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Logo of nihpaAbout Author manuscriptsSubmit a manuscriptHHS Public Access; Author Manuscript; Accepted for publication in peer reviewed journal;
J Immunol. Author manuscript; available in PMC 2013 September 19.
Published in final edited form as:
PMCID: PMC3777411

HLA-F complex without peptide binds to MHC class I protein in the open conformer form1


HLA-F has very low levels of polymorphism in humans and is highly conserved among primates suggesting a conserved function in the immune response. In this study we probed the structure of HLA-F on the surface of B-LCLs and activated lymphocytes by direct measurement of peptide binding of native HLA-F. Our findings suggested that HLA-F is expressed independently of bound peptide, at least with respect to peptide complexity profiles similar to those of either HLA-E or classical MHC-I. As a further probe of native HLA-F structure, we used a number of complementary approaches to explore the interactions of HLA-F with other molecules, at the cell surface, intracellularly, and in direct physical biochemical measurements. This analysis demonstrated that HLA-F surface expression was coincident with MHC-I heavy chain (HC) expression and was down regulated upon perturbation of MHC-I HC structure. It was further possible to directly demonstrate that MHC-I would only interact with HLA-F when in the form of open conformer free of peptide and not as trimeric complex. This interaction was directly observed by co-immunoprecipitation and by surface plasmon resonance and indirectly on the surface of cells through coincident tetramer and MHC-I HC co-localization. Together these data suggest that HLA-F is expressed independent of peptide and that a physical interaction specific to MHC-I HC plays a role in the function of MHC-I HC expression in activated lymphocytes.

Keywords: MHC-I open conformers, HLA-F, human, surface plasmon resonance


In the human system, MHC class I proteins comprise a group of molecules that perform a variety of functions, extending from the classical antigen presenting molecules HLA-A, -B, and -C to distantly related proteins including MHC class I-related chain A (MICA) that resides in the MHC and interacts with the activating immune receptor NKG2D (1-4). Classical MHC class I are expressed as trimeric complexes that consist of heavy chain (HC), β2-microglobulin (β2m) and peptide, usually from 8-10 amino acids in length, embedded in the polymorphic binding groove of the HC. Bound peptides are derived from intracellular proteins that have been cleaved by the proteosome and other cytoplasmic peptidases, and transported into the endoplasmic reticulum (ER), usually by the transporters associated with antigen processing (TAP). In the ER, peptides are loaded onto MHC class I via an assembly complex and the trimeric complex is subsequently expressed on the cell surface (5, 6).

While a large majority of studies have focused on MHC class I complexes as the structural component, MHC class I are also expressed on proliferating lymphoid cells as a stable pool of MHC-I HC (7). These HC are expressed devoid of peptide and/or β2m and appear to be derived from fully mature MHC-I molecules rather than arising from protein misfolding (8, 9). They were originally detected using monoclonal antibodies that do not react with MHC-I complex, but do react with denatured MHC-I. The reactivities of most of these antibodies have been mapped to epitopes located between residues 55-87 in the α1 domain, covering sequences that are directly interacting with peptide in the complex structure and thus not available as antibody epitopes when peptide is bound. While functional studies of MHC-I molecules have understandably focused on MHC-I complex structures for several decades, recent work has begun to bring to light potential alternative functions for MHC-I HC. These so-called ‘open conformers’ have been implicated in a number of interactions with other receptors both in trans and in cis, including the formation of homodimers, on the cell surface (10).

Also resident in the MHC, and more recently diverged from the classical MHC-I than is MICA, are the ‘non-classical’ MHC-I molecules HLA-E, HLA-F and HLA-G. HLA-G has been studied extensively after it was identified as being expressed exclusively in the placental trophoblast in alternative protein forms, each form derived from alternative splicing of the primary mRNA, (11-13). A function for HLA-G as an inhibitor of NK activity, through interaction with ILT2 or ILT4 NK receptors has been suggested (14, 15). HLA-E function has been elucidated through its interaction with CD94/NKG2 receptors (16). The interaction with such CD94/NKG2 heterodimers can augment, inhibit or have no effect on NK cell-mediated cytotoxicity and cytokine production (17). Surface expression of HLA-E requires nonamer peptides, including those derivative from the signal sequences of other HLA class I molecules including HLA-A, -B, -C, and -G but not HLA-F (18) and also forms stable complexes with limited numbers of structurally unrelated peptides (19). Similar to MHC-I, both HLA-G and HLA-E are expressed in complex forms with bound peptide, but are also expressed as HC under certain circumstances. Indeed, HLA-G free heavy chain is expressed on the surface of trophoblasts and may modulate the efficiency of the CD85J/LIR-1 and HLA-G interaction (20). An antibody specific for HLA-E free heavy chain has been described and expression has been observed on activated lymphocytes and B-LCLs, although no function has yet been suggested (18, 21).

The third nonclassical molecule HLA-F has been less studied and neither its native structure nor function is known. Evidence of a physical association of HLA-F and TAP was reported (22), but surface expression was not reduced in TAP negative mutant lines (23). Unlike classical MHC class I, the HLA-F cytoplasmic tail may be required for export from the endoplasmic reticulum implicating a function for HLA-F independent of peptide-loading in the ER (24). Our work using new monoclonal antibodies reactive with HLA-F showed that while HLA-F was not surface expressed on most cell lines that contained intracellular protein, HLA-F was expressed on the surface of B and some monocyte cell lines and in vivo on extravillous trophoblasts that had invaded the maternal decidua (12, 23). Further examination of peripheral blood lymphocytes demonstrated intracellular HLA-F protein expression in all resting lymphocyte subsets, including B, T, NK, and monocyte cells, and HLA-F surface expression was upregulated upon activation for all cell types (25).

