Resistance In Mantle Cell Lymphoma Research Articles

Impact of PIK3CA gain and PTEN loss on mantle cell lymphoma biology and sensitivity to targeted therapies

AbstractBesides many other mutations in known cancer driver genes, mantle cell lymphoma (MCL) is characterized by recurrent genetic alterations of important regulators of the phosphoinositol-3-kinase (PI3K) cascade including PIK3CA gains and PTEN losses. To evaluate the biological and functional consequences of these aberrations in MCL, we have introduced transgenic expression of PIK3CA (PIK3CA UP) and performed knockout/knockdown of PTEN gene (PTEN KO/KD) in 5 MCL cell lines. The modified cell lines were tested for associated phenotypes including dependence on upstream B-cell receptor (BCR) signaling (by an additional BCR knockout). PIK3CA overexpression decreased the dependence of the tested MCL on prosurvival signaling from BCR, decreased levels of oxidative phosphorylation, and increased resistance to 2-deoxy-glucose, a glycolysis inhibitor. Unchanged protein kinase B (AKT) phosphorylation status and unchanged sensitivity to a battery of PI3K inhibitors suggested that PIK3CA gain might affect MCL cells in AKT-independent manner. PTEN KO was associated with a more distinct phenotype: AKT hyperphosphorylation and overactivation, increased resistance to multiple inhibitors (most of the tested PI3K inhibitors, Bruton tyrosine kinase inhibitor ibrutinib, and BCL2 inhibitor venetoclax), increased glycolytic rates with resistance to 2-deoxy-glucose, and significantly decreased dependence on prosurvival BCR signaling. Our results suggest that the frequent aberrations of the PI3K pathway may rewire associated signaling with lower dependence on BCR signaling, better metabolic and hypoxic adaptation, and targeted therapy resistance in MCL.

Using the Iron Chelator Deferasirox to Overcome Venetoclax Resistance in Mantle Cell Lymphoma

Using the Iron Chelator Deferasirox to Overcome Venetoclax Resistance in Mantle Cell Lymphoma

MCL-229 Using the Iron Chelator Deferasirox to Overcome Venetoclax Resistance in Mantle Cell Lymphoma

MCL-229 Using the Iron Chelator Deferasirox to Overcome Venetoclax Resistance in Mantle Cell Lymphoma

Dialog between mantle cell lymphoma cells and lymphoma-associated macrophages underlies ibrutinib resistance

IntroductionPatients with mantle cell lymphoma (MCL) frequently develop resistance to ibrutinib. Lymphoma-associated macrophages (LAMs) may play a causal role in this resistance but remain underexplored in current literature. ObjectivesTo elucidate the role of LAMs in mediating ibrutinib resistance in MCL. MethodsWe investigated macrophage polarization through multiparameter flow cytometry (MPFC) using antibodies against CD206 and CD86 in blood and tissue samples from patients with MCL, both resistant and sensitive to ibrutinib. Subsequently, we developed an in vitro co-culture model utilizing MCL cell lines to identify cytokines associated with ibrutinib resistance and macrophage M2 polarization. The mechanisms underlying resistance were examined using MPFC, RNA sequencing, and Western blot analysis. Additionally, we assessed whether SB225002, a CXCR2 inhibitor, could reverse ibrutinib resistance through CCK-8 and caspase-3 assays, as well as in a mouse xenograft model involving an ibrutinib-resistant MCL cell line. ResultsIn patients exhibiting ibrutinib resistance, the ratio of M2 to M1 LAMs was significantly higher compared to sensitive patients. In co-cultures of LAMs and MCL cells, the percentage of M2 macrophages, the IC50 value for ibrutinib, and the concentrations of IL-8 and CXCL5 were significantly elevated. Mechanistically, CXCL5 secreted by LAMs interacted with the CXCR2 on MCL cells, leading to the activation of the Akt, p38, and STAT3 signaling pathways in the presence of ibrutinib; this activity was diminished upon blockade of the CXCL5/CXCR2 axis. The combination of SB225002 and ibrutinib significantly enhanced MCL cell apoptosis, suppressed lymphoma growth in the xenograft model, and reprogrammed macrophage phenotype compared to treatment with ibrutinib alone. ConclusionOur data indicate that M2-polarized LAMs are associated with ibrutinib resistance in a model of MCL, and that a CXCR2 inhibitor can reverse this resistance. These findings suggest a potential new therapeutic strategy.

Targeting DNMT3A-mediated oxidative phosphorylation to overcome ibrutinib resistance in mantle cell lymphoma

The use of Bruton tyrosine kinase (BTK) inhibitors such as ibrutinib achieves a remarkable clinical response in mantle cell lymphoma (MCL). Acquired drug resistance, however, is significant and affects long-term survival of MCL patients. Here, we demonstrate that DNA methyltransferase 3A (DNMT3A) is involved in ibrutinib resistance. We find that DNMT3A expression is upregulated upon ibrutinib treatment in ibrutinib-resistant MCL cells. Genetic and pharmacological analyses reveal that DNMT3A mediates ibrutinib resistance independent of its DNA-methylation function. Mechanistically, DNMT3A induces the expression of MYC target genes through interaction with the transcription factors MEF2B and MYC, thus mediating metabolic reprogramming to oxidative phosphorylation (OXPHOS). Targeting DNMT3A with low-dose decitabine inhibits the growth of ibrutinib-resistant lymphoma cells both invitro and in a patient-derived xenograft mouse model. These findings suggest that targeting DNMT3A-mediated metabolic reprogramming to OXPHOS with decitabine provides a potential therapeutic strategy to overcome ibrutinib resistance in relapsed/refractory MCL.

