Symbiotic bacteria-dependent expansion of MR1-reactive T cells causes autoimmunity in the absence of Bcl11b

Shibata, Kensuke; Motozono, Chihiro; Nagae, Masamichi; Shimizu, Takashi; Ishikawa, Eri; Motooka, Daisuke; Okuzaki, Daisuke; Izumi, Yoshihiro; Takahashi, Masatomo; Fujimori, Nao; Wing, James B.; Hayano, Takahide; Asai, Yoshiyuki; Bamba, Takeshi; Ogawa, Yoshihiro; Furutani-Seiki, Makoto; Shirai, Mutsunori; Yamasaki, Sho

doi:10.1038/s41467-022-34802-8

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Published: 14 November 2022

Symbiotic bacteria-dependent expansion of MR1-reactive T cells causes autoimmunity in the absence of Bcl11b

Nature Communications volume 13, Article number: 6948 (2022) Cite this article

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Abstract

MHC class I-related protein 1 (MR1) is a metabolite-presenting molecule that restricts MR1-reactive T cells including mucosal-associated invariant T (MAIT) cells. In contrast to MAIT cells, the function of other MR1-restricted T cell subsets is largely unknown. Here, we report that mice in which a T cell-specific transcription factor, B-cell lymphoma/leukemia 11B (Bcl11b), was ablated in immature thymocytes (Bcl11b^∆iThy mice) develop chronic inflammation. Bcl11b^∆iThy mice lack conventional T cells and MAIT cells, whereas CD4⁺IL-18R⁺ αβ T cells expressing skewed Traj33 (Jα33)⁺ T cell receptors (TCR) accumulate in the periphery, which are necessary and sufficient for the pathogenesis. The disorders observed in Bcl11b^∆iThy mice are ameliorated by MR1-deficiency, transfer of conventional T cells, or germ-free conditions. We further show the crystal structure of the TCR expressed by Traj33⁺ T cells expanded in Bcl11b^∆iThy mice. Overall, we establish that MR1-reactive T cells have pathogenic potential.

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Introduction

Unlike conventional T cells, unconventional T cells such as invariant NKT (iNKT) cells and mucosal-associated invariant T (MAIT) cells display restricted TCR repertoires characterized by the expression of invariant TCRα chains. For example, MAIT cells express TRAV1-2-TRAJ33 in humans and the orthologous Trav1-Traj33 in mice. These TCRs recognize microbial riboflavin precursors such as 5-(2-oxopropylideneamino)−6-D-ribitylaminouracil (5-OP-RU) presented by MHC class I-related 1 (MR1) proteins^1,2. Upon bacterial infection, MAIT cells are activated rapidly and elicit protective responses such as the production of IFNγ and IL-17A or cytotoxicity³. Although typical type 2 MAIT cells have not been reported, MAIT cells capable of producing type 2 cytokines were detected⁴. Recent reports have, in addition, identified non-canonical TRAV1^neg MR1-reactive T cells that do not express the TCR or markers characteristic of MAIT cells⁵. The physiological/pathological functions of these non-canonical MR1-reactive T cells have not yet been fully elucidated.

Bcl11b is a T cell-specific transcription factor essential for the transition from double-negative (DN) to double-positive (DP) thymocytes^6,7,8,9. Genetic deletion of Bcl11b in immature thymocytes (before the DP stage) (Bcl11b^flox/flox × Rag1^Cre/+; referred to as Bcl11b^ΔiThy mice) impaired the development of most T cell subsets. However, we previously observed that unconventional T cell subsets including Vγ1-bearing γδ T cells, develop from DN thymocytes in Bcl11b^ΔiThy mice¹⁰. Other similar “early developing” populations of lymphocytes have been recently identified^9,11,12. We have herein used our Bcl11b^ΔiThy mice to characterize a population of these additional, as yet unappreciated, unconventional cells that develop from early thymocytes. In the present study, we demonstrate that Trav1^neg atypical MR1-reactive T cells expand in Bcl11b^ΔiThy mice and acquire pathogenic potential, causing hypergammaglobulinemia and chronic inflammation in a process dependent on symbiotic bacteria.

Results

Bcl11b ^ΔiThy mice develop chronic inflammation

Bcl11b^flox/flox × Rag1^Cre/+ (Bcl11b^ΔiThy mice) were normal at birth¹⁰, but they did not gain weight at around 7 weeks of age and died by 15–20 weeks (Fig. 1a, b). Histological analysis of organs from Bcl11b^ΔiThy mice showed extensive infiltration of inflammatory cells into the periductal areas of the pancreas and disruption of acinar architecture (Fig. 1c). Bcl11b^ΔiThy mice also exhibited periductal fibrosis and atrophy of the exocrine portion of the pancreas (Fig. 1d). Serum lipase activity was elevated as inflammation progressed, indicating that Bcl11b^ΔiThy mice suffered severe pancreatic damage (Supplementary Fig. 1a). However, Bcl11b^ΔiThy mice did not develop diabetes (Fig. 1e), consistent with the observation that islets containing β cells were not damaged (Fig. 1c). In addition, we observed thickened lamina propria and shortened large intestines in Bcl11b^ΔiThy mice (Supplementary Fig. 1b, c). We also observed inflammation albeit less frequently in other organs such as the lung and lachrymal gland (Supplementary Fig. 1d). Thus, Bcl11b^ΔiThy mice develop spontaneous inflammation.

**Fig. 1: *Bcl11b*^ΔiThy mice spontaneously develop chronic inflammation.**

The inflammation and decreased survival in Bcl11b^ΔiThy mice were absent on a Rag2-deficient background (Fig. 1f, Supplementary Fig. 1e); this suggests that T lymphocytes are required for these defects since Bcl11b is not expressed in B cells^8,13. γδ T cells, which are present in Bcl11b^ΔiThy mice¹⁰, are not necessary for disease progression as Bcl11b^ΔiThy × Tcrd^–/– mice still displayed this lethal disorder (Fig. 1g); in contrast, survival was significantly prolonged on a pre-TCRα-deficient background (Bcl11b^ΔiThy × Ptcra^–/– mice) in which αβ T cells are absent (Fig. 1g). Notably, despite the DN2 arrest phenotype¹⁰ (Supplementary Fig. 2a, Fig. 1h, i), a few CD5⁺ αβTCR⁺ thymocytes were observed in 7-week-old Bcl11b^ΔiThy mice (Fig. 1k). In the periphery, αβTCR⁺ cells were extremely rare at an early age; however, the cell number gradually increased with age in Bcl11b^ΔiThy mice and exceeded that of WT mice (Fig. 1j). It is unlikely that this accumulation of mature T cells is due to incomplete deletion of Bcl11b in those cells, as Bcl11b protein could not be detected in peripheral αβ T cells from Bcl11b^ΔiThy mice (Fig. 1l). In the absence of preTCRα chains (Bcl11b^ΔiThy × Ptcra^–/– mice), such peripheral αβ T cells were eliminated (Fig. 1m), indicating that these T cells must undergo pre-TCR-mediated β-selection. Furthermore, adoptive transfer of T cells from Bcl11b^ΔiThy mice into CD3ε-deficient mice was sufficient to induce the disorders (Supplementary Fig. 2b). These data suggest that αβ T cells that develop in the absence of Bcl11b possess pathogenic potential.

