Genetically Defined Metabolic Targets Overcome Ibrutinib Resistance in Mantle Cell Lymphoma

Background: Mantle cell lymphoma (MCL), which accounts for around 7% of non-Hodgkin lymphomas, is currently incurable. MCL's key survival pathway is the B-cell receptor pathway, and Bruton's tyrosine kinase (BTK), the critical component of this pathway, is fundamentally activated in MCL. Ibrutinib, an agent that inhibits BTK, produced a 68% clinical response rate in patients with relapsed/refractory MCL, leading to its FDA approval. However, if MCL patients experience relapse following ibrutinib therapy or do not respond to ibrutinib, the 1-year survival rate is only 22%. Therefore, determining the mechanisms underlying ibrutinib resistance and identifying alternative therapeutic options are urgent unmet needs. Our group and others have shown that the BTK mutation associated with ibrutinib resistance is rare in MCL, and targeting alternative survival pathways to overcome ibrutinib resistance has not shown promising results.

Methods: To explore novel biomarkers or therapeutic targets, we performed whole exome and transcriptome sequencing and RNA-seq of ibrutinib-treated clinical specimens. Patient primary cells were isolated from MCL patients treated with ibrutinib either prior to treatment or at treatment discontinuation. Whole exome sequencing (WES) was performed to determine the mutational landscape of ibrutinib resistance. RNA-seq was employed to compare the gene expression profiles between ibrutinib-sensitive and -resistant patient samples. Gene set enrichment analysis was utilized to identify dysregulated molecular pathways associated with the resistant phenotype. The RNA-seq data were then validated with western blots. Functional studies targeting this molecular pathway were conducted, and in vivo efficacy was investigated in the ibrutinib-resistant MCL patient-derived xenograft (PDX) mouse model.

Results: Co-deletion of CDKN2A and MTAP was frequently detected in ibrutinib-resistant tumors but not in ibrutinib-sensitive tumors. We also found that metabolic reprogramming towards oxidative phosphorylation (OXPHOS) potentially drives ibrutinib resistance. IACS-010759, a small molecule developed by MD Anderson Cancer Center, inhibits OXPHOS and overcomes ibrutinib resistance in vitro and in PDX models. Nevertheless, the potential drivers of this observed metabolic reprogramming towards OXPHOS remain unclear. MTAP encodes 5-methylthioadenosine phosphorylase, a critical enzyme in the methionine salvage pathway, and is frequently lost in cancer cells, resulting in accumulation of metabolite methylthioadenosine and overexpression of protein arginine methyltransferase 5 (PRMT5). Thus, PRMT5 is a potential druggable therapeutic target to overcome ibrutinib resistance in MCL. We found that PRMT5 is highly expressed in ibrutinib-resistant MCL but not ibrutinib-sensitive MCL (7 ibrutinib-resistant vs. 15 ibrutinib-sensitive patient samples, p = 0.0051), especially in MTAP-deleted MCL specimens. Furthermore, patients with high PRMT5 levels had poor clinical outcomes on ibrutinib treatment. PRMT5 regulates tumor survival pathways by the methylation of histones H3R8, H4R3, and post-translational methylation of non-histone proteins, including p53, E2F1, BCL6, p65, and others. A novel PRMT5 inhibitor, GSK3226595, significantly inhibited tumor growth in an ibrutinib-resistant MCL PDX model (n = 5; vehicle vs. GSK3226595, p = 0.000048) and had no significant mouse body weight change (GSK3226595 vs. vehicle, p = 0.08).

Conclusion: This study may pave the way to develop a PRMT5/OXPHOS-based therapeutic strategy to overcome ibrutinib resistance in MCL.