Cx3Cr1-Cre induction leads to microglial activation and IFN-1 signaling caused by DNA damage in early postnatal brain.

Cx3cr1^CreER-driven Cre recombinase (Cre) is a widely used genetic tool for enabling gene manipulation in microglia and macrophages. However, an in-depth analysis of the possible detrimental effects of Cre activity in microglia, surprisingly, remains missing. Here, we demonstrate an age-dependent sensitivity of microglia to Cx3cr1-Cre toxicity, wherein Cre induction, specifically in early postnatal microglia, is detrimental to microglial development, proliferation, and function. Tamoxifen (TAM)-induced Cre activity leads to microglial activation, type 1 interferon (IFN-1) signaling, and increased phagocytosis, causing aberrant synaptic pruning during the early postnatal period and anxious behavior at later age. The detrimental effects of Cre induction are caused by DNA-damage-induced toxicity in microglia and are limited to the early postnatal period, showing no detrimental effects in adult microglia. Thus, our study reveals an age-dependent vulnerability of microglia to Cre activity, thereby highlighting age dependency of Cre action, which could be especially applicable in the broader context of environment-responsive cell types. [Display omitted] • Cx3cr1^CreER-driven neonatal Cre induction adversely affects microglial development • Cre induction causes DNA damage and IFN-1 signaling, affecting microglial functions • Adverse effects of Cx3cr1^CreER induction are limited to neonatal stages • Vehicle- versus TAM-treated Cre⁺ animal comparison is a critical control Sahasrabuddhe and Ghosh demonstrate that neonatal microglia are specifically vulnerable to Cre toxicity when Cre is driven via the Cx3cr1 promoter. This study uncovers the age and promoter dependence of Cre recombinase's action in microglia, highlighting the need for correct controls when using the Cre- loxP system for gene manipulation in general. [ABSTRACT FROM AUTHOR]