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2 TCR Repertoire Overlap in Different Anatomical Compartments of Healthy, Unrelated Rhesus Macaques1



*
Wisconsin Regional Primate Research Center; and
Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI 53715
| Abstract |
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|
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T cells show preferential homing that is characterized by
biased TCR repertoire at different anatomical locations. The processes
that regulate this compartmentalization are largely unknown. A model
that allows repeated multiple sample procurement under different
conditions and enables with relatively straightforward extrapolation to
a human situation will facilitate our understanding. The peripheral
blood V
2 T cell population is the best-characterized human 
T
cell subset. To determine its diversity at multiple immunocompartments
matching blood, colon, and vagina samples from rhesus macaques were
investigated. Four joining segments used in V
2-J
transcripts were
identified, including one segment with no human counterpart. Like in
humans, the rhesus peripheral blood V
2 TCR repertoire was limited
and contained common sequences that were shared by genetically
heterogeneous animals. Furthermore, this subset comprised several
phylogenetically conserved V
2 complementarity-determining region 3
(CDR3) motifs between rhesus and humans. Common sequences were also
found within the colon and vagina of the same animal, and within the
peripheral blood and intestine of different unrelated animals. These
results validate rhesus macaques as a useful model for 
TCR
repertoire and homing studies. Moreover, they provide evidence that the
concept of limited but overlapping V
TCR repertoire between
unrelated individuals can be extended including the mucosa of the
digestive and reproductive tract. | Introduction |
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2/V
2+ T cell subset of peripheral blood is
one of the largest circulating T cell populations in humans. This
population represents only a minor subset in neonates, but by adulthood
it is
48% of the circulating T cells, and
7090% of
circulating 
T cells (1, 2). The expansion of this
cell group is assumed to be driven by Ag-specific processes (3, 4). Their elevated cell numbers during numerous bacterial
infections, e.g., Mycobacterium tuberculosis
(5, 6, 7), Listeria (8, 9),
Plasmodium sp. (10, 11), Toxoplasma
(12), or Brucella melitensis
(13) suggest an important but yet unclarified role in the
immune response against these microorganisms.
V
2/V
2+ T cells form a minor population in
the mucosa (14, 15). Mechanisms that control the
translocation and retention of V
2/V
2+ T
cells at a particular tissue compartment are largely unknown, but are
of major significance in studies that aim to manipulate these
cells.
The Ag recognition of 
T cells is not MHC restricted
(16, 17, 18), and it does not require Ag processing via the
known Ag processing pathways (19, 20, 21). 
TCRs have
complementarity-determining region 3
(CDR3)4 length
diversity that are similar to Ig chains. Like the light chain of Igs
compared with the heavy ones,
TCR chains have more limited CDR3
length diversity than do
TCR chains (22, 23, 24). The
repertoire of peripheral blood V
2 TCR chain is limited by the
prevalent use of V
2-J
1.2 recombination (25), and by
the high frequency of canonical CDR3 sequence irrespective of age, sex,
or genetic background (26). V
2+ T
cells expressing germline-encoded CDR3 sequence seem to be of
extrathymic origin because they appear in the prethymic fetal liver in
a relatively high abundance (27). These cells are
functional because they respond to mycobacterial Ags by proliferation
and cytokine secretion. Furthermore, they are maintained through
adulthood as well (26). A subset of peripheral blood
V
2/V
2+ T cells are stimulated by small
alkylphosphate and/or alkylamine molecules that derive from
microorganisms, host cells, or the metabolism of nutrients
(28, 29, 30, 31, 32). Efforts to determine the significance of this
subset have been hindered by the lack of a well-established in vivo
model system that includes similar cells. 
T cells that recognize
alkylphosphate or alkylamine ligands have not been found in rodents.
However, rhesus macaques do have V
2/V
2+ T
cells that respond to these same molecules. In adult animals the
V
2+ and V
2+ T cell
subsets represent
0.7 and 0.4% of the lymphocyte population,
respectively (our unpublished observations, Ref. 33).
Although the relative proportion of the
V
2/V
2+ T cell subset in the peripheral
blood of rhesus monkeys remains to be established, an
2-fold
expansion of both the V
2+ (34)
and V
2+ subset (our unpublished observation)
as a function of age suggests that factors shaping the human
V
2+ TCR repertoire might also operate in
captive macaques. Previously we described that rhesus monkeys V
2
CDR3 length diversity is extremely limited and similar to the profile
of human beings. We also observed that this repertoire restriction
showed a tissue-specific pattern between peripheral blood and sigmoid
colon (34).
