Tapasin (Tpn) is a chaperone of the endoplasmic reticulum involved in peptide loading to MHC class I proteins. The influence of mouse Tpn (mTpn) on the HLA-B*2705-bound peptide repertoire was analyzed to characterize the species specificity of this chaperone. B*2705 was expressed on Tpn-deficient human 721.220 cells cotransfected with human (hTpn) or mTpn. The heterodimer to β2-microglobulin-free H chain ratio on the cell surface was reduced with mTpn, suggesting lower B*2705 stability. The B*2705-bound peptide repertoires loaded with hTpn or mTpn shared 94–97% identity, although significant differences in peptide amount were observed in 16–17% of the shared ligands. About 3–6% of peptides were bound only with either hTpn or mTpn. Nonamers differentially bound with mTpn had less suitable anchor residues and bound B*2705 less efficiently in vitro than those loaded only with hTpn or shared nonamers. Decamers showed a different pattern: those found only with mTpn had similarly suitable residues as shared decamers and bound B*2705 with high efficiency. Peptides differentially presented by B*2705 on human or mouse cells showed an analogous pattern of residue suitability, suggesting that the effect of mTpn on B*2705 loading is comparable in both cell types. Thus, mTpn has quantitative and qualitative effects on the B*2705-bound peptide repertoire, impairing presentation of some suitable ligands and allowing others with suboptimal anchor residues and lower affinity to be presented. Our results favor a size-dependent peptide editing role of Tpn for HLA-B*2705 that is species-dependent and suboptimally performed, at least for nonamers, by mTpn.

The MHC class I molecules bind a large array of peptides, arising mainly from proteasomal degradation of endogenous proteins and present them at the cell surface for recognition by CTL. Because the peptide-binding specificity of MHC I proteins is very broad, the peptide cargo of these molecules requires optimization to ensure selection of ligands with high stability, a feature that is important for immunogenicity (1). This optimization is conducted through a highly organized process of assisted loading, which involves several proteins collectively known as the peptide-loading complex. Besides the nascent MHC I and TAP molecules, this complex is formed by the lectin-like chaperone calreticulin (2), the thiol oxidoreductase ERp57 (3, 4, 5), and the MHC I-dedicated chaperone tapasin (Tpn)3 (2, 6). Numerous studies have demonstrated a pivotal role of Tpn in optimizing peptide binding to MHC I molecules (7, 8), by favoring loading of high affinity ligands (9). Indeed, MHC I molecules synthesized in the absence of Tpn are turned over more quickly and have higher ratios of open to folded conformers (10, 11). This idea was challenged in a recent study (12) reporting that peptide repertoires bound in the absence of Tpn showed comparable or higher overall affinity than those bound with this chaperone. On this basis, it was concluded that Tpn may act as a facilitator of peptide binding, rather than an editor selecting for high affinity ligands.

Tpn bridges MHC I and TAP (13), increases levels of peptide binding to TAP (14, 15), and contributes to the assembly of the peptide-loading complex. The precise mechanism by which Tpn contributes to optimizing the MHC I peptide cargo is unknown, but probably depends on interactions with multiple proteins (16, 17). For instance, the covalent interaction of Tpn with ERp57 is critical for the function of this protein in mediating the establishment of the disulfide bonds in the MHC molecule during folding (18, 19).

MHC I allotypes differ significantly in their Tpn dependency for peptide loading (20, 21). For instance, surface expression of HLA-B*2705 is relatively independent of Tpn, although in its absence B*2705 molecules at the cell surface are less stable (20), suggesting presentation of suboptimal peptides. Indeed, Tpn influences editing (22) and optimization (9) of the B*2705-bound peptide repertoire.

The species specificity of Tpn-mediated interactions is relevant in assessing the suitability of HLA class I expression in mouse cells for T cell Ag presentation and animal disease models. Human Tpn (hTpn) and mouse Tpn (mTpn) share 75% amino acid sequence identity (23, 24). The mouse chaperone is only slightly less efficient than its human counterpart in restoring surface expression of HLA-B5 and HLA-B8 on Tpn-deficient human cells (23), suggesting functional similarity.

The role and species-dependent effects of Tpn in peptide loading are especially relevant in the case of HLA-B27 for reasons related to its strong association with spondyloarthritis (25). First, HLA-B27-mediated peptide presentation might be involved in pathogenesis (26, 27). Second, HLA-B27 transgenic rats (28) and mice (29, 30, 31, 32) are used as animal models for HLA-B27-associated arthritis. Third, HLA-B27 H chain homodimers, which might also play a role in disease, are found at the cell surface following dissociation of MHC-peptide complexes (33, 34, 35). A suboptimal peptide repertoire might favor dissociation of these complexes and formation of homodimers, which might be recognized by autoaggressive T cells (36). This same process may lead to release of β2-microglobulin (β2m) that, if trapped in the synovia, might cause inflammation (37).

Despite many studies concerning the role of Tpn in peptide loading, systematic studies that characterize and quantify Tpn-dependent and Tpn-independent peptides are almost lacking. For HLA-B27, one study demonstrated that hTpn had significant quantitative and qualitative effects on the B*2705-bound peptide repertoire (22). More recently, we reported that a natural B*2705 ligand found in human cells but not in mouse B*2705 transfectants was at significantly lower levels in Tpn-deficient human cells reconstituted with mTpn, demonstrating species-dependent modulation of peptide loading for one particular ligand (38).

In the present study, we have addressed the modulation of the B*2705-bound peptide cargo by hTpn and mTpn. To this end, we have comparatively analyzed the B*2705-bound peptide pools from Tpn-deficient human cells reconstituted with hTpn or mTpn, or lacking this chaperone, identified individual ligands differentially expressed in a species-dependent way, and characterized their structural and binding properties as B*2705 ligands.

The cell line 721.220 (.220) is a human lymphoblastoid cell line in which HLA-A and -B genes have been deleted and a nonfunctional Tpn protein is expressed (39, 40). This cell line expresses low levels of endogenous HLA-Cw*0102. Transfection of HLA-B*2705 and wild-type hTpn or mTpn into .220 has been previously described (20). RMA-S is a TAP-deficient murine cell line (41, 42). RMA-S transfectant cells expressing B*2705 and human β2m have been previously described (43). These cells were cultured in RPMI 1640 medium supplemented with 10% FBS.

The mAb used in this study were W6/32 (IgG2a, specific for a monomorphic HLA-A, B, C determinant) (44), ME1 (IgG1, specific for HLA-B27, B7, B22) (45), and HC10 (IgG2a, specific for HLA class I H chain not associated to β2m) (46). Two polyclonal Abs were used. Ra 2223 is a rabbit Ab against the N terminus of mTpn (a gift from Ted Hansen, Washington University School of Medicine, St. Louis, MO), and GILES is a rabbit Ab against the N terminus of hTpn (a gift from B. Gao, University of Oxford, Oxford, U.K.).

Approximately 3 × 105 B*2705.220, hTpn-B*2705.220, and mTpn-B*2705.220 transfectant cells were washed twice in 200 μl of PBS and resuspended in 50 μl of purified mAb. After incubating for 30 min, cells were washed twice in 200 μl of PBS and resuspended in 50 μl of FITC-conjugated anti-mouse IgG rabbit antiserum (Calbiochem-Novabiochem), incubated for 30 min, and washed twice in 200 μl of PBS. All operations were done at 4°C. Flow cytometry was conducted on a Becton Dickinson FACSCalibur instrument using the CellQuest software.

Total RNA was extracted from .220 cells and B*2705.220 transfectants expressing hTpn or mTpn by the TRIZOL method, and 1-μg aliquots were reverse transcribed using MultiScribe reverse transcriptase and the archive kit reagents (Applied Biosystems) in a final volume of 100 μl.

The expression of hTpn and mTpn was quantified using two primers and a FAM-labeled TaqMan probe, all recognizing sequences in the translational enhancer from HTLV-1 present in the pMCFR vector (47, 48) in which both the hTpn and mTpn inserts were cloned. This region was chosen due to difficulties in designing appropriate primers from common sequences in the coding regions of the human and mouse chaperones. The primers and probe were designed and synthesized by Applied Biosystems. Various amounts (1, 4, and 10 ng) of each cDNA were subjected to quantitative RT-PCR in 96-well plates using a sequence detection system ABIPRISM 7000 (Applied Biosystems). cDNA samples were analyzed in triplicate with the Tpn construct-specific probe as well as with a ribosomal 18S-specific FAM-labeled probe (Hs99999901-s1; Applied Biosystems) used as an endogenous reference gene. PCR amplification was performed at 60°C for 40 cycles using TaqMan universal PCR master mix (Applied Biosystems) and Ct values were calculated using automatic adjustment of the threshold.

