Exposure of iPSC-derived human microglia to brain substrates enables the generation and manipulation of diverse transcriptional states in vitro

Abstract

Microglia, the macrophages of the brain parenchyma, are key players in neurodegenerative diseases such as Alzheimer’s disease. These cells adopt distinct transcriptional subtypes known as states. Understanding state function, especially in human microglia, has been elusive owing to a lack of tools to model and manipulate these cells. Here, we developed a platform for modeling human microglia transcriptional states in vitro. We found that exposure of human stem-cell-differentiated microglia to synaptosomes, myelin debris, apoptotic neurons or synthetic amyloid-beta fibrils generated transcriptional diversity that mapped to gene signatures identified in human brain microglia, including disease-associated microglia, a state enriched in neurodegenerative diseases. Using a new lentiviral approach, we demonstrated that the transcription factor MITF drives a disease-associated transcriptional signature and a highly phagocytic state. Together, these tools enable the manipulation and functional interrogation of human microglial states in both homeostatic and disease-relevant contexts.

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

“…Functional enrichment analysis revealed MITF, KLF12, and GLIS3 target genes involved in key biological processes for microglia function such as phagocytosis, cytokine production, and cellular response ( Figure 4F ). We find that MITF distinctly regulates phagocytic-related pathways in line with previous findings from in-vitro models 23 . In summary, by integrating SCENIC network inference with the analysis of differentially expressed genes in AD, we nominate MITF, KLF12, and GLIS3 as potential upstream master regulators of gene expression changes relevant to AD pathogenesis.…”

“…While we observe a close similarity between ADAM and PVM clusters ( Figure S2C ), we found a clear separation between the two when we enriched for conserved murine disease-associated microglia (DAM) signatures as well as human DAM signature from iPSC-derived microglia 23,24 ( Figure S2F ).…”

“…Through our GRN analysis, we prioritize MITF as the master regulator of AD risk signatures, governing the expression of numerous AD-associated genes, including APOE, DPYD, TREM2, and PTPRG 13,33,34 . The MITF network is specifically enriched for phagocytic activity markers and has previously been studied as a key regulator of homeostatic microglia functions, in particular for driving autophagic states, and for allowing microglia to move, sense, and clear Aβ/Tau proteinopathies 22,23,35–37 . Moreover, through our CCI analysis, we prioritize ligand-receptor interactions mediating the aggravation of AD progression and place ADAM as key players.…”

“…The final adaptive cluster, HSPA1A, is enriched for gene signatures responsible for adaptive response to unfolded protein, which is characterized by elevated activity of heat shock proteins and cellular stress response, with a potential role in AD neuropathology 21 . In addition, we identified a subtype, the GPNMB, which is predominantly observed in individuals with AD 22,23 . These AD-associated microglia (ADAM) feature elevated expression of GPNMB, MITF, and PTPRG genes, and functional enrichment analysis suggests increased phagocytic activity is a hallmark of these cells.…”

Triglyceride metabolism controls inflammation andAPOE4-associated disease states in microglia

“…Microglia, the resident immune cells of the CNS, are primary mediators of neuroinflammation; they adopt a variety of proinflammatory states in response to activating stimuli including pathogens, injury, protein aggregates, and cellular degeneration. Recent studies have characterized the multitude of microglial transcriptional states in mouse models, stem-cell derived human microglia, and human post-mortem brain tissue [1][2][3][4][5][6][7] . Taken together, these studies clarify that microglia are plastic and can adopt a myriad of states in response to their environment.…”