In these investigations we determined the V
2 TCR CDR3 repertoire
diversity of rhesus macaques in different anatomical compartments at
the nucleic acid level. We provide evidence for overlap of the V
2
TCR repertoire between distinct mucosal compartments within a single
animal. In addition, we present data that support the concept of a
restricted and shared V
2 TCR repertoire between distinct animals of
heterogeneous genetic background. Our results provide an initial
framework for future studies aimed at determining the homing mechanisms
of 
T cells.
| Materials and Methods |
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Rhesus macaques (Macaca mulatta) were housed at the
Wisconsin Regional Primate Research Center according to the National
Institutes of Health "Guide to the Care and Use of Laboratory
Animals". The animal cohort used in the primer extension length
profile analysis included nine clinically healthy animals aged between
4 and 14 years, among them six females and three males. In the CDR3
sequencing analysis, animals 1 and 2 were 4 years old, and animal 3 was
9 years old. Venous blood collection and vaginal and sigmoid biopsy
procedures were conducted under anesthesia using 20 mg/kg ketamine
hydrochloride and 0.03 mg/kg buprenorphine. Further pain management was
accomplished with 0.03 mg/kg buprenorphine administered i.m. at 3, 24,
and 32 h after the procedure. PBMC were isolated by density
gradient separation on Ficoll (Sigma, St. Louis, MO). Cells were washed
with PBS and stored as dry pellets at -80°C. Cells (3 x
106) were processed for mRNA isolation. One
vaginal punchbiopsy specimen (
16-mm3 size) and
four to five colon biopsy specimens (
12 mm3
each) were obtained and stored in RNALater solution (Ambion, Austin,
TX) at -20°C until mRNA isolation.
mRNA isolation and RT-PCR
PolyA RNA was isolated with the MicroFastTrack Kit (Invitrogen,
San Diego, CA) according to the manufacturer recommendation. cDNA
synthesis was accomplished in 20 µl volume using the Reverse
Transcription System (Promega, Madison, WI). PCR was performed in a
Perkin-Elmer (Applied Biosystems, Foster City, CA) 9600 thermal cycler
with the following thermal cycling profile: denaturation of cDNA at
94°C for 3 min, hot start at 65°C, denaturation 94°C for 45
s, annealing at 55°C for 45 s, and extension at 72°C for
90 s, with a final extension step (72°C for 10 min) when 40
cycles were completed. The reaction buffer consisted of 50 mM KCl, 20
mM Tris-HCl pH 8.3, 2 mM MgCl2, 100 µg/ml BSA,
1 mM of each primer, 0.2 mM of each dNTP, and 1.25 U of Taq
polymerase. PCR products were visualized on 1.5% agarose gels.
Oligodeoxynucleotide primers (Genosys; Sigma) were designed on the
basis of highly conserved sequences between human, chimpanzee, bovine,
pig, and mouse. The PCR products contained a segment of the TCR
variable region, spanning the CDR3 region and including the total
length of the J segment, and a small part of the constant region first
exon. The constant segment specific primer amplified both the C
1 and
C
2 genes (32). Oligonucleotide primer sequences were as
follows: V
2: AGA CCT GGT GAA GTC ATA C;
C
1&2: GTT GCT CTT CTT TTC TTG CC.
Primer extension product length determination
Five cycles of primer extension (94°C for 45 s, 60°C
for 45 s, 72°C for 45 s) were performed with V
2 TCR PCR
amplificates as templates using a 6-FAM-labeled primer that was
specific for
constant regions (35). The reaction
products were analyzed by capillary electrophoresis on a 310 Genetic
Analyzer (Perkin-Elmer), and fragment lengths were determined using
GeneScan 2.1 software and internal standards (Tamra 500; Perkin-Elmer).
The areas under each peak (sequences with identical CDR3 lengths) were
represented as a fraction of the total area of all peaks combined. The
6-FAM-labeled primer extension products contained a segment of the TCR
variable region and spanned the CDR3 region, including the total length
of the J segment with 40 bases of the constant domain first exon. The
6-FAM-labeled oligonucleotide primer used for primer extension reaction
was: AAT AGT GGG CTT GGG GGA AAC.