HLA-F has very low levels of polymorphism in humans and is highly conserved among primates (26, 27) which, combined with the structural similarities of HLA-F and other HLA class I, suggest a conserved function in the immune response possibly along broadly similar lines to those of HLA-E or -G. In this study we explored the structure of HLA-F on the surface of B-LCLs and activated lymphocytes by testing for similarities in peptide binding between native HLA-F and classical class I and its closer cousins HLA-E and HLA-G, which bind relatively restricted sets of peptides (18, 28). As a further probe of native HLA-F structure, we used a number of complementary approaches to explore the interactions of HLA-F with other molecules, at the cell surface, intracellularly, and in direct physical biochemical interactions.

Materials and Methods

Cells and cell culture

Cell lines NKL, OSP2, Daudi, MT2, Jurkat, Hut78, THP-1, Supt1, H9, Molt3, U937 were all obtained from America Type Culture Collection (Manassas, VA) and cultured according to the product information sheet provided. B-LCL cell lines (AMAI, BM9, BM15, Boleth, BSM, JY, BSM, Steinlin) were previously collected and studied by the International Histocompatibility Workshops & Conference and obtained directly from the International Histocompatibility Working Group (IHWG) in Seattle (29). LCL 721.221 was obtained from the ATCC and maintained in RPMI 1640 medium supplemented with 10% v/v FCS, 2 mM L-glutamine and 1 mM sodium pyruvate. Other B-LCL cell lines were grown in a culture medium of RPMI supplemented with 10% FBS, 100U/ml penicillin and 100U/mL streptomycin.


MHC class I monoclonal antibodies used in this study included W6/32 – specific for pan HLA class I MHC complex; HCA2 – specific for a subset of allelic HLA class I heavy chains (30); LA45 specific for a different subset of HLA class I heavy chains (31); 3D12 – specific for HLA-E complex and 7G3 – specific for HLA-E heavy chain without peptide (18); 3D11 and 4A11 – HLA-F specific mAbs previously described (23) and 4B4 – specific for intracellular HLA-F as described in this study; 16G1 – reactive with soluble HLA-G COOH terminus (32) and used as a control antibody for IgG1 isotype mAbs.

Immunofluorescence staining and FACS analysis

Cell surface expression of proteins was measured by indirect immunofluorescence staining as previously described (18). Briefly, cells were preincubated with saturating concentration of mAb followed by washing and labeling with FITC-conjugated goat F(ab')2 anti-mouse Ig (BioSource, Camarillo, CA). Samples were analyzed on a FACScan cytometer (Becton Dickinson, Mountain View, CA) and analysis was performed using FlowJo (Tree Star, Inc. Ashland, OR). For tetramer staining, 1μg of refolded H2-Db (control) or HLA-F monomer was incubated with 1.5μg of R-PE conjugated streptavidin (SAPE, Invitrogen, Carlsbad USA) per reaction at room temperature for 30 min. H2-Db and HLA-F tetramers were synthesized in vitro using previously described protocols and constructs (23, 33, 34). Briefly, recombinant MHC class-I heavy chain and beta2-microblobulin were expressed in E. coli and purified from the inclusion body. The peptide/MHC complex (pMHC) was refolded by dilution of the proteins, and subsequently purified by gel-filtration. The complex was biotinylated using BirA enzyme (Affinity, LLC, Denver, CO) and the biotinylated complex was re-purified by gel filtration. Tetramer was formed by mixing biotinylated pMHC complex with Alexa Fluor 647-conjugated Streptavidin (Invitrogen) at 4:1 ratio.

Acid treatment of cells was performed by resuspension of ~2.0×106 cells in 1 ml RPMI +10%FBS at pH 2.2 for 90 sec, followed by the addition of 13 ml of RPMI+10%FBS at pH 7.4. The cells were spun down and washed 2 times, then resusupended in cold FACS buffer (PBS +2% BSA, 0.1% NaN3) for staining. CD3 stimulation was performed using solid phase bound anti-CD3 mAb UCHT1 (Biolegend, San Diego, CA). 1.0×105 cells were incubated for 20 hours in separate wells of a 96 flat well plate coated with anti-CD3 or isotype control antibody. After 20 hours the cells were washed twice in cold FACS buffer and stained with the appropriate reagents. N-ethyl maleimide (NEM) treatment was performed by culture of ~1.0×105 cells in culture medium +100μM NEM for 20 mins (35), with or without the presence of mAb HCA2 or isotype control. The cells were spun down and washed an additional 2 times, then resusupended in FACS buffer for staining.

