Characterizing dysregulations via cell-cell communications in Alzheimer’s brains using single-cell transcriptomes

Abstract Alzheimer’s disease (AD) is a devastating neurodegenerative disorder affecting 44 million people worldwide, leading to cognitive decline, memory loss, and significant impairment in daily functioning. The recent single-cell sequencing technology has revolutionized genetic and genomic resolution by enabling scientists to explore the diversity of gene expression patterns at the finest resolution. Here, we leveraged the large-scale and publicly available single-nucleus RNA sequencing (snRNA-seq) in the human prefrontal cortex (PFC) from 23 AD samples and 13 controls to investigate cell-to-cell communication (C2C) in healthy brains and their perturbations in AD. Specifically, we first performed broad communication pattern analyses and discovered the inter-mixing of cell types and signaling pathways in AD brains. Secondly, we performed cell-type- centric analysis and found that excitatory neurons in AD have significantly increased their communications to inhibitory neurons, while inhibitory neurons and other supporting cells globally decreased theirs to all cells. Then, we delved deeper with a signaling-centric view, showing that canonical signaling pathways CSF, TGFβ, and CX3C are significantly dysregulated in their signaling to the cell type microglia/PVM and WNT pathway is dysregulated in its signaling from endothelial to neuronal cells in AD. Finally, after extracting 23 known AD risk genes, our intracellular communication analysis revealed a strong connection of extracellular ligand genes APP, APOE, and PSEN1 to intracellular AD risk genes TREM2, ABCA1, and APP in the communication from astrocytes and microglia to neurons. In summary, with the novel advances in single-cell sequencing technologies, we show that cellular signaling is regulated in a cell-type- specific manner and that improper regulation of extracellular signaling genes is linked to intracellular risk genes, connecting signaling to genetic differences manifested in AD. Author Summary Alzheimer’s is a devastating neurodegenerative disorder affecting 44 million people worldwide, leading to cognitive decline, memory loss, and significant impairment in daily functioning. The complex interplay of signaling genes suggests cells act in concert with other cells through cell-to-cell communication. Utilizing the recent advances in single-cell sequencing, we investigated dysregulated ligand-receptor gene pairs in the disease at the cell-type resolution. Specifically, our broad communication pattern analyses revealed the inter-mixing of cell types and signaling pathways in AD brains. Our cell-type-centric analysis found that excitatory neurons in AD have significantly increased their communications with inhibitory neurons, while inhibitory neurons and other supporting cells globally decreased theirs to all cells. With a signaling-centric view, we show that CSF, TGFβ, and CX3C pathways are significantly dysregulated in their signaling to the cell type microglia/PVM while the WNT pathway is dysregulated in its signaling from endothelial to neuronal cells in AD. Finally, our intracellular communication analysis revealed a strong connection of extracellular ligand genes APP, APOE, and PSEN1 to intracellular AD risk genes TREM2, ABCA1, and APP in the communication from astrocytes and microglia to neurons. In summary, performing a cell-to-cell communication analysis better explains the genetic differences manifested in Alzheimer’s.