Identification of B-cell clonal expansions using a modified
immunoglobulin VH gene fingerprinting assay
During normal B cell development, the processes of gene segment
recombination and coding end processing yield nucleotide HCDR3 lengths that are
characteristic and virtually invariant for an individual B-cell clone.
Therefore, these lengths can be used as signatures to identify members of a B
cell clone. The immunoglobulin V
H gene fingerprinting approach
[
23] takes advantage of the wide range of HCDR3 lengths
that can occur in human B cells (approximately 5-35 amino acids) to provide an
estimate of clonal diversity in polyclonal populations. When polyclonal B
lymphocytes from adults are analyzed using this assay, they display a Gaussian
HCDR3 length distribution around a mean of approximately 15 amino acids. The
presence of an individual dominant length that differs from this Gaussian
distribution can be used as an indication of a specific B-cell clonal
expansion.
Figure illustrates schematically the
two-stage immunoglobulin VH gene fingerprinting approach that we
utilized. Note that when cDNA prepared from normal peripheral blood B cells is
used as a template for these VH family-specific and
CH-specific assays, ladders of HCDR3 lengths that differ by three
nucleotides are identified. These individual HCDR3 lengths are signatures of
the various individual B-cell clones contained within the polyclonal
population. The intensities of the bands in virtually all of the ladders
illustrated in Figure are relatively uniformly
distributed around the mean. This indicates that there are no dominant HCDR3
lengths that skew the Gaussian distribution, and therefore that there are no
significant clonal expansions among the B cells that express most of these
VH–CH combinations. Similar results are obtained using
the genomic DNA-based assay, although these results cannot be interpreted in a
CH-specific manner (data not shown).
In the VH6-IgG combination (Fig. ), however, a non-Gaussian distribution is noted, even in this
normal individual. This could be a reflection of the numbers of VH
genes present in the VH family being analyzed (it is more likely to
see a non-Gaussian distribution in families with small numbers of individual
genes) or of the state of activation of a specific clone (because activated B
cells contain much higher levels of V gene messenger RNA than resting B cells).
We believe that in the instance illustrated in Figure
the latter possibility is more likely, because the small VH2 and
VH5 families (only two gene members per family) do not exhibit the
same degree of oligoclonality as that observed with the only somewhat smaller
VH6 family (one gene member).
Distinction between clonal expansion and clonal activation using
the modified immunoglobulin VH gene fingerprinting assay
Because B-cell activation and differentiation result in dramatic
increases in immunoglobulin V gene messenger RNA, these fingerprinting assays
cannot readily distinguish between clonal expansion and activation when cDNA is
used as a starting template. Because DNA levels are not appreciably altered by
cellular activation, however, the use of genomic DNA as well as cDNA from the
same sample of B cells helps to distinguish these two processes.
Thus, in the setting of specific B-cell clonal expansion without
concomitant cellular activation, the DNA-based fingerprinting assay will
indicate a dominant HCDR3 length, whereas the cDNA-based assay may not (data
not shown). Conversely, in the setting of specific B-cell clonal activation
without concomitant clonal expansion, the cDNA-based assay will indicate a
dominant HCDR3 length, whereas the DNA-based assay may not. Finally, in the
setting of specific B-cell clonal activation with concomitant clonal expansion,
both the cDNA- and the DNA-based assays will indicate a dominant HCDR3
length.
These distinctions were very reproducible in the following studies.
There were no situations in which evidence for cellular activation (either
selective or accompanied by clonal expansion) was present in one set of
analyses and not in a subsequent set using the same starting materials.
B cells in the blood, synovial fluid, and synovial tissue of
rheumatoid arthritis patients exhibit clonal expansions of activated and
resting B cells
We analyzed the peripheral blood, synovial fluid, and synovial
tissue B cells of rheumatoid arthritis patients (n = 20, 10, and 5,
respectively) using the genomic DNA- and cDNA-based fingerprinting assays to
develop an understanding of the diversity of the B cells in these compartments.
Figures and are illustrations
of representative patients for whom concomitant blood and synovial fluid or
blood and synovial tissue samples were available. In order to simplify the
Figures, only the results for two large VH families (VH1
and VH3) and two small VH families (VH5 and
VH6) are provided, although assays for each VH family and
each major CH family (μ,γ, and α) were performed and revealed
similar findings.
The genomic DNA-based assays in both patients indicated that clonal
expansions are common in the blood of rheumatoid arthritis patients. This type
of result was obtained with all individuals tested. It was most convincingly
demonstrated by the results in Figure obtained from B
cells expressing genes of the VH1 and VH3 families.
Because these VH families contain the largest numbers of
VH genes, they would be more likely to display a polyclonal
pattern.
An even more striking level of B-cell clonal dominance and expansion
was seen when the genomic DNA-based assay was used to analyze B cells from the
synovial fluid or synovial tissue (Figs and
). In these analyses, virtually all VH
families demonstrated extensive B-cell oligoclonality. It should be pointed out
that when an individual HCDR3 length comprises more than 50% of the radioactive
counts of a VH–CH ladder, clonality, based on DNA
sequencing, is very likely; when an individual length comprises more than 70%
of the radioactivity, clonality is virtually assured (data not shown).