Measurement of peptides bound to HLA-F

HLA-F was isolated from the detergent lysate of PLH cells as described previously (18), using three different HLA-F specific immunoaffinity columns constructed with each of 3D11, 4A11, and 4B4, an HLA-E specific 3D12 column, and a W6/32 column. A total of three separate isolations were carried out using different affinity column combinations connected in series: (1) 4A11, 4B4 and 3D12; (2) 3D12, 3D11, and 4B4; and (3) 4A11, 4B4, 3D12, and W632. MHC complexes were eluted with 2N acetic acid, and peptides were recovered in 2.5 N acetic acid by ultrafiltration using a Microcon filter with a 10,000 M.W. cutoff (Millipore), and concentrated by vacuum centrifugation. Eluted peptides were subjected to tandem mass spectrometry (MS/MS) carried out by the FHCRC Proteomics Resource.

Mass Spectrometry

The LC-MS setup consisted of a trap column (100 μm × 2 cm) made from an IntegraFrit (New Objective, Woburn, MA) packed with Magic C18AQ resin (5 μm, 200Å particles; Michrom Bioresources, Auburn, CA) followed by an analytical column (75 μm × 25 cm) made from a PicoFrit (New Objective) packed with Magic C18AQ resin (5-μm, 100Å resin; Michrom Bioresources). The columns were connected in-line to an Eksigent 1D+ nano-HPLC (Eksigent Technologies, Dublin, CA) in a vented column configuration to allow fast sample loading (36). The HPLC column setup was coupled to an LTQ-Orbitrap (Thermo Fisher Scientific, Waltham, MA) hybrid mass spectrometer using the nano-electrospray source. The MHC class peptide samples were analyzed by LC-MS/MS using a 60-minute gradient from 2% to 35% acetonitrile with 0.1% formic acid (against water with 0.1% formic acid) at a flow rate of 300 nL/minute. A spray voltage of 2.25 kV was applied to the nanospray tip. The mass spectrometer experiment consisted of a full MS scan in the Orbitrap (AGC target value 1e6, resolution 60K, 1 microscan, and injection time 500 ms) followed by up to 5 MS/MS spectra acquisitions in the linear ion trap. The 5 most intense ions from the Fourier-transform (FT) full MS scan were selected for fragmentation in the linear ion trap by collision-induced dissociation with a normalized collision energy of 35% (isolation width of 2 m/z, target value of 1e4, and injection time, 100 ms). Selected ions were dynamically excluded for 15 seconds with a list size of 100, a repeat count of 1, and repeat duration of 15 sec. The dynamic exclusion mass width around each precursor ion was -0.55 m/z to +1.55 m/z. Charge state screening was used allowing any ions with an identified charge state (+1 or higher) to be selected for MS/MS.

Database Identification

The LC-MS/MS data files were converted to the mzXML format and subsequently searched using the database search program X!Tandem (37) contained in the CPAS analysis system (38). The default scoring algorithm in X!Tandem was replaced with the k-score scoring algorithm contained in CPAS (39). The data was searched against the IPI human database (v. 3.59) where 3 trypsin (porcine and bovine) sequences have been added (80131 total sequences). The database search was performed with no enzyme specificity and a maximum peptide length of 50 amino acids. The database search results were analyzed using PeptideProphet (40) and also manually filtered for likely MHC class peptides using the following criteria: mass accuracy < 10ppm, peptide length < 13 amino acids, X!Tandem expectation value < 2. The purpose of the filtering criteria was to identify candidate peptide MS/MS scans that were then manually inspected to determine if the MS/MS fragment ions matched the identified peptide sequence.

Immunoprecipitation and Western blotting

Immunoprecipitation was performed as described (18, 23) with modifications. Briefly, 1 × 109 PLH cells were lysed in 1% NP-40, 140 mM NaCl, 200 mM PMSF, 10 mg/ml papstalin, 14 mg/ml aprotinin in 10 mM Tris pH 7.8, precleaned by control antibody, equally divided into three parts. Each part was subjected to a sequential immunoprecipitation by HLA-F specific antibody coupled Sepharose 4B in three distinct sequences: (i) 4B4, 3D11 then 4A11; (ii) 4A11, 3D11 then 4B4; (iii) 3D11, 4A11 then 4B4. After extensive washing with lysis buffer, antigen was eluted by 0.05 M diethylamine pH 11.2, neutralized by 1M Tris pH 6.8, separated on a 10% Tris- Glycine gel (Novex, San Diego, CA) and electroblotted as described (18). HLA protein was detected by mAb followed by horseradish peroxidase-labeled goat anti-mouse Ig's (BioSource) at 1:5,000 dilution and finally with an enhanced chemiluminescence system (ECL. Amersham, Arlington Heights, IL). Densitometry was performed by scanning the X-ray film with a Sharp JX-320 scanner and quantified with Image Quant 5.0 software (University of Virginia ITC-Academic Computing Health Sciences).

Expression and purification of recombinant HLA proteins

Construction of plasmid, protein expression and refolding was described previously for both HLA-E and HLA-F (21, 23). DNA sequences coding for a glycine-serine linker and a BirA substrate peptide were as described (41). β2-microglobulin (β2m) in pHN1+ was kindly provided by D. C. Wiley (Harvard University, Cambridge, MA) and expressed in E. coli strain XA90.

