Identification of a dysfunctional microglial population in human Alzheimer’s disease cortex using novel single-cell histology image analysis

In Alzheimer’s disease (AD), microglia are affected by disease processes, but may also drive pathogenesis. AD pathology-associated microglial populations have been identified with single-cell RNA-Seq, but have not been validated in human brain tissue with anatomical context. Here, we quantified myeloid cell markers to identify changes in AD pathology-associated microglial populations. We performed fluorescent immunohistochemistry on normal (n = 8) and AD (n = 8) middle temporal gyri, co-labelling the pan-myeloid cell marker, Iba1, with one of 11 markers of interest (MOIs): CD45, HLA-DR, CD14, CD74, CD33, CD206, CD32, CD163, P2RY12, TMEM119, L-Ferritin. Novel image analyses quantified the single-cell abundance of Iba1 and each MOI. Each cell was gated into one Iba1-MOI population (Iba1(low) MOI(high), Iba1(high) MOI(high), or Iba1(high) MOI(low)) and the abundance of each population was compared between AD and control. Triple-labelling of L-Ferritin and Iba1 with a subset of MOIs was performed to investigate L-Ferritin-MOI co-expression on Iba1(low) cells. Iba1(low) MOI(high) myeloid cell populations delineated by MOIs CD45, HLA-DR, CD14, CD74, CD33, CD32, and L-Ferritin were increased in AD. Further investigation of the Iba1(low) MOI(high) populations revealed that their abundances correlated with tau, but not amyloid beta, load in AD. The Iba1(low) microglial population highly expressed L-Ferritin, reflecting microglial dysfunction. The L-Ferritin(high) CD74(high) HLA-DR(high) phenotype of the Iba1(low) population mirrors that of a human AD pathology-associated microglial subpopulation previously identified using single-cell RNA-Seq. Our high-throughput immunohistochemical data with anatomical context support the microglial dysfunction hypothesis of AD. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s40478-020-01047-9) contains supplementary material, which is available to authorized users.