RBFOX1 Deficiency Induces Innate Microglia Generation in APOE4 Human Cerebral Organoids and Exacerbates Alzheimer's Disease Pathology

RBFOX1 has an important role in neuronal development, synapse formation, and is associated in several neuropsychiatric disorders. GWAS have suggested that RBFOX1 may be a risk factor for Alzheimer’s disease, with potential interactions with APOE4. We employed CRISPR/Cas9 and human cerebral organoids technologies to establish organoids of four genotypes: APOE3, APOE3_RBFOX1-KO, APOE4 and APOE4_RBFOX1-KO. Interestingly, RBFOX1 knockout promoted innate microglia generation in APOE4 organoids and induced DAM-like microglia, but not in APOE3. Similarly, in the presence of APOE4, RBFOX1 knockout prolonged mesoderm induction phase in embryonic body, potentially facilitating microglia development. RBFOX1 knockout also affected synaptic development and remodeling in organoids with APOE4. Furthermore, APOE4_RBFOX1-KO organoids secreted more pro-inflammatory factors, accumulated more lipid droplets, and exacerbated Tau phosphorylation and electrophysiological dysfunction, suggesting that RBFOX1 is a potential AD protective factor. Collectively, we developed an organoid model in which all cell types, including microglia, underwent self-organization. Our data suggest an antagonistic relation of RBFOX1 to APOE4-caused pathologies and produced microglia-containing organoids that can serve as an AD model with comprehensive pathological features, providing a valuable platform for AD research and therapeutic drug discovery.