Single-cell RNA-seq of telencephalic organoids from healthy CTRL and HD (Huntington’s disease) hESC (RUES2) grown as mono-culture or co-culture of chimeric organoids

Huntington's disease (HD) causes selective degeneration of striatal and cortical neurons, resulting in cell mosaicism of coexisting still functional and dysfunctional cells. The impact of non-cell autonomous mechanisms between these cellular states is poorly understood. Here we generated telencephalic organoids with healthy or HD cells, grown separately or as mosaics of the two genotypes. We used single-cell transcriptomics to test early HD selective cellular phenotypes by comparing healthy (CTRL) and pathologic (HD) telencephalic organoids at days 45 and 120 of differentiation. To test the influence and the interactions between healthy and HD cells, mosaic organoids composed of CTRL and HD cells juxtaposed within the same organoid were grown and analyzed by scRNAseq at day 120. Single-cell RNA sequencing revealed neurodevelopmental abnormalities in the ventral fate acquisition of HD organoids, confirmed by cytoarchitectural and transcriptional defects leading to fewer GABAergic neurons, while dorsal populations showed milder phenotypes mainly in the maturation trajectory. Healthy cells in mosaic organoids restored HD cell identity, trajectories, synaptic density, and communication pathways upon cell-cell contact while showing no significant alterations when grown with HD cells. These findings highlight cell-type-specific alterations in HD and beneficial non-cell autonomous effects of healthy cells, emphasizing the therapeutic potential of modulating cell-cell communication in disease progression and treatment.