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E4BP4 in macrophages induces an anti-inflammatory phenotype that ameliorates the severity of colitis

Transcription factor E4BP4 mediates the production of anti-inflammatory components that reduce the magnitude of intestinal inflammation in mice.


Macrophage dysregulation is implicated in inflammatory bowel disease. In this study, the upregulation of the transcription factor E4BP4 in macrophages reduced colitis severity in mice. RNA-seq and single-cell analyses showed that increased levels of E4BP4 raised the expression of anti-inflammatory genes and reduced the expression of pro-inflammatory genes. Knockout of E4BP4 increased proinflammatory gene expression and decreased anti-inflammatory gene expression. ChIP and ATAC-seq identified Il4ra as a target of E4BP4, which may drive polarization. This suggests that E4BP4 may regulate macrophage inflammatory phenotypes and is a potential therapeutic target in inflammatory bowel disease.

Main Points

  •  The authors generated transgenic mice highly expressing E4BP4 in macrophages, using dextran sulfate sodium (DSS) to induce colitis through epithelial damage and intestinal bacterial invasion. Mutant mice exhibited significantly decreased markers of inflammation and tissue damage than wild type (WT), showing preservation of their microbial diversity.
  • Single cell RNA-seq of lamina propria CD45 positive cells suggested milder inflammation in mutant compared to WT, an upregulation in anti-inflammatory genes C1q and ApoE, and concomitant downregulation of pro-inflammatory genes Iftim3, Plac8 and Thbs1. This suggested that E4BP4 is upregulated in macrophages during inflammation and may induce anti-inflammatory genes.
  • RNA-seq of cells overexpressing E4BP4 through lentiviral vector induction showed 708 differentially expressed genes, including increased expression of anti-inflammatory genes Il4a and C1qa and deceased expression of pro-inflammatory genes Txnrd, Odc1 and Mmp12. RNA-seq of murine macrophages subject to CRISPR/Cas9-mediated knockout of E4MP4 showed 2956 differentially expressed genes, including downregulation of Il4ra, C1qa and Ccl5 and upregulation of Pdc1 and Mmp12. Analysis of genes overlapping between the induction and knockout datasets showed 218 targets and identified the transcription factor CEBPB as a potential regulator of anti-inflammatory genes downstream of IL4ra.
  • Chromatin immunoprecipitation sequencing identified 56,329 potential binding sites for E4BP4, including in Per1. Gene ontology (GO) analysis showed an enrichment of genes associated with focal adhesion, migration, and interaction with the extracellular matrix. Transposase-accessible chromatin sequencing showed 3802 peaks where 1.4% located in promotor and TSS regions. GO analysis of genes identified by both ChIP-seq and ATAC-seq showed that E4BP4 binds to Il4ra and promotes its expression, inducing polarization towards an anti-inflammatory phenotype.


This study suggests that E4BP4 regulates Ilr4ra expression, inducing anti-inflammation in macrophages. It may play a role in adaptation to environmental changes, translating information such as circadian cycles, inflammation, and stress. Further elucidation of the role of E4BP4 in macrophages will help in the development of therapeutic strategies against pathologes like inflammatory bowel disease.




If you need to investigate acute and chronic colitis, Epistem can help. Our science team has in-depth experience across a range of techniques , including Immuno labelling.:

  • Epistem offer a range of models that allow researchers to look at the importance of different cell types for the development and maintenance of inflammatory bowel disease.  Models of both acute and chronic colitis are available. Key cell populations can be identified by immuno-labelling techniques and can be administered to control disease, or isolated for phenotyping and/or short-term culture and functional assays.A range of analytical platforms are available to support this work, including histology and quantitative image analysis, flow cytometry, luminex-based multiplex analysis of cytokines and chemokines andgene expression analysis