Both heavy- and light-chain (β2m) inclusion bodies were isolated from cell pellets, washed repeatedly in detergent and solubilized in 8 M urea, 25 mM MES pH 6.0, 10 mM EDTA and 0.1 mM DTT (solubilization buffer) as described (42). Refolding was accomplished using a variation of the method of O'Callaghan and coworkers (43) by dilution of 12 mg of β2m (in 2 ml of solubilization buffer) into 500 ml of 400 mM L-arginine, 100 mM Tris pH 8.0, 2 mM EDTA, 0.5 mM oxidized glutathione, 5 mM reduced glutathione and 0.2 mM PMSF (refolding buffer). After 1h at 4°C, 18.5 mg of heavy-chain (in 30 ml of solubilization buffer) and 17 mg of peptide (in DMSO at 1.7 mg/ml) were added (or no peptide in the cases of HLA-E open conformer refoldings). The initial molar ratio of heavy-chain: β2m:peptide was 1:2:30 respectively. The refolding mixture was pulsed three times with additional heavy-chain at 12 hr intervals. After 48 h, the refolding mixture was concentrated initially on a stir cell (Amicon, Beverly, MA) and subsequently in a 10 kDa cutoff Centriprep ultrafiltration unit (Amicon). Refolded HLA-E or HLA-F was separated from aggregates and buffer exchanged into 50 mM Pipes, pH 7.0, 150 mM NaCl, 1mM EDTA and 0.02% NaN3 on a Superdex 200 prep-grade size-exclusion chromatography column (Amersham/Pharmacia, NJ). Properly refolded complexes were purified by size exclusion chromatography (SEC) to yield protein >95% pure (21).

HLA-E complex was produced as above with two different peptides: VMAPRTLVL, from HLA-A2 and VMAPRTLFL, from HLA-G. HLA-A2 and HLA-A3 heavy chains were refolded with β2m in the presence of CMV pp65 (495-503) (NLVPMVATV) peptide and HIV Nef (73-82) (QVPLRPMTYK) peptide respectively (42). Refolding heavy chains with light chain in the absence of peptide failed to produce a well defined peak as assessed by FPLC for all MHC class I attempted with the exceptions of HLA-E and HLA-F. Instead, for HLA-A2 and -A3 the generation of putative empty, or peptide free, complexes was carried out using minor modifications of the method employing conditional ligands in MHC class I complexes (44). The optimal conditional ligands used for refolding A2 and A3 heavy chains with β2m were KILGFVFJV and RIYRJGATR respectively where J indicates the modified amino acid that is light sensitive/labile (45). Putative empty complexes were generated after a 5 min UV exposure and purified on an analytical Superdex 200 SEC column (Amersham Biosciences) in HBS-EP buffer (10 mM HEPES [pH 7.4], 150 mM NaCl, 3 mM EDTA, 0.005% v/v P-20 surfactant [Biacore AB, Uppsala, Sweden]). The proteins were injected on the SPR machine immediately after UV exposure and purification.

All the other proteins used for SPR binding studies were repurified by SEC in HBS-EP buffer within 24 h of use. All purified proteins showed the appropriate disulfide bonding state by comparative reducing/nonreducing SDS-PAGE and were monomeric by analytical SEC. Protein concentrations were determined by a bicinchoninic acid protein assay (Pierce; Rockford, IL).

Biosensor analysis of the interactions between HLA-F and heavy chains

SPR measurements were conducted in HBS-EP buffer using a Biacore 3000 system (Biacore AB). For SPR binding analysis of HLA-F/β2m complex, 10 mg/ml HLA-F/β2m in 10 mM sodium acetate (pH 4.5) and 10 mg/ml HLA-E/β2m (without peptide) in 10 mM sodium acetate (pH 5.0) were covalently immobilized on a CM5 research-grade sensor chip (Biacore AB) by standard amine coupling chemistry. The reference flow cell was left blank. Immobilization of 1700 response units (RU) for F/β2m and 2200 RU for E/β2m (without peptide) resulted in optimal responses for subsequent analyses. Injections of 85 ml containing various concentrations of heavy chains and control solutions were carried at 20 ml/min followed by a dissociation phase in buffer. Raw sensorgrams were corrected by subtracting the reference flow cell response.


Peptide elution suggests native HLA-F is expressed as an empty MHC class I

Previous molecular modeling of HLA-F had suggested a structure similar to other MHC-I complexes with possibly a partially open-ended peptide binding groove (46). However, an examination of the sequence of HLA-F had suggested fundamental structural differences from other MHC class I since 5 of 10 residues conserved in both human and mouse MHC class I and pointing into the antigen recognition site were substantially altered in HLA-F (47). Also, the altered cytoplasmic domain of HLA-F may direct surface expression through pathways independent of loading with peptides in the ER (24). In these respects, HLA-F is unique among MHC class I heavy chains indicating HLA-F might also be unique with regard to peptide binding characteristics.

In order to examine HLA-F for peptide binding we utilized B-LCLs since they express HLA-F on the cell surface (23). LCL PLH was chosen as we had measured surface levels of HLA-F that were highest among several LCLs examined. These cells also express HLA-E and HLA-A, B, C class I abundantly, providing convenient and important controls for the experimental variables. HLA-E and MHC-I also provided examples of two distinct ranges of peptide binding of MHC class I where HLA-E had been shown to bind small numbers of highly specific peptides that are derived from the available HLA class I expressed by the LCL being examined (18), while MHC-I as assessed by pan-MHC-I antibody W6/32, will contain hundreds to thousands of distinct peptides with peptide motifs predicted from those HLA class I expressed in the LCL (48).

