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Highlights of the advances in basic immunology in 2011

Abstract

In this review, we summarize the major fundamental advances in immunological research reported in 2011. The highlights focus on the improved understanding of key questions in basic immunology, including the initiation and activation of innate responses as well as mechanisms for the development and function of various T-cell subsets. The research includes the identification of novel cytosolic RNA and DNA sensors as well as the identification of the novel regulators of the Toll-like receptor (TLR) and retinoic acid-inducible gene I (RIG-I)-like receptor (RLR) signaling pathway. Moreover, remarkable advances have been made in the developmental and functional properties of innate lymphoid cells (ILCs). Helper T cells and regulatory T (Treg) cells play indispensable roles in orchestrating adaptive immunity. There have been exciting discoveries regarding the regulatory mechanisms of the development of distinct T-cell subsets, particularly Th17 cells and Treg cells. The emerging roles of microRNAs (miRNAs) in T cell immunity are discussed, as is the recent identification of a novel T-cell subset referred to as follicular regulatory T (TFR) cells.

Introduction

The immune system, a collection of tissues, cells and molecules, has evolved to recognize and eliminate invading pathogens. Broadly, the immune system can be divided into two categories, the innate immune system and the adaptive immune system. Although it has been known for many years that the innate immune system constitutes the first line of defense against pathogens, how the innate immune system senses danger signals from invading pathogens and distinguishes self from non-self was not understood until the identification of pattern-recognition receptors (PRRs). PRRs, which are expressed on a variety of different cell types, recognize a number of conserved structures in pathogens, termed pathogen-associated molecular patterns (PAMPs), and activate the downstream intracellular signaling pathways that mount inflammatory responses against invading pathogens at the early phase of infection.1 During the course of PRR-triggered innate immune responses, a number of endogenous molecules present in normal individuals exert dialectical regulatory effects on controlling the magnitude and duration of the inflammatory responses to avoid harmful immunopathogenesis.2 Recently, in addition to polymorphic nuclear leukocytes, antigen-presenting cells (including dendritic cells (DCs), monocytes and macrophages) and conventional natural killer (NK) cells, as well as novel cell subsets such as innate lymphoid cells (ILCs), have been identified as members of the innate immune system. The adaptive immune response develops in high-class vertebrates in the late phase of infection to eliminate pathogens that have evaded innate immunity. Adaptive immunity is characterized by the specificity of antigen recognition mediated by a broad repertoire of antigen-specific receptors and the memory responses to previously encountered antigens. T cells, because they control both the establishment and regulation of adaptive immunity, have attracted special attention in recent decades. Whereas Th1 and Th2 were first described in the 1980s, interest in several other T helper subsets, including regulatory T (Treg) cells, Th17 cells, follicular T helper (TFH) cells and regulatory follicular T (TFR) cells, has emerged in the last decade because of their unique cytokine profiles, functions and disease associations.3 In comparison with T cells, the function of B cells and their flexibility and elasticity in development remain more mysterious, and the further investigation of these cells has the potential for fascinating discoveries. In this review, we look back on the advances in basic immunological research that have had the greatest impact in 2011. We include new findings on pattern-recognition (special emphasis is placed on nucleic acid recognition and the regulation of innate immune responses); ILC; the developmental programs of T helper subsets including Th2, Th17, Treg, TFH and TFR cells; and T-cell homeostasis (the balance among naive, effector and memory T cells). Perspectives and the implications of these recent findings for health and diseases, with special emphasis on their indications for possible therapeutic strategies, are discussed.

Nucleic acid recognition

The recognition of the enormous diversity of potential invading pathogens by the innate immune system relies on the ability of the PRRs expressed on innate immune cells to detect the evolutionarily conserved structures on microbes, termed PAMPs. The PAMP engagement of PRRs causes the activation of a series of downstream signaling events that ultimately leads to the expression of pro-inflammatory cytokines and interferons (IFNs), which together orchestrate the early innate immune response and initiate the subsequent activation and shaping of adaptive immunity.4 To date, three families of PRRs, including Toll-like receptors (TLRs), retinoic acid-inducible gene I (RIG-I)-like receptors (RLRs) and nucleotide-binding oligomerization domain (NOD)-like receptors (NLRs), have been identified for their indispensable role in pathogen recognition and triggering of the antipathogen immune response. Nucleic acids are recognized as the essential components of viruses that are detected by innate immune receptors.5 However, because nucleic acids are commonly shared by the pathogen and host, the potential recognition of self nucleic acids by PRRs increases the risk of autoimmune or auto-inflammatory diseases. Thus, the specific and effective detection of microbial RNA and DNA is critical for an appropriate innate immune response against a pathogen.

Several transmembrane and cytosolic receptors have been identified for their ability to recognize multiple forms of RNA and DNA, including members of the TLRs, RLRs and several DNA sensors. To date, four TLR family members, TLR3, TLR7, TLR8 and TLR9, which are localized within endolysosomal compartments, have been studied extensively for their role in nucleic acid recognition and type I IFN induction.6

Because many viruses complete their entire infectious cycle in the cytosol, much attention has focused on discovering a mechanism for the detection of cytosolic viral RNA and DNA, which includes the identification of cytosolic PRRs, including the known RIG-I-like receptors that recognize cytosolic RNA and an analogous family of cytosolic DNA sensors. The recognition of nucleic acids by cytosolic PRRs activates the transcription factor IRF3 or IRF7 (IFN regulatory factor 3 or 7) signaling pathways and potently induces the production of type I IFN. In some cases, cytosolic DNA recognition also favors the activation of an inflammasome for the production of IL-1β. A number of the latest discoveries pertaining to the mechanisms of recognition of cytosolic RNA or DNA by PRRs are discussed below.

