A SCALABLE WORKFLOW FOR OMICS-BASED AD DRUG SCREENING USING A NOVEL 3D NEUROGLIAL MODEL

The increase of the global aging population demands efficacious disease modifying treatments to tackle Alzheimer’s dementia (AD). Both in vitro models with high translational power and platforms that capture the multitude of brain responses to neurodegenerative pathologies are a necessity to enable disease targeting drug discovery efforts. Here, we apply a novel 3D cortical brain tissue model (3BTM) constituted by human iPSC-derived neurons, astrocytes and microglia genetically engineered to carry APP mutations of familial AD (Swedish, Arctic, Iberian; knock in (KI) 3BTMs), leveraging single cell RNA sequencing (scRNA-seq) to assess cell type specific transcriptional responses to amyloid beta accumulation and drug perturbation. We first sought to characterize microglia in 3BTMs, evaluating their maturation level and investigating whether accumulation of amyloid beta would induce specific transcriptional changes. Notably, we found that three-month old microglia in 3BTMs approximate a postnatal-like development and adopt a consistently higher maturation state compared to 2D co-cultures. Upon amyloid beta accumulation in KI 3BTMs microglial cells acquire a neuroinflammatory phenotype characterized by upregulation of genes such as NFkB, C3 and TREM2. Lastly, to assess feasibility of implementation of single cell technology as drug screening readout and exploiting the benefits of this AD model, we tested a cost efficient combinatorial barcoding platform and recovered 95´073 cells after perturbation with 10 different small molecule drugs. Overall, our results offer a new alternative strategy for drug discovery in AD coupling scRNA-seq with a modular 3BTM model ensuring high throughput, reproducibility and resolution.