Pathogenic contribution of non-canonical MR1-reactive T cells

Most αβ T cells in Bcl11b^ΔiThy mice displayed a CD44^highCD62L^lowIL-18R^high phenotype, implying that they include unconventional T cells (Fig. 2a)³. However, CD1d-restricted iNKT cells were not detected in either the thymus or the periphery of Bcl11b^ΔiThy mice (Fig. 2b, c, Supplementary Fig. 2c, d). To evaluate the contribution of MR1-reactive αβ T cells to these disorders, Bcl11b^ΔiThy mice were crossed with MR1-deficient mice (Bcl11b^ΔiThy × Mr1^–/– mice). Pancreatitis was ameliorated in the resulting Bcl11b^ΔiThy × Mr1^–/– mice (Fig. 2e) and they survived longer (Fig. 2d). However, neither MR1 tetramer-positive (5-OP-RU-tet⁺) MAIT cells nor the canonical TCRα repertoire of MAIT cells (Trav1-Traj33) were detected in the spleens of Bcl11b^ΔiThy mice (Fig. 2b, c). Nevertheless, the proportion of CD44^high IL-18R^high αβ T cells observed in Bcl11b^ΔiThy mice was reduced to a level comparable to that of WT mice in Bcl11b^ΔiThy × Mr1^–/– mice (Fig. 2f). The T cells that accumulated in Bcl11b^ΔiThy mice did not express PLZF, which is a Bcl11b-dependent transcription factor characteristic of MAIT cells and iNKT cells (Supplementary Fig. 2e)¹⁴, confirming that they are not MAIT cells. Thus, the expansion of non-canonical MR1-reactive αβ T cells is associated with the development of chronic inflammation in Bcl11b^ΔiThy mice.

**Fig. 2: MR1-reactive αβ T cells are pathogenic in *Bcl11b*^ΔiThy mice.**

Correction of T cell insufficiency ameliorates chronic inflammation

Bcl11b^ΔiThy mice lack most conventional αβ T cells¹⁰. We therefore speculated that this T cell imbalance may allow the development/expansion of pathogenic innate-type T cells. After the transfer of bone marrow (BM) cells from Bcl11b^∆iThy mice into CD3ε-deficient mice, recipient mice experienced body weight loss in a lymphocyte-dependent (Rag1-dependent) manner (Fig. 2g). However, when BM cells from Bcl11b^ΔiThy and WT mice were mixed at a 1:1 ratio and the combination transferred, the body weights of recipient mice remained normal (Fig. 2g). Consistent with this, expansion of pathogenic CD4⁺ Bcl11b^ΔiThy T cells (Supplementary Fig. 2b) was constrained in the presence of WT cells (Fig. 2h–j), possibly due to the survival disadvantages¹⁵. Furthermore, chronic inflammation induced by Bcl11b^ΔiThy BM cells was eliminated by co-transfer with WT BM cells (Fig. 2k, Supplementary Fig. 2f). The effect of the presence of balanced T cells was also confirmed by using non-irradiated Bcl11b^ΔiThy recipient mice, as transfer of WT T cells limited the expansion of donor T cells (Fig. 2m), inflammations (Fig. 2k, Supplementary Fig. 2f) and fatal disorder independently of regulatory T cells (Treg) (Fig. 2l). These results suggest that the imbalance in T cells observed in the Bcl11b^ΔiThy genetic environment contributes to the pathogenesis.

MR1-dependent expansion of Traj33-bearing T cells in Bcl11b ^ΔiThy mice

To characterize the profiles and clonotypes of the pathogenic T cells at a clonal level, we performed single-cell-based TCR and RNA-sequencing (scTCR-RNAseq). In Bcl11b^ΔiThy mice, the TCR repertoire was highly skewed with small number of clones dominating (Fig. 3a). The most frequent clone in Bcl11b^ΔiThy mice accounted for 15% of total αβ T cells and expressed a Trav7-6-Traj33/Trbv13-2-Trbj1-1 TCR (designated as clonotype #1) with identical CDR3α and CDR3β sequences (Fig. 3a–c). Cells expressing clonotype #1 occupied 87% of all Traj33⁺ T cells in Bcl11b^ΔiThy mice (Fig. 3c, d, left panels). Furthermore, the TCRα and β chains of clonotype #1 preferentially paired with each other (Supplementary Fig. 3a, b). Although the Vα usage of clonotype #1 (Trav7-6) differed from the canonical Trav1⁺ MAIT TCR, the Traj33 Jα, which provides the critical amino acids for MR1 contact, was identical to typical MAIT cells¹⁶ (Fig. 3b, Supplementary Fig. 3c, d). We therefore solved the crystal structure of the apo form of the clonotype #1 TCR (Fig. 3e) and superimposed this structure onto the complex structure of the MR1-6-formylpterin (6FP)-MAIT TCR¹⁷. The comparison suggested that the Tyr residue in the SNYQ sequence, particularly Y⁹⁷, provided by the Jα33 chain, was located in a similar but different position to the Y⁹⁵ of canonical MAIT TCR, suggesting that it pointed toward the ligand binding pocket of MR1 in a slightly different manner¹⁸ (Fig. 3f, g, Supplementary Fig. 3e). Indeed, the frequency of Traj33⁺ T cells, including those expressing clonotype #1, was dramatically decreased on an MR1-deficient background (Fig. 3c, d, right panels), indicating that MR1 promotes the development and/or expansion of Traj33⁺ non-MAIT cells in Bcl11b^ΔiThy mice.

