Profiling senescent cells in human brains reveals neurons with CDKN2D/p19 and tau neuropathology

Senescent cells contribute to pathology and dysfunction in animal models1. Their sparse distribution and heterogenous phenotype have presented challenges to their detection in human tissues. We developed a senescence eigengene approach to identify these rare cells within large, diverse populations of postmortem human brain cells. Eigengenes are useful when no single gene reliably captures a phenotype, like senescence. They also help to reduce noise, which is impor-tant in large transcriptomic datasets where subtle signals from low-expressing genes can be lost. Each of our eigengenes detected similar to 2% senescent cells from a population of similar to 140,000 single nuclei derived from 76 postmortem human brains with various levels of Alzheimer's disease (AD) pathology. More than 97% of the senescent cells were excitatory neu-rons and overlapped with neurons containing neurofibrillary tangle (NFT) tau pathology. Cyclin-dependent kinase inhibi-tor 2D (CDKN2D/p19) was predicted as the most significant contributor to the primary senescence eigengene. RNAscope and immunofluorescence confirmed its elevated expression in AD brain tissue. The p19-expressing neuron population had 1.8-fold larger nuclei and significantly more cells with lipofus-cin than p19-negative neurons. These hallmark senescence phenotypes were further elevated in the presence of NFTs. Collectively, CDKN2D/p19-expressing neurons with NFTs represent a unique cellular population in human AD with a senescence-like phenotype. The eigengenes developed may be useful in future senescence profiling studies as they iden-tified senescent cells accurately in snRNA-Seq datasets and predicted biomarkers for histological investigation.

Automated summary

Senescent cells, contributing to pathology and dysfunction, were successfully identified in postmortem human brain tissues using a novel eigengene approach. These cells were found to be mainly excitatory neurons and overlapped with neurons containing neurofibrillary tangle pathology. The CDKN2D/p19 gene may play a significant role in these senescent cells.