miBRAIN snRNA-seq dataset — Cholesterol-mediated Lysosomal Dysfunction in APOE4 Astrocytes Promotes α-Synuclein Pathology in miBrains

The pathological hallmark of neurodegenerative disease is the aberrant post-translational modification and aggregation of proteins, leading to the formation of insoluble protein inclusions. Genetic factors like APOE4 are known to increase the prevalence and severity of tau, amyloid, and α-synuclein inclusions. However, the human brain is largely inaccessible during this process, limiting our mechanistic understanding. Here, we developed an iPSC-based 3D model that integrates neurons, glia, myelin, and cerebrovascular cells into a functional human brain tissue (“miBrain”). Single-nucleus RNA sequencing of miBrains confirmed the presence of diverse cell populations and revealed cell-type-specific transcriptional responses to synuclein pathology, including neuronal apoptotic and synaptic gene programs and astrocyte signatures of lipid dysregulation and reactivity. Like the human brain, we found that pathogenic phosphorylation and aggregation of α-synuclein are increased in the APOE4 miBrain. Combinatorial experiments revealed that endolysosomal dysfunction caused by cholesterol accumulation in APOE4 astrocytes impairs the degradation of α-synuclein and leads to a pathogenic transformation that seeds neuronal inclusions of α-synuclein. Collectively, this study establishes a robust model for investigating protein inclusions in human iPSC-derived brain tissue and highlights the role of astrocytes and cholesterol in APOE4-mediated pathologies, opening therapeutic opportunities.