Alzheimer’s disease (AD) is the most common form of dementia but has no effective treatment. A comprehensive investigation of cell type-specific responses and cellular heterogeneity in AD is required to provide precise molecular and cellular targets for therapeutic development. Accordingly, we perform single-nucleus transcriptome analysis of 169,496 nuclei from the prefrontal cortical samples of AD patients and normal control (NC) subjects. Differential analysis shows that the cell type-specific transcriptomic changes in AD are associated with the disruption of biological processes including angiogenesis, immune activation, synaptic signaling, and myelination. Subcluster analysis reveals that compared to NC brains, AD brains contain fewer neuroprotective astrocytes and oligodendrocytes. Importantly, our findings show that a subpopulation of angiogenic endothelial cells is induced in the brain in patients with AD. These angiogenic endothelial cells exhibit increased expression of angiogenic growth factors and their receptors (i.e., EGFL7, FLT1, and VWF) and antigen-presentation machinery (i.e., B2M and HLA-E). This suggests that these endothelial cells contribute to angiogenesis and immune response in AD pathogenesis. Thus, our comprehensive molecular profiling of brain samples from patients with AD reveals previously unknown molecular changes as well as cellular targets that potentially underlie the functional dysregulation of endothelial cells, astrocytes, and oligodendrocytes in AD, providing important insights for therapeutic development. Significance Alzheimer’s disease (AD) has complex pathological mechanisms. Our limited understanding of the molecular and cellular changes in AD hindered the identification of therapeutic targets. In this study, we profiled 169,496 nuclei from the prefrontal cortical samples of AD patients and healthy controls by single-nucleus RNA sequencing. The results indicated that there is a loss of neuroprotective glial cells in AD, which may contribute to impaired neurotransmitter recycling in astrocytes, demyelination in oligodendrocytes, and perturbed synaptic pruning in microglia. Moreover, the analysis revealed a role of antigen presentation by angiogenic endothelial cells in AD. Together, our findings offer important insights into the therapeutic potential of targeting glial- and endothelial-specific pathways to restore brain homeostasis in AD.

Significance: Dysfunction of the innate immune system is involved in the pathogenesis of Alzheimer’s disease (AD); however, the pathophysiological mechanisms underlying these dysfunctions are unclear. Here we report that stimulation of IL-33/ST2 signaling rescues memory deficits and reduces the accumulation of β-amyloid in APP/PS1 mice that exhibit select pathologies associated with AD. Although impaired IL-33/ST2 signaling is associated with early progression of AD, IL-33 injection rescues contextual memory deficits and reduces the accumulation of β-amyloid in APP/PS1 mice. IL-33 skews the microglia toward an alternative activation state with enhanced Aβ phagocytic capacity and elevated antiinflammatory gene expression, which results in a decreased proinflammatory response in the brain. Thus, this study suggests that IL-33 can be developed as a new therapeutic intervention for AD.

Significance: Synaptic loss and dysfunction is associated with cognitive impairment in Alzheimer’s disease (AD). However, the pathophysiological mechanisms underlying synaptic impairment are largely unknown. Here, we reveal a previously unidentified signaling pathway whereby activation of a receptor tyrosine kinase EphA4 is critical for synaptic dysfunctions in AD. Proof-of-concept studies undertaken in both in vitro and in vivo systems demonstrate its importance in mediating the deficit of synaptic transmission and hippocampal long-term potentiation in AD models. Specifically, blocking the EphA4-dependent pathway through knockdown studies or the use of small-molecule inhibitors effectively rescues the impaired synaptic transmission induced by Aβ and reverses impaired synaptic plasticity in AD mouse models. Thus, this study reveals a new disease-modifying therapeutic intervention for AD.

Neurotrophins are key regulators of neuronal survival and differentiation during development. Activation of their cognate receptors, Trk receptors, a family of receptor tyrosine kinases (RTKs), is pivotal for mediating the downstream functions of neurotrophins. Recent studies reveal that cyclin-dependent kinase 5 (Cdk5), a serine/threonine kinase, may modulate RTK signaling through phosphorylation of the receptor. Given the abundant expression of both Cdk5 and Trk receptors in the nervous system, and their mutual involvement in the regulation of neuronal architecture and synaptic functions, it is of interest to investigate if Cdk5 may also modulate Trk signaling. In the current study, we report the identification of TrkB as a Cdk5 substrate. Cdk5 phosphorylates TrkB at Ser478 at the intracellular juxtamembrane region of TrkB. Interestingly, attenuation of Cdk5 activity or overexpression of a TrkB mutant lacking the Cdk5 phosphorylation site essentially abolishes brain-derived neurotrophic factor (BDNF)–triggered dendritic growth in primary hippocampal neurons. In addition, we found that Cdk5 is involved in BDNF-induced activation of Rho GTPase Cdc42, which is essential for BDNF-triggered dendritic growth. Our observations therefore reveal an unanticipated role of Cdk5 in TrkB-mediated regulation of dendritic growth through modulation of BDNF-induced Cdc42 activation. Accurate transmission of information in the nervous system requires the precise formation of contact points between neurons. Regulation of these contact sites involves fine tuning the number and branching of dendritic processes on neurons. Throughout development, several secreted factors act to regulate dendrite number and branching. One important family of these factors is neurotrophins, which are indispensable for the survival and development of neurons. For example, stimulation of hippocampal neurons with one neurotrophin, brain-derived neurotrophic factor (BDNF), increases the number of dendrites directly extending from the cell body. Here, we report that BDNF-stimulated dendritic growth requires phosphorylation of the BDNF receptor, TrkB, by a kinase known as cyclin-dependent kinase 5 (Cdk5). Inhibiting phosphorylation of TrkB by Cdk5 essentially abolishes the induction of dendrites by BDNF. Our observations reveal that Cdk5 serves as a regulator of neurotrophin function. Since Cdk5 and neurotrophins both play essential roles in neuronal development, our findings suggest that the interplay between Cdk5 and TrkB may also be implicated in the regulation of other biological processes during development.