Subtyping Burkitt Lymphoma by DNA Methylation

Burkitt lymphoma (BL) is an aggressive germinal center B-cell-derived malignancy. Historically, sporadic, endemic, and immunodeficiency-associated epidemiological variants were distinguished which differ in the frequency of Epstein-Barr virus (EBV) association. Aiming at identifying subgroups based on DNA methylation patterns we here profiled 96 primary BL cases, 17 BL cell lines and 6 lymphoblastoid cell lines using Illumina BeadChip arrays. DNA methylation clustered the cases into each two subgroups according to EBV status, with each showing two underlying subgroups (EBV-positive: BL-mC1, BL-mC2 and EBV-negative: BL-mC3, BL-mC4). The subgroups BL-mC1/2 enriched for EBV-positive cases showed increased DNA methylation, epigenetic age and in part increased proliferation history compared to BL-mC3/4. CpGs hypermethylated in EBV-positive BLs were enriched for polycomb repressive complex 2 marks, while the CpGs hypomethylated in EBV-negative BLs were linked to B-cell receptor signaling. EBV-associated hypermethylation affected regulatory regions of genes frequently mutated in BL (e.g. CCND3, TP53), and impacted superenhancers, suggesting that hypermethylation may compensate for the lower mutation burden of oncogenic drivers in EBV-positive BLs. Though minor, but significant differences were also observed between EBV-positive endemic and sporadic cases (e.g. at the SOX11 and RUNX1 loci), our findings suggest that EBV status, rather than epidemiological variants, drive the DNA methylation-based subgrouping of BL. We collected 113 samples from patients with Burkitt lymphoma (sBL: n=70; eBL: n=20), Burkitt lymphoma-derived cell lines (n=17) and lymphoblastoid cell lines (n=6). The samples were analyzed using the Infinium HumanMethylation450 BeadChip array.