Innate control of Adaptive Immunity and Adaptive Instruction of Innate Immunity: Bi-Directional flow of information

Abstract

The ability of the innate and adaptive immune systems to communicate with each other is central to protective immune responses and maintenance of host health. Myeloid cells of the innate immune system are able to sense microbial ligands, perturbations in cellular homeostasis, and virulence factors, thereby allowing them to relay distinct pathogen-specific information to naïve T cells in the form of pathogen-derived peptides and a unique cytokine milieu. Once primed, effector T helper cells produce lineage-defining cytokines to help combat the original pathogen, and a subset of these cells persist as memory or effector-memory populations. These memory T cells then play a dual role in host protection by not only responding rapidly to reinfection, but by also directly instructing myeloid cells to express licensing cytokines. This means there is a bi-directional flow of information first from the innate to the adaptive immune system, and then from the adaptive back to innate immune system. Here, we focus on how signals, first from pathogens and then from primed effector and memory T cells, are integrated by myeloid cells and its consequences for protective immunity or systemic inflammation.

The ability of the innate and adaptive immune systems to communicate with each other is central to protective immune responses and maintenance of host health. Myeloid cells of the innate immune system are able to sense microbial ligands, perturbations in cellular homeostasis, and virulence factors, thereby allowing them to relay distinct pathogen-specific information to naïve T cells in the form of pathogen-derived peptides and a unique cytokine milieu. Once primed, effector T helper cells produce lineage-defining cytokines to help combat the original pathogen, and a subset of these cells persist as memory or effector-memory populations. These memory T cells then play a dual role in host protection by not only responding rapidly to reinfection, but by also directly instructing myeloid cells to express licensing cytokines. This means there is a bi-directional flow of information first from the innate to the adaptive immune system, and then from the adaptive back to innate immune system. Here, we focus on how signals, first from pathogens and then from primed effector and memory T cells, are integrated by myeloid cells and its consequences for protective immunity or systemic inflammation.

Introduction

Cells of the immune system constantly interact with and communicate amongst themselves to coordinate responses against invading pathogens. A prime example of this is when myeloid cells, following detection of invading microbes via pattern recognition receptors (PRRs) [1], present pathogen specific information to naïve T cells [2–4]. This process requires myeloid cells, particularly dendritic cells (DCs), to integrate complex pathogen-derived cues [5, 6]. In addition to presentation of pathogen-derived peptides and upregulation of costimulatory molecules, these signals lead to the production of priming cytokines – thus creating a unique cytokine milieu which influences primed T cells to differentiate into the appropriate T helper (Th) cell subset(s) [7, 8]. Pathogen-derived cues can be in the form of microbial structures [5], metabolites [9], and even certain pathogenic behaviors such as invasion, attachment, or production of virulence factors [10–14]. Importantly, the net outcome of the myeloid cell response is dependent on the nature of receptors activated, meaning that unique responses can be induced by different types of pathogens. This innate-to-adaptive relay of information has been broadly termed “innate control of adaptive immunity” and remains a fundamental principle governing our understanding of protective immunity [1, 7, 8].

Following resolution of infection, effector memory T cells (Tem) persist in the host to enable rapid protection in the event of reinfection [15–19]. Reactivation of Tem was initially thought to be independent of original priming signals [20, 21], however recent work has found that Tem continue to rely on APC-derived cues for sustained and optimal effector function [22–24]. In addition to costimulation, IL-1 family cytokines were found to “license” effector cytokine production by Tem following reactivation by cognate antigens [24]. It is critical to note here that both priming and licensing cytokines share a dependency on MyD88 signaling. While myeloid cell intrinsic MyD88, downstream of TLRs, is critical for production of priming cytokines [25], Tem intrinsic MyD88 is integral to their ability to sense IL-1 family of cytokines [26]. This evolutionarily conserved usage of MyD88-dependent signaling in regulating the life of a T cell, spanning from initial priming to memory reactivation, is a remarkable feature of the innate-adaptive cross talk.

