Epigenetic regulation of innate immune dynamics during inflammation

Abstract

Innate immune cells play essential roles in modulating both immune defense and inflammation by expressing a diverse array of cytokines and inflammatory mediators, phagocytizing pathogens to promote immune clearance, and assisting with the adaptive immune processes through antigen presentation. Rudimentary innate immune "memory" states such as training, tolerance, and exhaustion develop based on the nature, strength, and duration of immune challenge, thereby enabling dynamic transcriptional reprogramming to alter present and future cell behavior. Underlying transcriptional reprogramming are broad changes to the epigenome, or chromatin alterations above the level of DNA sequence. These changes include direct modification of DNA through cytosine methylation as well as indirect modifications through alterations to histones that comprise the protein core of nucleosomes. In this review, we will discuss recent advances in our understanding of how these epigenetic changes influence the dynamic behavior of the innate immune system during both acute and chronic inflammation, as well as how stable changes to the epigenome result in long-term alterations of innate cell behavior related to pathophysiology.

Keywords: DNA methylation; epigenetics; histones; inflammation; innate immune memory; innate immune system.

Figure 1 –. Modes of innate immune memory.

Innate immune cell exposure to pathogen-associated molecular patterns alters the cellular response to future immune challenges. Immune training (e.g. β-glucan exposure) exerts an immune enhancing effect that increases the strength of future immune responses. Tolerization (e.g. LPS exposure) produces the opposite effect, diminishing the immune response to future challenges. Prolonged exposure to immune pathogens results in innate immune exhaustion, during which cells exhibit immunosuppressive behavior and normal cellular functions are severely compromised. In contrast to the acute inflammation observed during initial immune stimulation, exhausted cells pro-inflammatory behavior is often chronic and debilitating.

Figure 2 –. Major forms of histone regulation of innate immune behavior.

A) Incorporation of histone variants into nucleosomes alters the local chromatin environment to increase or decrease gene expression. In the provided example, NAP1-mediated integration of variant H2A.Z into the Tnf promoter region results in an open chromatin environment conducive to increased Tnf expression. B) Covalent modification of histone tails regulates gene expression by influencing chromatin compaction and transcription factor recruitment through histone reader proteins. These covalent modifications can be transcriptionally repressive (e.g. H3K27me3) or activating (e.g. H3K27ac). In tolerized cells, H3K27me3 incorporation into the Tnf promoter prevents NF-κB binding and gene expression, while retention of H3K27ac in the non-tolerizable Ptges promoter permits sustained NF-κB binding and transcriptional activation. C) Altered expression of histone reader proteins influences signal integration of covalently modified histones. For example, diminished expression of H3K27me3 reader protein SP140 permits the expression of H3K27me3-marked genes normally repressed through SP140 binding. D) Histones incorporated into extruded genomic DNA during neutrophil NETosis signal to nearby immune cells in order to propagate inflammation.

Figure 3 –. Epigenetic priming.

Gene regulatory features are maintained in distinct epigenetic states based on the transcriptional demands of their affiliate genes. Inactive or quiescent genes are often marked with various heterochromatin features, including repressive histone modifications (e.g. H3K9me3 and H3K27me3) and DNA methylation. During epigenetic priming, removal of DNA methylation and H3K9me3 paired with the deposition of activating histone marks H3K4me1 (enhancers) or H3K4me3 (promoters) results in a bivalent epigenetic profile to suppress gene expression while remaining poised for rapid transcriptional activation in response to further signaling cues. Finally, replacement of H3K27me3 with activating H3K27ac creates an open chromatin environment permissive to transcription factor binding and gene expression.

Figure 4 –. Pathways for DNA demethylation.

Following DNA methylation through the enzymatic activity of DNMTs, several pathways exist to restore cytosine to its unmodified state. Suppression of DNMT activity permits the global loss of 5mC in the unmethylated daughter strand following DNA replication. Alternatively, in a site-specific manner, TET enzymes promote the iterative oxidation of specific 5mC residues to 5hmC, 5fC, or 5caC. These oxidized residues are not recognized by maintenance methyltransferase DNMT1, allowing for their passive loss through DNA replication. Alternatively, 5fC and 5caC are recognized by the enzyme TDG, which targets the residue for degylcosylation to generate an abasic site. Base excision repair then restores the unmodified cytosine in a process independent of DNA replication.

Figure 5 –. Mechanisms of TET-mediated regulation of innate inflammatory processes.

A) TET-mediated DNA demethylation promotes open chromatin formation to permit the binding of methyl-sensitive transcription factors. In the provided example, TET2-mediated demethylation of NF-κB/p65 binding sites promotes transcription and boosts the innate cell’s immunostimulatory potential. B) Non-catalytic TET activity influences gene expression through the recruitment of transcription regulators via protein-protein interactions. For example, in tolerizing DCs and macrophages, TET2-mediated recruitment of HDAC2 promotes histone deacetylation at the Il6 promoter to suppress its expression. C) TET enzymes oxidize methylated cytosines on RNA molecules to alter their stability and translation. In this example, TET2 oxidation of the 3’ UTR of Socs3 leads to ADAR1 binding and suppressed translation through the enzymes base editing activity. D) Various signaling pathways and gene regulatory activities have been proposed to be mediated through readers of oxidized cytosine residues.