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Molecular Biology and Genetics |
Institute for Cancer Genetics, and the Departments of Pathology and Genetics & Development, Columbia University, New York, NY 10032 [M. P. B., S. I., R. D-F.]; Hematology Unit, Division of Internal Medicine, Department of Medical Sciences, Amedeo Avogadro University of Eastern Piedmont, 28100 Novara, Italy [D. C., D. R., G. G.]; Cell Biology and Genetics Programs, Memorial Sloan-Kettering Cancer Center, New York, New York 10021 [P. H. R., P. N., D. C. L., S. C., R. S. K. C.]; and the Department of Pathology, British Columbia Cancer Agency, Vancouver, V5Z 4E6 Canada [T. A., R. D. G.]
| ABSTRACT |
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| INTRODUCTION |
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95% of mantle cell lymphomas, BCL-2 at 18q21 involved in 7090% of FLs (1)
, c-MYC at 8q24, which is found to be rearranged in 100% of Burkitts lymphoma (1)
, PAX-5 at 9p13 involved in 50% of lymphoplasmacytoid lymphomas (1)
, and BCL-6 at 3q27 rearranged in 3040% of DLBCLs and in 415% of FL cases (3, 4, 5)
. The BCL-6 gene encodes a nuclear phosphoprotein characterized by six COOH-terminal Kruppel-type zinc finger motifs, and an NH2-terminal POZ motif, shared by several zinc finger molecules, including the Drosophila developmental regulators Tramtrak and Broad-Complex, as well as the human KUP, ZID, and PLZF proteins (3) . BCL-6 has been shown to function as a potent transcriptional repressor of promoters linked to its DNA target sequence (6, 7, 8) . The BCL-6 protein is expressed in mature B-cells within germinal centers but not in immature B-cell precursors or in differentiated plasma cells (9) . Targeted disruption of the BCL-6 gene shows that BCL-6 is essential for germinal center formation, being involved in the control of Th2-type immune responses (10 , 11) .
Rearrangements involving the BCL-6 gene at 3q27 cluster mainly in a 4-kb genomic region, termed the MBR, which spans the first noncoding exon of the gene (3, 4, 5)
. Translocations affecting band 3q27 in NHL are not limited to the Ig loci but may involve numerous different partner chromosomes. The molecular characterization of several 3q27 chromosomal translocations has shown that the coding domain of the translocated BCL-6 gene becomes fused downstream to heterologous promoters. These include the Eµ and I
promoters of Ig genes in the case of t(3;14) as well as promoters of other genes, namely TTF, BOB-1, H4, in the case of t(3;4), t(3;11), and t(3;6), respectively (12, 13, 14, 15)
. A general feature of Rpromoters juxtaposed to translocated BCL-6 is their constitutive expression in B-cells, which leads to the inappropriate expression of BCL-6 (12, 13, 14, 15)
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Between 30 and 50% of the 3q27 chromosomal breakpoints found in lymphomas do not occur within the MBR of BCL-6, suggesting the presence of alternative breakpoints at 3q27 (3) . To address this question, we cloned a t(3;14)(q27;q32) occurring in a FL case shown to be negative for rearrangement at the MBR of BCL-6. We detected a novel breakpoint cluster located 245285 kb upstream of the first exon of the BCL-6 gene and termed ABR. This breakpoint site was shown to be recurrent in several lymphomas with 3q27 chromosomal translocations that lacked BCL-6 MBR rearrangement.
| MATERIALS AND METHODS |
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Southern and Northern Blot Analysis.
High molecular weight DNA was extracted by the SDS/proteinase K method followed by "salting out" and ethanol precipitation. Southern blot analysis was performed following standard procedures. The following probes were used for Southern blot analysis of Ig gene rearrangements: JH probe, represented by a 6.6-kb BamHI-HindIII fragment from the IgH locus (17)
; and Cµ probe, represented by a 1.3-kb EcoRI fragment from the IgH locus (17)
. Some of the BCL-6 ABR probes used in this study have been used in a previous study (18)
. For Northern blot analysis, RNA was extracted from cell lines and patient samples using the guanidinium thiocyanate/cesium chloride method, electrophoresed on a 1.0% agarose gel containing 2.2 mM formaldehyde and transferred to a nylon membrane (Hybond N; Stratagene).
