By
From the * Microbiology and Tumor Biology Center, Karolinska Institute, S-171 77, Stockholm,
Sweden; and Institute of Biochemistry and Molecular Biology, University of Ferrara Medical School,
44100 Ferrara, Italy
The T cell receptor (TCR) repertoires of cytotoxic responses to the immunodominant and
subdominant HLA A11-restricted epitopes in the Epstein-Barr virus (EBV) nuclear antigen-4
were investigated in four healthy virus carriers. The response to the subdominant epitope
(EBNA4 399-408, designated AVF) was highly restricted with conserved V usage and identical length and amino acid motifs in the third complementarity-determining regions (CDR3),
while a broad repertoire using different combinations of TCR-
/
V and J segments and
CDR3 regions was selected by the immunodominant epitope (EBNA4 416-424, designated
IVT). Distinct patterns of interaction with the A11-peptide complex were revealed for each AVF- or IVT-specific TCR clonotype by alanine scanning mutagenesis analysis. Blocking of
cytotoxic function by antibodies specific for the CD8 coreceptor indicated that, while AVF-specific TCRs are of high affinity, the oligoclonal response to the IVT epitope includes both
low- and high-affinity TCRs. Thus, comparison of the memory response to two epitopes derived from the same viral antigen and presented through the same MHC class I allele suggests that immunodominance may correlate with the capacity to maintain a broad TCR repertoire.
Recognition of MHC-peptide complexes by TCRs is
an essential step in the establishment of protective
immunity (1). The TCR is a heterodimer composed of
two polypeptide chains, CTLs expressing the TCR- Generation of CTL Cultures and Clones.
EBV-specific CTL cultures were obtained by stimulation of lymphocytes from the EBV
seropositive donors BK (HLA A2, A11, B7, B62), CA (HLA
A11, A32, B18, B35), ZA (HLA A3, A11, B35), and EA (HLA
A10, A11, B35.3, B51) with the autologous B95.8 virus transformed LCLs. After two or three consecutive restimulations the
cultures were expanded in complete medium supplemented with 10 U/ml recombinant IL-2 and 30% (vol/vol) culture supernatant from the gibbon lymphoma line MLA144 (16). Single cell
cloning was done by limiting dilution in IL-2-supplemented medium containing 105 irradiated (3,000 Rads) allogeneic PHA-pulsed PBLs as feeder. The EBV specificity and HLA class I restriction of the clones was assessed in 51Cr-release assays against a
panel of EBV-positive and -negative targets including the autologous lymphoblastoid cell lines (LCLs), allogeneic LCLs matched
through single class I alleles, at least two cell lines for each allele,
PHA activated blasts, HLA mismatched LCLs, and the prototype
NK-sensitive target K562. PHA blasts were preincubated with
10-9 M of the relevant synthetic peptide during 51Cr labeling followed by extensive washing before the cytotoxicity tests. Sensitivity to CD8 blocking was assessed by preincubating the targets
in the assay wells with the indicated amounts of purified anti-human CD8 mouse mAbs (OKT8 ATCC CRL8014) for 30 min
at room temperature before addition of the effectors.
RNA Extraction, First Strand cDNA Synthesis, PCR Amplification, and Sequencing.
Total RNA was extracted from 2-10 × 106
cells by the single-step acid guanidinium thiocyanate-phenol-chloroform method (17). For first-strand cDNA synthesis, 1-2
µg of total RNA were incubated at 42°C with 200 U of moloney
murine leukemia virus reverse transcriptase (Seikagaku America,
Inc., Rockville, MD), 30 pmol random hexamer primers (Clontech, UK), and 0.5 mM dNTP (Pharmacia, Uppsala, Sweden) in
a buffer containing 50 mM Tris-HCl, pH 8.3, 75 mM KCl, and 3 mM MgCl2 in a total volume of 30 µl. The reaction was run for 60 min and stopped by heating at 94°C for 5 min. PCR primers
specific for the variable and constant domains (Clontech, Palo
Alto, CA) were used to amplify 22 Memory CTL responses were reactivated in vitro by
stimulation of lymphocytes from four A11+ EBV carriers
with autologous EBV transformed LCL and EBV-specific T cell lines were cloned by limiting dilution. In accordance
with previous observations in polyclonal cultures (11), the
A11-restricted response was strongly dominated by CTL
clones specific for the IVT epitope in two of the donors,
BK and CA (Table 1). Two donors that yield cultures with
comparable IVT and AVF-specific activities (ZA and EA)
were included to avoid biases due to unequal representation of the two specificities.
