Innate and Innate-like Effector Lymphocytes in Health and Disease

Abstract

Lymphocytes can be functionally partitioned into subsets belonging to the innate or adaptive arms of the immune system. Subsets of innate and innate-like lymphocytes may or may not express antigen-specific receptors of the adaptive immune system, yet are poised to respond with innate-like speed to pathogenic insults but lack the capacity to develop classical immunological memory. These lymphocyte subsets display a number of common properties that permit them to integrate danger and stress signals dispatched by innate sensor cells to facilitate the generation of specialized effector immune responses tailored towards specific pathogens or other insults. Here, we review the functions of distinct subsets of innate and innate-like lymphocytes. A better understanding of the mechanisms by which these cells are activated in different contexts, their interactions with other immune cells, and their role in health and disease may inform the development of new or improved immunotherapies.

The immune response against infection or sterile insults involves coordination between different subsets of lymphocytes and innate effector cells to generate distinct immune effector modules, including a cytotoxic module and three types of helper modules (types 1–3) (1, 2). Innate lymphocytes can respond rapidly to the cytokines produced by innate sensor cells – such as dendritic cells (DCs), macrophages, mast cells and epithelial cells – that are activated by microbe- or damage-associated molecular patterns. Innate lymphocytes activated in this manner may assist myelomonocytic effector cells of the innate immune system as part of the inflammatory response and contribute to the induction of specialized effector T cells and class-switched B cells (3). In turn, adaptive effector lymphocytes amplify the activity of innate lymphocytes and rely on innate effector cells to clear the pathological insult. Hallmarks of an adaptive immune response are the clonal expansion of small numbers of antigen-specific B and T lymphocytes and the generation of long-term memory. Nevertheless, adaptive-like immune responses mediated by some innate lymphocytes such as natural killer (NK) cells have also been described (4), blurring the distinction between innate and adaptive immunity (5). Conversely, several subsets of lymphocytes expressing B or T cell receptors (BCRs or TCRs) exhibit limited capacity to generate classical antigen-specific immune memory responses (6). These innate-like, unconventional B and T cells are enriched in tissues and are further characterized by limited clonal diversity, rapid effector functions, and a tendency for autoreactivity. Additionally, some innate-like, conventional T cells, can generate memory responses in an antigen-independent manner and thus respond rapidly to an immune challenge (7). This Brief Review summarizes the effector and immune functions of the heterogeneous assortment of innate and innate-like lymphocytes (see Figure 1), providing examples of recent progress.

FIGURE 1. Subsets of innate, innate-like and adaptive effector lymphocytes.

Innate lymphocytes are divided into subsets of ILCs and a population of cells expressing iCD3 chains that are unique to the intestinal epithelium. Current nomenclature recognizes five subsets of ILCs: NK cells, three subsets of helper-like ILCs (i.e., ILC1–3), and fetal LTi cells. Innate-like T and B lymphocytes are divided into three groups: 1) innate-like unconventional T cells that include CD1d-restricted NKT cells, MR1-restricted MAIT cells, subsets of γδ T cells, Qa-1/HLA-E-restricted CD8⁺ T cells, H2-M3-restricted CD8⁺ T cells, and natural CD8αα⁺TCRαβ⁺ IELs, 2) innate-like conventional T cells that include innate and virtual memory CD8⁺ T cells, and 3) innate-like B cells that include B-1 cells and MZB cells (see Table I for the specificity of these cells). Adaptive lymphocytes are divided into subsets of effector T cells (i.e., CTLs,Th1, Th2, Th17 and Tfh cells, and Tregs) and B cells (i.e., FOB cells). Individual ILC subsets and their respective effector T cell counterparts are color-matched. Created with BioRender.com.

Innate lymphocytes

The family of innate lymphocytes includes 5 subsets of innate lymphoid cells (ILCs) (8) – NK cells, three subsets of helper-like ILCs (ILC1–3), and fetal lymphoid tissue inducer (LTi) cells – and a population of innate intraepithelial lymphocytes (IELs) in the intestine that express T cell markers (Figure 1) (9).

NK cells.