Abstract 676: The integrated stress activator BTM-3566 overcomes therapeutic resistance in mantle cell lymphoma

Abstract Successive generations of BTK inhibitors and CAR T-cell therapy have transformed the treatment of mantle cell lymphoma (MCL). However, treatment resistance has inevitably emerged, creating significant medical need. Recently a novel, clinical stage small molecule, BTM-3566, has been described that targets a mitochondrial process essential for Diffuse Large B-cell lymphoma (DLBCL) survival. BTM-3566 activates the mitochondrial protease OMA1, triggering the ATF4 integrated stress response (ISR). BTM-3566 has robust in vitro efficacy in DLBCL cell lines irrespective of genomic background and elicits complete tumor regression in multiple CDX and PDX mouse models of DLBCL. Based on the activity observed in DLBCL, we further explored the effectiveness of BTM-3566 in MCL models in vitro and in xenograft mouse models in vivo. BTM-3566 inhibited cell proliferation across a panel of MCL cell lines, irrespective of resistance status to ibrutinib and venetoclax (IC50s of 142.5-687.6 nM). Following a 24-hour treatment with BTM-3566, a dose-dependent increase in apoptosis was observed in four tested MCL cell lines—JeKo-1, JeKo-IBN-R, Mino, and Mino-VEN-R, as determined by increased caspase-3 activation and PARP cleavage. Similarly, western blot analysis revealed dose-dependent reductions in MCL-1 and c-MYC, accompanied by an increase in the transcription factor ATF4, indicative of activation of the stress response. We evaluated the in vivo efficacy of BTM-3566 in the JeKo-CDX mouse model. Daily oral administration of BTM-3566 at 10, 20 and 30 mg/kg (n = 5 for each group) in a 5-day on and 2-day off schedule resulted in tumor regression at all three doses (Treatment vs. Vehicle, p < 0.01). We expanded our investigation to PDX mouse models, including those derived from patients resistant to multiple therapies. Four PDX models encompassing naive, rituximab-resistant, BTKi-CAR T dual-resistant and BTKi-VEN-CAR T triple-resistant models were evaluated. BTM-3566 treatment results in nearly complete tumor growth inhibition associated with robust reductions in tumor burden in treated mice across all four PDX models (reduction in tumor weight at the study endpoint, p < 0.001). Notably, no toxicity was observed during the treatment period. In summary, BTM-3566 is effective in treating MCL in vitro and in vivo in preclinical studies. Citation Format: Yang Liu, Heng-Huan Lee, Joseph McIntosh, Yijing Li, Tianci Zhang, Wei Wang, Matthew J. Kostura, Michael Wang. The integrated stress activator BTM-3566 overcomes therapeutic resistance in mantle cell lymphoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 676.

Abstract 602: Targeting CDK9 with a novel potent and selective inhibitor, YX0798, in CAR-T-relapsed mantle cell lymphoma models

Abstract Introduction: Cyclin-dependent kinase (CDK) family members play critical roles in multiple cellular processes. CDK9 is a central regulator at several stages of PolII transcription, including initiation, elongation, and termination. CDK9 dysfunction resulted in transcriptomic reprogramming and promotion of the development of cancers, including lymphoma and leukemia. We and others reported that transcriptomic reprogramming is associated with disease progression and therapeutic resistance in mantle cell lymphoma (MCL). Targeting CDK9 with its inhibitors AZD4573 and enitociclib is safe and effective for treatment in preclinical MCL models, and they are currently under clinical investigation to assess their efficacy and safety. The data demonstrated that CDK9 is a promising therapeutic target. In this study, we developed a novel CDK9 inhibitor, YX0798, and assessed its potency and safety in preclinical MCL models. Method: Cell viability assays were conducted in a time- and dose-dependent manner to assess the in vitro efficacy of YX0798 as well as AZD4573. Apoptosis assays and western blots were used to determine the mechanism of action in MCL cells. Patient-derived xenograft models from primary MCL patient samples were established in immunodeficient mice and used to determine the therapeutic potential YX0798. Results: Next generation sequencing showed that CDK9 was upregulated and cancer hallmarks MYC-TARGETS-v1 and -v2 were highly enriched in CAR-T-relapsed MCL patients compared to CAR-T-naïve patients. We hypothesized that CDK9 overexpression and activity may greatly contribute to the enrichment of MYC-TARGETS-v1 and -v2 in patients with CAR-T resistance, so targeting CDK9 may overcome that resistance. YX0798 was developed to be a potent and selective CDK9 inhibitor. It markedly inhibited cell viability and induced robust apoptosis in MCL cell lines. As expected, it inhibited CDK9 kinase activity and suppressed the expression of short-lived proteins like c-MYC and MCL-1 that are critical for MCL cell survival and growth. YX0798 at 2 mg/kg for continuous 7 days via pump or at 5 mg/kg daily by oral administration potently inhibited the tumor growth of xenografts derived from a patient with therapeutic relapse to the CAR-T therapy in vivo (P<0.0001). This treatment efficacy was found to be similar at that of AZD4573 but at a higher dosage (15+15 mg/kg, 2 hours split, QW, IP). No adverse effects in mice were observed for any of treatments. Conclusion: These data show that our novel CDK9 inhibitor YX0798 is potent and efficacious in treating aggressive MCL models and overcame CAR-T resistance at a lower dosage than AZD4573. Citation Format: Vivian Jiang, Yu Xue, Hong Kim, Joseph McIntosh, Haiying Chen, Tianci Zhang, Yang Liu, Jia Zhou, Michael Wang. Targeting CDK9 with a novel potent and selective inhibitor, YX0798, in CAR-T-relapsed mantle cell lymphoma models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 602.

