Deep RNA Sequencing Uncovers a Repertoire of Human Macrophage Long Intergenic Noncoding RNAs Modulated by Macrophage Activation and Associated With Cardiometabolic Diseases

Abstract

BackgroundSustained and dysfunctional macrophage activation promotes inflammatory cardiometabolic disorders, but the role of long intergenic noncoding RNA (lincRNA) in human macrophage activation and cardiometabolic disorders is poorly defined. Through transcriptomics, bioinformatics, and selective functional studies, we sought to elucidate the lincRNA landscape of human macrophages.Methods and ResultsWe used deep RNA sequencing to assemble the lincRNA transcriptome of human monocyte‐derived macrophages at rest and following stimulation with lipopolysaccharide and IFN‐γ (interferon γ) for M1 activation and IL‐4 (interleukin 4) for M2 activation. Through de novo assembly, we identified 2766 macrophage lincRNAs, including 861 that were previously unannotated. The majority (≈85%) was nonsyntenic or was syntenic but not annotated as expressed in mouse. Many macrophage lincRNAs 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, suggesting potential roles in regulating macrophage inflammatory functions. A subset of lincRNAs overlapped genomewide association study loci for cardiometabolic disorders. MacORIS (macrophage‐enriched obesity‐associated lincRNA serving as a repressor of IFN‐γ signaling), a macrophage‐enriched lincRNA not expressed in mouse macrophages, harbors variants associated with central obesity. Knockdown of MacORIS , which is located in the cytoplasm, enhanced IFN‐γ–induced JAK2 (Janus kinase 2) and STAT1 (signal transducer and activator of transcription 1) phosphorylation in THP‐1 macrophages, suggesting a potential role as a repressor of IFN‐γ signaling. Induced pluripotent stem cell–derived macrophages recapitulated the lincRNA transcriptome of human monocyte‐derived macrophages and provided a high‐fidelity model with which to study lincRNAs in human macrophage biology, particularly those not conserved in mouse.ConclusionsHigh‐resolution transcriptomics identified lincRNAs that form part of the coordinated response during macrophage activation, including specific macrophage lincRNAs associated with human cardiometabolic disorders that modulate macrophage inflammatory functions.

Differentiation of Human‐Induced Pluripotent Stem Cells to Macrophages for Disease Modeling and Functional Genomics

“…Tumor‐derived monocytic cell lines, such as THP‐1 and U937, have unlimited proliferative potential and can be differentiated to macrophage‐like cells using phorbol 12‐myristate 13‐acetate that activates protein kinase C. However, these cells are karyotypically abnormal and functionally immature. Importantly, although small interfering RNA and antisense oligonucleotide‐mediated gene silencing have demonstrated some success in THP‐1 derived macrophages and HMDM (de Bruin et al., ; Zhang, Xue et al., ), clonal expansion of THP‐1 or U937 cell lines following genetic engineering to knockout target genes or introduce genetic mutations remains challenging. It is therefore imperative to develop and adapt novel experimental models that can recapitulate function and transcriptome profile of human primary macrophages and be also amenable to CRISPR/Cas9‐mediated genome engineering (Zhang, Shi et al., ).…”

“…One confluent 6‐well plate of iPSCs yields up to 2 × 10 7 of more than 95% CD45 + /CD18 + IPSDM (Zhang et al., ) and does not require positive selection using FACS or magnetic beads. Through deep RNA‐sequencing, we characterized the coding transcriptome (Zhang et al., ), alternative splicing events (Lin et al., ) and long non‐coding RNA profiles (Zhang, Xue et al., ) of isogenic IPSDM and HMDM cultured in the same macrophage culture medium at baseline and during activation, providing a comprehensive resource for planning IPSDM studies to model such events. (Zhang et al., ; Zhang, Shi et al., )…”

Profiles of Long Non-Coding RNAs and mRNA Expression in Human Macrophages Regulated by Interleukin-27

“…They modulate many pathophysiological pathways and are activated by pathogens. The role of lncRNAs in macrophage activation has been revealed by several studies [14,43]. Scacalossi et al recently reviewed the role of lncRNA in macrophage function such as in macrophage polarization, and innate and adaptive immune functions [13].…”

ASEP: gene-based detection of allele-specific expression in a population by RNA-seq

“…For example, LINC01001 , a long intergenic noncoding RNA (lincRNA), showed strong evidence of differential ASE (FDR adjusted P < 0.0001) ( Figure 6E ), and it might be involved in coordinated response during macrophage activation, and potentially regulates the inflammatory response in cardiometabolic disease. 31 Other genes of interest include NOTCH2 (FDR adjusted P < 0.0001), LILRB3 (FDR adjusted P = 0.0006), and TLN1 (FDR adjusted P = 0.0056) ( Figure S3 ). NOTCH2 plays a role in notch signaling that regulates macrophage activation in pro-inflammatory process.…”