Recognition of cytosolic RNA

RIG-I7 and MDA5 (melanoma differentiation-associated protein 5),8 both RLR family members, as well as NOD2,9 have been implicated in cytosolic RNA sensing. Pichlmair et al.10 reported that the IFN-induced gene product IFIT1 (IFN-induced protein with tetratricopeptide repeats 1) is a sensor for 5′-triphosphorylated RNAs of viral origin. The 5′-triphosphate group is a molecular signature within RNA that is responsible for its recognition by RIG-I.11, 12 Using an affinity proteomics approach, the authors determined that the antiviral protein IFIT1 binds PPP-RNA with nanomolar affinity. IFIT1, together with other IFIT family members, forms a larger protein complex that sequesters specific viral nucleic acids in the cytoplasm, which contributes to the inhibition of the growth and pathogenicity of viruses containing PPP-RNA.13 In studies by Zhang et al., the DDX1–DDX21–DHX36 complex14 and DHX915 were identified as cytosolic sensors for dsRNA in myeloid DCs. Through the isolation and sequencing of poly I:C-binding proteins, the authors showed that the RNA helicases DDX1, DDX21 and DHX36 form a complex with the TRIF [TIR (Toll-interleukin 1 receptor) domain-containing adaptor protein inducing interferon β] adaptor molecule to sense dsRNA in the cytosol and induce type I IFN and cytokine responses to poly I:C, influenza A virus, and reovirus in myeloid DCs. In addition, DHX9, a DExDc helicase family member, is another viral RNA sensor in myeloid DCs that specifically binds the dsRNA motif of poly I:C. DHX9 interacts with IPS-1 (IFN-β promoter stimulator 1, also known as MAVS/VISA/Cardif) to activate NF-κB (nuclear factor kappa B) and IRF3 pathways, ultimately leading to IFN-α/β and proinflammatory cytokine production in response to pathogenic RNA.

In addition to the identification of additional RNA sensors, investigators also focused on the molecular mechanisms of RNA sensing and the discrimination between host- and pathogen-derived RNA. RIG-I is a key innate immune PRR that initiates an antiviral immune response upon detection of the viral RNA PAMPs. Recently, Luo et al.,16 Kowalinski et al.17 and Jiang et al.18 independently clarified the molecular basis for RIG-I activation by RNA by revealing the conformational switch between the inactivated and activated state of RIG-I. Their work provides an insightful understanding of the molecular mechanism involved in the activation of RIG-I by pathogenic RNAs. Furthermore, Daffis et al.19 and Züst et al.20 recently identified the critical role of ribose 2′-O-methylation in the mechanism for discriminating between self and non-self mRNAs. The 5′ cap structures of higher eukaryote mRNAs and many viral RNAs contain ribose 2′-O-methylation; however, until these reports, the biological role of 2′-O-methylation was unknown. The studies demonstrated that 2′-O-methylation of the 5′ cap of viral RNA enabled several viruses to evade innate antiviral responses in the host, which was attributed to the reduced sensitivity to the antiviral effects exhibited by IFIT1 and the inhibition of type I IFN induction mediated by the cytosolic RNA sensor MDA5. Therefore, the studies indicate that the 2′-O-methylation of cellular mRNAs is a molecular signature for the discrimination of self and non-self mRNAs.21

Recognition of cytosolic DNA

Regarding the recognition of microbial DNA, investigators previously identified DAI (DNA-dependent activator of IFN-regulatory factors),22 AIM2 (absent in melanoma 2)23, 24, 25 and Pol III (DNA-dependent RNA polymerase III)26, 27 as major cytosolic DNA sensors. The recognition of cytosolic DNA by DAI triggers the production of type I IFN, similar to that triggered by cytosolic RNA sensing, whereas recognition by AIM2 activates multiple complexes, termed inflammasomes, which results in the processing and secretion of IL-1β. Pol III (DNA-dependent RNA polymerase III) recognizes and transcribes transfected poly (dA:dT) DNA to 5′-ppp dsRNA, which subsequently activates the RIG-I-dependent signaling pathway.28 Recently, several additional DNA sensors have been proposed. Unterholzner et al.29 identified IFI16 as an intracellular DNA sensor and showed that IFI16 (gamma-IFN-inducible protein 16) directly associates with viral DNA motifs and induces IRF3 and NF-κB activation through recruiting the adaptor STING (stimulator of IFN genes), which ultimately mediates the production of IFN-β. IFI16 and AIM2 are PYHIN (Pyrin and HIN domain-containing protein 1) proteins, which implicates a central role for PYHIN proteins in DNA sensing. A newly defined cytosolic DNA sensor, DDX41, was reported by Zhang et al.30 The study showed that DDX41 binds both DNA and STING in the cytosol and induces NF-κB and IRF3 activation, leading to type I IFN and cytokine production. Using a pull-down assay, Zhang et al.31 demonstrated that Ku70 is another novel DNA sensor that induces IFN-λ1 production through the activation of IRF-1 and IRF-7.32 In addition, LRRFIP1 (leucine-rich repeat flightless-interacting protein 1), previously identified by our lab, binds exogenous nucleic acids and increases the expression of IFN-β induced by both dsRNA and dsDNA. LRRFIP1 interacts with and promotes the activation of β-catenin, which increases IFN-β expression by binding to IRF3 and recruiting the acetyltransferase p300 to the IFN-β enhanceosome via IRF3.33

As discussed above, there has been exciting progress in the identification of new receptors involved in nucleic acid sensing and the mechanism that the sensors use to distinguish foreign and host nucleic acids. These studies provide a better understanding of the initiation of innate immune responses by invading pathogens and may potentially aid the design or modulation of antiviral treatments.

Activation and modulation of innate immune responses

TLR signaling

TLRs have been extensively studied in recent decades for their involvement in the recognition of multiple structures or components of microbes. TLRs are type I transmembrane molecules characterized by ectodomains containing varying leucine-rich-repeat motifs and cytoplasmic Toll-IL-1 receptor domains, which are required for the recognition of PAMPs and downstream signal transduction, respectively. MyD88 mediates the downstream signaling pathways of various TLRs, with the exception of the TLR3- and TLR4-mediated activation of IRF3, which signals mainly through a MyD88-independent but TRIF-dependent pathway. For the MyD88-dependent pathway, TLR agonists induce the recruitment of MyD88 [myeloid differentiation primary response gene (88)] and TIRAP [TIR domain containing adaptor protein], which activates IRAKs (interleukin-1 receptor-associated kinase) and TRAF6 (tumor necrosis factor receptor-associated factor 6). In combination with the E2 ubiquitin ligase complex of UBC13 (ubiquitin-conjugating enzyme 13) and UEV1A (ubiquitin-conjugating enzyme variant 1A), TRAF6 acts as an E3 ubiquitin ligase and catalyzes its own lysine 63-linked polyubiquitin chain and the NF-κB essential modulator NEMO (also known as IKKγ (IκB kinase γ)). Subsequently, this ubiquitination activates the TAK1 (transforming growth factor β-activated protein kinase 1) complex, resulting in the phosphorylation of NEMO and the activation of the IKK complex consisting of IKKα, IKKβ and IKKγ (also known as IKK1, IKK2 and NEMO, respectively) that phosphorylates IκB and leads to its dissociation from NF-κB. Free NF-κB translocates into the nucleus and promotes the expression of pro-inflammatory cytokine genes. TAK1 also activates the MAPK (mitogen activated protein kinase) cascades that lead to the induction of cytokine genes activated by AP-1 (activator protein 1). In the MyD88-independent pathway, TRIF is essential for the induction of non-typical IKKς, IKKε and TBK1 that mediate the activation of IRF3 and the production of IFN-β.34

