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Host immunomodulatory lipids created by symbionts from dietary amino acids

Nature volume 600, pages 302–307 (2021)Cite this article

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Abstract

Small molecules derived from symbiotic microbiota critically contribute to intestinal immune maturation and regulation1. However, little is known about the molecular mechanisms that control immune development in the host–microbiota environment. Here, using a targeted lipidomic analysis and synthetic approach, we carried out a multifaceted investigation of immunomodulatory α-galactosylceramides from the human symbiont Bacteroides fragilis (BfaGCs). The characteristic terminal branching of BfaGCs is the result of incorporation of branched-chain amino acids taken up in the host gut by B. fragilis. A B. fragilis knockout strain that cannot metabolize branched-chain amino acids showed reduced branching in BfaGCs, and mice monocolonized with this mutant strain had impaired colonic natural killer T (NKT) cell regulation, implying structure-specific immunomodulatory activity. The sphinganine chain branching of BfaGCs is a critical determinant of NKT cell activation, which induces specific immunomodulatory gene expression signatures and effector functions. Co-crystal structure and affinity analyses of CD1d–BfaGC–NKT cell receptor complexes confirmed the interaction of BfaGCs as CD1d-restricted ligands. We present a structural and molecular-level paradigm of immunomodulatory control by interactions of endobiotic metabolites with diet, microbiota and the immune system.

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Fig. 1: Chemical structure assignment of chain-length and branching variation in BfaGCs.
Fig. 2: BfaGC branching is dictated by host dietary BCAAs, and loss of BCAA utilization in B. fragilis impairs its ability to modulate host colonic NKT cells.
Fig. 3: BfaGCs cause distinct immunomodulatory signalling and actions.
Fig. 4: Crystal structure of 2C12 NKT cell receptor (TCR)–mCD1d–BfaGC ternary complexes showed conserved and distinct molecular interactions of BfaGCs with mCD1d and the 2C12 TCR.

Data availability

Raw data for NKT cell transcriptomic analysis was deposited in the NCBI Sequence Read Archive (SRA) with accession PRJNA750126. The crystal structures of the 2C12 TCR–mCD1d–SB2217 and 2C12 TCR–mCD1d–SB2219 ternary complexes were deposited in the Protein Data Bank under accession numbers 7M72 and 6XNG, respectively. Lipidomic analysis data containing MS1 scans were deposited to Metabolomics Workbench study number ST001910.

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Acknowledgements

We thank J. McCoy and E. J. Paik for manuscript preparation, R. T. Bronson for histopathological scoring, S. Iyer, L. Gebremedhin, E. Choi and T. Yanostang for technical assistance, and the staff at the Australian Synchrotron for assistance with data collection. This work was supported by National Institutes of Health (K01-DK102771 and R01-AT010268 to S.F.O., and R01-DK044319 to R.S.B.), Department of Defense (W81XWH-19-1-0625 to D.L.K.), Brigham and Women’s Hospital (Department of Anesthesiology, Perioperative and Pain Medicine Basic Science Grant to S.F.O.), the National Research Foundation of Korea (2014R1A3A2030423 and 2012M3A9C4048780 to S.B.P.), and the Australian Research Council (ARC) (CE140100011 and ARC Laureate Fellowship to J.R., and ARC Future Fellowship to J.L.N.). Graphical images used for the Fig. 2 were created with BioRender.com.

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Author notes

  1. These authors contributed equally: Sungwhan F. Oh, T. Praveena

Authors and Affiliations

  1. Department of Immunology, Blavatnik Institute of Harvard Medical School, Boston, MA, USA

    Sungwhan F. Oh, Deniz Erturk-Hasdemir, ChangWon C. Lee & Dennis L. Kasper

  2. Center for Experimental Therapeutics and Reperfusion Injury, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women’s Hospital, Boston, MA, USA