The HSP90-MYC-CDK9 network drives therapeutic resistance in mantle cell lymphoma

Brexucabtagene autoleucel CAR-T therapy is highly efficacious in overcoming resistance to Bruton’s tyrosine kinase inhibitors (BTKi) in mantle cell lymphoma. However, many patients relapse post CAR-T therapy with dismal outcomes. To dissect the underlying mechanisms of sequential resistance to BTKi and CAR-T therapy, we performed single-cell RNA sequencing analysis for 66 samples from 25 patients treated with BTKi and/or CAR-T therapy and conducted in-depth bioinformatics™ analysis. Our analysis revealed that MYC activity progressively increased with sequential resistance. HSP90AB1 (Heat shock protein 90 alpha family class B member 1), a MYC target, was identified as early driver of CAR-T resistance. CDK9 (Cyclin-dependent kinase 9), another MYC target, was significantly upregulated in Dual-R samples. Both HSP90AB1 and CDK9 expression were correlated with MYC activity levels. Pharmaceutical co-targeting of HSP90 and CDK9 synergistically diminished MYC activity, leading to potent anti-MCL activity. Collectively, our study revealed that HSP90-MYC-CDK9 network is the primary driving force of therapeutic resistance.

Exploring BiTE-Integrated CAR T-Cell Therapy to Overcome Tumor Antigen Escape and Reinforce CAR-T Therapy in Mantle Cell Lymphoma

Background T cell engagers (BiTEs) are bispecific T-cell engaging antibodies that redirect T cells to target antigen-expressing tumor cells. Combining a second antigen-targeted bispecific T cell engager (BiTE) with CAR T cells or incorporating bispecific engaging antibody-secreting T cells (engager-T cells) is expected to augment T-cell activation and proliferative capacity, and antitumor cytotoxicity, even towards tumor cells expressing tumor antigens heterogeneously. Here, we report a BiTE-integrated T-cell therapeutic strategy to overcome tumor antigen escape and reinforce the efficacy of CAR-T therapy in mantle cell lymphoma (MCL). Methods CD20-directed bispecific T-cell engager (CD20-BiTE) was constructed with a publicly available VHH fragment from an anti-CD20 single-domain antibody, and anti-CD3 scFv from OKT3 monoclonal antibody. CD19-directed CAR construct is comprised of anti-CD19 scFv from publicly available FMC63 monoclonal antibody, CD8 transmembrane-, 4-1BB costimulatory-, and CD3ζ signaling-domains. Human primary pan-T cells were isolated from PBMC derived from normal human donors (MD Anderson Blood Bank) or patients with MCL. Activated T cells were used for effector functional assay or transduced with lentivirus to produce CAR T or engager-T cells. Effector function of bispecific antibodies and T cells was determined via T-cell activation, cytokine release, and T-cell-dependent cytotoxicity assay in a co-culture model. Results Treatment with CD20-BiTE enhances the effector function of naïve T cells: the BiTE-Fc fusion protein was ectopically expressed in Expi293 and purified by immobilized Protein-A. The binding specificity of scFv(s) of CD20-BiTE was confirmed to bind strongly and specifically to CD20-expressing cells. In vitro functional analyses demonstrated that co-culture of naïve T cells with CD20-exressing cells in the presence of CD20-BiTE induced antigen-specific activation of the T cells (increase in the expression of CD25 and CD69). In the presence of naïve T cells and antigen-positive MCL cells, CD20-BiTE enhanced the secretion of cytokines (IFNγ and TNFα, > 2-fold increase) and CD8 T-cell cytotoxic molecule granzyme B by T cells, in a BiTE-dependent and CD20-specific manner. The enhanced effector function translated into improved antitumor cytotoxicity, as activated T cells treated with CD20-BiTE exerted 43- 72% increase in the killing efficacy of JeKo-1 BTK-KD cells. CD20-BiTE-combined CAR T cells endowed with enhanced antitumor activity overcome tumor antigen escape and resistance to current CD19-CAR T cell therapy: when primary T cells and CD19-CAR T cells were co-cultured with MCL cells, addition of CD20-BiTE potentiated T cell-dependent cytotoxicity ( p < 0.001). Since both CD19-dependent and -independent CAR T cell-resistance often develop during adoptive cell therapy in MCL, we sought to overcome the resistance in MCL by combining a second antigen-targeted CD20-BiTE with CAR T cells or incorporating CD20-BiTE secreting T cells (engager-T cells). Remarkably, when combined with CD19-CAR T cells, CD20-BiTE mediates significant increase in the antitumor cytotoxicity, compared to T cells alone ( p ≤ 0,001 and p < 0.001 for 2nM and 5nM of the BiTE, respectively), in a CD20-specific fashion, in both MCL cells with diminished CD19 expression, and CD19-CAR T-resistant primary MCL cells. Importantly, in a transwell assay, CD19-CAR T cells demonstrated restored potent killing (>3-fold increase over CAR T cells alone) of the CD19-low or CAR T therapy resistant tumor cells, but only when the engager-T cells were present in the insert, suggesting the engaging molecules were able to redirect CD19-CAR T cells to CD20-positive tumor cells regardless of their CD19 expression. The anti-lymphoma efficacy of engager-CAR T cell therapy will be further evaluated in our well-established unique PDX model for MCL. In summary, we have successfully generated a CD20-directed bispecific T-cellengaging antibody and CD20-BiTE engager-T cells that could be combined with CAR T cell therapy, which was demonstrated effective in overcoming tumor antigen escape and resistance to current CD19-CAR T cell therapy in MCL.

