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The Journal of Immunology, 2002, 168: 3801-3807.
Copyright © 2002 by The American Association of Immunologists

A Molecular Marker for Thymocyte-Positive Selection: Selection of CD4 Single-Positive Thymocytes with Shorter TCRB CDR3 During T Cell Development1

Maryam Yassai*, Kristin Ammon*, Joan Goverman{dagger}, Phillipa Marrack{ddagger}, Yuri Naumov* and Jack Gorski2,*

* Blood Research Institute, Blood Center of Southeastern Wisconsin, Milwaukee, WI 53201; {dagger} Department of Immunology, University of Washington, Seattle, WA 98105; and {ddagger} Howard Hughes Medical Institute, National Jewish Medical and Research Center, Denver, CO 80206


    Abstract
 Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 
The generation of the naive T cell repertoire is a direct result of maturation and selection events in the thymus. Although maturation events are judged predominantly on the expression of surface markers, molecular markers, more intimately involved in the selection process, can be informative. We have identified a molecular marker for selection in later stages of maturation in humans. Thymocytes are selected for the expression of TCR {beta}-chains with shorter CDR3 at the double-positive to single-positive (SP) transition. Here we extend these studies to the mouse and show that the selection phenotype is not related to {alpha}-chain pairing but is a function of the MHC haplotype. Interestingly, the selection is much more apparent in CD4 SP thymocytes than in CD8 SP cells. This is in contrast to human thymocytes, where the selection is equally apparent in both lineages. The involvement of MHC in the process argues that this is a positive selection stage. The difference in the extent of this selection between the two SP lineages may indicate a class difference in the nature of the TCR-MHC interaction, the role of coreceptors in the selection process, or both.


    Introduction
 Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 
Prior to exit from the thymus, T cells follow a developmental pathway that includes a number of selection events involving the TCR. The first of these is the selection of cells that have properly rearranged the TCRBV gene (1) that pairs with the pre-T {alpha}-chain (2), generating the pre-TCR. This occurs while the cells still lack expression of the three classical surface markers, CD3, CD4, and CD8. Selected cells expand and give rise to the CD4 and CD8 double-positive (DP)3 population. The next maturation stage involves generation of the mature TCR by the substitution of the pre-T {alpha}-chain with productively rearranged {alpha}-chains (3). This is followed by maturation from DP to single-positive (SP) cells. This last event marks the commitment to either the CD4 or CD8 lineage. Lineage commitment is thought to involve TCR recognition of the MHC, although there are two classes of models (4) that differ as to when in the lineage commitment process the MHC recognition takes place. The lineage commitment process is still the subject of study, and there are data that support both models (5, 6).

During maturation, thymocytes undergo two types of TCR-mediated selection processes, positive and negative. Negative selection is a relatively straightforward phenomenon, involving the elimination of thymocytes the TCR of which recognizes its thymic ligand too avidly (7). Because the MHC:peptide complexes present in the thymus are reflective of self, negative selection accounts for thymic tolerance (8). Positive selection is generally defined as any thymic developmental stage in which thymocyte survival requires the TCR to recognize MHC:peptide (9, 10). In many studies, lineage selection has been used as a readout for positive selection, although it is unclear whether the two are directly linked (11, 12). A number of studies have indicated that the DP-SP transition is the time at which most selection takes place (11, 13, 14). The events at this boundary may be complex including selection of properly paired {alpha}- and {beta}-chains ({alpha} selection), as well as positive and negative selection. A more detailed examination of these events is hampered by a lack of additional phenotypes that can be analyzed at the DP to SP boundary.

We analyzed the rearrangement profiles of TCR {beta}-chain genes at the DP and SP stages to test for an event that may indicate selection for well-paired receptors. Our recent observations with human thymocytes indicated that selection for thymocytes with shorter CDR3 is observed between the DP and SP stages (15). We were also able to determine that the selection occurred after pairing of the TCR {alpha}- and {beta}-chains. Here we use the genetic tools available in the mouse to extend our understanding and to test whether the short CDR3 phenotype represents a result of selection on MHC and/or peptide.


