Abstract 673: CHROMR Governs Interferon Signaling And Cholesterol Homeostasis In Human Atherosclerotic Plaque

Abstract

Long noncoding RNAs (lncRNA) have emerged as critical regulators of gene expression, yet their potential contribution to human disease remains poorly understood. We previously identified the primate-specific lncRNA CHROMR as a key regulator of cholesterol homeostasis. Here, we report a novel function for CHROMR in controlling interferon signaling, which is known to regulate innate and adaptive immune responses that drive atherosclerosis. Using single cell RNA-sequencing of human atheroma, we observed robust expression of CHROMR in plaque immune cell populations, which correlated strongly with the expression of two subsets of interferon-stimulated genes (ISG). Interrogation of these genesets using DisGeNET, a comprehensive catalogue of genes and variants associated to human diseases, revealed associations with atherosclerosis and coronary artery disease. Differential expression analysis of CHROMR -expressing versus non-expressing immune cells showed higher levels of ISGs particularly in the monocyte-macrophage cluster. To assess the impact of CHROMR depletion on inflammatory gene expression, we knocked down CHROMR in THP1 macrophages using GapmeR antisense oligonucleotides (or controls) and treated with the TLR3 agonist poly(I:C) to stimulate the interferon response. Transcriptome profiling and unsupervised hierarchical clustering of genes differentially expressed in CHROMR -sufficient and -depleted macrophages revealed that CHROMR silencing markedly repressed expression of key ISGs, including MX1 , IFI44L , STAT1 , and CXCL and CCL family chemokines ( CXCL10 , CXCL11, CCL2 ). Conversely, overexpression of CHROMR in THP1 macrophages increased expression of these ISGs. Furthermore, CHROMR depletion in macrophages reduced histone acetylation at regulatory regions of ISG loci. Mechanistically, we showed that CHROMR sequesters the interferon regulatory factor (IRF)-2-dependent transcriptional co-repressor IRF2BP2, thereby licensing IRF-dependent signaling and transcription of the ISG network. Taken together, our work unveils a critical role for CHROMR in coordinating interferon signaling responses in macrophages and suggests that targeting this lncRNA may reduce inflammation in atherosclerotic plaques.