Recently, Nrdp-1, a novel E3 ligase previously discovered by our lab, was identified as a positive regulator of the TLR pathway. Nrdp-1 induces MyD88 degradation and TBK1 activation to promote type I IFN production.35 In addition, our recent study36 provides new insights into the unexpected role of MHC class II in promoting TLR-triggered innate immune responses. We discovered that intracellular MHC class II molecules interact with Btk (Bruton's tyrosine kinase) via the costimulatory molecule CD40 and maintain the activation of Btk. Activated Btk interacts with the adaptor molecules MyD88 and TRIF, thereby promoting TLR signaling.37 A study by Tun-Kyi et al.38 described the role of prolyl isomerase Pin1 in the promotion of a TLR-triggered type I IFN response. The authors reported that Pin1, activated by TLR7 and TLR9 agonists, binds and activates IRAK1, leading to IRF7 activation and type I IFN production. In addition, Saitoh et al.39 suggested that the antiviral protein Viperin, induced after TLR7 or TLR9 stimulation, interacts with IRAK1 and TRAF6 and promotes the ubiquitination of IRAK1, leading to IRF7 activation and type I IFN production in pDC. These studies suggest potential targets for the treatment of various immune diseases related to type I IFN.

The correct magnitude and duration of TLR signaling is essential for appropriate innate immune responses and subsequent adaptive immune responses. The excessive activation of TLR signaling is associated with the pathogenesis of many autoimmune diseases. In normal individuals, a number of molecules have evolved that exert negative regulatory effects on TLR signaling.40 Over the past few years, several proteins have been described that are negative modulators of TLR signaling pathways, including A20,41 IRAK-M,42 SOCS-1 (suppressor of cytokine cignaling 1),43 SIGIRR (single immunoglobulin IL-1R-related molecule),44 ST245 and Tank.46

We identified an unexpected role for integrin CD11b; it negatively regulates TLR signaling pathways by mediating the degradation of Myd88 and TRIF.47 In addition, two molecules, orphan nuclear receptor SHP (small heterodimer partner) and a NOD-like receptor family member NLRX1, have been recently shown to negatively regulate TLR signaling. Yuk et al.48 reported that SHP represses the transactivation of the NF-κB p65 subunit and suppresses the polyubiquitination of the adaptor TRAF6, which ultimately results in the negative regulation of inflammatory cytokine production triggered by TLRs.49 Xia et al. and Allen et al. independently reported the function of a member of the nucleotide-binding domain and leucine-rich-repeat-containing (NLR) protein family, NLRX1, as a negative regulator of TLR and RIG-I signaling. NLRs are known as positive regulators of innate immune responses;50 however, new evidence suggests that NLRs can also act as inhibitors of TLR-mediated responses. Xia et al.51 demonstrated that NLRX1 is rapidly ubiquitinated in response to LPS stimulation, dissociating from TRAF6, and subsequently interacts with the IKK complex, which inhibits TLR-triggered NF-κB activation. In addition to the role of NLRX1 in the regulation of TRAF6-NF-κB signaling, Allen et al.52 provided further evidence that NLRX1 interferes with the RIG-I–MAVS pathway, thus preventing type I IFN and IL-6 responses to viral infection.

The regulators of TLR signaling described above were mainly identified by conventional approaches, such as the screening of inducible genes in response to TLR ligand stimuli or the identification of unknown components using mass spectrometry. However, the challenge is to discover more activators or modulators of TLR signaling using a more effective strategy and to integrate the dissecting signaling networks. Recently, Chevrier et al.53 reported a systematic strategy through which a series of previously unknown signaling components were identified, including Plk2 (Polo-like kinases 2) and Plk4 (Polo-like kinases 4), mediators of a novel mammalian antiviral response pathway. This strategy combined transcriptional profiling, genetic and small-molecule perturbation and unbiased phosphoproteomics. The findings are promising for the future investigation of TLRs and other signaling pathways, and they should lead to the systematic integrated mapping of signaling networks.

RLR signaling

As mentioned above, RIG-I is a cytosolic RNA receptor that triggers innate immune defenses against a variety of RNA viruses through recognizing 5′-triphosphate and/or polyuridine motifs present in the RNA. The activation of RIG-I-dependent signaling pathways induces the antiviral response and the production of type I IFN, which can activate both innate and adaptive immunity against viral replication and spread.54 The strength and duration of the RIG-I signal is finely regulated to ensure a beneficial outcome in response to foreign invaders.55 Hayakawa et al.56 recently reported a previously unknown role for poly(ADP-ribose) polymerase as a stimulator of RIG-I signaling. The study demonstrated that the zinc-finger antiviral protein shorter isoform, a member of the poly(ADP-ribose) polymerase family of proteins, interacts with RIG-I to promote the oligomerization and ATPase activity of RIG-I, which induces IRF3 and NF-κB activation and type I IFN and cytokine production. This study provides a potential strategy for enhancing the immune response to viral infection through the targeting of zinc-finger antiviral protein shorter isoform.

