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Blood, Vol. 95 No. 11 (June 1), 2000:
pp. 3534-3540
NEOPLASIA
From the Molecular Immunology Group, Tenovus Laboratory, Southampton
University Hospitals, Southampton, UK.
Somatic mutation in immunoglobulin variable (V) region genes occurs
largely in the germinal center and, after neoplastic transformation, imprints V genes of B-cell tumors with the mutational history of the
cell of origin. Recently, it has been found that chronic lymphocytic
leukemia (CLL) consists of 2 subsets, each with a different clinical
course, one with unmutated VH genes consistent with a naive
B cell, and the other with mutated VH genes consistent with
transit through the germinal center. However, somatic mutation also
occurs at another distinct locus, the 5' noncoding region of the
bcl-6 gene, in both B-cell tumors and in normal germinal center
B cells. To probe the suggestive link between the occurrence of
mutations in VH and bcl-6 genes, we analyzed the
nature of somatic mutation at these distinct loci in the 2 CLL subsets. Unexpectedly, we found no such link in the CLLs defined by unmutated VH genes, with 4 of 10 cases clearly showing mutations in
bcl-6. In those CLLs defined by somatically mutated
VH genes, 4 of 9 cases predictively showed bcl-6
mutations. The frequency of bcl-6 mutations was comparable in
both subsets, with mutations being biallelic, and in 3 of 8 cases
indicative of clonal origins. Surprisingly, intraclonal variation,
which is not a feature of VH genes in CLL, was found in 6 of 8 cases in both subsets. These data indicate that somatic mutation
of the VH and bcl-6 loci may not necessarily occur
in tandem in CLL, suggesting diverse pathways operating on the 2 genes.
(Blood. 2000;95:3534-3540)
V(D)J recombination in precursor B cells is the first
step in a multistage process to generate antibody
diversity.1 This process generates a unique signature CDR3
sequence that identifies derivative B-cell clones.1,2 After
antigen encounter, the V(D)J transcriptional unit is targeted by a
potent somatic hypermutation mechanism to generate high-affinity
antibody, which occurs by the selection of mutated
progeny.3 This process is thought to be largely restricted
to the germinal center.1-3 Consequently, analysis of V gene
somatic mutation in neoplastic B cells has enabled a characterization
of the clonal history of the cell of origin. B-cell tumors have
recently been classified in 3 categories: Those with unmutated V genes,
in which the cell of origin does not enter the germinal center; those
tumors with ongoing V gene mutations, such as follicle center lymphoma
(FCL), which arise and remain in the germinal center environment; and
tumors with mutated stable V genes, such as multiple myeloma, which
have traversed the germinal center and exit, never to
return.4
These distinctions have also revealed a significant and clinically
relevant division of chronic lymphocytic leukemia (CLL) into 2 subsets,
one of which has V-gene sequences in germline configuration, and the
other with somatically mutated V genes, a finding independently
reported in several studies.5-8 The initial concept that
all CLLs arose from a naive B cell clearly had to be revised. In our
early study of 22 cases of CLL with the common phenotype of
CD5+, CD23+, low-surface immunoglobulin (Ig),
we found that unmutated VH genes were associated with
atypical morphology and trisomy 12, both features of a less favorable
prognosis.8 Expansion of these analyses has confirmed that
unmutated V genes, found in approximately 50% of CLLs, are highly
associated with a poorer clinical outcome, even at stage
A.5 These findings indicate that CLL is derived from B
cells arrested at 2 distinct stages of differentiation, with the more
mature cell that has encountered the somatic mutation mechanism, being
less malignant. In contrast to FCL, however, the mutational pattern in
CLL appears stable, with no intraclonal heterogeneity.4-9
It is now known that somatic mutation also targets nonimmunoglobulin
loci, to date characterized in the 5'-intronic region of the
bcl-6 gene.10 BCL-6 is a proto-oncogene,
encoding a transcriptionally active protein with a POZ/Zinc finger
motif,11 and maps to chromosome 3q27.12 Its
expression regulates germinal center formation and B-cell activity at
this site, as well as Th2 T-cell responses.13,14 A high
frequency of chromosomal translocations in non-Hodgkin lymphoma, particularly diffuse large-cell lymphoma
(DLCL), cluster at band 3q27, specifically at the bcl-6
promoter and first noncoding exon regions, and may lead to
deregulated bcl-6 function with a potential role in
lymphomagenesis.14-16 Mutations in bcl-6 at this
locus also occur in the absence of translocation events, with a target
region approximately 2 kilobase (kb) 3' from the transcription
initiation site.10 These mutations may be biallelic and are
characterized by single point mutations, insertions and deletional
events.10,17,18 Single base-point mutations predominate, favoring transitions over transversions,10,17-19 with
evidence for strand specificity,18 and although the
frequency of mutations in bcl-6 is notably higher than basal
rates, in general, it appears to be lower than the frequency of V gene
mutations.17,18
Somatic mutation targets both the VH and bcl-6 loci
in normal B cells, and is found only in memory and not naive B
cells.17-19 In a study at the single cell level, bcl-6
mutation tended to occur in normal B cells containing mutations in
their VH genes.17 Although 80% to 100% of
these cells displayed mutations in VH, only approximately
30% of the cells had corresponding mutations in bcl-6,
implicating differences in targeting of the 2 loci. Bcl-6
mutations also occur in a range of B-cell tumors, and a correlation
between mutational status in VH and bcl-6 in B cell has been suggested. However, there were many exceptions, particularly among cases of Burkitt's lymphoma and multiple myeloma.17
Overall, more than half the numbers of germinal centers
(GCs) or post-GC cell-derived B-cell tumors studied,
which would certainly be expected to harbor VH mutations,
did not show mutations in bcl-6.17 Furthermore, GC-resident lymphoma cells characteristically show high levels of
intraclonal variation in tumor VH gene sequences, which to date has not been described as a feature of bcl-6 mutations in these tumor cells. Interestingly, this intraclonal variation in bcl-6 sequence has been reported in normal tonsil GC B
cells.19 The question that is raised from these findings is
whether the same mutational pathway is invariably involved.
