MAIT cell homing in intestinal homeostasis and inflammation

Abstract

Mucosa-associated invariant T (MAIT) cells are a large population of unconventional T cells widely distributed in the human gastrointestinal tract. Their homing to the gut is central to maintaining mucosal homeostasis and immunity. This review discusses the potential mechanisms that guide MAIT cells to the intestinal mucosa during homeostasis and inflammation, emphasizing the roles of chemokines, chemokine receptors, and tissue adhesion molecules. The potential influence of the gut microbiota on MAIT cell homing to different regions of the human gut is also discussed. Last, we introduce how organoid technology offers a potentially valuable approach to advance our understanding of MAIT cell tissue homing by providing a more physiologically relevant model that mimics the human gut tissue. These models may enable a detailed investigation of the gut-specific homing mechanisms of MAIT cells. By understanding the regulation of MAIT cell homing to the human gut, potential avenues for therapeutic interventions targeting gut inflammatory conditions such as inflammatory bowel diseases (IBD) may emerge.

MAIT cell homing to the gut in health and disease provides insights to guide therapeutic development for intestinal inflammation.

INTRODUCTION TO MAIT CELLS

Mucosal-associated invariant T (MAIT) cells constitute a large population of innate-like T cells in humans. Unlike classical T cells, MAIT cells express a semi-invariant T cell receptor (TCR) composed of an invariant TCR Vα and Jα segment (TRAV1-2-TRAJ33/12/20), paired with a limited set of TCRβ chains, predominantly TRBV20 or TRBV6 in humans (1, 2). This unique TCR arrangement allows MAIT cells to recognize various pyrimidine-related antigenic metabolites presented by the nonpolymorphic major histocompatibility complex class I–related protein (MR1) (3, 4), including those derived from microbial metabolites derived from riboflavin biosynthesis (4, 5). The MR1 gene is highly evolutionarily conserved among mammals, and of all the MHC class I–like proteins, MR1 shows the highest conservation among eutherian mammals, including in various ungulates and chiropterans (6–8). Among the antigenic metabolites of riboflavin biosynthesis that MAIT cells recognize, the most potent stimulatory MR1-binding ligands found are 5-OP-RU [5-(2-oxopropylideneamino)-5-d-ribitylaminouracil] and 5-OE-RU [5-(2-oxoethylideneamino)-5-d-ribitylaminouracil] (5).

In the human blood, the majority of MAIT cells are CD4⁻CD8⁺ subsets; ~10 to 15% CD4⁻CD8⁻ subsets and less than ~5 to 10% CD4⁺CD8⁻ and CD4⁺CD8⁺ subsets [reviewed in (9)]. MAIT cells exhibit innate-like immune responses, which are in part driven by the transcription factor promyelocytic leukemia zinc finger to respond quickly to infections (10). MAIT cells expressing T-box transcription factor TBX21 (T-bet), Eomesodermin (Eomes), and B lymphocyte–induced maturation protein 1 (BLIMP-1) have type 1 immunity through secretion of interferon-γ (IFN-γ), tumor necrosis factor (TNF), and cytolytic proteins including granzyme B, perforin, and granulysin when detecting bacterial infection. Activated MAIT cells can also produce type 17 immune responses, primarily identified by their interleukin-17 (IL-17) secretion that is driven by retinoic acid receptor-related orphan receptor gamma (RORγt) and signal transducer and activator of transcription 3 (STAT3), which are highly relevant in the mucosal sites (11, 12). Interestingly, IL-17–producing human MAIT cells have the capacity to switch to secreting IFN-γ following TCR stimulation in the presence of polarizing cytokines (13). Prolonged TCR stimulation can induce MAIT cells to produce type 2 cytokines, including IL-4, IL-10, and IL-13 (14–16). Follicular helper–like MAIT cells have also been identified in human tonsils, which help in B cell differentiation and the generation of high-quality antibody responses (17). In addition, there exist regulatory-type MAIT cells characterized by the expression of forkhead box (Fox) P3, Helios, and CD39 (18–21). In summary, there is substantial heterogeneity and plasticity within the human MAIT cell population, with their diverse functional roles in health and various diseases still requiring further exploration.

CELLULAR DISTRIBUTION OF MAIT CELLS IN THE HUMAN GUT MUCOSA

Because of the challenges of obtaining gut tissue samples from healthy humans, our understanding of MAIT cell distribution within the gut mucosa has been somewhat limited. However, recent research has revealed that MAIT cells are indeed present in the human gut, with varying levels of abundance across different regions and tissue compartments (21–28). This growing body of evidence provides valuable insights into the specific localization and frequency of MAIT cells within the gut, contributing to a better understanding of their role in gut immunity.

