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The Journal of Immunology, 2007, 178: 33-37.
Copyright © 2007 by The American Association of Immunologists, Inc.

CUTTING EDGE

Cutting Edge: Allele-Specific and Peptide-Dependent Interactions between KIR3DL1 and HLA-A and HLA-B1,2

Hathairat Thananchai*, Geraldine Gillespie*, Maureen P. Martin{dagger}, Arman Bashirova{ddagger}, Nobuyo Yawata§, Makoto Yawata§, Philippa Easterbrook, Daniel W. McVicar||, Katsumi Maenaka#, Peter Parham§, Mary Carrington{dagger}, Tao Dong3,4,* and Sarah Rowland-Jones3,4,*

* Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, Oxford, United Kingdom; {dagger} Laboratory of Genomic Diversity, Science Applications International Corporation-Frederick, National Cancer Institute, Frederick, MD 21702; {ddagger} Johns Hopkins University School of Medicine, Baltimore, MD 21205; § Department of Structural Biology and Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305; Department of HIV/Genitourinary Medicine, The Guy’s, Kings’, and St. Thomas’ School of Medicine, London, United Kingdom; || Laboratory of Experimental Immunology, National Cancer Institute, Frederick, MD 21702; and # Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan


   Abstract
Top
 Abstract
Introduction
 Materials and Methods
 Results and Discussion
 Disclosures
 References
 
Although it is clear that KIR3DL1 recognizes Bw4+ HLA-B, the role of Bw4+ HLA-A allotypes as KIR3DL1 ligands is controversial. We therefore examined the binding of tetrameric HLA-A and –B complexes, including HLA*2402, a common Bw4+ HLA-A allotype, to KIR3DL1*001, *005, *007, and *1502 allotypes. Only Bw4+ tetramers bound KIR3DL1. Three of four HLA-A*2402 tetramers bound one or more KIR3DL1 allotypes and all four KIR3DL1 allotypes bound to one or more HLA-A*2402 tetramers, but with different binding specificities. Only KIR3DL1*005 bound both HLA-A*2402 and HLA-B*5703 tetramers. HLA-A*2402-expressing target cells were resistant to lysis by NK cells expressing KIR3DL1*001 or *005. This study shows that HLA-A*2402 is a ligand for KIR3DL1 and demonstrates how the binding of KIR3DL1 to Bw4+ ligands depends upon the bound peptide as well as HLA and KIR3DL1 polymorphism.


   Introduction
Top
 Abstract
 Introduction
Materials and Methods
 Results and Discussion
 Disclosures
 References
 
Natural killer cells represent a major component of innate immunity; they can kill tumor or virus-infected cells without prior sensitization and play an important role in the control of virus infections (1, 2). NK lysis is inhibited when their inhibitory receptors interact with class I HLA molecules on target cells. Receptors for the classical HLA-A, -B, and -C molecules are encoded by genes in the killer cell Ig-like receptor (KIR)5 gene complex (3, 4); like HLA-A, B and C, the KIR genes are highly polymorphic. KIRs are type I transmembrane proteins comprising two (KIR2D) or three (KIR3D) extracellular Ig-like domains. In general, KIRs with long cytoplasmic tails (KIR2DL and KIR3DL) transduce an inhibitory signal to inhibit NK cell lysis, whereas KIRs with short cytoplasmic tails (KIR2DS and KIR3DS) activate NK cell function (5, 6). An exception is KIR2DL4, the HLA-G receptor, which combines a long cytoplasmic tail with activating function (7).