Cloning and sequencing
RT-PCR products were isolated from a 1% agarose gel, purified
by filter through a PCR cleanup spin column (Wizard PCR preps DNA
Purification System; Promega), and ligated with a pCRII-TOPO vector
(Invitrogen) for 5 min at room temperature. A portion of the ligation
was used to transform DH10 cells according to the manufacturer
recommendations (Invitrogen). Transformants were plated on
Luria-Bertani agar with ampicillin prespread with
5-bromo-4-chloro-3-indolyl-
-D-galactopyranoside (40
mg/ml in dimethylformamide) and
isopropyl-thio-
-D-galactopyranoside (5 mM in
H2O). Lac- colonies were
processed by standard alkaline lysis. Pellets containing plasmid DNA
were washed with 70% ETOH. Plasmids were sequenced using C
182
primer and the BigDye fluorescent sequencing kit (Applied Biosystems).
Sequencing products were analyzed with ABI 377XL automated fluorescence
sequencer (Applied Biosystems). Sequence data were analyzed with
MacVector 6.5 software (Oxford Molecular Group, Hunt Valley,
MD).
| Results |
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2 and J
TCR
segments
Our initial approach was to determine the extent of homology of
V
2 and J
TCR segments between M. mulatta and
Homo sapiens. Germline sequences of TCR chain gene segments
of rhesus macaques have not been published so far. Having used cDNA
samples, our analysis is limited to consensus sequences derived from
data of five unrelated animals. For the same reason, we defined the
position of nucleic and amino acid replacements on the basis of
corresponding human data (36, 37, 38, 39). We sequenced the V
2
TCR chain segment that is adjacent to the 3' end of CDR2 hypervariable
regions stretching from amino acid residue at position 81 to the
carboxyl-terminal of the chain segment. At this region four of the
detected eight mutations were nonsynonymous. At the amino acid level,
these exchanges resulted in a glycine to serine at the 84th residue, an
isoleucine to leucine at the 95th residue, and a glutamic acid to
lysine replacement at the 97th residue (Fig. 1
). The extent of homology was >93% at
nucleic acid and 93% at amino acid levels.
|
sequences have been identified and
designated as J
1.1, J
1.2, J
1.3, J
2.1, and J
2.3
(37, 38, 39). Having sequenced >500 clones, we encountered
four different
-joining (J
) segments. On the basis of sequence
homology, we designated them as J
1.1, J
rh, J
1.2, and J
2.3.
We did not identify sequences that would match the human J
1.3 or
J
2.1 gene segments. The region showing the highest homology to the
human J
1.1 sequence had only one, nonsynonymous mutation, which
changed the phenylalanine at the fourth residue to an isoleucine (Fig. 1
rh. J
rh showed the highest homology to the J
1.1
segment, and five nonsynonymous mutations caused changes of glycine to
tryptophan at the second residue, phenylalanine to isoleucine at the
fourth residue, isoleucine to lysine at the sixth residue, and lysine
to arginine at the 12th residue (Fig. 1
rh and human J
1.1 was >93% at the nucleic
acid, and 75% at the amino acid level. Whether this domain represents
an allotypic variant or a distinct joining gene segment will require
further studies.
We observed the greatest variation in the J
1.2 segment. All four
amino acid replacements were localized to the NH2
terminus of the protein segment (Fig. 1
). The extent of homology was
90% at nucleic acid and 76% at protein level. Surprisingly, we found
no mutation at all in the J
2.3 sequences. Altogether these data
point out several differences and confirm the anticipated high homology
of
TCR chain gene segments between rhesus monkeys and human
beings.
Limited diversity of amino acid sequences coded by V
2-J
1.2
CDR3 regions in peripheral blood; shared sequences between different
unrelated animals
Previously we established that the diversity of V
2 CDR3 lengths
in rhesus macaque peripheral blood is extremely restricted
(34). To understand the molecular basis for this
restriction we sequenced samples from three adult unrelated animals.
The V
2-J
1.2 junction region was preferentially expressed in all
three animals (Fig. 2
),
and V
2-J
2.3 junctions were detected less frequently. J
1.1 and
J
rh joining regions were underrepresented in all three animals.
Almost all of the V
2-J
1.2,
30% of the V
2-J
2.3, and 20%
of the V
2-J
rh recombinations were in frame. More than 70% of the
J
1.2-containing segments had six-amino-acid-long CDR3 regions. The
CDR3 lengths encompassed by V
2-J
2.3 junctions were more diverse.
