Poster Presentation CD1-MR1 Workshop 2025

Deciphering the molecular basis of headless lipid recognition by NKT cells   (#120)

Praveena Thirunavukkarasu 1 , Tan-Yun Cheng 2 , Srinath Govindarajan 3 4 , Catarina F. Almeida 5 , Daniel G. Pellicci 5 , Wellington C. Arkins 2 , Ildiko Van Rhijn 2 , Koen Venken 3 4 , Dirk Elewaut 3 4 , Dale I. Godfrey 5 , D. Branch Moody 2 , Jamie Rossjohn 6 7
  1. Infection and Immunity program, Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
  2. Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
  3. Molecular Immunology and Inflammation Unit, Vlaams Instituut voor Biotechnologie, Center for Inflammation Research, Ghent University, Ghent, Belgium
  4. Faculty of Medicine and Health Sciences, Department of Internal Medicine and Pediatrics (Rheumatology unit), Ghent University, Ghent, Belgium
  5. Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
  6. Infection and Immunity Program, Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
  7. Institute of Infection and Immunity, Cardiff University, Heath Park, Cardiff, UK

In the absence of foreign lipids, NKT cells display self-reactivity in conditions like autoimmunity, tumour immunity and graft-versus-host disease. Identifying natural self-lipids is a central aspect of understanding NKT cell self-reactivity. Using a high-throughput lipidomics approach, we have identified several CD1d-bound self-lipids from mammalian cells that could act as binders or blockers. Interestingly, most of these lipids lacked the polar sugar head group, which serves as an epitope for NKT TCR recognition. Our structural studies using X-ray crystallography on one such CD1d-presented headless lipid antigen, ceramide, in complex with a type I NKT TCR revealed that the T cell receptor adopted a parallel docking topology, positioning itself atop the F′-pocket of CD1d. The absence of the sugar headgroup abolished key interactions with the NKT TCR, and, nevertheless, the overall conserved docking pattern was maintained. Surprisingly, the majority of the intermolecular interactions in the complex were formed between CD1d and TCR itself, with minimal interactions in contacting the lipid. Of note, the NKT TCR recognised the CD1d-headless lipid with micromolar affinities as measured by Surface Plasmon Resonance. Collectively, this study provides the first detailed insights into how a CD1d-presented headless lipid is recognised by the NKT TCR. Our data provides proof of concept that small naturally occurring headless lipids could function as CD1d ligands in activating NKT cells.

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(* denotes co-first authors)

Cheng TY*, Praveena T*, Govindarajan S*, Almeida CF*, Pellicci DG, Arkins WC, Van Rhijn I, Venken K, Elewaut D, Godfrey DI, Rossjohn J, Moody DB. Lipidomic scanning of self-lipids identifies headless antigens for natural killer T cells PNAS. 2024 Aug 20;121(34):e2321686121.