Astrocyte transcriptomic changes along the spatiotemporal progression of Alzheimer’s disease

Background Alzheimer’s disease (AD) is defined by widespread accumulation of Ab plaques and phospho‐tau neurofibrillary tangles throughout the brain, with the latter following a stereotypical hierarchical spatiotemporal pattern along neural networks. These AD neuropathological changes are accompanied by a dramatic loss of synapses and neurons as well as prominent morphological and functional changes of astrocytes, collectively termed reactive astrogliosis. Astrocytes also play a critical role in maintaining brain homeostasis. However, their changes along the spatiotemporal progression of AD neuropathology remain largely unknown. To investigate these astrocyte changes, we performed single‐nucleus RNA‐sequencing on 5 brain regions along the stereotypical progression of AD neuropathology from 32 donors representing the entire normal aging‐severe AD spectrum. Method Nuclei were isolated from five brain areas of n = 32 donors with increasing AD neuropathology (total n = 160 samples). The five brain areas were chosen based on their hierarchical accumulation of tau pathology: entorhinal cortex (EC)> inferior temporal gyrus (BA20) > dorsolateral prefrontal cortex (BA46) > secondary visual cortex (V2 or BA18/19) > primary visual cortex (V1 or BA17). To enrich in astrocytic nuclei, NEUN+ and OLIG2+ nuclei were separated via FACS, whereas NEUN‐/OLIG2‐ nuclei (including astrocytes) were subjected to snRNA‐seq resulting in a transcriptomic dataset of 629,755 astrocyte nuclei, which were subsequently examined for common and region‐specific AD related changes. Result We discovered temporal gene‐expression‐trajectories with gene sets differentially activated at various disease stages. Surprisingly, a gene set enriched in proteostasis (genes encoding heat shock proteins) and energy metabolism (e.g., ATP synthases) was upregulated at late‐stage but unexpectedly returned to baseline levels at end‐stage, suggesting exhaustion of response in “burnt‐out” astrocytes. The spatial gene‐expression‐trajectories revealed that genes related to tripartite synapses (e.g., GLUL, GRIA2, NRXN1, SLC1A2) are dysregulated in parallel to the stereotypical progression of tangle pathology across regions. In addition, we identified substantial astrocyte heterogeneity across brain regions with a continuum from homeostatic to reactive cells through “intermediate” transitional states. Conclusion Our astrocyte snRNA‐seq dataset encompassing five regions of control and AD brains revealed distinct spat