    Sungwhan F. Oh, Ji-Sun Yoo & Da-Jung Jung

  3. Infection and Immunity Program & Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia

    T. Praveena, Jérôme Le Nours & Jamie Rossjohn

  4. CRI Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul, Republic of Korea

    Heebum Song, Yoon Soo Hwang, Hyunsoo Kim, Jesang Lee & Seung Bum Park

  5. Division of Gastroenterology, Hepatology and Endoscopy, Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA

    Richard S. Blumberg

  6. Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia

    Jamie Rossjohn

  7. Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK

    Jamie Rossjohn

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Contributions

S.F.O., D.L.K. and R.S.B. conceived the idea and designed the outline of the research. S.F.O., H.B.S. and S.B.P. designed the structures of synthetic BfaGCs; H.B.S., Y.S.H., H.K. and J.L. synthesized BfaGC molecules. T.P., J.L.N. and J.R. generated crystals of 2C12 TCR–CD1d–BfaGCs and carried out X-ray crystallography analysis as well as affinity measurements by SPR. S.F.O., J.-S.Y. and C.C.L. designed and carried out all experiments with microorganisms. S.F.O., D.-J.J. and D.E.-H. executed in vitro and in vivo cytokine assays. S.F.O. and D.-J.J. designed and carried out all animal experiments. J.-S.Y. carried out transcriptomic analysis. S.F.O., S.B.P., J.R. and D.L.K. wrote the manuscript, and all authors contributed to relevant discussions.

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Correspondence to Sungwhan F. Oh, Jamie Rossjohn, Seung Bum Park or Dennis L. Kasper.

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Competing interests

S.F.O., R.S.B. and D.L.K. have filed a patent on the functions of BfaGCs and related structures (US patent 10,329,315). S.F.O., S.B.P. and D.L.K. filed a patent on the functions of BfaGCs and related structures (under review).

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Extended data figures and tables

Extended Data Fig. 1 Molecular structures of prototypic NKT agonist KRN7000, OCH and a representative B. fragilis-derived aGC (SB2217).

.

Extended Data Fig. 2 LC-MS profile of BfaGCs.

(A) Representative extracted ion chromatograms (XICs) of C32–C36 BfaGCs. (B) C34 BfaGCs are the major component of B. fragilis glycosphingolipids (N=5).

Extended Data Fig. 3 LC-MS/MS assignment of C34 BfaGC structural variants.

(A) The MS/MS-XIC of total C34 BfaGCs (762→698) shows that BfaGCs are isobaric mixtures separated by RP-HPLC. (B, C) MS/MS-XICs of C34 BfaGCs reveal co-eluting chemical homologues. Two isobaric species with aliphatic chains of C17/C17 (B) and C18/C16 (C) were assigned MS/MS fingerprints of 490 and 504, respectively. (D) MS/MS fingerprints of three peaks show a distinct difference in relative intensity between MS/MS fragments of 490 (C17/C17) and 504 (C18/C16), implying that the latter two peaks are a mixture of chain-length homologues. Chromatograms and spectra represent triplicate observations. (E-H) MS/MS spectra of the most abundant peaks of (E) C32, (F) C33, (G) C35 and (H) C36 BfaGCs. MS/MS fingerprint of 462–518 indicates lengths of sphinganine and acyl chains. Spectra are representative of triplicate observation.

Extended Data Fig. 4 Chemical structures of 23 synthetic BfaGCs.

(SB2201–SB2223).

Extended Data Fig. 5 BCAA dictates branching of BfaGCs by direct incorporation in vivo.

(A–E) Ratios among differently branched C34 BfaGCs (MS1 XIC=762.57, as [M+HCOO-]) are clearly different for B. fragilis grown in rich medium (A) and B. fragilis grown in minimal medium (B). Supplementation with individual BCAAs (C–E) on defined medium increases production of branched-chain (both dibranched and monobranched) BfaGCs. (F–H) MS/MS fingerprints confirm the incorporation of leucine and isoleucine into the C17/C17 ceramide backbone (via C5 branched acyl-CoA) and of valine into the C18/C16 backbone (via C4 branched acyl-CoA). Chromatograms and spectra are representative of triplicate observations. (I) An MS/MS-XIC of d3- and d6-C34 BfaGC shows that deuterium-labeled leucine is actively incorporated into BfaGC. (J-K) MS/MS pattern shows distinctive differences between gut luminal BfaGC (M+3 isotopolog) in (J) presence or (K) absence of d3-leucine, showing MS2 fragments in presence of d3-leucine reflect inclusion of deuterium-labeled leucine in the structure. Chromatograms and spectra are representative results of four mice.

