Research Projects

Mutations in repetitive DNA sequences, such as microsatellite repeats, can lead to repeat expansion disorders. More than 50 untreatable human diseases, including the most common form of motor neuron disease Amyotrophic lateral sclerosis (ALS), Spinocerebellar ataxias (SCAs), Fragile X-associated tremor/ataxia syndrome (FXTAS), and Huntington’s disease (HD) are linked to repeat expansion mutations. Despite substantial ongoing research, none of these diseases currently have effective therapies, largely due to the multitude of effects as follows: 1. Expansions of DNA repeats, particularly in the promoter regions, can induce transcriptional gene silencing, leading to loss-of-function of the repeat harboring gene. 2. Repeat DNA elements are transcribed to highly structured RNAs like stem loops and G-quadruplexes, which can sequester critical RNA-binding proteins (RBPs), precluding their normal functions. 3. Finally, repeated RNAs can get translated through canonical or non-canonical processes to produce toxic, aggregation-prone repetitive peptides. Therefore, a key challenge in treating these diseases lies in understanding the repeat RNA-RBP interactions, which are often difficult to study due to the experimental challenges posed by long, repetitive sequences. This project aims to leverage advanced technologies such as APEX2 proximity labeling to identify disease-specific RBPs involved in ALS (GGGGCC repeat expansion), SCA36 (GGCCTG repeat expansion), and FXTAS (CGG repeat expansion); and characterize how repeat RNA-RBP interactions contribute to disease mechanisms across various repeat expansion disorders. We hypothesize that a comparative analysis of the RNA-protein interaction networks associated with these repeat expansions will reveal the molecular basis of disease-specific RBP sequestration, as well as the RNA-RBP interactions that are crucial for unique disease manifestation. We propose to use an innovative adaptation of the APEX2 proximity labeling system to identify proteins that interact with expanded repeat RNAs in a disease-specific and cellular compartment-specific manner in vivo. Our multi-pronged approach will include in vitro, mammalian cell-based, and Drosophila (fly) disease models to assess the role of critical RBPs in core cellular pathomechanisms underlying these diseases. This work will provide broader insights into repeat RNA metabolism and its role in neurodegenerative diseases. If successfully executed, this project will open new avenues for understanding the molecular basis of RNA toxicity underlying repeat expansion diseases, with potential applications in drug discovery and therapeutic development.