DNMT3B functions as tumor suppressor in mantle cell lymphoma

Abstract DNA methyltransferases (DNMTs) are an evolutionarily conserved family of DNA methylases responsible for establishing and maintaining DNA methylation patterns. Accumulating evidence demonstrates that the regulation of DNA methylation by DNMTs is critical for normal hematopoiesis. Aberrant DNA methylation and expression due to DNMT dysregulation and mutations are recognized as important molecular events in various hematological malignancies. However, the precise function of DNMT3B in human mantle cell lymphoma (MCL) and the mechanism by which DNMT3B regulates MCL remain undefined. In this study, we used mantle cell lymphoma cell lines to generate DNMT3B knockout and overexpression models. RNA sequencing of DNMT3B knockout (sgDNMT3B) cells revealed differentially expressed genes and pathways compared to the control group. Notably, MYC target genes and the oxidative phosphorylation (OXPHOS) pathway were upregulated in the DNMT3B knockout group, suggesting that DNMT3B may suppress MYC activity and modulate the OXPHOS process. Furthermore, we performed immunohistochemistry (IHC) staining on a tissue microarray containing 58 tumor samples and 12 normal tissues (6 lymph nodes and 6 tonsil tissues) and found significantly lower DNMT3B expression in the tumor group. Consistently, cell viability and proliferation assays showed an increased growth rate in DNMT3B knockout cells, supporting a tumor-suppressive role for DNMT3B. Additionally, using MitoTracker, we detected a reduced mitochondrial membrane potential in DNMT3B-overexpressing cells, suggesting a role for DNMT3B in regulating mitochondrial function. By performing ChIP-seq, we identified genome-wide DNMT3B binding sites and potential co-factors. Among them, PAX5 emerged as a prominent candidate. PAX5 is an important transcription factor involved in regulating B-cell development and differentiation, although its role in lymphomagenesis remains poorly understood. We confirmed the physical interaction between DNMT3B and PAX5 by immunoprecipitation (IP). Notably, IHC staining demonstrated an inverse correlation between DNMT3B and PAX5 protein levels, supporting their opposing functions in MCL pathogenesis. Taken together, our findings highlight the tumor-suppressor role of DNMT3B and indicate that DNMT3B may inhibit the OXPHOS pathway in mantle cell lymphoma. Moreover, we identify a potential regulatory axis between DNMT3B and PAX5 in MCL, although the underlying mechanisms warrant further investigation.