An Epigenetic Insight into NLRP3 Inflammasome Activation in Inflammation-Related Processes

Abstract

Aberrant NLRP3 (NOD-, LRR-, and pyrin domain-containing protein 3) inflammasome activation in innate immune cells, triggered by diverse cellular danger signals, leads to the production of inflammatory cytokines (IL-1β and IL-18) and cell death by pyroptosis. These processes are involved in the pathogenesis of a wide range of diseases such as autoimmune, neurodegenerative, renal, metabolic, vascular diseases and cancer, and during physiological processes such as aging. Epigenetic dynamics mediated by changes in DNA methylation patterns, chromatin assembly and non-coding RNA expression are key regulators of the expression of inflammasome components and its further activation. Here, we review the role of the epigenome in the expression, assembly, and activation of the NLRP3 inflammasome, providing a critical overview of its involvement in the disease and discussing how targeting these mechanisms by epigenetic treatments could be a useful strategy for controlling NLRP3-related inflammatory diseases.

Keywords: DNA methylation; IL-1β; NLRP3; acetylation; epigenetics; inflammasome; pyroptosis.

Figure 1

Pathways involved in NLRP3 inflammasome priming and activation. (A). Activation of the NLRP3 inflammasome requires an initial priming step aimed to upregulate the expression of inflammasome components. That first signal, or priming (left panel), is provided by PAMPs that induce NF-_kB activation, thereby triggering the transcription of NLRP3, caspase-1, pro-IL-1β, and pro-IL-18. The FADD-caspase-8 complex is essential in this step since it allows NF-_kB to be activated. After that, the second signal is accomplished by a wide range of stimuli, such as RNA viruses, pore-forming toxins, extracellular ATP, and crystals. These stimuli alter cellular homeostasis (changes in Ca²⁺, K⁺ and Cl⁻ flux, ROS production, mitochondrial dysfunction) triggering the assembly of NLRP3, ASC caspase-1 and NEK7 proteins, and establishing the activation of the NLRP3 inflammasome. Otherwise, a non-canonical pathway is activated when LPS from Gram-negative bacteria is internalized. Human caspase-4/5 or mouse caspase-11 can directly recognize the LPS and cut GSDMD, promoting the formation of pores in the plasma membrane. At the same time, these pores facilitate the egress of intracellular K⁺, thereby triggering the activation of the NLRP3 inflammasome. In monocytes, the recognition of LPS by TLR4 guides the activation of the alternative pathway in which priming is the only necessary step. The inflammasome is activated by the multiprotein complex FADD-RIPK1-caspase-8, independently of the K+ efflux, that leads to a gradual release of IL-1β and IL-18. (B). After assembly and activation of the NLRP3 inflammasome components by the different pathways, caspase-1 is activated inducing the cleavage of the immature forms of IL-1β and IL-18 cytokines and their further release to the extracellular medium. Moreover, active caspase-1 cleaves gasdermin D (GSDMD), which forms pores in the plasma membrane that give rise to cell death by a process named pyroptosis. Although this last process is not triggered by the alternative pathway.IL-1R: IL-1β receptor. TNFR: TNF receptor. PAMPs: pathogen-associated molecular patterns. FADD: FAS-associated death domain protein. PYD: pyrin domain. LRR: leucine-rich repeat. ASC: apoptosis-associated speck-like protein. NEK7: NIMA-related kinase 7.

Figure 2

Direct and indirect mechanisms of epigenetic regulation modulating NLRP3 inflammasome activation. A variety of epigenetic mechanisms (DNA methylation, acetylation/deacetylation dynamics and miRNAs) are directly involved in the transcriptional regulation of inflammasome components. They are also indirectly involved through the modulation of factors and processes that participate in the assembly and activation of the NLRP3 inflammasome. (A). DNA methylation: During differentiation of monocytes to macrophages, regulatory regions of the ASC, CASP1, and IL1B genes are demethylated, thus enabling them to be expressed. In fact, NLRP3 is hypomethylated in infections and idiopathic syndromes to allow its transcription and further activation. ASC hypermethylation could condition the survival of tumor cells, and also contributes to alleviate cardiac failure, when exercise prevents its demethylation. (B). Acetylation/deacetylation dynamics: changes in the acetylation dynamics of genes involved in the NF-κB pathway lead to alterations in NLRP3, ASC, Caspase-1 and IL-1β transcription. During Leishmania amazonensis infection, impaired acetylation of H3K9 and H3K14 in MYD88 and RelA, blocks IκBα phosphorylation and NF-κB activation. Similarly, in acute gouty arthritis and cerebral ischemia, overexpression of BRD4 allows the expression of inflammasome components through activation of the NF-κB pathway. The recruitment of p-STAT3 and the acetylation of histones H3(K9) and H4 in the NLRP3 promoter region triggers its expression. Moreover, acetylation of the PYD domain of NLRP3 in macrophages is required for proper assembly with ASC. (C). miRNAs: downregulation of diverse miRNAs (miR-223, miR-7, miR-30e, miR-22, and miR-495) or hypermethylation of miR-145 during the development of the diseases leads to increased expression of all inflammasome components and further NLRP3 inflammasome activation. (D). Indirect regulation: epigenetic mechanisms involved in the expression of transcription factors (N2, C/EBPβ, CtBPs and XBP1), modulators of ROS production (TXNIP, and UCP2), genes encoding microtubule stabilization proteins, such as MARK4, and autophagy (ATG5) could facilitate changes in the expression of NLRP3 inflammasome components and stop the inflammasome activation.