Many accessory proteins have been identified that play a critical role in mediating the downstream signaling triggered by RLRs, including MAVS (mitochondrial antiviral signaling, also known as IPS-1, CARDIF and VISA),57 TRIM25 (tripartite motif-containing 25),58 STING (stimulator of IFN gene, also known as MITA and ERIS)59 and EYA4 (eyes absent 4).60 MAVS is a critical adaptor for RIG-I, MDA5 and NOD2 signaling, mediating the activation of IRF3 and the subsequent production of type I IFNs. Despite a growing understanding of the critical role of MAVS in RLR signaling, little is known about the mechanism underlying the activation of MAVS. A very recent study by Hou et al.61 demonstrated that the sequential binding of RIG-I to viral RNA (5′-ppp RNA) and K63 ubiquitin chains induces the formation of large MAVS aggregates, which behave like prions with a potent ability to activate NF-κB and IRF3. The authors suggest that a prion-like conformational switch occurs in MAVS that activates and amplifies antiviral responses and provides a mechanism to mediate robust antiviral responses. Unlike MAVS, STING is required for signaling triggered by both RIG-I and DNA sensors, including DAI but not MDA5, to induce type I IFNs. Recently, Chen et al.62 identified a critical role for STAT6 (signal transducer and activator of transcription 6), activated by STING, in antiviral infection. The authors provide evidence that STAT6 is recruited by and interacts with STING in response to viral infection, and the phosphorylation of STAT6 subsequently induces the target genes responsible for immune cell homing. Furthermore, the authors show that STAT6 is required for the antiviral response in vivo. The work clarifies the regulation of RIG-I signaling and reveals a previously unrecognized role for STAT6 in antiviral responses.

Future perspectives for innate signaling

There has been substantial progress in our understanding of the initiation and activation of innate immune responses to pathogen infection, especially for novel sensors of cytosolic nucleic acids, as well as the molecular regulation and crosstalk between the comprehensive signaling pathways. However, some areas of the innate immune response require further investigation. For example, more information regarding the components and regulators of cytosolic PRRs and their downstream signaling pathways and the role of these molecules in activating immune responses in vivo are required. In addition, the relationships between the TLR system and cytosolic PRRs and the integration of different signaling pathways between different immune cells remain to be investigated. Furthermore, additional mechanisms that ensure reliable self and non-self distinction have yet to be discovered.

Innate lymphoid cells

Discovery of ILC

Lymphoid cells derived from common lymphoid progenitors include B cells and T cells, the major types of lymphocytes that orchestrate adaptive immunity and ILCs. ILCs are a recently identified family of heterogeneous cell subsets that are developmentally related and evolutionarily conserved. This family of cells includes NK cells, lymphoid tissue-inducer cells and cells that produce IL-5, IL-13, IL-17 and IL-22. ILCs are mostly enriched in mucosal tissues and are important for innate protection against infectious microorganisms, lymphoid tissue formation, tissue remodeling and the homeostasis of tissue stromal cells. Currently, all known ILCs are derived from Id2-expressing ILC precursors, and distinct transcription factors and cytokines play essential roles in orchestrating the differentiation of the distinct ILCs. According to their distinct transcription factor- or cytokine-dependence, cytokine profiles, biological functions and disease associations, the known ILCs are grouped into the following three categories: NK, helper and RORγt (retinoid-related orphan receptor γt). The NK ILCs include conventional cytotoxic NK cells and IFN-γ+ ILC1 subsets, which require IL-15 for their development, produce IFN-γ and function to limit infection by viruses and intracellular pathogens. Helper ILCs contain the ILC2 subset that produces abundant IL-13 in response to IL-25 and IL-33, and these cells function to control infection by extracellular parasites. The RORγt+ ILCs include lymphoid tissue-inducer cells, IL-17-producing ILC (ILC17) and IL-22-producing innate cells (ILC22), which require IL-7 for their development, express heterotrimers of LT-α and LT-β and produce IL-17 and IL-22, respectively. These ILCs participate in the host defense against extracellular bacteria. The dysfunction of helper ILCs and RORγt ILCs is associated with allergic diseases and some autoimmune diseases, respectively.63 Discussed below are some of this year's latest findings regarding the development and function of several ILC subsets.

Development of RORγt+ ILC

Distinct transcription factors are essential for the development of the different ILC subsets. For example, the transcription factor NFIL3 (E4bp4) is required for the development of NK cells,64 and RORγt is essential for the development of RORγt+ ILCs,65 including lymphoid tissue-inducer, ILC22 and ILC17. The identification of transcription factors or candidate molecules that regulate distinct ILC lineage commitment is currently a hot topic. Recently, researchers have discovered a number of signaling molecules that are involved in the development of ILC subsets.

Possot et al. and Lee et al. independently demonstrated that Notch signaling is required for the development of a number of RORγt+ ILC subsets. Possot et al.66 determined that Notch2 signaling is specifically required for the development of adult RORγt+ ILCs but not fetal liver RORγt+ ILCs, whereas Lee et al.67 revealed that Notch is required for the development of NKp46+ ILCs, a subset of the ILC22 family.

Possot et al.66 demonstrated that fetal and adult bone marrow-derived RORγt+ ILCs mature in the fetal liver environment and peripheral organs, respectively. In addition, the study showed that fetal liver common lymphoid progenitors differentiate into RORγt+ ILCs as they successively acquire the expression of the integrin α4β7 and chemokine receptor CXCR6, which is accompanied by the loss of B-cell and T-cell potential. Thus, CXCR6 is an additional marker of ILC lineage commitment.

The ligand-dependent transcription factor aryl hydrocarbon receptor (AHR) participates in the regulation of Treg and Th17 cell generation,68 and it plays a critical role in regulating IL-22 production by T cells.69 It has been shown that RORγt+ ILCs express the AHR;70 however, the role of AHR in the development of ILCs is unknown. Recently, Kiss et al. and Lee et al. independently demonstrated that AHR is required for the development of intestinal RORγt+ ILC and ILC22 cells, respectively. Kiss et al.71 described the essential role of AHR in the postnatal expansion of intestinal RORγt+ ILC and the formation of intestinal lymphoid follicles. The study shows that AHR within RORγt+ ILCs is activated by dietary ligands and thus serves as a molecular link between nutrients and intestinal homeostasis and immunity. Meanwhile, Lee et al.67 demonstrated that AHR is necessary for the development of ILC22 cells and the formation of postnatal lymphoid tissues including cryptopatches and isolated lymphoid follicles, thus playing an essential role in the host defense against intestinal bacterial infections. In addition, Li et al.72 demonstrated that AHR is highly expressed in intraepithelial lymphocytes and plays a crucial role in regulating the maintenance of these cells. Intraepithelial lymphocytes reside in the body's surfaces, organizing an epithelial barrier against infection. Collectively, the studies describe a critical role for AHR in the development of RORγt+ ILCs and intraepithelial lymphocytes, and they establish a link between dietary compounds, the intestinal immune system, and the microbiota.