In the first experiment, lysate from 2×1010 cells was passed through columns constructed with antibodies 4A11 (anti-HLA-F) and 4B4 (anti-HLA-F intracellular form) arranged in series. After acid treatment and elution, samples were analyzed by mass spectrometry to characterize eluted peptides. In order to confirm these results we repeated these experiments two additional times using different sequential antibody columns and with the addition of the anti-HLA-F reagent 3D11 (anti-HLA-F all forms), not tested in the first experiment. Positive controls were provided by the addition of W6/32 at the end of the third series, and 3D12 (anti-HLA-E) in the second and third series. Sequential column arrangements and the number of specific peptides identified in each experiment are reported in Table 1.

Table 1
Peptide elution summary.

After filtering out nonspecific results from complex mixtures of peptides, 789 putative peptides eluted from the W6/32 column were identified (Table 1). Given the HLA type of PLH as A*0301, B*4701, Cw*0602, these peptides were analyzed using the HLA Peptide Binding Predictions web site which provides access to software that ranks potential 8-mer, 9-mer, or 10-mer peptides based on a predicted half-time of dissociation to HLA class I molecules (49). Of the 789 putative peptides eluted from the W6/32 column 265 had the motif of for HLA-A*0301 and 98 showed the HLA-Cw*0602 motif. Several of these peptides were confirmed by MS/MS analysis. The motif for B*4701 was not available for comparison. In two experiments we were able to unambiguously identify the expected peptides bound to HLA-E, including nonamers derived from HLA-A*0301 and B*4701 both expressed on the target LCL (Table 2). In addition, 6 peptides not previously reported as binding to HLA-E, some of which have motifs substantially distinct from the class I derived nonamers, were identified independently from both separate anti-HLA-E columns. Six of these peptides were confirmed as binding to HLA-E through in vitro refolding and three of these through subsequent peptide elution analysis (data not shown).

Table 2
Peptides verified by intersection and MS/MS

Using the same filtering criteria, from 3 to 53 peptides were identified from the repeat runs of the total of six anti-F columns, on the order of the numbers identified from the HLA-E columns. However, no peptides with a molar abundance relative to heavy chain within 20-fold of those obtained for HLA-E were found from any of the anti-HLA-F columns (Fig. 1). In addition, none of the peptides identified in anti-HLA-F antibody columns were identical between different runs, neither between antibodies in the same serial isolation nor between the same antibody from different isolations (Table 1). The results for HLA-E and pan MHC indicate a sound technical approach, supporting these negative results from the anti-HLA-F columns analyzed within the same experiments.

Figure 1
Peptide elution from MHC class I. MS elution times are charted against relative abundance for each of three MHC class I antibodies W6/32 (pan class I), 4B4 (anti-HLA-F), and 3D12 (anti-HLA-E) as indicated. The relative intensity of the highest peak within ...

MHC class I heavy chain (MHCI-HC) modulates HLA-F surface expression

Since it was possible to refold HLA-F with β2m we initially attempted to identify a receptor for HLA-F by analyzing differential patterns of HLA-F tetramer binding to a diverse panel of cell lines followed by attempts to generate antibodies that would replicate these patterns and block tetramer binding. Despite repeated attempts, we were unable to obtain any antibodies producing the expected binding patterns. At the same time, we were investigating blocking of tetramer using existing antibodies and observed a potential interaction between MHCI-HC antibodies and HLA-F. Reactivities of two of these antibodies, HCA2 and LA45 have been well characterized with HCA2 reacting preferentially with a subset of HLA-A locus heavy chains (30) while the LA45 epitope includes about half the alleles of both HLA-A and -B loci heavy chains (31). Our initial experiments indicated that HCA2 or LA45 antibody binding interfered with HLA-F antibody binding since prior addition of either antibody resulted in reduced binding of the anti-HLA-F reagents (Fig. 2A). However, neither HC antibody blocked the levels of F tetramer binding and none of the anti-HLA-F reagents interfered with HCA2 or LA45 binding (Fig. 2A). The effect of HC antibodies was specific since LCLs that expressed different combinations of HCA2 and LA45 epitopes affected HLA-F detection on these cells in accord with the presence or absence of those epitopes (Fig. 2B). The observation that 3D11 did not block HCA2 binding and that HCA2 did not interfere with F-tetramer binding suggested the possibility that HCA2 and LA45 were instead down modulating HLA-F or changing surface levels through other means such as HLA-F proteolytic release.

Figure 2
HLA-F surface expression is downregulated in response to MHC-I heavy chain mAb. (A) B-LCL SAVC cells without (solid lines) and following addition of MHC-I heavy chain mAbs HCA2, LA45, or anti-HLA-F 3D11 as indicated within brackets (dotted lines). The ...

To test for proteolytic release of HLA-F we examined supernatants for HLA-F protein after treatment with HCA2 incubation. No HLA-F protein was detected in supernatants of cells treated with HCA2 as assessed with an HLA-F specific ELISA suggesting the alternative possibility that HLA-F is internalized in response to HC antibody. Accordingly, we repeated these experiments in the presence of 100 mM NEM, which inhibits transcytosis and endocytosis preventing the uptake of surface proteins (50). While HCA2 substantially down modulated HLA-F expression on B-LCL AMAI, the same experimental conditions resulted in no change of HLA-F levels when NEM was present at appropriate concentrations (Fig. 2C). These results further suggested that HLA-F was down-modulated upon the addition of HCA2 rather than HCA2 blocking 3D11 binding.

