Developing a single cell map of the aging human brain relevant to Alzheimer's disease

National Institute On Aging

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Abstract

To establish appropriate methodologies, we initially performed single nuclear RNA-Seq (snRNA-Seq) on 180,000 nuclei from 16 defined donors taken from our prior collection of dorsolateral prefrontal cortex. This is part of the North American Brain Expression Consortium, where we have substantial genomic data including whole genome sequencing, DNA methylation and bulk RNA-Seq for 250 individuals across the adult human lifespan. This data demonstrated that we are able to identify most major cell types and can discriminate subtypes of neurons with multiple identified groups of both inhibitory and excitatory neurons as well as non-neuronal cells. Subsequently, we obtained tissues from four brain regions (entorhinal cortex, middle temporal gyrus, putamen and subventricular zone) from a series of samples representing relatively younger and older donors (n=6-7 per group for each region). We used a pooling strategy to perform efficient snRNA-Seq in several experimental batches then deconvoluted pools to individual donors based on known genotypes. We were able to discriminate many cell types with expected differences between regions based on known marker genes. There appear to be only modest differences in cellular proportions between the younger and older groups but substantial signal in terms of differential gene expression as a function of age. In particular, we have noted that while some cell types have a tendency to show downregulation of gene expression between age groups others show increase in expression. We particularly note that immune cells of the brain show distinct patterns of age-dependent gene expression not seen in neurons. A larger follow up study is in place to validate any observations that will also include epigenetic measurements.