Accordingly, Sawa et al.73 recently identified a cross-regulation mechanism among intestinal symbionts, adaptive immunity and RORγt+ ILCs. The authors demonstrated that RORγt+ ILCs constitutively produce most of the intestinal IL-22. Although the symbiotic microbiota and adaptive immunity could inhibit the production of IL-22, epithelial damage restored this function for the benefit of tissue repair.

Novel findings in ILC2 cells

The type 2 cytokine–producing innate lymphoid ILC2 subset includes nuocytes and natural helper (NH) cells that produce abundant Th2 cytokine IL-13 in response to IL-25 and IL-33. These cells also express CD127 (IL-7 receptor α-chain), IL-33R and IL-17RB and engage in the control of extracellular parasites. Although ILC2 cells in mice have attracted interest, ILC2 cells in humans are poorly defined. Recently, Monticelli et al.74 identified a population of lung-resident ILCs in mice and humans that resembles the phenotype and cytokine profile of ILC2 cells and is critical for airway epithelial integrity and tissue remodeling after infection with influenza virus. These lung-resident ILC2 cells produce amphiregulin following stimulation with infectious agents, which promotes epithelial cell proliferation through the EGFR receptor.75 In addition, Mjösberg et al.76 defined a unique population of CD127+CRTH2+CD161+ ILCs in humans that are potent producers of IL-13 in response to IL-25 and IL-33. However, because CRTH2+ ILCs accumulate in nasal polyps in chronic rhinosinusitis, the IL-5 and IL-13 secreted by these cells can potentially induce the symptoms of allergic disease and thus play a pathogenic role in respiratory immune responses.

A recent report by Chang et al.77 described the function of NH cells in airway inflammation, thus describing a previously unrecognized role for innate immunity in viral-induced asthma. The study demonstrated that infection with influenza causes the development of airway hyper-reactivity, a characteristic feature of asthma, independent of the adaptive immune system but requiring the activation of the IL-13-IL-33 axis and natural helper cells.78, 79

Future perspectives for ILC research

There is increasing evidence for the importance of ILCs in the defense against invading pathogens as well as lymphoid formation and tissue homeostasis. Continuing research into the diversified phenotype and function of distinct ILCs subsets, the regulation mechanism for development of ILCs and the interaction of ILCs with environmental factors and other immune cells or molecules will further clarify the biological characteristics of this family of cell subsets and their roles in health and disease.

Differentiation and function of T-cell subsets

Brief history of the identification of T-cell subsets

In 1986, Mosmann and Coffman discovered the helper T (Th) cells, Th1 and Th2, based on their distinct pattern of cytokine production and function.80 Since then, our knowledge of the differentiation and function of various T-cell subsets has greatly expanded. Upon recognition of the antigen peptide-MHC complex T-cell receptor, naive CD4+ T cells are induced to differentiate into specific T effector cells in the presence of costimulatory signals provided by antigen-presenting cells and a complicated cytokine microenvironment from the innate immune and adaptive immune systems. To date, four distinct T-cell subsets have been characterized, Th1, Th2, Th17 and iTreg cells, which shape the adaptive immune responses mainly through distinct cytokine profiles and participate in the pathological processes of various diseases. Briefly, Th1 cells produce IFN-γ and IL-2 and mediate immune responses against intracellular pathogens, whereas Th2 cells, which produce IL-4, IL-5, IL-9, IL-10 and IL-13, mediate humoral responses and immunity against extracellular parasites including helminthes.81 Th17 cells express IL-17A, IL-17F, IL-21 and IL-22 (and IL-26 in humans) and participate in immune responses against extracellular bacteria and fungi as well as multiple autoimmunity processes.82 Treg cells play critical roles in maintaining self-tolerance and in regulating immune responses through the secretion of transforming growth factor-β (TGF-β) and IL-10 and by contact-dependent mechanisms.83 The development of the T helper subsets is dictated by their master transcription factors, T-bet (Th1-specific T box transcription factor) for Th1, GATA-3 (GATA binding protein 3) for Th2, RORγt for Th17 and Foxp3 for Treg cells. Nevertheless, growing evidence has indicated a considerable flexibility and plasticity among committed T-cell subsets through complex crosstalk between distinct transcription factors.84 Understanding the developmental programs of these T-cell subsets and the mechanisms involved in the regulation of their functions has been a major focus in recent years. In this section, we will summarize some of the latest discoveries in the developmental regulation of the distinct T-cell lineages by cytokines and transcription factors and their roles in different immune responses and diseases. Special emphasis will be placed on research pertaining to Th17 and Treg cells.

Th2 cells: development and trafficking

GATA-3 is an essential regulator of Th2 differentiation85 and activates the genes encoding Th2 cytokines through epigenetic modifications including histone acetylation and chromatin remodeling.86 Recently, the molecular basis for GATA-3 directing the Th2 lineage commitment has been further clarified by Tanaka et al.87 The study shows that the DNase I-hypersensitive site 2 (HS2) element, located in the second intron of IL-4 locus (Il4), functions as a critical enhancer that is strictly controlled by GATA-3. HS2 is uniquely essential for the production of specific IL-4 but not IL-5 and IL-13. HS2 is a target of GATA-3 that regulates the chromosomal modification of Il4, including the trimethylation of histone H3 at Lys4 and the acetylation of histone H3 at Lys9 and Lys14.88, 89

The work described above sheds new light on the detailed mechanism of how GATA-3 functions to determine Th2 commitment at a transcriptional level. In other studies by Kool et al. and Kuroda et al., a novel molecular mechanism by which immunogenic particles initiate Th2 cell responses is described. Uric acid crystals are a known cause of gout; however, there are few reports of the role that uric acid plays in other inflammatory process, especially in T-cell commitment. Kool et al.90 provided evidence that uric acid, which is released from asthmatic airways, is critical for Th2 cell immunity and alum- and house dust mite allergen-induced type 2 immunity in DC in a spleen tyrosine kinase- and PI3-kinase δ signaling-dependent manner. Accordingly, Kuroda et al. also indicated that silica crystals and aluminum salts induce type 2 immune responses in a NALP3 inflammasome-independent and PGE2 (prostaglandin E2)-dependent manner.91 Whereas the NLRP3 inflammasome is required for alum-induced adjuvanticity,92 these two studies identified an inflammasome-independent pathway through which type 2 immune responses are activated by aluminum salts. These results may help reveal the molecular mechanism behind alum adjuvanticity.93, 94