Extended Data Fig. 6 Genetic study of B. fragilis Bcat orthologue (BF9343-3671).

(A) Confirmation of the target gene deletion by PCR. (B) The knockout strain (BF9343-Δ3671) shows comparable growth pattern to isogenic WT strain (grown in duplicate per group), and a complemented strain of KO strain with empty vector shows same pattern to BF9343-3671 complemented strain. (C) BF9343-Δ3671 complementation can recover the production of di-branched C17/C17 BfaGC production to wild-type level. (D) WT and mutant strain (N=5 for each group) can colonize mouse in comparable density. All results represent of two independent experiments with similar trend. For gel source data, see Supplementary Fig. 1.

Extended Data Fig. 7 Structure-specific actions of BfaGCs.

(A) NKT cell–APC co-culture assays show that branching of sphinganine chain is, but 3’-OH group is not, critical for IL-2 inducing activity. Results are shown in duplicate and represent three independent experiment sets with similar trend (p=0.017 for 100nM and p=0.026 for 1000nM). (B-C) When injected intraperitoneally (N=5 per group, one sample in OCH group in panel C was lost), unlike Th1- or Th2-skewed prototypic ligands such as KRN7000 or OCH, SB2217 only weakly induce IFN-γ and did not induce IL-4 in vivo. (D-F) SB2217 weakly induced expression of co-stimulatory molecules such as CD86, CD40 and CD80 in splenic DCs, where SB2219 did not (N=5 per group).

Extended Data Fig. 8 Transcriptomic landscape of splenic NKT cells in responses to agonists.

(A) A heatmap shown with the Euclidean distances between different treatment groups. (B) Transcriptomic profile comparison of SB2217, SB2219 and OCH. (C) Pathway enrichment analysis of SB2217 reveals increased expression of immunoregulatory pathways in NKT cells when compared to vehicle or SB2219.

Extended Data Fig. 9 Comparison between SB2217 and SB2219 in mCD1d-BfaGC-2C12 complexes.

(A) 2Fo-Fc electron density map (in blue) contoured at a 0.8σ level of the BfaGCs within each ternary complex. (B) Fo-Fc electron density map (in brown) contoured at a 2.2σ level of the BfaGCs and spacer lipids within each ternary complex. SB2217 is shown as blue and SB2219 is shown as green; Spacer lipids are shown as black sticks. (C) Superimposition of the headgroups of BfaGCs and KRN7000 (PDB code: 6BNK). (D) 2C12 TCR molecular interactions with SB2217 (in blue). mCD1d and CDR loops are colored as in Fig. 4a. Hydrogen bonds are shown as red dashed lines. (E-F) The mCD1d–SB2217 complex shows higher affinity to 2C12 TCR than the mCD1d–SB2219 complex. (E) Each SPR datapoint is mean of techincal duplicate and KD values (mean±SD) were calculated from two independent results, using a single-site binding model with KD as a shared variable. (F) The sensorgrams are results of single experiment.

Extended Data Fig. 10 BfaGC profile in human microbiota-associated mice.

(A) BfaGC and B. fragilis abundance shows positive correlation in B. fragilis-gavaged HMB mice. Results are from longitudinally collected samples (2, 3 and 7 days after B. fragilis oral introduction) from five mice (total N=15). (B) BfaGC (C17/C17 dibranched and monobranched) are identified from neonatal (p14) GI contents. Chromatogram and spectrum represent seven samples.

Supplementary information

Supplementary Information

This file contains Supplementary Tables; Supplementary Figs. 1 (raw gel data) and 2 (FACS gating strategies for immune cell analysis); raw data (weight monitoring over disease time course) of in vivo experiment (oxazolone colitis); and total organic synthesis of BfaGC analogue (SB2201‐SB2223) library.

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Oh, S.F., Praveena, T., Song, H. et al. Host immunomodulatory lipids created by symbionts from dietary amino acids. Nature 600, 302–307 (2021). https://doi.org/10.1038/s41586-021-04083-0

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