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* Blood Research Institute, Blood Center of Southeastern Wisconsin, Milwaukee, WI 53201;
Department of Immunology, University of Washington, Seattle, WA 98105; and
Howard Hughes Medical Institute, National Jewish Medical and Research Center, Denver, CO 80206
| Abstract |
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-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
-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 |
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-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
-chain with productively rearranged
-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
- and
-chains (
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
-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
- and
-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 |
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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
-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
null mice (19) on the BL6 x 129 background
were obtained from The Jackson Laboratory. Mice used in the experiments
were 34 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-
-FITC conjugate (clone
H57-597); CD4-Tri-Color conjugate and CD8 R-PE conjugate (Caltag
Laboratories. San Francisco, CA); and V
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 I
. 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. 1
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
-chain DNA constant region. The titration procedure is
described in greater detail in Ref. 21 .
|
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| Results |
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|
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-chain CDR3 than do
thymocytes
The studies presented here use rearrangement analysis of TCR
-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. 1
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
-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
-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. 1
C) yielding the
difference in RF (
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
RF plot. To generate a measure of the extent of
shortening, the
RF to the right of the inflection point are summed
(Fig. 1
C). 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
RF was determined for

- DP and 
+ CD4
SP thymocytes from two BL/6 mice. Fig. 2
, 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. 2
E, described below).
|
The analysis was extended to the 
+ CD8
SP population. There is much less evidence for the selection of
thymocytes with shorter CDR3 in the 
+ CD8
SP thymocyte population (Fig. 2
, C and D). There
is still evidence for selection given that there is a tendency for the
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
RF of the 
- DP
populations in both mice is compared (Fig. 2
E). We would
expect that the two distributions should be identical. The data do not
show a large difference in
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. 2
, 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
- and
-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
-chain and the
-chain. We took advantage of the fact that mice
expressing a transgenic TCR
-chain gene can predominantly express
the transgenic
-chain, resulting in a sizable population of DP

+ thymocytes than can be identified by the
expression of the
-chain. This facilitates the analysis of these
cells. Mice analyzed in these experiments express the V
2 chain of
the 172.10 TCR, which is specificity for the myelin basic protein
peptide 111 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
-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
-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
-chain or for the V
2 chain gave very similar
profiles, indicating that most of the TCR on the surface use the V
2
chain (Fig. 3
A). Therefore,
the CDR3 analysis was performed on the 
-
DP, 
low DP, and

high CD4 SP thymocyte populations from
-transgenic mice on the DBA background. Cells were sorted on the
basis of 
TCR, CD4, and CD8 expression into three subsets:

- DP, 
low DP
and 
high CD4 SP (Fig. 3
B). The
RF comparison between the 
low DP and CD4
SP populations showed a definite selection for short CDR3 (Fig. 3
C), whereas there was no evidence of selection for short
CDR3 between the 
- and

low DP populations (Fig. 3
D). If
the selection phenotype is a function of the ability of the two TCR
chains to pair and generate 
+ thymocytes,
the expected result would be the observation of shorter CDR3 in the

low DP cells. Because the selection was
observed between the 
low DP population and
the 
+ CD4 SP population, the CDR3 length
selection process does not correlate with the act of pairing of the two
receptors at the DP stage.
|
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
RF were compared between 
-
DP and 
+ CD4 SP thymocytes from these mice
(Fig. 4
A). The results in
these two strains were compared with those for B10 and 129 that are
H-2b (Fig. 4
B). 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. 2
and 4
, as well as the analysis of additional PL, B10.PL, and 129
mice, are shown in Table II
. 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.
|
|
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
peptide tethered to I-Ab as the only
surface MHC molecule is shown in Fig. 5
.
The sorted thymocyte populations, and an example of the CDR3 length
data are shown in Fig. 5
A. 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. 5
B) is not that different
from that observed in the control animal (Fig. 5
C). There is
a small difference in the
RF pattern with a number of positive
values in the negative (left) portion of Fig. 5
B.
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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| Discussion |
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-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
and the
acquisition of
-chain production, the selection could be a function
of the ability of the two chains to pair. The importance of
-chain
pairing is shown by the fact that in-frame
-chain rearrangements are
often observed in excision circles (25, 26) during the
ongoing
-chain rearrangement process (27). Analyzing
the shortening in TCR AV2 transgenic mice, which owing to the
precocious expression of the
chain generate a sizable population of
TCR expressing DP cells, tested this possibility. If the shortening is
a function of generating a viable 
pair, we should observe the
shorter CDR3 in the 
+ DP thymocytes. In
fact, the length selection occurred between the

+ DP and 
+ CD4
SP stage and not between the 
- DP and

+ 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
selection as evidenced by
selection of in-frame
-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
-chain with the
-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
-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
-chain CDR3. Because the
-chain
CDR3 comes in contact with the upward bulging portion of the MHCII
-chain
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
-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
-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 |
|---|
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 ![]()
3 Abbreviations used in this paper: DP, double-positive; SP, single-positive; RF, relative frequency;
RF, difference in RF. ![]()
Received for publication May 2, 2001. Accepted for publication February 6, 2002.
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