SCRN: Single-cell Gene Regulatory Network Identification in Alzheimer's Disease

Alzheimer's disease (AD) is the most common neurodegenerative disease, and it consumes considerable medical resources with increasing number of patients every year. Mounting evidence show that the regulatory disruptions altering the intrinsic activity of genes in brain cells contribute to AD pathogenesis. To gain insights into the underlying gene regulation in AD, we proposed a graph learning method, Single-Cell based Regulatory Network (SCRN), to identify the regulatory mechanisms based on single-cell data. SCRN implements the γ-decaying heuristic link prediction based on graph neural networks and can identify reliable gene regulatory networks using locally closed subgraphs. In this work, we first performed UMAP dimension reduction analysis on single-cell RNA sequencing (scRNA-seq) data of AD and normal samples. Then we used SCRN to construct the gene regulatory network based on three well-recognized AD genes (APOE, CX3CR1, and P2RY12). Enrichment analysis of the regulatory network revealed significant pathways including NGF signaling, ERBB2 signaling, and hemostasis. These findings demonstrate the feasibility of using SCRN to uncover potential biomarkers and therapeutic targets related to AD.