**Fig. 3: Identification of pathogenic T cells by single cell analysis.**

Simultaneous single-cell RNA-seq analysis implied that clonotype #1 was detected in different clusters including Mki67^high proliferating cells, and Mki67^neg cells expressing Il4, Ifng or Gzmb (Fig. 3h). No IL-17A-positive cluster was detected. Pseudotime analysis of clonotype #1 allowed us to visualize three distinct differentiation pathways when Mki67^high cells were defined as a root for the analysis (Fig. 3i, j). Along the pseudotime dimension, the proliferative ability identified by Mki67 expression gradually decreased to the end, suggesting that functional differentiation occurred after proliferation (Fig. 3k). One of the three computationally predicted lineages (Lin 1) was characterized by Il4 expression and gradually acquired expression of T_FH marker genes such as Bcl6, Cxcr5, Pdcd1, Il21, Sostdc1 and Rgs16^19,20,21 (Fig. 3k, Supplementary Fig. 3g). Another lineage (Lin 2) (Fig. 3j) overlapped with a CTL-like cluster (Supplementary Fig. 3h). Importantly, the T cells bearing Trav7-6-Traj33 was also detected in other individual Bcl11b^ΔiThy mice and even in WT mice at a low frequency (Supplementary Fig. 3f), suggesting that these T cells are not arisen sporadically and aberrantly under Bcl11b-deficient conditions.

Thus, Traj33⁺ T cells bearing non-MAIT TCRs are clonally expanded in the presence of MR1 and proceed through functional differentiation in Bcl11b^ΔiThy mice.

Elevated serum immunoglobulin and autoantibodies in Bcl11b ^ΔiThy mice

Consistent with the expansion of T_FH-like cells expressing IL-4, IgG levels in the serum of Bcl11b^ΔiThy mice began to increase at about the same age as when αβ T cells began to be detected (Fig. 4a). All IgG subclasses were significantly higher in Bcl11b^ΔiThy mice (Fig. 4b). Sera from individual Bcl11b^ΔiThy mice reacted to lysates from mouse pancreas, suggesting the presence of autoantibodies (Fig. 4c). Furthermore, IgG1 antibodies were deposited around pancreatic ductal sites in Bcl11b^ΔiThy mice; this was not observed on an MR1-deficient background (Fig. 4d). Both the number of IgG1⁺ B cells and IgG1 production were increased in the peripheral blood of Bcl11b^ΔiThy mice in the presence of MR1 (Fig. 4e, f) and pre-TCRα (Supplementary Fig. 4a). These data suggest that Bcl11b^ΔiThy mice develop hyperimmunoglobulinemia including autoantibodies in an MR1-restricted T cell-dependent manner. Indeed, preventing the expansion of such pathogenic T cells by adoptive transfer of WT T cells recovered Bcl11b^ΔiThy mice from hyperimmunoglobulinemia (Supplementary Fig. 4b).

**Fig. 4: Autoantibody production is dependent on MR1-reactive T cells.**

Consistent with the high IgG1 production in Bcl11b^ΔiThy mice, mass cytometric analysis showed increases in germinal center (GC) B cells and T_FH-like cells in Bcl11b^ΔiThy mice (Fig. 4g, Supplementary Fig. 4c, d). We also observed peanut agglutinin positive (PNA⁺) germinal center-like structures in the enlarged pancreatic lymph nodes of Bcl11b^ΔiThy mice, which was not observed in WT mice (Supplementary Fig. 4e). Consistent with these observations, CD4⁺ αβ T cells in Bcl11b^ΔiThy mice expressed CD40L (Fig. 4h) and produced IL-4 (Fig. 4i). IL-4-GFP reporter fluorescence was also detected in pancreatic LN T cells from Bcl11b^ΔiThy × Il4^GFP/+ mice (Fig. 4j). On either a B cell-deficient (μMT) or IL-4-deficient (Il4^GFP/GFP) background, Bcl11b^ΔiThy mice did not survive longer (Supplementary Fig. 4f). The inflamed pancreases of Bcl11b^ΔiThy mice were infiltrated with some IgG1⁺ B cells and CD4⁺ αβ T cells in an MR1-dependent manner (Supplementary Fig. 4g, h). These clinical features are similar to those in human autoimmune pancreatitis (AIP)²², which has been characterized by the high levels of serum human IgG4 (a putative counterpart of mouse IgG1²³), periductal pancreatitis, lymphocyte infiltration and steroid responsiveness²⁴. Indeed, steroid treatment ameliorated elevation of serum IgG and pancreatitis in Bcl11b^ΔiThy mice (Fig. 4k, l).

Remission of pancreatitis in Bcl11b ^ΔiThy mice under germ free condition

A canonical MAIT cell antigen, 5-OP-RU, is provided mainly by microbiota^1,25,26. We thus assessed whether symbiotic microbes affect the pathogenic T cells and disorders observed in Bcl11b^ΔiThy mice by generating germ-free (GF) Bcl11b^ΔiThy mice. Under germ-free conditions, we did not observe weight loss (Fig. 5a), a survival defect (Fig. 5b), T cell expansion (Fig. 5c), pancreatitis (Fig. 5d) or hypergammaglobulinemia (Fig. 5e) in Bcl11b^ΔiThy mice. Furthermore, the number of peripheral αβ T cells expressing high levels of IL-18R was reduced in GF Bcl11b^ΔiThy mice compared with Bcl11b^ΔiThy mice under specific pathogen-free (SPF) conditions (Fig. 5f–h). We also performed scTCR-RNA-seq on T cells from GF Bcl11b^ΔiThy mice and did not detect clonotype #1 (Fig. 5i), although this clonotype accumulated in SPF Bcl11b^ΔiThy mice (Fig. 3c). These results suggest that symbiotic microbes are required for the fatal disorders in Bcl11b^ΔiThy mice. Indeed, like germ-free conditions, treatment with antibiotics also ameliorated chronic inflammation (Fig. 5j) and improved survival (Fig. 5k) in Bcl11b^ΔiThy mice.

**Fig. 5: Microbiota are essential for the development of the disorders in *Bcl11b*^ΔiThy mice.**

Clonotype #1 responds to fecal components

The above observations suggest that symbiotic microbes may provide an antigen(s) to clonotype #1 to support clonal expansion and/or activation. We thus reconstituted the expression of clonotype #1 TCRα (Trav7-6-Traj33) and TCRβ (Trbv13-2-Trbj1-1) in a TCRαβ-deficient reporter cell line (Fig. 6a). To identify antigenic components, fecal extracts from SPF mice were fractionated and tested for stimulatory activity towards reporter cells expressing the clonotype #1 TCR in the presence of MR1-expressing antigen-presenting cells. Fraction #54 was found to induce NFAT reporter activity in an MR1-dependent manner (Fig. 6b), as it was suppressed in the presence of Ac-6-FP (Fig. 6c). To determine the active component(s) in fraction #54, we analyzed these seventy fractions by non-targeted metabolomics²⁷. Twenty-two candidates were selectively and reproducibly present in fraction #54 (Fig. 6d, Supplementary Fig. 5a, b). Among them, only one candidate (#54-6) had similar m/z value to the exact mass of a known metabolite (human metabolome database, https://hmdb.ca), riboflavin (RF) (Supplementary Fig. 5b). MS/MS analysis confirmed that this precursor ion is derived from RF (Fig. 6e). Indeed, synthetic RF stabilized the surface expression of MR1 (Fig. 6f), suggesting that RF specifically binds to MR1 as recently reported²⁸. Although RF was not recognized by MAIT TCRs (Fig. 6g, blue)²⁸, it activated cells expressing the clonotype #1 (Fig. 6g, red) and this activation was blocked by both Ac-6-FP and anti-MR1 antibody (Fig. 6g, black). As predicted from its TCR sequence (Fig. 3b, Supplementary Fig. 3c), clonotype #1 did not react with an authentic MAIT cell antigen, 5-OP-RU (Fig. 6h). These results suggest that non-canonical MR1-reactive T cells recognize metabolites presented by MR1 that are distinct from MAIT cell antigens.