KIR2D recognizes HLA-C determinants, whereas KIR3D receptors recognize HLA-A and -B alleles (5). Polymorphisms in the C terminus of the HLA class I {alpha}1 helix (residues 77–83) strongly influence KIR interactions. For HLA-A and -B this is also the site of the serological Bw4 and Bw6 epitopes and their corresponding sequence motifs (8). KIR3DL1 specificity was originally defined in cellular assays that examined the ability of different HLA class I molecules to protect targets from NK cell lysis. In one such analysis of NK clones Cella et al. (9) found that both Bw4+ HLA-A and -B allotypes were inhibitory; they emphasized the strong, but incomplete, correlation with the presence of isoleucine 80 (I80). In contrast, the analysis of NK cell clones from other donors by Gumperz et al. (10) correlated inhibition with Bw4+ HLA-B allotypes irrespective of the position 80 residue and found no interaction with two Bw4+ HLA-A allotypes, A*2501 and A*2403. Subsequent comparison of five HLA-B27 subtypes (all Bw4+) showed that the four subtypes with threonine 80 (B*2701, *2703, *2704, *2705, and *2706) were strong inhibitors of NK cells, whereas the one subtype with I80 (B*2702) did not inhibit (11). The molecular basis for these functional differences was not determined and while there has been increasing evidence for KIR3DL1 interactions with Bw4+ HLA-B, the significance of interactions with Bw4+ HLA-A (which all have I80) remains uncertain.

A possible cause of the differences observed in the HLA-A and -B specificity of KIR3DL1 is genetic polymorphism of KIR3DL1, which we now know is extensive (12, 13, 14) but was not appreciated at the time of the earlier studies (9, 10, 11). Thus, the NK cell clones may well have expressed different forms of KIR3DL1, potentially with different HLA class I specificities. To address this question, we used well-defined peptide-HLA class I tetrameric complexes ("tetramers") to dissect the interactions between polymorphic variants of KIR3DL1 and HLA-A and -B.


   Materials and Methods
Top
 Abstract
 Introduction
 Materials and Methods
Results and Discussion
 Disclosures
 References
 
Generation of NK clones

PBMCs were obtained from laboratory workers and members of a previously described HIV-1-infected, long-term nonprogressor (LTNP) cohort (ethically approved by the Research Ethics Committee of King’s College Hospital, London, U.K.) (15). NK cells were negatively selected using anti-CD3, anti-CD14, and anti-CD19-coated magnetic beads (Dynal Biotech) and then cocultured with irradiated allogeneic PBMCs in RPMI 1640 medium supplemented with 10% heat-inactivated human AB serum (H10) and recombinant human (rh) IL-2 at 100U/ml for 2 wk. NK cell clones were generated by limiting dilution and cultured in H10 with rhIL-2 at 200U/ml and rhIL-15 at 10 µg/ml with irradiated feeder cells.

KIR3DL1 transfectant cell lines

cDNA clones encoding KIR3DL1 alleles were isolated from NK cells as described (16). KIR3DL1*005, *007, and *1502 cDNA were cloned into the pEF6/V5-His-TOPO vector (Invitrogen Life Technologies). The corresponding plasmids (30 µg each) were electroporated into Jurkat cells using a BTX square wave electroporator. Transfected cells were selected in 20 µg/ml blasticidin S (Invitrogen Life Technologies) and then dilution cloned. Individual clones were screened by flow cytometry using anti-KIR3DL1 mAb (DX9) and maintained in 10 µg/ml blasticidin S.

Tetramer staining

NK clones or KIR3DL1 transfectants cell were stained with a panel of class I "tetramers." Briefly, 2 x 105 cells were washed and resuspended with wash buffer (PBS containing 0.1% BSA and 0.1% azide). Two micrograms of tetramer was added followed by incubation at 37°C for 15 min. Cells were washed and fixed with wash buffer. For blocking experiments, cells were incubated on ice with DX9 or isotype control Ab for 30 min before adding a tetramer.

Cytotoxicity assays

The killing activity of NK clones was assessed using 51Cr release assays. Class I-deficient 221 lymphoblastoid cells were used as target cells, either without treatment or following infection with recombinant vaccinia virus containing A*2402, A*0201, or no insert. A*2402 and A*0201 expressions were comparable as determined by anti-MHC class I Ab. 221 cells expressing A*2402 and A*0201 were pulsed with 100 µmol of peptides and washed before use in the assay.