We often found transcripts shared either by all three, or just two of
the animals or we detected clones with identical amino acid sequences.
The amino acid motif WEVQQF was abundant, being represented by clones
with four distinct coding sequences. The CDR3 regions WEVQGQF, WEGQQF,
WEVKQF, WESQQF, and WEVGQF were found in two or all three of the
monkeys, sometimes with identical transcripts. In the case of
V
2-J
2.3 recombination we found no shared nucleic or amino acid
sequences. Overall, repeated encounters with common V
2-J
1.2, but
not V
2-J
2.3 motifs in three unrelated adult animals provide
evidence for a strong, permanent selection for these receptor sequences
that was independent of genetic background.
|
2-J
2.3 transcripts in the sigmoid
colon; shared motifs between different animals
To assess the extent of V
2 TCR diversity in mucosal
compartments, we sequenced cDNA samples derived from sigmoid colon
biopsies. V
2-C
transcripts from peripheral blood samples were
characterized by a dominant 284-base-long primer extension product
length (Fig. 3
A). (The size of
this product is determined by our choice of primer sequences and is
used here for identification only.) In contrast, V
2-C
transcripts
from intestinal samples cannot be characterized by one predominant
length, but usually they contain products of shorter lengths (Fig. 3
B). Sequencing revealed that the majority of transcripts
are V
2-J
2.3 recombinations. However, a significant number of the
V
2-J
2.3 recombinations produced out of frame sequences, and we
even detected a higher number of out of frame V
2-J
1.2
recombinations (Fig. 4
).
Next we determined whether the functional transcripts still display a
similar length pattern in the blood and sigmoid colon. We found an
enrichment for shorter functional transcripts in the intestine, the
pattern of which was primarily due to an increased usage of the shorter
J
2.3 joining segment (Fig. 5
).
|
|
|
2-J
2.3
transcript expressing the CDR3 motif WEVRYK in two animals; in one of
them it was a repeated transcript, suggesting previous expansion of
this clone.
To assess the reproducibility of our sampling method we simultaneously
processed two pools of samples (biopsies taken at the same time) from
the same animal. We observed significant overlap between the two sets
of clones, irrespective of whether the recombinations were in frame or
not (Fig. 4
, animal 3/1 and 2 bold-faced sequences). We also compared
the retrieved sequences with a set of clones that was derived from
specimens taken 2 months previously. Again common motifs were detected
with both in and out of frame recombinations (Fig. 4
, animal 3/3
bold-faced sequences). Altogether, the excellent reproducibility of
V
2 TCR chain repertoire in parallel samples argues against sampling
errors. These results indicate that the sigmoid colon contains an
oligoclonally expanded V
2 TCR+ cell subset,
and the repertoire is shared among genetically distinct animals.
Common V
2-C
motifs between intestinal and vaginal samples of
the same animal
To determine the diversity of V
2 TCR repertoire at another
mucosal site, we analyzed vaginal samples from six animals. We found
that the average primer extension product length diversity is very
similar to the peripheral blood (Fig. 6
).
Sequence data derived from two animals showed no elevated frequency of
V
2-J
2.3 transcripts (Fig. 7
). As
expected on the basis of published human data (40, 41, 42, 43),
there was a significant overlap between the vaginal and matching blood
V
2 TCR repertoires. Because the female reproductive tract is highly
vascularized, additional experiments are needed to show whether this
overlap can be attributed to contaminating blood cells. Remarkably, we
found two in frame transcripts, one of them V
2-J
1.2 and the other
V
2-J
2.3, which were present in both the vaginal and intestinal
repertoires. These sequences were not encountered in the peripheral
blood. V
2-J
2.3 transcript WEIKPSYYK was found repeatedly in both
mucosal tissues, suggesting that it represents a T cell population that
is common at both tissue sites.