The Selective CDK9 Inhibitor VIP152 Overcame Therapeutic Resistance in Mantle Cell Lymphoma

Introduction Mantle cell lymphoma (MCL) is an aggressive subtype of non-Hodgkin lymphoma. Even most advanced therapies are generally followed by resistance and relapse, creating an urgent need for novel drugs to overcome resistance. Our and other studies have shown transcriptome is abnormally reprogrammed in patients with therapeutic resistance. CDK9, as a master transcriptional regulator, is overexpressed in tumors after subsequent relapses to BTK inhibitors (BTKi) and CAR-T therapy. VIP152 is a highly potent and selective CDK9 inhibitor under preclinical and early clinical development. As yet, its potency and safety in patients with MCL, especially those with multiple therapeutic resistances, has not been addressed. Method We performed single-cell RNA sequencing and bulk RNA sequencing to investigate enriched cancer hallmarks in MCL. Cell viability assays were conducted in a time- and dose-dependent manner to assess the in vitro efficacy of VIP152. Apoptosis assays and western blots were used to identify relevant pathways in bypassing resistances. Cell line-derived xenograft and patient-derived xenograft models of MCL created in immunodeficient mice were used to monitor tumor growth and thus determine the in vivo efficacy of VIP152 in overcoming therapeutic resistances. Results Based on single-cell RNA sequencing and bulk RNA sequencing, we found that the cancer hallmark MYC-TARGETS is progressively enriched in MCL patients with subsequent failures to BTKi and CAR-T therapy. CDK9 was found to be overexpressed in CAR-T-relapsed patients compared to CAR-T-naïve but BTKi-refractory/relapsed patients. We hypothesized that CDK9 overexpression and activity may greatly contribute to the transcriptomic reprogramming in patients with therapeutic resistance. Targeting CDK9-mediated transcription with the specific CDK9 inhibitor VIP152 was highly effective in MCL cell lines at low nanomolar range (55-172 nM). VIP152 robustly induced apoptosis in a time- and dose-dependent manner, which was largely dependent on caspase-3 activity. It markedly inhibited CDK9 phosphorylation and down streaming signaling, and suppressed the expression of short-lived proteins like MYC, MCL-1, and cyclin D1 that are critical for MCL cell survival and proliferation. VIP152 effectively inhibited the tumor growth of MCL cell line-derived xenograft models in vivo (P<0.001) with no apparent adverse effects in mice. Moreover, VIP152 markedly inhibited the growth of three patient-derived xenograft tumor models, overcoming BTKi resistance (P<0.001), BTKi-venetoclax dual resistance (P<0.01), and BTKi-CAR-T dual resistance (P<0.001). Conclusion These data showed that CDK9 was a promising target for treating MCL and using VIP152 to specifically target it was efficacious in overcoming a variety of therapeutic resistances in MCL.

Harnessing Btki Therapy By CDK4/6i Control of T Effector Memory Cells and T Cell Surveillance in Mantle Cell Lymphoma