Cloning of Chromosomal Breakpoints.
High molecular weight DNA from NHL case 1952 was digested with BamHI and size fractionated by running on a 0.7% low-melting agarose gel. Fragments ranging from 12 to 23 kb were gel-purified and ligated into the
Dash-II vector (Stratagene, La Jolla, CA) and subsequently in vitro packaged using Gigapack III Gold packaging extract (Stratagene, La Jolla, CA). Recombinant phage clones (1 x 106) were screened by plaque hybridization using the JH and Cµ Ig probes. Isolation of germ-line 3q27 sequences was achieved by screening a human placenta library (Stratagene) with probe 2.1 B/H derived from phage
19522 {corresponding to der(14)
} (Fig. 1)
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FISH.
Briefly, probes were labeled by nick translation with biotin-16-dUTP or digoxigenin-11-dUTP and detected by indirect immunofluorescence using fluorescein isothiocyanate-conjugated avidin and rhodamine-conjugated anti-digoxigenin, respectively. Chromosomes were counterstained with 4',6-diamidino-2-phenylindole. Images were captured with a cooled chargecoupled device camera (Photometrics, Tucson AZ) attached to a Nikon Microphot-SA microscope and processed using Smart capture imaging system (Vysis, Downers Grove, IL).
DNA Sequencing.
DNA sequencing was performed by the dideoxy chain termination method using the ABI 373A automated sequencing system (Applied Biosystems, Foster City, CA).
| RESULTS |
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, and C
sequences showed the presence of three rearranged J fragments, two of which did not comigrate with any constant gene region probe (data not shown) as observed previously in several cases of chromosomal translocations involving the IgH locus (20)
. We then proceeded to clone the rearranged BamHI fragments containing JH and Cµ sequences from a recombinant phage library constructed from BamHI-digested DNA from case 1952, which was screened by both JH and Cµ probes. Restriction mapping and hybridization analysis revealed that the recombinant phage clones contained JH and Cµ sequences juxtaposed to sequences unrelated to the IgH locus. To determine the chromosomal origin of these sequences, a 2.1-kb BamHI-HindIII fragment from
1952-2, as well as a 1.3-kb XbaI fragment from
1952-23 (Fig. 1)
1952-2 was then used to screen a genomic placenta library to clone the corresponding normal locus on chromosome 3, represented by phage clones
1952-15 and
1952-11 (Fig. 2)
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1952-15/11) as a probe revealed signals on chromosomal derivatives (3)
and (14)
as well as normal chromosome 3, band q27, thus confirming the derivation of these phages from a t(3;14) (data not shown). By sequencing analysis, the typical Ig switch pentameric repeat motifs were seen in the immediate vicinity of the cloned breakpoint. No apparent homology was detectable between chromosome 14 and chromosome 3 sequences near the breakpoint.
Relationship between the 3q27 Breakpoint of Case 1952 and the BCL-6 Gene.
To define the position of the newly identified 3q27 breakpoint, a contig of P1, PAC, and YAC clones was constructed linking the newly cloned ABR to the BCL-6 locus (Fig. 2)
. A restriction map of the YAC clone 19GA10 is given in Fig. 2
, showing MluI and EagI restriction enzyme sites identified by double enzyme digestion and by hybridization analysis using YAC/PAC clone ends. By Southern blot hybridization analysis, probe 1.3 X from ABR (Fig. 2)
hybridized only to YAC clone 19GA10 in the contig. It hybridized specifically to a 220-kb MluI restriction fragment of YAC clone 19GA10. An adjacent ABR probe, termed 2.5 B/H, hybridized to a different MluI restriction fragment of 85 kb (see Fig. 2
). This indicates that the ABR is located 220 kb from the left YAC arm terminus, 19GA10L. By Southern blot hybridization analysis, probe 19GA10L hybridizes to both P1371O8 and PAC133M19. The 5' marker of P1371O8 (T7 end) is positioned
65 kb 5' to exon 1 of BCL-6 by a combination of PFGE and hybridization analysis (Fig. 2)
. Marker 133M19T7 maps 25 kb 5' to BCL-6 as determined by restriction fingerprint analysis and hybridization analysis (data not shown). Overall, these results indicate that ABR is positioned at a distance of 245285 kb 5' to BCL-6.
