising primarily molecular chaperones and the ubiquitin‒proteasome system (UPS), is essential for maintaining protein homeostasis by regulating protein folding, trafficking, and degradation. Notably, polyQ proteins can disrupt the PQC system by sequestering its critical components and impairing its proteasomal functions. Therefore, restoring the PQC system through genetic or pharmacological interventions could potentially offer beneficial effects and alleviate the symptoms of the disease. Here, we will provide a review on the distribution, expression, and genetic or pharmacological intervention of protein quality control system in cellular or animal models of PolyQ SCAs.