In this study, we have investigated whether somatic mutation of the
bcl-6 gene occurs conjointly with VH mutations in the 2 CLL disease subsets. Previously, Pasqualucci et al17
examined bcl-6 mutations in 33 cases of CLL by SSCP analysis,
and a parallel presence of VH and bcl-6 mutations
was observed in 5 cases by sequence analysis. Our results from this
study suggest distinct routes for VH and bcl-6
mutations in CLL, with ongoing somatic mutations in bcl-6,
even in cases with no VH mutations.
Patients
Cytogenetics
Preparation of genomic DNA
Amplification of VH genes These methods were reported previously.5Polymerase chain reaction analysis of -globin ( G), polymerase chain reaction (PCR)
primers were designed to amplify a 724-base pair (bp) fragment of
intronic DNA, spanning exons 2 and 3 (GenBank accession no. V00499). The forward G primer was 5'-AGG AAG GGG AGA AGT AAC and the
reverse primer was 5'-AAT CCA GCC TTA TCC CAA, each primer used
at a final concentration of 400 mmol/L. DNA (5 µL) isolated from
patients A.G. and D.B. was amplified using the Advantage-HF2 PCR Kit
(Clontech, Hants, UK) in a 50 µL volume and the following PCR
conditions: 95°C for 5' (1 cycle), followed by 95°C for
1', 54°C for 1', 72°C for 3' (30 cycles), and
72°C for 10' (1 cycle). Contamination was checked in control
reactions with no added template, and stringent working conditions for
PCR analysis were used as recommended.20
Cloning and sequencing of PCR products Gel-purified PCR products of a predicted size were cloned into the pGEM-TA vector as described and used to transform JM109 competent cells.21 Randomly selected clones found to contain an insert of an appropriate size by restriction analysis of plasmid DNA were sequenced using M13 universal primers, primers used for PCR amplification, or internal primers (bcl-6 sense 5'-AGC AGA GAG GAC GAG ACA GTG CTT; antisense 5'-GAA AAA ACA CAG CCG CAC GAA TCC AGA). Mutations were confirmed by at least 2 separate primers by bidirectional sequencing. Both for VH and bcl-6, a minimum of 4 clones were analyzed per patient.
Cytogenetic features of patients studied In 18 of 19 patients studied in this report, data were available from karyotype analysis (Tables 1 and 2 and Hamblin et al5), and did not reveal any chromosome 3 abnormality. In our initial cohort of 84 patients with CLL,5 only 2 patients exhibited a karyotype with a chromosome 3 abnormality, del(3)(p21) and t(3;11)(q25:q25), respectively, suggesting a low incidence in the CLL disease.VH analysis in CLL subsets Data showing a clear demarcation of the 2 CLL subsets in a large cohort of 84 patients have been reported previously,5 and are reproduced in part in Tables 1 and 2 for reference. VH gene use by 2 additional patients included in this study (B.P.S. and A.G.) was in germline configuration, and has been deposited in the GenBank/EMBL database (accession no. AJ272398/9). Of note, 4 cases (C.W., D.F., J.B., and N.O.) each showed identical VH sequences in 4 tumor-derived clones.bcl-6 5'-intron sequence In all patients analyzed, a 7-base difference (at positions 607, 769-771, 889, and 987) was observed from the reported germline database sequence (GenBank accession no. Z79581). The first nucleotide of bcl-6 complementary DNA (cDNA) from this reported sequence was arbitrarily chosen as position +1,10 and the amplified bcl-6 5' intronic region spanned +415 to +1140.Taq polymerase error rate In the characterization of bcl-6 mutations in normal and malignant B cells, Pasqualucci et al17 used a 394-bp intron fragment of G to assess Taq misincorporation rate, which was
consistently found to be unmutated, indicating that this gene is not
targeted for somatic mutation, and is suitable as an internal control
to assess bcl-6 mutations. To match the target length of
bcl-6 under investigation in this study, a 724-bp fragment of
intronic DNA spanning exons 2 and 3 of the G gene was amplified.
