Dr. Hyejung Won (Associate Professor, Genetics) was awarded a seed grant from the Amyotrophic Lateral Sclerosis Association for her project titled 鈥淒eciphering higher-order chromatin mechanisms for C9orf72-mediated ALS鈥�.
The project is based on the findings that one of the leading causes of amyotrophic lateral sclerosis (ALS) is GGGGCC (G4C2) short tandem repeats (STRs) in the intron of C9orf72. While the genetic cause is clear, progress towards developing disease-altering therapies in C9orf72-mediated ALS (C9-ALS) has been slow due to the incomplete mechanistic understanding of the disease. Three broad mechanisms have been proposed for C9-ALS: (1) downregulation of C9orf72, (2) transcribed STRs form RNA foci that sequester RNA binding proteins (RBPs), and (3) translated dipeptide repeats (DPRs) form toxic protein aggregates. Recently, another mechanism was proposed that STRs may cause disease by altering three-dimensional (3D) chromatin structure. To investigate the impact of C9orf72 G4C2 STRs (C9-STRs) on 3D chromatin structure, Dr. Won acquired genome-wide chromosome conformation maps of neurons and glia sorted from the cortex of C9-ALS. Notably, Dr. Won鈥檚 lab found ectopic loop formation in C9-ALS neurons, but not in glia. Based on this finding, they are proposing a new mechanism by which C9-STRs contribute to the ALS pathophysiology: transcribed STRs interact with DNA and induce ectopic loop formation, which can lead to widespread transcriptional dysregulation observed in C9-ALS brains. Because ectopic loops in C9-ALS can arise from the compensatory mechanism in postmortem brain samples, they propose to recapitulate these findings in isogenic induced pluripotent stem cell (iPSC) lines with and without C9-STRs. After differentiating isogenic iPSCs into neurons, they will generate genome-wide chromosome conformation maps to identify C9-STR-mediated changes in chromatin looping and leverage Capture Hybridization Analysis of RNA Targets (CHART) to identify DNA targets that interact with C9-STR RNA. The successful completion of this proposal will begin to elucidate the role of STRs in regulating 3D chromatin structure and pathophysiology of neurodegenerative diseases.