Diffuse Large B-cell Lymphoma Cell Lines Research Articles

Abstract ND05: The discovery of ARV-393, a potent, orally bioavailable BCL6 targeting PROTAC® for the treatment of Non-Hodgkin’s Lymphoma

Abstract Discovery of ARV-393, a potent, orally bioavailable BCL6 targeting PROTAC® for the treatment of Non-Hodgkin’s Lymphoma (NHL)Dan Sherman, Sheryl M. Gough, Lynn DeCarr, Sarah Eaton, Mark Bookbinder, Jennifer Pizzano, Elizabeth Bortolon, John Corradi, Rashaun Wilson, Daniel Rogoz, Ram Lingamaneni, Wei Zhang, Michelle Zhang, Xin Chen, Gan Wang, Hanqing Dong, Michael Berlin, Keith R. Hornberger, Lawrence Snyder, Achal Pashine and Ian Taylor. Arvinas, Inc., 5 Science Park, New Haven, CT, USA. Approximately 18,000 cases of Diffuse large B-cell lymphomas (DLBCL) are diagnosed worldwide per year making this cancer the most prevalent (30%) of the non-Hodgkin’s Lymphomas (NHL). Despite the success of R-CHOP treatment, approximately 40% of patients are refractory or relapse. While much progress has been made with CAR-Ts and bi-specific antibodies following frontline therapy in recent years, there remains a need for an orally bioavailable small-molecule that targets molecular drivers of NHL. The BCL6 transcription factor has long been known as an oncogenic driver of B-cell malignancy. The BCL6 gene has been found to be translocated and/or mutated resulting in deregulation of its expression, predominantly in DLBCL and Burkitt’s lymphoma (BL). The deregulated expression and scaffolding role of BCL6 in the transcriptional repressor complex make it an ideal target for the PROteolysis Targeting Chimera (PROTAC®) technology with one BCL6 degrader recently entering Phase 1 trials. We undertook a medicinal chemistry campaign to identify a BCL6-targeting PROTAC®. This effort identified ARV-393, an orally bioavailable PROTAC® that recruits BCL6 and the E3 ligase cereblon to rapidly degrade BCL6 via the cell’s natural ubiquitin proteasome system. ARV-393 is potent, demonstrating DC50 and GI50 values <1 nM in numerous DLBCL and BL cell lines. This agent demonstrates deep BCL6 degradation in vitro and in vivo, resulting in excellent TGI in several tumor xenograft models supporting a first-in-human trial in 1H 2024. We will present the chemical structure of ARV-393 and selected pre-clinical data. Citation Format: Dan Sherman. The discovery of ARV-393, a potent, orally bioavailable BCL6 targeting PROTAC® for the treatment of Non-Hodgkin’s Lymphoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr ND05.

Abstract 605: ABBV-101, a highly potent and selective clinical stage Bruton tyrosine kinase degrader, overcomes BTK mutation-induced resistance to BTK inhibitors

Abstract Bruton tyrosine kinase (BTK), a clinically validated target for various B-cell malignancies, plays a critical role in regulating cell growth, adhesion, and homing to lymphoid tissues that provide a microenvironment favorable to cancer cells. Despite the success of approved covalent BTK inhibitors in diseases such as CLL, most patients do not achieve complete response with monotherapy and eventually relapse, often via the emergence of the BTK-C481S mutation. Although second-generation reversible BTK inhibitors may temporarily overcome the C481S mutation, novel BTK mutations associated with resistance emerged in the clinic recently. Additionally, covalent BTK inhibitors have not shown sufficient differentiation from standard-of-care (SoC) in B-cell malignancies, such as diffuse large B cell lymphoma (DLBCL) to warrant approval to date. To address these unmet needs, a next-generation orally bioavailable BTK degrader ABBV-101 has been developed. Unlike BTK inhibitors that solely bind to and impede the catalytic domain of BTK, ABBV-101 eliminates the protein in a highly selective fashion. This degradation mechanism targets both the catalytic and scaffolding functions of BTK, and thus may enable deeper and more durable responses in patients with B-cell malignancies. Cellular activity of ABBV-101 was determined in a panel of DLBCL cell lines. We show that most non-germinal center B cell DLBCL (non-GCB-DLBCL) cell lines are sensitive to ABBV-101. To determine whether ABBV-101 could overcome BTK mutations-induced resistance, we engineered human DLBCL cell line TMD8 using CRISPR technology to express these BTK mutations and tested for sensitivity to ABBV-101 and BTK inhibitors. We show that ABBV-101 demonstrates similar potent activity against all BTK mutations associated with resistance to both covalent and reversible BTK inhibitors. The modulation of downstream pathway by ABBV-101 and how it differentiates from other BTK inhibitors will be presented. Further, ABBV-101 induces complete tumor regression in the BTK-C481S TMD8 DLBCL xenograft model. A spontaneous mouse CLL model carrying BTK-C481S mutation was developed through crossing BTK-C481S knock-in mice with the Emu-TCL1 transgenic mice in the C57BL/6 background. ABBV-101 completely inhibits BTK-C481S Emu-TCL1 CLL burden increase in the blood compartment and reduces CLL burden in the spleen and lymph nodes, whereas covalent BTK inhibitors show no activity. Finally, combination with a BCL-2 inhibitor enhances the efficacy of ABBV-101 in CLL and DLBCL models. Taken together, our results suggest that ABBV-101 has potent in vitro and in vivo efficacy. ABBV-101 is currently in phase 1 clinical trial for a variety of B-cell malignancies. ClinicalTrials.gov identifier: NCT05753501 Citation Format: Chin Pan, Jacob Riehm, Tarikere L. Gururaja, Haiyan Li, Henry Nguyen, Yongjiao Zhai, Xiaoping Xie, Rong-Xian Ding, Rebecca Matthew, Hana Y. Hoh, Zhaozhong J. Jia, Bo Liu, Cassandra P. Shu, Claudina A. Stevenson, Christine Will, Federico Innocenti, Wissam Assaily, Lloyd T. Lam, Alexey Rivkin. ABBV-101, a highly potent and selective clinical stage Bruton tyrosine kinase degrader, overcomes BTK mutation-induced resistance to BTK inhibitors [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 605.

