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Daly AE, Yeh G, Soltero S, Smale ST. Selective regulation of a defined subset of inflammatory and immunoregulatory genes by an NF-κB p50-IκBζ pathway. Genes Dev 2024; 38:536-553. [PMID: 38918046 PMCID: PMC11293394 DOI: 10.1101/gad.351630.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 05/29/2024] [Indexed: 06/27/2024]
Abstract
The five NF-κB family members and three nuclear IκB proteins play important biological roles, but the mechanisms by which distinct members of these protein families contribute to selective gene transcription remain poorly understood, especially at a genome-wide scale. Using nascent transcript RNA-seq, we observed considerable overlap between p50-dependent and IκBζ-dependent genes in Toll-like receptor 4 (TLR4)-activated macrophages. Key immunoregulatory genes, including Il6, Il1b, Nos2, Lcn2, and Batf, are among the p50-IκBζ-codependent genes. IκBζ-bound genomic sites are occupied at earlier time points by NF-κB dimers. However, p50-IκBζ codependence does not coincide with preferential binding of either p50 or IκBζ, as RelA co-occupies hundreds of genomic sites with the two proteins. A common feature of p50-IκBζ-codependent genes is a nearby p50/RelA/IκBζ-cobound site exhibiting p50-dependent binding of both RelA and IκBζ. This and other results suggest that IκBζ acts in concert with RelA:p50 heterodimers. Notably, p50-IκBζ-codependent genes comprise a high percentage of genes exhibiting the greatest differential expression between TLR4-stimulated and tumor necrosis factor receptor (TNFR)-stimulated macrophages. Thus, our genome-centric analysis reveals a defined p50-IκBζ pathway that selectively activates a set of key immunoregulatory genes and serves as an important contributor to differential TNFR and TLR4 responses.
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Affiliation(s)
- Allison E Daly
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - George Yeh
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Sofia Soltero
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California 90095, USA
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Stephen T Smale
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, California 90095, USA;
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California 90095, USA
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, California 90095, USA
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Lucas RM, Luo L, Stow JL. ERK1/2 in immune signalling. Biochem Soc Trans 2022; 50:1341-1352. [PMID: 36281999 PMCID: PMC9704528 DOI: 10.1042/bst20220271] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 10/07/2022] [Accepted: 10/10/2022] [Indexed: 07/30/2023]
Abstract
Extracellular signal-related kinases 1 and 2 (ERK1/2) are the final components of the mitogen-activated protein kinase (MAPK) phosphorylation cascade, an integral module in a diverse array of signalling pathways for shaping cell behaviour and fate. More recently, studies have shown that ERK1/2 plays an essential role downstream of immune receptors to elicit inflammatory gene expression in response to infection and cell or tissue damage. Much of this work has studied ERK1/2 activation in Toll-like receptor (TLR) pathways, providing mechanistic insights into its recruitment, compartmentalisation and activation in cells of the innate immune system. In this review, we summarise the typical activation of ERK1/2 in growth factor receptor pathways before discussing its known roles in immune cell signalling with a focus downstream of TLRs. We examine emerging research uncovering evidence of dysfunctional ERK1/2 signalling in inflammatory diseases and discuss the potential therapeutic benefit of targeting ERK1/2 pathways in inflammation.
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Affiliation(s)
- Richard M. Lucas
- Institute for Molecular Bioscience (IMB) and Centre for Inflammation and Disease Research, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Lin Luo
- Institute for Molecular Bioscience (IMB) and Centre for Inflammation and Disease Research, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Jennifer L. Stow
- Institute for Molecular Bioscience (IMB) and Centre for Inflammation and Disease Research, The University of Queensland, St Lucia, QLD 4072, Australia
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