**Fig. 6: Clonotype #1 recognizes riboflavin in an MR1-dependent manner.**

Discussion

In the present study, we demonstrate that non-canonical MR1-reactive αβ T cells acquire pathogenic potential through microbiota-dependent clonal expansion. RF metabolites, such as 5-OP-RU, are agonistic antigens for MAIT cells², whereas RF itself is a weak antagonist of MAIT cells²⁸. Considering its different action on expanded clonotypes in our study, RF might regulate MR1-reactive T cells as both an agonist and an antagonist depending on the TCR repertoire²⁸. RF may contribute to the maintenance of MR1-reactive T cells in normal setting; however, excessive intake of RF might influence inflammation in particular T-imbalanced settings. It is also possible that, in addition to RF, the active fraction #54 contains an antigen(s) which has not yet been annotated (Fig. 6d and Supplementary Fig. 5b). Taken together with recent reports^{28,29,30,31,32}, more diverse metabolites than previously demonstrated may regulate various mouse and human MR1-reactive T cells.

An important question arising is whether pathogenic T cells, such as clonotype #1, are also detected in Bcl11b-sufficient mice. CDR3-matched Trav7-6-Traj33 TCRs were identified by bulk TCR sequencing of WT mice; however, such cells exist at low frequency (Supplementary Fig. 3f) and are not pathogenic. Thus, a normal environment in which innate T cell subsets are balanced is likely to restrict excessive expansion of such clonotypes, thus preventing pathogenic conversion^10,33. Development of probes, such as specific tetramers or clonotypic mAbs, would enable us to monitor the status of these clonotypes during various experimental settings.

It should be noted that Bcl11b is critical for the development and function of Treg cells, since CD4-Cre-driven Bcl11b-deficient mice develop inflammatory diseases due to the dysregulated activation of effector Th17 cells via defective Treg function³⁴. This scenario, however, may not explain the symptoms observed in Rag1-Cre-driven Bcl11b-deficient (Bcl11b^∆iThy) mice, as the correction of T-imbalance could suppress the disease in the absence of Treg (Fig. 2l). Furthermore, most conventional αβ T cells do not develop in these mice and thus effector Th17 cells were extremely rare in Bcl11b^∆iThy mice (Fig. 3i). Rather, MR1-reactive T cells possessing T_FH potential accumulated (Fig. 3i, l). It is possible that these cells may provide B cell help for autoantibody production in a non-cognate manner as recently reported³⁵.

It is interesting that canonical type 2 MAIT cells have not been clearly defined³⁶, given that type 2 lymphocytes are a well-established and conserved subset across the wide variety of T lymphocytes and innate lymphocyte lineages^37,38,39. The identification of Trav1^negTraj33^pos non-canonical MR1-reactive T cells that produce IL-4 might represent MR1-reactive type 2 T cells, together with recent reports on IL-4-producing MAIT cells⁴. Still, we cannot exclude the possibility that the absence of Bcl11b results in the derepression of IL-4-related genes in these cells⁴⁰. Detailed immune profile analysis of clonotype #1 T cells present in WT mice would clarify this issue.

The observation of incomplete symptom suppression in Bcl11b^∆iThy mice on a μMT- or Il4^–/–-background suggests that antibodies are not the sole effectors contributing to these disorders. As previously proposed, the cytotoxic effector molecules, granzymes, could be an additional candidate for causing direct tissue damage⁴¹. The immune profile of the second most frequent T cell clone (clonotype #2) expanding in Bcl11b^∆iThy mice might support this assumption; these cells included a granzyme B⁺ population whose development was also dependent on MR1 and microbiota (Supplementary Fig. 3i, j).

Although Bcl11b is required for early T cell development, Bcl11b-null mice are neonatal lethal due to its importance in neural development¹³. Thus, genetic modification of Bcl11b specifically in immature thymocytes within ‘viable’ mice allowed us to detect previously unappreciated αβ T cell subsets. Such type 2 skewing of the remaining T cells may partly explain the exacerbated type 2 immunity in humans bearing hypomorphic Bcl11b mutations⁴². Currently, whether αβ T cells in Bcl11b^ΔiThy mice develop through the DP stage is unclear; it is possible that they develop into mature T cells from the DN2 stage, in a process similar to an IFNγ-producing γδ T subset^10,43. The reported “DN2 arrest phenotype of Bcl11b-deficient cells^6,7,8” and the “requirement of pre-TCR-mediated β-selection (generally thought to accompany the DN to DP transition)” in the present study are apparently contradictory observations. Still, these T cells in Bcl11b^ΔiThy mice express CD5, a marker indicative of having experienced TCR engagement during positive selection. Typical MAIT and iNKT cells are positively selected by DP thymocytes and express PLZF, a lineage-defining transcription factor for these innate T lymphocytes³. However, a subpopulation of MR1-restricted T cells is selected by non-hematopoietic cells and is PLZF-negative²⁶, as observed in the T cells of Bcl11b^ΔiThy mice (Supplementary Fig. 2e). Given that antigen-presenting DP cells are lacking in the Bcl11b^∆iThy thymus, T cells might be selected by thymic epithelial cells. The introduction of fine fate-mapping alleles in mixed chimera experiments may clarify this issue.

Under GF conditions, inflammatory symptoms in many autoimmune models worsen^44,45,46. In contrast, the complete remission of inflammation in GF Bcl11b^∆iThy mice indicates that the effector mechanisms are distinct from typical autoimmune diseases. Indeed, the generation of pathogenic T cells and inflammation in the current model require microbiota, presumably because microbiota provide antigens for MR1-restricted T cells, as was also recently shown for MAIT cells^2,26,41,47. Similarly, as yet unidentified “mobile” metabolites from symbiotic bacteria may also activate the MR1-reactive T cells in the intestine and pancreas, which are anatomically connected via pancreatic ducts^48,49. It is also possible that cytokine milieu, such as IL-12 or IL-1/18, present under SPF conditions might activate MR1-reactive T cells independently of the TCR⁵⁰.

