The immune system discriminates between the body’s own cells and foreign invaders largely by auditing proteins. Cells digest proteins into short fragments and load them onto the major histocompatibility complex (MHC), which presents the peptide to T cells for inspection. Using a parallel strategy, cells can also present lipids to T cells via a protein called cluster of differentiation 1 (CD1).1 Although scientists knew of the existence of lipid antigens, most immunology research has focused on protein antigens, leaving much to demystify about the role of CD1 and lipids.
In a study spanning 14 years, a team of immunologists took on the challenge of characterizing CD1. Published in the journal Cell, they showed that CD1 can onboard hundreds of lipids to present to T cells.2
“We’ve never had such an in-depth map of the CD1 lipidome available,” said Patricia Barral, an immunologist at King’s College London who was not involved with the work. “It will enable us to start thinking about different types of lipids that may function as activatory or as inhibitory lipids, and whether they can control T cell responses in different contexts.”
Immunologists have spent more than 40 years studying how T cells respond to peptide antigens rather than lipid ones, according to Branch Moody, an immunologist at Harvard University and study coauthor. A protein’s amino acid sequence is easy to deduce from the gene sequence, which may be one reason for the protein bias. Lipid structures are harder to uncover, and past studies have focused on individual CD1 types rather than the whole ensemble, which includes four different variants (CD1a to CD1d), making comparisons difficult. In this study, “we have all four proteins together that allow us to figure the patterns that belong to each specific isoform,” said Shouxiong Huang, coauthor and immunologist at the University of Cincinnati.
The team surveyed lipids that naturally bind CD1. Previously, researchers had to use a detergent that dissolves the cell membrane to isolate CD1, but this also washes away the loaded lipids.3 To avoid losing the lipids, Huang and his colleagues dispensed with the detergent and created a secreted form of CD1 by deleting the membrane region.
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Next, they harvested the loaded lipids and used high-performance liquid chromatography to separate them according to how quickly they pass through a vertical column under pressure. Depending on the lipid’s structure, some stuck poorly to the column wall and passed through quickly, whereas others stuck firmly and passed through later, allowing the lipids to separate with time. Each lipid was then broken into fragments and run through a mass spectrometer to determine the mass and charge of each fragment. From this data, the researchers pieced together the structure and identity of each lipid, culminating in a long list of lipids that possibly influence T cells.
Only a small number of lipids were known to bind CD1, but the new lipidomic analysis increased the count to more than 1600.4 Moreover, all four CD1 types shared more than half of the lipids, an overlap Barral hypothesized might boost the immunosurveillance capabilities of T cells. “Even if it’s the same lipid, it doesn’t necessarily sit in the same way in the different CD1 molecules,” she speculated. “This will affect what the T cell receptor sees.”
The team found that CD1 varieties preferentially loaded some lipids according to chain length. For example, CD1a preferred shorter chains (38 to 40 carbons) than CD1d (42 to 46 carbons). Of particular interest to the researchers was CD1b, a molecule that preferred short lipids with a chain length of 30 to 38 carbons even though its groove is large enough to hold twice that size. This led the team to hypothesize that the CD1b groove could hold two short lipids simultaneously. By resolving the crystal structure of the CD1b-lipid complex, they found that two lipids occupied the upper and lower chambers of the groove, suggesting that only the upper lipid contacts the T cell receptors (TCR).
The lower lipid may possibly serve as molecular stool for the upper one and might remain in place when short lipids exchange in the upper chamber. Moody and his team found that CD1b preferentially onboards shorter lipids. “In a 2001 paper, we found somewhat mysteriously that it’s very easy to get short-chain lipids loaded and presented, and it’s very hard to get long-chain lipids,” Moody commented.5 “Now we understand why. To get the big lipids inside CD1, you have to kick out two placeholders” instead of just the upper one.
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Proteins are trimmed into short yet distinct peptide fragments before they are presented to TCR, but the loaded lipids did not undergo detectable processing.6 This isn’t surprising because lipid chains contain many repeating units that wouldn’t be distinctive if trimmed down. They’re also difficult for cells to digest, mentioned Moody. “A chemically saturated hydrocarbon is extraordinarily stable. You can boil them in acid, and they’ll be just fine.”
These lipid antigens originate from human cells and might serve to train T cells to discriminate the body’s own lipids from those of infectious microbes. Moody noted that some of these lipids might influence the immune response in autoimmune conditions or cancer, too. Alternatively, a few might have no immune role but serve as placeholders in the hydrophobic, water-repelling groove until a lipid antigen is loaded. Some of the most frequently loaded lipids might include placeholders, like derivates of sphingomyelin and phosphatidylcholine, but the team couldn’t find a single dominant lipid, implying that a variety plug the groove.
In the future, the team hopes that their lipidomic strategy will be used to study how cells present microbial lipids to T cells during infection. CD1 loads a few microbial lipids, but this type of lipidomic analysis may reveal many more.7
Targeting CD1 might also have therapeutic benefits, and the researchers are looking for molecules that block CD1 from presenting lipids to T cells, thereby dampening immune responses. Barral supports this idea, noting that CD1 receptors do not vary considerably in humans. “This can make them specifically a very good target for therapeutic interventions,” she noted.
Conflicts of Interest
Moody consults for Pfizer and holds intellectual property through Mass General Brigham (filing 29618-0390P01).
- Ogg G, et al. Capturing the antigen landscape: HLA-E, CD1 and MR1. Curr Opin Immunol. 2019;59:121-129.
- Huang S, et al. CD1 lipidomes reveal lipid-binding motifs and size-based antigen-display mechanisms. Cell. 2023;186(21):4583-4596.
- Adams EJ. Lipid presentation by human CD1 molecules and the diverse T cell populations that respond to them. Curr Opin Immunol. 2014;26:1-6.
- Shahine A, et al. Novel molecular insights into human lipid-mediated T cell immunity. Int J Mol Sci. 2021;22(5):2617.
- Moody DB, et al. Lipid length controls antigen entry into endosomal and nonendosomal pathways for CD1b presentation. Nat Immunol. 2002;3:435-442.
- Evnouchidou I, van Endert P. Peptide trimming by endoplasmic reticulum aminopeptidases: Role of MHC class I binding and ERAP dimerization. Hum Immunol. 2019;80(5):290-295.
- Burchill L, Williams SJ. From the banal to the bizarre: Unravelling immune recognition and response to microbial lipids. Chem Commun (Camb). 2022;58(7):925-940.