The initial discovery revealed that human TRAV1-2-TRAJ33 MAIT cells were located specifically in the lamina propria (LP) of the gut, based on analysis of gut biopsies that included tissue from the epithelium, Peyer’s patches, and LP (3). In addition, MAIT cells have been identified in the LP of the human stomach, where they exhibit a memory phenotype comparable to those found in peripheral blood (22). In healthy human jejunal tissue, only small numbers of intraepithelial (IE) MAIT cells were detected using in situ TRAV1-2⁺ CD161⁺ staining, with confirmation via MR1 tetramer staining (1, 25). Although only a subset of TRAV1-2⁺ CD161hi T cells in intestinal tissues reacted to the MR1-5-OP-RU tetramer, a definitive marker for MAIT cells, these cells were observed in both the LP and IE layers of the gastrointestinal mucosa, with their abundance varying across these compartments (25). Furthermore, MAIT cells were found in colectomy samples of both colon adenocarcinomas and unaffected colon tissue, with similar frequencies observed in the IE compartment and LP (23). In patients with colorectal cancer or cecal appendix cancer, a comparison of MAIT cell frequencies among intraepithelial lymphocytes (IELs) and lamina propria lymphocytes showed that the cecum harbored substantially higher frequencies of MAIT cells in the IEL compartment compared to the colon (24). Immunohistochemistry also revealed that TRAV1-2⁺ cells were predominantly found in the LP of the colon but were also present in IE regions of the cecum (24). Collectively, it is evident that MAIT cells are primarily located within the LP of the gut mucosa while also present at lower numbers in the IE compartment, reflecting their widespread distribution within the gut mucosa.

MAIT CELL FUNCTION WITHIN THE HUMAN GUT

MAIT cells mediate effector functions through two key mechanisms: the TCR-dependent and TCR-independent pathways. In the TCR-dependent pathway, MAIT cells recognize riboflavin metabolites presented by MR1 molecules, which triggers the release of proinflammatory cytokines such as IFN-γ and TNF, as well as cytotoxic molecules, including granulysin, granzymes, and perforin (29–32). This pathway is essential for responding to microbial infections such as riboflavin-producing bacteria and fungi (11, 30, 33). Alternatively, the TCR-independent pathway driven by cytokines such as IL-12 and IL-18 enables MAIT cells to respond even when riboflavin metabolites are absent, broadening their role to include infection caused by viruses and nonriboflavin-producing microbes (10, 27, 34–36), cancer, and noninfectious inflammation in the intestine (37). Other cytokines, including IL-7, IL-15, and type I IFNs, further enhance MAIT cell activity, allowing them to produce cytotoxic molecules and inflammatory cytokines (12, 29, 38). These two activation pathways often work together, resulting in stronger effector responses, with MAIT cells producing higher levels of cytokines and chemokines (36, 38). In addition, glycolytic, lipid, and oxidative phosphorylative metabolic pathways regulate the development and function of human MAIT cells in circulation and the lung (39–41). Whether such metabolic programming shapes gut resident MAIT cell effector responses is yet to be established.

Although studies indicate that MAIT cells are proinflammatory and may promote tissue damage, including within the human gut (22, 26, 42–47), there is an increasing appreciation of the tissue repair and healing roles of MAIT cells [reviewed in (27)]. Such studies showed the expression of tissue repair gene signatures following TCR stimulations (34, 36, 38) and production of tissue repair factors, including the cytokines IL-17 and IL-22 (21, 26, 48, 49), FURIN, CCL3 (C-C motif chemokine ligand 3), VEGFB (vascular endothelial growth factor B), CSF2 (granulocyte-macrophage colony-stimulating factor), and AREG (amphiregulin), which initiate tissue repair and reinforce barrier integrity (34, 36, 38, 50, 51). In a mouse model of colitis, MAIT cell ligands generated in the colon were found to rapidly cross the intestinal barrier, activating MAIT cells, which in turn expressed tissue repair genes and produced barrier-promoting mediators, including HIF1A (hypoxia-inducible factor 1 subunit alpha) and FURIN (52). Mice lacking MAIT cells were shown to be more susceptible to chronic colitis and colitis-induced colorectal cancer (CRC) (52). Interestingly, topical administration of the prototypical MR1 ligand 5-OP-RU was sufficient to stimulate wound healing by recruiting cutaneous MAIT cells and production of IL-17 (50). Similarly, in a human-like mouse model of full-thickness skin injury, MAIT cells express a tissue repair transcriptomic program and promote skin wound healing through their recruitment into the wound site in a TCR-independent but CXCR6-dependent manner (51). AREG-deficient mice exhibited appreciably delayed wound healing, indicating the role of Areg in the tissue healing function of MAIT cells (51). These findings underscore the importance of MAIT cells in tissue repair and maintaining barrier integrity during both infection and inflammatory conditions. However, while MAIT cells in the appendix produce IL-17 and IL-22 in response to bacterial stimulation (26), and intestinal MAIT cells have demonstrated regulatory functions that may contribute to barrier protection (21), further research is needed to determine whether MAIT cells are involved in other tissue repair processes within the human gut.

