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The neuronal ceroid lipofuscinoses (NCLs, Batten disease) are fatal inherited lysosomal storage diseases of children characterized by increasing blindness, seizures and profound neurodegeneration but the mechanisms leading to these pathological changes remain unclear. Sheep with a CLN6 form that have a human-like brain and disease progression are invaluable for studying pathogenesis. A study of preclinical pathology in these sheep revealed localized glial activation at only 12 days of age, particularly in cortical regions that subsequently degenerate. This has been extended by examining fetal tissue from 60 days of gestation onwards. A striking feature was the presence of reactive astrocytes and the hypertrophy and proliferation of perivascular cells noted within the developing white matter of the cerebral cortex 40 days before birth. Astrocytic activation was evident within the cortical gray matter 20 days before birth, and was confined to the superficial laminae 12 days after birth. Clusters of activated microglia were detected in upper neocortical gray matter laminae shortly after birth. Neuronal development in affected sheep was undisturbed at these early ages. This prenatal activation of non-neuronal cells within the affected brain indicates the onset of pathogenesis during brain development and that an ordered sequence of glial activation precedes neurodegeneration.