An efficient, non-viral arrayed CRISPR screening platform for iPSC-derived myeloid and microglia models

Authors:
Sonja Meier, Anne Sofie Gry Larsen, Florian Wanke, Nicolas Mercado, Arianna Mei, Livia Takacs, Eva Suszanna Mracsko, Ludovic Collin, Martin Kampmann, Filip Roudnicky, Ravi Jagasia
In:
Source: Stem Cell Reports
Publication Date: (2025)
Issue: 0:  2213-6711
Research Area:
Immunotherapy / Hematology
Neurobiology
Stem Cells
Basic Research
Molecular Biology
Regenerative medicine
Drug Discovery
Cells used in publication:
Macrophage, human
Species: human
Tissue Origin: blood
Microglia, mouse
Species: mouse
Tissue Origin: brain
Culture Media:
Platform:
4D-Nucleofector® 96-well Systems
Experiment

Optimized nucleofection protocol for preMacs with subsequent microglia differentiation

25 pmol of sgRNA was complexed with 2 µg of TrueCut Cas9 protein v2 (Invitrogen) for 20 min at room temperature. 50,000 preMacs per reaction were resuspended in 20 µL P3 Primary Cell Nucleofector solution (Lonza) and mixed with CRISPR-Cas9 RNPs before nucleofection with CM-137 pulse code using a 4D-Nucleofector 96-well Shuttle nucleofector (Lonza). After nucleofection, cells were allowed to rest for 5 min before 80 µL microglia differentiation medium (see earlier text) was added per well and suspension was transferred to a fibronectin-coated seeding plate (PhenoPlate, PerkinElmer) containing 100 µL differentiation medium. 75% of the medium was changed the day post-nucleofection, and then 50% medium changes were carried out every two days. 

Abstract

Here, we developed a CRISPR-Cas9 arrayed screen to investigate lipid handling pathways in human induced pluripotent stem cell (iPSC)-derived microglia. We established a robust method for the nucleofection of CRISPR-Cas9 ribonucleoprotein complexes into iPSC-derived myeloid cells, enabling genetic perturbations. Using this approach, we performed a targeted screen to identify key regulators of lipid droplet formation dependent on Apolipoprotein E (APOE). We identify the Mammalian Target of Rapamycin Complex 1 (mTORC1) signaling pathway as a critical modulator of lipid storage in both APOE3 and APOE knockout microglia. This study is a proof of concept underscoring the utility of CRISPR-Cas9 technology in elucidating the molecular pathways of lipid dysregulation associated with Alzheimer’s disease and neuroinflammation.