Mutational landscape of high-grade B-cell lymphoma with MYC-, BCL2 and/or BCL6 rearrangements characterized by whole-exome sequencing

Abstract

High-grade B-cell lymphoma accompanied with MYC and BCL2 and/or BCL6 rearrangements (HGBL-DH/TH) poses a cytogenetically-defined provisional entity among aggressive B-cell lymphomas that is traditionally associated with unfavorable prognosis. To better understand the mutational and molecular landscape of HGBL-DH/TH we here performed whole-exome sequencing and deep panel next-generation-sequencing (NGS) of 47 clinically annotated cases. Oncogenic drivers, mutational signatures and perturbed pathways were compared with data from follicular lymphoma (FL), diffuse large-B-cell lymphoma (DLBCL) and Burkitt lymphoma (BL). We find an accumulation of oncogenic mutations in NOTCH, IL6/JAK/STAT and NFκB signaling pathways and delineate the mutational relationship within the continuum between FL/DLBCL, HGBL-DH/TH and BL. Further, we provide evidence of a molecular divergence between BCL2 and BCL6 rearranged HGBL-DH. Beyond a significant congruency with the C3/EZB DLBCL cluster in BCL2 rearranged cases on an exome-wide level, we observe an enrichment of the SBS6 mutation signature in BCL6 rearranged cases. Differential gene set enrichment and subsequent network propagation analysis according to cytogenetically defined subgroups revealed an impairment of TP53 and MYC pathway signaling in BCL2 rearranged cases, whereas BCL6 rearranged cases lacked this enrichment, but instead exhibited showed impairment of E2F targets. Intriguingly, HGBL-TH displayed intermediate mutational features in all three aspects. This study elucidates a recurrent pattern of mutational events driving FL into MYC-driven BCL2 rearranged HGBL, unveiling the mutational pathogenesis of this provisional entity. Through this refinement of the molecular taxonomy for aggressive, germinal-center derived B-cell lymphomas, this calls into question the current WHO classification system, especially regarding the status of MYC/BCL6 rearranged HGBL.

"Clinical Heterogeneity of High-Grade B-Cell Lymphoma"

“…Beyond a significant congruency with the C3/EZB DLBCL cluster in BCL2 rearranged cases on an exome-wide level, they observed an enrichment of the SBS6 mutation signature in BCL6 rearranged cases. SBS6 is associated with defective DNA mismatch repair and is found in microsatellite unstable tumors [9]. Differential gene set enrichment and subsequent network propagation analysis according to cytogenetically defined subgroups revealed an impairment of TP53 and MYC pathway signaling in BCL2 rearranged cases, whereas BCL6 rearranged cases lacked this enrichment, but instead exhibited showed impairment of E2F targets.…”

“…Differential gene set enrichment and subsequent network propagation analysis according to cytogenetically defined subgroups revealed an impairment of TP53 and MYC pathway signaling in BCL2 rearranged cases, whereas BCL6 rearranged cases lacked this enrichment, but instead exhibited showed impairment of E2F targets. Oncogenic drivers, mutational signatures and perturbed pathways were compared with data from follicular lymphoma (FL), diffuse large-B-cell lymphoma (DLBCL) and Burkitt lymphoma (BL) [9]. C-MYC/BCL2 HGBL DH usually attended to GCB lymphomas.…”

Copy Number Alteration and Mutational Profile of High-Grade B-Cell Lymphoma with MYC and BCL2 and/or BCL6 Rearrangements, Diffuse Large B-Cell Lymphoma with MYC-Rearrangement, and Diffuse Large B-Cell Lymphoma with MYC-Cluster Amplification

“…KMT2D , SOCS1 , and BCL2 were frequently mutated in DHL/THL but not in SHL. Previously reported NGS data of DHL/THL showed CREBBP , BCL2 , KMT2D , MYC , EZH2 , IGLL5 , FOXO1 , SOCS1 and SI are frequently mutated genes [ 16 , 17 , 18 ]. Evrard et al stated that for DHL/THL, the most frequently mutated genes were like those reported in DLBCL NOS, especially in GCB-DLBCL, but the percentage of DHL/THL with mutations on eight genes ( CREBBP , BCL2 , KMT2D , MYC , EZH2 , IGLL5 , FOXO1 and SOCS1 ) was significantly higher than that of reported DLBCL, NOS [ 16 ].…”

“…Aukema SM et al demonstrated that comparative copy number alteration (CNA) of DHL/THL had higher frequencies of gains at chromosome loci 8q and 12q compared with SHL (9). Next-generation target sequencing (NGS) demonstrated that the mutational profile of DHL/THL differed from that of DLBCL, NOS [ 16 , 17 , 18 ]. Gene expression profile analyses of DHL/THL revealed that DHL with BCL2 -R (DHL- BCL2 ) and THL had germinal center B-cell-like (GCB) profiles [ 6 , 9 , 19 , 20 , 21 ].…”

Cytological Diagnosis of Aggressive Small-Cell Lymphomas

“…In BL, we already assessed the prognostic role of MYC insertions or concomitant BCL2 and BCL6 mutations [46, 51]. In B-ALL/LBL and HGBL with MYC and BCL2 and/or BCL6 rearrangements, NGS sequencing has shown recurrent variants of genes coding for transcription factors (MYC, FOXO1), epigenetic modulators (KMT2D, EZH2, and CREBBP), and antiapoptotic proteins (BCL2) [51, 52]. In PTCL, NGS profiling matches with PCR-based T-cell clonality assessment [53].…”