NEURONAL APOPTOSIS SHAPES DISEASE-ASSOCIATED MICROGLIAL TRAJECTORIES IN PRESYMPTOMATIC ALZHEIMER’S PATIENT-DERIVED IPSC MODELS

This study aimed to investigate how microglia from presymptomatic Alzheimer’s disease (AD) patients react to an AD-like neuronal environment using patient-derived induced pluripotent stem cell (iPSC) models.
Twenty iPSC lines from presymptomatic AD participants from the Deep and Frequent Phenotyping study were differentiated into microglia. iPSC-microglia were exposed to non-apoptotic (NAN) or apoptotic neurons (AN) and subjected to scRNA-sequencing. After quality control, 14 lines (11 APOE3/E4, 3 APOE4/E4) were retained. Preprocessing was performed with the Panpipes pipeline, cells were annotated using published microglia atlases. Clustering, batch correction, and trajectory inference were performed with Monocle3. EdgeR was used for abundance analysis. Differential gene expression analysis was conducted using Seurat, and gene ontology enrichment (GOE) was performed with ClusterProfiler package.
Trajectory analysis identified two trajectories leading from cycling to disease-associated microglia (DAM). Trajectory towards GPNMB-high CXCR4+ TREM2+ Lipox-DAM via TREM2+ IFN responsive microglia was preferred in NAN environment. Alternatively, when subjected to AN, trajectory towards LPL-high TREM2+ DAM via MITO-high DAM was more prominent. Comparing microglia subtype ratios between NAN and AN environments showed a decrease in TREM2-IFN responsive microglia (14.2% in NAN to 1.0% in AN, p<0.05) and an increase in MITO-high DAM (7.2% in NAN to 15.3% in AN, p<0.05). In comparison to TREM2+ IFN-responsive microglia, GOE highlighted MITO-high DAM upregulation of endocytosis-related pathways and downregulation of immune response pathways.
In conclusion, presymptomatic AD iPSC-microglia follow two distinct trajectories toward DAM, with an apoptotic neuron environment favouring a MITO-high intermediate. Transcriptomically, MITO-high DAM appears more endocytic than immune-responsive.