The migration of Th2 cells from the lymph nodes to peripheral tissues is the key step for inflammatory responses; however, the mechanism regulating the Th2 cell migration is not fully understood. Recently, two findings have increased our understanding of Th2 cell trafficking. Islam et al.95 identified a critical role for the CCL8–CCR8 axis in Th2 cell migration. This study demonstrated that CCL8 is an agonist for the chemokine receptor CCR8, which is expressed in IL-5+Th2 cells and promotes IL-5-mediated chronic allergic inflammation by recruiting Th2 cells in allergen-inflamed skin.96 In addition, Li et al.97 demonstrated that the extracellular matrix protein-1 is highly and selectively expressed in Th2 cells and is essential for the Th2 cell egress from lymphoid tissues through the re-expression of S1P1 (sphingosine-1 phosphate receptor 1). The work indicates a potential strategy for the treatment of related allergies by influencing Th2 cell migration.98

Th17: differentiation and function

Th17 cells and their effector cytokines play crucial roles in infectious, inflammatory and autoimmune diseases. Multiple cytokines have been implicated in the regulation of Th17 cell differentiation, for example, IL-6 and TGF-β potently initiate Th17 cell differentiation. Likewise, IL-21 controls the generation of Th17 cells, and IL-23, IL-1 and IL-18 have also been implicated in Th17 cell differentiation. In contrast, IFN-γ, IL-4, IL-27 and IL-2 negatively regulate Th17 cell differentiation.99 Several transcription factors have been implicated in the control of Th17 cell development, such as RORα and RORγt, establishing the expression of a Th17 cell-specific gene program. Foxp3, STAT1, STAT5 and ETS1 (V-Ets erythroblastosis virus E26 oncogene homolog 1) negatively regulate TH17 cell differentiation.100

Several groups have described in detail the regulation of Th17 cell differentiation by distinct transcription factors. Dang et al.101 identified hypoxia-inducible factor 1 as a key metabolic sensor that favors Th17 cell generation, but inhibits Treg cell generation. This study shows that hypoxia-inducible factor 1 is induced under Th17 skewing conditions and drives the differentiation of Th17 cells via cooperation with RORγt, STAT3 and p300, whereas hypoxia-inducible factor 1 inhibits Treg cell development by mediating Foxp3 protein degradation. The work demonstrates how metabolic signals regulate the balance between inflammation and tolerance and provide a potential therapeutic opportunity for the treatment of diseases.102 Lazarevic et al.103 demonstrated that T-bet, a master regulator of Th1 cells, inhibits Th17 cell generation by preventing the transcription factor Runx1-mediated activation of the gene encoding RORγt. The interaction of T-bet with Runx1 blocks the Runx1-mediated transactivation of Rorc. The STAT proteins selectively regulate T helper cell differentiation, and Yang et al.104 recently elucidated the direct reciprocal action of STAT3 and STAT5 in the regulation of IL-17 production by Th17 cells. In this study, the direct binding of STAT3 and STAT5 to multiple common sites across the Il17a–Il17f locus was observed. STAT3 binding induces IL-17 and RORγt but inhibits Foxp3, and IL-2 inhibits IL-17 through promoting STAT5 binding and limiting STAT3 binding at these sites. Thus, a competition between STAT3 and STAT5 binding, controlled by IL-2, modulates Th17 cell differentiation. In addition, Maruyama et al.124 reported that Id3 (DNA-binding protein inhibitor 3) plays an opposing role in the differentiation of Treg cells and Th17 cells, as discussed in section 5.4 (Treg cells: differentiation).

In addition to transcription factors, a number of cytokines are involved in the fine-tuned regulation of Th17 cell differentiation. Recently, the leukemia inhibitory factor was reported to be an inhibitor of Th17 cell differentiation;105 the administration of neural progenitor cells ameliorates experimental autoimmune encephalomyelitis through the selective inhibition of Th17 cells, and the secretion of leukemia inhibitory factor is responsible for the control of Th17 cells and experimental autoimmune encephalomyelitis by neural progenitor cells through upregulating SOCS3, which leads to the downregulation of STAT3 activity. The study identifies leukemia inhibitory factor as a novel regulator of Th17 cell differentiation and provides insights into the mechanisms of the effects of neural progenitor cell in the treatment of neurodegenerative diseases.106 In addition, Solt et al.107 demonstrated that SR1001, a high-affinity synthetic ligand that is specific to both RORα and RORγt, significantly inhibits Th17 cell differentiation and function, thus providing a potential target for the treatment of autoimmune diseases.108 IL-23 is required for the complete differentiation and function of Th17 cells;109 however, the factors that mediate the pathogenic function of Th17 have remained elusive. Studies by Codarri et al.110 and EI-Behi et al.111 independently identified a critical role for granulocyte-macrophage colony-stimulating factor in the initiation of Th17-mediated autoimmune neuro-inflammation induced by IL-23. Using a model of EAE, IL-23 was shown to induce a positive feedback loop whereby granulocyte-macrophage colony-stimulating factor produced by Th17 cells promotes antigen-presenting cells to secret IL-23. This study defines a chief mechanism underlying the important role of IL-23 in inducing Th17 encephalitogenicity in autoimmune diseases of the central nervous system.112

Th17 cell-derived cytokines, mainly consisting of IL-17A–F and other cytokines, such as IL-22, not only enhance innate defense against infection but also mediate inflammatory tissue damage in the pathogenesis of autoimmune diseases. The secretion and mechanisms of action of these cytokines are precisely regulated by the microenvironmental factors surrounding the Th17 cells and the interactions with their receptors.113 Among the IL-17 members and their receptors, only IL-17A and its receptor have been extensively studied for their molecular structures, biological functions and signaling pathways. Recently, Song et al., Ramirez-Carrozzi et al. and Chang et al. independently reported the mechanism underlying IL17C function. Song et al.114 and Ramirez-Carrozzi et al.115 demonstrated that IL-17C is induced in colon epithelial cells during infection and activates downstream signaling through binding to the IL-17RE–IL-17RA complex, leading to the production of antibacterial peptides and pro-inflammatory molecules by epithelial cells; thus, IL-17C plays an important role in early innate immunity to intestinal pathogens.116 Chang et al.,117 however, demonstrated the role of IL-17C in the pathogenesis of autoimmune diseases. IL-17C binds and forms a complex with IL-17RE expressed on Th17 cells and subsequently induces the activation of Act1 and IκBζ, thus activating the Th17 cell response. This work sheds new light on the function and signaling pathway of IL-17 and its receptor.