Classical NK cells were originally described as large granular lymphocytes that can lyse tumor cells without prior sensitization (10, 11). NK cells are found widespread throughout lymphoid and nonlymphoid tissues where they may display a remarkable level of phenotypic and functional diversity (12). Their maturation is critically dependent on the transcription factors T-bet and Eomesodermin (Eomes). The reactivity of these cells to susceptible targets is controlled by the balance of signals received from a broad repertoire of activating and inhibitory receptors (13). NK cells can be activated by target cells expressing virus- or stress-induced ligands that engage NK cell activating receptors, or by cells lacking expression of classical MHC class I (class Ia) proteins that engage NK cell inhibitory receptors. NK cells also express Fcγ receptors (FcγRIII/CD16) that, upon interaction with the constant region of IgG antibodies attached to target cells, trigger antibody-dependent cell-mediated cytotoxicity. The activity of these cells is augmented by a variety of cytokines, most notably type I interferons, IL-2, IL-12, IL-15 and IL-18. In addition to exhibiting cytotoxicity via perforin/granzyme and Fas/FasL pathways, activated NK cells are capable of producing cytokines such as IFN-γ and TNF-α, which potently stimulate macrophages and contribute to the generation of cytotoxic and type 1 immunity. As such, NK cells represent the innate counterpart to cytotoxic T lymphocytes in the adaptive immune system.

The role of NK cells in tumor immunosurveillance has been exploited in cancer immunotherapy, for example by adoptive transfer of NK cells engineered to enhance their cytolytic activities (14). NK cells play a critical role in innate defense against viral pathogens, as illustrated by the susceptibility of patients with NK cell deficiency disorders to herpes virus infections (15). These cells also contribute to a multitude of other immune responses, including graft-versus-host disease, allergic inflammation, and autoimmunity. The remarkable heterogeneity of NK cells in different tissues is perhaps best illustrated in the pregnant uterus, where these cells play a critical role in the establishment of the fetal-maternal interface and immune surveillance. For example, a recent study showed that human NK cells in the uterus can clear Listeria monocytogenes bacteria from the developing fetus by delivering the antimicrobial protein granulysin into placental trophoblasts through nanotubes (16). In the central nervous system (CNS), NK cells can modulate cognitive function during aging (17) and neurodegenerative disease (18, 19).

Helper-like ILCs.

Helper-like ILCs are considered the innate counterparts of effector CD4⁺ T helper (Th) cells, with ILC1, ILC2 and ILC3 exhibiting effector functions similar to Th1, Th2 and Th17 cells, respectively (20, 21). All three helper-like ILC subsets arise from a common progenitor cell characterized by expression of the transcription factor promyelocytic leukemia zinc finger (PLZF) (22), which is also critical for the acquisition of innate effector functions in some subsets of innate-like T cells (see below). They share key transcription factors, homing receptors and cytokine production profiles with their adaptive counterparts. Similar to polarized CD4⁺ Th cells, helper-like ILCs can respond to their local microenvironment by altering their cytokine profiles and this plasticity may contribute to their biological functions (23). These cells are predominantly tissue resident and particularly abundant at mucosal barrier sites exposed to environmental antigens, commensal microorganisms, and pathogens (24). Although these cells can play critical roles in tissue homeostasis, immune surveillance, and tissue inflammation, patients with a long-term deficiency in helper-like ILCs and NK cells lack a severe clinical phenotype, which has led to the suggestion that these cells may be largely dispensable for warding off disease when normal T and B cell function is preserved (25).

ILC1s are found in a variety of tissues such as liver, small intestine, skin, adipose, uterus, and salivary gland. These cells bear similarities with NK cells such as responsiveness to IL-12 and IL-18 produced by macrophages and DCs, many surface receptors, a requirement of T-bet for their function, and capacity to produce IFN-γ, yet ILC1s require GATA-3 but not Eomes for their differentiation. Although most ILC1s were thought to lack cytotoxicity, new studies have revealed the capacity of many ILC1s to gain cytotoxic potential during effector differentiation, in a manner dependent in part on the transcription factor Hobit (26, 27). IFN-γ produced by these cells can promote macrophage activation and Th1 cell differentiation. Consistent with their similarity to Th1 cells, ILC1s play critical roles in host defense against intracellular bacteria such as L. monocytogenes and Salmonella enterica. They can also promote inflammation and tissue injury such as colitis in the intestine, ischemia-reperfusion injury in the kidney, and adipose tissue inflammation in obesity. Conversely, these cells can protect mice from acute liver injury (28).

