Innate Immune Sensors in Health and Disease

Abstract

The immune system constantly patrols the body, identifying and responding to deviations from homeostasis. These deviations can include pathogens, foreign substances (such as inert particles or allergens), or signs of host tissue damage (e.g., from trauma or radiation). A robust host response is essential to resolve these challenges. Both immune and nonimmune cells work together to initiate these critical responses. All cells express a variety of pattern recognition receptors (PRRs) that detect potential threats. These PRRs recognize molecular patterns associated with pathogens, known as pathogen-associated molecular patterns (PAMPs), or molecular patterns derived from damaged host tissue, known as damage-associated molecular patterns (DAMPs) (Figure 1).

One of the major classes of pattern recognition receptors (PRRs) includes membrane-bound Toll-like receptors (TLRs). As membrane-bound receptors, TLRs recognize extracellular threats, including PAMPs and DAMPs present in the extracellular milieu or within endosomes. Humans possess 10 functional TLRs, designated TLR1 to TLR10 [1]. In contrast, mice—the most used model system in research—have twelve functional TLRs, including TLR1 to TLR9 and then TLR11 to TLR13 [1]. Similarly, C-type lectin receptors (CLRs) [2] and formyl peptide receptors (FPRs) [3] are membrane-bound PRRs that recognize distinct extracellular PAMPs and DAMPs. Collectively, these membrane-bound PRRs initiate signaling pathways, including nuclear factor kappa B (NFκB), mitogen-activated protein kinases (MAPK) and interferon (IFN) signaling. This activation ultimately leads to the production of pro-inflammatory cytokines and promotes a protective immune response.

While membrane-bound PRRs effectively detect extracellular PAMPs and DAMPs, they are less suited for sensing intracellular threats. Many pathogens—including viruses, bacteria, and protozoa—have evolved to survive within intracellular niches. Additionally, cellular damage within the intracellular milieu (i.e., damage of organelles) must also be detected, a task that membrane-bound PRRs cannot perform. Fortunately, immune cells are equipped with a diverse array of cytoplasmic PRRs to detect intracellular PAMPs and DAMPs. These cytoplasmic sensors can be broadly classified into three major groups: Nod-like receptors (NLRs), AIM2-like receptors (ALRs) and RIG-I-like receptors (RLRs). Additionally, broad classes of RNA and DNA sensors—including DEAD/H-box helicases and ZBP1—play crucial roles in intracellular immune surveillance. These have been reviewed in this issue and will be discussed in brief below.

The innate immune response is a double-edged sword. An insufficient immune response can result in uncontrolled infections and impaired tissue repair, whereas an overactive or dysregulated immune response can lead to autoinflammation and immunopathology. Our understanding of the roles of cytoplasmic PRRs in health and disease continues to evolve. In this review, we compile and summarize current knowledge on various innate immune sensors in different infections and disease conditions. In particular, we highlight the role of the NLRP3 inflammasome in multiple pathological contexts, which will be briefly discussed in the following sections.

Cytoplasmic sensors are unique in that some members of this group can assemble into a multiprotein complex known as the inflammasome. The term inflammasome—coined by Dr. Jürg Tschopp—refers to a multimeric protein complex composed of a cytoplasmic PRR, the adaptor protein ASC, and the cysteine protease caspase-1 [4]. Extensive research in this field has now identified exceptions to this classical composition. For instance, CARD-containing PRRs can bypass the requirement for ASC in certain settings (e.g., The NLRC4 inflammasome) [5], while caspase-11 (and caspase-4/−5 in humans) can substitute for caspase-1 in noncanonical inflammasomes [6]. Several inflammasomes have been extensively studied, including NLRP1, NLRP3, NLRC4, AIM2, and Pyrin. However, recent discoveries have expanded the list of inflammasome-forming sensors to include NLRP6, NLRP7, NLRP9, NLRP10, NLRP11, NLRP12, CARD8, and MxA [7]. In this issue, Pandey et al. [8] provide a comprehensive list of inflammasome-forming sensors in both mice and humans, highlighting similarities and differences between the two species. More importantly, they detail the various pathogen- and self-derived triggers sensed by these cytoplasmic PRRs, the mechanisms of their activation, and the molecular and signaling pathways driving the assembly of these emerging inflammasomes [8]. A common consequence of inflammasome activation—including the newly identified ones discussed in this review—is the production of pro-inflammatory cytokines IL-1β and IL-18, as well as gasdermin D (GSDMD)-mediated pyroptotic cell death [8].

