Comparative gene regulatory networks modulatingAPOEexpression in microglia and astrocytes

Abstract

AbstractBackgroundSingle-cell technologies have unveiled various transcriptional states in different brain cell types. Transcription factors (TFs) regulate the expression of related gene sets, thereby controlling these diverse expression states. Apolipoprotein E (APOE), a pivotal risk-modifying gene in Alzheimer’s disease (AD), is expressed in specific glial transcriptional states associated with AD. However, it is still unknown whether the upstream regulatory programs that modulate its expression are shared across brain cell types or specific to microglia and astrocytes.MethodsWe used pySCENIC to construct state-specific gene regulatory networks (GRNs) for resting and activated cell states within microglia and astrocytes based on single-nucleus RNA sequencing data from AD patients’ cortices from the Knight ADRC-DIAN cohort. We then identified replicating TF using data from the ROSMAP cohort. We identified sets of genes co-regulated withAPOEby clustering the GRN target genes and identifying genes differentially expressed after the virtual knockout of TFs regulatingAPOE. We performed enrichment analyses on these gene sets and evaluated their overlap with genes found in AD GWAS loci.ResultsWe identified an average of 96 replicating regulators for each microglial and astrocyte cell state. Our analysis identified the CEBP, JUN, FOS, and FOXO TF families as key regulators of microglial APOE expression. The steroid/thyroid hormone receptor families, including the THR TF family, consistently regulated APOE across astrocyte states, while CEBP and JUN TF families were also involved in resting astrocytes. AD GWAS-associated genes (PGRN,FCGR3A,CTSH,ABCA1,MARCKS,CTSB,SQSTM1,TSC22D4,FCER1G, and HLA genes) are co-regulated with APOE. We also uncovered that APOE-regulating TFs were linked to circadian rhythm (BHLHE40,DBP,XBP1,CREM,SREBF1,FOXO3, andNR2F1).ConclusionsOur findings reveal a novel perspective on the transcriptional regulation ofAPOEin the human brain. We found a comprehensive and cell-type-specific regulatory landscape forAPOE, revealing distinct and shared regulatory mechanisms across microglia and astrocytes, underscoring the complexity ofAPOEregulation.APOE-co-regulated genes might also affect AD risk. Furthermore, our study uncovers a potential link between circadian rhythm disruption andAPOEregulation, shedding new light on the pathogenesis of AD.