ILC2s are most abundant in barrier tissues such as lung, gut and skin. They are activated by the cytokines TSLP (thymic stromal lymphopoietin), IL-25 and IL-33 produced by epithelial cells, require GATA-3 for their development, and upon activation produce the type 2 cytokines IL-5, IL-13, and to a lesser extent IL-4, and also produce the growth factor amphiregulin. In the intestine, activated ILC2s may also produce the immune suppressive cytokine IL-10 (29). ILC2s stimulate mucus production in goblet cells, induce smooth muscle contraction, activate eosinophils, and promote Th2 differentiation to expel helminths such as Nippostrongylus brasiliensis. Surprisingly, the capacity of ILC2s to promote type 2 immunity and helminth expulsion requires their expression of MHC class II and interaction with antigen-specific T cells (30). These cells can also promote airway hyperresponsiveness in viral infections mediated by influenza A virus or respiratory syncytial virus infection. The type 2 cytokines they produce are a major source for the generation of allergic reactions in asthma and atopic dermatitis. ILC2s are also an important source of IL-5 for induction of IgM and IgA antibody production by B-1 cells (31). By producing amphiregulin, these cells can also promote wound healing, a key component of type 2 immunity. In adipose tissue ILC2s promote homeostasis in part by recruiting and maintaining eosinophils and M2 macrophages. Adipose ILC2s can also respond to neurotrophic factors produced by mesenchymal stromal cells, which induces them to produce type 2 cytokines and endogenous opioid peptides that nurture the generation of beige adipocytes, thus promoting energy expenditure and reducing adiposity and obesity (32, 33).

ILC3s are particularly abundant in the gut mucosa and in tonsils, and are also found in spleen, skin and decidua. They are activated by the cytokines IL-1β and IL-23 produced by macrophages and DCs, require the transcription factor RORγt for their development, and can produce the cytokines IL-17 and IL-22. Three subsets of ILC3s can be distinguished based on surface expression of chemokine receptor CCR6 and natural cytotoxicity receptors (NCRs): CCR6⁻NCR⁺ ILC3s and their CCR6⁻NCR⁻ precursors, and CCR6⁺NCR⁻ ILC3s. The latter subset phenotypically resembles fetal LTi cells and is therefore called LTi-like ILC3s. Whereas LTi cells play critical roles in the fetal organogenesis of secondary lymphoid organs (see below), LTi-like ILC3s are important for the postnatal generation of tertiary lymphoid structures such as cryptopatches in the intestine (34).

The effector functions of ILC3s are tightly controlled by the transcription factors RORγt, RORα and T-bet (35, 36). RORγt-deficient mice lack lymph nodes, illustrating the critical role of RORγt-dependent lymphoid cells in lymph node organogenesis. However, the additional absence of T-bet was able to rescue this defect, which was associated with the fetal expansion of RORα-dependent ILC precursors expressing central LTi factors. Since RORγt-deficient mice contain an expanded population of ILC1s, these findings suggest that RORγt opposes the T-bet-driven differentiation of ILC precursors towards the ILC1 lineage.

The cytokines produced by ILC3s can recruit neutrophils, induce antimicrobial peptides, promote epithelial cell survival, facilitate Th17 cell differentiation, and support Tregs in the intestine. Additionally, by providing survival and co-stimulatory signals, ILC3s can enhance T cell-independent IgG3 antibody responses from marginal zone B (MZB) cells (37). ILC3s play critical roles in immune responses against extracellular microbes such as Citrobacter rodentium. Remarkably, the LTi-like ILC3s express MHC class II and can present antigens from commensal microorganisms to CD4⁺ T cells in the absence of co-stimulation, inhibiting such T cell responses to promote intestinal homeostasis and limit pathological immune responses to commensal microbes (38). Nevertheless, under some conditions such interactions may also promote immune responses in the intestine as well as in the microenvironment of tumors to facilitate tumor immunity (39). Similarly, in a mouse model of multiple sclerosis, MHC class II-expressing ILC3s with an inflammatory phenotype were recruited from the circulation to the CNS and promoted myelin-specific T cell responses and neuroinflammation (40).

Fetal LTi cells.

Fetal LTi cells are closely related to LTi-like ILC3s. Both are dependent on RORγt, but the latter and not the former are derived from a PLZF-expressing precursor (41, 42). Fetal LTi cells are derived from the fetal liver, whereas LTi-like ILC3s are derived from the bone marrow. Fetal LTi cells are critically important for the generation of secondary lymphoid tissues such as the lymph nodes and Peyer patches. Following their generation in the fetal liver, LTi precursors migrate towards the lymph node anlagen where they respond to signals such as retinoic acid and RANK-L (receptor activator of nuclear factor kappa-B ligand) by producing IL-17, IL-22 and especially lymphotoxin, which activates lymphoid tissue organizer cells to promote lymph node development. These cells can also stimulate the generation of tertiary lymphoid structures, but other lymphotoxin-inducing cells can do so as well (43).