Increased HCA2 binding on cells correlates with increased HLA-F tetramer binding

Mild acid treatment of resting cells is known to destabilize class I MHC complexes on the cell surface, causing peptide and β2m to dissociate generating MHC-I HC (51). We thus reasoned that if HLA-F is interacting with MHC-I HC, specific binding of F tetramer should increase coincident with increased levels of MHC-I HC. We first examined cells that are negative for HLA-F expression and for MHC-I HC including the T cell lymphoma cell lines Jurkat, Molt-3, HUT-78 and H9, and monomyelocytic cell line U937 as well as class I bare, β2m deficient Burkitts lymphoma cell line Daudi. All of these cells were analyzed for HCA2 binding and HLA-F tetramer binding before and after mild acid treatment (Fig. 3A and B). On untreated cells, no HLA-F tetramer binding was observed, while after mild acid treatment all cell lines except class I bare cell line Daudi became both HCA2 reactive and bound HLA-F tetramer in a manner closely associated with the intensity of HCA2 staining (Fig. 3B). Control HLA-A*0201 tetramer did not bind to either untreated or acid treated cells (not shown).

Figure 3
Acid induced free class I heavy chain expression facilitates HLA-F tetramer binding. HLA-F negative and free Class I Heavy Chain negative T cell lines Jurkat, Molt-3, HUT78, H9 and monocytic cell line U937, as well as Class I bare cell line Daudi were ...

A second measure of coincidence between HCA2 expression and HLA-F tetramer binding was taken by activation of cell line OSP2, which can be activated upon treatment with anti-CD3 antibody. Consistent with the results obtained after acid treatment, upregulation of HCA2 was observed and was found coincident with increased F tetramer binding (Fig. 3C). Essentially similar results were obtained with a T cell clone after activation and expansion and activated T cell clone 1C7-7 stained with both HCA2 and HLA-F tetramer showed coincident expression of the two signals as did H9 cells after acid treatment (Fig. 3D). These latter experiments showed that while HCA2 is not always coincident with HLA-F antibodies or with F tetramer, the latter are always found overlapping with HC.

Co-immunoprecipitation of HLA-F with MHCI-HC including HLA-E

If MHC-I HC does bind directly to HLA-F it might be possible to isolate both proteins as part of a complex depending on the strength of the interactions. In order to test this possibility further, we performed sequential immunoprecipitations (IPs) of HLA-F from LCL PLH with three anti-F reagents (Fig. 4). Earlier experiments had not detected any other MHC-I protein coprecipitating with HLA-F but were limited in their experimentation with different detergents for lysis and had not included all available antibodies reactive with HLA-F (23). One antibody we isolated, 4B4, does not react with surface HLA-F on any cell lines tested but does IP HLA-F from all of the same cell lines. In addition, antibodies 3D11 and 4A11 also have distinct reactivities at specific times after activation of lymphocytes (25) indicating each of the three anti-HLA-F antibodies react with distinct forms of HLA-F.

Figure 4
MHCI-HC, including HLA-E HC, co-precipitate with HLA-F. Cells were lysed directly in NP40 buffer containing freshly prepared 50 mM iodoacetamide. Three sets of sequential immunoprecipitations of total cell lysate from LCL PLH were carried out and separated ...

These considerations motivated experimentation with a variety of detergents and further testing of available anti-F reagents. In an experiment designed under conditions similar to the peptide isolations described above, we performed sequential IPs with antibodies 4B4, 3D11, and 4A11 in each of the three possible sequences followed by western analysis with anti HC antibodies. Representative results of these experiments are presented in Fig. 4. Three features of these results are noteworthy. First, within each of the HLA-F antibody IP series it was possible to co-precipitate HCA2 reactive proteins with antibody 4B4 regardless of the order in IP sequence. This IP product included HLA-F (Fig. 4, left) and three bands reactive with HCA2. Control experiments had shown that HLA-F is not reactive with HCA2 under the conditions used for western analysis (not shown). Of the three HCA2 reactive bands observed the lower HCA2 reactive band corresponds in size to soluble HLA class I and may be produced in cells as a result of proteolytic cleavage as described (52). Second, blotting of an identical IP with anti-HLA-E-HC antibody 7G3 showed the middle fainter band identified by HCA2 was in fact HLA-E (Fig. 4, right). A third feature is the higher molecular weight band reactive with 3D11 and found only in the 3D11 IP, and present despite that these gels were run under reducing conditions.

Direct measurement of HLA-F and MHC-I HC interactions

As an additional and more direct method for measuring HLA-F and MHC-I HC interactions we used label-free surface plasmon resonance (SPR) based technology for studying these biomolecular interactions in real time. Our hypothesis to this point was that HLA-F physically interacts with MHC-I HC but not with complex form. This was based on the coincidence of HLA-F and MHC-I HC in cell binding assays and modulation of HLA-F surface levels as described above. However, a direct measurement required producing heavy chain open conformer presumably without peptide in an homogeneous and reproducible manner. Because it was not possible in our hands to refold sufficient quantities of HLA-A2 or -A3 without peptide we took advantage of the method of conditional MHC ligands recently described to produce the appropriate empty class I molecules (44). This method was developed to allow for refolding of stable complex, which can then be UV treated to produce empty or at least peptide-receptive MHC molecules that can then be charged with a peptide of choice (45). After refolding HLA-A2 and -A3 with peptides that can form corresponding complexes but that can be cleaved upon UV irradiation, we were able to produce homogeneous preparations of putative empty MHC molecules after purification by size-exclusion chromatography. It is possible that a small fragment remains, depending on its affinity, after UV-treatment. However, considerable data on MHC-I peptide binding indicates that no peptides of 5 amino acids have been demonstrated to stabilize classical MHC-I, supporting the likelihood that our UV-treated complexes are indeed empty. But even if complexes do have some portion of peptide bound, when contrasted with peptide-bound complexes where there is little or no binding, the affinity for HLA-F is clearly markedly changed (Fig. 5). Further, these results are consistent with the HLA-E binding where we have direct evidence of empty HLA-E.

