Protein Kinase CK2 regulates epigenetic plasticity in diffuse large B-cell lymphoma

Diffuse Large B-Cell Lymphoma (DLBCL) is the most prevalent and heterogeneous subtype of non-Hodgkin lymphoma and is characterized by profound transcriptional and epigenetic deregulation. In the germinal center (GC) subtype, malignant B cells acquire a survival advantage by maintaining a pseudo-germinal center state, driven by epigenetic mechanisms that stabilize a proliferative, anti-differentiation program. A major contributor to this malignant epigenetic identity is the Polycomb Repressive Complex 2 (PRC2). Its enzymatic core, EZH2, catalyzes trimethylation of histone H3 at lysine 27 (H3K27me3), a repressive chromatin mark that silences tumor suppressors and prevents terminal differentiation. Gain of function mutations of EZH2, particularly at Y641, are largely present in GC-DLBCL, enabling lymphoma cells to remain transcriptionally frozen in a germinal center-like state, bypass apoptosis, and proliferate aggressively. Protein kinase CK2 is a constitutively active Ser/Thr kinase that has emerged as an epigenetic regulator in cancer. CK2 phosphorylates numerous chromatin associated proteins, integrates metabolic signals, and modulates survival pathways such as NF-κB and AKT. However, its functional crosstalk with PRC2 remains poorly characterized, particularly in DLBCL. Previous studies revealed a biochemical link between CK2 and PRC2 through the phosphorylation of SUZ12, a structural component of the complex; nevertheless, the mechanistic relationship between CK2 and EZH2, remains unexplored, especially in germinal center lymphomas. In this work, we investigated the epigenetic consequences of CK2 inhibition in GC-derived DLBCL cell lines, hypothesizing that CK2 activity is essential for maintaining the malignant epigenetic identity through a delicate balance of activation and repression marks. We found that CK2 blockade led to a robust, yet paradoxical, upregulation of repressive H3K27me3 and H3K9me3 markers in total cell lysate, despite no change in EZH2 levels. Crucially, this hypermethylation was absent in purified histones, suggesting a mechanism of uncoupling between histone synthesis and deposition. Concurrently, CK2 inhibition downregulated the global H3 acetylation. We demonstrated that this hypoacetylation is linked to the collapse of the CK2-AKT-ACLY metabolic axis: the inhibition of CK2 leads to reduced the activating phosphorylation of ACLY at Ser455, thereby diminishing the nuclear supply of Acetyl-CoA required by Histone Acetyltransferases. Furthermore, we detected a significant reduction in DNMT1, the major maintenance DNA methyltransferase, revealing that CK2 inhibition simultaneously perturbs the DNA methylation machinery. Collectively, these findings suggest that CK2 acts as a central epigenetic hub, sustaining a chromatin environment favorable to oncogenic transcription by integrating metabolic flux regulation, maintaining DNA methylation, and preventing the excessive repressive methylation of nucleosomes. Importantly, we found that pretreatment of GC-DLBCL cells with the EZH2 inhibitor tazemetostat, followed by CK2 inhibition, significantly enhanced apoptotic cell death revealing that PRC2 dependent methylation and CK2 mediated epigenetic control operate in a cooperative manner. Disrupting both pathways destabilizes the epigenetic equilibrium required for the survival of GC like lymphoma cells. Collectively, our findings highlight CK2 as a regulator of PRC2 activity, whose interactions extend beyond SUZ12 phosphorylation and ultimately could influence EZH2-dependent chromatin silencing. By simultaneously controlling histone methylation and acetylation, DNA methylation, and acetyl-CoA metabolism, CK2 could maintain the malignant identity of GC-DLBCL. These results not only uncover a mechanistic rationale for combined targeting of CK2 and EZH2 but also highlight CK2 as a master epigenetic player that sustains tumor survival by preventing differentiation-inducing repressive chromatin states.