Tpn expression was confirmed in B2705.220 transfectants using either hTpn- or mTpn-specific Abs. Cell lysates were separated on 10% SDS-PAGE and transferred onto PVDF membrane (PerkinElmer Life and Analytical Sciences). The membrane was blocked in 3% skimmed milk in PBS containing 0.05% Tween 20 (BDH Laboratory Supplies) and probed with either GILES (anti-hTpn) or Ra2223 (anti-mTpn) antisera, washed in PBS milk, and probed with sheep anti-rabbit Ig-HRP conjugate (Silenus Laboratories) and Tpn visualized by using Renaissance chemiluminescence substrate (PerkinElmer Life and Analytical Sciences).

This was conducted from 3.5 × 109 .220 transfectant cells lysed in 1% Nonidet P-40 in the presence of a mixture of protease inhibitors, after immunopurification of HLA-B27 with the W6/32 mAb and acid extraction, exactly as described elsewhere (49). HLA-B27-bound peptide pools were fractionated by HPLC at a flow rate of 100 μl/min as previously described (50), and 50-μl fractions were collected.

The peptide composition of HPLC fractions was analyzed by MALDI-TOF mass spectrometry (MS) using a Bruker Reflex III MALDI-TOF mass spectrometer (Bruker-Franzen Analytic) equipped with the SCOUT source in positive ion reflector mode. A 0.5 μl of each sample was deposited onto the AnchorChip probe and allowed to dry at room temperature. Then, 0.5 μl of matrix solution (1 mg/ml α-cyano-4-hydroxycinnamic acid in 33% aqueous acetonitrile and 0.1% trifluoroacetic acid) was added and allowed to dry before analysis.

Peptide sequencing was conducted using quadrupole ion trap microelectrospray MS/MS in an LCQ instrument (Finnigan ThermoQuest), as described elsewhere (51), except that samples were injected through an HPLC equipped with a C18 capillary column (150 × 0.18 mm) connected online, at a flow rate of 1.5 μl/min. In a few cases sequencing was conducted by MALDI-TOF/TOF using the Applied Biosystems 4700 proteomics analyzer. Dried HPLC fractions were dissolved in 5 μl of 0.1% aqueous trifluoroacetic acid, 50% acetonitrile. A 0.5-μl aliquot was mixed with 0.5 μl of matrix (3 mg/ml α-cyano-4-hydroxicynnamic acid in 50% acetonitrile). Full scan MS was conducted by MALDI-TOF, and the selected ion peaks were subjected to MS/MS.

In a previous study (52) we compiled 174 natural ligands of B*2705 sequenced from human cells, including 108 nonamers and 39 decamers. The availability of this extensive series of peptides with the same size allowed us to determine reliable residue frequencies (RF) at each peptide position (P) among nonamers and decamers. Thus, the RF of any given residue found in a given position in a nonamer or a decamer is the percentage of frequency value of that residue at that position among the available database of constitutive B*2705 nonamer or decamer ligands, respectively. In addition, because the mean frequency of any amino acid residue among human proteins is known (〈www.ebi.ac.uk/proteome/index.html〉), it is possible to determine how many times the frequency of a residue in a given peptide position is increased or decreased among B*2705 ligands, relative to the frequency of that residue among all human proteins (deviation from mean frequency in the human proteome (DMP)). Both of these related parameters define the suitability of a residue in a given position for presentation by B*2705 in human cells with intact Ag-processing loading machineries and no heterologous components.

We calculated a double score for individual peptides as the added RF and DMP values corresponding to the residues at all peptide positions, except P2. This position, which is the main anchor for B*2705, was excluded because there was R2 in all the peptides analyzed in this study, as in nearly all natural B*2705 ligands (52). In addition, to assess the global suitability of peptide sets as B*2705 ligands and to compare peptide series among each other, we calculated the mean RF and DMP scores corresponding to all the residues in a given position within the peptide series, and estimated the overall suitability of the peptide series for B*2705 presentation as the Σmean RF or Σmean DMP for all peptide positions, except P2. A similar analysis, restricted to the P1, P3, PΩ-2, and PΩ anchor positions, was also conducted. These analyses were separately done for nonamers and decamers. We considered that the higher the RF and/or DMP scores the more suitable was a peptide, a peptide position, or a peptide series for B*2705 presentation, because the RF and DMP parameters reflect the natural selection of B*2705 ligands in vivo. Our approach is different but has some analogies with another method previously reported for the qualitative assessment of MHC class I ligands (53).

Peptides were synthesized using the standard solid-phase Fmoc chemistry, and were purified by HPLC. The correct composition and molecular mass of purified peptides were confirmed by amino acid analysis using a 6300 amino acid analyzer (Beckman Coulter), which also allowed their quantification.

The assay used to measure peptide binding was performed as described (54). Briefly, B*2705-RMA-S transfectant cells were incubated at 26°C for 22 h in RPMI 1640 medium supplemented with 10% heat-inactivated FBS. They were then washed three times in serum-free medium, incubated for 1 h at 26°C with various peptide concentrations without FBS, transferred to 37°C, and collected for flow cytometry after 4 h. HLA-B27 expression was measured using 50 μl of hybridoma culture supernatant containing the mAb ME1. Binding of the natural B*2705 ligand RRYQKSTEL, used as positive control, was expressed as C50, which is the molar concentration of the peptide at 50% of the maximum fluorescence obtained at the concentration range used (10−4 to 10−8 M). Binding of other peptides was assessed as the concentration of peptide required to obtain the fluorescence value at the C50 of the control peptide. This was designated as EC50. Peptides with EC50 < 10 μM were considered to bind with high affinity. EC50 values between 10 and 50 μM were considered to reflect intermediate affinity, and EC50 > 50 μM indicated low affinity.

A previously described (55) cell surface MHC-peptide complex stability assay was used with slight modifications. Briefly, T2-B*2705 cells (5 × 105 cells/well) were incubated overnight at 37°C, in serum-free AIM-V cell culture medium (Invitrogen Life Technologies), in the presence of 100 μM peptide and 100 nM β2m. After washing, cells were incubated for 1 h at 37°C in RPMI 1640, containing 10% FBS (Invitrogen Life Technologies) and brefeldin A (10 μg/ml) to block egress of newly synthesized class I molecules. Cells were washed, and incubation continued in the presence of 0.5 μg/ml brefeldin A at 37°C. Cells were removed at various times (0, 8, 24, and 30 h) and stained with the ME1 mAb, as described above. The decay of B*2705-peptide complexes was determined as follows: percentage of mean linear fluorescence (MLF) remaining = MLFt(+pep) − MLFt(−pep)/MLFt=0(+pep) − MLFt=0(−pep).

Fluorescence values at the various time points were adjusted by linear regression analysis, and only those experiments with R2 ≥ 0.9 were taken into account. Stability was measured as DC50. This is the time required to obtain 50% of the fluorescence value at t = 0.

The χ2 test with Yates correction or, for small data sets, the Fisher’s exact test, were used.

The expression levels of hTpn and mTpn in the B*2705.220 transfectants used in this study were determined by quantitative RT-PCR. The amount of mTpn relative to hTpn, as assessed by this method, was somewhat higher (1.67 ± 0.37) (Fig. 1 A).

FIGURE 1.

Expression of hTpn and mTpn in transfectant cells. A, Relative expression of hTpn (white bars) and mTpn (black bars) in B*2705.220 transfectants, assessed by quantitative RT-PCR. The results of five independent experiments using 1 ng (Expts. 1 and 2), 4 ng (Expt. 3), or 10 ng (Expts. 4 and 5) are shown. Each experiment is the mean of triplicate (Expts. 1 and 4) or duplicate (Expts. 2, 3, and 5) measurements. The mean ± SD of the five experiments is indicated. The results are expressed as relative quantity and are normalized to the amount of hTpn. B, Expression of hTpn and mTpn in B*2705.220 cells. Cross-reactivity of the anti-hTpn serum with mTpn was observed: note a weaker band with anti-hTpn for 2.5 × 106 B2705.220.mTpn cell equivalents and no band with anti-mTpn serum for 2.5 × 106 B2705.220.hTpn cell equivalents. No Tpn band was observed for Tpn-deficient B2705.220 cells in either blot (not shown). Because different antisera were used, the titers obtained for hTpn and mTpn in these blots are not comparable.

FIGURE 1.

