Nonclassical MHC Class Ib Molecules Research Articles

Immunodominant, Qa-1-restricted CD8 T cell response elicited against a non-canonical translation product in influenza A virus

Abstract The extent to which non-canonical translation products drive antiviral T cell responses is incompletely understood. We explored this question using an immunopeptidomic approach in an influenza virus model. C57Bl/6 mouse-derived cells were infected with influenza virus A/Puerto Rico/8/1934 (PR8), and MHC-bound peptides were eluted and analyzed by tandem mass spectrometry. Mass spectra were searched against a database of all viral gene segments translated in all possible reading frames, irrespective of the presence of start codons. We identified a 9-mer peptide, here termed M-SL9, that maps to an alternative reading frame of the sequence encoding matrix protein 1 (M1). To validate M-SL9 as a T cell epitope, we infected C57Bl/6 mice with PR8, collected tissues, and measured T cell reactivation by synthetic M-SL9 peptide. Remarkably, 10% of all CD8 T cells in the lung were specifically reactivated by M-SL9 peptide, and the vast majority of these were polyfunctional, producing two or more Th1 cytokines. An analysis of M-SL9 processing and presentation revealed that M-SL9 is restricted to the non-classical MHC class Ib molecule, Qa-1, and that presentation is dependent on the second 5′-proximal AUG codon within the M1-coding sequence, suggesting that its translation results from leaky ribosomal scanning. These data contribute to a growing body of work showing the importance of non-canonical MHC presentation in protective immune responses.

Peptide Binding to HLA-E Molecules in Humans, Nonhuman Primates, and Mice Reveals Unique Binding Peptides but Remarkably Conserved Anchor Residues.

Ag presentation via the nonclassical MHC class Ib molecule HLA-E, with nearly complete identity between the two alleles expressed in humans, HLA-E*01:01 and HLA-E*01:03, can lead to the activation of unconventional T cells in humans. Despite this virtual genetic monomorphism, differences in peptide repertoires binding to the two allelic variants have been reported. To further dissect and compare peptide binding to HLA-E*01:01 and HLA-E*01:03, we used an UV-mediated peptide exchange binding assay and an HPLC-based competition binding assay. In addition, we investigated binding of these same peptides to Mamu-E, the nonhuman primate homologue of human HLA-E, and to the HLA-E-like molecule Qa-1b in mice. We next exploited the differences and homologies in the peptide binding pockets of these four molecules to identify allele specific as well as common features of peptide binding motifs across species. Our results reveal differences in peptide binding preferences and intensities for each human HLA-E variant compared with Mamu-E and Qa-1b Using extended peptide libraries, we identified and refined the peptide binding motifs for each of the four molecules and found that they share main anchor positions, evidenced by conserved amino acid preferences across the four HLA-E molecules studied. In addition, we also identified differences in peptide binding motifs, which could explain the observed variations in peptide binding preferences and affinities for each of the four HLA-E-like molecules. Our results could help with guiding the selection of candidate pathogen-derived peptides with the capacity to target HLA-E-restricted T cells that could be mobilized in vaccination and immunotherapeutic strategies.

The Role of MHC-E in T Cell Immunity Is Conserved among Humans, Rhesus Macaques, and Cynomolgus Macaques.

MHC-E is a highly conserved nonclassical MHC class Ib molecule that predominantly binds and presents MHC class Ia leader sequence-derived peptides for NK cell regulation. However, MHC-E also binds pathogen-derived peptide Ags for presentation to CD8+ T cells. Given this role in adaptive immunity and its highly monomorphic nature in the human population, HLA-E is an attractive target for novel vaccine and immunotherapeutic modalities. Development of HLA-E-targeted therapies will require a physiologically relevant animal model that recapitulates HLA-E-restricted T cell biology. In this study, we investigated MHC-E immunobiology in two common nonhuman primate species, Indian-origin rhesus macaques (RM) and Mauritian-origin cynomolgus macaques (MCM). Compared to humans and MCM, RM expressed a greater number of MHC-E alleles at both the population and individual level. Despite this difference, human, RM, and MCM MHC-E molecules were expressed at similar levels across immune cell subsets, equivalently upregulated by viral pathogens, and bound and presented identical peptides to CD8+ T cells. Indeed, SIV-specific, Mamu-E-restricted CD8+ T cells from RM recognized antigenic peptides presented by all MHC-E molecules tested, including cross-species recognition of human and MCM SIV-infected CD4+ T cells. Thus, MHC-E is functionally conserved among humans, RM, and MCM, and both RM and MCM represent physiologically relevant animal models of HLA-E-restricted T cell immunobiology.