MAIT CELL SEEDING INTO THE GUT MUCOSAL TISSUES DURING DEVELOPMENT

During thymic development in mice, MAIT cells undergo positive selection via MR1 molecules expressed by CD4⁺ CD8⁺ double-positive (DP) thymocytes (53, 54). Human MAIT cells also develop within the thymus, and their intrathymic development follows three distinct stages, as outlined in a seminal study by Koay and colleagues (55). In the first stage, MAIT cells express both the CD4 and CD8 coreceptors (CD4⁺CD8⁺ DP cells) but notably lack expression of CD27 and key MAIT cell markers, CD161 and IL-18 receptor α-subunit (IL-18Rα). These receptors are progressively up-regulated during the second and third stages of MAIT cell development (55). MAIT cells exit the thymus primarily as either CD8⁺ single-positive cells or as double-negative (DN; CD4⁻ CD8⁻) cells in a naive state (55, 56).

In the periphery, the maturation and expansion of naive MAIT cells are primarily driven by microbial exposure, particularly through riboflavin metabolites (55, 57). The gut microbiota plays a crucial role in this process, as commensal bacteria producing the riboflavin metabolites are essential for MAIT cell maturation (50, 57, 58) and germ-free mice have substantially fewer MAIT cells (3, 55). Interestingly, MAIT cells are already present in low numbers within the gut mucosae of second-trimester human fetuses and exhibit innate-like antimicrobial responses before the establishment of commensal microflora in the gut (59). This suggests that the seeding and functionality of MAIT cells in the human gut may occur independently of microbial colonization (59). However, since MR1 ligands can enter the circulation from barrier tissues and contribute to the development and accumulation of MAIT cells at distal sites (50, 57), it is tempting to speculate that these ligands may cross the placenta during pregnancy, entering the fetal circulation. This process could facilitate the seeding and functional maturation of MAIT cells in the fetal gut. Further insights from mouse models revealed that cytotoxicity-associated genes were only expressed by MAIT1 cells in the thymus (60). However, MAIT cells in the mouse intestine not only expressed cytotoxic genes but also up-regulated a tissue repair gene signature, indicating that MAIT cells undergo additional functional maturation after leaving the thymus (60). This highlights their ability to adapt and acquire tissue-specific roles.

Within human circulation, the frequency of MAIT cells increased from birth until about 25 years of age, after which they declined (61–65). Interestingly, single-nucleotide polymorphisms of IL7RA—the gene encoding IL-7 receptor α-subunit—are associated with increased MAIT cell levels within the circulation, further highlighting the potent influence of IL-7 on MAIT cell biology (66). Following adulthood, the CD8⁺ MAIT cell population decreases, while the DN MAIT cell population appears to accumulate with age (63, 67, 68). Subsequent investigations reveal that this may be contributed by the differentiation of the dominant CD8⁺ MAIT cell population into DN MAIT cells (67). Furthermore, progressively mature DN MAIT cells accumulate in human fetal tissues, while the CD8⁺ subset contracts in response (67). This suggests that the differentiation of peripheral CD8⁺ MAIT cells into the DN subpopulation might also occur without a fully established microbiota in the mucosal tissues. The DN MAIT cells exhibit distinct functional characteristics, including enhanced IL-17 production and increased susceptibility to apoptosis (67). In contrast, CD8⁺ MAIT cells show increased IFN-γ and TNF production (67, 69). This enhanced function in CD8⁺ MAIT cells is due to the interaction of CD8 with MR1, which acts as a functional coreceptor for these cells (69). Collectively, this sequence of studies supports the importance of both microbial interactions and the local environment in the maturation and functional diversification of MAIT cells, albeit that fully established microbiota may not be essential in certain circumstances.

THE POTENTIAL ROLE OF THE GUT MICROBIOTA AND MAIT CELL DISTRIBUTION IN THE HUMAN GUT

The gut harbors complex and dynamic microbial communities, influenced by multiple factors, including environment, diet, and age (Fig. 1) (70). These microbiota communities play a crucial role in shaping the distribution and function of the gut immune cell populations. Whether varied MAIT cell population in the intestine [reviewed in (27)] is associated with various microbial compositions and related riboflavin biosynthesis (71) as the microbiota composition shifts with age, diet, and environmental factors remains little understood (Fig. 2).

Fig. 1. The changes of commensal bacteria in intestinal tract along with age.

Lactobacillales and Bacillales may be detected at low levels in meconium, although the microbiome is predominantly established only after birth. The gut is rapidly colonized by Bifidobacteriales, Bacteroidales, and Clostridiales after birth and then replaced by a diverse mixture of Clostridiales and Oscillospirales between 6 and 24 months. By around 2 to 3 years of age, the composition of bacterial community resembles adult-like biomass with the dominance of Bacteroidales, Oscillospirales, and Lactobacillales. The microbial community shifts with an increased abundance of Bacteroidales and Clostridiales in the older individuals. Created with BioRender.com.

Fig. 2. The potential association of MAIT cell distribution and commensal bacteria in the intestinal tract.

