Transcriptomic profiling of myeloid cells in Alzheimer’s Disease brain illustrates heterogeneity of microglia endolysosomal subtypes

Abstract

AbstractBackgroundMicroglia‐mediated neuroinflammation contributes to disease progression in Alzheimer’s Disease (AD). Microglia demonstrate heterogeneous states with proposed beneficial, harmful, and disease‐specific subtypes. Defining the spectrum of microglia phenotypes is crucially important to the design of neuroinflammation‐modulating therapies.MethodWe performed single‐nucleus RNA‐seq on over 120,000 microglia nuclei isolated from dorsolateral prefrontal cortices collected from 12 AD and 10 controls. Nuclei were sorted for PU.1 expression using fluorescence activated nucleus sorting.ResultsWe detected several microglia clusters that expressed features of “activation” as well as three previously unrecognized microglia transcriptomic subpopulations. These newly described subpopulations are defined by predominant endolysosomal gene expression patterns heterogeneous for metabolic and inflammatory signatures. One endolysosomal subtype is more abundant in AD individuals and uniquely enriched for transcripts involved in nucleic acid detection and interferon signaling. This population is distinct from a classic inflammatory subpopulation also present in our cohort, which upregulates NFKB, TLR and interferon related pathways but does not share the endolysosomal signature. Network analysis revealed subtype specific enrichment of IRF3 and IRF5 regulomes. AD individuals also exhibited increased expression of unfolded protein response and inflammatory genes in homeostatic microglia subpopulations.ConclusionWe demonstrate significant heterogeneity in human brain microglia subtypes including identifying multiple endolysosomal subpopulations. Like neuroinflammation, alterations in the endolysosomal system have been identified as a key component of AD pathology; however, how endolysosomal dysfunction contributes to AD progression remains unresolved. Our study is the first to identify a subpopulation of microglia in human AD brain correlating endolysosomal activity and interferon pathway induction supporting a relationship between these two pathways in AD pathogenesis. These results highlight the heterogenous nature of the microglia response to AD pathology and inform efforts to target specific subtypes of microglia in the development of novel AD therapies.