Two different nonclassical MHC class I-restricted invariant T cell lineages with non-overlapping antiviral and anti-mycobacterial immune functions in the amphibian Xenopus

Abstract Unconventional T cells, including disparate populations of MHC class Ib-reactive innate T (iT) cells are emerging as key factors in the immune system partly due to their public antigen specificities and rapid effector responses. The biological relevance and evolutionary conservation of iT cells have, over the past few years, been strengthened by studies in the amphibian Xenopus, which have revealed an overrepresentation of several invariant TCRs in tadpoles and identified a prominent subset of iT cells (invariant Vα6 [iVα6]) restricted by the nonclassical MHC class Ib molecule XNC10. Recently, we showed that similar to CD1d restricted iNKT cells in humans and mice Xenopus iVα6 T cells are critical for early antiviral immunity. Here, using RNAi loss-of-function by transgenesis targeting another Xenopus nonclassical gene, XNC4, we have identified a different XNC4-dependent iT cell population expressing one of the 6 previously identified overrepresented TCRα rearrangements (TRAV45 joined to TRAJ1.14). We show that this invariant Vα45 [iVα45] T cell population is critical for antibacterial immunity against Mycobacterium marinum. These data suggest that functionally distinct populations of MHC class Ib-reactive iT cell populations play a prominent role in amphibian immune defense and as such may represent a more primordial immune cell type that previously thought.

Broadly targeted CD8 + T cell responses restricted by major histocompatibility complex E

Major histocompatibility complex E (MHC-E) is a highly conserved, ubiquitously expressed, nonclassical MHC class Ib molecule with limited polymorphism that is primarily involved in the regulation of natural killer (NK) cells. We found that vaccinating rhesus macaques with rhesus cytomegalovirus vectors in which genes Rh157.5 and Rh157.4 are deleted results in MHC-E-restricted presentation of highly varied peptide epitopes to CD8αβ(+) T cells, at ~4 distinct epitopes per 100 amino acids in all tested antigens. Computational structural analysis revealed that MHC-E provides heterogeneous chemical environments for diverse side-chain interactions within a stable, open binding groove. Because MHC-E is up-regulated to evade NK cell activity in cells infected with HIV, simian immunodeficiency virus, and other persistent viruses, MHC-E-restricted CD8(+) T cell responses have the potential to exploit pathogen immune-evasion adaptations, a capability that might endow these unconventional responses with superior efficacy.

Population genetic structure for gene HLA-G in NorthWest Russia

HLA-G is a nonclassical MHC class Ib molecule predominantly expressed in cytotrophoblasts and also under pathological conditions in chronically inflamed and malignant tissues. Polymorphisms of the HLA-G gene, some of which are functionally important, may potentially affect both the coding and noncoding regions of this gene. Using the PCR method we studied polymorphism of the HLA-G gene (alleles G*0101–0107,–725C/G, and 3741del/ins14) in 118 individuals aged from 20 to 40 years and living in the NorthWest Region of Russia (St. Petersburg). In order to determine major alleles of the HLA-G gene, the system of primers for multiplex allele-specific PCR was elaborated. The HLA-G allele distribution in residents of the NorthWest Region of Russia was determined. The minor allele frequencies varied in wide ranges, from 0% to 39%. Cluster analysis was carried out and the genetic distances between the Spanish, Chinese, Japanese, Danish, Indian, African Shona, Brazilian, Polish, and German populations, as well as the population of the NorthWest Region of Russia, were calculated. The similarity of the distribution of frequencies of alleles G*0101–0107 and polymorphism 3741del/ins14 in the Danish, German, and NorthWest Region’s populations was shown.

Nonclassical MHC-Restricted Invariant Vα6 T Cells Are Critical for Efficient Early Innate Antiviral Immunity in the Amphibian Xenopus laevis.

