Cryo-ET of prion-infected neurons reveals nanopathology shared with Huntington disease models

‘Prion-like’ mechanisms have informed wider neurodegenerative disease research for decades, yet much is unknown about how prion assemblies propagate in the environment of a neuron. Here we establish a cryo-correlative light and electron microscopy (cryo-CLEM) workflow to study prion infection of primary neurons at nanometre resolution under near-native conditions. Cryo-electron tomography (cryo-ET) of fluorescently tagged ex vivo prion (PrPSc) seeds and live-immunolabelled nascent disease-associated prion assemblies (PrPd) reveals distinct fibril morphologies in situ. PrPd fibrils appear fragmented, frequently confined within membrane-bound compartments, and often surrounded by highly electron-dense sheet aggregate structures, previously identified by cryo-ET in Huntington disease patient iPSC-derived and mouse primary neurons. Another shared feature was mitochondrial pathology, manifesting with the accumulation of enlarged electron-dense granules. These nanoscale findings suggest common mechanisms leading to neuronal dysfunction in different neurodegenerative diseases.