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

Mice of the strains C57BL/6, 129Sv, C57BL/10, B10PL, PL, and DBA/1 were obtained from The Jackson Laboratory (Bar Harbor, ME) . The generation (16) and the characterization (17) of the {alpha}-chain TCR-transgenic mice used in these experiments have been described previously as well as the generation and characterization of the single-tethered peptide mice (18). H2-DM{alpha} null mice (19) on the BL6 x 129 background were obtained from The Jackson Laboratory. Mice used in the experiments were 3–4 wk old and were not matched for gender.

Fluorescent staining and sorting

Thymi or spleens were disaggregated by passing through a wire mesh. Cells were suspended in RPMI (Life Technologies, Gaithersburg, MD), 0.1% sodium azide, and 2% FCS (Life Technologies). In the case of spleen, RBC were lysed by adding 0.5 ml filtered distilled water to the cell pellet and immediately adding medium containing 10% FCS. Thymocytes and splenocytes were analyzed by staining 0.5 x 106 cells with mouse mAbs specific for the murine cell surface markers: CD3-FITC conjugate; TCR-{beta}-FITC conjugate (clone H57-597); CD4-Tri-Color conjugate and CD8 R-PE conjugate (Caltag Laboratories. San Francisco, CA); and V{alpha}2-FITC (BD PharMingen. San Diego, CA). The stained cells were analyzed using FACScan (BD Biosciences, San Jose, CA) and sorted on a FACStar (BD Biosciences). Cells were collected into 0.5 ml FCS to a final volume of 5 ml, so that the final FCS concentration in the tube was 10%.

Preparation of DNA from sorted cells

Cells were spun down and resuspended in nucleic lysis buffer, pH 8.2 (10 mM Tris, 0.4 M NaCl, 2 mM EDTA) in the presence of SDS and proteinase K. The cells were incubated overnight at 45°C to ensure complete lysis. After incubation, proteins were precipitated by adding 5.3 M NaCl, and DNA was isolated from the supernatant by ethanol precipitation (20).

Rearrangement analysis

Rearrangement analysis was performed by PCR amplification of the TCR CDR3 using V and J region-specific primers. The primers used in these experiments are described in Table IGo. The V or J region primer was labeled with fluorescein, and the PCR products were analyzed on denaturing polyacrylamide gels. The fluorescent PCR products quantitated using a FluorImager (Molecular Dynamics, Sunnyvale, CA). The gel data were collected as a 16-bit TIFF file, and the intensities could be analyzed using software (ImageQuant) provided by Molecular Dynamics. Band intensities can be further analyzed using ImageQuant and spreadsheet software. For calculation of CDR3 length changes, band intensities originally measured as relative fluorescence units by the FluorImager were converted to the relative frequency (RF) of each band over the total band intensity. The relative band intensities correct for minor fluctuations in the data. Use of RF to calculate shortening is shown in Fig. 1Go and described in Refs. 15 and 21 . The analyses were performed on DNA samples that were titrated to ensure equal efficiency of amplification of the {beta}-chain DNA constant region. The titration procedure is described in greater detail in Ref. 21 .


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Table I. Primers used for CDR3 length analysis1

 


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FIGURE 1. Recombination analysis of TCR {beta}-chain CDR3 regions from thymocytes and splenocytes. A, 129 mouse; B, BL/6 mouse. The analysis shows the CDR3 length profiles of BV8.3 recombining with J1.1, J1.2, or J1.3. The J region analyzed is identified above each pair of lanes. Lane S, splenocyte data; lane T, thymocyte data. C, Plot of the {Delta}RF between lanes T and S for the 129 mouse data in A, and calculation of the skew. The bands compared are identified in A.

 

    Results
 Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 
Peripheral T cells have shorter TCR {beta}-chain CDR3 than do thymocytes

The studies presented here use rearrangement analysis of TCR {beta}-chain CDR3. In this method, the CDR3 is PCR amplified using BV- and BJ-specific primers, and the different CDR3 lengths resolved on denaturing polyacrylamide gels. The approach is similar to that used by Mallick et al. (1), Dudley et al. (22), and Pannetier et al. (23). As long as the PCR is in a range where all signals are a function of input (21), the measurement gives a global view of the CDR3 length distributions of a particular V-J rearrangement.