and
or
and
, which contain
a variable domain, involved in antigen recognition, and a
constant domain which is important for membrane attachment and T cell activation (2). The variable domain is encoded by multiple variable (V), diversity (D), and joining
(J) gene segments. Somatic DNA rearrangement during
lymphocyte differentiation in the thymus juxtapose V-J or
V-D-J segments that code for the
/
and
/
chains, respectively. This combinatorial capacity creates an array of
unique TCRs capable of recognizing a large variety of
epitopes. The diversity is further increased by several possible
/
or
/
pairings and by nucleotide additions and/or trimming at the V(D)J junctions. The size of the repertoire
that may potentially interact with a given antigen is narrowed by positive and negative selection in the thymus (3,
4). Further restrictions are imposed on the peripheral repertoire by the nature of the antigenic stimulus where the antigenic load and the persistence of the stimulus over a long period of time are likely to be important parameters (5).
/
-heterodimer and CD8
coreceptor play a critical role in controlling infection by
EBV, a widespread human herpes virus that persists in
healthy carriers as a latent infection of B cells (6, 7). In spite
of the large complexity of the virus, which encodes for at
least 9 proteins expressed in latently infected B lymphocytes, the CTL response detected during primary EBV infection appears to be preferentially focused on only few epitopes
that are mainly derived from the high molecular weight
Epstein-Barr virus nuclear antigens (EBNA)1 3, 4, and 6 (also known as EBNA 3A, 3B, and 3C) (8, 9). The reason
for this strong focusing is presently unknown, but it is remarkable that a very similar hierarchy of epitope choice is
maintained in the memory CTL responses that can be reactivated by in vitro stimulation of lymphocytes from healthy
virus carriers. We have previously reported that EBV-specific
CTL responses of HLA A11+ Caucasians are frequently
dominated by A11-restricted CTLs that are directed to several epitopes derived from EBNA4 (10). The cognate
peptides of two epitopes have been mapped within EBNA4 residues 416-424 (IVTDFSVIK, designated IVT) and 399-408 (AVFDRKSDAK, designated AVF) (11, 12). IVT-specific
effectors may account for as much as 80% of the EBV-specific CTL clones isolated from these donors indicating that
this is the immunodominant epitope (13). The immunodominance of the IVT epitope has recently been confirmed in a study that compared the frequency of specific
CTL precursors in primary and memory response (14).
Mutations affecting the anchor residues of the IVT peptide
were shown to abrogate CTL recognition in EBV isolates
from Southeast Asia, where HLA A11 is expressed in
>50% of the population. Only half of the Southeast Asian
isolates carried concomitant mutations within the AVF
peptide, suggesting that CTL responses to IVT may exert a
stronger selective pressure in vivo (12, 15). We have exploited these features to examine to what extent immunogenicity may affect the diversity of TCR repertoires specific for different viral epitopes during long-term persistent
infection, where the opportunity for selection of T cell
clones with maximal affinity might be optimal.