Expression of hTpn and mTpn in transfectant cells. A, Relative expression of hTpn (white bars) and mTpn (black bars) in B*2705.220 transfectants, assessed by quantitative RT-PCR. The results of five independent experiments using 1 ng (Expts. 1 and 2), 4 ng (Expt. 3), or 10 ng (Expts. 4 and 5) are shown. Each experiment is the mean of triplicate (Expts. 1 and 4) or duplicate (Expts. 2, 3, and 5) measurements. The mean ± SD of the five experiments is indicated. The results are expressed as relative quantity and are normalized to the amount of hTpn. B, Expression of hTpn and mTpn in B*2705.220 cells. Cross-reactivity of the anti-hTpn serum with mTpn was observed: note a weaker band with anti-hTpn for 2.5 × 106 B2705.220.mTpn cell equivalents and no band with anti-mTpn serum for 2.5 × 106 B2705.220.hTpn cell equivalents. No Tpn band was observed for Tpn-deficient B2705.220 cells in either blot (not shown). Because different antisera were used, the titers obtained for hTpn and mTpn in these blots are not comparable.

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Expression of the hTpn and mTpn proteins was confirmed by Western blot (Fig. 1 B). Two high affinity polyclonal antisera, raised against hTpn or mTpn, respectively, were used. The former antiserum cross-reacted more weakly with mTpn, precluding a quantitative comparison. Titration of cell equivalents using separate antisera for each protein suggested high expression levels of hTpn and mTpn in the corresponding transfectants. Although titration of mTpn was higher, consistent with results from RT-PCR, the blots cannot be formally compared because different antisera were used.

The surface expression of HLA-B*2705 was analyzed on .220 cells transfected either with only B*2705 or with this allotype plus hTpn or mTpn. Expression of the B*2705 heterodimer was clearly but moderately increased in the presence of Tpn, relative to Tpn-deficient cells, as determined with the ME1 and W6/32 mAbs. The effects of hTpn and mTpn were indistinguishable with these antibodies. (Fig. 2,A, Table I).

FIGURE 2.

Tpn-dependent cell surface expression of HLA-B*2705. Flow cytometry analysis of B*2705.220 cells (Tpn) or transfectants of this cell line expressing hTpn or mTpn with the ME1 (A) or HC10 (B) mAb. A representative experiment is shown. Mean channel fluorescence for Tpn, hTpn, and mTpn transfectants in this experiment were 120, 246, and 259, respectively (A) and 29, 23, and 42, respectively (B) (see also Table I). Dotted lines represent staining with only the fluorescence-labeled rabbit anti-mouse IgG Ab.

FIGURE 2.

Tpn-dependent cell surface expression of HLA-B*2705. Flow cytometry analysis of B*2705.220 cells (Tpn) or transfectants of this cell line expressing hTpn or mTpn with the ME1 (A) or HC10 (B) mAb. A representative experiment is shown. Mean channel fluorescence for Tpn, hTpn, and mTpn transfectants in this experiment were 120, 246, and 259, respectively (A) and 29, 23, and 42, respectively (B) (see also Table I). Dotted lines represent staining with only the fluorescence-labeled rabbit anti-mouse IgG Ab.

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Table I.

Tpn-dependent surface expression of HLA-B*2705a

mAbB*2705.220
TpnNhTpnNmTpnN
W6/32 191 ± 36 11 349 ± 86 348 ± 91 
ME1 126 ± 19 13 242 ± 70 246 ± 78 13 
HC10 34 ± 11 12 23 ± 8 40 ± 14 14 
HC10:W6/32 ratio (%) 20 ± 7% 6 ± 2% 12 ± 3% 
HC10:ME1 ratio (%) 25 ± 9% 12 9 ± 3% 17 ± 6% 13 
mAbB*2705.220
TpnNhTpnNmTpnN
W6/32 191 ± 36 11 349 ± 86 348 ± 91 
ME1 126 ± 19 13 242 ± 70 246 ± 78 13 
HC10 34 ± 11 12 23 ± 8 40 ± 14 14 
HC10:W6/32 ratio (%) 20 ± 7% 6 ± 2% 12 ± 3% 
HC10:ME1 ratio (%) 25 ± 9% 12 9 ± 3% 17 ± 6% 13 
a

Data are expressed as mean fluorescence ± SD of N experiments. The percentage of HC10-associated fluorescence relative to the W6/32- or ME1-associated fluorescence is indicated for each cell line.

Surface expression of free HLA class I H chain as measured with the HC10 mAb was low in all three cases, but lowest with hTpn (Fig. 2,B). The presence of this chaperone resulted in ∼3-fold reduction of HC10-associated fluorescence, relative to that of the heterodimer. With mTpn HC10-associated fluorescence, relative to that of the heterodimer, was intermediate between Tpn-deficient cells (∼1.5-fold reduction) and those expressing hTpn (Table I). These results indicate that the presence of hTpn results in slightly more stable B*2705 molecules on the cell surface than with mTpn, but in both situations B*2705 is more stable than in the absence of the chaperone. These results are compatible with better optimization of the B*2705-bound peptide repertoire by hTpn.

B*2705-bound peptide pools were isolated from similar numbers of B*2705.220 cells expressing either hTpn or mTpn, fractionated by HPLC under the same conditions and consecutive runs, and each individual fraction was analyzed by MALDI-TOF MS. The overall peptide yield as estimated by the total area of absorbance peaks (at 210 nm) corresponding to peptide-containing HPLC fractions was similar for both pools (3.6 × 107 and 4 × 107 U, respectively), which is consistent with the similar expression levels of B*2705 on both transfectants (Table I, Fig. 2 A).

A systematic comparison of B*2705-bound peptides loaded in the presence of hTpn or mTpn was conducted on the basis of their retention time and molecular mass, as in previous studies from our laboratory (38, 56, 57, 58, 59, 60). Briefly, the MALDI-TOF MS spectrum of each HPLC fraction from one peptide pool was compared with the correlative, and adjacent HPLC fractions from the other pool. This was done to account for slight shifts in the retention time of individual peptides that might occur between consecutive chromatographic runs. Ion peaks with the same (±0.7) mass-to-charge (m/z) ratio found in HPLC fractions with the same retention times were assigned as identical peptides. Our previous studies have shown that this is the case in the overwhelming majority of cases in which the corresponding peptides were sequenced from the two peptide pools compared. Ion peaks found only in one peptide pool in two independent experiments were assigned as peptides differentially present in that pool. An example of this comparison is shown in Fig. 3.

FIGURE 3.

Comparison of correlative HPLC fractions from the B*2705-bound peptide pools isolated from .220 cells transfected with mTpn or hTpn. In this example the MALDI-TOF MS spectrum of fraction N.101 from the mTpn transfectant is compared with the corresponding spectra of HPLC fractions N.100–102 from hTpn cells. Ion peaks in mTpn 101 for which a counterpart of the same m/z ratio was found in hTpn 100–102 fractions were assigned as shared ligands. They are labeled with asterisks. Ion peaks labeled with two asterisks (∗∗) are shared ligands assigned as quantitative differences predominant in the corresponding peptide pool (see text). The ion peak at m/z 1239.5 in hTpn 100 and 101 had its counterpart in mTpn 99 and 100 (not shown). Ion peaks labeled with arrows in mTpn 101 lacked a detectable counterpart in the correlative hTpn 100–102 fractions and were assigned as differential peptides loaded only with mTpn. The small (unlabeled) ion peak 14 m/z units to the left of that at m/z 1570.6 in mTpn 101 is related to this ion peak and was not counted.

FIGURE 3.

Comparison of correlative HPLC fractions from the B*2705-bound peptide pools isolated from .220 cells transfected with mTpn or hTpn. In this example the MALDI-TOF MS spectrum of fraction N.101 from the mTpn transfectant is compared with the corresponding spectra of HPLC fractions N.100–102 from hTpn cells. Ion peaks in mTpn 101 for which a counterpart of the same m/z ratio was found in hTpn 100–102 fractions were assigned as shared ligands. They are labeled with asterisks. Ion peaks labeled with two asterisks (∗∗) are shared ligands assigned as quantitative differences predominant in the corresponding peptide pool (see text). The ion peak at m/z 1239.5 in hTpn 100 and 101 had its counterpart in mTpn 99 and 100 (not shown). Ion peaks labeled with arrows in mTpn 101 lacked a detectable counterpart in the correlative hTpn 100–102 fractions and were assigned as differential peptides loaded only with mTpn. The small (unlabeled) ion peak 14 m/z units to the left of that at m/z 1570.6 in mTpn 101 is related to this ion peak and was not counted.

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Upon comparing >1000 ion peaks (Table II), both peptide pools shared ∼94–97% of ligands. Thus, 3–6% of the peptides from each pool was specifically loaded with either hTpn or mTpn. The average mass of peptides differentially presented with mTpn was only 13 Da smaller than that of hTpn-specific peptides.

Table II.

