Analysis of the human monocyte-derived macrophage transcriptome and response to lipopolysaccharide provides new insights into genetic aetiology of inflammatory bowel disease

Abstract

The FANTOM5 consortium utilised cap analysis of gene expression (CAGE) to provide an unprecedented insight into transcriptional regulation in human cells and tissues. In the current study, we have used CAGE-based transcriptional profiling on an extended dense time course of the response of human monocyte-derived macrophages grown in macrophage colony-stimulating factor (CSF1) to bacterial lipopolysaccharide (LPS). We propose that this system provides a model for the differentiation and adaptation of monocytes entering the intestinal lamina propria. The response to LPS is shown to be a cascade of successive waves of transient gene expression extending over at least 48 hours, with hundreds of positive and negative regulatory loops. Promoter analysis using motif activity response analysis (MARA) identified some of the transcription factors likely to be responsible for the temporal profile of transcriptional activation. Each LPS-inducible locus was associated with multiple inducible enhancers, and in each case, transient eRNA transcription at multiple sites detected by CAGE preceded the appearance of promoter-associated transcripts. LPS-inducible long non-coding RNAs were commonly associated with clusters of inducible enhancers. We used these data to re-examine the hundreds of loci associated with susceptibility to inflammatory bowel disease (IBD) in genome-wide association studies. Loci associated with IBD were strongly and specifically (relative to rheumatoid arthritis and unrelated traits) enriched for promoters that were regulated in monocyte differentiation or activation. Amongst previously-identified IBD susceptibility loci, the vast majority contained at least one promoter that was regulated in CSF1-dependent monocyte-macrophage transitions and/or in response to LPS. On this basis, we concluded that IBD loci are strongly-enriched for monocyte-specific genes, and identified at least 134 additional candidate genes associated with IBD susceptibility from reanalysis of published GWA studies. We propose that dysregulation of monocyte adaptation to the environment of the gastrointestinal mucosa is the key process leading to inflammatory bowel disease.

Effects of anti-inflammatory drugs on the expression of tryptophan-metabolism genes by human macrophages

“…The scale of the transcriptional response to LPS and IFNα in these data was comparable to previous studies. LPS is itself known to induce type 1 IFNs (mainly IFNβ) in MDM, which act in an autocrine manner via IFNAR1, itself induced by LPS 27. Accordingly, the response to exogenous type 1 IFN (IFNα) was largely a subset of the LPS response, as reported in previous studies 24, 28, 50, 51, 54.…”

“…LPS also caused significant down‐regulation of genes coding kynurenine metabolic enzymes ( AFMID and CCBL7 ). Other tryptophan transporters in human macrophages, the heavy chain Y+L SLC3A2 (CD98) and SLC7A7 are expressed constitutively at high levels 27. IFNα challenge resulted in a similar profile of effects on the expression of genes encoding the kynurenine metabolic enzymes, but did not produce significant elevation of the tryptophan transporter genes (Fig.…”

“…None of the anti‐inflammatory agents we examined completely prevented the response to either challenge and, although prednisolone and anti‐TNFα both reduced expression of many genes that were up‐ or down‐regulated by the inflammatory challenges, each had a distinctive transcriptional effect. This diversity likely reflects the complex feed‐forward and negative feedback loops that characterize the response to LPS27, 55 and the different mode of action of each drug.…”

“…As part of the FANTOM5 consortium, we have recently generated extensive promotor‐level data on the time‐course of the response of MDM 27. IFNα is a type‐1 IFN and was chosen as a stimulus because of the clinical data indicating that this agent can cause a depressive syndrome in patients 6, 7.…”

“…Neutralizing anti‐TNFα antibodies act by binding to TNFα in circulation, thus blocking its proinflammatory effects mediated by action at TNF receptors 29. TNFα acts in an autocrine manner on stimulated macrophages to induce downstream targets and amplify the initial induction of proinflammatory target genes 27, 30. Indomethacin acts by inhibiting cyclooxygenase (COX) or prostaglandin synthase enzymes (COX1/COX2; PTGS1/PTGS2) 31.…”