Nonclassical MHC class Ib-restricted invariant T (iT) cell subsets are attracting interest because of their potential to regulate immune responses against various pathogens. The biological relevance and evolutionary conservation of iT cells have recently been strengthened by the identification of iT cells (invariant Vα6 [iVα6]) restricted by the nonclassical MHC class Ib molecule XNC10 in the amphibian Xenopus laevis. These iVα6 T cells are functionally similar to mammalian CD1d-restricted invariant NKT cells. Using the amphibian pathogen frog virus 3 (FV3) in combination with XNC10 tetramers and RNA interference loss of function by transgenesis, we show that XNC10-restricted iVα6 T cells are critical for early antiviral immunity in adult X. laevis. Within hours following i.p. FV3 infection, iVα6 T cells were specifically recruited from the spleen into the peritoneum. XNC10 deficiency and concomitant lack of iVα6 T cells resulted in less effective antiviral and macrophage antimicrobial responses, which led to impaired viral clearance, increased viral dissemination, and more pronounced FV3-induced kidney damage. Together, these findings imply that X. laevis XNC10-restricted iVα6 T cells play important roles in the early anti-FV3 response and that, as has been suggested for mammalian invariant NKT cells, they may serve as immune regulators polarizing macrophage effector functions toward more effective antiviral states.

Human CD8 T lymphocytes recognize Mycobacterium tuberculosis antigens presented by HLA-E during active tuberculosis and express type 2 cytokines.

CD8 T cells contribute to protective immunity against Mycobacterium tuberculosis. In humans, M. tuberculosis reactive CD8 T cells typically recognize peptides associated to classical MHC class Ia molecules, but little information is available on CD8 T cells recognizing M. tuberculosis Ags presented by nonclassical MHC class Ib molecules. We show here that CD8 T cells from tuberculosis (TB) patients recognize HLA-E-binding M. tuberculosis peptides in a CD3/TCR αβ mediated and CD8-dependent manner, and represent an additional type of effector cells playing a role in immune response to M. tuberculosis during active infection. HLA-E-restricted recognition of M. tuberculosis peptides is detectable by a significant enhanced ex vivo frequency of tetramer-specific circulating CD8 T cells during active TB. These CD8 T cells produce type 2 cytokines upon antigenic in vitro stimulation, help B cells for Ab production, and mediate limited TRAIL-dependent cytolytic and microbicidal activity toward M. tuberculosis infected target cells. Our results, together with the finding that HLA-E/M. tuberculosis peptide specific CD8 T cells are detected in TB patients with or without HIV coinfection, suggest that this is a new human T-cell population that participates in immune response in TB.

Population genetic structure of HLA-G gene in North-west Region of Russian Federation

Background. HLA-G is a non-classical MHC class Ib molecule predominantly expressed in cytotrophoblasts and under pathological conditions also in chronically inflamed and in malignant tissues. Polymorphic sites present in coding and non-coding regions of the HLA-G gene may potentially affect all of these biological features. Materials and methods: Using the PCR method we have studied polymorphism of HLA G gene (alleles G*0101-G0107, -725C/G , 3741del/ins14.) in 118 people aged from 20 till 40 years of the North-West Region of Russia (St. Petersburg). Results: To determine the common alleles of the HLA-G gene the system of allele-specific PCR primers was elaborated. We have determined HLA-G allele distribution in North-west Region of Russian Federation. The minor allele frequencies varied in wide ranges - from 0 % to 39 %. The genetic distances among the Spanish, Chinese, Japanese, Danish, Indian, African Shona, Brazilian, Polish, German and North-west Region of Russian Federation were calculated. Conclusion: The evaluation of alleles rates in North-west of Russian Federation and in populations of other countries revealed the similarity in alleles G*0101-G0107 and polymorphism 3741del/ins14 distribution among the Danish, German and North-west Region populations.

