Plasticity of Human Microglia and Brain Perivascular Macrophages in Aging and Alzheimer’s Disease

Microglia and perivascular macrophages, myeloid-origin resident immune cells in the human brain, play crucial roles in Alzheimer’s disease (AD)[1][1]–[4][2]. However, the field lacks a unified taxonomy describing their heterogeneity and plasticity[5][3]. To address this, we applied single-cell profiling to two independent, demographically diverse cohorts. The first comprises 543,012 viable myeloid cells from 137 unique postmortem brain specimens, while the second consists of 289,493 myeloid nuclei from 1,470 donors. Collectively, they cover the human lifespan and varying degrees of AD neuropathology. We identify 13 transcriptionally distinct myeloid subtypes, including the “GPNMB” subtype that proliferates with AD. We distinguish two contrasting homeostatic microglial states in AD and with aging: the first (“FRMD4A”) wanes over time, while the second (“PICALM”) becomes more prevalent. By prioritizing AD-risk genes, including PTPRG, DPYD, and IL15, and placing them into a regulatory hierarchy, we identify common upstream transcriptional regulators, namely MITF and KLF12, that regulate the expression of AD-risk genes in the opposite directions. Through the construction of cell-to-cell interaction networks, we identify candidate ligand-receptor pairs, including APOE:SORL1 and APOE:TREM2, associated with AD progression. We show polygenic risk for AD predisposes and prioritize the GPNMB subtype as a therapeutic target of early intervention. Our findings delineate the relationship between distinct functional states of myeloid cells and their pathophysiological response to aging and AD, providing a significant step toward the mechanistic understanding of the roles of microglia in AD and the identification of novel therapeutics. ### Competing Interest Statement F.J.T. consults for Immunai Inc., Singularity Bio B.V., CytoReason Ltd, Omniscope Ltd, Cellarity, and has ownership interest in Dermagnostix GmbH and Cellarity. The remaining authors declare no competing interests. ### Funding Statement We acknowledge the National Institute on Aging for their generous support in funding this research with the following NIH grants: R01AG065582 (PR, VH), R01AG067025 (PR, VH), and R01AG082185 (PR, VH, DL). ROSMAP is supported by P30AG10161, P30AG72975, R01AG15819, R01AG17917. U01AG46152, U01AG61356.Human Brain Collection Core (HBCC) at the National Institute of Mental Health-Intramural Research Program is supported by the NIMH-IRP under project ZIC MH002903. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Ethics committee/IRB of Mount Sinai gave ethical approval for this work. Ethics committee/IRB of James J. Peters Department of Veterans Affairs Medical Center gave ethical approval for this work. Ethics committee/IRB of Rush Alzheimer's Disease Center gave ethical approval for this work. Ethics committee/IRB of National Institute of Mental Health Human Brain Collection Core gave ethical approval for this work. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes [1]: #ref-1 [2]: #ref-4 [3]: #ref-5