Values indicate the mean or range of MAIT cell frequency in the relevant tissues as percentages of total T cells. (+) indicates riboflavin-producing bacteria. (−) indicates nonriboflavin-producing bacteria. (+/−) indicates that parts of the bacterial Order produce riboflavin (71). The abundance of Bifidobacteriales and Lactobacillales appears to be higher in faecal/luminal samples than in the mucosa, whereas Clostridiales and Lactobacillales are detected in the mucus layer as well as crypts of intestinal epithelium (84, 85). Created with BioRender.com.

The gut microbiota composition undergoes substantial changes across the life span, beginning with rapid colonization after birth, followed by the establishment of a more diverse and stable microbiota in early childhood, and eventual shifts in older age (Fig. 1) (70, 72, 73). These age-related variations in microbial communities could influence the early seeding of MAIT cells to the gut, given that MAIT cells recognize microbial metabolites produced through the riboflavin biosynthesis pathway, which is common among gut bacteria, including Bacteroidales, Bacillales, Vellionellales, and Clostridiales (74). Notably, sulfated secondary bile acids, which represent a distinct class of MR1 ligands, are produced through the metabolic activity of the microbiome and lead to MAIT cell survival and the expression of a homeostatic gene signature (75). In neonates, the predominance of early colonizers such as Lactobacillales and Bacillales (76–78) may limit the availability of riboflavin-dependent bacteria and may influence MAIT cell activity during this period. As the infant’s gut transitions to a more diverse bacterial community with the introduction of solid foods, the presence of Clostridiales and Oscillospirales increases (79–81), potentially promoting greater MAIT cell localization and functionality to areas of high microbial density, such as the ileum and colon. In adults, the microbial community shifts toward increased Bacteroidales and Clostridiales abundance (73). These taxa are known to express the riboflavin biosynthesis pathway (71). The age-associated changes in bacterial composition may thus potentially influence MAIT cell localization and functionality in the human gut and their role in maintaining gut immune homeostasis.

The varying composition of bacteria across different sections of the gut may further influence the distribution and function of MAIT cells in different parts of the gut. In the small intestine, which has a relatively low bacterial biomass, MAIT cell localization may be limited due to the lower abundance of riboflavin-producing bacteria such as the Vellionellales, Bacillales, Clostridiales, Bacteroidales, and Enterobacterales (71). The colon contains abundant bacterial loads and is dominated by obligate anaerobes such as Bacteroidales, Clostridiales, and Bifidobacteriales (82). The variation in bacterial composition between the proximal and distal parts of the colon, with Bacteroidales being prevalent in the rectum (83), might result in localized differences in MAIT cell distribution and activity. These anaerobic bacterial taxa are known to produce riboflavin (71), potentially explaining the higher concentrations of MAIT cells in the large intestines (Fig. 2) (27). Such abundance may also lead to enhanced MAIT cell function, particularly in immune surveillance and response to microbial pathogens in these parts of the gut. In addition, the variation in bacterial distribution between the mucus layer and fecal content may also affect MAIT cell positioning and function (81, 84, 85), as different microbial niches within the gut could offer distinct signals for MAIT cell recruitment and retention (Fig. 2).

In summary, the composition of the gut microbiota, particularly the riboflavin-producing taxa, may influence the distribution and functional responses of MAIT cells within various parts of the human gut across different age groups. The link between microbial composition and MAIT cell distribution and function remains an important area for further research, with potential implications for understanding MAIT cell regulation in gut health and disease.

MECHANISMS OF MAIT CELL HOMING TO THE HUMAN GUT IN HEALTH AND PATHOLOGICAL CONDITIONS

The homing of MAIT cells to the gut and their retention involve several key factors, including chemokines, chemokine receptors, and tissue adhesion molecules (Fig. 3). These molecular signals coordinate MAIT cell migration and residence in the human gut, allowing them to perform immune effector and tissue repair roles. Dysregulation of these homing signals is often observed in pathological gut conditions, including during infection, inflammation, and malignancies. These perturbations may enhance MAIT cell recruitment and retention at these sites and promote increased effector responses that may exacerbate inflammation and tissue damage. Indeed, in multiple gut pathologies, MAIT cells frequently increase within the gut mucosal tissues, whereas their circulatory counterparts concomitantly decrease (27). Together, these observations indicate that circulating MAIT cells are commonly recruited during these gut pathologies. Here, we discuss various potential mechanisms that may guide MAIT cells to home to the gut in health and disease.

Fig. 3. MAIT cell homing to the gut in health and inflammation.