The premise behind innate control of adaptive immunity means that, by design, priming cytokines are produced downstream of PRR signaling [1]. While PRR-dependent production of IL-1β aids T cell priming and clonal expansion [27, 28], this cytokine continues to play a critical role in Tem reactivation by licensing the production of their effector cytokines. Interestingly, in the context of Tem reactivation, myeloid production of IL-1β is completely independent of PRR activation, but instead requires TNF receptor super family (TNFRSF) signaling [29]. As Tem were the source for TNFRSF ligands, this means that myeloid cells can sense presence of pathogens (through PRRs) or presence of memory T cells (through TNFRSFs) leading to production of priming or licensing cytokines, respectively. Although beneficial for host protection, licensing cytokines can also have detrimental consequences particularly in the context of T cell mediated autoimmunity [29, 30]. Here, we will focus on how myeloid cells integrate complex cues first from pathogens and then from Tem, and the costs as well as benefits associated with this bidirectional communication network.

Innate recognition of pathogen: signal integration

The concept of innate control of adaptive immunity was proposed in 1989 by Charles Janeway Jr. [1] and has since expanded to encompass sensing of conserved microbial ligands as well as virulence factors [7, 8, 31, 32]. PRR activation relays pathogen-specific information to myeloid cells, including overt pathogenic class, subcellular localization, and life-stage of the microbe [14, 32, 33]. In general, adaptors act downstream of multiple receptors and converge on a defined set of transcription factors [7, 33, 34]. While much is known about signaling pathways downstream of individual PRRs, complex pathogens rarely activate PRRs in isolation. Complexity in pathogen-induced responses therefore arises from the integration of signals downstream of multiple receptors (Figure 1).

Figure 1:

Integration of PRR signaling. Sensing of extracellular or endosomal pathogens by TLRs leads to the recruitment of TLR specific adaptor proteins. Usage of MyD88 by cell-surface TLRs leads to NF-κB activation. Endosomal TLRs that signal through MyD88 predominately activate IRF7, while usage of TRIF by TLR4 and TLR3, in the endosomes, activates IRF3. Intracellular pathogens can be sensed via microbial lipids (NOD), or by nucleic acids exposed during replication (RIG-I, MDA5, cGAS). Adaptors for these receptors are found anchored in the mitochondria (MAVS) or endoplasmic reticulum (ER) (STING). Stimulation through NOD1/2 leads to NF-κB and MAPK activation. STING signaling leads to the transcriptional activation of IRF3, while MAVS can activate both IRF3/7. Pathogen disruption of normal cellular homeostatic processes can also be sensed by host cells. Usage of host transcriptional machinery by pathogens can lead to ER stress, detected by ATF6, PERK, or IRE-1. This leads to the activation of ATF4/6 or XBP1 which results in abrogation of protein synthesis. Perturbations in host ubiquitin homeostasis triggers NOX2-dependent production of reactive oxygen species (ROS). Amino acid scarcity can be sensed through GCN2, leading to phosphorylation of eIF2 and activation of ATF4. Integration of these microbial recognition and homeostatic sensing pathways can occur at either the level of signaling or transcription, leading to responses which are distinct from the sum of their parts.

Signal integration can occur within members of the same or different PRR family [35, 36]. Simultaneous signaling of Toll-like receptor (TLR) 3 or TLR4 with TLR3, TLR7, or TLR9 leads to synergistic induction of TNF, IL-6, and IL-12 [35, 37–39]. This is due to the integration of MyD88 and TRIF signaling pathways, whereby activation of transcription factors NF-κB, c-Jun, and IRF5 are sustained [37, 39, 40]. In vivo, this synergy is beneficial for robust cytokine production and is critical for protection against MCMV, M. tuberculosis, and T. cruzi [41]. Certain viruses have also evolved to exploit this synergy as a method to enhance viral spreading [42].

