Transcriptional landscape of human microglia reveals robust gene expression signatures that implicates age, sex and APOE-related immunometabolic pathway perturbations

Microglia have fundamental roles in health and disease, however effects of age, sex and genetic factors on human microglia have not been fully explored. We applied bulk and single cell approaches to comprehensively characterize human microglia transcriptomes and their associations with age, sex and APOE . We identified a novel microglial signature, characterized its expression in bulk data from 1,306 brain samples across 6 regions and in single cell microglia transcriptome. We discovered microglial co-expression network modules associated with age, sex and APOE -ε4 that are enriched for lipid and carbohydrate metabolism genes. Integrated analyses of modules with single cell transcriptomes revealed significant overlap between age-associated module genes and both pro-inflammatory and disease-associated microglial clusters. These modules and clusters harbor known neurodegenerative disease genes including APOE, PLCG2 and BIN1 . These data represent a well-characterized human microglial transcriptome resource; and highlight age, sex and APOE -related microglial immunometabolism perturbations with potential relevance in neurodegeneration. ### Competing Interest Statement The authors have declared no competing interest. * AD : Alzheimer’s disease APOE : Apolipoprotein EBM : Brodmann’s area BSA : Bovine serum albumin CERAD : Consortium to Establish a Registry for Alzheimer’s Disease CNS : Central nervous system CQN : Conditional quantile normalization DAM : Disease-associated microglia DPBS : Dulbecco’s phosphate buffered saline FACS : Fluorescence-activated cell sorting FPKM : Fragments per kilobase of transcript per million mapped reads GEM : Gel bead-in emulsion GO : Gene ontology MACS : Magnetic-activated cell sorting ME : Module eigengenes MM : Module membership PBS : Phosphate buffered saline PC : Principal component PCA : Principle component analysis PFA : Paraformaldehyde QC : Quality control RNAseq : RNA sequencing ROSMAP : Rush University Religious Order Study-Memory and Aging Project scRNAseq : Single cell RNA sequencing snRNAseq : Single nuclei RNA sequencing UMI : Unique molecular identifier WGCNA : Weighted gene co-expression network analysis