Collectively, these data indicate that the B-cell repertoire of
rheumatoid arthritis patients is skewed away from the typical, apparently
random representation of normal individuals. The reason for this discrepancy is
not clear, although one possibility is that restricted antigenic exposure
alters the composition of the repertoire in favor of B cells reactive with the
putative antigen(s). If this is so, the progressive narrowing of the repertoire
from the blood to the synovial tissue is consistent with the ideas that the
antigenic exposures are originating at these sites and that the synovial
compartment is supporting clonal amplification. Because these are true clonal
expansions (ie increased numbers of B cells per specific clone), it is likely
that the antigenic exposures are chronic and therefore are increasing the
numbers of memory B cells reactive with these determinants.
In order to confirm that these clonally expanded B cells were
receiving ongoing antigenic stimulation and not limited solely to the memory
compartment, we employed the cDNA-based assay to distinguish clonal expansions
of activated B cells from resting (memory) cells. As illustrated in Figure
, activated B-cell clones (identified by the letter
'A' in Fig. ) expressing each of the
immunoglobulin heavy-chain isotypes were easily identified in all the
VH families studied. In some instances, these activated clones were
also expanded numerically (as defined by the genomic DNA-based assays, and
identified by the letter 'E' in Fig. ). In
other cases, these activated clones did not appear to be numerically expanded.
Similar examples can be found in Figures and
, but they are not identified by letters in order to
simplify the Figures.
Thus, it appears that many discrete B-cell clones exist in the
synovial compartment of rheumatoid arthritis patients, and that these are
increased in number, consistent with a response to a restricted antigenic
challenge(s). Furthermore, these B-cell clones appear to be of both the resting
(memory) and the activated types, suggesting that these antigenic challenges
are chronic and ongoing. Thus, these data support and extend previous findings
[
18,
19,
20,
21,
22] by
indicating that specific B-cell clonal amplifications can occur both in
previously stimulated B cells and in currently activated B cells. The presence
of activated B cells that are not increased in number is consistent either with
recent
in situ synovium-specific stimulation of these B-cell clones,
or with the influx of activated B cells that were stimulated by antigens
outside of and not necessarily relevant to the synovial compartment.
B-cell clonal expansions in the blood and synovial compartments
can be restricted to one or another compartment, or be common to the two
Because the preceding data indicated that the B-cell repertoire of
rheumatoid arthritis patients contains expanded clones of B cells that can be
resting or activated, we investigated whether the same clones could be
identified in both the blood and synovial compartments. Figures and illustrate data that suggest that
there are expanded clones that are blood restricted, joint restricted, or are
common to both compartments. Examples of blood-restricted clones are
highlighted on Figures and with
the

symbol, those that are joint-restricted with the
![[open triangle]](/corehtml/pmc/pmcents/x25B9.gif)
symbol, and those
that are common to the two compartments with the ♦ symbol. These findings
suggest that there may be a degree of cellular trafficking between the blood
and the synovial tissues.
In order to address this issue, we studied the B cells of the blood
and two synovial sites (right and left hip) that were obtained from the same
patient within 3 h of each other (Fig. ). In this
patient, the DNA-based assay provided examples of clonal expansions that were
present in only one joint (eg the VH3–JH and
VH5–JH combinations in Figure ),
and the companion cDNA-based assays indicated that in some instances these
expansions were either activated or resting. In only rare instances, however,
did the data suggest that a similar clone was present in two different synovial
tissues. DNA sequence analyses confirmed the rarity of this event (data not
shown). Thus it appears that in most instances the clonal amplifications occur
in situ and are not the result of trafficking from one anatomic site
to another. If so, this would suggest that the antigenic challenges driving
these clonal expansions may not be common to all synovial tissues, but may be
generated independently at each site, possibly by ongoing tissue breakdown.
Clonal persistence in the synovial fluid compartment
If the clonal expansions identified in the joints of rheumatoid
arthritis patients are due to an ongoing response to antigen, then one would
predict that at least some of the clones would persist over time. To test this,
we studied the synovial fluid B cells from the same joints of three patients on
two occasions spanning several months. Most of the clonal expansions detected
on the initial samples were not present in the subsequent samples. In a few
instances, however, B-cell clonal persistence was found.
Figure illustrates the best example of this
phenomenon in a patient who was studied over a 4-month interval. The DNA-based
assay using VH4 family-specific primers indicated the presence of
two similar clones on days 0 and 120, whereas the other
VH4-expressing clones detected at the first analysis were
no longer present at the time of the second analysis. DNA sequence analyses of
one of these two clones confirmed their identity, because each displayed the
same rearranged VHDJH gene with identical VH
mutations and identical HCDR3 sequences (data not shown). Therefore, certain
clones can persist locally over time, suggesting that a common and persistent
antigenic stimulation was operable in the joint of this rheumatoid arthritis
patient.
The lack of persistence of the other B-cell clones suggests two
possibilities. First, the initial set of B-cell clones might have been replaced
by others that recognized and responded to different antigenic epitopes on the
same original immunogenic protein. This type of clonal evolution to the
recognition of different epitopes on the same immunogenic moiety is common in
experimental situations in which repetitive immunizations with a defined
antigen are delivered [
29,
30,
31]. The other possibility is that
the B cells that disappeared over time were not reactive with tissue antigens.
These could have been stimulated by irrelevant antigens in the periphery and
therefore, after entering the synovial compartment, could not be restimulated
and hence could not enter the memory pool and take up residence in the synovial
tissue.