PRR members from different families can also synergize, as is the case of TLRs and NOD1/2 or NOD-like receptors (NLRs) [43]. Simultaneous stimulation of NOD1/2 and TLR2 or TLR4 leads to the synergistic induction of proinflammatory cytokines and myeloid cell maturation markers [44–46]. Mechanistically, TLR and NOD signaling converges at the level of TAK1 and NEMO, leading to the rapid degradation of IkBα [47]. Further work suggests that NOD/TLR synergy could also be due to the receptors’ differential induction of TNF gene transcription or translation, respectively [48]. NOD/TLR synergy is one mechanism behind systemic inflammation seen during sepsis [49, 50], and antagonists are currently being developed as potential therapeutic options [51]. Signal integration between TLRs and NLRs is fundamentally different from NOD/TLR synergy, as sensing of both extracellular and intracellular virulence factors leads to assembly of a distinct signaling complex called inflammasome [52]. In the case of inflammasome, TLR signals act as a “priming” step allowing for the transcriptional upregulation of NF-κB targets [53, 54], while NLR stimulation triggers “activation” and assembly of the inflammasome with procaspase-1 [52, 55]. Priming-independent inflammasome activation results from simultaneous TLR and NLR stimulation, whereby IRAK1 coordinates rapid secretion of pre-synthesized proIL-18 [56, 57]. This two-step process leading to the production of IL-1β and IL-18 acts as a safeguard against unnecessary production of such tissue-damaging cytokines and ensures that inflammasome is only activated when specific virulent pathogens are detected [58, 59].

Virulence factors perturbing cellular homeostasis can also integrate with microbial cues [31]. Pathogens that rely on host translational machinery, for example, often activate host unfolded protein response (UPR) [60]. UPR directly activates MAPK and NF-κΒ, however simultaneous PRR signaling synergizes with these signals [60, 61]. Multiple pathogens also modulate host ubiquitination machinery, and subsequent ubiquitin homeostasis, to evade or exploit normal immune responses [62–64]. Perturbations in ubiquitin homeostasis were recently found to result in ROS production by macrophages, which potentiated TLR signaling [65]. Accumulation of lipid byproducts [66], or limitations in availability of nutrients [67, 68] and amino acids [69, 70] can also modulate innate immune responses [71]. While signal integration between PRRs and sensors of cellular homeostasis directly influence outcomes of innate immunity, whether they are also important for generating tailored adaptive immune responses against specific pathogens is an area of immense interest.

Dendritic cells as a bridge to adaptive immunity

The innate immune system achieves functional diversity through the division of labor across multiple specialized cells. While macrophages are well suited for rapid pathogen responses [72], type 1 and type 2 conventional DCs (cDC1s, cDC2s) are critical for priming naïve T cells [73–76], and are therefore the predominant node of integration for many pathogen-derived signals. While numerous myeloid subsets, including neutrophils and macrophages, utilize mechanisms of cell death to provide protection against pathogens [77–79], untimely death of cDCs can have negative consequences for the host if adaptive immune responses are not primed [80]. In fact, a virulence strategy utilized by measles and hepatitis C is to trigger premature cDC death [81, 82], effectively blunting priming and Tem development. One method utilized by DCs to avoid premature death is upregulation of c-FLIP during maturation [83], rendering mature DCs resistant to FasL-mediated apoptosis [84–87]. Recent work has also demonstrated that cDCs are particularly resistant to inflammatory death pathways [88–90]. Specifically, cDCs suppress inflammasome activation and pyroptosis, thereby allowing for priming of pathogen-specific T cell responses [89]. Other studies have shown that certain phagocytes can separate inflammasome activation from pyroptosis, allowing for the cell to enter a state of hyperactivation resulting in sustained secretion of IL-1β [91, 92]. While premature cDC death is detrimental to protective immune responses, it is important to note that cDC death is a natural step in limiting the overactivation of lymphocytes [93–95].

