CD1c tetramers detect ex vivo T cell responses to processed phosphomycoketide antigens

Cluster of differentiation 1c (CD1c)-dependent self-reactive T cells are abundant in human blood, but self-antigens presented by CD1c to the T-cell receptors of these cells are poorly understood. Here we present a crystal structure of CD1c determined at 2.4 Å revealing an extended ligand binding potential of the antigen groove and a substantially different conformation compared with known CD1c structures. Computational simulations exploring different occupancy states of the groove reenacted these different CD1c conformations and suggested cholesteryl esters (CE) and acylated steryl glycosides (ASG) as new ligand classes for CD1c. Confirming this, we show that binding of CE and ASG to CD1c enables the binding of human CD1c self-reactive T-cell receptors. Hence, human CD1c adopts different conformations dependent on ligand occupancy of its groove, with CE and ASG stabilizing CD1c conformations that provide a footprint for binding of CD1c self-reactive T-cell receptors.CD1 | lipid antigen | antigen presentation | T cell | cholesteryl ester C luster of differentiation 1 (CD1) proteins are a family of MHC class I-like glycoproteins that present lipid antigens to T cells. CD1 restricted T cells are abundant in humans and play important roles in host defense and immune regulation. Human CD1 proteins comprise five CD1 isoforms, CD1a, CD1b, CD1c, CD1d, and CD1e, which exhibit different intracellular trafficking behaviors and ligand binding preferences (1). Structurally, the main differences between these CD1 isoforms lie in the architecture of their lipophilic ligand binding grooves. Whereas all CD1 isoforms share a highly conserved A′ channel (or pocket) for binding C18-C26 acyl chains, specialization is provided by further connecting channels (2-7). In CD1a, the A′ channel is "fused" to a wide and shallow F′ channel, enabling binding of lipopeptides such as mycobacterial didehydroxymycobactin (DDM) (8). CD1b features a unique T′ tunnel that connects A′ and F′, thereby forming a "superchannel" for accommodating very long acyl chains (e.g., mycobacterial mycolates) (2, 4). CD1d, the only isoform also conserved in rodents, exhibits a twobranched ligand binding groove with two linear channels A′ and F′ connected near the main portal into the groove, known as the F′ portal. A similar two-branched arrangement of A′ and F′ is seen in CD1e, the only CD1 isoform not expressed on the cell surface. Compared with CD1d, CD1a, and CD1b, the portal into the groove in CD1e is widely exposed, consistent with its known role in lipid transfer processes inside lysosomes (6).CD1c presents foreign-(9, 10) as well as self-lipid antigens to T cells (11). Two recent crystal structures of human CD1c revealed a two-branched design similar to that of CD1d and CD1e, with two channels A′ and F′ connecting near the groove portal. In these structures, a mycobacterial phosphomycoketide (PM) or mannosyl-β1-phosphomycoketide (MPM) occupied the A′ channel, whereas an undefined short ligand was present in the F′ channel (7, 12). The spatial arrangement of...

Section: Discussionmentioning

confidence: 99%

Cholesteryl esters stabilize human CD1c conformations for recognition by self-reactive T cells

Mansour

Tocheva

Cave-Ayland

et al. 2016

“…Prior work using human T-cell clones (3)(4)(5)(6)(7) and the recently developed human CD1a, CD1b, and CD1c tetramers (8)(9)(10) has demonstrated the existence of mycobacteria-reactive T cells, including polyclonal T cells with stereotyped T-cell receptors (TCRs), known as germline-encoded mycolyl lipid-reactive T cells (11) and LDN5-like T cells (12). At this time, nearly all known foreign antigens presented by CD1b, including mycolic acid, glucose monomycolate, glycerol monomycolate, and sulfoglycolipids, are selectively synthesized by Mycobacterium tuberculosis and related mycobacterial species.…”