Drug resistance remains a formidable challenge in mantle cell lymphoma (MCL). Cell cycle dysregulation driven by aberrant Cyclin D1 and CDK4 expression is a hallmark for MCL, providing a rationale for targeting the cell cycle in MCL therapy. We have demonstrated in preclinical studies that inhibition of CDK4/6 not only induces early G1 cell cycle arrest, but also reprograms MCL cells for cytotoxic killing. On this basis, we investigated if inhibition of cyclin D1/CDK4 with palbociclib (CDK4/6 inhibitor) could reprogram recurrent MCL to deepen and prolong the ibrutinib (BTK inhibitor) response in a phase I clinical trial, and the resistance mechanism by longitudinal genomic analysis of sequential samples from individual patients in the context of the clinical response. Palbociclib was administered to MCL patients on days 1-21 of a 28-day cycle; ibrutinib was given continuously. For longitudinal genomic analysis, sequential tissue and blood specimens from 27 evaluable MCL patients before and during therapy, and on progression were collected. Single cell RNA-seq (scRNA-seq) of PBMC or the monocytic fractions from bone marrow and lymph node (53 samples) was performed using a unique in house MCL cell-specific library. PBMC from normal donors (n=4) and untreated MCL patients (n=4) served as controls. The data were then subject to multiplex analysis with whole transcriptome sequencing and whole exome sequencing of MCL cells isolated from the same specimens, as well as flowcytometry in conjunction with IHC. Total numbers of MCL and immune cells in each specimen were deduced by integrating complete blood counts (CBC) with differential with scRNA-seq or flowcytometry. CDK4/6 Inhibition appears to deepen and prolong the BTKi response, with a CR rate of 42% and 5 patients (2 CR and 3 PR) remained on therapy for ~ 9 years. Longitudinal scRNA-seq (210,000 cells) revealed that MCL cells comprise 4 major transcriptomically distinct clusters. Cluster 1 (C1) resembles quiescent normal B cells; C2 mimics hyper-activated B cells that are enriched for signatures of BCR and cytokine signaling; C3 represents non-proliferating, long-lived MCL cells; and C4 is highly proliferative. RNA velocity analysis further indicates that having progressed to late G1 after evading CDK4/6 inhibition, MCL cells in C2 are in transit to C4. By contrast, C3 is a terminal node of MCL cells arrested in late G1 with elevated BCL2 expression Primary resistance and progression on therapy were associated with a marked expansion of either long-live non-proliferating C3 MCL cells, or C2 MCL cells that fuel the proliferating C4 MCL cells. Resistance was also associated with a profound reduction in MHC I and MHC II expression on MCL cells in some patients. Moreover, concurrent with disease progression, CD8+ T and CD+T cells were rapidly depleted by different mechanisms ( Figure 1). CD8+ T cells were proliferating and eliminated by exhaustion, as evidenced by the marked expression of LAG3 TIGIT and TIM3, and a failure to maintain CD8+ T effector memory cells. By contrast, CD4+ T cells were not proliferating and appeared die from glucose starvation. Collectively, these data suggest that T cell maintenance and surveillance is pivotal in sustaining a durable clinical response to combined inhibition of CDK4/6 and BTK. Guided by these discoveries, we have now restored BTKi sensitivity ex vivo in MCL cells from resistant patientsby targeting patient-specific expansion of C2 or C3 in vivo. In one resistant patient, this led to the maintenance of CD4+ and CD8+ T effector memory cells and a CR in response to venetoclax plus BTKi for nearly 3 years and continuing. In summary, by integrated longitudinal scRNA-seq analysis of a hypothesis-driven therapy, we have provided the first evidence that 1) MCL cells comprise 4 major transcriptomically distinct clusters; 2) resistance to CDK4/6i is associated with expansion of C2 that fuels the proliferating C4 MCL cells, or the long-lived C3 MCL cells with elevated BCL2 expression; 3) CDK4/6i harnesses BTKi response by promoting the maintenance of effector memory T cells; 4) combined inhibition of BCL2 and BTK overrides resistance to CDK4/6i and BTKi, leading to a durable clinical response; and 5) T cell surveillance is pivotal for a durable response to CDK4/6, BTK or BCL2 inhibition; implicating genome-guided combination therapy to overcome therapy resistance in MCL.

Combined treatment with crizotinib and temsirolimus is an effective strategy in mantle cell lymphoma and can overcome acquired resistance to temsirolimus.

Constitutive activation of the PI3K/AKT/mTOR-pathway plays an important role in the pathogenesis of mantle cell lymphoma (MCL), leading to approval of the mTOR inhibitor temsirolimus for relapsed or refractory MCL. Yet, despite favorable initial response rates, early relapses under treatment have been observed. Therefore, understanding the underlying mechanisms of temsirolimus resistance and developing strategies to overcome it is highly warranted. Here, we established a new temsirolimus-resistant MCL cell line to evaluate the molecular background of resistance to this drug. Transcriptome profiling and gene set enrichment analysis comparing temsirolimus-sensitive and -resistant cell lines showed significant upregulation of PI3K/AKT/mTor-, RAS signaling- and the RTK-dependent PDGFR-, FGFR-, Met- and ALK-signaling-pathways in the resistant cells. Furthermore, MET, known as important proto-oncogene and mediator of drug resistance, was among the most upregulated genes in the resistant cells. Importantly, Met protein was overexpressed in both, MCL cells with acquired as well as intrinsic temsirolimus resistance, but could not be detected in any of the temsirolimus sensitive ones. Combined pharmacological inhibition of mTOR and Met signaling with temsirolimus and the RTK inhibitor crizotinib significantly restored sensitivity to temsirolimus. Furthermore, this combined treatment proved to be synergistic in all MCL cell lines investigated and was also active in primary MCL cells. In summary, we showed for the first time that overexpression of MET plays an important role for mediating temsirolimus resistance in MCL and combined treatment with temsirolimus and crizotinib is a very promising therapeutic approach for MCL and an effective strategy to overcome temsirolimus resistance.