chain and 24
chain TCR
families. Each PCR reaction contained 0.5 µM of primers, 2% of
the product of the cDNA synthesis, 0.2 mM dNTP, 2U Taq
polymerase (Amersham International, Amersham, UK), 10 mM
Tris-HCl, pH 8, 50 mM KCl, 1.5 mM MgCl2, and 0.01% gelatin
in a final volume of 50 µl. The reaction was overlaid with 50 µl
of mineral oil and amplification was run for 30 cycles of 1 min
denaturation at 95°C, 1 min annealing at 55°C, and 1-min extension at 72°C. 10% of the PCR product was analyzed in a 1.8%
agarose gel containing 0.5 µg/ml ethidium bromide. The amplified fragments were then cloned into the EcoRV site of the pGEM plasmid (Promega Corp., Madison, WI). 10 µg of the recombinant plasmid DNA was denatured for 10 min with NaOH,
neutralized with sodium acetate, pH 4.8, ethanol precipitated,
and used for sequencing. The M13 universal (CGACGTTGTAAAACGACGGCCAGT) and M13 reverse oligonucleotides (CAGGAAACAGCTATGAC) were fluorescein labeled and used to
prime upstream and downstream of the cloning site. 5 pmol of
the fluorescent primer was annealed to denatured plasmid DNA
for 5 min at 65°C followed by 10 min at 37°C and 10 min at
room temperature in a 14 µl buffer containing 140 mM Tris-HCl, pH 7.6, and 14 mM MgCl2. 8 U T7 DNA polymerase, 3 µl
of DMSO and 1 µl of a mix containing 300 mM citric acid, 325 mM DTT, and 40 mM MnCl2 were added and the reaction was
split in four aliquots. Each aliquot was incubated with one of the
four dideoxynucleotides (Pharmacia) for 5 min at 37°C. The reactions were terminated by adding an equal volume of deionized
formamide and 5 µg/µl blue dextran. Samples were loaded onto
a 0.5-mm-thick 6% polyacrylamide gel containing 7 M urea and
run in an A.L.F. DNA sequencer (Pharmacia). Alternatively, recombinant plasmid DNA was used as template for PCR amplification using primers located downstream and upstream of the
cloning site in the pGEM vector (coordinates 2874-2892 and
222-241). One of the primers was biotinylated at the 5
end. PCR
amplified material was separated with Dynabeads M280-streptavidin (Dynal, Norway) and the immobilized double strand DNA
was denatured with 0.1 N NaOH at room temperature for 6 min.
The biotinylated single-strand template DNA was primed and sequenced as described with the only modification that annealing
was performed at 60°C for 10 min. From each CTL clone, between three and six independent TCR
and
chain clones
were sequenced.
The TCR and
chain usage of a representative panel
of 19 AVF-specific clones from the four donors and 24 IVT-specific clones from three of the donors was determined by polymerase chain reaction (PCR)-assisted cDNA
amplification. All AVF-specific clones expressed TCRBV3S1
(Table 2). This was paired to TCRAV1S4 in clones derived from three of the donors (BK, CA, and ZA; AVF
type I), while all clones from EA expressed the closely related TCRAV16S1 (AVF type II). Sequencing of the PCR
products demonstrated the regular rearrangement of BV3S1
to BJ2S2, AV1S4 to AJ21, and AV16S1 to AJ40. Comparison of the predicted amino acid sequences of the 19 V
chains revealed CDR3 regions of equal length and identical
protein sequence in all clones expressing a given VJ combination, with variations in codon usage restricted to the N
regions (Fig. 1 A). The codon for Asp at position 94 was
generated by N additions and was consistently preceded by
the codons for Gly in clones expressing AV1S4J21, or Ser
in the AV16S1J40 clones. The V
sequences of clones expressing the AVF type I receptor also showed a remarkable
similarity. A conserved Thr-Ser-Ala motif was generated in
the NDN region of all but one sequence that carried a Thr
to Ala substitution. This motif was not present in the junctional region of the AVF type II TCRs, although a strict
requirement for length maintenance in the CDR3 loop
was suggested by the replacement of two germ line encoded Ser residues at positions 94 and 95 with ND encoded Thr and Gly. A remarkable conservation of TCR
V
usage was previously reported in EBV-specific CTLs
that recognize the EBNA3 325-333 epitope. Identical amino
acid and nucleotide sequences were detected in the V