The phenotypic and functional properties of Th17 cells have been extensively studied in recent years. However, future work that focuses on the additional transcription factors involved in Th17 differentiation, the additional roles of Th17-derived inflammatory cytokines and the additional mechanisms of Th17 cells interaction with other cell subsets will broaden our understanding of the developmental and clinical significance of Th17 cells.118

Treg cells: differentiation

Since the identification of the transcription factor Foxp3, it has been widely accepted by the immunological community that the CD4+CD25+ T cells are regulatory T cells. Treg cells can be divided into two groups according to their distinct origins; naturally occurring Treg cells that are produced in the thymus from CD4+ thymocytes119 and induced Treg (iTreg) cells that are induced in the periphery from naïve CD4+ T cells in response to the low-dose engagement of the TCR, TGF-β and IL-2.120 Despite remarkable advances in the understanding of the cellular and molecular mechanism of Treg cell development and function in recent years, some questions remain. This year, the substantial progress in this field shared a common focus: the regulation of Treg cell generation.

Foxp3 is the master transcription factor for the differentiation of Treg cells, which are essential for maintaining self-tolerance and immune homeostasis.121 Recently, much attention has focused on the phenotypic and functional diversity of Treg cells, which is driven by the regulation of Foxp3 expression and specific transcription factors distinct from Foxp3. A recent study by Cretney et al.122 indicated that the transcription factors Blimp-1 and IRF4 jointly define a novel pathway that leads to the acquisition of a particular Treg cell effector function. The study reports that the expression of Blimp-1 defines a population of Treg cells that has an effector phenotype, localizes to mucosal sites and produces IL-10. Furthermore, the expression of IRF4 is essential for Blimp-1 expression and for the differentiation of all effector Treg cells, thus describing a previously unknown role for the IRF4–Blimp-1 axis in the effector function of Treg cells and revealing how distinct transcription factors interact with each other in an immune network.123 In addition, Maruyama et al.124 demonstrated that the DNA-binding inhibitor Id3 plays a critical role in controlling the differentiation of Treg cells and Th17 cells. They found that the deletion of Id3 leads to the defective generation of Treg cells but the enhanced differentiation into Th17 cells. Mechanistically, an Id3 deficiency leads to the defective binding of E2A protein to the Foxp3 promoter and the defective removal of inhibition by GATA-3 at the Foxp3 promoter. Rorc activation and the subsequent Th17 differentiation are also regulated by E2A.125 Thus, the cooperative network of Id3, E2A and GATA-3 regulates Foxp3 expression. Interestingly, Wang et al.126 recently challenged the conventional theory that GATA-3 negatively regulates Foxp3 expression127 by providing evidence that GATA-3 is essential for Treg cell function and that GATA-3 promotes Foxp3 expression through binding with Foxp3 elements.128

A recent study by Beal et al.129 demonstrated that in addition to transcription factors, the adaptor molecule Ndfip1 influences the differentiation of iTreg cells. In this study, Ndfip1 was shown to play a role in sustaining normal amounts of Foxp3 expressed in iTreg cells. Ndfip1 expression is transiently upregulated during the course of iTreg cell differentiation in a TGF-β-dependent manner and promotes the E3 ubiquitin ligase Itch-mediated degradation of the transcription factor JunB, thus preventing IL-4 production. Therefore, the mechanism underlying the role of TGF-β signaling in iTreg cell differentiation by inducing Ndfip1 expression to silence IL-4 production is proposed.

In addition, from an epigenetic perspective, a recent study by Beyer et al.130 revealed the mechanism underlying the shift between effector T cell function and suppressive T cell function. SATB1, a genome organizer that regulates chromatin structure and gene expression, was found to be required for establishing effector T cell differentiation and the induction of effector T-cell cytokines. Foxp3 suppresses SATB1 activity directly through the maintenance of a repressive chromatin state at the SATB1 locus and indirectly through inducing the binding of microRNAs (miRNAs) to the SATB1 3′ untranslated region. Therefore, SATB1 is a proposed molecular switch that directs Treg cell reprogramming to effector T cells.

TFR cells versus TFH cells

TFH cells represent a novel subset that promotes the function of B cells distinguishable from other Th subsets. These cells are characterized by the significant expression of CXCR5 and their specific location in B-cell follicles.131 TFH cells potently stimulate the differentiation of B cells into antibody-forming cells through the secretion of IL-21, which promotes the generation of TFH cells using a feedback mechanism.132 The dysfunction of TFH cells and their associated molecules, such as inducible costimulatory molecule or IL-21, may contribute to the pathogenesis of certain autoimmune diseases or immunodeficiencies.133 The transcription factor Bcl-6 has been shown to direct the lineage commitment of TFH cells,134, 135, 136 whereas the inducible costimulatory molecule provides a critical early signal for inducing the expression of Bcl6 that subsequently induces CXCR5 and regulates IL-21 production by TFH cells.137 B cells are required for the maintenance of Bcl6 and TFH cell commitment. The interfollicular zone is the site where germinal center B cell and TFH cell differentiation is initiated. Plasma cells also negatively regulate the TFH cell program through the inhibition of Bcl-6 and IL-21 expression.138 Recently, Morita et al.139 presented the interesting finding that human blood CXCR5+CD4+ T cells may be circulating TFH cells and contain specific subsets, such as CXCR5+Th2 and CXCR5+Th17 cells, which differentially support antibody secretion via IL-21. These authors also propose that an altered balance of TFH cell subsets toward CXCR5+Th2 and CXCR5+Th17 cells is related to juvenile dermatomyositis, a systemic human autoimmune disease.

