DNA Methylation-Based Burkitt Lymphoma Epitypes Have Distinct Molecular and Clinical Features

Introduction: Genome-wide hypomethylation coupled with hypermethylation of tumor suppressor genes is a hallmark of many cancers. Consistent changes in DNA methylation patterns are also a feature of immune cells as they undergo terminal differentiation and maturation. In previous studies, it has been shown that malignant B cells harbor a combination of de novo methylation while retaining some epigenetic features characteristic of their cell of origin. Although information on the genetic features of Burkitt Lymphoma (BL) is expanding, limited information exists on the methylation landscape and its role in pathogenesis. We sought to identify consistent DNA methylation changes and their interplay between BL pathogenesis and other features such as EBV status and somatic mutations. We performed an integrative analysis using comprehensive genome-wide CpG methylation profiling, whole genome sequencing, and gene expression analysis.

Methods: Samples were collected as part of the Burkitt Lymphoma Genome Sequencing Project (BLGSP). DNA from 218 primary BL tumors (154 pediatric (111 EBV+), 64 adult (19 EBV+)), 13 BL cell lines (6 EBV+), and 6 normal centroblast (CB) samples were profiled using the Illumina EPIC array. DNA and RNA from biopsies and cell lines underwent whole genome and RNA sequencing to enable the correlation of DNA methylation status with gene expression and genomic alterations. Nine of the BL samples were separately subjected to whole genome sequencing using the PromethION (Oxford Nanopore) to infer genome-wide methylation landscape. Publicly available data from 1595 B cell samples representing both normal subpopulations and tumor subtypes were used for further comparison. To search for methylation patterns within BL, beta values from the 10000 most variable CpGs were used as features for non-negative matrix factorization (NMF) clustering.

Results: Clustering revealed two distinct epigenetic subgroups (epitypes) within BL, which we have named hyperBL (cluster1) and hypoBL (cluster2). We found pediatric and adult tumors to be proportionally split across the two epitypes; however, we noted an over-representation of EBV+ tumors in hyperBL. PCA analysis comparing BL with the additional B-cell samples revealed a separation between the epitypes, with hyperBL projecting farther along the trajectory of B cell differentiation, suggestive of a more terminally differentiated B-cell. Investigating the differential methylation between epitypes revealed hyperBL to be associated with greater hypermethylation compared to hypoBL and CBs. The hypermethylated CpGs in hyperBL mainly affected promoter regions within CpG islands while hypomethylated CpGs were mostly intergenic or in open seas. Using PromethION data to allow for genome-wide analyses, we found hypermethylated regions of hyperBL were enriched for binding motifs for several transcription factors involved in B cell development including: IRF4, PAX5, YY1, BCL6, SP1, STAT3, and KLF9. We used mitotic clock estimates based on DNA methylation (epiCMIT) and found hyperBL had significantly elevated values, suggesting a greater proliferative history of these tumors. To further establish a molecular basis for these epitypes, we searched for gene expression differences and distinct driver mutation patterns. The genomes of hyperBL tumors harbored an overall greater mutation burden and significantly higher mutation burden within regions affected by aberrant somatic hypermutation (aSHM), which was associated with a higher frequency of mutations attributed to the SBS9 mutational signature. Gene expression differences indicate hypoBL tumors have upregulation of IRF4 induced pathways. To determine the clinical relevance of the unique epigenetic clusters we conducted survival analyses and found hyperBL samples to have significantly inferior progression free survival.

Conclusion: This work identifies novel epigenetic subgroups within BL with characteristic genetic differences between them. HyperBL is associated with hypermethylation, a higher mutation burden, elevated rates of aSHM, and inferior PFS. These results establish a subset of patients with distinct epigenetic, molecular and clinical features and further elucidates key mechanisms underlying BL pathogenesis. Together these data highlight the need and potential for strategies that exploit these epigenetic changes as a therapeutic target.