In homeostasis (left), MAIT cell homing to the stomach may rely on the chemokine receptor G protein–coupled receptor 25 (GPR25) and its ligand chemokine CXCL17, whereas in the small intestine, MAIT cells may depend on CCR9. GPR15 and its ligand GPR15LG contribute to MAIT cell homing to the large intestine. Subsequently, MAIT cells transmigrate from the gut microvasculature via the interaction of α4β7 integrin with mucosal addressin cell adhesion molecule–1 (MAdCAM-1) expressed on endothelial cells. α4β7 and α4β1 integrins may also interact with low levels of vascular cell adhesion molecule–1 (VCAM-1) expressed at these sites. MAIT cells may up-regulate αEβ7 integrin to interact with E-cadherin within the mucosal LP and IE layer. During inflammation (right), such as acute appendicitis, IBDs, and CRC, inflammatory chemokines increase at barrier sites and lead to the recruitment of MAIT cells through various chemokine receptors such as CCR1, CCR2, CCR4, CCR6, CCR9, CXCR3, and CXCR6. Increased levels of inflammatory cytokines at these sites partly contribute to the up-regulation of these chemokine receptors. Concomitantly, there is an increase in the expression of tissue adhesion molecules including MAdCAM-1, VCAM-1, and intercellular adhesion molecule–1 (ICAM-1), further enhancing MAIT cell entry into the gut mucosae. The balance between homeostasis and inflammation may lead to different recruitment mechanisms of MAIT cells and possibly different effector roles (protective versus pathogenic). Created with BioRender.com.

Chemokines and chemokine receptors

Chemokines are small signaling proteins and are among the first mobilizers of host responses in homeostasis and disease processes (86–88). The main function of chemokines is to guide the migration of immune cells during homeostasis, infection, and inflammation. By binding to G protein–coupled chemokine receptors expressed on immune cells, chemokines orchestrate the directed movement of immune cells toward sites of infection or tissue damage (89). Circulating MAIT cells express high levels of tissue-homing chemokine receptors (Table 1), including C-C motif chemokine receptor 6 (CCR6), CCR9, and C-X-C motif chemokine receptor 6 (CXCR6), as well as CCR2, CCR5, and CXCR3, allowing them to migrate (26, 90, 91). Chemokine and chemokine receptors, including CCR9 and its ligand CCL25, are important for the homing of MAIT cells to the gut, particularly to the small intestine, while other chemokine receptors including CCR6 and CXCR6 may also play roles (23, 92). The G protein–coupled receptor GPR25 and its ligand CXCL17 (C-X-C motif chemokine ligand 7) specifically recruit T cells into the upper gastrointestinal tract, such as the stomach, whereas GPR15 and its ligand GPR15LG to the colon (93–95). Human tonsillar MAIT cells migrated to both CXCL17 and GPR15LG in transwell experiments, suggesting the role of these chemokine receptor–ligand axes in MAIT cell recruitment to the stomach and colon, respectively (93). In other tissues, MAIT cells appear to migrate via different chemokine-chemokine receptor axes. For instance, circulating MAIT cells migrate to the intervillous region of the placenta via macrophage migration inhibitory factor (MIF), CCL20, and CCL25 (96). In another study, MAIT cells may egress from the tissues and recirculate within the lymphatic system, possibly via CCR7 (97).

Table 1. Expression of chemokine receptors on circulating MAIT cells at steady state and their potential chemokine ligands.

The expression of chemokine receptors by peripheral blood MAIT cells in a steady state may change during inflammatory conditions. The chemokine receptors and their ligands that are up-regulated during gut inflammation are depicted in Fig. 3.

Chemokine receptors	Potential chemokine ligands
CCR2 (26, 91, 132)	CCL2, CCL7, CCL8, CCL13, and CCL16
CCR5 (26, 91, 132)	CCL3, CCL4, CCL5, CCL14, CCL16, and CCL3L1
CCR6 (26, 42, 91, 132)	CCL20
CCR9 (42, 91)	CCL25
CXCR3 (42, 91, 132)	CXCL9, CXCL10, and CXCL11
CXCR4 (91, 132)	CXCL12
CXCR6 (26, 42)	CXCL16

CD26/dipeptidylpeptidase IV is widely expressed in blood and tissues [reviewed in (98)]. A large number of human chemokines, including CXCL2, CXCL6, CXCL9, CXCL10, CXCL11, CXCL12, CCL3L1, CCL4, CCL5, CCL11, CCL14, and CCL22, are cleaved by CD26 (98). NH₂-terminal cleavage of chemokines by CD26 has prominent effects on their receptor binding and signaling (99–102). Through modulation of chemokine activity, CD26 regulates leukocyte migration and progenitor cell release from the bone marrow (98, 103–105). Interestingly, MAIT cells uniformly express high levels of CD26 (61, 106, 107). However, it is now unclear whether CD26 expressed by MAIT cells may play roles on cleaving certain chemokines and influence MAIT cell migration to the gut.

During acute infection and inflammation of the gut, MAIT cells are also recruited to the pathological sites through different sets of chemokines and chemokine receptors. Recently, we reported the recruitment of circulating MAIT cells into the appendix tissues during acute appendicitis in children (26). Acute appendicitis is a severe inflammation as an outcome of bacterial infection in the appendix tissues, usually caused by gram-negative enteric bacteria. MAIT cell recruitment in acute appendicitis was mediated by CCR1 and CCR2 via their chemokine ligands CCL2, CCL3, and CCL8, as well as by CCR4 via their chemokine ligands CCL17 and CCL22, all of which were elevated in both plasma and inflamed appendix tissues (26). During Vibrio cholerae infection, there appears to be MAIT cell clonotype redistribution from the circulation into the duodenum following infection (45). In cases of necrotizing enterocolitis (NEC), another severe intestinal inflammation as an outcome of bacterial infection in the newly born, a decrease in circulating MAIT cells was observed, while there was an enrichment of these cells in the ileal tissues of patients with NEC (46). In a human challenge trial involving controlled infection with Salmonella enterica serovar Paratyphi A, MAIT cells were activated in the blood during infection, with an early decrease in their frequency occurring before the clinical diagnosis of enteric fever (108). Together, these bodies of studies strongly support the hypothesis that MAIT cells are actively recruited to the sites of acute infection and the accompanying inflammation.

