Abstract
Background
Recent genetics studies for Alzheimer’s disease have identified multiple risk variants affecting amyloid processing, immune response, lipid transport, and endocytosis, among ...others 1. More than half the risk genes associated with late‐onset AD are selectively expressed in microglia and peripheral myeloid cells. Yet, we know little about the underlying biology or how myeloid cells contribute to AD pathogenesis.
Method
To gain insights into the broad impact of genetics on microglia, we selected 50 cell lines from the CIRM biobank with variable APOE genotypes and polygenic risk scores (PRS). Building on our in vitro platform that recapitulates microglia states in vitro 2, we used villages 3, or pooled culture, to differentiate these lines into microglia and assessed key microglia functions, transcriptional profiles, and response to various perturbations.
Result
Cell villages allow us to compare phenotypes across lines with little technical variability robustly. Our data determined functional phenotypes that were altered by PRS and others that were affected by APOE genotypes. Moreover, quantitative trait locus (QTL) analysis identified new variants affecting phagocytosis, proliferation, and response to lipids. Finally, single‐cell RNA sequencing of our village pinpointed key microglia pathways altered between high and low PRS individuals.
Conclusion
Cell village allows for the characterization of up to hundreds of cell lines while minimizing technical variability allowing us to identify phenotypes dysregulated across various genetic backgrounds. Our data pinpointed the impact of a novel Alzheimer’s disease PRS on microglia states and functions and identified new variants affecting microglia functions.
1. Sims, R., Hill, M. & Williams, J.
Nat Neurosci
23
, 311‐322 (2020). 2. Dolan, M.‐J.
et al. Biorxiv
2022.05.02.490100 (2022)
https://doi.org/10.1101/2022.05.02.490100
. 3. Wells, M. F. et al. Biorxiv 2021.11.08.467815 (2021)
https://doi.org/10.1101/2021.11.08.467815
.
Abstract
Background
Emerging genetic studies of late‐onset Alzheimer’s Disease (LOAD) implicate microglia, the brain’s resident macrophages. More than half the risk genes associated with LOAD are ...expressed in microglia, yet we know little about the underlying biology or how myeloid cells contribute to LOAD pathogenesis. Single‐cell transcriptomic studies reveal diverse microglial states in patients and mouse models; however, we lack tools to track these states and understand the impact of environmental challenges or genetic susceptibility.
Method
We used human embryonic and induced pluripotent stem cell models to gain insights into microglia. These cells can be differentiated into microglia, enabling the broad characterization of cells
in vitro
and understanding their impact on the other cell types in xenograft models, allowing us to gain biological insight into disease pathogenesis.
Result
Our lab has developed a novel human stem cell‐based platform1 which induces stem cell‐derived microglia (iMGLs) to take on diverse transcriptional signatures similar to those found in the human brain in response to exposure to brain‐relevant substrates. Moreover, we conceived a lentiviral protocol that allows for efficient genetic manipulation of microglia (>90% transduction). Building on these systems, we generated reporters of microglia state to track the expression of key microglial genes and adapted iPSC “villages”2, or pooled cultures, that combine iPSC cell lines in the same dish. Using these tools
in vitro
and in xenograft models3,4, we identified genetic regulators and functional changes of microglia states in LOAD.
Conclusion
Together, these tools represent a broad toolset that will allow us to answer some of the most pressing questions, such as when and how in disease these states are formed, what is their impact on disease progression, and how plastic they are. These tools will be invaluable to understanding the role of microglia in AD and the brain in general.
1. Dolan, M.‐J.
et al. Biorxiv
2022.05.02.490100 (2022)
2. Wells, M. F. et al.
Biorxiv
2021.11.08.467815 (2021)
3. Hasselmann, J. et al.
Neuron
103
, 1016‐1033.e10 (2019)
4. Mancuso, R. et al.
Nature Neuroscience
22
, 2111‐2116 (2019)
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.
