Single nuclei RNA-sequencing of GWAS loci variant carriers elucidates cell-types and transcriptional profile alterations associated with Alzheimer disease.

Abstract

AD has a substantial genetic, molecular and cellular heterogeneity associated with its etiology. We sought to investigate the glial and neuronal pathways affected by AD at a cell specific resolution. To do so, we generated single-nuclei RNA-seq (snRNA-seq) from the parietal cortex of Mendelian mutation carriers, sporadic AD and neuropath-free donors from the Knight-ADRC and Dominantly Inherited Alzheimer Network banks. We generated snRNAseq (10X chemistry v3) for 18 APP and PSEN1 mutation carriers, 36 sporadic AD and 9 controls. After data cleaning and quality control, 336,892 nuclei remained for clustering and downstream analyses (Figure 1). Our analytical approach is based on the identification of cellular states (subclusters), their characterization and identification of genes associated with AD genetic strata. We identified a myriad of transcriptional states for the most representative brain cell-types (Figure 1) with distinguishing expression profiles (mean of 600 genes overexpressed; FDR<0.05). We identified that neuronal and glial cells have specific transcriptional states enriched in nuclei from brains with APP and PSEN1 mutations. For example, an astrocyte cell state specific for these brains shows overexpression of genes identified in the Disease Associated Astrocytes (DAA) expression signature. We also noted a microglia cell state enriched for a subset of TREM2 variant carriers showing overexpression of genes related to cell migration and lamellipodium assembly. We developed a unique molecular atlas to study the pathways dysregulated in AD. Our analyses indicate that in the backdrop of neuropath free and even sporadic AD brains, ADAD samples have distinctive cell states and altered pathways in neurons and glia.