mentioning

confidence: 99%

Human autoreactive T cells recognize CD1b and phospholipids

Rhijn

Berlo

Hilmenyuk

et al. 2015

Self Cite

101

In contrast with the common detection of T cells that recognize MHC, CD1a, CD1c, or CD1d proteins, CD1b autoreactive T cells have been difficult to isolate in humans. Here we report the development of polyvalent complexes of CD1b proteins and carbohydrate backbones (dextramers) and their use in identifying CD1b autoreactive T cells from human donors. Activation is mediated by αβ T-cell receptors (TCRs) binding to CD1b-phospholipid complexes, which is sufficient to activate autoreactive responses to CD1b-expressing cells. Using mass spectrometry and T-cell responses to scan through the major classes of phospholipids, we identified phosphatidylglycerol (PG) as the immunodominant lipid antigen. T cells did not discriminate the chemical differences that distinguish mammalian PG from bacterial PG. Whereas most models of T-cell recognition emphasize TCR discrimination of differing self and foreign structures, CD1b autoreactive T cells recognize lipids with dual self and foreign origin. PG is rare in the cellular membranes that carry CD1b proteins. However, bacteria and mitochondria are rich in PG, so these data point to a more general mechanism of immune detection of infection- or stress-associated lipids.

“…These antigens include synthetic mannosyl phosphodolichols that are structurally related to mycobacterial mannosyl-β1-phosphomycoketide (MPM) (7)(8)(9) and recently described phosphomycoketide (PM) (10). The unusual methyl branches associated with these mycoketide antigens, synthesized by polyketide synthase 12 (pks12), serve as a molecular signature for M. tuberculosis and are required for loading into the CD1c antigen binding groove (8,10). MPM binds in the A′ pocket of CD1c and the mannose head group extends out of ligand binding groove to become accessible to a TCR for recognition (11).…”

mentioning

confidence: 99%

Molecular basis of mycobacterial lipid antigen presentation by CD1c and its recognition by αβ T cells

Roy¹,

Li³

et al. 2014

Self Cite

CD1c is a member of the group 1 CD1 family of proteins that are specialized for lipid antigen presentation. Despite high cell surface expression of CD1c on key antigen-presenting cells and the discovery of its mycobacterial lipid antigen presentation capability, the molecular basis of CD1c recognition by T cells is unknown. Here we present a comprehensive functional and molecular analysis of αβ T-cell receptor (TCR) recognition of CD1c presenting mycobacterial phosphomycoketide antigens. Our structure of CD1c with the mycobacterial phosphomycoketide (PM) shows similarities to that of CD1c-mannosyl-β1-phosphomycoketide in that the A' pocket accommodates the mycoketide alkyl chain; however, the phosphate head-group of PM is shifted ∼6 Å in relation to that of mannosyl-β1-PM. We also demonstrate a bona fide interaction between six human TCRs and CD1c-mycoketide complexes, measuring high to moderate affinities. The crystal structure of the DN6 TCR and mutagenic studies reveal a requirement of five complementarity determining region (CDR) loops for CD1c recognition. Furthermore, mutagenesis of CD1c reveals residues in both the α1 and α2 helices involved in TCR recognition, yet not entirely overlapping among the examined TCRs. Unlike patterns for MHC I, no archetypical binding footprint is predicted to be shared by CD1c-reactive TCRs, even when recognizing the same or similar antigens.group 1 CD1 | Mycobacterium tuberculosis | T-cell reactivity H uman CD1 molecules are antigen-presenting proteins that capture and display lipid antigens to T cells (1). CD1 proteins are categorized based on their genomic organization, sequence homology, and cellular function into group 1 (CD1a, CD1b, and CD1c), group 2 (CD1d), and group 3 (CD1e) (2, 3). Our understanding of CD1 antigen presentation and recognition by a T-cell receptor (TCR) is largely based on CD1d/natural killer T (NKT) cell receptor interactions (4). However, the five human CD1 molecules are markedly different in the architecture of their antigen binding pockets, which in turn gives rise to distinct antigen specificities. Furthermore, each CD1 family member exhibits different tissue expression profiles and intracellular trafficking patterns, demonstrating that CD1 molecules perform specific, nonredundant immunological tasks (5). CD1c, in particular, is a common and broadly expressed antigen-presenting molecule in the human immune system, where it is found at high surface density on most myeloid dendritic cells and marginal zone B cells.A number of Mycobacterium tuberculosis lipid antigens have been identified that are presented by group 1 CD1 molecules (6). CD1c molecules present several mycobacterial or synthetic lipid antigens that share a key chemical motif: methylated alkyl chains. These antigens include synthetic mannosyl phosphodolichols that are structurally related to mycobacterial mannosyl-β1-phosphomycoketide (MPM) (7-9) and recently described phosphomycoketide (PM) (10). The unusual methyl branches associated with these mycoketide antigens, synthesized by p...