Comparison of B*2705-bound peptides in the presence of hTpn or mTpn

B*2705.220
hTpnmTpn
Total peptides compared 1155 1184 
Shared peptides 1118 (97%) 1118 (94%) 
Specific peptides 37 (3%) 66 (6%) 
Average mass of shared peptides 1244 Da 1244 Da 
Average mass of specific peptides 1251 Da 1238 Da 
Average mass of total peptides 1244 Da 1244 Da 
Major ion peaks counteda 226 226 
Quantitative differences 36 (16%) 38 (17%) 
B*2705.220
hTpnmTpn
Total peptides compared 1155 1184 
Shared peptides 1118 (97%) 1118 (94%) 
Specific peptides 37 (3%) 66 (6%) 
Average mass of shared peptides 1244 Da 1244 Da 
Average mass of specific peptides 1251 Da 1238 Da 
Average mass of total peptides 1244 Da 1244 Da 
Major ion peaks counteda 226 226 
Quantitative differences 36 (16%) 38 (17%) 
a

Ion peaks showing 50% or more of the maximal intensity value in the corresponding MALDI-TOF MS spectrum.

The reliability of assigning species-specific peptide differences depends on the intensity of the corresponding ion peaks. It is possible that ion peaks found only in one peptide pool might escape detection in the other if the corresponding peptides were below the detection levels of our MALDI-TOF analysis. In our comparison, 61 and 64% of the peptides assigned as hTpn- or mTpn-specific, respectively, showed strong signal (≥50% of the maximal intensity of the MALDI-TOF MS spectrum). Examples of major and minor ion peaks assigned as species-specific differences are shown in Fig. 3.

Quantitative differences in the expression of shared ligands with either hTpn or mTpn was estimated as follows. Shared ion peaks showing 50% or more of the maximal intensity value in each MALDI-TOF MS spectrum were selected. Their intensity was compared with those of their counterparts in the other peptide pool. Ion peaks showing 10-fold or more intensity difference were considered as quantitative differences predominant in the corresponding peptide pool. This procedure provides only an approximate estimation, because MALDI-TOF MS is not quantitative. Nevertheless, control experiments showed that MALDI-TOF MS spectra of equivalent HPLC fractions were largely reproducible (data not shown; also see Refs. 22 and 61). A total of 226 major ion peaks corresponding to shared ligands were compared in this way. Of these, 36 (16%) and 38 (17%) were assigned as peptides expressed at significantly higher levels with hTpn or mTpn, respectively (Table II). Thus, in addition to determining species-specific expression of a limited number of peptides, hTpn and mTpn modulate peptide levels for a significant number of B*2705 ligands in a species-dependent way.

The sequence of 46 shared ligands, including 26 nonamers, was determined (Fig. 4). A systematic comparison of residue frequencies among these nonamers with a series of 108 B*2705-bound nonamers previously sequenced from human lymphoid cells (52), showed no statistically significant differences, except for a marginal increase of M8 (p = 0.045). These results are in agreement with the very high sharing between the B*2705-bound peptide repertoires loaded with mTpn or hTpn.

FIGURE 4.

Amino acid sequence of HLA-B*2705 ligands from .220 cells transfected with hTpn or mTpn. Sequences were determined by quadrupole/ion trap electrospray MS/MS, except for four peptides whose sequence, labeled with asterisk (∗), was determined by MALDI-TOF/TOF. Isobaric residues (I/L, K/Q) were assigned on the basis of unambiguous matching with human sequences in the protein database. The putative parental protein, with which full match was obtained, and the corresponding accession number in the Swissprot database (〈www.ebi.ac.uk/swissprot/access.htm〉) is indicated. The one or more cell line from which the sequence was determined is also indicated. When a peptide was sequenced from only one cell line, its presence in the other one was inferred from the finding of an ion peak of equal m/z and retention time. Peptides that were previously reported as natural ligands of B*2705 and/or other HLA-B27 subtypes in human cells (52 ) are labeled with asterisk (∗) in the right column.

FIGURE 4.

Amino acid sequence of HLA-B*2705 ligands from .220 cells transfected with hTpn or mTpn. Sequences were determined by quadrupole/ion trap electrospray MS/MS, except for four peptides whose sequence, labeled with asterisk (∗), was determined by MALDI-TOF/TOF. Isobaric residues (I/L, K/Q) were assigned on the basis of unambiguous matching with human sequences in the protein database. The putative parental protein, with which full match was obtained, and the corresponding accession number in the Swissprot database (〈www.ebi.ac.uk/swissprot/access.htm〉) is indicated. The one or more cell line from which the sequence was determined is also indicated. When a peptide was sequenced from only one cell line, its presence in the other one was inferred from the finding of an ion peak of equal m/z and retention time. Peptides that were previously reported as natural ligands of B*2705 and/or other HLA-B27 subtypes in human cells (52 ) are labeled with asterisk (∗) in the right column.

Close modal

The sequences of 8 and 12 peptides found only with hTpn or mTpn, respectively, were determined (Fig. 5 A). Residue usage at the P1, P3, and PΩ anchor positions was compared using the Fisher’s exact test. A few statistically significant differences (p < 0.05) were observed at P1 and P3 between both peptide sets. The most conspicuous one concerned A3. This residue was found in 6 (50%) mTpn-specific and none of the hTpn-specific peptides. A3 has low frequency (5.2%) among natural B*2705 ligands sequenced from human cells (52), so that the high frequency of this residue among mTpn-specific peptides was also statistically significant when compared with this series. In a previous study (62), in which we scanned poly-Ala analogues for binding to B*2705, A3 was less favored than more bulky aliphatic or aromatic residues. In addition, 4 other mTpn-specific peptides had P3 residues less favored than A (E, Q, R). Thus, 10 of 12 (83%) mTpn-specific peptides had a suboptimal P3 residue, relative to 3 (R, T, E) of 8 (37.5%) hTpn-specific peptides. These results indicate that mTpn allows presentation of peptides with weak P3 anchor residues that are less frequently found among B*2705 ligands in the presence of hTpn.

FIGURE 5.

Amino acid sequence of HLA-B*2705 ligands differentially presented with hTpn or mTpn. A, B*2705 ligands differentially found in .220 cells transfected with either hTpn or mTpn. B, Shared B*2705 ligands predominant in the presence of hTpn or mTpn from the same transfectant cells. All sequences were determined by quadrupole/ion trap electrospray MS/MS, except in one case whose sequence, labeled with asterisk (∗), was determined by MALDI-TOF/TOF. Peptides that were previously reported as natural ligands of B*2705 and/or other HLA-B27 subtypes in human cells (52 ) are labeled with asterisk (∗) in the right column. Other conventions are also as in Fig. 4.

FIGURE 5.

Amino acid sequence of HLA-B*2705 ligands differentially presented with hTpn or mTpn. A, B*2705 ligands differentially found in .220 cells transfected with either hTpn or mTpn. B, Shared B*2705 ligands predominant in the presence of hTpn or mTpn from the same transfectant cells. All sequences were determined by quadrupole/ion trap electrospray MS/MS, except in one case whose sequence, labeled with asterisk (∗), was determined by MALDI-TOF/TOF. Peptides that were previously reported as natural ligands of B*2705 and/or other HLA-B27 subtypes in human cells (52 ) are labeled with asterisk (∗) in the right column. Other conventions are also as in Fig. 4.

Close modal

At PΩ, 5 (41.7%) mTpn-specific and none of the hTpn-specific peptides showed a basic residue. The percentage of peptides with C-terminal R or K residues among B*2705-bound peptides is 26.6% (52). Thus, although the difference did not reach statistical significance, our results suggest that peptides with C-terminal basic residues might be under-represented among hTpn-specific ligands. Two mTpn-specific peptides (16.7%) had C-terminal A. This is significantly high, relative to the very low frequency of C-terminal A (2 of 174: 1.1%) among B*2705-bound peptides (52), suggesting that this weak C-terminal anchor is more easily allowed in the presence of mTpn.

The previous comparison suggested that mTpn might allow peptides with suboptimal anchor residues to bind B*2705. To assess this possibility, we compared residue usage among hTpn-specific, mTpn-specific, and shared peptides, using the RF and DMP scores, as defined in Materials and Methods. The results (Table III) showed that both scores were consistently higher for hTpn than for mTpn-specific peptides. Shared nonamers showed global frequency scores (ΣP1-P9 and Σanchor) higher than mTpn-specific nonamers and similar or slightly lower than the hTpn-specific counterparts. The strongest score differences were mainly at anchor positions. Mouse Tpn-specific nonamers used, on an average, P1 and P3 residues with lower RF than those used by hTpn-specific or shared nonamers, and with mean DMP values <1. In contrast, score differences at P9 were smaller between hTpn- and mTpn-specific nonamers and similar between mTpn-specific and shared nonamers. These results suggest that, in the presence of mTpn, suboptimal nonamers are allowed that are not presented with hTpn. Conversely, some highly suitable nonamers that are presented by B*2705 with hTpn, are not allowed in the presence of mTpn.