For blocking experiments, effector cells were preincubated with 10 µg/ml DX9 or IgG1 isotype control at 4°C for 30 min. The ratio of NK cells to target cells varied from 5:1 to 10:1, and they were incubated at 37°C for 4 h. Specific lysis was calculated using the following formula: percentage specific lysis = 100% x [(experimental lysis – spontaneous lysis)/(maximum lysis – spontaneous lysis)].

KIR3DL1 genotyping

Genomic DNA was isolated from PBMCs using the PureGene DNA isolation kit (GentraSystems). Following PCR, KIR3DL1 was sequenced using the following primers: exon 3, 5'-TTCTTGGTCCAGAGGGCCGGT-3' (forward) and 5'-CTGTGACCATGATCACCAC-3' (reverse); exon 4, 5'-GAAACCACAGAAAACCTTCCC-3' (forward) and 5'-AGAGAGAAGGTTTCTCATATG-3' (reverse); exon 5, 5'-GCCTCTTCTCCTTCCAGGTCC-3' (forward) and 5'-CACCTGTGACAGAAACAAG-3' (reverse); exons 7–9, 5'-AGTGGTCATCATCCTCTTCATC-3' (forward) and 5'-GTGTACAAGATGG TATCTGTA-3' (reverse). Cycle sequencing was performed using the ABI BigDye terminator cycle sequencing ready reaction kit (Applied Biosystems) and samples were run on an ABI 3730xl sequencer.


   Results and Discussion
Top
 Abstract
 Introduction
 Materials and Methods
 Results and Discussion
Disclosures
 References
 
We previously used HLA class I tetramers to show that KIR3DL2 specificity depends upon both the MHC class I molecule, either HLA-A3 or –A11, and a specific bound peptide derived from the EBV (17). We used a similar strategy to investigate the binding of HLA class I ligands to four KIR3DL1 allotypes.

KIR3DL1 binds to HLA-A*2402 tetramers

Four NK clones from three donors either expressed 3DL1*001 or 3DL1*005 or lacked 3DL1 (Table I); these were stained with a panel of tetramers containing different antigenic peptides. Correct tetramer folding was confirmed by staining well-characterized specific cytotoxic T cell lines (18, 19). Three of the four NK clones bound to HLA-A*2402 tetramers containing different epitope peptides from HIV-1 nef, HIV-1 gag p17, and human cytomegalovirus (Fig. 1A and Table I). The ability to bind A*2402 tetramers correlated with KIR3DL1 expression as defined by staining with the anti-KIR3DL1 mAb, DX9. These data show that A*2402 binds to KIR3DL1; this was confirmed using a 3DL1*001 transfectant of the mouse Baf3 cell line that bound the same three A*2402 tetramers as the KIR3DL1+ NK clones. Abrogation of tetramer binding in the presence of DX9 Ab, but not by isotype control Ab, showed that binding was specific for KIR3DL1 (Fig. 1B and data not shown). These results demonstrate that the complexes of HLA-A*2402 with several virus-derived peptides are ligands for KIR3DL1.


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  		Table I. Phenotype and genotype of NK clones and their ability to bind HLA-A*2402 tetramers

 

Figure 1
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  		FIGURE 1. A and B, HLA-A*2402 tetramers can bind specifically to NK clones and transfectants expressing KIR3DL1*001. A, DX9+ NK clone LTNP208-43 was stained with A*2402 tetramers. B, Baf3 cells transfected with 3DL1*001 were stained with an A*2402 tetramer refolded with HIV-1 nef peptide alone and with the addition of isotype Ig control or DX9 mAb. C and D, Expression of KIR3DL1 on transfectant cell lines. 3DL1*001-transfected Baf3 (C) or 3DL1*005-transfected Jurkat cells (D) were stained with DX9 mAb. Gray shaded histograms show staining of untransfected cells and black lines show staining of 3DL1-transfected cells. E and F, KIR3DL1*005 binds both HLA-A*2402 and HLA-B*5703 tetramers. 3DL1*005-transfected Jurkat cells were stained with HLA class I tetramers in the presence of isotype control Ab (black line) or DX9 Ab (dashed line). Transfectant cells were stained with A*2402 nef (E) or B*5703 KAF (F). These data are representative of three replicate experiments.