The reliance of the immune system on cDCs in eliciting adaptive immune responses is a powerful driving force for their divergence from other myeloid lineages. In fact, the ability of cDCs to suppress inflammasome activation and pyroptosis relies on expression of lineage-defining transcription factors IRF4 and IRF8 [89], suggesting that this feature is intimately intertwined with cDC development itself. Other functional implications of IRF4 and IRF8 expression in cDCs have been reported [96–100]. Although sensing of conserved microbial ligands and virulence factors can lead to qualitatively different responses from macrophages, cDCs’ resistance to specific virulence outcomes preserves their ability to prime T cells against both virulent as well as non-virulent pathogens. This division of labor and cellular segregation of function between macrophages and cDCs is integral for protective immune responses against microbes.

Innate cytokines as drivers of adaptive immunity

Signal integration at the subcellular level and diversity at the cellular level results in the production of a specific cytokine milieu which shapes adaptive immune responses. The identity of priming cytokines leading to differentiation of various Th lineages have been reviewed in depth elsewhere [8, 101, 102]. Importantly, these cues can be derived from myeloid [7, 8], stromal [103, 104], or epithelial origins [105, 106] meaning that T cells can integrate numerous signals necessary for proper effector differentiation. Subsequently, the resulting effector Th cell populations are now poised to neutralize the original invading pathogen. Following clearance of pathogen, a subset of memory T cells persists in secondary lymphoid organs (central memory T cell) or in the periphery (Tem) [107]. Should Tem see cognate peptide again, they are capable of rapidly proliferating and secreting effector cytokines to quickly combat reinfection [17, 18, 108, 109]. While reactivation is largely independent of original priming signals, recent work has demonstrated that Tem reactivation is still enhanced by co-stimulation and innate cytokines provided by APCs [20, 24, 107, 110]. Interestingly, these innate cytokines which we refer to as “licensing” cytokines are distinct from the original priming cytokines and are largely composed of IL-1 family members [24, 111–115].

Despite their different identities, priming and licensing cytokines share conserved dependency on MyD88 signaling. During priming, myeloid-intrinsic MyD88 links TLR ligation to downstream NF-κB activation, resulting in induction of T cell priming cytokines [116]. On the other hand, IL-1 family of cytokines signal through Tem intrinsic MyD88 to license their effector function [25, 117, 118]. The importance of MyD88 signaling downstream of IL-1R has previously been implicated in Tem responses [119, 120], presumably partially due to their lack of response to licensing cytokines. While IL-1β regulates effector cytokine production across all Th lineages, its ability to control murine and human Th17 cytokine production is most striking [24, 121]. We hypothesize that other IL-1 family members, like IL-18 for Th1 and IL-33 for Th2, play similar and more lineage specific roles in amplifying effector function of Tem cells. Whether these cytokines are made by myeloid cells in a MyD88-independent fashion remains an open and exciting area of investigation.

Adaptive instruction of innate immunity

In addition to sensing various pathogenic signals, myeloid cells can also sense cues provided by interacting CD4 T cells (Figure 2). The role of this communication has been suggested to be important during T cell priming where CD40 signaling in myeloid cells enhances their production of priming cytokines, although in these studies it is unclear if CD40L expression by recently activated naïve or newly generated effector T cells engaged CD40 on myeloid cells [122–124]. Upregulation of CD40L by naïve T cells is indeed dependent on their activation [125, 126], meaning that APCs must first be activated (to upregulate pMHC and costimulatory molecules). Therefore, PRR signaling is still a critical first step for APC activation during T cell priming, while TNFRSF signals originating from newly activated T cells may amplify this response [76].