Table III.

Residue frequency scores for hTpn-specific, mTpn-specific, and shared B*2705 ligandsa

hTpn Nonamers (N = 5)mTpn Nonamers (N = 4)Shared Nonamers (N = 26)
Mean RFMean DMPMean RFMean DMPMean RFMean DMP
P1 10.5 1.7 P1 3.7 0.7 P1 13.0 2.1 
P3 12.3 2.3 P3 1.4 0.2 P3 9.8 2.1 
P4 8.7 1.5 P4 6.1 1.0 P4 7.9 1.3 
P5 9.1 1.4 P5 9.8 1.7 P5 8.7 1.5 
P6 12.4 2.5 P6 6.7 1.1 P6 7.1 1.3 
P7 7.4 1.5 P7 7.0 1.5 P7 7.9 1.4 
P8 9.4 1.9 P8 7.2 1.0 P8 7.1 1.3 
P9 24.6 3.1 P9 17.8 3.1 P9 17.1 3.5 
ΣP1–P9 94.4 15.9 ΣP1–P9 59.7 10.3 ΣP1–P9 78.6 14.5 
Anchor 54.8 8.6 Anchor 29.9 5.5 Anchor 47.8 9.1 
Non-anchor 39.6 7.3 Non-anchor 29.8 4.8 Non-anchor 30.8 5.4 
hTpn Nonamers (N = 5)mTpn Nonamers (N = 4)Shared Nonamers (N = 26)
Mean RFMean DMPMean RFMean DMPMean RFMean DMP
P1 10.5 1.7 P1 3.7 0.7 P1 13.0 2.1 
P3 12.3 2.3 P3 1.4 0.2 P3 9.8 2.1 
P4 8.7 1.5 P4 6.1 1.0 P4 7.9 1.3 
P5 9.1 1.4 P5 9.8 1.7 P5 8.7 1.5 
P6 12.4 2.5 P6 6.7 1.1 P6 7.1 1.3 
P7 7.4 1.5 P7 7.0 1.5 P7 7.9 1.4 
P8 9.4 1.9 P8 7.2 1.0 P8 7.1 1.3 
P9 24.6 3.1 P9 17.8 3.1 P9 17.1 3.5 
ΣP1–P9 94.4 15.9 ΣP1–P9 59.7 10.3 ΣP1–P9 78.6 14.5 
Anchor 54.8 8.6 Anchor 29.9 5.5 Anchor 47.8 9.1 
Non-anchor 39.6 7.3 Non-anchor 29.8 4.8 Non-anchor 30.8 5.4 
Decamers (N = 1)Decamers (N = 5)Decamers (N = 9)
 RF DMP  Mean RF Mean DMP  Mean RF Mean DMP 
P1 28.2 4.9 P1 13.3 2.6 P1 13.1 1.9 
P3 5.1 0.5 P3 9.8 2.4 P3 12.3 3.2 
P4 12.8 1.9 P4 8.2 1.2 P4 8.5 1.3 
P5 7.7 1.2 P5 8.7 1.4 P5 6.5 1.0 
P6 10.3 1.7 P6 12.3 2.3 P6↓ 6.8 1.1 
P7 12.8 2.0 P7 10.3 1.7 P7↓ 4.3 1.0 
P8 10.3 1.6 P8 6.2 1.1 P8 6.6 1.1 
P9 20.5 3.1 P9 9.2 1.5 P9↓ 5.7 0.8 
P10 23.1 2.3 P10 16.9 3.6 P10 23.9 5.8 
ΣP1–P10 130.8 19.2 ΣP1–P10 94.9 17.8 ΣP1–P10 87.7 17.2 
Anchor 66.7 9.3 Anchor 46.2 9.7 Anchor 55.9 12.0 
Non-anchor 64.1 9.9 Non-anchor 48.7 8.1 Non-anchor 31.8↓ 5.2↓ 
Decamers (N = 1)Decamers (N = 5)Decamers (N = 9)
 RF DMP  Mean RF Mean DMP  Mean RF Mean DMP 
P1 28.2 4.9 P1 13.3 2.6 P1 13.1 1.9 
P3 5.1 0.5 P3 9.8 2.4 P3 12.3 3.2 
P4 12.8 1.9 P4 8.2 1.2 P4 8.5 1.3 
P5 7.7 1.2 P5 8.7 1.4 P5 6.5 1.0 
P6 10.3 1.7 P6 12.3 2.3 P6↓ 6.8 1.1 
P7 12.8 2.0 P7 10.3 1.7 P7↓ 4.3 1.0 
P8 10.3 1.6 P8 6.2 1.1 P8 6.6 1.1 
P9 20.5 3.1 P9 9.2 1.5 P9↓ 5.7 0.8 
P10 23.1 2.3 P10 16.9 3.6 P10 23.9 5.8 
ΣP1–P10 130.8 19.2 ΣP1–P10 94.9 17.8 ΣP1–P10 87.7 17.2 
Anchor 66.7 9.3 Anchor 46.2 9.7 Anchor 55.9 12.0 
Non-anchor 64.1 9.9 Non-anchor 48.7 8.1 Non-anchor 31.8↓ 5.2↓ 
a

See Materials and Methods. Briefly, for each series the frequency of each residue at each peptide position was obtained from a previous compilation of B*2705 ligands (52 ), and the mean RF at each position was calculated. A score was derived as the added mean RF for all peptide positions within each series (Σmean RF), except P2. A second score (Σmean DMP) was calculated based on the number of times that residue frequencies at a given position deviated from mean residue frequencies among human proteins. Analogous scores were calculated for only the P1, P3, PΩ-2, and PΩ anchor positions. This analysis was separately performed for nonamers and decamers. Score differences showing >1.5-fold increase in mean RF or DMP between hTpn- and mTpn- specific peptides, and the corresponding positions, are in boldface and underlined. Shared ligand score values >1.5-fold higher than those of mTpn-specific peptides are highlighted in the same way. Arrows (↓) indicate positions in which shared ligands showed score values >1.5-fold lower than mTpn-specific peptides.

The only sequenced hTpn-specific decamer scored higher than the mTpn-specific counterparts, but the difference was less pronounced than for nonamers. Moreover, in contrast to nonamers, shared decamers showed global scores that were either lower (ΣP1-P10 and Σnon-anchor) or only slightly higher (Σanchor) than for mTpn-specific decamers, suggesting that both mTpn-specific and shared decamers were similarly suitable.

In conclusion, hTpn-specific peptides tend to include highly suitable B*2705 ligands. Mouse Tpn allows loading of a majority of the natural B*2705 ligands, but also of some suboptimal nonamers not found in the constitutive B*2705-bound peptide repertoire of human cells. The influence of mTpn on selection of nonamers and decamers does not seem to be identical.

To test the suitability of peptides differentially presented by B*2705 with hTpn or mTpn their binding efficiency was compared in an epitope stabilization assay using B*2705-RMA-S transfectant cells (Table IV). Of four hTpn-specific nonamers tested, three bound with a high efficiency (EC50 < 10 μM), and one bound with intermediate efficiency (10 μM < EC50 < 50 μM). In contrast, the four peptides differentially presented with mTpn showed intermediate or low (EC50 > 50 μM) binding. Cell surface stability, as assessed with a variant of the epitope stabilization assay that measured the decay of B*2705 surface expression on T2 transfectant cells at 37°C as a function of time, showed similar differences. The results correlated with the RF/DMP scores of these peptides, supporting the validity of this scoring approach to assess the suitability of nonamers as B*2705 ligands and demonstrated that nonamers specifically presented by B*2705 with mTpn tend to be suboptimal B*2705 binders.

Table IV.