Among all inflammasomes, the NLRP3 inflammasome is one of the most extensively studied. Unlike other inflammasome sensors, NLRP3 does not recognize a specific stimulus or a ligand; rather, it detects common intracellular ionic changes triggered by a variety of stimuli such as ATP, nigericin, and monosodium urate. Specifically, a decrease in intracellular potassium levels has been proposed as a converging mechanism through which these diverse stimuli activate NLRP3 [9]. The exact mechanism by which NLRP3 senses potassium fluctuations remains unclear. However, recent studies suggest that NEK7 may act as an intermediary molecule facilitating this process [10].

The activation of the NLRP3 inflammasome occurs through a two-step process: (1) a priming step whereby activation of NFκB and MAPK signaling leads to the upregulation of NLRP3, pro-IL-1β, and pro-IL-18, and (2) an activation step whereby specific stimuli promote NLRP3 oligomerization and the formation of the NLRP3 inflammasome complex. A deeper analysis of the priming step reveals it is not merely about upregulating NLRP3, pro-IL-1β, and pro-IL-18, but also about “licensing” NLRP3 for activation through a process of deubiquitylation [11]. MAPK, including ERK, JNK, and p38, plays essential roles in the priming, licensing, and activation of the NLRP3 inflammasome. Vervaeke and Lamkanfi [12] provide a detailed review of this process in this issue. Specifically, they discuss (1) recent advances in our understanding of MAPK-induced AP-1 signaling in the transcriptional regulation of NLRP3, (2) the specific roles of ERK and JNK in NLRP3 licensing, and (3) the role of TAK1 in linking death receptor signals to NLRP3 inflammasome activation [12]. Additionally, Vervaeke and Lamkanfi [12] also review the role of MAPK in regulating the NLRP1 inflammasome.

Mitochondria are key intracellular organelles essential for the spatial regulation of the NLRP3 inflammasome. Beyond providing critical signals for the NLRP3 inflammasome—such as mitochondrial DNA, reactive oxygen species (ROS), and free ATP—mitochondria also serve as a platform for NLRP3 inflammasome nucleation [13]. Specifically, cardiolipin, expressed by damaged mitochondria, can directly bind and recruit NLRP3, initiating inflammasome activation [14]. Unsurprisingly, autophagy and mitophagy—the cell's cleanup mechanisms—help limit NLRP3 inflammasome activation by processing damaged mitochondrial components and mitigating NLRP3-activating signals. Gupta et al. [15] review the roles of autophagy and mitophagy in regulating the NLRP3 inflammasome and discuss recent advances in this area. Furthermore, their review explores the impact of these processes in lung diseases, specifically linking them to NLRP3 inflammasome regulation [15]. Given the requirement for NLRP3 localization to specific organelles such as mitochondria, the endoplasmic reticulum and the Golgi apparatus, recent research has highlighted the crucial role of lipids in recruiting and assembling NLRP3 at these sites, ultimately driving inflammasome activation. In this issue, Anand reviews the importance of lipid biosynthesis—specifically cholesterol and palmitate—in NLRP3 inflammasome activation [16]. Additionally, Anand's review discusses the role of fatty acyl chains and lipid peroxidation in NLRP3 activation, emphasizing their potential link to metabolic diseases [16].

In the next review, Li et al. [17] discuss the role of ROS in inflammasome activation and how maintaining a balance in ROS regulation is crucial for preventing colorectal cancer. There are two primary sources of ROS: mitochondria and NADPH oxidases. NCF4, a component of the NADPH oxidase, contributes to ROS generation in myeloid cells. Li et al. [17] provide insights into how NCF4 functions as a ROS sensor to regulate ROS levels and NLRP3 inflammasome activation.

The recognition of pathogenic bacteria by different cytoplasmic sensors triggers inflammasome activation, leading to the activation of caspase-1. This, in turn, results in (1) the processing of pro-IL-1β and pro-IL-18 into their bioactive forms, IL-1β and IL-18, which play a key role in recruiting immune cells, and (2) the cleavage of GSDMD, releasing the N-terminal fragment that initiates inflammatory cell death, known as pyroptosis. While IL-1β and IL-18 are crucial for immune cell recruitment, pyroptosis directly contributes to pathogen control by eliminating the pathogen's niche and further attracting immune cells. However, the immunological consequences of pyroptotic cell death vary depending on the type of cells undergoing pyroptosis. Oh et al. [18] review the role of pyroptosis during Gram-negative bacterial infections, highlighting how mechanisms and outcomes differ across macrophages, neutrophils, and epithelial cells. Macrophage undergoing pyroptosis form pore-induced intracellular traps (PITs), which can capture invading bacteria and facilitate their clearance by phagocytes, such as neutrophils. Neutrophils during pyroptosis promote the formation of peptidyl arginine deiminases (PAD)-dependent neutrophil extracellular traps (NETs), which help immobilize pathogens for clearance. Epithelial cells, during bacterial invasion, undergo pyroptosis, leading to cell extrusion and their release into the lumen. Oh et al. [18] discuss the consequences of these events in the context of in vivo infections.