Figure 2:

Crosstalk between innate and adaptive immune cells. During T cell priming, APCs provide three distinct signals to naïve T cells: pathogen-derived peptide on the surface of MHCII (1), costimulatory molecules (2), and priming cytokine production (3). These three signals are PRR-dependent. Newly activated T cells upregulate TNFRSF ligands including CD40L, which signal back to the APC to amplify cytokine production. Following clearance of pathogen, effector memory T cells (Tem) retain expression of TNFRSF ligands. During reactivation, in addition to cognate MHC-TCR engagement (1*), Tem expression of TNFα and FasL (2*) leads to myeloid cell transcription and cleavage of proIL-1β (3*), respectively. This adaptive instruction of innate immunity leads to production of licensing cytokines which are necessary for optimal Tem effector function, but autoreactive T cell engagement of this pathway can also lead to tissue damage and systemic inflammation.

In contrast to naïve T cell priming, Tem reactivation and function are largely independent of innate immune PRR activation [19, 21, 127]. Evolutionarily, this is a sound strategy as Tem have already passed rigorous checkpoints during priming. However, even though PRR activation is not necessary, Tem continue to rely on myeloid-derived licensing cytokines [24]. A mechanism of PRR-independent IL-1β production was recently described, where Tem expression of TNFRSF ligands induces proIL-1β synthesis and cleavage in interacting myeloid cells [29]. This is consistent with reports of rapid upregulation of TNFRSF ligands by Tem following TCR ligation [121, 122, 125, 128]. Together, this suggests that while myeloid cells sense microbial signals through PRRs to prime T cells, they can also sense the presence of pre-existing memory through TNFRSF. Tem essentially appear to replace microbial signals, thereby driving PRR-independent activation of the innate immune system. While PRR-independent production of IL-1β was described to occur for Tem across all Th lineages [29], it is important to note that lineage specific usage of other TNFRSF ligands has been reported [129–133]. It remains an intriguing possibility that lineage specific usage of TNFRSF signaling may provide further specification during adaptive instruction of innate immunity. Invariant NKT cells also utilize FasL expression to induce myeloid production of inflammasome-independent IL-1β, suggesting that TNFRSF-mediated instruction of myeloid cells may play a meaningful role in additional cellular contexts [134].

The physiological significance of Tem instruction of myeloid cells is that protective immunity becomes uncoupled from direct microbial recognition. This is an advantageous strategy, should the pathogen inhibit PRR signaling [135–139]. An inherent cost of this uncoupling, however, is that autoreactive Tem interacting with self-peptide(s) expressed by myeloid cells can trigger widespread production of licensing cytokines, leading to systemic inflammation [29]. In fact, numerous autoimmune diseases including rheumatoid arthritis and psoriasis are linked to pathological IL-1β production, and IL-1β blockade can ameliorate disease symptoms [140]. As there is not a clear link between inflammasome activation and many T cell driven autoimmune diseases [141], we predict that adaptive instruction of innate immune cells via engagement of TNFRSF members is a likely cause of pathology and systemic inflammation during T cell mediated autoimmunity.

Concluding remarks

When studying the interplay between innate and adaptive immune responses, much of the focus has previously been on the relay of information from innate to adaptive immune cells. While we have developed a broad understanding of the inflammatory outcomes of simultaneous engagement of multiple PRRs, the impact of such signal integration on generating tailored adaptive immune responses is not entirely clear. The influence of adaptive immunity on innate immune responses has largely been considered through their production of effector cytokines and chemokines to mobilize innate cells. Here, we have outlined how adaptive instruction of innate immunity, facilitated by cognate interaction between Tem and myeloid cells, makes a critical contribution to this bi-directional communication underlying protective immunity. While PRR signaling is necessary for DC activation during initial T cell priming, here we propose that TNFRSF signaling, initiated by Tem cells, replaces PRR signaling to activate the innate immune system.

Highlights.

• Myeloid cells sense and integrate numerous pathogen-derived signals leading to priming of a tailored Th cell response.

• Dendritic cells are a critical node for pathogen-derived signal integration, and are resistant to pathogen-induced inflammatory cell death.

• Effector CD4 T cells instruct interacting myeloid cells to produce licensing cytokines which support their optimal reactivation.