Inflammatory Bowel Disease (IBD) is a chronic inflammatory condition affecting the intestines, characterized by repetitive episodes of inflammation of the gastrointestinal tract caused by abnormal immune responses (109). IBD primarily consists of Crohn’s disease (CD) and ulcerative colitis (UC); while CD affects the entire gastrointestinal tract, UC predominantly affects the large intestine (110). In this chronic inflammation, MAIT cells were activated, leading to enhanced recruitment to inflamed tissues, a shift in their phenotype, and alterations in their cytokine secretion patterns (42–44, 47). While MAIT cell frequency in the blood of patients with IBD was notably lower than in healthy donors, it was notably higher in inflamed colons compared to healthy colons (47). In addition, the expression of chemokines such as CCL20, CXCL10, CXCL16, and CCL25 was elevated in inflamed intestinal tissues compared to non-inflamed tissues (42). In patients with UC, the frequency of MAIT cells in peripheral blood was lower compared to healthy controls but elevated in inflamed mucosa, correlating with clinical and endoscopic disease activity (44). In another study, in both UC and CD patients, MAIT cell frequency was lower not only in peripheral blood but also in inflamed intestinal mucosa compared to non-IBD controls. This reduction may be due to the proapoptotic characteristics exhibited by MAIT cells in patients with IBD (111). In mouse models of spontaneous (112) and chemically induced colitis (113), MAIT cells appear to play a pathogenic role as MR1 deficiency or suppressing MAIT cell activation in these models lessened the severity of colitis without compromising gut integrity. In a contrasting study, MR1 ligands generated in the colon led to the secretion of tissue repair factors by MAIT cells and better colitis outcomes (52).

Patients with mucosal-associated malignancies, including gastric, colon, and lung cancers, had markedly lower circulating MAIT cell levels (114–116). MAIT cell levels in such cancer tissues were higher than in peripheral blood suggesting their recruitment (114, 115), with infiltration into the cancer tissues in some studies (114, 115). Circulating MAIT cells had high levels of CCR6 and CXCR6, and their chemokines, such as CCL20 and CXCL16, were highly expressed in colon cancer tissues (115). Interestingly, chemokine responsiveness is similar in both unaffected mucosa and tumor-associated MAIT cells (23).

Although viruses do not have riboflavin synthesis pathway and thus do not activate MAIT cells directly through the TCR-dependent pathways, they provoke various innate and proinflammatory cytokines and stimulate MAIT cells via this cytokine-driven pathway [reviewed in (117)]. In chronically infected HIV-1 patients, there is a distinct decrease of MAIT cells in the circulation (35, 118). Interestingly, MAIT cells were maintained or even increased in the colorectal tissues (35, 118, 119), suggesting that MAIT cells are recruited to the gut during chronic HIV-1 infection. Going forward, it will be important to determine the mechanisms underlying MAIT cell trafficking in chronic viral infections affecting the gut mucosa such as HIV-1 infection.

Tissue adhesion molecules

Integrins are the primary adhesion molecules that immune cells use to home into tissues. Their roles in guiding MAIT cell homing into tissues are less well understood than the more extensively studied chemokine-chemokine receptor axis that governs their migration. Given the limited studies on this subject, in this Review, we infer from the well-characterized roles of integrins in the homing mechanisms of conventional gut-resident T cells. In these T cells, integrins such as α4β1 and α4β7 play a crucial role in mediating homing to the intestinal mucosa (110), where they use these integrins to interact with the ligands on vascular endothelial cells (110). Certain chemokines activate integrins such as α4β1 and α4β7, which then bind to vascular cell adhesion molecule–1 (VCAM-1) and mucosal addressin cell adhesion molecule–1 (MAdCAM-1), respectively (110, 120). These molecules are expressed in the Peyer’s patches and mesenteric lymph nodes, facilitating the transmigration of T cells into gut tissues (121). Once in the gut, T cells adhere to the intestinal epithelium by interacting with E-cadherin through αEβ7 integrin, contributing to the immune effector processes (110, 120, 122). Other integrins, such as integrin αLβ2 (LFA-1) may additionally contribute to the accumulation of T cells into the gut tissues during inflammation through its interaction with intercellular adhesion molecule–1 (ICAM-1) [reviewed in (123)].