Binding properties and anchor residue scoring of hTpn- and mTpn-specific B*2705 ligandsa

PeptideEC50 ± SDDC50 ± SDRFaDMPa
Nonamers     
 RRYQKSTEL 2 ± 0.5 29 ± 3 61.1 10.6 
hTpn     
 SRYTGINQF 7 ± 2 n.d. 41.6 11.1 
 KRFGKAYNL 8 ± 1 n.d. 55.5 10.8 
 RRLGVQQSL 5 ± 1 30 ± 3 64.1 8.2 
 QRTDVLTGL 29 ± 6 n.d. 47.2 6.8 
Mean score   52.1 9.2 
mTpn     
 KRQAIKTAF 26 ± 12 n.d. 34.2 8.0 
 IRENPVYEK 38 ± 18 14 ± 0.5 26.0 6.4 
 ERAIQESLL >100 n.d. 38.9 4.2 
 TRQGGSPAK >100 19 ± 1 20.4 3.5 
Mean score   28.4 4.7 
Decamers     
hTpn     
 RRLGPVPPGL 28 ± 3 66.7 9.3 
mTpn     
 IRAFPNKQGY 3 ± 1 26 ± 7 46.2 10.2 
 KRFAGKVTTA 4 ± 2 24 ± 2 43.6 10.2 
 ARIPPVAVRL 5 ± 1 n.d. 61.6 9.4 
 HRAGKIVVNL 3 ± 0.2 n.d. 43.7 7.9 
 RRAGIKVTVA 4 ± 2 n.d. 36.0 6.2 
Mean score   44.7 10.2 
PeptideEC50 ± SDDC50 ± SDRFaDMPa
Nonamers     
 RRYQKSTEL 2 ± 0.5 29 ± 3 61.1 10.6 
hTpn     
 SRYTGINQF 7 ± 2 n.d. 41.6 11.1 
 KRFGKAYNL 8 ± 1 n.d. 55.5 10.8 
 RRLGVQQSL 5 ± 1 30 ± 3 64.1 8.2 
 QRTDVLTGL 29 ± 6 n.d. 47.2 6.8 
Mean score   52.1 9.2 
mTpn     
 KRQAIKTAF 26 ± 12 n.d. 34.2 8.0 
 IRENPVYEK 38 ± 18 14 ± 0.5 26.0 6.4 
 ERAIQESLL >100 n.d. 38.9 4.2 
 TRQGGSPAK >100 19 ± 1 20.4 3.5 
Mean score   28.4 4.7 
Decamers     
hTpn     
 RRLGPVPPGL 28 ± 3 66.7 9.3 
mTpn     
 IRAFPNKQGY 3 ± 1 26 ± 7 46.2 10.2 
 KRFAGKVTTA 4 ± 2 24 ± 2 43.6 10.2 
 ARIPPVAVRL 5 ± 1 n.d. 61.6 9.4 
 HRAGKIVVNL 3 ± 0.2 n.d. 43.7 7.9 
 RRAGIKVTVA 4 ± 2 n.d. 36.0 6.2 
Mean score   44.7 10.2 
a

RRYQKSTEL is a high affinity shared ligand used as control; EC50 (μM) and DC50 (hours) measure binding efficiency and cell surface stability, respectively, of the peptides bound to B*2705 (see Materials and Methods). Data are means of at least three experiments. RFa and DMPa are scores for anchor positions (P1 + P3 + PΩ-2 + PΩ).

In contrast, five decamers specifically presented with mTpn bound B*2705 with high efficiency. The surface stability of the mTpn-specific decamers tested in complex with B*2705 was also similar to the hTpn-specific decamer sequenced. This ruled out the possibility that stability differences between the hTpn- and mTpn-specific decamers were masked in the epitope stabilization assay.

The sequences of eight peptides assigned as quantitative differences, six predominant with hTpn and two predominant with mTpn, were determined (Fig. 5,B). The nonamers predominant with hTpn had mean RF and DMP values (ΣP1–P9) similar to those of hTpn-specific nonamers and higher than the only sequenced nonamer predominant with mTpn (Table V). This peptide had RF and DMP scores (ΣP1–P9) only slightly higher than those of mTpn-specific nonamers (Table III). Despite a suitable P1 residue, it used an unusual P9 anchor, which had a strong negative effect on scoring. The global RF of the anchor positions for the only sequenced decamer predominant with hTpn was similar to the corresponding value for the hTpn-specific decamer (Table III), due to very suitable anchor residues.

Table V.

Residue frequency scores for B*2705 ligands with quantitative Tpn-dependent expressiona

hTpn Nonamers (N = 4)mTpn Nonamers (N = 1)hTpn Decamers (N = 1)
Mean RFMean DMPRFDMPRFDMP
P1 13.2 2.1 P1 20.4 3.6 P1 15.4 2.2 
P3 8.8 1.6 P3 12 P3 10.3 3.9 
P4 6.5 1.1 P4 6.5 1.4 P4 5.1 0.7 
P5 6.5 1.2 P5 1.9 0.5 P5 5.1 1.4 
P6 9.5 2.1 P6 2.8 1.1 P6 5.1 0.8 
P7 10.9 1.3 P7 15.7 1.6 P7 
P8 7.7 1.4 P8 7.4 1.1 P8 2.6 
P9 19.2 4.5 P9 P9 7.7 0.9 
      P10 33.3 12.8 
ΣP1–P9 82.2 15.4 ΣP1–P9 66.7 11.3 ΣP1–P10 84.6 23.7 
Anchor 51.1 9.5 Anchor 48.1 7.2 Anchor 61.6 19.9 
Non-anchor 31.1 5.9 Non-anchor 18.6 4.3 Non-anchor 23.0 3.8 
hTpn Nonamers (N = 4)mTpn Nonamers (N = 1)hTpn Decamers (N = 1)
Mean RFMean DMPRFDMPRFDMP
P1 13.2 2.1 P1 20.4 3.6 P1 15.4 2.2 
P3 8.8 1.6 P3 12 P3 10.3 3.9 
P4 6.5 1.1 P4 6.5 1.4 P4 5.1 0.7 
P5 6.5 1.2 P5 1.9 0.5 P5 5.1 1.4 
P6 9.5 2.1 P6 2.8 1.1 P6 5.1 0.8 
P7 10.9 1.3 P7 15.7 1.6 P7 
P8 7.7 1.4 P8 7.4 1.1 P8 2.6 
P9 19.2 4.5 P9 P9 7.7 0.9 
      P10 33.3 12.8 
ΣP1–P9 82.2 15.4 ΣP1–P9 66.7 11.3 ΣP1–P10 84.6 23.7 
Anchor 51.1 9.5 Anchor 48.1 7.2 Anchor 61.6 19.9 
Non-anchor 31.1 5.9 Non-anchor 18.6 4.3 Non-anchor 23.0 3.8 
a

See footnote to Table III. Highlighting was done only for nonamers. Anchor: P1 + P3 + PΩ-2 + PΩ.

Thus, peptides showing Tpn species-dependent expression levels have global residue frequencies comparable to those of hTpn or mTpn-specific peptides. This suggests that both qualitative and quantitative species-dependent modulation of peptide loading by Tpn are based on structural suitability for binding to B*2705.

We next addressed whether mTpn had an intermediate effect between absence and presence of hTpn on HLA-B27 loading or had a distinct editing function. To this end, we compared the B*2705-bound peptide repertoires from B*2705.220 transfectants lacking Tpn or expressing the human or mouse chaperone. The total peptide yield obtained from similar cell numbers (∼3.5 × 109 cells) was 3-fold higher with hTpn or mTpn than in the absence of this chaperone (Table VI). Systematic peptide comparisons revealed that only 2% of the Tpn-independent B*2705 ligands were not found in the presence of hTpn or mTpn (Fig. 6,A, Table VI). In contrast, 26–27% of the B*2705 ligands bound with hTpn or mTpn were not detected in the absence of this chaperone (Table VI). It is unlikely that the observed differences in peptide sharing are due to the lower peptide yields from Tpn-deficient cells, because many differential ion peaks had significant intensity and did not correspond to minor signals that could be missed in a less abundant peptide pool (Fig. 6 B).

Table VI.

Comparison between B*2705-bound peptides from Tpn-deficient and hTpn or mTpn .220 cells

B*2705.220B*2705.220
TpnhTpnTpnmTpn
Total peptide yield (HPLC area units) 1.2 × 107 3.6 × 107 1.2 × 107 4 × 107 
Total peptides compared 876 1155 882 1183 
Shared peptides 855 (98%) 855 (74%) 861 (98%) 861 (73%) 
Differential peptides 21 (2%) 300 (26%) 21 (2%) 322 (27%) 
B*2705.220B*2705.220
TpnhTpnTpnmTpn
Total peptide yield (HPLC area units) 1.2 × 107 3.6 × 107 1.2 × 107 4 × 107 
Total peptides compared 876 1155 882 1183 
Shared peptides 855 (98%) 855 (74%) 861 (98%) 861 (73%) 
Differential peptides 21 (2%) 300 (26%) 21 (2%) 322 (27%) 
Differentially Presented B*2705 Ligandsa
hTpn mTpn Tpn No. of Peptides 
− − 21 
− 
− − 60 
− 262 
− − 38 
− 
Differentially Presented B*2705 Ligandsa
hTpn mTpn Tpn No. of Peptides 
− − 21 
− 
− − 60 
− 262 
− − 38 
− 
a

Signs (+ and −) indicate presence or absence, respectively, of the corresponding peptides in the B*2705-bound peptide pools from the hTpn, mTpn, and Tpn-deficient .220 transfectant cells.