Figure 5
MHC class I heavy chain, but not complex, binds directly and specifically to HLA-F. Surface plasmon resonance binding sensograms were analyzed using surfaces coated with refolded F β2m on the left or with two channels simultaneously, containing ...

To examine direct binding we tested a surface coupled with HLA-F refolded with β2m. Since we were interested in distinguishing between MHC-I in complex with peptide versus empty MHC-I binding, we passed HLA-A2 refolded with conditional ligand before and after UV treatment over the HLA-F/β2m surface. HLA-A2 UV treated prooftein showed binding to the HLA-F/β2m surface and increasing amounts (2.5uM and 7.5 uM) of the HLA-A2 UV treated protein resulted in proportional increases in SPR signals (Fir. 5A, left). Further, No binding was observed when HLA-A2 was used before the UV treatment or when the HLA-A2 was refolded with conventional ligand. In order to demonstrate the specificity of the binding to HLA-F/β2m, a second surface coupled with HLA-EG2m was used and 2.5μM HLA-A2 after UV treatment was injected over both surfaces, resulting in significantly stronger binding to the HLA-F/β2m surface (Fig. 5A, right). The HLA-EG2m surface signal accounts for non-specific binding of HLA-A2 to the surface. Essentially similar results were obtained with HLA-A3 where signal from UV treated complex was measured with increasing protein amounts and no background binding to HLA-F was observed without UV treatment or when conventional peptide was used for refolding. Again, the binding was specific for HLA-F as evidenced by background levels of HLA-A3 binding to the empty HLA-E coated surface (Fig. 5B).

Motivated by the identification of HLA-E in co-immunoprecipitations described above, we extended these results to include a comparative binding of HLA-E refolded with and without peptide. Our prior work had shown that it was possible to refold sufficient quantities of HLA-E without peptide obviating the need for a similar conditional ligand strategy (21). Refolded forms of both allelic variants were available for analysis. When either allele was refolded with conventional nonamer peptides derived from either HLA-A2 or HLA-G signal sequences (18), binding was detected at background levels on either HLA-F or control HLA-E surfaces, whereas strong binding was evident when empty versions of either HLA-E allele were exposed to the HLA-F surface (Fig. 5C and D). The binding patterns of the HLA-EG and ER alleles were essentially similar at the level of analysis performed, and although binding of HLA-ER appears quantitatively stronger in the results shown, variation in protein preparation and purification prevent a quantitative comparison between experiments.


Our findings combined with previous data demonstrate that HLA-F is expressed independent of bound peptide, at least with respect to peptide complexity profiles similar to those of either HLA-E or classical MHC-I. In addition, we were able to demonstrate that not only was HLA-F surface expression coincident with MHC-I HC expression, but that HLA-F surface expression was down regulated upon perturbation of MHC-I HC structure. It was further possible to directly demonstrate that MHC-I would only interact with HLA-F in the form of open conformer probably free of peptide and not as peptide bound complex. This interaction was directly observed intracellularly through co-immunoprecipitation and surface plasmon resonance and indirectly on the surface of cells through coincident tetramer and MHC-I HC co-localization. Together these data suggest that HLA-F is expressed independent of peptide and that a physical interaction specific to MHC-I HC plays a role in the functional consequence of MHC-I HC expression in activated lymphocytes.

Although our results suggest that HLA-F is expressed as HC without peptide, immunoprecipitations using our panel of HLA-F specific antibodies do coprecipitate β2m in subequimolar amounts (23, 25). Based on this data and the differential coimmunoprecipitation experiments reported here (Fig. 4), it appears likely that more than one complex form of HLA-F is expressed, with a portion complexed with β2m, and some or all complexed with MHC-I HC. In total there is evidence of at least three different forms of HLA-F based on differential staining of surface HLA-F using antibodies 4A11 and 3D11 over the course of lymphocyte activation and the unique 4B4 binding pattern. In light of this, it is also possible that HLA-F may bind larger peptides, beyond the limits of our analysis of 13mers, or may be stabilized by interactions with proteins other than MHC class I or other biomolecules such as phospholipids similar to CD1d (53). Interestingly, the HLA-F protein is entirely dependent on its cytoplasmic tail for export from the ER and the HLA-F cytoplasmic sequence contains motifs that are overlapping with those of CD1d (24, 54).