Transcriptomic analysis reveals that MAIT cells express multiple integrins, including ITGA1, ITGA4, ITGA5, ITGB1, and ITGB3 in the murine thymus (124), suggesting that these integrins may guide them to specific tissues. However, their exact functions are not fully understood. Indeed, human MAIT cells are known to express several integrins under normal physiology and during inflammation, including α4β7 and αEβ7 (26, 49). The presence of tissue-resident-like MAIT cells expressing CD69 and αE integrin (CD103) has been shown in the gastrointestinal tract, including in the oral mucosae (49), the appendix (26), and the intestine (21).

In diseases characterized by an overactive immune response, such as IBD, extensive infiltration of T cells into the intestinal tissue is observed. Integrins such as α4β1 and α4β7 regulate this tissue invasion, resulting in the accumulation of T cells during inflammation (120, 122). It is currently unclear what are the roles of integrins for MAIT cells during gut inflammation. However, perturbations of the α4β7 and αEβ7 expression have been observed in acute appendicitis (26). In addition, MAIT cells expressing the αLβ2 integrin can secrete IFN-γ through binding to ICAM-1, potentially targeting ICAM-rich endothelial vessels during inflammatory responses (125). During mycobacterial pulmonary infection, α4β1-expressing MAIT cells are recruited to the lungs through interaction with VCAM-1, potentially providing early immune protection in this mouse model of tuberculosis infection (126). Thus, integrin signaling in MAIT cells during inflammatory processes may not only increase the recruitment of MAIT cells but also enhance their effector functions.

The influence of gut dysbiosis on MAIT cell homing to the gut

Gut dysbiosis has been observed in various diseases, including infectious colitis, IBD, cancer, and obesity (127). Dysbiosis typically features a bloom of pathobionts and loss of commensal number or diversity, potentially leading to changes in riboflavin metabolite production in the gut (28, 128). Furthermore, dysbiosis may affect the levels and patterns of chemokines, chemokine receptors, and tissue adhesion molecules (129). Therefore, a dysbiotic microbiota may influence MAIT cell distribution and function in pathological conditions through the shift in the riboflavin metabolite antigen availability and the perturbation in the molecular signaling that governs MAIT cell homing to the gut and their retention within tissues.

Following exposure to bacteria-derived metabolic products, gut epithelial cells and immune cells residing within the intestinal epithelium express chemokines and adhesion molecules (129). The transplantation of mixed human fecal bacteria strains has been shown to up-regulate the expression of chemokines CXCL9 and CXCL10 in mouse epithelial cells (130). These chemokines are ligands for CXCR3, which is expressed by MAIT cells (91). In addition, gut dysbiosis induces the production of CCL5 from mouse colonic epithelial cells (131), potentially recruiting circulating MAIT cells to the intestine through a CCL5-CCR5 interaction. Interestingly, a high-fat diet, known to be a risk factor for gut microbiota dysbiosis, results in the activation of the CCL2-CCR2 axis in the small intestine, which may attract MAIT cells to the gut (26, 90, 132). Moreover, after antibiotic treatment, the recolonization of guts in mice by Enterocloster species down-regulates the expression of ileal MAdCAM-1 (133), the ligand for integrin α4β7 expressed by MAIT cells. In parallel, a positive correlation has been found between fecal Ruminococcus and VCAM-1 levels in the serum of obese children (134), which may enhance MAIT cell retention in the gut through interaction with integrin α4β1. Interestingly, the presence of aerotolerant bacteria in the microbiome is related to the protective function of MAIT cells in the mouse colitis model (52).

Our group recently showed that inflamed appendix tissues from most acute pediatric appendicitis patients were infected by riboflavin metabolite–producing Escherichia coli (26, 67, 135). Certain pathogenic E. coli strains, such as the adherentinvasive E. coli (136) promote the secretion of IL-1β, IL-23, and the chemokine CCL5 (137, 138). Indeed, in our study, we observed substantially increased levels of IL-1β, IL-18, and IL-23 (26). Such elevated proinflammatory cytokines activate circulating MAIT cells, leading to notable changes in the chemokine receptor expression pattern, including CCR1, CCR2, CCR4, CCR6, CXCR1, and CXCR6 (26). These changes are associated with the recruitment of MAIT cells to the appendix due to increased levels of the chemokines CCL2, CCL3, CCL8, CCL17, CCL20, CCL22, and CXCL8 within the inflamed tissues (26).

In summary, MAIT cell homing to the gut is driven by complex interactions of chemokines, chemokine receptors, and tissue adhesion molecules. These processes are crucial for immune surveillance in health but are dysregulated in many gut pathologies. Inflammation and dysbiosis may perturb the gut-homing activity of MAIT cells through changes to the riboflavin-related metabolite availability and the chemokine and tissue adhesion molecule profiles. Such conditions may promote excessive MAIT cell recruitment to affected tissues, where they often adopt inflammatory phenotypes. The redistribution of MAIT cells from circulation to inflamed sites consistently shown in multiple studies strongly supports their role in mucosal immunity and their contribution to pathogenesis. On the basis of these insights, we further discuss explorations going forward to understand better the mechanisms behind MAIT cell recruitment and function in disease contexts.