HARNESSING BTKI THERAPY BY CDK4/6I CONTROL OF T CELL SURVEILLANCE

Introduction: Drug resistance remains a formidable challenge in mantle cell lymphoma (MCL). Cell cycle dysregulation driven by aberrant Cyclin D1 and CDK4 expression is a hallmark for MCL. By inhibition of CDK4/6, we have developed a novel strategy that both inhibits proliferation of MCL cells and reprograms them for cytotoxic killing. In a phase I clinical trial we investigated if inhibition of cyclin D1/CDK4 with palbociclib could reprogram recurrent MCL to deepen and prolong the ibrutinib response, and the mechanism for resistance by longitudinal genomic analysis of sequential samples from individual patients in the context of the clinical response. Methods: Palbociclib was administered to recurrent MCL patients on days 1–21 of a 28-day cycle; ibrutinib was given continuously. For longitudinal genomic analysis, sequential tissue and blood specimens from 27 evaluable MCL patients before, during therapy and on progression were collected. Single cell RNA-seq (scRNA-seq) of PBMC or the monocytic fractions from bone marrow and lymph node was performed using a unique in house MCL-specific library. The data were then subject to multiplex analysis with whole transcriptome sequencing and whole exome sequencing of purified MCL cells and flowcytometry of the same samples in conjunction with IHC. Results: Palbociclib appears to deepen and prolong the ibrutinib response; the CR rate was 42% CR, and 5 patients (2 CR and 3 PR) remained on therapy for >8 years. Longitudinal scRNA-seq further revealed that MCL cells comprise 4 major transcriptomically distinct clusters (C)s. Primary resistance and progression on therapy were associated with a marked expansion of either long-live non-proliferating C3 cells or C2 cells that fuel the proliferating C4 cells. Resistance was associated with a profound reduction in MHC I and MHC II expression and disease progression was further accompanied by a rapid loss of both CD8+ and CD+ T cells. This suggests T cell surveillance plays a critical role in maintaining a durable ibrutinib response. Guided by our discoveries, we have restored ibrutinib sensitivity by target patient-specific expansion of C2 or C3 MCL cells ex vivo. In one patient, this led to restoration of CD4+ and CD8+T cells and a CR over 2.5 years. Conclusion: T cell surveillance plays a critical role in prolonging the ibrutinib response by CDK4/6 inhibition, implicating genome-guided combination therapy to overcome ibrutinib resistance in MCL. The research was funded by: PO1 grant from the National Cancer Institute MCL-RI grant from Leukemia and Lymphoma Society Keywords: combination therapies, genomics, epigenomics, and other-omics, tumor biology and heterogeneity No conflicts of interests pertinent to the abstract.

BV6, AN ANTAGONIST OF INHIBITOR OF APOPTOSIS PROTEINS, SENSITIZES RESISTANT MANTLE CELL LYMPHOMA CELLS TO VENETOCLAX

Introduction: Although Bruton’s tyrosine kinase inhibitors (BTKi) and CAR T-cell therapy have achieved remarkable efficacy in the treatment of mantle cell lymphoma (MCL), it remains incurable due to the inevitable development of therapeutic resistance. The BCL-2 inhibitor venetoclax is effective in many relapsed MCL patients, including those who progressed on BTKi, but subsequent relapse to venetoclax yields poor clinical outcomes. Hence, novel therapeutics and combination therapies are required to tackle the clinical challenges. Here, we investigated BV6, an antagonist of inhibitor of apoptosis proteins (IAPs), alone and in combination with venetoclax in multiple therapy-resistant MCL models. Methods: We performed single-cell RNA-seq to assess gene expression in ibrutinib-sensitive, ibrutinib-resistant, and dual ibrutinib-/CAR T-resistant MCL patients. Cell lines with acquired resistance to ibrutinib or venetoclax, as well as primary tumor cells from patients who relapsed after multiple therapies, were used as models of MCL resistance. CellTiter-Glo® luminescent assay was used to measure cell viability; annexin V/PI staining was used to measure the induction of apoptosis; and western blotting was used to assess IAP and apoptosis signaling protein expression across MCL cell lines after drug treatment. Results: The single-cell RNA-seq analysis demonstrated that IAP gene expression was not influenced by patient response to ibrutinib and CAR T-cell therapy, and western blotting showed that IAP proteins were broadly expressed across all MCL cell lines. To determine the on-target effects of BV6, we treated JeKo-1, JeKo-IBN-R, Mino, and Mino-VEN-R cells with BV6 and examined the expression of IAPs. BV6 treatment for 4h markedly reduced c-IAP1 and c-IAP2 expression, and moderately reduced XIAP expression. BV6 inhibited cell viability in both ibrutinib- and venetoclax-resistant cell lines, and BV6 treatment for 24 h dose-dependently induced apoptosis in MCL cells, including not only cell lines with acquired resistance but also patient primary cells, independent of their resistance to ibrutinib, venetoclax, and CAR T-cell therapy. We observed a striking and significant synergy in the cell viability assay when ibrutinib- or venetoclax-resistant cells were treated with BV6 combined with venetoclax (combination index < 1), and a dramatic enhancement of apoptosis (p < 0.001). The combination eradicated c-IAP1 and c-IAP2 expression, while XIAP was synergistically diminished. This was accompanied by strong caspase-3 activation and PARP cleavage. This combination therapy is currently under evaluation in venetoclax-resistant mouse model in vivo. Conclusions: Our findings indicate that a combination of IAP antagonists with apoptosis inducers can be exploited as a rational strategy to overcome therapeutic resistance in MCL. This study was supported by philanthropic funds from the Kimmel Research fund and various donor funds. Keywords: Aggressive B-cell non-Hodgkin lymphoma, Combination Therapies, Molecular Targeted Therapies No conflicts of interests pertinent to the abstract.

Concurrent Inhibition of Akt and ERK Using TIC-10 Can Overcome Venetoclax Resistance in Mantle Cell Lymphoma.

Venetoclax, a BCL-2 inhibitor, has proven to be effective in several hematological malignancies, including mantle cell lymphoma (MCL). However, development of venetoclax resistance is inevitable and understanding its underlying molecular mechanisms can optimize treatment response. We performed a thorough genetic, epigenetic and transcriptomic analysis of venetoclax-sensitive and resistant MCL cell lines, also evaluating the role of the stromal microenvironment using human and murine co-cultures. In our model, venetoclax resistance was associated with abrogated TP53 activity through an acquired mutation and transcriptional downregulation leading to a diminished apoptotic response. Venetoclax-resistant cells also exhibited an upregulation of the PI3K/Akt pathway, and pharmacological inhibition of Akt and ERK with TIC-10 led to cell death in all venetoclax-resistant cell lines. Overall, we highlight the importance of targeted therapies, such as TIC-10, against venetoclax resistance-related pathways, which might represent future therapeutic prospects.

