Selective vulnerability of layer 5a corticostriatal neurons in Huntington's disease (HD) is highlighted by the loss of these neurons in the cerebral cortex, particularly in early stages of the disease. Using serial fluorescence-activated nuclear sorting (sFANS) and single-nucleus RNA sequencing (snRNA-seq), researchers identified that layer 5a pyramidal neurons are selectively vulnerable in HD. Extensive somatic CAG expansions of the mutant huntingtin (mHTT) allele occur in both vulnerable and resilient neurons, including Betz cells and layers 6a and 6b neurons. Gene expression analyses indicate altered synaptic function in layers 5 and 6 neurons. Retrograde tracing in macaque brains confirmed that layer 5a neurons are corticostriatal pyramidal cells. The study suggests that enhanced somatic mHTT CAG expansion and altered synaptic function contribute to corticostriatal disconnection and neuronal vulnerability in HD. The findings demonstrate that extensive somatic CAG expansions occur in both vulnerable and resilient deep layer cortical neurons, and that synaptic dysfunction and corticostriatal disconnection may play a role in HD neurodegeneration. The study also shows that L5a HTR2C expressing neurons are corticostriatal projection neurons in primates, and that their loss is associated with selective vulnerability in HD. The data indicate that transcriptional programs are disturbed in HD, with genes involved in synaptic and dendritic functions being downregulated. These findings contribute to understanding HD pathophysiology at the molecular level in the human cerebral cortex.Selective vulnerability of layer 5a corticostriatal neurons in Huntington's disease (HD) is highlighted by the loss of these neurons in the cerebral cortex, particularly in early stages of the disease. Using serial fluorescence-activated nuclear sorting (sFANS) and single-nucleus RNA sequencing (snRNA-seq), researchers identified that layer 5a pyramidal neurons are selectively vulnerable in HD. Extensive somatic CAG expansions of the mutant huntingtin (mHTT) allele occur in both vulnerable and resilient neurons, including Betz cells and layers 6a and 6b neurons. Gene expression analyses indicate altered synaptic function in layers 5 and 6 neurons. Retrograde tracing in macaque brains confirmed that layer 5a neurons are corticostriatal pyramidal cells. The study suggests that enhanced somatic mHTT CAG expansion and altered synaptic function contribute to corticostriatal disconnection and neuronal vulnerability in HD. The findings demonstrate that extensive somatic CAG expansions occur in both vulnerable and resilient deep layer cortical neurons, and that synaptic dysfunction and corticostriatal disconnection may play a role in HD neurodegeneration. The study also shows that L5a HTR2C expressing neurons are corticostriatal projection neurons in primates, and that their loss is associated with selective vulnerability in HD. The data indicate that transcriptional programs are disturbed in HD, with genes involved in synaptic and dendritic functions being downregulated. These findings contribute to understanding HD pathophysiology at the molecular level in the human cerebral cortex.