 
Interaction of HLA-A*2402 with KIR3DL1 inhibits NK cell lysis

To investigate the function of the HLA-A24/KIR3DL1 interaction, we determined whether A*2402 expression protected target cells from lysis by KIR3DL1+ NK clones. A*2402 expression protected 221 cells from lysis by NK cell clones expressing either 3DL1*005 (H002-2) or 3DL1*001 (LTNP208-43), and lysis was restored in the presence of DX9 mAb (Fig. 2, A–D). In contrast, the expression of HLA-A*0201 (either in the presence or absence of the HIV-1 p17 peptide) did not protect 221 target cells from killing by KIR3DL1+ NK clones (Fig. 2, C and D). The KIR3DL1– NK clone (LTNP208-16) lysed 221 cells expressing A*2402, further demonstrating the specificity of the inhibitory interaction (Fig. 2E). Additionally, the expression of other receptors on NK clones was determined by cell surface staining with anti-KIR3DL2 (DX31), anti-ILT2, and anti-CD94 (Table I). Although some KIR3DL1+ NK clones expressed KIR3DL2, it is clear that the inhibition is due solely to interaction between HLA-A24 and KIR3DL1, because DX9+ NK cell clones are no longer inhibited in the presence of the anti-KIR3DL1 Ab. Taken together, these data show that KIR3DL1 recognition of HLA-A*2402 inhibits NK cell effector function.


Figure 2
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  		FIGURE 2. The interactions between KIR3DL1*001 and 005 and HLA-A*2402 are peptide specific. A and B, NK clones were stained with a panel of HLA-A*2402 tetramers folded with different viral epitope peptides. NK clones LTNP208-43 (3DL1*001) (A) and H002-2 (3DL1*005) (B) could interact with an A*2402 tetramer refolded with HIV-1 nef and p17 peptides. C–E, Killing of 221 cells expressing HLA-A*2402 and HLA-A*0201, pulsed or unpulsed, with HIV peptides by DX9+ NK clones LTNP208-43 (C) and H002-2 (D). E shows representative DX9– NK clone LTNP208-16. Gray bars show killing without DX9 mAb. Filled (black) bars show killing in the presence of isotype Ig control. Open bars show killing in the presence of DX9 mAb. The E:T ratio varied from 5:1 to10:1. These data are representative of two replicate experiments. wt, Wild type.

 
KIR3DL1 allotypes differ in their ability to bind HLA class I tetramers

Previous studies showed that heterogeneous levels of KIR3DL1 expression on NK and T cells reflect KIR3DL1 gene polymorphism (16). In this study we compared the binding of four different KIR3DL1 allotypes to our panel of HLA class I tetramers by using Baf3 or Jurkat cell lines transfected with the 3DL1*001, 3DL1*005, 3DL1*007, and 3DL1*01502 alleles (Table II). The levels of KIR3DL1 allotype expression on the transfected cell lines were comparable (Fig. 1, C and D, and data not shown).