FIGURE 6.

Comparison of HLA-B*2705-bound peptides presented in Tpn-deficient, hTpn, and mTpn transfectant cells. A, B*2705 ligands specifically presented in the absence of Tpn. In this example the MALDI-TOF MS spectra of HPLC fractions N.139 from the B*2705-bound peptide pools isolated from Tpn-deficient, hTpn, and mTpn .220 transfectant cells are compared. Ion peaks labeled with asterisk (*) are found in the three peptide pools. The ion peak at m/z 1109.7 from the Tpn-deficient MS spectrum (labeled with an arrow) lacks a counterpart in the corresponding MS spectra of hTpn and mTpn. B, Comparison of correlative HPLC fractions of the B*2705-bound peptide pools from Tpn-deficient, hTpn, and mTpn.220 transfectant cells. In this example the MALDI-TOF MS spectra of HPLC fractions N.199 from the three peptide pools are shown. Ion peaks at m/z 1300.5/1300.6 and 1443.5/1443.7 (labeled with arrows) correspond to Tpn-dependent peptides, not found in Tpn-deficient cells. Ion peaks labeled with asterisk (∗) were found in the 3 peptide pools. Ion peaks at m/z 1238.2 (Tpn), 1244.5, and 1250.5/1250.6 (hTpn and mTpn) were found in adjacent fractions of the other peptide pools (not shown).

FIGURE 6.

Comparison of HLA-B*2705-bound peptides presented in Tpn-deficient, hTpn, and mTpn transfectant cells. A, B*2705 ligands specifically presented in the absence of Tpn. In this example the MALDI-TOF MS spectra of HPLC fractions N.139 from the B*2705-bound peptide pools isolated from Tpn-deficient, hTpn, and mTpn .220 transfectant cells are compared. Ion peaks labeled with asterisk (*) are found in the three peptide pools. The ion peak at m/z 1109.7 from the Tpn-deficient MS spectrum (labeled with an arrow) lacks a counterpart in the corresponding MS spectra of hTpn and mTpn. B, Comparison of correlative HPLC fractions of the B*2705-bound peptide pools from Tpn-deficient, hTpn, and mTpn.220 transfectant cells. In this example the MALDI-TOF MS spectra of HPLC fractions N.199 from the three peptide pools are shown. Ion peaks at m/z 1300.5/1300.6 and 1443.5/1443.7 (labeled with arrows) correspond to Tpn-dependent peptides, not found in Tpn-deficient cells. Ion peaks labeled with asterisk (∗) were found in the 3 peptide pools. Ion peaks at m/z 1238.2 (Tpn), 1244.5, and 1250.5/1250.6 (hTpn and mTpn) were found in adjacent fractions of the other peptide pools (not shown).

Close modal

Of 66 peptides loaded with mTpn but not hTpn, only 6 (9%) were found in the absence of the chaperone (Table VI). This indicates that a subset of peptides (60 of 66 in our analysis) that fail to bind B*2705 in the absence of Tpn are allowed with mTpn but not with hTpn. We found no peptides bound with hTpn and without this chaperone but absent with mTpn. These results are consistent with an intermediate role of mTpn in shaping the B*2705-bound peptide repertoire.

We reported a number of peptide sequences corresponding to B*2705 ligands, whose differential presentation in human or mouse cells (B*2705-C1R and B*2705-P815, respectively) was accounted for only by differences in Ag-processing-loading between species (38). Nine of these sequences (five human specific and four mouse specific) corresponded to nonamers or decamers. We calculated their RF and DMP scores to examine whether mTpn in mouse cells had a similar or a different behavior than in human cells for B*2705 loading, because homologous or heterologous interactions with non-MHC components of the loading complex may modulate Tpn function. As shown in Table VII, human-specific nonamers had higher RF and/or DMP scores at anchor positions (P1, P3, PΩ-2, PΩ) than mouse-specific nonamers. The mean RF and DMP scores for the anchor positions of human-specific and mouse-specific nonamers were also similar to the corresponding values for hTpn- and mTpn-specific peptides from human cells, respectively (Table III). The situation was similar for decamers, but their smaller number precluded any detailed comparisons. These results strongly suggest that mTpn in the presence of components of the mouse peptide-loading complex behaves similarly as in human cells in allowing presentation of B*2705 ligands with suboptimal anchor residues.

Table VII.

Residue frequency scores for the anchor positions of species-specific B*2705 ligandsa

Human-specific peptidesMouse-specific peptides
GRVAPRSGL   ARDERRFRV   
IRNDEELNK   NRYDGIYKV   
LRNPLIAGK   QRTPKIQVY   
HRFEQAFYTY   SRISLPLPTF   
SRVNIPKVLR      
Human-specific peptidesMouse-specific peptides
GRVAPRSGL   ARDERRFRV   
IRNDEELNK   NRYDGIYKV   
LRNPLIAGK   QRTPKIQVY   
HRFEQAFYTY   SRISLPLPTF   
SRVNIPKVLR      
Human Nonamers (N = 3)Mouse Nonamers (N = 3)
 Mean RF Mean DMP  Mean RF Mean DMP 
P1 11.4 1.8 P1 7.1 1.3 
P3 8.9 2.1 P3 5.2 1.5 
P7 10.2 1.2 P7 4.0 1.3 
P9 17.3 2.4 P9 10.2 2.5 
Σanchor 47.8 7.5 Σanchor 26.5 6.6 
Human Nonamers (N = 3)Mouse Nonamers (N = 3)
 Mean RF Mean DMP  Mean RF Mean DMP 
P1 11.4 1.8 P1 7.1 1.3 
P3 8.9 2.1 P3 5.2 1.5 
P7 10.2 1.2 P7 4.0 1.3 
P9 17.3 2.4 P9 10.2 2.5 
Σanchor 47.8 7.5 Σanchor 26.5 6.6 
Decamers (N = 2)Decamers (N = 1)
 Mean RF Mean DMP  RF DMP 
P1 9.0 2.4 P1 7.7 0.9 
P3 16.7 4.2 P3 15.4 3.6 
P8 5.2 1.2 P8 10.3 1.6 
P10 23.1 7.5 P10 7.7 2.1 
Σanchor 54.0 15.3 Σanchor 41.1 8.2 
Decamers (N = 2)Decamers (N = 1)
 Mean RF Mean DMP  RF DMP 
P1 9.0 2.4 P1 7.7 0.9 
P3 16.7 4.2 P3 15.4 3.6 
P8 5.2 1.2 P8 10.3 1.6 
P10 23.1 7.5 P10 7.7 2.1 
Σanchor 54.0 15.3 Σanchor 41.1 8.2 
a

Peptide sequences have been previously reported (38 ). See footnote to Table III.

Species-dependent effects of Tpn for HLA class I loading have been reported in several studies concerning mainly B*4402, a strongly Tpn-dependent allotype that is poorly expressed on mouse cells (17, 20). In particular, Tan et al. (17) reported that the B*4402-bound peptide repertoires from .220 transfectants expressing either hTpn or mTpn were different, although this was analyzed only in a qualitative way. In contrast, B*2705 is relatively independent of Tpn (20) and is expressed at high levels on mouse cells. In a recent study (38), a peptide was more efficiently presented on .220 cells expressing hTpn than mTpn. This peptide was not found in B*2705-transfected mouse cells despite being normally produced by the murine 20S proteasome, suggesting that species-dependent effects of Tpn also influenced B*2705 loading.

In this study, we have 1) quantified the effect of the heterologous expression of mTpn in human cells on the cell surface stability and peptide repertoire of B*2705; 2) identified peptides whose presentation was specifically dependent or quantitatively modulated by Tpn in a species-dependent way; 3) demonstrated that residue usage among hTpn-specific peptides is biased toward residues that are frequent among the constitutive B*2705-bound peptide repertoire, whereas among mTpn-specific peptides is biased toward less frequent residues; 4) shown that mTpn-specific nonamers, but not mTpn-specific decamers, are suboptimal B*2705 binders; 5) determined that the effect of mTpn on peptide selection for B*2705 was intermediate between absence and presence of hTpn; and 6) shown that residue usage among peptides specifically presented by B*2705 on mouse cells is similarly suboptimal as for peptides specifically presented on human cells with mTpn, so that homologous interactions of this chaperone with non-MHC proteins in the loading complex do not improve the B*2705 cargo. This suggests a peptide-modulating role of Tpn that is dependent on its direct interaction with B*2705.