Despite the increasing understanding of the differentiation and function of TFH cells, little is known about how TFH cell numbers and functions are controlled. Treg cells have been shown to suppress Th1,140 Th2141 and Th17142 cell responses through interfering with T-bet, IRF-4 and RORγt signaling, respectively. Recent studies by Linterman et al.,143 Chung et al.144 and Wollenberg et al.145 independently identified a unique T-cell subset located in the germinal center that shares phenotypic characteristics with TFH cells and conventional Foxp3+ regulatory Treg cells, yet are distinct from both. This T-cell subset, designated TFR cells, consists of Foxp3+Blimp-1+CXCR5highPD-1highCD4+ and potently inhibits T cell proliferation and TFH cell numbers as well as controlling germinal center B cell selection. TFR cells originate from thymic Foxp3+ precursors, which further develop in the periphery depending on Bcl-6, SLAM-associated protein, CD28 and B cells. TFR cells may thus provide a potential target for maintaining immune tolerance to prevent autoantibody-associated autoimmunity.146, 147

Naive, effector and memory T cells

One of the research highlights of the last year was the discovery of the transcriptional programs that regulate T-cell differentiation into effector T cells versus memory T cells. Yang et al. and Ji et al. independently identified Id3 as a key transcriptional regulator in controlling effector T cells differentiation into memory T cells. Yang et al.148 reported that a deficiency in Id2 (DNA-binding protein inhibitor 2) or Id3 results in the loss of distinct CD8+ effector and memory populations, whereas Ji et al.149 consistently demonstrated that the enforced expression of Id3 strengthens the recall responses. Ji et al. further demonstrated that the transcriptional repressor Blimp-1 represses the expression Id3 in short-lived effector T cells and thus limits the ability of the short-lived effector T cells to persist as memory cells.

In addition to transcriptional regulators, recent evidence shows that the target for rapamycin (mTOR) is critical for memory CD8+ T-cell differentiation in mammals. mTOR is an evolutionarily conserved PI3-kinase family member that plays a central role in the regulation of amino-acid metabolism, energy balance and cell survival. It has been previously shown that mTOR plays a negative role in memory CD8+ T-cell differentiation.150 mTOR functions to promote the effector versus memory cell fate of antigen-specific CD8+ T cells by regulating the expression of the transcription factors T-bet and Eomesodermin (Eomes).151 Recently, Li et al.152 further elucidated the critical role of mTOR in homeostatic proliferation-induced CD8+ T-cell memory and tumor immunity. The inhibition of mTOR in CD8+ T cells promotes homeostatic proliferation-induced CD8+ T-cell memory and anti-tumor effects. Homeostatic proliferation-induced mTOR enhances transcription factor T-bet and CD122 expression, which sensitizes IL-15-dependent CD8+ T-cell memory formation by inducing the expression of transcription factor Eomes over T-bet.

Recently, in addition to its role in the differentiation of memory T cells, an emerging role for mTOR in directing T-cell activation and differentiation has been reported.153, 154, 155 mTOR promotes the differentiation of CD4+ T cell into effector cells versus Treg cells in response to appropriate skewing conditions.156 The distinct signaling complexes mTORC1 and mTORC2 are formed around mTOR. Delgoffe et al.157 recently demonstrated that mTORC1 and mTORC2 regulate the fates of Th cells in different ways. Th1 and Th17 cell differentiation is selectively regulated by Rheb-dependent mTORC1 signaling, whereas Th2 generation is selectively regulated by mTORC2 signaling. The distinct effect of mTORC1 and mTORC2 on T-cell differentiation is associated with the differential inhibition of SOCS proteins. In addition, Michalek et al.158 identified the essential role of metabolic programs in the specific generation of Teff and Treg cells. Effector T cells require a glycolytic metabolism and an activated mTOR, whereas Treg cells have high levels of activated MAPK and require lipid oxidation. Future studies focusing on the detailed mechanism of the mTOR-mediated regulation of effector, memory or Treg cell differentiation, as well as additional functions for mTOR signaling in T cells and their involvement in infection and autoimmune diseases, will further clarify the expanding role of mTLR in T cell-mediated biological and pathological processes.

miRNA and T-cell functions

miRNAs play pivotal roles in the regulation of multiple immune processes.159 In addition to their potent roles in regulating the innate immune responses of macrophages,160 dendritic cells161 and NK cells,162 miRNAs are also involved in T-cell differentiation and function in many ways. For example, miR-181a,163, 164 miR-182165 and miR-146a166 are potent regulators of T-cell development and function, whereas miR-155167 and miR-326168 specifically regulate the differentiation and function of Th17 cells. Recently, studies by Ma et al. and Steiner et al.171 independently described miRNA-29 as a suppressor of IFN-γ production through different mechanisms. Ma et al.170 demonstrated that miR-29 suppressed IFN-γ production by directly targeting the 3′ UTR (untranslated regions) of Ifng mRNA. Furthermore, increased IFN-γ production and the more effective clearance of Listeria monocytogenes, as well as enhanced Th1 responses and greater resistance to mycobacterial infection, were observed in miR-29 sponge-transgenic mice compared with their littermates. miR-29 suppresses immune responses to intracellular pathogens by directly targeting IFN-γ. A study by Leavy,169 however, demonstrated that the repression of IFN-γ production by miR-29 is attributed to the direct targeting of the 3′ UTRs of Tbx21 and Eomes, but that Ifng is not targeted. The transcription factors Tbx21 (encodes T-bet) and Eomes are known to promote IFN-γ production independently. Together, these data suggest an important role for miR-29 in the regulation IFN-γ production and provide potential clues for the treatment of inflammatory diseases though the elucidation of the exact mechanism of the suppressive function of miR-29.

Furthermore, Rossi et al. demonstrated that miR-125b is a signature miRNA of naive CD4+ T cells and regulates the expression of genes involved in T-cell differentiation, including IFNG, IL2RB, IL10RA and PRDM1. The identification of an ‘atlas’ of specific microRNA expression in human lymphocytes and in different subsets through microRNA profiling analysis was also reported.172 In a study by Oertli et al.,173 miR-155 expression was shown to be required for the control of H. pylori infections and infection-associated immunopathologies through regulating Th17/Th1 cell differentiation. Blüml et al.174 also reported an essential role for miR-155 in the adaptive and innate immune reactions, including Th17 polarization, leading to autoimmune arthritis.

Over the past few years, substantial advances have been achieved in elucidating the role of miRNAs in the development and function of the immune system. Continuing work concentrating on the identification of additional miRNAs involved in immune responses and diseases as well as in the regulation and mechanism of miRNA targeting will advance this research area even further.175

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Liu, J., Liu, S. & Cao, X. Highlights of the advances in basic immunology in 2011. Cell Mol Immunol 9, 197–207 (2012). https://doi.org/10.1038/cmi.2012.12

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Keywords

  • ILC
  • innate immunity
  • Th17 cells
  • TFR cells
  • TLR

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