Introduction: Sustained and dysfunctional macrophage activation promotes inflammatory cardiometabolic disorders (CMDs), but the role of long non-coding RNAs in human macrophage activation and CMDs is poorly defined.
Objective: We aim to elucidate the long intergenic non-coding RNA (lincRNA) landscape of human macrophages through RNA-sequencing (RNA-seq), genomics and bioinformatics, as well as selective translational and functional studies.
Methods and Results: Using deep RNA-seq and de novo assembly of the lincRNA transcriptome of human monocyte-derived macrophages (HMDM) at resting and stimulated with lipopolysaccharide and interferon-gamma (IFN-γ) for M1-activation, and interleukin-4 for M2-activation, we identified 2,766 macrophage lincRNAs including 861 previously unannotated ones. The majority (~85%) was non-syntenic, or syntenic but not annotated, in the mouse genome. Many macrophage lincRNAs also demonstrated tissue-enriched transcription patterns (21.5%) and enhancer-like chromatin signatures (60.9%). Macrophage activation, particularly to the M1 phenotype, markedly altered the lincRNA expression profiles revealing 96 lincRNAs differentially expressed (fold-change >2 and FDR <0.01), suggesting potential role of many lincRNAs in regulating macrophage inflammatory functions. A subset of macrophage lincRNAs overlapped genome-wide association study loci for CMDs. For example, MacORIS, a syntenic lincRNA not annotated in the mouse genome, harbors variants associated with central obesity. MacORIS is macrophage-enriched and predominantly located in cytoplasm. Knockdown of MacORIS enhanced IFN-γ induced JAK2/STAT1 phosphorylation, suggesting its potential role as a repressor of IFN-γ signaling. Induced pluripotent stem cell-derived macrophages (IPSDM) recapitulated lincRNA transcriptome of primary macrophage and provide a high-fidelity model to study, in particular non-conserved, lincRNAs in human macrophage biology.
Conclusion: In summary, high-resolution transcriptomics identified 100s of lincRNAs that form part of the coordinated response during macrophage activation including specific macrophage lincRNAs associated with human CMDs that modulate macrophage inflammatory functions.