Transcriptomic Characterization Reveals Disrupted Medium Spiny Neuron Trajectories in Huntington's Disease and Possible Therapeutic Avenues [bulk RNA-seq]

Huntington's Disease (HD) is a neurodegenerative disorder caused by an expansion of CAG repeats in exon 1 of the HTT gene, ultimately resulting in the generation of a mutant HTT (mHTT) protein. Although mHTT is expressed in various tissues, it significantly affects medium spiny neurons (MSNs) in the striatum, resulting in their loss and the subsequent motor function impairment found in HD. While HD symptoms typically emerge in midlife, disrupted MSN neurodevelopment plays an important role. To explore the effects of HD on MSN development, we differentiated induced HD pluripotent stem cells (iPSC) and isogenic control into neuronal stem cells, and then generated a developing MSN population encompassing early, intermediate progenitors, and mature MSNs. Single cell RNA sequencing (scRNAseq) revealed that the developmental trajectory of MSNs in our model closely emulated the trajectory of fetal striatal neurons. However, in the HD MSN cultures, this process was by downregulating several crucial genes for required for proper MSN maturation, including ASCL1 and members of the DLX family of transcription factors. Our analysis also uncovered a progressive dysregulation of multiple HD-related pathways as MSNs matured, including the NRF2-mediated oxidative stress response and ERK/MAPK signaling. Using the transcriptional profile of developing HD MSNs, we searched the L1000 dataset for small molecules that induce an opposite gene expression pattern. Our analysis pinpointed numerous small molecules with known benefits in HD models, as well as previously untested novel molecules. A top novel candidate, Cerulenin, demonstrated a partial restoration of DARPP-32 levels and electrical activity in HD MSNs, while also modulating genes involved in in multiple HD related pathways.