Systematic characterization of brain cellular crosstalk signaling networks in Alzheimer's disease reveals a novel role for SEMA6D in TREM2-dependent microglial activation

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. ### Competing Interest Statement T.-W.K. is a cofounder of BL Melanis Co. Ltd.