Systematic analysis of cellular crosstalk reveals a role for SEMA6D-TREM2 regulating microglial function in Alzheimer’s disease

Abstract

Disrupted cross-cellular communication signaling (cellular crosstalk) has been implicated in neurodegenerative diseases, including Alzheimer's disease (AD). However, there is currently no systematic characterization of brain crosstalk networks in health and disease. We systematically characterized brain cellular crosstalk networks using single-nucleus transcriptomics data from a large cohort of control and AD brain donors (n=67). We found that crosstalk interactions between microglia and neurons were highly enriched to directly involve reported AD risk genes as ligands or receptors. Computational reconstruction of the co-expression networks associated with neuron-microglia crosstalk revealed they perturb additional known AD risk genes in microglia. We identified the interaction of neuronal SEMA6D (a PLXNA1 ligand) with a highly connected microglial regulatory sub-network involving TREM2, APOE, and HLA genes, which we predict is disrupted in late AD stages. Using CRISPR-modified human induced pluripotent stem cell (iPSC)-derived microglia and treatment with recombinant SEMA6D, we experimentally demonstrated that SEMA6D promotes microglial phagocytosis and cytokine (TNFα and IL-6) release in a TREM2-dependent manner. The novel discovery that the SEMA6D-PLXNA1/TREM2 signaling axis is involved in the regulation of microglia function demonstrates that our systematic characterization of cellular crosstalk networks is an important strategy for discovering specific mediators of significant cross-cellular interactions important to AD pathogenesis, gaining wider insights into the biology of this disease, and uncovering novel therapeutics.

Evaluation of altered cell-cell communication between glia and neurons in the hippocampus of 3xTg-AD mice at two time points

“…Therefore, our results corroborate previous findings indicating increased association to AD-risk genes of microglia-associated CCC. [34][35][36][37] Most signaling mediators of predicted AD-associated interactions were not significantly differentially expressed in the 3xTg-AD hippocampus. Due to processes like post-transcriptional modifications and downstream differential expression of additional mediators, signaling mediators can be differentially regulated, regardless of the lack of significant differential expression in inhibitory and excitatory neurons.…”

“…Our findings corroborate those from a previous study that determined enrichment for AD-risk genes in neuron-microglia interactions in the human postmortem superior parietal cortex. 35 The remaining 12 To further investigate AD-risk gene-associated interactions, we constructed GRNs using ligand-receptor and target gene signaling information from the NicheNet v2 prior, a database that includes ligand, receptor, signaling mediator, and target gene information. 60 By considering any node adjacent to our predicted receptors as potential signaling mediators of AD-associated LRTs, we identified 26 signaling mediators in our receiver cell types (Bottom of Fig 5B, Table S7).…”

Altered Glia-Neuron Communication in Alzheimer’s Disease Affects WNT, p53, and NFkB Signaling Determined by snRNA-seq

“…Recently, multiple computational cell-cell communication (CCC) inference tools, which use single-nucleus RNA-sequencing (snRNA-seq) data to infer ligands and receptors, were developed to predict signaling patterns between cell types (reviewed in [28]). Using these approaches, CCC patterns in the human postmortem prefrontal cortex (PFC) were previously shown to be disrupted in AD compared to control patients [29,30]. For example, chandelier neurons were associated with an inhibitory signaling pattern in control PFC, though in AD they were associated with excitatory signaling involved in the WNT signaling pathway [29].…”

Unraveling the intercellular communication disruption and key pathways in Alzheimer's disease: An integrative study of single-nucleus transcriptomes and genetic association

“…These activated cells exert downstream effects on neurons, further implicating them in diseases including Alzheimer's Disease (AD) [6, 7]. Recent studies have leveraged single-nucleus RNA sequencing (snRNAseq) data [8-10] and intercellular communication analysis tools [11,12] to identify complex intercellular communication within the postmortem AD brains [13][14][15]. Most ndings suggest that microglia may contribute to AD's pathogenesis through ligand-receptor (LR) axis communication alterations [13][14][15], but the role of astrocytes in perturbed interactions remains largely unexplored.…”

“…Recent studies have leveraged single-nucleus RNA sequencing (snRNAseq) data [8-10] and intercellular communication analysis tools [11,12] to identify complex intercellular communication within the postmortem AD brains [13][14][15]. Most ndings suggest that microglia may contribute to AD's pathogenesis through ligand-receptor (LR) axis communication alterations [13][14][15], but the role of astrocytes in perturbed interactions remains largely unexplored. Hence, a more thorough intercellular communication analysis using snRNA-seq data is crucial for deeper insights into the interplay between non-neuronal and neuronal cells in AD.Understanding the biological relevance of dysregulated intercellular signals in AD requires a comprehensive assessment of their associated pathways [4].…”