Viral infections, including influenza virus, respiratory syncytial virus, and more recently, SARS-CoV-2, have been implicated in inflammasome activation, which plays a crucial role in regulating subsequent immune responses. Importantly, several virus-encoded proteins have been shown to inhibit inflammasome activation, allowing viruses to evade host immunity. Rodrigues and Zamboni [19] focus on RNA respiratory viruses with special emphasis on Influenza virus and SARS-CoV-2, providing a robust discussion on the mechanisms leading to inflammasome activation. They also highlight various viral components that negatively regulate these pathways. Additionally, the review explores current therapeutic strategies aimed at modulating these pathways to mitigate viral pathogenesis [19]. On a related note, Woolls et al. [20] offer a comprehensive overview of how NLRs regulate immune responses during viral infections. Functionally, NLRs can be classified into four major groups: (1) NLRs that form inflammasomes, which are discussed extensively in this issue concerning their roles in health and disease, (2) NLRs that positively regulate signaling pathways, (3) NLRs that negatively regulate signaling pathways, and (4) NLRs that function as transcriptional regulators [21]. Woolls et al. [20] review how viruses activate a diverse range of NLRs leading to inflammasome activation (e.g., NLRP1, NLRP3, NLRP6, and NLRC4), positive regulation of immune signaling (e.g., NOD1, NOD2), and negative regulation of immune pathways (e.g., NLRP12, NLRC3, and NLRX1). The review further explores how these NLRs contribute to antiviral immunity.

The role of the NLRP3 inflammasome in neuroinflammation has gained significant attention over the past decade, with several NLRP3 inhibitors currently under investigation as potential therapeutics for neurodegenerative diseases such as Alzheimer's disease (AD), Parkinson's disease (PD), multiple sclerosis (MS), and amyotrophic lateral sclerosis (ALS) [22]. One promising molecule in this context is beta-hydroxybutyrate (BHB)—a ketone body generated from fatty acids—which has been shown to negatively regulate NLRP3 inflammasome activation [23]. Notably, BHB levels inversely correlate with AD pathology, and supplementation with BHB has been demonstrated to mitigate AD progression in a mouse model [24]. In their review, Shippy et al. [24] summarize how ketone bodies—specifically BHB—are derived from fatty acids during ketogenesis and utilized as an alternate energy source. Additionally, the authors discuss BHB metabolism in microglia, the brain's resident immune cells, and provide a mechanistic perspective on how BHB inhibits NLRP3 inflammasome activation [24]. Finally, they review existing literature and explore how targeting ketone body metabolism could be leveraged as a therapeutic approach for AD [24]. Like AD, epilepsy is a neurologic disorder; however, unlike AD, the role of inflammasomes and neuroinflammation in epilepsy remains poorly understood. Hollis and Lukens [25] provide an in-depth review of DAMPs, inflammasome sensors (NLRP1, NLRP3, NLRC4, and AIM2), and their effector cytokines (IL-1β, IL-18) and GSDMD in epilepsy pathogenesis. The review also discusses various immune therapies aimed at regulating inflammasome activation in epilepsy models [25]. Collectively, these reviews underscore the critical role of inflammasomes in neuroinflammation and suggest that targeting these pathways could offer much-needed therapeutic strategies for neurodegenerative diseases and epilepsy.

The sensing of pathogen-associated RNA and DNA molecules is critical for eliciting effective immune responses. In the context of viral infections, members of the DEAD/H-box helicase family, including RIG-I and MDA5, play essential roles in detecting viral RNA and initiating downstream signaling pathways necessary for pathogen control. However, mutations in several DEAD/H-box helicases have also been linked to autoimmunity. In their comprehensive review, Parthun et al. [26] explore the diverse functions of DEAD/H-box helicases, summarizing current literature on their role in antiviral immunity. Notably, the review also highlights the noncanonical functions of these helicases, including their involvement in viral replication and propagation, their roles in nonviral infections, and their contribution to autoimmune diseases and cancer [26]. Given their broad immunological functions, DEAD/H-box helicases have emerged as promising targets for novel therapeutic development in recent years. Parthun et al. [26] provide a detailed discussion on the latest advancements in this area, shedding light on potential therapeutic strategies targeting these RNA heicases.