A link between lymphopenia and autoimmunity has been reported⁵¹. Under lymphopenic conditions, the compensatory expansion of T cells exhibiting innate T cell/T_FH cell profiles, converts these cells into pathogenic effectors^52,53,54. Taken together, the present study suggests a possible contribution of non-canonical innate T cells to autoimmune diseases under T cell-imbalanced conditions and/or dysbiosis.

Methods

Mice

This study was approved by the Committee of Ethics on Animal Experiments in the Faculty of Medicine of Kyushu University, Science Research Center of Institute of Life Science and Medicine of Yamaguchi University and Research Institute for Microbial Diseases of Osaka University. Experiments were carried out under the control of the Guidelines for Animal Experiments. Mice were maintained under 12 h dark/light cycle and constant conditions of temperature (18–23 °C) and humidity (40–60%). C57BL/6 mice were purchased from SLC (Shizuoka, Japan). Bcl11b^flox/flox mice were provided by R. Kominami (Niigata University, Japan). Rag1^Cre/+ mice were provided by T. Rabbitts (Leeds Institute of Molecular Medicine, United Kingdom) by courtesy of K. Akashi (Kyushu University, Japan). Il4^GFP/GFP mice were provided by Dr. W.E. Paul (National Institute for Health, USA). μMT mice were provided by D. Kitamura (Tokyo University of Science, Japan). Bcl11b^flox/flox, Rag1^Cre/+ Il4^GFP/GFP. and μMT mice were backcrossed to C57BL/6 mice more than ten generation. Mr1^–/– mice provided by Dr. Susan Gilfillan (Washington University, USA) on the courtesy of Dr. K. Iwabuchi (Kitazato University, Japan) were backcrossed to C57BL/6 mice for at least twenty generations. Throughout the study, we mostly used littermate mice for control groups and designated Rag1-, Bcl11b- and MR1-sufficient mice (Rag1^{Cre/+ or +/+} × Bcl11b^+/+ × Mr1^+/–, Rag1^{Cre/+ or +/+} × Bcl11b^flox/+ × Mr1^+/–, Rag1^+/+ × Bcl11b^{flox/flox or flox/+} × Mr1^+/+, Rag1^+/+ × Bcl11b^flox/flox × Mr1^{+/+ or +/–}, Rag1^+/+ × Bcl11b^flox/+ × Mr1^+/+ mice) as WT mice. Germ-free Bcl11b^ΔiThy mice are generated by in vitro fertilization at the CLEA Japan. Germ-free mice were bred and maintained in vinyl isolators within the facility in CLEA Japan. For steroid treatment, Bcl11b^ΔiThy mice were sequentially administrated from 5 weeks of age with an increased amount of dexamethasone (Cat. No.D4902, Sigma) (1, 3, 10 mg/kg) three times for every two weeks intraperitoneally, in accordance with human therapy⁵⁵ and analyzed at 12 weeks of age. For treatment with antibiotics, mice (5 weeks old) were given for 13 weeks with ampicillin (Cat. No.19769-64) (1 g/L), vancomycin (Cat. No.35575-94) (500 mg/L), neomycin sulfate (Cat. No.19767-42) (1 g/L), and metronidazole (Cat. No.23254-64) (1 g/L) in drinking water. All antibiotics were purchased from Nakarai Tesque, Inc.

Cell lines

Reporter cell line expressing clonotype #1 αβTCR or MAIT TCR was generated by retroviral gene transduction to TCR-negative mouse T cell hybridoma with an NFAT-GFP reporter gene, a kind gift from Dr. H. Arase (Osaka University, Japan). Mouse MR1-expressing antigen-presenting cells were generated by retroviral gene transduction of mouse MR1 to mouse fibroblastic cell line NIH3T3 (Cat. No.CRL1658, ATCC).

Compounds

Ac-6-FP (Cat.No.11.418) was purchased from Schircks laboratories. 5-A-RU (Cat.No.A629245) was purchased from Toronto Research Chemicals. Methylglyoxal solution (Cat.No.M0252) and riboflavin (Cat.No.R9504) were purchased from Sigma-Aldrich. 5-OP-RU was generated by reacting 5-A-RU with equal molar ratio of methylglyoxal. 5-OP-RU concentrations are shown under assumption that all 5-A-RU is converted to 5-OP-RU.

Flowcytometric analysis

αGC-loaded CD1d tetramers were prepared following the manufacturer’s instructions (Cat No.TS-MCD-1, Medical & Biological Laboratories co., LTD). For staining of mouse MAIT cells, APC-labeled mouse MR1 tetramer provided by NIH Tetramer core facility was used². FITC-conjugated anti-mouse (m) CD45.1 (A20, 1:40 dilution, Cat No.110705), anti-mCD45.2 (104, 1:100 dilution, Cat No.109805) mAbs, PE-conjugated anti-mCD5 (53-7.3, 1:100 dilution, Cat No.100607), anti-mCD8α (53-6.7, 1:80 dilution, Cat No.100707), anti-mCD40L/CD154 (MR1, 1:100 dilution, Cat No.106505), anti-mCD117 (2B8, 1:40 dilution, Cat No.105807), and anti-MR1 (26.5, 1:40 dilution, Cat No.361105) mAbs, PECy7-conjugated anti-mCD4 (RM4-5, 1:200 dilution, Cat No.100527) mAb, PerCP-Cy5.5-conjugated anti-mI-A/I-E (M5/114.15.2, 1:200 dilution, Cat No.107623) and anti-mCD44 (IM7, 1:200 dilution, Cat No.103031) mAbs, APC-conjugated anti-mTCRβ (H57-597, 1:40 dilution, Cat No.109211), anti-mCD4 (RM4-5, 1:100 dilution, Cat No.100515), anti-mIL-18Rα (A17071D, 1:100 dilution, Cat No.157905), anti-mCD25 (PC61, 1:200 dilution, Cat No.102011), anti-mCD44 (IM7, 1:200 dilution, Cat No.103011), anti-mCD45.2 (104, 1:40 dilution, Cat No.109813) and anti-mCD62L (MEL-14, 1:100 dilution, Cat No.104411) mAbs, AF700-conjugated mCD8 (53-6.7, 1:100 dilution, Cat No.100729) mAb, APCCy7-conjugated mTCRβ (H57-597, 1:40 dilution, Cat No.109219) mAb, BV421-conjugated mTCRβ (H57-597, 1:40 dilution, Cat No.109229) and mCD8α (53-6.7, 1:80 dilution, Cat No.100737) mAbs, BV510-conjugated mB220 (RA3-6B2, 1:100 dilution, Cat No.103247) and anti-mCD4 (RM4-5, 1:100 dilution, Cat No.100553) mAbs were purchased from BioLegend. FITC-conjugated anti-mIgG1 (A85-1, 1:50 dilution, Cat No.553443) mAb was purchased from BD Biosciences. PE-conjugated anti-mIL-18R (P3TUNYA, 1:80, Cat No.12-5183-82) and APC-eFluor780 conjugated anti-mTCRβ (H57-597, 1:20, Cat No.47-5961-82) mAbs were purchased from Thermo Fisher Scientific. Dead cells were stained with 7AAD (7-amino-actinomycin D, Cat No.420403, BioLegend) and viable cells were analyzed by FACS Verse (BD Biosciences) or Gallios flow cytometer (Beckman Coulter). The data were analyzed using FlowJo software (TreeStar).