Innate IELs expressing CD3 chains.

The intestinal epithelium contains multiple subsets of innate lymphocytes (9). Some of these cells resemble ILC subsets found outside of the intestinal epithelium. Additionally, the intestinal epithelium contains TCR⁻ lymphocytes that are developmentally distinct from ILCs, express intracellular CD3 (iCD3) chains, and require IL-15 for their development (44). The latter cells are expanded in a refractory form of celiac disease with the potential to transform into lymphomas. This population of iCD3⁺ IELs contains a subset (termed iCD8α cells) expressing CD8αα homodimers, which are responsive to cytokines such as IL-12, express MHC class II, exhibit phagocytic properties and produce the cytokines IFN-γ and osteopontin (45). iCD8α cells have been implicated in murine colitis and immune responses against Citrobacter rodentium, and are expanded in human newborn infants with necrotizing enterocolitis (9, 45).

Innate-like B cells

The innate-like B cell population includes B-1 cells and MZB cells (Figure 1 and Table I) (46). These B cell subsets arise from distinct developmental pathways but share many properties and functions.

Table I.

Specificity of innate-like B and T lymphocytes.

Cell type	MHC	Antigen or other ligand
Innate-like B cells
B-1	N/A	self and foreign carbohydrates, glycolipids and glycoproteins
MZB	N/A	microbial carbohydrates and proteins
Innate-like unconventional T cells
Type I NKT or iNKT	CD1d	self and microbial glycolipids, including α-linked glycosylceramides such as α-GalCer
Type II NKT or dNKT	CD1d	self and microbial glycolipids such as sulfatide and lysophosphatidylcholine, and non-lipidic sulfa drugs
MAIT	MR1	vitamin B metabolites, small drugs and drug-like molecules
Qa-1/HLA-E-restricted CD8+ T	Qa-1 (mouse), HLA-E (human)	peptides from MHC class Ia signal sequence, self and microbial heat shock proteins, etc.
H2-M3-restricted CD8+ T	H2-M3 (mouse)	N-formylated peptides from bacteria or mitochondria
γδ T	class Ia, Ib, class I-related, class II, or none	peptide, lipid, BTN plus phosphoantigen (human), BTN-like, etc.
Natural TCRαβ+ IELs	class Ia or Ib?	peptide?
Innate-like conventional T cells
CD8+ innate memory T	class Ia	peptide
CD8+ virtual memory T	class Ia	peptide

N/A, not applicable

B-1 cells.

B-1 cells develop early during development from hematopoietic precursors in the fetal yolk sac or fetal liver and maintain their population during adulthood largely by self-renewal (47). B-1 cells constitute a major proportion of the B cells found in the peritoneal and pleural cavities, although they can also be found in other organs such as spleen and adipose tissue. These cells express high surface levels of IgM and low levels of IgD, and also express low levels of CD1d, permitting them to present antigens to natural killer T (NKT) cells (see below). The majority of these cells also express the inhibitory molecule CD5 and are called B-1a cells, whereas those lacking CD5 are called B-1b cells. B-1 cells express a limited BCR repertoire, in part because they undergo recombination in the absence of terminal deoxynucleotidyl transferase (TdT).

B-1a cells are the major source of so-called natural IgM autoantibodies that are reactive to a variety of self-derived carbohydrates, glycolipids and glycoproteins. These autoantibodies are thought to promote the clearance of senescent cells and to react with molecular patterns common to many microbes, thus providing an early source of immunity to diverse pathogens and to protect against sepsis (48). B-1 cells can also produce IgG3 and IgA antibodies in response to host microbiota, to which they react mainly through toll-like receptor (TLR) rather than BCR stimuli, generally in a T cell-independent manner. Although B-1 cell-mediated responses often lack antigen-dependence and immune memory, exceptions have been noted (48).