The primary observation indicating a difference in the CDR3 length distribution in immature and mature T cells that led us to investigate this phenomenon in both mice and humans came from the comparison of the rearrangement profiles of CDR3 from thymocytes and peripheral T cells. An example of such data is shown in Fig. 1Go for a 129 and a BL/6 mouse. Each pair of lanes shows the rearrangement profile of a PCR amplification with a BV1 and a particular JB primer (identified above the lanes). The DNA used was normalized on the basis of amplifiable {beta}-chain C-region DNA. Visual inspection provides evidence that the band intensity distribution of total thymocytes is skewed toward higher molecular mass bands. This indicates that peripheral T cells constitute a population that has been selected for those having rearranged TCR {beta}-chains with a shorter CDR3.

Although individual rearrangement assays can be analyzed by visual inspection, analyzing a larger data set requires a more quantitative approach. To do so, the difference between the relative frequency distributions of the bands in two or more populations is calculated. This has been described in our previous work in human thymocytes (15). The fluorescent scan of the gel bands is converted to the RF of each band by dividing the band intensity by the total of all band intensities. The RF for each spleen band is subtracted from that of the corresponding thymus band (Fig. 1GoC) yielding the difference in RF ({Delta}RF). Positive values indicate an increased frequency for that particular CDR length in the thymus, whereas negative values indicate increased frequency in the spleen. Shortening is indicated by a cluster of positive values on the right of an inflection point with a corresponding cluster of negative values to the left of the inflection point. The increased incidence of T cells with shorter CDR3 in the spleen as compared with thymus can be easily determined from the {Delta}RF plot. To generate a measure of the extent of shortening, the {Delta}RF to the right of the inflection point are summed (Fig. 1GoC). If there are both positive and negative values in this region, the values will cancel out. If all values are positive, this will result in a higher value. This measure is referred to as the skew. For a valid comparison of two (or more) skew values, the same V-J rearrangements must be analyzed.

Selection for thymocytes with shorter CDR3 takes place at the DP->SP boundary

To determine where in T cell maturation the selection was taking place in mice, the {Delta}RF was determined for {alpha}{beta}- DP and {alpha}{beta}+ CD4 SP thymocytes from two BL/6 mice. Fig. 2Go, A and B, shows the results for the analysis of BV1 gene rearrangements with the six BJ2 genes for the two mice. The accumulation of CD4 SP with shorter CDR3 can be seen for most of the BJ combinations. BJ2.1 is an example where the skew is minimal. The skew values for both mice are much higher than the control (Fig. 2GoE, described below).



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FIGURE 2. Analysis of shortening in two different BL/6 mice. Rearrangements between BV1 and all the BJ2 are shown. The identity of the J region analyzed is given in the inset. A and B, {Delta}RF between {alpha}{beta}- DP and {alpha}{beta}+ CD4 SP data from the two mice, respectively. The skew values indicating the overall shortening are similar for the two animals. C and D, {Delta}RF between {alpha}{beta}- DP and {alpha}{beta}+ CD8 SP data for the two mice. As a control, E shows the {Delta}RF between the DP populations of the two mice. Because the CDR3 length distributions should be similar in the DP of two different mice, the {Delta}RF values should fluctuate around zero. In keeping with a lack of shortening, the skew values are very low.

 
Selection for shorter CDR3 occurs to a much greater extent in the CD4 SP compartment than in the CD8 SP compartment

The analysis was extended to the {alpha}{beta}+ CD8 SP population. There is much less evidence for the selection of thymocytes with shorter CDR3 in the {alpha}{beta}+ CD8 SP thymocyte population (Fig. 2Go, C and D). There is still evidence for selection given that there is a tendency for the {Delta}RF to be positive on the right and negative on the left; however, the overall skew is greatly reduced as compared with the CD4 SP.

As a control, the {Delta}RF of the {alpha}{beta}- DP populations in both mice is compared (Fig. 2GoE). We would expect that the two distributions should be identical. The data do not show a large difference in {Delta}RF between the two mice, and there is no clustered pattern of positive or negative values. Choosing an inflection point in a data set such as these is not evident, and the ones used are based on the inflections observed in Fig. 2Go, A and B. However, changing the inflection point did not greatly alter the actual value, because both positive and negative values are added on either side. The low skew value of this control indicates that the observation of a low level of shortening in CD8 SP cells is biologically significant. Nevertheless, a much higher degree of CDR3 length selection takes place in the CD4 lineage.