Double Positive Thymocytes Select Mucosal-Associated Invariant T Cells

NKT and mucosal-associated invariant T (MAIT) cells express semi-invariant TCR and restriction by nonclassical MHC class Ib molecules. Despite common features, the respective development of NKT and MAIT subsets is distinct. NKTs proliferate extensively and acquire effector properties prior to thymic export. MAIT cells exit the thymus as naive cells and acquire an effector/memory phenotype in a process requiring both commensal flora and B cells. During thymic development, NKTs are selected by CD1d-expressing cortical thymocytes; however, the hematopoietic cell type responsible for MAIT cell selection remains unresolved. Using reaggregated thymic organ culture and bone marrow chimeras, we demonstrate that positive selection of mouse iVα19 transgenic and Vβ6 transgenic MAIT cell progenitors requires MHC-related 1-expressing CD4(+)CD8(+) double positive thymocytes, whereas thymic B cells, macrophages, and dendritic cell subsets are dispensable. Preincubation of double positive thymocytes with exogenous bacterial ligand increases MHC-related 1 surface expression and enhances mature MAIT cell activation in the in vitro cocultures. The revelation of a common cell type for the selection of both NKT and MAIT subsets raises questions about the mechanisms underlying acquisition of their specific features.

NKG2C, HLA‐E and their association with psoriasis

Natural killer (NK) cell activation is regulated by the integration of signals from inhibitory and activating cell surface receptors. Both NKG2A and NKG2C pair with CD94 to form inhibitory and activating receptors specific for the HLA-E-canonical peptide complex. HLA-E is a non-classical MHC class Ib molecule with limited polymorphism. It preferentially binds to and presents leader sequence peptides derived from classical MHC class I molecules. Wilson et al. have identified an association between NKG2C deficiency and psoriasis. They have also discovered an HLA-C-dependent association between HLA-E and psoriasis. Their research highlights the importance of NK cells in the pathophysiology of psoriasis. Herein, we propose two different models to explain the association between NKG2C, HLA-E and psoriasis. In the first model, we hypothesize that NKG2C deficiency and/or HLA-E O1:01 can inhibit the ability of NK cells to regulate autoreactive T cells, predisposing to psoriasis. The second model proposes that HLA-E 01:03 can disrupt the presentation of the psoriasis-inducing self-determinant by HLA-C, thereby protecting against psoriasis.

Increased HLA-E expression in white matter lesions in multiple sclerosis.

The molecular mechanisms underpinning central nervous system damage in multiple sclerosis (MS) are complex and it is widely accepted that there is an autoimmune component. Both adaptive and innate immune effector mechanisms are believed to contribute to tissue disease aetiology. HLA-E is a non-classical MHC class Ib molecule that acts as the ligand for the NKG2A inhibitory receptor present on natural killer (NK) and CD8+ cells. Peptide binding and stabilization of HLA-E is often considered to signal infection or cell stress. Here we examine the up-regulation of HLA-E in MS brain tissue. Expression is significantly increased in white matter lesions in the brain of MS patients compared with white matter of neurologically healthy controls. Furthermore, using quantitative immunohistochemistry and confocal microscopy, we show increased HLA-E protein expression in endothelial cells of active MS lesions. Non-inflammatory chronic lesions express significantly less HLA-E protein, comparable to levels found in white matter from controls. Increased HLA-E protein levels were associated with higher scores of inflammation. These results suggest the potential for an effect in central nervous system pathogenesis from HLA-E modulation in stressed tissue. Co-localization with infiltrating CD8+ cells implicates a possible role for HLA-E-restricted regulatory CD8+ cells, as has been proposed in other autoimmune diseases.

An MHC Class Ib-Restricted CD8+ T Cell Response to Lymphocytic Choriomeningitis Virus