Among DNA sensors, Z-nucleic acid binding protein 1 (ZBP1) has gained significant attention for its role in initiating innate immune responses, inflammation, and cell death pathways. Through its Zαβ-domains, ZBP1 detects both RNA and DNA in their Z-confirmation. Given the critical involvement of inflammation and cell death in various diseases, ZBP1 has become a promising therapeutic target. In their review, Mishra et al. [27] provide a detailed historical background on ZBP1 and the mechanisms that regulate ZBP1-mediated cell death following Z-nucleic acid sensing. Their review comprehensively covers both infection-dependent (including viruses, bacteria, fungi, and protozoa) and infection-independent (endogenous Z-RNA-mediated inflammation) roles of ZBP1 in regulating infectious and autoinflammatory diseases [27]. Recent research has also identified a direct link between ZBP1, adenosine deaminase acting on RNA-1 (ADAR1), and cyclic GMP-AMP synthase (cGAS), highlighting their involvement in nucleic acid sensing and cancer. These findings suggest that targeting ZBP1 activation could serve as a potential therapeutic strategy for cancer, a topic explored in detail by Mishra et al. [27] in their review.

As discussed above, both foreign and self-DNA can activate the immune system by stimulating various DNA sensors. The immune system is equipped with a diverse set of DNA sensors, including TLR9, cGAS, AIM2, IFI16, DNA-PK, and DDX41, which play crucial roles in detecting pathogen-associated DNA fragments and controlling infections. However, the detection of self-DNA can lead to unwanted inflammation and contribute to metabolic disorders. In their review, Kwak et al. [28] explore the potential sources of self-DNA accumulation in metabolic diseases and discuss how different DNA sensors recognize this DNA, ultimately impacting metabolic disorders and cardiovascular diseases. The review provides an in-depth analysis of how these DNA sensors contribute to conditions such as obesity, diabetes, fatty liver disease, and cardiovascular disease [28].

The final two reviews in this issue examine the innate immune system in the context of disease. Lee and Lupfer [29] review current literature on COVID-19 infections caused by the SARS-CoV-2 virus, detailing the immunological characteristics of the disease from an innate immune perspective. Studies have shown that the intensity of innate immune responses correlates with the severity of COVID-19 infections in humans. Various clinical trials have explored targeting these pathways to mitigate COVID-19-associated morbidity, mortality, and complications. In their review, Lee and Lupfer [29] provide a comprehensive analysis of clinical trials that investigated the therapeutic potential of targeting different inflammatory pathways, including tyrosine kinase inhibitors, JAK inhibitors, TNF inhibitors, inflammasome and IL-1β inhibitors, IL-6 inhibitors, complement inhibitors, anti-inflammatory drugs, and corticosteroids.

In the final review of this issue, Saini and Gurung [30] examine the immunopathology associated with acute radiation exposure, highlighting the cellular consequences and proximal signaling pathways that are activated in response to radiation. Specifically, the review focuses on cellular responses to DNA damage, including DNA damage recognition, cell cycle arrest, and DNA repair mechanisms. Innate immune sensors play a crucial role in detecting DAMPs generated by radiation-induced DNA damage. The review discusses the involvement of TLRs and cytoplasmic sensors in regulating radiation-induced lethality [30]. One of the major consequences of radiation exposure is cell death, and Saini and Gurung [30] provide a comprehensive overview of the various cell death pathways that are engaged following radiation exposure.

Our innate immune system employs a wide assortment of PRRs to detect PAMPs and DAMPs. As evident from the collection of reviews in this issue—though not exhaustive—we possess multiple redundant PRRs to ensure rapid detection of threats and the maintenance of homeostasis. However, the resulting inflammatory responses must be tightly regulated. When the immune system becomes dysregulated, it can lead to immunopathology, autoinflammation, and metabolic diseases. Despite significant scientific advancements, many innate immune sensors remain poorly understood, necessitating further research to uncover their precise functions. These studies will help reveal novel therapeutic targets for treating infectious and inflammatory diseases.

The author declares no conflicts of interest.