Epigenetic regulation of Leukocyte associated immunoglobulin-like receptors 1 and 2 by interferon signaling in macrophages and T cells

Background Inhibitory immune receptors are important for maintaining immune homeostasis. We recently identified epigenetic alterations in two members of this group, LAIR1 and LAIR2, in patients with inflammatory tissue damage and recurrent skin and soft tissue infections. We therefore hypothesized that the expression of LAIR1 and LAIR2 may be controlled by immune stimuli acting on discrete transcriptional regulatory elements. Methods We used flow cytometry, qRT-PCR, and RNAseq to assay LAIR1 and LAIR2 expression in human and murine immune cell subsets at baseline and post-treatment with immune mediators, including type I and II interferons, tumor necrosis factor-alpha (TNF-ɑ), and lipopolysaccharide (LPS). Using chromatin immunoprecipitation sequencing (ChIP-seq), we identified candidate transcriptional regulatory elements of LAIR genes and evaluated their regulatory activity using luciferase reporters. Results Both human and murine macrophages significantly upregulate LAIR1 expression as they differentiate from monocytes to macrophages. In response to interferons, LAIR1 protein levels increase, while LPS causes a relative reduction. Regulatory elements flanking LAIR genes exhibit distinct patterns of enhancer activity with variable responses to immune stimuli. These responses are related to discrete sets of transcription factors in inflammatory pathways that correlate with cell-specific LAIR expression patterns. In addition, we identified LAIR1 and LAIR2 regulatory elements that act as foci of 3D genome interactions with other highly active regulatory elements. Conclusions Our findings define the complex regulatory landscapes of human and mouse LAIR genes and reveal new insights into the transcriptional regulatory mechanisms that control the expression of these important immune modulatory proteins. ### Competing Interest Statement The authors have declared no competing interest.