In addition to antibodies, B-1 cells are potent producers of immunoregulatory cytokines. For example, in response to sepsis or pneumonia, B-1a cells in serosal sites can migrate to the spleen and lung where they differentiate into so-called innate response activator (IRA) B cells that secrete growth factors such as GM-CSF and IL-3, which, in turn, amplify inflammation, while also producing polyreactive IgM antibodies that protect against infection (49). Additionally, a large proportion of B-1 cells can produce immune suppressive cytokines such as IL-10 or IL-27, and are thus included in the burgeoning family of regulatory B cells (Bregs) (50–52). These immunoregulatory B-1 cells can protect against sepsis, dissemination of Staphylococcus aureus, autoimmunity, obesity-associated insulin-resistance, and inflammation following myocardial infarction (50, 53, 54).

MZB cells.

MZB cells and follicular B (FOB) cells, jointly called B-2 cells, are derived from a common bone marrow precursor and diverge largely from each other at the transitional T2 stage (55). While new FOB cells are generated throughout life, MZB cells are predominantly generated early in life and are long-lived. MZB cells are located within the marginal zone of the spleen that forms the interface between the lymphoid white pulp and the non-lymphoid red pulp that represents the main point of antigen entry to the organ. Like B-1 cells, MZB cells express high levels of IgM and low levels of IgD. These cells also express CD1d, at levels higher than B-1 cells, but lack expression of CD5. Consistent with their early life origin, most MZB cells generate BCRs without TdT involvement, and exhibit a restricted BCR repertoire similar to B-1 cells that is biased towards common bacterial carbohydrate antigens.

The contribution of MZB cells to the normal pool of natural IgM autoantibodies is likely limited. However, these cells are critical for the rapid generation of T cell-independent IgM and IgG immune responses against blood-borne pathogens. Consequently, individuals without a spleen are at risk of severe disease and sepsis caused by encapsulated bacteria. Such organisms also contain T cell-dependent antigens and MZB cells can generate antibody responses to them as well, following interaction with T follicular helper (Tfh) or NKT cells. A recent study showed that MZB cells can capture peptide-MHC class II complexes from DCs, in a manner that involves binding of complement component C3 with peptide-class II complexes on DCs, followed by plasma membrane transfer to MZB cells via complement receptor 2 in a process called trogocytosis, thus endowing MZB cells with DC-like functions (56). The capacity of MZB cells to generate memory responses remains uncertain.

Like B-1 cells, IL-10-producing MZB cells have been identified. These cells may restrain immune responses against microbial pathogens or autoantigens (50).

Unconventional T cells with innate-like functions

Unconventional T cells are defined as T cells that do not react with classical peptide-MHC complexes (57). This family includes NKT cells, CD1a/b/c-restricted T cells, mucosal-associated invariant T (MAIT) cells, Qa-1/HLA-E-restricted T cells, H2-M3-restricted T cells, γδ T cells, and TCRαβ⁺CD8αα⁺ IELs (Figure 1 and Table I) (57–61). We will focus here on those subsets that most clearly belong to the group of innate-like T cells, based on their pre-activated state, rapid effector responses, and lack of classical immune memory.

NKT cells.

NKT cells recognize glycolipid antigens presented by the MHC class I-related protein CD1d, which is expressed by a variety of immune and epithelial cells (62–67). Two distinct subsets of NKT cells have been recognized: type I or invariant NKT (iNKT) cells that express semi-invariant TCRs (Vα14-Jα18 paired with Vβ8.2, Vβ7, or Vβ2 in mice and Vα24-Jα18 paired with Vβ11 in humans) and type II or diverse NKT (dNKT) cells that express more diverse TCRs (68). In mice, iNKT cells outnumber dNKT cells, whereas in humans, dNKT cells are more prevalent. These cells are enriched in tissues such as liver, but are also found in the intestine, lymphoid organs (including a mature population of iNKT cells in the thymus), and adipose tissue. Both NKT cell subsets can react with a variety of foreign and self-lipid antigens. All iNKT cells react with the prototypical antigen α-galactosylceramide (α-GalCer) that was isolated from a marine sponge but is likely derived from its commensal bacteria (65, 69). This antigen bears striking similarity to the α-linked glycosylceramides produced by some gut microbiota (70) and those serving as endogenous iNKT ligands in mammalian cells (71, 72). Owing to their more diverse TCRs, dNKT cells can react with a broader range of antigens compared to iNKT cells, including the self-lipids sulfatide and β-glucosylceramide, and non-lipidic small molecule sulfa drugs (73–75). In addition to TCR stimuli, iNKT cells can be activated by cytokines such as IL-12, IL-18, and type I interferons produced by TLR-activated DCs (76). This latter mode of activation may also apply to dNKT cells, as shown by studies with the TLR9 agonist CpG (77).