TCR {alpha}- and {beta}-chain pairing is not associated with selection of cells with short CDR3

It was of interest to determine whether the selection for short CDR3 sequences is a function of the pairing process between the {beta}-chain and the {alpha}-chain. We took advantage of the fact that mice expressing a transgenic TCR {alpha}-chain gene can predominantly express the transgenic {alpha}-chain, resulting in a sizable population of DP {alpha}{beta}+ thymocytes than can be identified by the expression of the {alpha}-chain. This facilitates the analysis of these cells. Mice analyzed in these experiments express the V{alpha}2 chain of the 172.10 TCR, which is specificity for the myelin basic protein peptide 1–11 presented by I-Au. The transgene has been bred onto two backgrounds, B10.PL and DBA, which differ in their ability to select for the TCR {beta}-chain that corresponds to the hybridoma of origin (14). Preliminary experiments comparing thymocytes and splenocytes showed that the selection for a short CDR3 in CD4 SP can be observed in {beta}-chains of wild-type DBA mice whereas the effect was much reduced in B10PL mice. Thus, the DBA strain was used. Staining of transgenic DBA thymocytes with mAbs specific for the TCR {beta}-chain or for the V{alpha}2 chain gave very similar profiles, indicating that most of the TCR on the surface use the V{alpha}2 chain (Fig. 3GoA). Therefore, the CDR3 analysis was performed on the {alpha}{beta}- DP, {alpha}{beta}low DP, and {alpha}{beta}high CD4 SP thymocyte populations from {alpha}-transgenic mice on the DBA background. Cells were sorted on the basis of {alpha}{beta} TCR, CD4, and CD8 expression into three subsets: {alpha}{beta}- DP, {alpha}{beta}low DP and {alpha}{beta}high CD4 SP (Fig. 3GoB). The {Delta}RF comparison between the {alpha}{beta}low DP and CD4 SP populations showed a definite selection for short CDR3 (Fig. 3GoC), whereas there was no evidence of selection for short CDR3 between the {alpha}{beta}- and {alpha}{beta}low DP populations (Fig. 3GoD). If the selection phenotype is a function of the ability of the two TCR chains to pair and generate {alpha}{beta}+ thymocytes, the expected result would be the observation of shorter CDR3 in the {alpha}{beta}low DP cells. Because the selection was observed between the {alpha}{beta}low DP population and the {alpha}{beta}+ CD4 SP population, the CDR3 length selection process does not correlate with the act of pairing of the two receptors at the DP stage.



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FIGURE 3. Analysis of CDR3 lengths in thymocyte populations from {alpha}-transgenic mice on the DBA background. A, Comparison of thymocytes stained with a TCR-{beta}-chain-specific mAb (gray) and an AV2-specific mAb (white). B, Definition of sort gates. Thymocytes were fractionated on the basis of TCR{beta} expression into three regions. These were further fractionated on the basis of CD4 and CD8 expression into {alpha}{beta}- DP, {alpha}{beta}low DP, and {alpha}{beta}high CD4 SP. C, {Delta}RF analysis of the transgenic animals comparing the {alpha}{beta}low DP and the CD4 SP populations. D, {Delta}RF analysis of the two DP populations ({alpha}{beta}- and {alpha}{beta}low). The V-J combinations used for the analysis are described in the inset.

 
Selection for shorter CDR3 is a function of the class II MHC

In comparing B10.PL and DBA strains, we had observed strain-specific differences in the extent to which selection of shorter length CDR3 can be observed. This was investigated in more detail by analyzing the process in a number of mouse strains that shared different MHC loci. The strain that was originally identified as showing very low levels of shortening was B10.PL, and the possible role of the H-2u haplotype investigated by analysis of PL mice. The {Delta}RF were compared between {alpha}{beta}- DP and {alpha}{beta}+ CD4 SP thymocytes from these mice (Fig. 4GoA). The results in these two strains were compared with those for B10 and 129 that are H-2b (Fig. 4GoB). The BV1 rearrangements with all the BJ2 genes were analyzed. The skew values for the H-2u strains is lower than that for the H-2b strains. The data from Figs. 2Go and 4Go, as well as the analysis of additional PL, B10.PL, and 129 mice, are shown in Table IIGo. The reproducibility of the shortening analysis is shown by the similar skew values of the additional mice. Thus, the skew of the H-2b strains is 2 times that observed for the H-2u strains.