CDR3 regions of the EBNA3 325-333-specific TCRs isolated from four individuals (18). However, the usage of
germ line sequences indicates that a preferentially favored
rearrangement may contribute to the conservation of this
response. This is clearly not the case in the AVF-specific
response. The significant differences between the
and
chain nucleotide sequences and the regular occurrence of
N additions confirm the origin of AVF-specific TCRs from independent recombination events even in clones derived from the same individuals (Fig. 1, donor BK). This
finding stresses the importance of the conserved features of
the AVF-specific TCRs for interaction with the A11-peptide complex. A different scenario was revealed by analysis
of the repertoire specific for the immunodominant IVT
epitope. Each of the 24 IVT-specific clones analyzed expressed one of nine distinct TCR-
/
heterodimers (Table
2). Four IVT-specific clonotypes were identified in donor
BK, one in CA, and four in EA with no identical or even
similar TCR isolated from more than one donor. Sequence
comparison showed no preferential usage of TCRJ segments and no apparent conservation of CDR3 amino acid composition. Different sets of N or NDN additions resulted in the generation of CDR3 loops of variable length
and amino acid composition (Fig. 1 B).
|
To determine how the TCR structural differences related to target recognition, the fine specificity of clones
representing the two AVF-specific and nine IVT-specific
TCR types was determined using peptide analogues in
which each residue of IVT or AVF was sequentially substituted by Ala. Analysis of the HLA A11 binding motif (19)
and molecular modeling of the IVT- and AVF-containing complexes (20) indicate that Val at position 2 (P2) and the carboxy-terminal Lys serve as the main anchors. In accordance, the IVT-A9 and AVF-A10 analogues failed to stabilize A11 expression in transporter associated with antigen
presentation (TAP) mutant cells (not shown) and were not
included in this study. Residues at P1, P4, P5, P7, and P8
of IVT are predicted to point away from the binding
groove and be accessible to TCR while the side chains of
residues in P3 and P6 are likely to face the cleft, serving as
accessory anchors. Sequence variations between IVT-specific TCR types were reflected in unique fine specificity
patterns (Fig. 2). Whereas all clones were affected by substitutions at P4 and P5, that may represent important TCR
contact sites, the type-IX TCR interacted stringently only
with the central residues of the peptide and the remaining
TCRs appeared to scan the complex with preferential recognition shifting from the COOH terminus (IVT types I,
VI, II) to the NH2 terminus (IVT type VIII). The full array
of potential contact residues was recognized by TCR type III, V, VII, and IV, albeit with different stringency. The effect of substitutions in P2, P3, and P6 suggests that they
may induce conformational changes that indirectly affect
the interaction with certain TCRs. It should be noted that
all clones recognized equally well the wild-type peptide
with half-maximal lysis observed at concentrations between
5 and 10 pM, confirming that the different recognition of
the analogues is not an artifact due to different efficiency of
the CTLs (not shown). As predicted by the conserved TCR usage, AVF-specific clones showed a homogeneous
pattern of interaction with the Ala replacement set. All type
I TCRs were sensitive to substitution of the solvent exposed residues in P4, P6, and P8 of the AVF peptide, and
were also affected by replacement of the Phe in P3, probably due to significant conformational changes. Differences
were observed when clones expressing BV3S1D2J2S2 chains containing Arg, Val, Pro, or Leu at position 96 were compared for recognition of the wild-type peptide presented by
other members of the HLA A11 family (A1, A3, and Aw68,
not shown), suggesting a possible role of this residue in
contacting the -helix. The Thr(Ala)-Ser-Ala motif may
interact with the peptide since the type II clones, that lack
the motif, were not affected by substitution of the Asp in P4.