Conventional MHC class Ia-restricted CD8(+) T cells play a dominant role in the host response to virus infections, but recent studies indicate that T cells with specificity for nonclassical MHC class Ib molecules may also participate in host defense. To investigate the potential role of class Ib molecules in anti-viral immune responses, K(b-/-)D(b-/-)CIITA(-/-) mice lacking expression of MHC class Ia and class II molecules were infected with lymphocytic choriomeningitis virus (LCMV). These animals have a large class Ib-selected CD8(+) T cell population and they were observed to mediate partial (but incomplete) virus clearance during acute LCMV infection as compared with K(b-/-)D(b-/-)β(2)-microglobulin(-/-) mice that lack expression of both MHC class Ia and class Ib molecules. Infection was associated with expansion of splenic CD8(+) T cells and induction of granzyme B and IFN-γ effector molecules in CD8(+) T cells. Partial virus clearance was dependent on CD8(+) cells. In vitro T cell restimulation assays demonstrated induction of a population of β(2)-microglobulin-dependent, MHC class Ib-restricted CD8(+) T cells with specificity for viral Ags and yet to be defined nonclassical MHC molecules. MHC class Ib-restricted CD8(+) T cell responses were also observed after infection of K(b-/-)D(b-/-)mice despite the low number of CD8(+) T cells in these animals. Long-term infection studies demonstrated chronic infection and gradual depletion of CD8(+) T cells in K(b-/-)D(b-/-)CIITA(-/-) mice, demonstrating that class Ia molecules are required for viral clearance. These findings demonstrate that class Ib-restricted CD8(+) T cells have the potential to participate in the host immune response to LCMV.

Xenopus, a unique comparative model to explore the role of certain heat shock proteins and non-classical MHC class Ib gene products in immune surveillance.

The heat shock proteins (HSPs) gp96 and hsp70 can elicit potent anti-tumor responses and as such have significant clinical potential. Besides cytotoxic CD8 T cell (CTLs) effectors, evidence suggests that natural killer (NK) cells and other less well-characterized cell types also play a critical role in HSP-mediated anti-tumor responses. Owing to their high degree of phylogenetic conservation, we have proposed that HSPs are ancestral agents of immune surveillance; and postulated that their immunological properties, if important, should have been conserved during evolution. We are investigating this issue using a unique non-mammalian comparative tumor-immunity model in the frog Xenopus, which allows us to focus on the relationship between HSPs, classical MHC class Ia, and non-classical MHC class Ib molecules. In addition to a transplantable lymphoid tumor in genetically defined cloned Xenopus, we are generating transgenic frogs with inducible or knocked-down (RNAi) gene expression.

Tumorigenesis and anti-tumor immune responses in Xenopus.

Despite intense study, the role of the immune system in detecting (immunosurveillance), controlling and remodeling (immunoediting) neoplasia remains elusive. We present here a comparative view of the complex interactions between neoplasia and the host immune system. We provide evidence, in the amphibian Xenopus laevis, consistent with an evolutionarily conserved and crucial role of the immune system in controlling neoplasia, which involves a striking variety of anti-tumoral immune effectors including conventional CTLs, classical MHC class Ia unrestricted CTLs (CCU-CTLs) that interact with nonclassical MHC class Ib molecules, CD8 NKT-like cells and NK cells. We also review the tumors found in X. laevis with an emphasis on thymic lymphoid tumors and a rare ovarian dysgerminoma. Finally, we consider the use of X. laevis for in vivo study of tumorigenesis. Given our current knowledge, the experimental systems already established in X. laevis, and the rapid accumulation of genetic resources for the sister species Silurana (Xenopus) tropicalis, it is our conviction that these species provide an ideal alternative to the murine system for studying tumorigenesis and tumor immunity.

Cover Picture: Involvement of nonclassical MHC class Ib molecules in heat shock protein‐mediated anti‐tumor responses – Eur. J. Immunol. 6/2007

AbstractThe image of the jumping frog was kindly provided by Jacques Robert and created by his son by Adrien. Anti‐tumor responses, both in vitro and in vivo, are studied using Xenopus laevis by Robert and colleagues (pp. 1494–1501); non‐classical MHC class Ib molecules are shown, by RNA interference, to be important for the gp96‐induced CTL response against class Ia‐negative tumors in Xenopus. The conservation of the class Ia‐unrestricted response from Xenopus to mammals indicates the importance of this anti‐tumor immune mechanism.