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FIGURE 4. Comparison of {Delta}RF profiles from H2u and H2b strains. A, H2u strains; B, H2b strains. Mice were sorted for CD3-; DP and CD3+; CD4SP and CD3 lengths were analyzed. The difference in the overall shortening is 2-fold higher in the H2b strains as indicated by the skew values. Data are for BV1 rearrangements, and the mouse and J region analyzed is described in the inset.

 

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Table II. {alpha}{beta}-DP - CD4 SP skew values for a number of strains

 
The sensitivity of the measurement is shown by a mixing experiment in which the skew was calculated between thymocytes and splenocytes from 129 and from PL mice, as well as between thymocytes and a 50:50 mixture of splenocytes from the 129 and PL mice. The same V-J combinations were analyzed as in the strain analysis. The skew value of the 50:50 mixture (0.45) was almost identical with that of 50% of the sum of the independent skews from the 129 (0.56) and PL (0.32) mice (0.5 x (0.56 + 0.32) = 0.44). Thus, we could easily observe intermediate skew values if such had been present.

The difference in extent of shortening between these mouse strains strongly suggests that the selection for thymocytes with shorter length CDR3 is a function of the MHC. Because, the shortening is predominantly a CD4 phenomenon, we would expect that it is the class II MHC that is involved.

Shortening is observed with low peptide complexity

The data in the previous sections show that the nature of the MHC has an effect on the selection phenotype. It was therefore of interest to determine whether the peptides bound by the MHC could also have an effect. As a first test of this, we took advantage of the availability of mice expressing a single peptide tethered to I-A. On an Ii-/-I-A-/- background, almost all of the I-A molecules are loaded with the tethered peptide. The total I-A on the surface of thymus and spleen can be all accounted for by the expression of the peptide specific epitope (24). Mice expressing two such constructs, wherein the peptide differed only in a TCR-contact residue, increased the complexity of the repertoire in an additive manner (24). Using such mice in our rearrangement assay may show differences from the normal selection for thymocyte with shorter CDR3. If peptide contacts are important, with some peptides having a large effect and other peptides having no effect, then a perturbation of the phenotype may be possible. The results of the analysis of a mouse expressing the I-E{alpha} peptide tethered to I-Ab as the only surface MHC molecule is shown in Fig. 5Go. The sorted thymocyte populations, and an example of the CDR3 length data are shown in Fig. 5GoA. There is evidence of a selection for short CDR3 in the CD4 SP population. The extent of shortening as defined by the skew value (Fig. 5GoB) is not that different from that observed in the control animal (Fig. 5GoC). There is a small difference in the {Delta}RF pattern with a number of positive values in the negative (left) portion of Fig. 5GoB. This irregularity may point to some subtle differences in the selection process. Similar results were obtained in mice in which class I MHC was expressed in addition to the tethered peptide-class II molecule. The replacement of the normal multiplicity of peptides presented by class II with a single peptide had a minimal effect on the CDR3 length selection.



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FIGURE 5. Rearrangement analysis of thymocytes from single peptide:MHC mice. Thymocytes from mice expressing a tethered I-E{alpha} peptide bound to I-Ab on a Inv-/-I-A{beta}-/-{beta}2m-/- background were fractionated and analyzed. A, Sorting gate for CD3+ cells fractionated by CD4 and CD8. Only CD4 SP and a small number of DP cells are observed in the CD3+ population. The gel shows the data for CD3- DP cells and the CD4 SP cells. B, {Delta}RF analysis of DP-CD4 SP cells for BV1 and all J2 regions for the single peptide mouse. C, Positive control, {Delta}RF analysis from a mouse expressing I-A as well as the tethered peptide on a Inv-/-{beta}2m-/- background. The J regions analyzed are identified in the inset.

