<i>BCL3</i> rearrangements in B-cell lymphoid neoplasms occur in two breakpoint clusters associated with different diseases

Abstract

The t(14;19)(q32;q13) often juxtaposes BCL3 with IGH resulting in overexpression of the gene. In contrast to other oncogenic translocations, BCL3-rearrangement (BCL3-R) has been associated with a broad spectrum of lymphoid neoplasms. Here we report an integrative whole-genome sequence, transcriptomic, and DNA methylation analysis of 13 lymphoid neoplasms with BCL3-R. The resolution of the breakpoints at single base-pair revealed that they occur in two clusters at 5’ (n=9) and 3’ (n=4) regions of BCL3 associated with two different biological and clinical entities. Both breakpoints were mediated by aberrant class switch recombination of the IGH locus. However, the 5’ breakpoints (upstream) juxtaposed BCL3 next to an IGH enhancer leading to overexpression of the gene whereas the 3’ breakpoints (downstream) positioned BCL3 outside the influence of the IGH and were not associated with its expression. Upstream BCL3-R tumors had unmutated IGHV, trisomy 12, and mutated genes frequently seen in CLL but had an atypical CLL morphology, immunophenotype, DNA methylome, and expression profile that differ from conventional CLL. In contrast, downstream BCL3-R neoplasms were atypical splenic or nodal marginal zone lymphomas (MZL) with mutated IGHV, complex karyotypes and mutated genes typical of MZL. Two of the latter 4 tumors transformed to a large B-cell lymphoma. We designed a novel FISH assay that recognizes the two different breakpoints and validated these findings in 17 independent tumors. Overall, upstream or downstream breakpoints of BCL3-R are mainly associated with two subtypes of lymphoid neoplasms with different (epi)genomic, expression, and clinicopathological features resembling atypical CLL and MZL, respectively.

Diverse B-cell tumors associated with t(14;19)(q32;q13)/<i>IGH</i>::<i>BCL3</i> identified by G-banding and fluorescence <i>in situ</i> hybridization

“…Indeed, a recent study using next-generation sequencing (NGS) found rearrangements of upstream CEACAM16 and downstream CBLC and BCAM with IGH . 19 However, in cases with the latter two rearrangements, the tumors showed marginal zone lymphoma histopathology and lacked expression of BCL3, being clearly different from cases in our study. Bright nuclear staining of BCL3 by IHC observed in cases 3 and 4 suggests that, even though the (14;19)(q32;q13) breakpoints in these two cases were not within the same region as those in cases 1 and 2, they still occurred in the vicinity of BCL3 , resulting in the high level expression of the gene product under the influence of juxtaposed IGH .…”

“…However, IGHD and IDHJ breakpoints were identified in a NGS-based study, 30 and switch regions associated with IGHG1 , IGHG2 , and IGHG3 were also affected in another study. 19 Currently, it is unclear whether the preferential Sα involvement observed in our series was due to a bias in case selection or difference in methods between us and others. Nevertheless, the presence of t(14;19)(q32;q13) and t(2;14)(p13;q32), the latter of which also involved Sγ2 switch regions and, therefore, was considered to be mediated by erroneous CSR mechanisms, 27 , 28 in IGHV -unmutated B-cell tumor cells supports the possibility that CSR can occur outside the germinal center in a T-cell-independent manner and before the initiation of somatic mutations in the IGH gene.…”

“…The BCL3 -side breakpoints of t(14;19)(q32;q21)/ IGH :: BCL3 described in B-CLL/SLL cases were located within a range of the upstream sequences of BCL3 , 2 , 3 , 19 and those in the majority of cases were clustered immediately 5′ of BCL3 exon 1, 2 , 3 , 5 as observed in cases 1 and 2 ( Figure 6 ). The IGH -side breakpoints, on the other hand, preferentially occurred in the Sα1 or Sα2 switch region in our previous studies, 2 , 3 , 5 and the Sα1 breakpoints were confirmed by the current study, suggesting that class switch recombination (CSR) from IGHM and IGHA potentially mediates the generation of t(14;19)(q32;q21).…”

“…Here, we characterized 5 B-cell tumors that carried t(14;19)(q32;q13) identified by G-banding and the IGH :: BCL3 fusion gene determined by FISH. As described previously, 19 , 20 the tumors were categorized into two clinically and molecularly different groups: one included B-CLL/SLL cases requiring treatments, and the other was composed of de novo cases of aggressive B-cell lymphoma ( Table 1 ). Although both groups carried IGHV , used by B-CLL cells at higher frequencies than observed in normal B cells, 29 the genes were unmutated in the former group and significantly mutated in the latter.…”

“… 7 The t(14;19)(q32;q13) in these tumors is identical to that in B-CLL/SLL at the cytogenetic level, but not necessarily at the DNA level. 19 In this study, we present 5 B-cell tumors with t(14;19)(q32;q13) characterized in our laboratory and describe their clinical, histopathologic, and cytogenetic features in detail.…”