Tolerance to self antigens may diversify the peripheral
repertoire specific for a given epitope by deleting cross-reactive TCRs of high affinity (21). We sought to determine whether a similar phenomenon may explain the
discrepancy between IVT- and AVF-specific responses. In
vitro studies with soluble molecules have revealed that CD8
enhances the T cell receptor interaction with its ligand
(25). The triggering of cytotoxic functions is regulated by
the cooperative influence of several factors where, in the
presence of equal ligand density, TCR affinity correlates with resistance to blocking of the CD8 coreceptor (26, 27). The IVT and AVF peptides bind equally well to HLA A11
and similar titration curves are obtained when IVT- and
AVF-specific effectors are compared for lysis of peptide-pulsed targets (13). Taking advantage of these features, we
tested the effect of increasing amounts of anti-CD8 antibodies on the cytotoxic activity of clones expressing different TCRs (Fig. 3). Reproducible levels of inhibition were
observed in repeated experiments performed with each
clone. The AVF-specific effectors were not affected by addition of 60 ng of the purified antibody and <50% inhibition was achieved at 75-fold higher concentrations suggesting that they express TCRs of high affinity. In contrast, the
IVT-specific repertoire included TCRs of both high and
low affinity, with each TCR type falling in a distinct range
of sensitivity. This and the demonstration that all potential
TCR contact residues are recognized by at least some of
the IVT-specific effectors supports the view that the diversity of this repertoire is not caused by elimination of a self-reactive TCR.
We have shown that the differences in immunogenicity of the AVF and IVT epitopes correlate with the diversity of the epitope-specific T cell repertoire recruited in memory response. Antigen load is likely to play a crucial role in the maintenance of this repertoire. An interesting parallel may be drawn with the development of antibody responses. When antigen becomes scarce in the late phase of the response, clones expressing low-affinity immunoglobulin receptors develop into plasma cells, whereas clones carrying high-affinity receptors remain in the proliferating pool for additional cycles of replication (28, 29). It is tempting to speculate that antigen load may operate in a similar fashion in the peripheral selection of distinct populations of specific T cells. This would predict a direct correlation between the efficiency of presentation of a given epitope and the degree of diversity of the selected repertoire. In line with this prediction, we have recently reported that 10-fold higher amounts of the immunodominant IVT epitope can be recovered from HLA A11 positive LCLs as compared to the subdominant AVF (13). It is likely that chronic stimulation by cells presenting a low density of ligands, as in the case of the AVF epitope, would favor the generation of homogeneous responses composed of clones with high affinity TCRs. Conversely, the higher IVT load would allow the selection of both high and low affinity resulting in a broader response.
To our knowledge, this is the first demonstration that a highly restricted or a diverse repertoire may be recruited in the memory response by two epitopes derived from the same protein and restricted through the same class I allele. Our data suggest that the diversity of the peripheral repertoire is principally a function of the antigenic peptide itself and is influenced by the degree of immunogenicity. Antigen load is likely to account for our findings, although the structure of the epitopes, notably the TCR contact surface of AVF, with three charged residues in adjacent positions (Asp-P4, Lys-P6, and Asp-P8), may also play a role. Differences in the repertoire may already exist before peripheral selection as fewer naive cells may meet the TCR-CDR3 charge requirements for efficient docking to the AVF epitope. Ligand density would superimpose further selection in the periphery to generate the final profile of the memory repertoire. Further studies of TCR usage in conditions where these epitopes are not in short supply, as during primary EBV infection, are needed to assess to which extent the repertoires detected in memory responses reflect the preservation of selected T cell clones.
Address correspondence to Maria G. Masucci, Microbiology and Tumor Biology Center, Karolinska Insitute, S-171 77 Stockholm, Sweden. Phone: 46-8-728-64-00; FAX: 46-8-33-04-98.
Received for publication 30 January 1997 and in revised form 4 April 1997.
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