The TREM2-R47H Variant Drives Alzheimer's-Relevant Alterations in Forebrain Organoids Beyond Microglial Populations

Recent genetic studies have underscored the central role of microglia in orchestrating neurodegenerative pathology, particularly in Alzheimers disease (AD). However, contributions of other cell types are complex and poorly understood. Studying specific genetic mutations related to the disease is limited by the lack of robust in vitro models. To address this, we investigated the impact of the high-risk AD-associated TREM2-R47H variant using iPSC-derived forebrain organoids co-cultured with microglia, comparing mutant and isogenic control lines. Organoids were cultured up to 173 days, co-cultured with microglia and profiled using single-cell transcriptomics, bulk RNA sequencing, and confocal microscopy. Our findings demonstrate that the mutant co-culture model exhibits AD-specific signatures in vitro. Notably, confocal imaging revealed that control microglia internalized phosphorylated-Tau throughout the tissue, while R47H microglia showed no such uptake. Single-cell and bulk RNA profiling uncovered alterations in gene expression associated with oxidative phosphorylation, lysosomal activity and pathways of neurodegeneration. Interestingly, signs of neurodegeneration appeared as early as day 139 in variant organoids cultured without microglia, whereas wild-type (WT) organoids did not exhibit comparable changes at the whole-organoid level. By day 163, robust neurodegenerative profiles spanning neuronal and glial populations were evident exclusively in TREM2-R47H samples. These data suggest that the TREM2-R47H variant impairs microglial clearance of pathological proteins and may affect broader cellular networks beyond microglia, challenging current assumptions about its role and opening avenues for redefining AD pathogenesis.