Mass cytometry analysis

Antibodies were conjugated with the MaxPar conjugation kit according to the manufacturer’s instructions with the exception of cisplatin-labeled antibodies. Metal isotopes were obtained from Standard BioTools with the exception of Indium 113 and 115 (Trace Sciences). Conjugated antibodies were stored in PBS‐based Ab stabilizer (Candor Biosciences) and all antibodies were titrated for optimal staining concentrations with control mouse tissues. Full details of the staining panel are provided in Supplementary Table 1. For staining, 1 × 10⁶ cells per sample were initially barcoded with metal-conjugated CD45 antibodies in the presence of Fc blocker for 30 min at RT and then washed twice in CyFACS buffer (PBS with 0.1% BSA and 2 mM EDTA) and then barcoded cells were pooled. Pooled cells were stained with a metal-conjugated surface stain antibody cocktail for 45 min at RT. Cells were then washed twice in CyFACS buffer, stained for viability with the cisplatin analogue dichloro-(ethylenediamine) palladium (II) in PBS for 5 min at RT and then fixed and permeabilized using the Foxp3 Transcription Factor Staining Buffer Set according to the manufacturer’s protocol (Thermo Fisher Scientific). Cells were subsequently stained with an intracellular antibody cocktail for 45 min at 4 °C. Cells were then washed twice in CyFACS buffer and once in PBS. Cells were then fixed overnight in 2% formaldehyde solution containing DNA Cell-ID Intercalator-103Rh (Standard BioTools). Prior to acquisition, cells were washed once in CyFACS buffer and twice in H₂O. Cells were then diluted to 1 × 10⁶ cells/ml in H₂O containing 15% EQ Four Element Calibration Beads (Standard BioTools) and filtered. Cells were acquired at a rate of 200–300 cells/s using a Helios mass cytometer (Standard BioTools). Flow Cytometry Standard files were normalized to EQ bead signal. Initial gating and debarcoding was performed in CytoBank software. Clustering was then performed after gating on B cells (B220⁺CD3^–) or CD4 T cells (CD4⁺CD3⁺TCRβ⁺B220^–) by FlowSOM within the CATALYST Bioconductor package referring to CyTOF workflow (version 3)⁵⁶. Differential abundance analysis of clusters was performed with edgeR, calculating adjusted p-values.

Bone marrow and T cell transplantation

BM cells from CD45.1⁺ WT or CD45.2⁺ Bcl11b^ΔiThy mice were suspended in phosphate-buffered saline (PBS) and 1 × 10⁷ cells were injected into 8 Gy-irradiated Cd3e^–/– mice. For mixed BM transfer, Cd3e^–/– mice received 1:1 ratio of CD45.1⁺ WT and CD45.2⁺ Bcl11b^ΔiThy BM cells. The body weight and the frequency of CD4⁺ T cells in the peripheral blood were analyzed weekly. For T cell transfer, 1 × 10⁷ cells of CD4⁺ T cells or CD4⁺ T cells lacking CD25⁺ Treg cells from CD45.1⁺ WT mice were transferred into CD45.2⁺ Bcl11b^ΔiThy mice.

Single cell-based transcriptome and TCR analysis

Libraries for mouse T cells were prepared using following reagents; Chromium Single Cell 5′ Library & Gel Bead Kit, PN-1000014; Chromium Single Cell A Chip Kit, PN-1000009; Chromium i7 Multiplex Kit, PN-120262; Chromium Single Cell V(D)J Enrichment Kit, Mouse T Cell, PN-1000071. Approximately 2 × 10⁴ cells are loaded into Chromium microfluidic chips to generate single-cell gel-bead emulsions using the Chromium controller (10X Genomics) according to the manufacturer’s recommendations. Suspensions containing ∼16,000 cells were loaded on the instrument. RNA from each sample was subsequently reverse-transcribed in a Veriti Thermal Cycler (Thermo Fisher Scientific), and all subsequent steps to generate single-cell libraries were performed according to the manufacturer’s protocol, with 14 cycles used for cDNA amplification. Then ∼50 ng of cDNA was used for gene expression library amplification by 14 cycles in parallel with cDNA enrichment and library construction for T cell libraries. Fragment size of the libraries were confirmed with the Agilent 2100 Bioanalyzer (Agilent). Libraries were sequenced on an Illumina NovaSeq 6000 as paired-end mode (read1: 28 bp; read2: 91 bp). The raw reads were processed by cellranger 3.1.0 (10X Genomics). Clonotype analysis was done using Loupe Cell Browsers provided by 10x Genomics (https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest#loupetab). After identification of TCR clonotypes by the loupe V(D)J browser, transcriptome analysis of these clusters was further performed by the loupe browser.

Bulk RNA-sequencing analysis

Single-cell suspensions from splenocytes were dissolved in the TRIzol (Cat. No.15596026, Thermo Fisher Scientific) and applied for bulk RNA-sequencing analysis was applied for TCR repertoire analysis using the SMARTer Mouse TCR a/b Profiling Kit (Takara Bio USA Inc).

Pseudotime analysis

For inferring cell lineages and pseudotimes, a Bioconductor package “slingshot⁵⁷” and their lineage inference workflow to predict cell lineage (s) and pseudotime (s) were used. The output value “filtered_feature_bc_matrix” from the Cell Ranger was used as count data for slingshot. An R clustering package “mclust” was applied to the t-SNE matrix generated by Cell Ranger to infer clusters, yielding a final repertoire of 7 clusters (“chartreuse”, “cyan”, “khaki”, “plum”, “orange”, “orangered”, “sienna”). The “getLineages” function of slingshot was used to obtain lineage structure of the t-SNE matrix and their pseudotime (s). We specified the initial cluster as chartreuse based on gene expression of Mki67. We also used the “getCurves” function of slingshot to construct smooth curve in each lineage which inferred by getLineages function using default parameter setting except for extend = “n” and stretch = 0. For gene expression in the t-SNE dimension, the natural logarithm of the given value plus one (log1p) of the count data of each gene was plotted by plotGeneCount functions of a Bioconductor package “tradeSeq⁵⁸”. We customized the plotGeneCount script to change color and position of the log1p color scales (Supplementary_code.txt).