DECIPHERING POTENTIAL MECHANISMS OF MAIT CELL HOMING TO THE GUT THROUGH ORGANOID CULTURE SYSTEM

One of the primary challenges in fully understanding the mechanisms of MAIT cell homing to the human gut is the lack of effective human model systems. While MAIT cell migration and tissue homing are typically studied in vivo using animal models, there are limitations to this approach. MAIT cell biology in these animal models differs appreciably from humans, and the low number of MAIT cells in these models often necessitates genetic or biological manipulation to increase their levels, potentially altering their natural biology. To address this, a fully human system for studying MAIT cell biology is essential. However, conventional in vitro two-dimensional (2D) cell cultures and ex vivo methods are insufficient for this purpose. A potential alternative approach is the use of organoid models, which offer a more physiologically relevant environment. Unlike traditional 2D cultures, organoids can mimic in vivo tissue structures and functions (139), providing a more accurate platform for studying MAIT cell behaviors.

In a recent study, we successfully established a patient-derived intestinal organoid model where we examined the mechanism of MAIT cell recruitment during appendicitis and their interactions with the intestinal epithelial cells in 3D settings (26). Through this model system, we identified a previously unknown mechanism of MAIT cell recruitment toward inflamed human intestinal tissues, including the CCR4-CCL17/CCL22–mediated migration of MAIT cells (26). We further demonstrate the potentially pathological roles of MAIT cells in the setting of acute appendicitis through their activation and secretion of proinflammatory cytokines and cytotoxicity toward bacterially infected intestinal cells (26). Interestingly, in a separate study of MAIT cell roles in biliary atresia, biliary organoid models were used to demonstrate the tissue repair capacity of MAIT cells via the secretion of Areg (140). In addition, a murine intestinal organoid model has been used to explore the role of closely related invariant natural killer T cells in regulating intestinal epithelial cell homeostasis in mice (141).

While the use of organoid models to understand MAIT cell biology and their potential application in precision medicine and personalized treatment is still in its infancy, these models may hold considerable promise. Organoids could offer a more realistic, complex tissue-like environment that mimics human gut mucosal tissues, potentially enabling a deeper understanding of MAIT cell behavior in conditions including IBD, infections, and cancer. Patient-derived organoids could also be used to test targeted therapies that may lead to the development of more personalized treatments in diseases driven by MAIT cell dysregulation [reviewed in (27)]. As these models are further developed, refined, and integrated with tools such as drug screening, gene editing, and single-cell sequencing, they may further enhance our understanding of MAIT cells and their therapeutic potential in the gut.

FUTURE PERSPECTIVES AND CONCLUDING REMARKS

MAIT cells play dual roles in intestinal mucosal immunity, contributing to barrier integrity and tissue repair during homeostasis while driving inflammation in pathological conditions. It remains unclear whether these functions represent distinct roles of MAIT cells at different stages of tissue repairs following the precipitating insults. Tissue healing typically progresses through three phases: inflammation, regenerative tissue formation, and remodeling (142). MAIT cells may adapt their functions to support these distinct stages, or there could be distinct populations involved in different phases of tissue healing. Notably, tissue-resident MAIT cells may focus on maintaining homeostasis and repair, whereas circulating MAIT cells recruited to the pathological sites may mediate inflammation. Understanding these differences could reveal alternative therapeutic strategies to enhance repair without exacerbating inflammation. This knowledge could also inform the optimization of MAIT cell expansion protocols in vitro (132), potentially improving their therapeutic application.

Targeting specific chemokine pathways and integrin interactions may further promote MAIT cell homing to the gut, improving mucosal immunity and tissue repair. Conversely, blocking these pathways could help control inflammation and tissue damage. Various drugs have been developed to inhibit T cell infiltration into inflamed tissue, with antibody or receptor antagonist therapies targeting integrins and chemokine receptors being a key focus (110, 120, 143). For instance, the monoclonal antibody against CCR4 (mogamulizumab) approved to treat mycosis fungoides or Sézary syndrome (144, 145) and a dual antagonist targeting CCR2 and CCR5 (cenicriviroc) under evaluation for the treatment of HIV-1 infection and liver fibrosis (144, 146) may be repurposed to block MAIT cell migration in cases of acute intestinal inflammation (26). In addition, monoclonal antibodies against integrins now approved or under evaluation for the treatment of IBD, including those targeting α4β7 (vedolizumab) (147, 148), α4β7/αEβ7 (etrolizumab) (149, 150), or α4β1/α4β7 (natalizumab) (151), could also potentially block MAIT cell adhesion during intestinal inflammation (26). Combining chemokine receptor and integrin antagonists offers a potential strategy for regulating MAIT cell recruitment in inflammatory gut diseases by preventing excessive MAIT cell migration, adhesion, and retention while promoting egress from tissues. This potentially synergistic approach may help to reduce inflammation and tissue damage further.

In conclusion, targeting MAIT cell homing represents a promising therapeutic strategy for various gut-related diseases by modulating the processes that govern MAIT cell migration and activity in the gut. Future research will be crucial in translating these concepts into effective therapies.