Involvement of nonclassical MHC class Ib molecules in heat shock protein‐mediated anti‐tumor responses

Nonclassical MHC class Ib (class Ib) genes are found in all jawed vertebrates, and their products are hypothesized to be indicators of intracellular stress and malignancy. They may be involved in immune recognition of classical MHC class Ia (class Ia)-low or -negative tumor cells through their interaction with T cell receptors and/or non-T cell inhibitory or triggering receptors expressed by NK cells and T cells. In the frog Xenopus, the molecular chaperone gp96 mediates a potent immune response involving antigen-specific classical class Ia-unrestricted CD8+ CTL (CCU-CTL) against a transplantable thymic tumor (15/0) that does not express class Ia molecules. We hypothesized that Xenopus nonclassical class Ib gene products (XNC) are involved in gp96-mediated CCU-CTL anti-tumor responses. To investigate the involvement of class Ib gene products in Xenopus anti-tumor responses, we generated, for the first time in ectothermic vertebrates, stable tumor transfectants expressing short hairpin RNA (shRNA) to silence either XNC directly or beta2m to prevent class Ib surface expression. Both types of 15/0 transfectants are more resistant to CCU-CTL killing, more tumorigenic and more susceptible to NK-like cell killing. This study provides in vitro and in vivo evidence of the evolutionary conservation of class Ib involvement in anti-tumor CD8+ T cell responses.

The 14-bp deletion polymorphism in the HLA-G gene displays significant differences between ulcerative colitis and Crohn's disease and is associated with ileocecal resection in Crohn's disease

HLA-G is a non-classical MHC class Ib molecule predominantly expressed in cytotrophoblasts and under pathological conditions also in chronically inflamed and in malignant tissues. Recently an increased expression of HLA-G was found in ulcerative colitis (UC), but not in Crohn's disease (CD). The HLA-G gene is located in IBD3, a linkage region for inflammatory bowel disease (IBD). A 14-bp deletion polymorphism (Del+/Del-) within exon 8 of the HLA-G gene might influence transcription activity and is therefore of potential functional relevance. To investigate whether the 14-bp deletion polymorphism is associated with IBD, 371 patients with CD, 257 patients with UC and 739 controls were genotyped. The heterozygous genotype (P = 0.031) and the Del+ phenotype (P = 0.038) were significantly increased, whereas the homozygous Del- phenotype (P = 0.038) was significantly decreased in UC when compared with CD. Thus, the 14-bp deletion polymorphism within the HLA-G gene displayed significant differences between UC and CD. Moreover, a significant increase of the Del+ allele (P = 0.002) and the Del+/Del+ genotype (P = 0.013) and a consecutive decrease of the Del-/- genotype (P = 0.024) were observed in those CD cases positive for ileocecal resection. Thus, a potential effect of the HLA-G gene in IBD may affect both UC and CD. Other polymorphisms linked to the 14-bp deletion polymorphism might also contribute to immunopathogenesis. As there are several partly functional polymorphisms within the promoter region potentially influencing HLA-G expression, further studies in IBD are necessary in the context of differential expression of HLA-G between UC and CD.

Induction of classical and nonclassical MHC-I on mouse brain astrocytes by Japanese encephalitis virus

Infection with Flaviviruses upregulates the cell surface expression of MHC-I, MHC-II, ICAM-1 (CD54), VCAM-1 (CD106) and TAP proteins. Although all these studies have been confirmed using West Nile virus and other Flaviviruses, there are few reports that have examined the effects of Japanese encephalitis virus (JEV) infection directly on nonclassical and classical MHC expression in astrocytes. We show in this report that JEV infection of mouse brain astrocytes results in induction of the nonclassical MHC Class Ib genes, H-2T23, H-2Q4 and H-2T10 in addition to MHC-I, Type I ( α/ β) IFNs, TAP-1, TAP-2, Tapasin, LMP-2, LMP-7 and LMP-10 but not IFNγ, CD80, CD86 and MHC-II genes. The increased cell surface expression of these antigens as well as induction of the genes mentioned above as measured by RT-PCR suggests that JEV infection may lead to the induction of classical MHC Class Ia as well as nonclassical MHC Class Ib molecules.

HLA-G and MIC expression in tumors and their role in anti-tumor immunity

Non-classical MHC class Ib molecules have attracted growing interest in recent years, especially because they interact with non-T-cell inhibitory or triggering receptors expressed on natural killer (NK) and T cells, suggesting that they have a role in immune recognition. Abnormalities in MHC class Ib expression are frequently found in human tumors of various histologies and might be associated with poor clinical outcome despite the local accumulation of immune competent cells. Available data suggest that the balance between activating and suppressing signals significantly influences the efficacy of the immune response and consequently of tumor progression.