 
To test this in another manner, we used mice in which the class II MHC molecule, H2-DM, has been eliminated. These mice express I-A with a very restricted peptide repertoire, and a large part of the I-A molecules on the surface are bound to the invariant chain derived CLIP peptide (19). Analysis of thymocyte subsets revealed that the selection for short CDR3 in CD4 SP cells is also observed (Fig. 6Go). In this case, it was interesting to note that extent of selection as measured by the skew value was quite high. Thus, although the limited number of peptides in these animals did not show a profound effect on the CDR3 length selection, there appeared to be a possible effect in the form of an increased level of selection.



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FIGURE 6. Rearrangement analysis in H2-DM-/- mice. Thymocytes from DM{alpha} null mice were fractionated on the basis of CD3, CD4, and CD8. Top, Example of the gel analysis for BV1-J2.5 rearrangements; bottom, summary of the data for all VB1-J2 rearrangements comparing CD3- DP with CD3 plus CD4 SP profiles. The skew value is almost twice that observed for any of the H2b strains in Fig. 4Go.

 

    Discussion
 Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 
We have analyzed the thymic maturation steps leading from DP to SP thymocytes and observed that there is a selection for shorter CDR3 length of the TCR {beta}-chain. Our previous observations in humans (12) are extended here in the mouse. By using a number of mouse strains and mutants, a more detailed analysis is possible. Analysis of thymocyte populations showed, as in humans, that the shortening of the mean size of the CDR3 was observed between the DP and CD4 SP stage. The extent of selection varied with the V-J combination. The absolute length and size distribution of the mouse CDR3 are functions of the V and J regions analyzed (22), and the shortening also appears to be a function of the V-J region analyzed.

As the time of selection coincides with the loss of pre-T{alpha} and the acquisition of {alpha}-chain production, the selection could be a function of the ability of the two chains to pair. The importance of {alpha}-chain pairing is shown by the fact that in-frame {alpha}-chain rearrangements are often observed in excision circles (25, 26) during the ongoing {alpha}-chain rearrangement process (27). Analyzing the shortening in TCR AV2 transgenic mice, which owing to the precocious expression of the {alpha} chain generate a sizable population of TCR expressing DP cells, tested this possibility. If the shortening is a function of generating a viable {alpha}{beta} pair, we should observe the shorter CDR3 in the {alpha}{beta}+ DP thymocytes. In fact, the length selection occurred between the {alpha}{beta}+ DP and {alpha}{beta}+ CD4 SP stage and not between the {alpha}{beta}- DP and {alpha}{beta}+ DP stages. Because the selection for thymocytes with shorter CDR3 is preferentially observed only in the CD4 SP population, it is difficult to see how the length of the CDR3 would influence pairing only in those cells that are destined to become CD4 SP. In humans, a sizable population of DP thymocytes that express low levels of CD3 was shown to have undergone {alpha} selection as evidenced by selection of in-frame {alpha}-chains. There was no evidence of CDR3 length selection in this CD3low DP population (15). Taken together, these data make it unlikely that the CDR3 length selection results from structural constraints due to pairing of the {beta}-chain with the {alpha}-chain.

Further insight into the CDR3 length selection process was gained by an analysis of MHC matched vs disparate strains. For the BV1 gene, the extent of shortening was much reduced in the H2u strains, PL or B.10 PL, in comparison with the H2b strains B10, B6, or 129. Thus, there appears to be a strong effect of the MHC on the selection process. An additional observation implicating the MHC in the selection process is that the selection phenotype was much more evident in CD4 cells than in CD8 cells.

The nature of the peptide bound by the class II MHC had much less of an effect on the phenotype. Selection for shorter CDR3 could be observed in animals expressing a single peptide derived from the I-E {alpha}-chain. The pattern of shortening was more irregular in these mice, suggesting a slight effect of the peptide. H2-DM-/- mice, which express a limited number of peptides predominant among which is class II-associated invariant chain peptide, showed an increase in the level of selection for short CDR3. The role of the class II bound peptide in positive selection has been firmly established using mice expressing single peptides (18, 24, 28) or a reduced complexity of peptides (29, 30, 31) as well as mice deficient in thymic Ag processing (32). The small qualitative differences observed using the single peptide mice could be due to the reported skewing of the repertoire selected on the single peptide (33). The increased selection in DM null mice could be a function of other factors influenced by incomplete Ag processing that is thought to be associated with these animals. However, these smaller effects could also signal that the nature of the peptide may be playing a role in the selection process.