Preparation of fractionated tissue homogenates

After snap-frozen tissues in liquid nitrogen were smashed in a mortar, homogenates were centrifuged (15,000 × g for 20 min at 4 °C). The homogenates were resuspended in water with 0.1% TFA and fractionated by HPLC (JASCO LC-NetII/ADC) using COSMOSIL 5C₁₈-MS-II 4.6 mmID × 250 mm (Cat. No. 38020-41, Nakalai tesque). After loading, 70 fractions were collected by increasing Acetonitrile to 80%. Fractions were dried and stored at −80 °C until use.

Reporter assay

Reporter cell lines were cocultured with mouse MR1-expressing NIH3T3 cells in the presence of homogenates⁵⁹. One day after the coculture, GFP expressions in reporter cells were analyzed by flowcytometry after gating on CD3⁺ reporter cells.

Histological analysis

Histological analysis was performed after freshly isolated tissue samples were fixed with formalin and then embedded in paraffin or OCT compound (Cat No.45833, Sakura Finetek). Sections were stained with Hematoxylin and Eosin (H&E) for detecting inflammatory cells or with Sirius red for the assessment of collagen contents using Picrosirius Red Stain Kit (Cat. No.24901, Polyscience). OCT compound-embedded sections of mouse pancreatic tissues were stained with antibodies against mIgG1 (0.5 μg/ml, A85-1, Cat. No.553443, BD Biosciences), mCD4 (10 μg/ml, GK1.5, Cat. No.100407, BioLegend) or B220 (5 μg/ml, RA3-6B2, Cat. No.103225, BioLegend) or biotinylated PNA (20 μg/ml, Cat. No.BK-1000, Vector laboratories) overnight at 4 °C. For PNA staining, Alexa Fluor 647-conjugated Streptavidin (1 μg/ml, Cat. No.405237, BioLegend) was applied on the tissues and incubated for 2 h at 37 °C. Stained tissues were visualized using an FV3000 confocal microscope (Olympus). Inflammatory score was determined as described previously⁶⁰. The degrees of cell infiltration judged by histology using H&E staining of pancreatic tissues were scored as follows: 0, no detectable infiltration; 1, a focus of perivascular infiltration; 2, several foci of perivascular infiltration; 3, cellular infiltration in more than 50% of vasculature; 4, cellular infiltration in more than 80% of vasculature; and 5, massive infiltration. For quantification of the percentage of Picrosirius Red-positive area, images of pancreatic tissue were binarized using a fixed threshold by ImageJ and positive pixel ratio was calculated.

Determination of isotype-specific immunoglobulins, blood glucose levels, and lipase activities in serum

Concentrations of polyclonal mIgM (Cat. No. E99-101), mIgG1 (Cat. No. E99-105), IgG2a (Cat. No. E99-107), mIgG3 (Cat. No. E99-111) and mIgA (Cat. No. E99-103) were analyzed by isotype-specific enzyme-linked immunosorbent assay (Bethyl Laboratories, Inc). Blood glucose level was analyzed by ACCU–CHEK Aviva System Blood Glucose Meter (Roche). Lipase activity was analyzed with Lipase Color Liquid (Roche).

Immunoblot analysis

For analysis of sorted CD4⁺ αβ T cells, cells were lysed for 5 min at 95 ˚C in SDS lysis buffer (20 mM EDTA, 10 mM Tris HCl, 150 mM NaCl and 1% NP40). For analysis of pancreatic homogenates, tissues from Rag1-deficient mice were sonicated and then suspended in RIPA buffer. Proteins were resolved by SDS-PAGE and transferred to Immobilon–P membranes. Membranes were blocked by Blocking One (Cat. No. 03953-66, Nakalai tesque) and were detected by immunoblot analysis. The rabbit anti-mBcl11b polyclonal Ab was kind gift from Yukio Mishima (Niigata University). Anti-β-actin (2F1-1) mAb (Cat. No.622101, BioLegend) was used as an internal control. For pancreatic homogenates, serums from indicated mice were used as the first antibody. The first antibody was detected by peroxidase-labeled Goat anti-mIgG (H + L) (Cat. No.115-035-003, Jackson ImmunoResearch Laboratories Inc.). Signals were detected using LAS4000mini (GE healthcare).

Electrospray ionization-quadrupole Orbitrap high-resolution tandem mass spectrometry (ESI-HRMS/MS) analysis and data mining

Soluble fractions were dissolved in 50 μl of methanol/water (95:5, vol/vol). Flow injection analysis was performed using a Nexera LC system (Shimadzu Co., Kyoto, Japan) coupled with Q Exactive, a high performance bentchtop quadrupole Orbitrap mass spectrometer (Thermo Fisher Scientific, Waltham, MA), equipped with an electron spray ionization source. The flow injection conditions in the positive and negative ionization modes were described previously⁶¹. Data mining procedure was described previously²⁷. In short, Compound Discoverer 3.0 software (Thermo Fisher Scientific) was used for data processing, involving peak detection, data grouping, and filling gaps. Differential analysis (fraction #54 vs. other fractions, fold change > 5) was performed using an XLSM extension developed with Visual Basic for applications in Microsoft Excel 2013. Among more than 20,000 ion peaks (including isotopes and adducts detected in the positive and negative ionization), 22 candidates were detected selectively and reproducibly present in fraction #54.

Expression and purification of clonotype #1 ectodomain

Expression and purification of clonotype #1 αβ ectodomain was performed as described recently⁶². In brief, both clonotype #1 α and β ectodomains were expressed as fusion proteins with N-terminal hexahistidine tag and Tabaco Etch Virus (TEV) protease cleavage site. The clonotype #1 α and β ectodomains were separately expressed in Escherichia coli as inclusion bodies. The inclusion bodies were solubilized with 6 M guanidine hydroxychloride. The solubilized clonotype #1 α and β ectodomains were mixed, refolded, and then dialyzed. Clonotype #1 αβ heterodimer was applied to Ni-NTA agarose. After the removal of histidine tag by TEV protease treatment, the proteins were applied to size exclusion and anion change chromatography. The purities of proteins were assessed by SDS-PAGE.

