Intersecting impact of CAG repeat and Huntingtin knockout in stem cell-derived cortical neurons [ESC]

Huntington’s Disease (HD) is caused by a CAG repeat expansion in the gene encoding Huntingtin (HTT). While normal HTT function appears impacted by the mutation, the specific pathways unique to CAG repeat expansion versus loss of normal function are unclear. To understand the impact of the CAG repeat expansion, we evaluated biological signatures of HTT knockout (HTT KO) versus those that occur from the CAG repeat expansion by applying multi-omics, live cell imaging, survival analysis and a novel feature- based pipeline to study cortical neurons (eCNs) derived from an isogenic human embryonic stem cell series (RUES2). HTT KO and the CAG repeat expansion influence developmental trajectories of eCNs, with opposing effects on the growth. Network analyses of differentially expressed genes and proteins associated with enriched epigenetic motifs identified subnetworks common to CAG repeat expansion and HTT KO that include neuronal differentiation, cell cycle regulation, and mechanisms related to transcriptional repression and may represent gain-of-function mechanisms that cannot be explained by HTT loss of function alone. A combination of dominant and loss-of-function mechanisms are likely involved in the aberrant neurodevelopmental and neurodegenerative features of HD that can help inform therapeutic strategies. We performed ATAC-seq and ChIP-seq in embryonic stem cell and ESC-derived cortical neuron models of Huntington's disease. In the ChIP-seq experiments we measured H3K27me3, H3K27Ac, H3K4me1 and H3K4me3 histone modifications. All measurements were performed in control cells, cells wtih HTT CAG repeat expansion (56CAG and 72CAG), and cells with HTT knockdown.