Genetic dissection of microglia functions in complement-mediated synapse loss in Alzheimer s disease

Microglia are the macrophages of the brain and become activated in response to amyloid. Recently, single cell sequencing has defined multiple activated states of microglia including two states that are robustly induced in animals of Alzheimer’s disease (AD): disease associated microglia (DAM), and interferon responding microglia (IRM). It is now established that in response to amyloid microglia initiate the classical pathway of the complement cascade, and that the complement cascade is a critical mediator of neuronal synapse loss during disease progression. Synapse loss is among the strongest neurobiological correlates of cognitive decline in AD. Global ablation of the C1 complex (via C1qa gene knockout) preserves synapses in AD mouse models, highlighting the importance of determining the mechanisms determining the role of microglia in complement-mediated synapse loss. Yet despite much work, key knowledge gaps remain. First, the relationships among the different transcriptionally defined microglia states have not been determined. Second, all microglia express C1Q and it remains unknown whether microglia belonging to distinct states trigger synapse loss on neurons. Third, the complement cascade requires downstream components such as complement factors C2 through C9 that are not expressed by microglia, but virtually nothing is known about the spatial and temporal coordination of the specific cell types expressing these components in the brain. Filling these knowledge gaps may lead to new therapeutic avenues that prevent or intervene in synapse loss in AD. By leveraging floxed alleles of Csf1r, Trem2, Sting1, C1qa, C3, C5 and C7, microglia state specific Cre driver lines such as Cx3cr1-cre, Tmem119-cre, Itgax-cre, and Mx1-cre, and reporter lines to lineage trace distinct states, we will take a multi-modal approach based on genetic strategies to address these questions with cellular specificity. We will use distinct mouse genetic contexts we have shown are susceptible (C57BL/6J) or resilient (PWK/PhJ) to synapse loss, and we will employ state-of-the- art methodologies including single cell myeloid cell sequencing, spatial transcriptomics and protein visualization, and circuit-specific labeling of synapses. In three aims we will test the model that IRM are an intermediate microglia state necessary to recruit DAM to plaques, and that DAM are the critical state driving complement- mediated synapse loss. In Aim 1, to test whether IRM are the intermediate state between homeostatic microglia and DAM, we will lineage trace IRM, ablate DAM or IRM, and conditionally delete Sting1 (a key mediator of interferon signaling) from DAM. In Aim 2, to determine whether DAM are the primary initiators of complement mediated synapse loss, we will conditionally delete Trem2 from homeostatic microglia, ablate DAM, and conditionally delete C1qa from DAM. In Aim 3, to uncover the cell types producing the downstream components of the complement cascade, we will perform spatial transcriptomics and protein visualization. We will then conditionally delete a downstream component from its parent cell type. Successful completion of these aims will result in the identification of critical cellular and genetic contributors to complement-mediate synapse loss in AD. Project Number: 1R01AG096489-01 | Fiscal Year: 2026 | NIH Institute/Center: National Institute on Aging (NIA) | Principal Investigator: Gareth Howell (+1 co-PI) | Institution: JACKSON LABORATORY, BAR HARBOR, ME | Award Amount: $716,579 | Activity Code: R01 | Study Section: Special Emphasis Panel[ZRG1 BN-S (90)] View on NIH RePORTER: https://reporter.nih.gov/project-details/11230350