Because we observe a clear effect of the nature of the MHC on the selection process, we propose that it is an example of positive selection. There are two possible ways to explain the presence or absence of the positive selection in the various MHC settings. A more complicated explanation would involve separate mechanisms for the class I and class II observations. Thus, the differences within class II may be due to I-Au-specific peptides, and the class I and class II differences may be due to the coreceptor interaction. The latter possibility could also explain the species differences observed for class I between mice and humans, given that there could be species-specific differences in the coreceptor-MHC interactions.

However, there may be one mechanism to relate all the results, and this would invoke structural differences in TCR-MHC contacts. Differences in TCR-MHC contacts have been recently described between class II and class I MHC on the basis of crystal structures (34, 35). These data indicate that the geometry of the TCR-class II interaction is orthogonal whereas that of the previously analyzed TCR-class I structures are diagonal. It is also possible that the actual CDR footprints might be different between the two classes (36). We propose a relationship between an orthogonal geometry and the length of the {beta}-chain CDR3. Because the {beta}-chain CDR3 comes in contact with the upward bulging portion of the MHCII {beta}-chain {alpha} helix, a longer CDR3 could interfere with peptide contact, which is the predominant role of the CDR3. The selection for shorter CDR3 would be viewed as an affinity process favoring closer approximation of the TCR and MHC. The shape correlation statistic, which measures snugness of fit between the two molecules, is higher for the TCR in the orthogonal mode than in the diagonal mode (35). The two human class I-TCR structures do show the most orthogonal geometry of the class I molecules studied to date (34, 37). Thus, the geometry argument could help explain the species differences observed in class I MHC selection. Because the rearrangement data represent a population analysis, it could be expected that not all class I MHC-TCR structures would fall into a strict structural categorization.

We propose that a test of the interrelation of the TCR contact angle and the length of the {beta}-chain CDR3 will be the structure of the TCR-MHCII complex using I-Au. According to our hypothesis, these interactions would show a "class I-like" diagonal geometry. Although we relate our data to TCR-MHC geometry, this does not explain why there is a selection for the short CDR3/orthogonal binding mode in those situations where it is observed. Using the standard evolutionary argument that if selection is observed it must be "favorable" to the function, the general rule would be that orthogonal binding/short CDR3 must offer an advantage in terms of affinity/avidity for most class II MHC. Structural insights into this "favorable" interaction are still required. An additional test of the role of TCR-MHC interactions in this regard might be to use mutant mice in which the importance of TCR signaling has been partially or completely bypassed (38, 39, 40). We predict that the CD4-CD8 differences in selection for short CDR3 would not be observed in such animals and that the CDR3 lengths would remain unchanged between DP and SP thymocytes.

The data presented here more clearly define a selection stage associated with thymocyte maturation. The phenotype of selection of thymocytes that express TCR with shorter {beta}-chain CDR3 is a function of the MHC and peptide and thus involves a positive selection step. The lack of this selection in the CD8 SP lineage further indicates a role of the class of MHC or perhaps of the coreceptor in this process. This phenotype should allow the further delineation of thymic maturation events at the DP to SP transition. The data may also have implications for our current view of TCR-MHC interactions, and we speculate that there may be a connection between shorter CDR3 and the orthogonal binding mode.


    Footnotes
 
1 This work was supported by the Blood Center Research Foundation and National Institutes of Health Grant AI26085. Back

2 Address correspondence and reprint requests to Dr. Jack Gorski, Blood Research Institute, P.O. Box 2178, Milwaukee, WI 53201-2178. E-mail address: Jack{at}bcsew.edu Back

3 Abbreviations used in this paper: DP, double-positive; SP, single-positive; RF, relative frequency; {Delta}RF, difference in RF. Back

Received for publication May 2, 2001. Accepted for publication February 6, 2002.


    References
 Top
 Abstract
 Introduction
 Materials and Methods
 Results
 Discussion
 References
 

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