Recurrency of the BCL-6 ABR in Lymphomas.
To assess the frequency of ABR, we collected a series of lymphomas (n = 12) with cytogenetic evidence of t(3q27) translocations but absence of rearrangement involving the MBR of BCL-6. The histological and partial cytogenetic profiles of these NHL cases are presented in Table 1
. Southern blots of HindIII-, BgIII-, and BamHI-digested tumor DNAs were prepared and hybridized sequentially with probes derived from phages
1952-15/11, exploring a genomic distance of
40 kb surrounding the breakpoint of case 1952. All rearrangements reported were confirmed by analysis with a second enzyme digest. Representative results of hybridization analyses with probes from the ABR on Southern blots of t(3q27) NHL cases are shown in Fig. 3
. Using probes 1.3 X and 0.4 HaeIII on HindIII, BgIII, and BamHI Southern blot digests of lymphoma cases (Fig. 3)
, rearrangements were seen in 42% (5 of 12) of NHL cases that had cytogenetic evidence of t(3q27) chromosomal translocations and that showed germ-line configuration of the MBR (Table 1)
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BCL-6 Expression Levels in NHL Cases with ABR Rearrangement.
To analyze the effect of ABR rearrangement on BCL-6 gene expression, we examined the levels of BCL-6 expression in lymphoma cases 1952 (FL) and 1188 (DLBCL) (both rearranged at ABR), as compared with two control FLs (cases 2065 and 1992) showing no rearrangement at the ABR or MBR of BCL-6 (Fig. 4)
. BCL-6 RNA levels were similar, independent of the BCL-6 genomic status. In addition, BCL-6 expression levels of case 1952 were also comparable with those of DLBCL cell line LY18 with germ-line BCL-6, as well as of immunoblastic lymphoma LY8 carrying a MBR rearrangement. Overall, these results indicate that cases with ABR rearrangement express BCL-6 at levels comparable with phenotypically similar cases with MBR rearrangement or lacking 3q27 abnormalities.
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| DISCUSSION |
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5060% of lymphoma cases carrrying the 3q27 translocation (3, 4, 5)
. The occurrence of lymphomas harboring 3q27 breaks but devoid of BCL-6 MBR rearrangements point to the putative existence of other BCL-6 breakpoint clusters. Here we report the identification of a novel ABR, which, together with the BCL-6 MBR, accounts for
70% of the total number of 3q27 chromosomal breakpoints detectable in NHL cases.
The BCL-6 ABR is located at a distance of
280 kb telomeric to BCL-6, raising the question of how the translocation induces BCL-6 deregulation. On the basis of the model of several other lymphoma translocations, the ABR breaks may exert several possible modes of BCL-6 deregulation. These include substitution of enhancer regions, a mechanism which has been well demonstrated for many B-cell-associated oncogenes, including BCL-1, BCL-2, c-MYC, PAX-5, BCL-8, and BCL-9 (1)
. Enhancer substitution results from the insertion of various IgH transcriptional control elements, such as the potent JH-CH intron enhancer Eµ, the 3'
E, or the 3'
-hs4, at the junction region of the translocation breakpoint (23)
. An alternative mode of BCL-6 deregulation by ABR translocations consists in the removal of cis-acting regulatory domains in a fashion similar to that suggested for some rearrangements involving the c-MYC locus (24)
. In the case of NHL cases rearranged at the ABR but not involving the Ig genes, it is conceivable that BCL-6 is deregulated by enhancer substitution of genes other than Ig genes. Finally, it cannot be formally excluded that ABR breaks affect genes mapping to 3q27 but unrelated to BCL-6. However, the genomic region surrounding ABR analyzed to date failed to reveal any functionally proven gene.