Targeting glutaminase is therapeutically effective in ibrutinib-resistant mantle cell lymphoma.

Mantle cell lymphoma (MCL) is an incurable B-cell non-Hodgkin lymphoma characterized by frequent relapses. The development of resistance to ibrutinib therapy remains a major challenge in MCL. We previously showed that glutaminolysis is associated with resistance to ibrutinib. In this study, we confirmed that glutaminase (GLS), the first enzyme in glutaminolysis, is overexpressed in ibrutinib-resistant MCL cells, and that its expression correlates well with elevated glutamine dependency and glutaminolysis. Furthermore, we discovered that GLS expression correlates with MYC expression and the functioning of the glutamine transporter ASCT2. Depletion of glutamine or GLS significantly reduced cell growth, while GLS overexpression enhanced glutamine dependency and ibrutinib resistance. Consistent with this, GLS inhibition by its specific inhibitor telaglenastat suppressed MCL cell growth both in vitro and in vivo. Moreover, telaglenastat showed anti-MCL synergy when combined with ibrutinib or venetoclax in vitro, which was confirmed using an MCL patient-derived xenograft model. Our study provides the first evidence that targeting GLS with telaglenastat, alone or in combination with ibrutinib or venetoclax, is a promising strategy to overcome ibrutinib resistance in MCL.

Bcl-2 Family Members Bcl-xL and Bax Cooperatively Contribute to Bortezomib Resistance in Mantle Cell Lymphoma.

Mantle cell lymphoma (MCL) is an aggressive non-Hodgkin lymphoma with poor prognosis, due to the inevitable development of drug resistance. Despite being the first-in-class proteasome inhibitor for relapsed/refractory MCL, resistance to bortezomib (BTZ) in MCL patients remains a major hurdle of effective therapy, and relapse following BTZ is frequent. Understanding the mechanisms underlying BTZ resistance is, therefore, important for improving the clinical outcome and developing novel therapeutic strategies. Here, we established de novo BTZ-resistant human MCL-derived cells with the highest resistance index of 300-fold compared to parental cells. We provided compelling evidence that both Bcl-xL and Bax are key mediators in determining BTZ sensitivity in MCL cells. Overexpression of antiapoptotic Bcl-xL and depletion of proapoptotic Bax cooperatively protected MCL cells against BTZ-induced apoptosis, causing acquired BTZ resistance, likely by tilting the balance of Bcl-2 family proteins toward antiapoptotic signaling. Bioinformatics analyses suggested that high BCL2L1 (encoded Bcl-xL) and low BAX were, in part, associated with poor prognosis of MCL patients, e.g., when combined with low OGT, which regulates cellular O-GlcNAcylation. Our findings support recent strategies in small molecule drug discovery co-targeting antiapoptotic Bcl-2 family proteins using BH3 mimetics and Bax using Bax activators to overcome cancer drug resistance.

Inhibition of MAPK-ERK Signaling Pathway Overcomes Microrna-Mediated Ibrutinib Resistance in Mantle Cell Lymphoma

Inhibition of MAPK-ERK Signaling Pathway Overcomes Microrna-Mediated Ibrutinib Resistance in Mantle Cell Lymphoma

DNMT3A-Mediated Oxidative Phosphorylation and Ibrutinib Resistance in Mantle Cell Lymphoma

Mantle cell lymphoma (MCL), a B cell non-Hodgkin lymphoma, is incurable with current treatment modalities. Targeting Bruton tyrosine kinase (BTK) in the early B cell receptor signaling pathway by ibrutinib has shown remarkable anti-tumor activity, with the overall response rate of 68% in relapsed/refractory MCL patients. However, almost all the responders relapsed after ibrutinib treatment, with the 1-year survival rate of 22%. To overcome primary and acquired resistance to ibrutinib, novel treatment strategies are urgently needed. The presence of a relapse-specific C481S mutation in BTK associated with acquired ibrutinib resistance has been frequently identified in chronic lymphocytic leukemia but is rare in clinical MCL specimens based on sequencing results. Thissuggests that non-genetic aberrations likely play a role in ibrutinib resistance. The recent emergence of mitochondrial oxidative phosphorylation (OXPHOS) as a driver of ibrutinib resistance warrants the necessity to identify the components that govern OXPHOS in MCL. This study identifies the de novo DNA methyltransferase 3A (DNMT3A) as a mediator of mitochondrial biogenesis and OXPHOS in MCL. Using multiomics and functional approaches, we found that DNMT3A is required and sufficient to confers ibrutinib resistance in MCL. We show that DNMT3A promotes MCL growth by enhancing mitochondrial biogenesis, mitochondrial functions and OXPHOS. These effects are mediated by its interaction with MEF2B, a transcriptional activator of MYC, to enhance MYC-mediated transcription of genes involved in mitochondrial biogenesis. More importantly, the level of DNMT3A protein increases after ibrutinib treatment in primary MCL, which is consistent with a previous finding that the expression of DNMT3A was higher in ibrutinib-resistant than in ibrutinib-sensitive MCL patients. We demonstrate that DNMT3A knockout sensitizes ibrutinib-resistant cells to ibrutinib treatment. Conversely, the overexpression of DNMT3A cDNA de-sensitizes ibrutinib-sensitive cell lines. Interestingly, the overexpression of a catalytically dead DNMT3A confers resistance to ibrutinib in ibrutinib-sensitive cell lines, suggesting that DNMT3A-mediated ibrutinib resistance is independent of its enzymatic activity. Finally, we demonstrate that targeting DNMT3A by a low dose of decitabine, which induces the degradation of DNMT3A protein, synergizes with IM156, an inhibitor of mitochondrial complex I and currently in phase I clinical trial, in killing ibrutinib-resistant cell lines and primary MCL cells. Currently, we are testing this synergistic effect using patient-derived xenograft mouse models. Therefore, our study reveals a novel noncatalytic function of DNMT3A and suggests that DNMT3A is a potential biomarker and molecular target in treating MCL (Figure 1). Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Mutation Spectrum, Characteristics and Impact of Mutation Profiling on Prognosis, Outcome and Treatment Responses in Patients (pts) with Mantle Cell Lymphoma

