Exploring the Mechanism of SETDB1 in Regulating Neuroinflammation and Anxiety-Depression-like Behaviors [RNA-seq]

Depression is a globally prevalent disabling mental illness with serious social hazards. Previous studies suggest that neuroinflammation plays an important role in the pathogenesis of depression, but the underlying mechanism remains elusive. Endogenous retrovirus (ERVs) is a type of transposable elements (TEs), consists around 8% of human genome but are mostly silenced in vivo. Repressive histone modifications H3K9me3 mediated by the methyltransferase SETDB1 plays a key role in maintaining silencing of ERVs. In this study, we constructed Setdb1-CK-cKO (KO) transgenic mice. Behavioral tests showed that the KO mice exhibited anxiety-depression-like behaviors compared to wild type (WT). Cortex snRNA-seq analysis revealed significant changes in astrocytes in addition to excitatory neurons, with the emergence of a new sub cluster of astrocytes in the KO whose transcriptional profile exhibited specific ERVs activation. We observed a large number of GFAP-positive cells in the KO cortex and striatum by Immunostaining, suggesting reactive astrogliosis. Transcriptomic analysis of astrocytes revealed significant upregulation of genes associated with inflammation in the KO cortex, including multiple chemokine genes. To investigate the potential molecular mechanism underlying "endogenous" neuroinflammation in KO mice, we focused on the purinergic receptor P2X7R, which has been reported to play an important role in mediating neuroinflammation and emotional behaviors. Most importantly, we found that the expression of P2rx7 was significantly upregulated in the KO neuron. We applied multiple epigenomic methods (RNA-seq, ATAC-seq, H3K9me3 ChIP-seq) to analyze in detail the molecular mechanism by which SETDB1 regulates the P2rx7 gene expression, and identified a novel enhancer fragment, mE1. We further constructed a SETDB1 knockout human 293T cell line and examined chromatin accessibility by ATAC-seq. We found a regulatory fragment hE1 with enhancer activity, which was present at a similar location in the human P2RX7 locus, suggesting that this mechanism is conserved between human and mouse. Knockout of P2X7R effectively ameliorated neuroinflammation and partially alleviated neuronal dysfunction as well as behaviors in Setdb1-CK-cKO mice.