Both NKT cell subsets exhibit an effector phenotype, which they acquire during thymic development and requires PLZF expression (77–79). For iNKT cells, this also involves the intrathymic generation of subsets – IFN-γ-producing NKT1, IL-4-producing-NKT2 and IL-17-producing NKT17 cells – imprinted with a polarized cytokine production profile (80). Additional PLZF-independent subsets, including IL-10-producing NKT10 cells that are enriched in adipose tissues and IL-21-producing follicular helper NKT (NKTfh) cells, are generated in the periphery. The effector functions of iNKT cells are also significantly shaped by the microbiota they are exposed to early in life (81–83). dNKT cells can also produce a variety of cytokines, including IFN-γ, IL-4 and IL-13, but whether these are secreted by distinct subsets remains unclear. The cytokines produced by NKT cells can modulate the activity of a variety of innate, innate-like and adaptive immune cells. Key examples include the capacity of iNKT cells to enhance DC functions, promote NK cell activation, provide help to B cells, and induce Treg cell activity (84).

Owing to their tissue residence, iNKT cells are often one of the first immune cell types to respond to pathogens, including organisms that lack cognate antigens (85). They frequently facilitate protective immune responses against pathogenic microorganisms, but can also contribute to pathology and immune suppression seen following bacterial sepsis (86). iNKT cells also play a role in natural immunity against tumors and contribute to the pathogenesis of a multitude of autoimmune and inflammatory diseases. These activities of iNKT cells have been exploited in vaccines and immune therapies, employing α-GalCer or related antigens (87). dNKT cells can also induce protective (or sometimes pathogenic) immune responses against infectious agents and tumors, and in autoimmune and inflammatory diseases (73, 74, 85). Sulfatide-activated dNKT cells can protect against inflammation of the CNS and liver (73). In some models of cancer or fatty liver disease, iNKT and dNKT cells appear to play opposing roles (74).

MAIT cells.

MAIT cells recognize antigens in the context of the ubiquitously expressed MHC-related 1 (MR1) protein (63, 67, 88–90). These cells are rare in mice but quite abundant in humans, and are found in a variety of tissues such as liver, lungs and intestine. Like iNKT cells, MAIT cells express semi-invariant TCRs (Vα19-Jα33 paired with Vβ6 or Vβ8 in mice and Vα7.2-Jα33 paired with Vβ2 or Vβ13 in humans). These cells react with vitamin B metabolites derived from a variety of microorganisms (91). MR1 can also bind with a number of pharmaceutic agents and their derivatives that can weakly stimulate MAIT cells or compete for binding with agonistic antigens (92). Like iNKT cells, these cells can be activated in a TCR-independent manner, by cytokines such as IL-12 and IL-18. Most MAIT cells exhibit an effector phenotype that is acquired in the thymus and requires PLZF expression (93). MAIT cell subsets with a biased cytokine production profile have been identified (88, 94, 95), including IFN-γ-producing MAIT1 cells and a more abundant population of IL-17-producing MAIT17 cells. The MAIT1 and MAIT17 lineages develop in the thymus, which is facilitated by microbiota-derived vitamin B metabolites that traffic to the thymus to expand developing MAIT cells (96). MAIT cells contribute to protective immune responses against a variety of pathogens, including organisms lacking vitamin B biosynthetic pathways. These cells can also positively or negatively influence the progression of autoimmune and inflammatory diseases. Consistent with their response to microbial metabolites, these cells promote intestinal inflammation and dysbiosis, such as during obesity (97). Another critical function of MAIT cells is to promote wound healing by responding to commensal microorganisms (61, 98, 99). The potential utility of MAIT cell antigens as vaccine adjuvants or therapeutics remains to be explored.

Qa-1/HLA-E-restricted T cell subsets.