Subcloning of G PCR DNA and subsequent sequence analysis enabled a
quantitation of Taq error rate. For 2 patients (A.G. and D.B.),
15 and 12 clones respectively from the G PCR products were
completely sequenced, and 5 mutations were detected in 19 548-bp
sequenced, giving a background error rate of
2.6 × 10 4 bp 1 (less than
0.03%). The same PCR amplification conditions were used for
bcl-6 analysis.
bcl-6 polymorphic alleles Two nucleotide changes likely to represent polymorphic variants were observed, a G-C change at position +753 in 16 clones from 5 cases (also described by Migliazza et al10) and a single base deletion ( T) at position +875, which was observed in 15 clones from 4 cases
(Tables 3, 4,
and 5). Polymorphic changes permitted
identification of biallelic mutations in bcl-6.
bcl-6 mutations in CLL The overriding criterion in determining the significance of low levels of bcl-6 mutations is the Taq error rate. Of the CLL cases identified as carrying bcl-6 mutations (Tables 3 and 4), 2 patients, A.G. and D.B., both from the VH unmutated CLL subset, were selected for simultaneous analysis of the frequency of mutations in bcl-6 and -G genes, using identical amounts of template genomic DNA, from
the same preparations. It was apparent (Table 5) that in both cases the
level of bcl-6 mutation detected was significant, approximately
4-fold higher than the level of Taq misincorporation as
assessed by the reference -G gene. This finding was based on
a replicate PCR analysis of bcl-6 in these 2 cases (Table 5). As an internal control, replicate PCR analysis of patient A.W. confirmed an absence of mutations in bcl-6 (Table 4), negating any influence of the bcl-6 target gene on Taq error
rate at levels present in the isolated genomic DNA in these samples.
The analysis of plasmid DNA carrying an unmutated bcl-6 insert,
discussed above, confirmed that localized motifs in bcl-6
sequence do not interfere adversely with Taq misincorporation.
Nature of bcl-6 mutations Single nucleotide substitutions predominated as the type of mutation detected. The overall characteristics of mutational changes are shown in Table 6. There was no apparent difference between the frequency of mutations affecting each base in the 2 subsets (data not shown). The low number of bcl-6 mutations in this study excluded statistical analysis. However, transitions (86%) predominated over transversions (14%), with a preferential bias for T:N over A:N target bases. Each mutation was assessed for influence of flanking bases, and only 2 mutations, G-A (733) in clone CW1 and G-A (721) in clone AG2, occurred in G within an RGYW motif.
Analysis of intraclonal heterogeneity of bcl-6 mutations To confirm that cloning was a prerequisite to identify low levels of heterogeneous bcl-6 mutations in tumor-derived clones, a mixing experiment was undertaken: 8 clones showing no bcl-6 mutations were mixed with 2 clones showing 2 mutations each in the bcl-6 intron, and the mix PCR amplified. PCR DNA was eluted, and directly sequenced. None of the mutations expected from the 2 parental clones were visible in the resultant chromatogram, confirming the necessity of cloning before bcl-6 sequence analysis.
The price of somatic mutation in immunoglobulin V genes of B cells, so essential for the development of high-affinity antibodies, is the danger of exposing the genome to potentially damaging mutation in other genes. Generally, it appears that control of the mechanism is tight and that extraneous mutation is rare. However, recent findings on the bcl-6 gene have revealed nucleotide changes, and it has been suggested that this gene may be a target for the same mutational process. This has been supported by the finding that mutations in bcl-6 tend to be more common in B cells, both normal and neoplastic, which have encountered the germinal center environment, where somatic mutation in V genes occurs.1-3
We would like to thank Dr Gianluca Gaidano, Amedeo Avogadro University of Eastern Piedmont, Novara, Italy, for useful discussions.
Submitted August 17, 1999; accepted February 3, 2000.
Supported by The Leukaemia Research Fund and Tenovus UK.
Reprints: Surinder S. Sahota, Molecular Immunology Group, Tenovus Laboratory, Southampton University Hospitals, Tremona Rd, Southampton SO16 6YD, UK; email: sss1{at}soton.ac.uk.
The publication costs of this article were defrayed in part by page charge payment. Therefore, and solely to indicate this fact, this article is hereby marked "advertisement" in accordance with 18 U.S.C. section 1734.
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