Shared mechanisms of resistance to zanubrutinib and ibrutinib via EGR1 and DNMT3A in mantle cell lymphoma

Abstract Mantle cell lymphoma (MCL), a B-cell malignancy comprising ~6% of non-Hodgkin lymphomas, remains incurable due to frequent relapse and acquired resistance to therapies, including Bruton's tyrosine kinase (BTK) inhibitors. While second-generation BTK inhibitors (e.g., zanubrutinib, acalabrutinib) offer improved selectivity and reduced toxicity compared to ibrutinib, resistance persists, and no standard of care has been established for relapsed/refractory MCL. We previously identified two key mediators of ibrutinib resistance—EGR1 and DNMT3A—which support mitochondrial metabolism via distinct mechanisms. EGR1 upregulates PDP1, enhancing PDH activity and linking glycolysis to oxidative phosphorylation (OXPHOS), while DNMT3A forms a transcriptional complex with MEF2B and MYC, driving mitochondrial biogenesis and OXPHOS. Both genes are upregulated in ibrutinib-resistant (IBR) MCL cells, and their inhibition restores drug sensitivity. Importantly, we observed similar overexpression of EGR1 and DNMT3A in MCL cells treated with zanubrutinib, suggesting a conserved resistance mechanism across BTK inhibitors. Ectopic expression of either gene reduced zanubrutinib sensitivity in vitro. Notably, IM156, a clinical-grade OXPHOS inhibitor and metformin analog, synergized with zanubrutinib to induce cell death in primary MCL cells with ibrutinib resistance. These findings will be further validated using patient-derived xenograft (PDX) models. Together, our results highlight mitochondrial metabolism—via EGR1 and DNMT3A—as a key vulnerability in BTK inhibitor-resistant MCL and support combination strategies targeting OXPHOS to improve therapeutic outcomes.