The murine nonclassical MHC class I (class Ib) protein Qa-1 (encoded by the H2-T23 gene) and its human ortholog HLA-E are ubiquitously expressed and can bind with peptides derived from a variety of endogenous and exogenous sources (100, 101). Qa-1 is typically occupied by peptides derived from the signal sequence of MHC class Ia proteins, and this complex interacts with CD94/NKG2 receptors on NK cells and subsets of CD8 T cells, leading to inhibition (via CD94/NKG2A) or less commonly activation (via CD94/NKG2C). Qa-1 can also bind with peptides derived from host or bacterial heat shock proteins, insulin, TCR Vβ chains, and a variety of self-peptides that are enriched in cells deficient in factors (i.e., TAP [transporter associated with antigen processing] or ERAAP [ER-associated aminopeptidase]) controlling MHC class I-restricted antigen presentation (102, 103). The Qa-1-restricted CD8 T cells reactive to some of these antigens may exhibit pro- or anti-inflammatory responses in different contexts (101, 104, 105). A regulatory Qa-1-restricted T cell population that expresses CD8αα and PLZF has been identified in the liver, and these cells can restrain autoimmunity in the CNS and intestine (106). The Qa-1-restricted CD8 T cell populations specific for immunodominant ligands on TAP- or ERAAP-deficient cells showed features of innate-like T cells, including expression of an invariant TCRα chain and a memory phenotype (102, 103). Upon activation, these cells became cytotoxic and produced IFN-γ, but their immune functions remain unclear. Finally, a population of HLA-E-restricted CD8⁺ T cells expands during human cytomegalovirus infection to adopt an NK cell-like phenotype with the capacity to lyse virally-infected cells via engagement of CD94/NKG2C in the absence of TCR stimulation (107).

H2-M3-restricted T cells.

The ubiquitously expressed mouse class Ib protein H2-M3 binds with N-formylated peptides (108), and is thus uniquely suited to present bacterially or mitochondrially derived peptides to CD8 T cells. Although H2-M3-restricted CD8 T cells display a diverse TCR repertoire, they exhibit a pre-activated phenotype to rapidly gain cytotoxicity and produce IFN-γ to bacterial pathogens, and generate diminished memory responses (105, 109–111). They play a non-redundant role in protective immunity against L. monocytogenes infection (112, 113). A recent study showed that these cells produce IL-17 and amphiregulin to commensal bacteria in the skin, providing antimicrobial protection while accelerating skin wound healing (114).

γδ T cell subsets.

γδ T cells are most abundant in barrier tissues, including skin, intestine and lungs, where subsets expressing particular TCR Vγ and Vδ combinations reside (115, 116). Subsets of γδ T cells with a variety of specificities have been identified. For example, human Vγ9Vδ2 T cells react with bacterial phosphoantigens bound by members of the butyrophilin (BTN) family of proteins that are related to the B7 family of co-stimulatory molecules. BTN-like proteins also control the development and function of γδ T cells in the skin of mice (i.e., DETC [dendritic epidermal T cells]) and in the intestinal epithelium of mice and humans (i.e., natural γδ IELs). Other subsets of γδ T cells interact with MHC class I-related proteins such as CD1, MR1, mouse T10/T22, human MICA and MICB (MHC class I-related A and B), and UL16-binding protein 4 (ULBP4), either in the presence (e.g., CD1, MR1) or absence (e.g., T10/T22, MICA/B, and ULBP4) of bound antigen (117). Some of these factors may be induced by cellular stress and also activate γδ T cells by binding with NKG2D (e.g., MICA/B and ULBPs). γδ T cell subsets develop in waves from embryonic to early neonatal life to populate specific peripheral sites. Subsets of γδ T cells (γδT1, γδT2 and γδT17 cells) that are thymically programmed to produce type 1–3 cytokines have been described, and some (γδT2 and γδT17 subsets) are dependent on PLZF for their development (80, 118). In addition to TCR- and NKG2D-mediated responses, these cells can be activated by cytokines such as IL-12 and IL-18. Although some γδ T cells can generate immune memory, others cannot (119). Consistent with their diverse tissue distribution and effector functions, γδ T cells have been implicated in protective immune responses against a variety of pathogens, can contribute either positively or negatively to tumor immunity, and control the pathogenesis of autoimmune and inflammatory diseases (115, 116). For example, recent studies with human Vγ9Vδ2 T cells have shown two pathways by which these cells can sense and constrain blood stage malaria parasite infection (120): firstly, their TCRs can interact with parasite-derived phosphoantigens bound with BTN proteins on red blood cells to trigger red blood cell lysis, and secondly, in the presence of patient serum, these cells can phagocytose and degrade the malaria parasites. Other recent studies have identified a subset of γδT17 cells that accumulate in adipose tissue where they are able to influence Treg cell homeostasis, promote sympathetic innervation, and control thermogenesis (121, 122). DETC that reside in the murine epidermis have been implicated in regulating cutaneous malignancy and skin antimicrobial barrier function (123, 124). Finally, natural γδ IELs in the intestine play a role in parasite expulsion, tissue repair following mucosal injury, and oral tolerance (9, 125).