|
|
| Discussion |
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|
|
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2 TCR repertoire
at different anatomical compartments in rhesus macaques to establish an
in vivo model for V
2 T cell repertoire studies. We observed that the
CDR3 length diversity for the V
2 T cell subset in peripheral blood
is similarly limited in humans and rhesus macaques (25, 26, 34). In these studies we show that this similarity relies on
extensive structural homology within the peripheral blood V
2 TCR
repertoire for M. mulatta and H. sapiens. Rhesus
monkeys have four counterparts of the known human J
segments
(38, 39) but, like in humans, the V
2-J
1.2 junctions
predominate. The overwhelming majority of these junctions have CDR3
length of 6 ± 1 amino acids in both humans and macaques. In
humans the canonical V
2-J
1.2 junction encodes the amino acid
sequence WEVQEL. Although rhesus monkeys do not express this particular
sequence, a CDR3 region was identified that encoded the motif WEVQQF
and was frequently encountered at multiple anatomical locations in all
of the investigated animals. On the basis of consensus sequences of
rhesus V
2-J
1.2 recombinations and sequence homology between human
and rhesus, we postulate that this sequence might be a canonical
sequence in macaques. A common CDR3 motif WEVXEL was observed in
3050% of human peripheral blood V
2-J
1.2 junctions
(26). In rhesus the WEVXQF motif was observed at similar
frequencies (20.844.7% of the blood V
2-J
1.2 junctions).
Finally, several motifs that included the carboxyl-terminal of V
2
segment and amino acids encoded by palindrome/N-nucleotides were found
in both humans and rhesus monkeys (WEVQ, WESQ, WEAQ, WEVG). These
phylogenetically conserved sequences suggest strong selection for the
structures represented by them. The mechanism of selection remains to
be established; however, it equally well could be attributed to the
presence of ubiquitous Ags (44), a diversifying machinery
of limited capacity (45), or a selection pressure for
certain
-chain conformations that may or may not have direct contact
with the Ag (46).
The diversity of V
2 TCR chain in the intestine is restricted, but
different from peripheral blood, suggesting that selection mechanisms
operating in blood are absent, or overruled in the intestine. There are
no published examples of shared 
TCR CDR3 sequences in adult
human intestinal samples. However, common V
2 and V
2 TCR CDR3
motifs have been observed between different fetal tissues (including
gut and liver) of the same individual or between genetically distinct
subjects (27, 47). Our results identify common V
2 TCR
species in the colon of unrelated adult animals, suggesting a dominant
and ubiquitous selection mechanism. Further studies are necessary to
explore different possible explanations for this unexpected
observation, e.g., shared sequences of V
but not V
TCR might also
exist in adult humans, or shared CDR3 motifs might be frequent in some
mammals and appear in early human ontogeny, mainly as a reiteration of
phylogeny.
In mice, the nonoverlapping
TCR chain variable gene segment usage
of tissue resident 
T cell populations (48, 49, 50, 51, 52, 53) and,
in humans, the nonoverlapping CDR3 repertoire of
TCR chains between
intestine and blood (54, 55, 56) indicated strict
compartmentalization of 
T cell subsets. In human beings,
TCR
chain repertoires found at distant locations in the intestine
(duodenum, colon) from a single individual contained common clones,
suggesting the presence of ubiquitous Ags distributed throughout the
digestive tract, or the original population of these sites by a small
number of progenitor cells (56). Our data are the first to
show that although the V
2 T cell repertoire of colon and vagina is
mostly distinct, shared sequences can be detected. This observation
might indicate the presence of common Ag(s) and/or a possible 
T
cell trafficking between the reproductive and digestive tract of
healthy animals.
Processes controlling 
T cell trafficking and tissue targeting
remain largely unknown. Our results are consistent with studies that
showed anatomical compartmentalization of 
T cells. Within
mucosal tissue sites, the 
T cell populations are largely
distinct, but the occasional appearance of common V
2 sequences
suggests either cell trafficking between these sites or some overlap in
the Ags that might be responsible for selecting and maintaining the
local 
T cell repertoire. The extensive similarity between V
2
TCR repertoire in rhesus and human shows that this animal model will be
useful for elucidating mechanisms that control 
cell biology.
| Acknowledgments |
|---|
| Footnotes |
|---|
2 Current address: Institute of Human Virology, Medical Biotechnology Center, 725 West Lombard Street, Baltimore, MD 21201. ![]()
3 Address correspondence and reprint requests to Dr. Eva Rakasz, University of Wisconsin-Madison, Wisconsin Regional Primate Research Center, 1220 Capitol Court, Madison, WI 53715. ![]()
4 Abbreviation used in this paper: CDR3, complementarity-determining region 3. ![]()
Received for publication August 17, 2000. Accepted for publication November 27, 2000.
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