It is possible to refold HLA-F with β2m without peptide which forms a stable structure that can be used in tetramer binding ((55) and Fig. 3). Open conformer MHC-I are relatively unstable in comparison but are up-regulated by cold treatment, while HLA-F is not, suggesting that there is likely a threshold of stability that MHC class I HC must reach to traffic to and remain on the cell surface. The possibility that HLA-F is required for the formation of the open conformer is raised considering their coincident surface expression and physical interaction. Since HLA-F is otherwise expressed intracellularly in resting lymphocytes it is also possible that the formation of MHC-I HC upon activation induces complex formation between HLA-F and MHC-I HC, which then signals transport to the surface.

When free HC antibodies bind to MHC-I HC on the cell surface, the conformation of the HC may be changed to more closely resemble MHC complex with peptide. Whether HLA-F recycles with MHC-I HC as suggested by internalization upon addition of HC antibodies would clearly add an important dimension to studies of the trafficking of MHC-I HC. As an interesting supplement, HLA-F does have a tyrosine based internalization motif (TSQA) similar to that proposed to regulate MHC-I endocytosis and intracellular trafficking, while HLA-C an HLA-G do not (56). This may be relevant to HLA-C and HLA-G cycling in trophoblast cells in light of the coincident expression of these molecules in conjunction with HLA-F in the placental environment (12). It is not known whether HLA-C is expressed as a free heavy chain in trophoblasts, but evidently HLA-G is (15, 20) and in tropohoblasts that have invaded the maternal decidua, HLA-F and HLA-G are co-expressed on the surface. It would be interesting to explore the idea that the lack of the internalization motif on HLA-C and HLA-G was directly related to their expression in the placental environment.

Our data do not address whether HLA-F interacts with all MHC-I HC since we were able to analyze only those MHC-I for which a conditional ligand was available to us (HLA-A2 and -A3) or that we were able to refold without peptide (HLA-E). Considering the extensive polymorphism of MHC class I, it is possible that HLA-F interacts with only a subset of MHC-I alleles or more generally stated that the affinity between HLA-F and different MHC-I alleles will differ substantially. Our analysis of the three MHC-I HC studied in this report was not carried out under conditions that allowed for precise quantitative measurement, however differences could be detected between HLA-A2 or HLA-A3 and HLA-E. While we do not have detail on the interaction points between HLA-F and MHC-I HC, a logical presumption from this work would be that they are restricted to regions exposed upon removal of peptide.

The reactivities of MHC-I HC specific mAbs has been mapped to epitopes formed by residues within positions 57-84 in the a1 domain that are specific to the open conformer (10). These residues are in contact with peptide or otherwise hidden in the peptide bound molecule but become exposed in the MHC-I HC conformer. HCA2 has been mapped to residues 77-84 probably ruling this segment out since HLA-F and HCA2 do not compete for binding to MHC-I, but a similar comparative analysis with other MHC-I HC specific antibodies could be useful in mapping the HLA-F contact residues. Further insight may come from comparative sequence analysis with HLA-F homologues expressed in other primates. For example, HLA-F homologues are found in macaques with as few as 10 amino acid differences in the α1 to α3 domains (26).

These findings leave open the possibility that HLA-F binds to a specific receptor(s) or even that HLA-F and MHC-I HC interactions can occur in trans between cells. Addressing the former possibility, while our immunoprecipitations with 3D11 and 4A11 did not co-precipitate equimolar amounts of MHC-I as did 4B4, it is unlikely that this evidence argues against an interaction of HLA-F and MHC-I HC on the surface. Subequimolar amounts were detected with both antibodies and it is not clear that this was due to experimental conditions (e.g. the detergent used) and possibly compounded by antibody specificities. In fact, there is a strong correlation with binding of HLA-F tetramer and the presence of surface MHC-I HC (Fig. 3). In addition, surface HLA-F is internalized upon addition of free HC antibodies, which could implicate an interaction between the two molecules prior to the addition of HC antibody. If heterodimers of MHC-I HC and HLA-F or similar complexes of homodimers of each species do exist on the surface. it would suggest the possibility for interaction with a unique receptor in trans, perhaps another polymorphic locus or group of genes.

MHC-I interactions with other proteins have been demonstrated in cis, including insulin and epidermal growth factor receptors, and evidence points to that interaction being exclusively with MHC-I HC (57-59). Indeed a relatively long list of reported cis-associations between MHC-I and other surface receptors and proteins can be compiled from the literature (10). Whether all of these associations are formed between the MHC-I open conformer remains to be determined, but the discovery we report here may place a new light on these interactions and indeed may refocus some emphasis on this aspect of MHC-I function.

Further functional data will clarify the role that interaction between HLA-F and MHC-I plays in class I presentation by activated cells. However, the high conservation of HLA-F and the binding to MHC-I HC together suggest a role as chaperone to stabilize MHC-I HC expression in the absence of peptide. This escort function could be operating in both directions, bringing MHC-I HC to the surface and internalizing MHC-I HC after appropriate signals have been delivered, although we have no direct evidence in support of the latter possibility. The coincident internalization of HLA-F may therefore suggest an involvement in internalization of MHC-I upon encounter with the formation of an alternative stable complex.


We thank Ofer Majdic for providing mAb LA45, Huib Ovaa and Ruiwert Hoppes for conditional ligands, Jianhong Cao for tetramers, Julio Vasquez for microscopy, Thomas Spies for HCA2, and Roland Strong for help with surface plasmon resonance.

Abbreviations used in this paper

endoplasmic reticulum
Major Histocompatibility Class I heavy chain form


1This work was supported by National Institutes of Health grants HD045813 to D.E.G.


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