We initiated the systematic profiling of the dorsolateral prefrontal cortex obtained from a subset of autopsied individuals enrolled in the Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP), which are jointly designed prospective studies of aging and dementia with detailed, longitudinal cognitive phenotyping during life and a quantitative, structured neuropathologic examination after death. They include over 3,322 subjects. Here, we outline the first generation of data including genome-wide genotypes (n=2,090), whole genome sequencing (n=1,179), DNA methylation (n=740), chromatin immunoprecipitation with sequencing using an anti-Histone 3 Lysine 9 acetylation (H3K9Ac) antibody (n=712), RNA sequencing (n=638), and miRNA profile (n=702). Generation of other omic data including ATACseq, proteomic and metabolomics profiles is ongoing. Thanks to its prospective design and recruitment of older, non-demented individuals, these data can be repurposed to investigate a large number of syndromic and quantitative neuroscience phenotypes. The many subjects that are cognitively non-impaired at death also offer insights into the biology of the human brain in older non-impaired individuals.

The extent of microglial heterogeneity in humans remains a central yet poorly explored question in light of the development of therapies targeting this cell type. Here, we investigate the population structure of live microglia purified from human cerebral cortex samples obtained at autopsy and during neurosurgical procedures. Using single cell RNA sequencing, we find that some subsets are enriched for disease-related genes and RNA signatures. We confirm the presence of four of these microglial subpopulations histologically and illustrate the utility of our data by characterizing further microglial cluster 7, enriched for genes depleted in the cortex of individuals with Alzheimer’s disease (AD). Histologically, these cluster 7 microglia are reduced in frequency in AD tissue, and we validate this observation in an independent set of single nucleus data. Thus, our live human microglia identify a range of subtypes, and we prioritize one of these as being altered in AD.

Background The extent of microglial heterogeneity in the aging human brain remains a central, yet poorly explored question in light of the development of therapies targeting this cell type in age related neurodegenerative diseases, such as Alzheimer’s disease. Methods Using single cell RNA sequencing, we investigated the population structure of microglia purified from human cerebral cortex of aged donors with and without Alzheimer’s disease. Results We describe the population structure of microglia in the aged human brain and establish the divergent association of the different microglia subsets to age related neuropathologies and measures of cognitive decline. We confirm the presence of the identified microglial subpopulations histologically and explore their topological relationship to histopathological hallmarks of aging and AD in situ. Based on our data we prioritize one microglial cluster, cluster 7, which is enriched for genes involved in endosomal/vacuolar pathway. Interestingly we find that the signature gene set of cluster 7 is depleted in the cortical transcriptomic profile of individuals with AD. Histologically, these cluster 7 microglia are reduced in frequency in AD tissue, and we validate this observation in an independent set of single nucleus data. Conclusions Thus, single cell transcriptomic profiling of live human microglia identifies a range of microglia subtypes in the aged human brain, and we prioritize one of these as being altered in AD.