Natural TCRαβ⁺CD8αα⁺ IELs.

In addition to innate IELs and natural γδ IELs discussed above, the intestinal epithelium contains αβ IELs with innate-like characteristics and functions (9, 125). These natural αβ IELs express CD8αα in the absence of CD8αβ or CD4 and are derived from thymic precursors that upon leaving the thymus during a narrow time window in early life rapidly seed the epithelium and induce CD8αα expression in response to TGF-β signaling (9, 125, 126). The specificity of these cells is uncertain but likely involves both classical and nonclassical MHC products. These cells display an oligoclonal TCR repertoire, exhibit an effector or memory phenotype, depend on IL-15 for their maintenance and/or differentiation, and show similarities with thymus-derived Tregs (127). The functions of these cells are incompletely understood, but they may be involved in sensing damaged epithelia and regulating intestinal inflammation (9, 125). Recent studies have shown that natural TCR⁺ IELs can modulate systemic metabolism and accelerate cardiovascular disease to a fat- and sugar-rich diet (128).

Conventional T cells with innate-like functions

A substantial proportion of antigen-inexperienced T cells in unmanipulated mice express phenotypic markers of immune memory (7, 129, 130). These cells have been primarily defined within the CD8⁺ T cell lineage of mice. These antigen-inexperienced memory T cells can be partitioned into subsets whose innate-like memory phenotype is imprinted intra-thymically (i.e., innate memory T cells) or acquired extra-thymically (i.e., virtual memory T cells) (Figure 1 and Table I). Although the precise developmental, phenotypic and functional relationships between these two subsets are under debate (7), it has been recently suggested that these subsets can be distinguished based on differential surface expression levels of CD122 (131). Thymic innate memory CD8⁺ T cells are formed via IL-4 produced by NKT2 cells and prevail in young mice with high thymic IL-4 output (131, 132). Virtual memory T cells are thought to represent CD8 T cells with high levels of autoreactivity that are converted to innate-like memory T cells in the periphery via cytokines such as IL-15, IL-7 and/or IL-4 (133–135). Virtual memory T cells are more prevalent in aged mice, probably owing to age-related lymphopenia (136). Innate-like memory T cells express NKG2D and can respond to cytokine signals (e.g., IL-12 and IL-18) to induce IFN-γ production and bystander killing in an antigen-independent manner. These cells contribute to clearance of bacterial and viral infections while maintaining tolerance against self-antigens (7, 129, 130). These cells can also infiltrate tumors where they express PD-1 (programmed death 1) and may serve as targets for checkpoint inhibitors (133).

Conclusions

Innate and innate-like lymphocytes can sense danger and stress signals that evoke their rapid effector responses to promote early immune surveillance and modulate adaptive immunity. Distinct subsets of innate and innate-like lymphocytes exhibit specialized effector functions that mirror those of their adaptive cousins. These cells therefore play integral roles in each of the major immune effector modules. Despite this progress, many questions regarding the diverse functions of innate and innate-like lymphocytes remain to be fully addressed (Table II). A better understanding of the biology of these cells and their roles in health and disease will undoubtedly advance novel approaches for the development of vaccines and immunotherapies.

Table II.

Outstanding questions regarding the functions of innate and innate-like effector lymphocytes.

How similar or different are they between humans and mice?

What are the mechanisms that elicit their effector functions?

To what extent do tissues imprint resident populations with unique features?

How do they interact with other immune and non-immune cells?

Are the functions of individual subsets redundant or unique?

Do they make distinct contributions to primary vs. secondary immune responses?

Considering the alterations observed in some of these cells during SARS-CoV-2 infection (137–140), do they influence COVID-19 disease progression?

How can we better target these cells in vaccines and immunotherapies?

Abbreviations used in this article:

Breg

regulatory B

BTN

butyrophilin

DETC

dendritic epidermal T cell

dNKT

diverse NKT

Eomes

Eomesodermin

FOB

follicular B

IEL

intraepithelial lymphocyte

ILC

innate lymphoid cell

iNKT

invariant NKT

LTi

lymphoid tissue inducer

MAIT

mucosal-associated invariant T

MIC

MHC class I-related

MR1

MHC-related 1

MZB

marginal zone B

NCR

natural cytotoxicity receptor

NK

natural killer

NKT

natural killer T

PLZF

promyelocytic leukemia zinc finger

Tfh

T follicular helper

Treg

regulatory T

ULBP

UL16-binding protein