Our survey of BCL-6 ABR breakpoints in B-cell lymphoma defines that the frequency of ABR rearrangements is substantially lower than that of BCL-6 MBR. In fact, MBR rearrangements seem to be involved in
75% of DLBCL cases with cytogenetically detectable 327 breakpoints (3q27+) (3)
, whereas ABR rearrangements account for only a fraction (4 of 7, >50% in this study) of the remaining MBR-negative 3q27+ cases. Thus, ABR rearrangements are expected to account for
12% of all 3q27 rearrangements, corresponding to an expected frequency of 4% in the overall DLBCL populations and consistent with the actual frequency observed in this initial study (2 of 84). Conversely, it is curious that the frequency of ABR rearrangements in FL appears to be similar, or possibly higher, than that of MBR rearrangements. Future studies on large panels of cases are needed to define whether BCL-6 ABR rearrangements preferentially associate with FL.
From a diagnostic standpoint, the results of this study point to the need of long range DNA analysis for the correct identification of all BCL-6 breakpoints occurring in lymphomas. In this respect, FISH provides a powerful tool to detect both MBR and ABR BCL-6 breakpoints, thereby surpassing the capabilities of conventional Southern blot hybridization analysis. In particular, highly predictive analysis of BCL-6 rearrangements can be performed by FISH using as a probe a 650-kb clone contig designed to detect breakpoints occurring both at the MBR and ABR, as well as those which scatter around the BCL-6 locus. Because a fraction of 3q27 breaks cannot be currently explained by BCL-6 breaks at MBR or ABR, FISH studies may also lead to the discovery of additional BCL-6 breakpoint clusters that, together with MBR and ABR, will recapitulate the molecular pathology of 3q27 breaks in B-cell lymphoma.
| FOOTNOTES |
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1 Supported in part by the National Institute of Health Grant CA-37295 (to R. D-F.); Istituto Superiore di Sanità, III Programma Nazionale di Ricerca sullAIDS 1999 - Progetto Patologia, Clinica e Terapia dellAIDS, Rome, Italy (to G. G.); and Fondazione "Piera Pietro e Giovanni Ferrero," Alba, Italy (to G. G.). M. P. B. was supported in part by the Mater College, Dublin, Ireland, and the Vocational Education Committee Co., Donegal, Ireland. M. P. B. was registered in the PhD program of medicine in University College Dublin, Ireland. D. C. is supported by a fellowship from Federazione Italiana Ricerca Cancro, Milan, Italy. ![]()
2 To whom requests for reprints should be addressed, at Institute for Cancer Genetics, Columbia University, Russ Berrie Science Pavilion, 1150 Saint Nicholas Avenue, Room 303B, New York, NY 10032. Phone: (212) 851-5273; Fax (212) 851-5256; E-mail: rd10{at}columbia.edu ![]()
3 The abbreviations used are: NHL, non-Hodgkins lymphoma; Ig, immunoglobulin; FL, follicular lymphoma; DLBCL, diffuse large B-cell lymphoma; MBR, major breakpoint region; ABR, alternative breakpoint region; FISH, fluorescent in situ hybridization; PFGE, pulsed-field gel electrophoresis. ![]()
Received 2/ 1/02. Accepted 5/17/02.
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-enhancers from a distance of at least 30 kb but not by elements located within 50 kb of the unaltered c-myc locus in vivo. Oncogene, 12: 1299-1307, 1996.[Medline]This article has been cited by other articles:
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Y.-W. Chen, X.-T. Hu, A. C. Liang, W.-Y. Au, C.-C. So, M. L. Wong, L. Shen, Q. Tao, K.-M. Chu, Y.-L. Kwong, et al. High BCL6 expression predicts better prognosis, independent of BCL6 translocation status, translocation partner, or BCL6-deregulating mutations, in gastric lymphoma Blood, October 1, 2006; 108(7): 2373 - 2383. [Abstract] [Full Text] [PDF] |
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H. Niu, G. Cattoretti, and R. Dalla-Favera BCL6 Controls the Expression of the B7-1/CD80 Costimulatory Receptor in Germinal Center B Cells J. Exp. Med., July 21, 2003; 198(2): 211 - 221. [Abstract] [Full Text] [PDF] |
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L. Pasqualucci, A. Migliazza, K. Basso, J. Houldsworth, R. S. K. Chaganti, and R. Dalla-Favera Mutations of the BCL6 proto-oncogene disrupt its negative autoregulation in diffuse large B-cell lymphoma Blood, April 15, 2003; 101(8): 2914 - 2923. [Abstract] [Full Text] [PDF] |
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