Research Projects

Neurodegenerative diseases (NDs) are a group of disorders marked by progressive neuronal loss and shared pathological hallmarks such as the accumulation of misfolded proteins, synaptic dysfunction, and eventual cell death. These disorders are underpinned by complex molecular mechanisms, including disrupted proteostasis, cytoskeletal abnormalities, metabolic dysregulation, neuroinflammation, and impaired RNA regulation (Ricci 2024). While some NDs are caused by inherited mutations, many are sporadic and influenced by combinations of genetic variants that increase disease susceptibility. Notably, the same genes are often implicated in both familial and sporadic forms of disease, indicating the presence of common molecular pathways (Gan et al. 2018). A major class of proteins involved in NDs are RNA-binding proteins (RBPs) containing intrinsically disordered regions (IDRs), which facilitate Ribonucleoprotein (RNP) granule formation (Ramaswami, Taylor, and Parker 2013). Disease-associated mutations frequently occur within these IDRs, promoting aberrant aggregation of RBPs with RNA in either the cytoplasm or nucleus. Among them, TDP-43 is of particular interest due to its abnormal cytoplasmic accumulation in several neurodegenerative conditions. The hallmark mislocalization of TDP-43 from the nucleus to the cytoplasm is strongly associated with Amyotrophic Lateral Sclerosis (ALS), frontotemporal dementia (FTD), and other disorders (Wood et al. 2021). The pathogenicity of TDP-43 is believed to result from both toxic gain-of-function effects in the cytoplasm and loss of nuclear function. Ataxin-2 is a well-characterized gene associated with multiple dominantly inherited NDs, including ALS, FTD, and spinocerebellar ataxia type 2 (SCA2). The most common pathogenic mechanism involves expansion of an N-terminal polyglutamine (polyQ) tract beyond 33 repeats (Butland et al. 2007; Pulst et al. 1996). Interest in Ataxin-2 has grown due to findings that its reduction, via knockout or knockdown, can suppress disease progression in several neurodegeneration models. These observations position Ataxin-2 as a compelling therapeutic target, particularly in diseases linked to RNA toxicity (Bakthavachalu et al. 2018; Becker et al. 2017; Scoles et al. 2017). Our lab has extensively investigated Ataxin-2’s role in RNA regulation using Drosophila models and has demonstrated its importance in maintaining neuronal function. We have also shown that disease-linked human proteins expression in flies induces neurotoxicity, which can be rescued by either reducing Ataxin-2 levels or disrupting its recruitment into RNP granules (Bakthavachalu et al. 2018; Petrauskas et al. 2024; Singh et al. 2021). These findings prompted us to explore the mechanistic relationship between Ataxin-2 and TDP-43. Using the TRIBE (Targets of RNA-Binding Proteins Identified by Editing) approach in human cells, we identified significant overlap in RNA targets bound by both Ataxin-2 and TDP-43, suggesting a previously unrecognized co-regulatory mechanism. This observation raises a critical question: How does Ataxin-2 modulate TDP-43 function, and how does this regulation influence neurodegenerative processes? To address this, we propose a comprehensive set of experiments combining advanced molecular techniques. We will use TRIBE to map the in vivo RNA targets of both proteins and CRISPR genome engineering to generate gene knockouts and domain-specific mutants to dissect their interaction and functional interdependence. Our preliminary results from both TRIBE and CRISPR experiments support the feasibility of this approach and validate our central hypothesis. The expected outcomes of this project will extend our current understanding of Ataxin-2’s role in RNA metabolism and its functional interaction with TDP-43. This work will not only complement ongoing studies in our lab but also provide critical mechanistic insight into a potentially druggable pathway in ND.