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  		Table II. HLA class I tetramers refolded with various antigenic peptides were tested for binding to different KIR3DL1 transfected cell lines

 
The four KIR3DL1 allotypes exhibited three different patterns of tetramer binding (Table II). The 3DL1*001 transfectant cell line bound the A24 p17, A24 nef, and A24 CMV tetramers, but not the A24 D2 tetramer or any HLA-B tetramers. In contrast, the 3DL1*005 transfectant cell line bound to A24 p17, A24 nef (Fig. 1E and data not shown), and the two B57 tetramers (Fig. 1F and data not shown). Only the A24 nef tetramer bound to the 3DL1*007 and 3DL1*1502 transfectant cell lines. All of the positive reactions were with HLA allotypes having the Bw4 motif; no binding was detected with the HLA-B7, B8, and B*3501 tetramers with the alternative Bw6 motif. These data show first that KIR3DL1 allotypes can have different specificities of HLA binding and second that binding can depend upon the bound peptide as well as the HLA class I allotype. Consequently, the potential variability in KIR3DL1 recognition of HLA class I is much greater than previously appreciated, which clearly warrants further studies to dissect the pattern of HLA class I and peptide recognition for all common KIR3DL1 allotypes.

Structural models for the distinctive HLA class I specificity of KIR3DL1*005

The tetramer binding studies indicate that 3DL1*005 has a broader specificity for HLA class I than 3DL1*001, 007, and 1502, which includes both Bw4+ HLA-A and -B allotypes. Another distinguishing feature of 3DL1*005 is that it combines low cell surface expression with a high inhibitory capacity (20). From amino acid sequence comparisons, the structural basis for these functional differences appears to be two substitutions, serine for proline at position 182 in the D1 domain and leucine for tryptophan at position 183 in the D0 domain. Mutagenesis experiments (21) are consistent with a model in which the D1 and D2 domains of KIR3DL1 interact with HLA class I in a similar manner to that seen in the crystallographic structure of the KIR2DL1-HLA-Cw4 complex (22). Mutagenesis has also shown that the substitution of serine for leucine at position 182 decreases cell surface expression of KIR3DL1 (23).

Computer modeling of the KIR3DL1 structure (24) indicates that residue 283 is located in the hydrophobic core of the interface between the D1 and D2 domains. Consequently, the substitution of leucine for tryptophan at position 283 in 3DL1*005 is likely to change the relative orientation of the D1 and D2 domains. A computer-generated model of 3DL1*005 bound to B*5703 was made from the crystallographic structure of B*5703 bound to the KAF peptide and the structure of the KIR2DL1-HLA-Cw4 complex (Fig. 3A). In this model, the elbow surface of D1-D2 domains interacts with a region that includes the Bw4 epitope and the C-terminal part of the bound peptide. Two features can be identified that could contribute to the specificity of the 3DL1*005-B*5703 interaction. One is that changes in the orientation of D1 and D2 caused by leucine 283 alters the elbow surface to favor interaction with B*5703. The other is that the unusual central bulge of the 11-mer KAF peptide when bound to B*5703 (19) favors binding to the A'B loop of the D1 domain of 3DL1*005, providing additional interactions that could increase the binding affinity. Further study is needed to determine the contribution of these two potential mechanisms. Crystal structures for A*2402 (25) and B*5101 (24), a well-characterized ligand for KIR3DL1 (24), are similar in both the C-terminal part of the bound peptide and the {alpha}1 domain helix (Fig. 3B). Thus, the A*2402 structure is compatible with it being a ligand for KIR3DL1, as we have demonstrated.


Figure 3
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  		FIGURE 3. Computer models of the interaction of KIR3DL1 with peptide HLA class I complexes. A, Model of the bulged-out region of the 11-residue peptide in the B*5703–3DL1 complex. The B*5703 sequence is superimposed onto the structure of the KIR2DL1-HLA-Cw4 complex (19 22 ). Yellow, KIR2DL1 (modeling for KIR3DL1); dark blue, B*5703; white, bound peptide. The A'B loop of the KIR (red dotted circle) is close enough to interact with the bulged-out region of the 11-residue peptide (green dotted circle) bound to B*5703. B, The three-dimensional structural of A*2402 is compatible with KIR interaction. The structure in the Bw4 epitope region of A*2402 is compared with the corresponding region of B*5101, a known KIR3DL1 ligand. Residues 77–83, comprising the Bw4 motif, are indicated by the dotted circle. The bound peptides of A*2402 and B*5101 are shown in pink and dark blue, respectively. Because the structures of the two molecules are sufficiently similar, A*2402 is predicted to bind KIR3DL1 in a manner like that of B*5101.

