Molecular Signatures of Resilience to Alzheimer’s Disease in Neocortical Layer 4 Neurons

Single-cell omics is advancing our understanding of selective neuronal vulnerability in Alzheimer’s disease (AD), revealing specific subtypes that are either susceptible or resilient to neurodegeneration. Using single-nucleus and spatial transcriptomics to compare neocortical regions affected early (prefrontal cortex and precuneus) or late (primary visual cortex) in AD, we identified a resilient excitatory population in layer 4 of the primary visual cortex expressing RORB, CUX2, and EYA4. Layer 4 neurons in association neocortex shared overlapping molecular signatures of resilience. Early in the disease, resilient neurons upregulated genes associated with synapse maintenance, synaptic plasticity, calcium homeostasis, and neuroprotective factors, including GRIN2A, RORA, NRXN1, NLGN1, NCAM2, FGF14, NRG3, NEGR1, and CSMD1. We also identified KCNIP4, which encodes a voltage-gated potassium (Kv) channel-interacting protein that interacts with Kv4.2 channels and presenilins, as a key factor linked to resilience. KCNIP4 was consistently upregulated in the early stages of pathology. Furthermore, AAV-mediated overexpression of Kcnip4 in a humanized AD mouse model reduced the expression of the activity-dependent genes Arc and c-Fos, suggesting compensatory mechanisms against neuronal hyperexcitability. Our dataset provides a valuable resource for investigating mechanisms underlying resilience to neurodegeneration. This single-nucleus RNAseq dataset was generated from postmortem fresh frozen human cerebral cortex from patients who died with Alzheimer’s disease (AD) and age-matched healthy controls. It contains ~ 500,000 nuclei, of which ~ 80% are neurons, from the prefrontal (BA9), precuneus (BA7) and primary visual (BA17) cortices from 46 donors, including 18 donors with no or low AD pathology (Braak 0-II), 10 with intermediate AD pathology (Braak IIII-IV), and 18 with high AD pathology (Braak V-VI). The samples were processed as described in our protocol at https://www.protocols.io/view/isolation-of-single-nuclei-from-postmortem-fresh-f-6tuhenw. Each sample was sorted by FANS (fluorescence-activated nucleus sorting) to collect two populations, one consisting of all nuclei and the other enriched for neurons (NeuN+). We annotated 18 excitatory and 19 inhibitory neuronal cell types, as well as glial and vascular cells.