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Burkitt-like lymphoma with 11q aberration
Supplementary Figure S2), two cases had only an 11q termi- nal deletion, one case showed a complex 11q alteration with two gains and two losses, and finally one case had an 11q23.3-q25 copy number neutral loss of heterozygosity in addition to gain (Online Supplementary Figure S2). Two min- imal regions of gain were identified (chr11:103326831- 111737912/11q22.3-q23.1 and chr11:114767237- 116764582/11q23.3,hg19) whereas the minimal region of loss was in chr11:128214400-132020453/11q24.3-q25 (including the ETS1 and FLI1 genes). No cases with homozygous deletions of these two targets were observed in our series. The breakpoint region between gain and loss was not conserved and spanned from chr11:118352769 to chr11:121062860. Amplifications in the 11q arm were observed in four cases, with a minimal region chr11:118347020-120155799/11q23.3, including the USP2 gene (Online Supplementary Figure S5). The most recurrent copy number aberrations other than 11q were 12q12-q21.1 gains and 6q12.1-q21 losses (Figure 2A).
BLL-11q cases displayed similar levels of complexity as MYC-positive BL (7.1 vs. 6 alterations/case),20 but signifi- cantly lower than those of GCB-DLBCL (7.1 vs. 19, alter- ations/case P<0.0001).13 The BLL-11q genomic profile dif- fered from that of BL and DLBCL (Online Supplementary Figure S6). BLL-11q had frequent gains of 5q21.3-q32 and losses of 6q12.1-q21 and lacked the 1q gains seen in MYC- positive BL. BLL-11q also lacked alterations typically seen in GCB-DLBCL such as gains of 2p16.1 and 7p and losses of 1p36.32.
The six tumors negative for both MYC and 11q-aberra- tions in patients younger than 40 years had similar levels of genomic complexity as those observed in BLL-11q (11.8 vs. 7.1 alterations/case) (Online Supplementary Figure S7A). The unique significant aberration that distinguished the two groups was the presence/absence of the 11q aberration.
The review of the literature regarding other lymphoid neoplasms confirmed that the 11q alteration observed in BLL-11q is mainly absent in other lymphoma entities with the exception of transformed follicular lymphoma (16%) (Online Supplementary Results).22
Next-generation sequencing and gene expression analysis
Target next-generation sequencing showed a total of 49 potential driver mutations affecting 27 different genes (mean=4.9 mutations per case) (Figure 2C, D, Online Supplementary Figures S8 and S9; Online Supplementary Table S7). Interestingly, all cases lacked the typical BL mutations in ID3, TCF3, or CCND3 genes, and their muta- tional profile was more similar to that of other GC- derived lymphomas with recurrent mutations affecting BTG2 (4 cases), DDX3X, ETS1, EP300, and GNA13 (3 cases each) (Online Supplementary Table S8). Five cases had mutations in epigenetic modifier genes such as EP300, CREBBP, KMT2C, EZH2, ARID1A, KMT2D, HIST1H1D and HIST1H2BC. Two cases had concomitant TMEM30A deleterious mutations associated with a 6q14.1 deletion as seen in DLBCL but not in BL (Figure 2C).14-16
BTG2 mutations, found in four cases, comprised three missense mutations and one deletion in a splicing site. BTG2 is a tumor suppressor gene with an important role in G1/S transition through inhibition of CCND1 in a pRb- dependent mechanism.23 These BTG2-inactivating muta- tions could release CCND1 inhibition and accelerate G1/S transition. GNA13 mutations were found in three cases
including four missense and two nonsense mutations, and one missense mutation in a splicing site. Two MYC mis- sense mutations occurred in the central domain of the pro- tein, but did not affect threonine phosphorylation sites (Online Supplementary Table S7).24 ETS1 mutations have been previously described in BLL-11q and activated B-cell DLBCL13,17 but not in conventional BL (Online Supplementary Table S8).14,15 We detected three coding mutations located on the winged helix-turn-helix DNA- binding domain but the previously described exon 1 mutations (NM_005238) were absent in this series. ETS1 RNA expression was lower in BLL-11q than in MYC-pos- itive BL (relative expression 6.6 vs. 19.3, P<0.001) and was also lower in ETS1-mutated than wild-type BLL-11q (rela- tive expression 1.9 vs. 8.6, P=0.03) (Online Supplementary Figure S4B).
The mutational profile of four MYC-negative/11q alter- ation-negative cases with material available was analyzed using the same approach. No mutations in BTG2, EP300 or ETS1 genes were observed. Moreover, three out of four did not harbor any BL-related mutation on ID3, TCF3 and CCND3 whereas the fourth case had a mutational profile commonly seen in BL with MYC, DDX3X, SMARC4, CCND3 and TP53 mutations (Online Supplementary Figure S7B).
Discussion
BLL-11q was initially recognized as a particular subset of HGBCL that had an expression profile and some patho- logical characteristics similar to those of BL but lacked MYC-translocations and alternatively shared a common pattern of gains at 11q23 associated with losses at 11q24- qter. The particular features of these cases raise some uncertainty on their precise categorization as a variant of BL or a tumor related to other HGBCL.1,4-6,9-11 On the other hand, the limited number of cases reported and the differ- ent methodologies used for their recognition do not pro- vide a clear view of their incidence and clinico-pathologi- cal characteristics.
In this study we searched our files for cases that could be reclassified as BLL-11q among 95 tumors previously classified as BL, atypical BL, or HGBCL, NOS and found eight (8%) cases with the chromosomal aberration. These cases, together with three additional cases received on consultation, were investigated for copy number alter- ations and mutational profiles and compared to the genomic aberrations recently identified in BL, DLBCL, and HGBCL.13-17 The complexity of BLL-11q was similar to that of MYC-positive BL,20 but significantly lower than that of GCB-DLBCL.13 The BLL-11q genomic profile differed from that of BL and DLBCL (Online Supplementary Figure S6). BLL-11q had frequent gains of 5q21.3-q32 and losses of 6q12.1-q21 and lacked the 1q gains seen in MYC-posi- tive BL. BLL-11q also lacked alterations typically seen in GCB-DLBCL such as gains of 2p16.1 and 7p and losses of 1p36.32. Additionally, we identified a mutational profile in BLL-11q which was different from that of MYC-posi- tive BL since all cases lacked the typical BL mutations in ID3, TCF3, or CCND3 genes and had mutations in BTG2, DDX3X, and ETS1 not seen in BL. In addition, BLL-11q had mutations in epigenetic modifier genes such as EP300, CREBBP, KMT2C, EZH2, ARID1A, KMT2D, HIST1H1D and HIST1H2BC, which are common in DLBCL, particu-
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