 
Concluding remarks

This study examined the direct interaction of soluble tetrameric complexes of a defined peptide and HLA class I allotype with cells expressing four KIR3DL1 allotypes. Three of four HLA-A*2402 tetramers bound to one or more KIR3DL1 allotypes, indicating that this common Bw4+ HLA-A allotype is probably an important KIR3DL1 ligand. The four KIR3DL1 allotypes exhibited three different specificities for the four A*2402 tetramers, showing that the binding is dependent upon the KIR3DL1 allele and the bound peptide as well as the HLA class I allotype.

Such molecular heterogeneity implies that KIR3DL1 allotypes will be differentially inhibited by HLA-A*2402, as has been reported for B*5101, B*2705, and B*5801 (20, 26). Of the six Bw4+ tetramers tested, four bound 3DL1*005, three bound 3DL1*001, and only one bound 3DL1*007 and 3DL1*1502. If this small sample of pathogen-derived peptides extends to self-peptides, then the proportion of Bw4+ HLA class I molecules at the cell surface that actually serve as inhibitory ligands will vary with the KIR3DL1 allotype. The number of KIR3DL1 allotypes and the differences in their specificity for Bw4+ peptide-HLA class I complexes can readily explain why KIR3DL1+ NK cells from some donors are susceptible to inhibition by Bw4+ HLA-A (9) whereas others are not (10).

KIR3DS1 is an activating receptor with ligand-binding extracellular domains similar to those of KIR3DL1. The combination of KIR3DS1 and an HLA-B allotype with I80 was associated with delayed progression to AIDS in HIV-1 infection (27). Although the activating (KIR2DS1) and inhibitory (KIR2DL1) forms of KIR2D recognize a similar repertoire of peptides bound to HLA-Cw4 (28), similar studies have not been performed for KIR3DS1. Our results demonstrate that KIR3DL1 allotypes interact with HLA-A24 and HLA-B57 bound to HIV-1 peptides in an allele-specific manner. This raises two possibilities: 1) KIR3DS1 has its own unique preferences for HLA-peptide complexes; and 2) KIR3DL1 polymorphism might also influence disease progression in HIV-1 infected individuals.


   Acknowledgments
 
We are very grateful to the donors who gave blood for this study. We also thank Laura Quigley for providing KIR3DL1 transfected Jurkat cell lines.


   Disclosures
Top
 Abstract
 Introduction
 Materials and Methods
 Results and Discussion
 Disclosures
References
 
The authors have no financial conflict of interest.


   Footnotes
 
The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked advertisement in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

1 This work was funded by the Medical Research Council, United Kingdom and in part with federal funds under the Intramural Research Program of the National Cancer Institute, National Institutes of Health under Contract N01-CO-12400. H.T. was funded by the Royal Thai Government. Back

2 The content of this publication does not necessarily reflect the views or policies of the Department of Health and Human Services, nor does mention of trade names, commercial products, or organizations imply endorsements by the U.S. government. Back

3 T.D. and S.R.-J. contributed equally to this work. Back

4 Address correspondence and reprint requests to Dr. Tao Dong and Dr. Sarah Rowland-Jones, Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford OX3 9DS, United Kingdom. E-mail addresses: TDong{at}hammer.imm.ox.ac.uk and sarah.rowland-jones{at}ndm.ox.ac.uk Back

5 Abbreviations used in this paper: KIR, killer Ig-like receptor; LTNP, long-term nonprogressor; rh, recombinant human. Back

Received for publication May 19, 2006. Accepted for publication October 17, 2006.


   References
Top
 Abstract
 Introduction
 Materials and Methods
 Results and Discussion
 Disclosures
 References
 

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