DNA replication stress-induced transcriptome of Human Burkitt’s lymphoma identifies MBD1 as a novel suppressor of BCL6 rearrangements in germinal center derived B-lymphomagenesis

Abstract BCL6 is a master transcriptional regulator of germinal center (GC) B cells. BCL6 is frequently translocated at the major translocation cluster (MTC) within intron 1 of the BCL6 locus, a hotspot commonly rearranged in diffuse large B cell lymphomas (DLBCLs). BCL6 amplifications are associated with therapeutic resistance and poor survival outcomes in hematological and solid cancers. However the mechanisms suppressing genome instability at the BCL6 -MTC preventing BCL6 rearragements remain unclear. Here, transcriptome analysis and genome-wide mapping of histone H3 lysine 4 trimethylation (H3K4me3) in hydroxyurea (HU)-treated Raji cells (a Burkitt’s lymphoma model) revealed the induced expression of MBD1 , encoding the DNA CpG methylation-binding protein. Functional studies using shRNA silencing and ectopic overexpression demonstrated that MBD1 suppresses BCL6 transcription whose promoter harbours conserved CpG methylation sites, suggesting a DNA methylation-dependent regulation of BCL6 trasncription by MBD1. Conversely, BCL6 repressed MBD1 expression by binding to its promoter. MBD1 -depleted Raji cells exhibited increased genomic instability at the BCL6 -MTC upon HU treatment, heightened sensitivity to DNA replication inhibitors (HU, gemcitabine, and etoposide), and reduced tumorigenicity in xenograft mouse models. We propose that MBD1 prevents genomic instability at the BCL6 -MTC to suppress DLBCL formation. Moreover, MBD1 promotes genomic stability and cell viability during DNA replication stress. MBD1 thus represents a potential therapeutic target for cancers exhibiting resistance to chemotherapies targeting DNA replication. Key Points MBD1 suppresses BCL6 expression under the DNA replication stress MBD1 suppresses genomic instability at BCL6 translocation hotspots MBD1 depletion is associated with reduced tumorigenicity in mouse xenograft and sensitivity to DNA replication inhibitors.