Genomic Characterization and Classification of BCL6 Rearranged Follicular Lymphomas
Authors: Amallraja Anu , Gundem Gunes , Domenico Dylan , Arango Ossa Juan E , Aypar Umut , Baik Jeeyeon , Kluk Michael , Sethi Shenon , Lopez Katherine , Qualls David A. , Salles Gilles , Papaemmanuil Elli , Galera Pallavi , Dogan Ahmet 
Published: December 2024

Introduction
Follicular lymphoma (FL) is the most common type of indolent non-Hodgkin's lymphoma with BCL6 rearrangements (BCL6-R) observed in 5-15% of cases. BCL6-R FL frequently exhibit concurrent canonical BCL2 rearrangements (BCL2-R). However, a subset presents with BCL6-R exclusively and shares biological features with the recently described genomic subgroup of diffuse large B-cell lymphoma, BN2, characterized by BCL6-R and a mutational profile suggestive of marginal zone lymphoma (MZL) (Schmitz 2018). In this study, we analyzed 14 BCL6-R FL samples to study the mechanisms generating the BCL6 and BCL2 rearrangements.
Methods
WGS was performed in 14 FL tumors determined to be BCL6 rearranged by clinical cytogenetics (median coverage 71x) and matched germline controls (median coverage 41x). Bioinformatics analysis was performed to align sequencing reads, call somatic variants - mutations, indels, rearrangements, and detect mutational signatures and clonal structures as described (Shukla, Levine, Gundem 2022). Kataegis was detected using {katdetectR} (Hazelaar 2023) and Ig loci were characterized by IgCaller (Nadeu 2020). The LymphGen classification algorithm was run on the NCI website (Wright 2020).
Results and Discussion
Genome-wide mutation calling identified a median of 16.7k SNVs, 10.7k Indels and 0.2k SVs per sample. Driver events were detected in all 14 samples with 93% of samples having at least 5 events. Mutations in epigenetic modifier genes like KMT2D, CREBBP, ARID1A and deletions in the CDKN2A/CDKN2B/MTAP locus were the most frequent. Non-canonical (SBS9) and canonical (SBS84) AID mutational signatures were detected in all samples.
Recurrent driver rearrangements were identified in BCL6 (n = 14) and BCL2 (n = 10). BCL2-R (n = 8) were found to be predominantly created by RAG mediated aberrant VDJ recombination, whereas most BCL6-R (n = 11) were found to be generated through AID mediated aberrant class switch recombination or somatic hypermutation. These results suggest that in cases with concurrent BCL2-R and BCL6-R, BCL2-R occurred early in the B-cell ontogeny within the bone marrow whereas BCL6-R occurred later within the germinal center. Most BCL6-R associated with a BCL2-R involved non-Ig partners (n = 8), whereas exclusive BCL6-R were partnered with IgH.
The LymphGen algorithm classified samples into EZB (n = 11, 78.57%), BN2 (n = 2, 14.28%), EZB/A53 (n = 1, 7.14%). Two cases with exclusive BCL6-R showed mutational profiles similar to MZL, including mutations in the NOTCH pathway, and were classified as BN2.
Conclusions
WGS-based comprehensive genomic profiling of BCL6-R FL revealed that BCL6-R are generated by AID mediated CSR or somatic hypermutation, regardless of whether they were the primary driver (BCL6-R only) or secondary to existing BCL2-R. Exclusive BCL6-R were associated IgH gene region enhancers and are likely to be pathogenic drivers associated with overexpression of the BCL6 protein, whereas BCL6-R with concurrent BCL2-R revealed different partners and might represent passenger events rather than true oncogenic drivers. Cases with BCL6-R only exhibit MZL like mutations and may represent a unique subset of B-cell lymphomas biologically closer to MZL than to FL.