Background: Genomic profiles of mantle cell lymphoma (MCL) are associated with clinical outcomes. BTKi Resistance in MCL can be predicted with mutation profile. Identifying these patients (pts) early can help guide therapy decisions and predict outcomes. We describe results from a clinical NGS based assay with a customized 162-gene panel in routine work-ups of MCL pts. Materials and Methods: We reviewed data from MCL patients who underwent CLIA approved lymphoma gene panel testing at MDACC from October 2020 until the end of June 2022. Data on treatment response, outcomes, and patient characteristics were collected. Mutation panel testing was conducted on various patient samples. Genomic DNA was isolated from fresh bone marrow (BM) aspirate, formalin-fixed paraffin-embedded (FFPE) tissues, fine needle aspirate (FNA) and peripheral blood (PB) specimens. Sequencing was performed using the Illumina NextSeq platform (Illumina, San Diego, CA). Variant calling was performed using Agilent SureCall software v4.1 and post-variant call analysis and annotation were performed using an in-house bioinformatics pipeline (OncoSeek v 1.1). Analytical sensitivity of the assay was established at 2% using a per base coverage cut-off of 200x. The assay was performed in cases with >10% lymphoma cells in the sample. Results: We included 227 MCL pts in this study: 129 treatment naïve and 97 with prior therapies. The distribution of patients according to the sample type included: BM (n=107), FFPE (n=50; 24 lymph node, 20 GI tract, and 6 miscellaneous tissues), FNA from involved nodal and non-nodal tissues (n=50) and PB (n=20). Baseline pt features included a median age of 67 years (range, 38-88 years). There were 164 men and 63 women. Histomorphology was classic in 165 pts, blastoid in 31, pleomorphic in 19 and blastoid/pleomorphic in 2. Ten pts had unclear histomorphology. Ki-67% in involved tissues was evaluable in 180 pts (in 47 pts Ki-67% was not available). Ki-67% was high (>=30%) in 98 and low in 82 biopsy specimens. Among the 97 previously treated pts, 47 had BTKi refractory disease. Twenty-three pts were treated with standard of care brexucabtagene autoleucel (CART). The spectrum of gene mutations is depicted by both previously untreated and pts with prior therapy in figure-1A. The most common mutated genes were: ATM (51.5%), TP53 (29.5%), KMT2D (21.1%), CCND1 (19.3%), BIRC3 (16.2%), NSD2 (11.4%), SMARCA4 (10.1%), UBR5 (9%), NOTCH1 (8.3%), CARD11 (7%), SAMHD1 (7%), NFKB1E (6.6%), SP140 (6.6%), S1PR1 (6.6%), DNMT3A (6%), NOTCH2 (6%), IGLL5 (6%), TRAF2 (5%), TET2 (5%). Unlike chronic lymphocytic leukemia, mutations of BTK (n=5; 2%) and PLCg (n=4; 2%) were rare. BTK mutations included missense mutations: C481Y, C481R, T474I and 2 with L528W. All patients with BTK mutations were resistant to prior BTKi and 4/5 died with refractory disease. Additional mutations of prognostic interest in other lymphomas were detected at very low frequency (<3%) and included CDKN2A, CD79b, MYD88, MEF2B, MAP3K14, Rb1, PAX5, SPEN, SF3B1, DIS3. We also evaluated pt survival from the date of gene panel testing and noted that TP53 mutant MCL pts had significantly inferior survival. We further divided the pts based on >=3 mutations (n=77) vs < 3 mutations (n=150) and identified that pts with a higher number of mutations had inferior survival, P <0.0001 (Figure 1C). Pts with SMARCA4 and TRAF2 mutations also demonstrated shorter survival compared to those which were wild type (not shown). Twenty-three pts received CART therapy and 7 had progressed and 16 have not. The distribution of mutations before CART in the two groups was not significantly different. Among the 47 BTKi refractory MCL, the frequency of certain mutations was higher: TP53 (49%), ATM (55%), KMT2D (31%), CCND1 (23%), 10% each for SMARCA4, NSD2 and SP140. Currently, we are utilizing this test to evaluate and include pts with high risk MCL on our clinical trials in MCL and treat with risk stratified treatments. Conclusion: The clinical NGS-based assay for MCL pts at our institution has proven to have prognostic significance. Resistant MCL pts exhibit a preponderance of mutations involving TP53, epigenetic modifier and chromatin regulator genes. Comprehensive risk stratification of pts early on and during therapy is very useful and improves patient care, helps design next generation clinical trials and improves our understanding of the biology of resistant MCL in the BTKi and CART era. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal