Molecular signatures underlying neurofibrillary tangle susceptibility in Alzheimer’s disease

Tau aggregation in neurofibrillary tangles (NFTs) is closely associated with neurodegeneration and cognitive decline in Alzheimer’s disease (AD). However, the molecular signatures that distinguish between aggregation-prone and aggregation-resistant cell states are unknown. We developed methods for the high-throughput isolation and transcriptome profiling of single somas with NFTs fro¬m human AD brain, quantified the susceptibility of 20 neocortical subtypes for NFT formation and death, and identified both shared and cell-type-specific signatures. NFT-bearing neurons shared a marked upregulation of synaptic transmission-related genes, including a core set of 63 genes enriched for synaptic vesicle cycling. Oxidative phosphorylation and mitochondrial dysfunction were highly cell-type dependent. Apoptosis was only modestly enriched, and the susceptibilities of NFT-bearing and NFT-free neurons for death were highly similar. Our analysis suggests that NFTs represent cell-type-specific responses to stress and synaptic dysfunction. We provide a resource for biomarker discovery and the investigation of tau-dependent and tau-independent mechanisms of neurodegeneration. Fresh frozen brain tissue from the prefrontal cortex (BA9) of eight Braak stage VI AD and eight age-matched healthy control donors was micro-dissected and dissociated without detergents or enzymatic digestion. Immunostaining and FACS using an antibody to detect pathological tau aggregates (AT8) and the pan-neuronal marker MAP2 was used to isolate somas with NFTs (n = 24,660) and neighboring NFT-free neurons (n = 38,465) from AD donors and control NFT-free somas (n = 63,110). RNA capture and library preparation was performed using the 10× Genomics Chromium Single Cell 3’ v2 or v3 assay. The generated paired-end libraries were sequenced on Illumina Novaseq 6000. Paired-end sequence reads were processed using the 10× Genomics software package Cell Ranger and the R-based Seurat package. Raw data is available in SRA with Study accession SRP189891 and Bioproject accession PRJNA528824.