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Huntington disease (HD) is an adult onset neurodegenerative disorder that predominantly affects the striatum and cortex despite ubiquitous expression of mutant huntingtin (htt). Here we demonstrate that this pattern of selective degeneration is present in the YAC128 mouse model of HD. At 12 months, YAC128 mice show significant atrophy in the striatum, globus pallidus and cortex with relative sparing of the hippocampus and cerebellum (striatum: −10.4%, P <0.001; globus pallidus: −10.8%, P =0.04; cortex: −8.6%, P =0.001; hippocampus: +0.3%, P =0.9; cerebellum: +2.9%, P =0.6). Similarly, neuronal loss at this age is present in the striatum (−9.1%, P <0.001) and cortex of YAC128 mice (−8.3%, P =0.02) but is not detected in the hippocampus (+1.5%, P =0.72). Mutant htt expression levels …