Crystallization, data collection, and structure determination of clone #1 ectodomain

All crystallization trials were performed by sitting drop vapor diffusion method as described previously⁶². Initial crystallization conditions were searched using Index (Hampton Research) and SG1 Screen (Molecular Dimensions). Diffraction-quality crystals were obtained under the condition of 0.1 M Bis-tris (pH 5.5), 0.2 M lithium acetate and 17% (w/v) polyethylene glycol 10,000 at 293 K. Crystals were soaked into reservoir containing 10% (v/v) glycerol and rapidly frozen in liquid nitrogen. X-ray diffraction data were collected on the beamline BL-1A at Photon Factory (Tsukuba, Japan). All data sets were integrated with program XDS and scaled with the program Scala. The phases of the crystal were determined by molecular replacement with program Molrep using TCR-017 ectodomain (PDB code: 7EA6) as a search model. Further model building was manually performed with program Coot. Refinement was initially conducted using program Refmac5 and then Phenix.refine for final model. The stereochemical quality of the final model was assessed by Molprobity. Data collection and refinement statistics were summarized in Supplementary Table 2. Structural factors and coordinates have been deposited on Protein Data Bank under accession code 7F5K. All structural figures were depicted by program PyMOL2.0 (The PyMOL Molecular Graphics System, Version 2.0 Schrödinger, LLC.). Structural superposition was performed with program SUPERPOSE.

Statistical analyses

Statistical significance was calculated using Prism software (GraphPad, San Diego, CA). Differences with values for p < 0.05 were considered statistically significant.

Reporting summary

Further information on research design is available in the Nature Portfolio Reporting Summary linked to this article.

Data availability

Bulk RNA-sequencing and single-cell RNA-sequencing data have been deposited at the DNA Data Bank of Japan (DDBJ) database under the accession number DRA011320 within the Bioproject PRJDB10983. Structure factor and 3D coordinates of clone #1 TCR ectodomain have been deposited in the Protein Data Bank under the accession code, 7F5K. Source data are provided with this paper.

Code availability

The customized plotGeneCount script and source data for Fig. 3k are provided as Supplementary Code. The script code provided in the supplementary material is available under the MIT License (Copyright 2022, Takahide Hayano). The original code was included in the package “tradeSeq” (https://bioconductor.org/packages/release/bioc/html/tradeSeq.html) which is distributed under the MIT License (Copyright 2019, Koen Van den Berge; Hector Roux de Bezieux). See https://opensource.org/licenses/mit-license.php for the full text of the MIT license.

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Acknowledgements

We thank S. Iwai, M. Kurata, S. Mondoon, M. Kawano, M. Shiokawa, K. Toyonaga, A. Kubota, X. Lu, Y. Harima, A. Tanaka, E. Ito, T. Oono, K. Kawabe, D. N. Azizah and T. Ito for technical support; S. Inuki, KH. Sonoda and Y. Yoshikai for discussions; M. Tanaka and K. Kaseda for embryonic engineering; the Cooperative Research Project Program of the Medical Institute of Bioregulation, Kyushu University and Science Research Center of Yamaguchi University for technical support. We also thank the beamline staff at the Photon Factory for crystallographic data collection. This research was supported by AMED (JP20gm0910010, JP20ak0101070, and JP20fk0108075), JSPS KAKENHI (JP20H00505 and JP16K08740), the Kurozumi Medical Foundation (K.S.), and the Takeda Science foundation (M.F.S.). The MR1 tetramer technology was developed jointly by Dr. James McCluskey, Dr. Jamie Rossjohn, and Dr. David Fairlie, and the material was produced by the NIH Tetramer Core Facility as permitted to be distributed by the University of Melbourne.

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Authors and Affiliations

Department of Microbiology and Immunology, Graduate School of Medicine, Yamaguchi University, Ube, 755-8505, Japan
Kensuke Shibata & Mutsunori Shirai
Department of Ophthalmology, Department of Ocular Pathology and Imaging Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
Kensuke Shibata
Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, 565-0871, Japan
Kensuke Shibata, Chihiro Motozono, Masamichi Nagae, Takashi Shimizu, Eri Ishikawa & Sho Yamasaki
Division of Infection and Immunity, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, 860-0871, Japan
Chihiro Motozono
Laboratory of Molecular Immunology, Immunology Frontier Research Center, Osaka University, Suita, 565-0871, Japan
Masamichi Nagae, Eri Ishikawa & Sho Yamasaki
Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, 565-0871, Japan
Daisuke Motooka
Single Cell Genomics, Human Immunology, World Premier International Research Center Initiative Immunology Frontier Research Center, Osaka University, Suita, 565-0871, Japan
Daisuke Okuzaki
Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, 565-0871, Japan
Daisuke Okuzaki
Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
Yoshihiro Izumi, Masatomo Takahashi & Takeshi Bamba
Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
Nao Fujimori & Yoshihiro Ogawa
Laboratory of Human Immunology (Single Cell Immunology), World Premier International Immunology Frontier Research Center, Osaka University, Suita, 565-0871, Japan
James B. Wing
Laboratory of Experimental Immunology, World Premier International Immunology Frontier Research Center, Osaka University, Suita, 565-0871, Japan
James B. Wing
Department of Systems Bioinformatics, Graduate School of Medicine, Yamaguchi University, Ube, 755-8505, Japan
Takahide Hayano & Yoshiyuki Asai
Japan Agency for Medical Research and Development, Core Research for Evolutional Science and Technology, Tokyo, 100-0004, Japan
Yoshihiro Ogawa
Department of Molecular Medicine and Metabolism, Research Institute of Environmental Medicine, Nagoya University, Nagoya, 464-8601, Japan
Yoshihiro Ogawa
Systems Biochemistry in Pathology and Regeneration, Graduate School of Medicine, Yamaguchi University, Ube, 755-8505, Japan
Makoto Furutani-Seiki
Division of Molecular Design, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
Sho Yamasaki
Division of Molecular Immunology, Medical Mycology Research Center, Chiba University, Chiba, 260-8673, Japan
Sho Yamasaki

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Kensuke Shibata
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Chihiro Motozono
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Masamichi Nagae
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Takashi Shimizu
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Eri Ishikawa
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James B. Wing
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Takahide Hayano
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Makoto Furutani-Seiki
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Mutsunori Shirai
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Sho Yamasaki
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Contributions

K.S. and S.Y. conceptualized research; K.S., C.M., T.S., E.I., Y.I., M.T., and M.N. did investigation; N.F. and Y.O. provided resources; K.S., C.M., D.M., D.O., J.B.W., T.H., Y.A., and T.B. did data curation; M.F.S., M.S., and S.Y. supervised the research; K.S. and S.Y. wrote the manuscript.

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Correspondence to Sho Yamasaki.

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Shibata, K., Motozono, C., Nagae, M. et al. Symbiotic bacteria-dependent expansion of MR1-reactive T cells causes autoimmunity in the absence of Bcl11b. Nat Commun 13, 6948 (2022). https://doi.org/10.1038/s41467-022-34802-8

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Received: 18 October 2021
Accepted: 08 November 2022
Published: 14 November 2022
DOI: https://doi.org/10.1038/s41467-022-34802-8

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