Surface expression of B*2705 on Tpn-deficient .220 cells was only slightly lower than with hTpn. Although with mTpn B*2705 levels were indistinguishable from those with hTpn, slightly increased dissociation was compatible with the possibility that B*2705 on the surface of cells containing mTpn presented peptides with suboptimal stability and that these were a small fraction of the B*2705-bound repertoire. An alternative possibility was hypothesized by Zarling et al. (12): Tpn would influence MHC I stability not on the basis of peptide affinity, but by conditioning the conformational state of the class I molecule after peptide binding in a way that remained undefined.

Identification of the peptides bound to B*2705 in the presence of hTpn or mTpn helped us to distinguish between both alternatives and to characterize the effect of heterologous interactions involving Tpn on the B*2705-bound peptide repertoire. First, mTpn allowed binding of ∼95% of the native B*2705 ligands, which is significantly more than the already large percentage (∼75%) bound in the absence of Tpn. However, ∼5% of each peptide repertoire was differentially presented by B*2705 in the presence of hTpn or mTpn, and ∼30% of shared ligands were expressed at significantly different levels. Thus, there was a clear Tpn species-dependent modulation of B*2705 loading.

The molecular mechanism by which Tpn influences B*2705 loading and cell surface stability may be inferred from the molecular features of differentially presented peptides. We took advantage of our knowledge of many B*2705 ligand sequences, and of the most suitable anchor residues for this allotype, to compare the suitability of structural features between differentially bound peptides. This approach was based on a previous analysis of residue frequencies at every peptide position among nearly 200 natural B*2705 ligands (52). Thus, any amino acid residue at a given peptide position could be scored on the basis of its frequency among natural B*2705 ligands, giving an unbiased indication of the suitability of a peptide for B*2705 presentation in human cells with an intact Ag-processing-loading system.

When this analysis was applied to individual positions of differentially bound peptides, the subset found only with hTpn scored significantly higher than the mTpn-specific subset, particularly at anchor positions. Shared nonamers scored similarly or slightly lower than the hTpn-specific ones, but higher than the mTpn-specific counterparts. However, this was not the case for shared decamers. These results suggested that differential presentation of nonamers is largely based on affinity. Low binding of mTpn-specific nonamers to B*2705 in vitro, confirmed the conclusions derived from residue scoring. The results explain the small but clear decrease in cell surface stability of B*2705 in .220 cells transfected with mTpn, because suboptimal peptides are a small fraction of the total B*2705-bound repertoire in these transfectants.

In contrast, decamers presented with mTpn scored similarly as shared ligands and bound in vitro with high efficiency. Two aspects of this result should be discussed. First, it is possible that the RF and/or DMP scores might be less reliable for decamers than for nonamers, because these are based on >100 peptides, relative to only 39 decamers (52). Moreover, the epitope stabilization assays may not fully reflect peptide binding in vivo. Although we cannot rule out these possibilities, the fact remains that for both nonamers and decamers there is a correlation between residue scoring and binding efficiency in vitro; whereas mTpn-specific nonamers scored lower than shared nonamers and bound poorly, the mTpn-specific decamers scored similarly as shared decamers and bound with high efficiency. Thus, our results suggest that the role of Tpn in mediating peptide loading may not be identical for nonamers and decamers and that optimization of the peptide cargo is more strictly performed for nonamers. The mechanism for this differential effect is currently unclear to us.

Species-dependent effects of mTpn in human cells have been ascribed, in studies with B*4402, not only to bridging MHC and TAP, but also to defective interactions with other components of the peptide-loading complex (16, 17). Mouse Tpn was reported to be as efficient as its human counterpart in stabilizing TAP levels in B*4402.220 transfectants (17). It is possible that alterations in the stability, composition, or stoichiometry of the loading complex, resulting from heterologous interactions of mTpn with calreticulin and ERp57(17), may influence suboptimal B*2705 loading on human cells transfected with the mTpn. However, the fact that suboptimal residue scoring was also observed among B*2705 ligands specifically loaded in mouse cells argues against a dominant influence of heterologous interactions between Tpn and non-MHC I proteins on suboptimal B*2705 loading and supports a direct role of Tpn in this process.

It is generally accepted that Tpn contributes to stabilize a peptide-receptive conformation of the HLA class I molecule, facilitating peptide binding. After this is accomplished, the HLA molecule dissociates from the loading complex and migrates to the cell surface. On the basis of our results, we would like to hypothesize that dissociation of the HLA class I molecule from the loading complex requires a minimum affinity threshold. Because of suboptimal stabilization of the human loading complex by mTpn, the peptide affinity threshold for dissociation of the MHC molecule from this complex might be lower, allowing for suboptimal ligands to reach the cell surface. The fact that some highly suitable peptides were presented only with hTpn is compatible with this model, because their selective expression might result from lower competition among peptides for productive binding to B*2705 when the affinity threshold is higher and, therefore, more restrictive. However, given the complexity and incomplete knowledge of the interactions among components of the peptide-loading complex other alternatives cannot be ruled out. For instance, hTpn and mTpn might stabilize empty class I molecules in slightly different conformations, one more receptive to only high affinity peptides and the other somewhat more permissive.

Our results argue against the view (12) that Tpn functions as a facilitator of peptide binding, rather than as a peptide editor favoring loading of high affinity MHC ligands. This conclusion was largely based on the observation that the average affinity, as measured in vitro with whole peptide pools, of HLA-B8 or HLA-A2 ligands from Tpn-deficient cells was higher or similar, respectively, than the corresponding peptide pools from Tpn-proficient cells. In addition, HLA-B8 ligands from Tpn-deficient or Tpn-proficient cells had similar anchor residues. In contrast, our results with B*2705 show that individual mTpn-specific nonamers tend to have both suboptimal residues and low binding efficiency, fully consistent with an editor role of Tpn. Our results also suggest that this function may be peptide size dependent, because mTpn-specific decamers were good B*2705 binders.

There could be various explanations for the apparent disparity between our results and those of Zarling et al. (12). For instance, the effect of Tpn on shaping MHC class I-bound peptide repertoires might be variable among allotypes. Another possibility is that, in the binding assay using whole peptide pools, the presence of individual ligands with lower affinity might be masked by a dominant effect of peptides with high affinity in the same pool. For instance, many of the peptides bound in the absence of Tpn are also bound in its presence and may have an affinity that is comparable to the Tpn-dependent ligands, as we have previously shown for B*2705 (22). To our knowledge, affinity measurements of individual HLA class I-bound ligands presented in the absence, but not in the presence of Tpn, have not been reported. Whatever the explanation, the differences we observed between nonamers and decamers point out to unsuspected complexities in the way Tpn modulates peptide loading.

In conclusion, our study provides evidence for suboptimal editing of the B*2705-bound peptide repertoire by mTpn, leading to presentation of peptides with less suitable residues and lower affinity, lack of presentation of some ligands that bind with hTpn, and quantitative alterations in the expression level of shared ligands. As a result, surface expressed B*2705 is slightly less stable in the presence of mTpn. These results have obvious implications for animal models of HLA-B27-associated disease. We previously reported that more than half of the peptides differentially presented by B*2705 on human and mouse cells do not arise from species-related protein polymorphism, but from differences in Ag processing (38). Now we have quantified the effect of mTpn as the only heterologous component in the loading complex on peptide presentation by B*2705. Although it remains to be proven, it is likely that the effects on peptide selection will be similar or larger on mouse cells, in which the only human component is HLA-B27. This was suggested by results concerning a single peptide in our previous study (38). Now we have shown that B*2705 ligands arising from conserved sequences between mouse and man, but differentially expressed on human cells have more suitable residues than those differentially expressed on mouse cells, in a pattern very similar to that found for human or mTpn-specific peptides from .220 cells. This suggests that the function of mTpn for B*2705 peptide loading is not improved when other components of the loading complex are also of mouse origin. Therefore, suboptimal peptide presentation, relative to humans, is to be expected when B*2705 is expressed on mouse cells and transgenic mice.

We thank Anabel Marina and Ricardo Ramos (Centro de Biología Molecular Severo Ochoa, Madrid, Spain) for assistance in MS and RT-PCR, respectively, Juan J. Cragnolini and Elena Merino for their help, and Luis Antón for critical comments.

The authors have no financial conflict of interest.

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 supported by Grants SAF2002/00125 and SAF2003/02213 from the Ministry of Science and Technology, 08.3/0005/2001.1 from the Comunidad Autónoma de Madrid, and an institutional grant of the Fundación Ramón Areces to the Centro de Biología Molecular Severo Ochoa. A.W.P. is a recipient of the Russell Grimwade Fellowship.

3

Abbreviations used in this paper: Tpn, tapasin; hTpn, human Tpn; mTpn, mouse Tpn; .220, 721.220; β2m, β2-microblobulin; MS, mass spectrometry; MS/MS, tandem MS; RF, residue frequency; DMP, deviation from mean frequency in the human proteome; m/z, mass-to-charge.

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