Abstract 1912: Targeting Trop-2 with sacituzumab govitecan (IMMU-132) suppresses the tumor growth in diffuse large B cell lymphoma

Abstract Introduction: Sacituzumab govitecan (SG), also termed IMMU-132, is an antibody-drug conjugate, linking an anti-Trop-2 antibody and the topoisomerase I inhibitor, SN-38. Clinically, SG has shown promising therapeutic effects in patients with human epidermal growth factor receptor 2 (HER2)-negative metastatic breast cancer. However, the efficacy of SG in diffuse large B-cell lymphoma (DLBCL) remains unexplored. In this study, we sought to determine whether SG can efficiently inhibit cell proliferation and tumor growth of DLBCL by using both in vitro and in vivo models. Methods: We examined the cytotoxicity of SG in the activated B-cell like (ABC)-subtype-DLBCL cell lines, Riva (Ri-1), HBL-1, and SU-DHL-2, and the germinal center B-cell (GCB)-subtype-DLBCL cell lines, SU-DHL-4, SU-DHL-5, and SU-DHL-6 by MTT assay. We assessed the distributions of cell cycle phase and apoptosis in the aforementioned DLBCL cell lines treated with SG for 24 h or 48 h using flow cytometry and Annexin V staining. We confirmed apoptosis (cleavage of poly ADP-ribose polymerase [PARP] and caspase-3) and detected DNA damage (γH2AX and 53BP1)-related protein expression in SU-DHL-2 and SU-DHL-6 cell lines treated with SG at various concentrations for 48 h using western blotting, compared to untreated cells. To examine the anti-tumor effect of SG in vivo, NOD-SCID nude mice of Riva-xenograft mouse models were randomized into a control group and an SG-treated group. Results: Flow cytometry and western blotting revealed overexpression of Trop-2 on the surface of untreated ABC-DLBCL and GCB-DLBCL cell lines. In this study, we showed that SG treatment reduced cell viability in all six DLBCL cell lines with nanomolar IC50 values. Exposing SG to DLBCL cells significantly increased cell cycle arrest at the G2/M and sub-G1 phases of all six DLBCL cell lines. Annexin V staining revealed that SG induced apoptosis in all six DLBCL cell lines. Western blotting confirmed apoptosis induction by showing a dose-dependent upregulation of cleaved PARP and cleaved caspases-3 by SG treatment, along with decreased expression of survivin in both SU-DHL-2 and SU-DHL-6 cells. SG also upregulated the expression of γH2AX and 53BP1 in both SU-DHL-2 and SU-DHL-6 cells. Furthermore, we found that tumor growth of Riva cells in vivo was significantly reduced by treatment with SG when compared with untreated control. Conclusion: SG suppresses tumor growth of ABC-DLBCL and GCB-DLBCL cells in both in vitro and in vivo models by inducing cell cycle arrest, apoptosis, and DNA damage. These findings provide a rationale for transitioning SG to clinical trials for treating patients with relapsed or refractory DLBCL. Citation Format: Jakie Ting, Ming-Feng Wei, Hsiao-Wei Lee, Keng-Hsueh Lan, Ann-Lii Cheng, Sung-Hsin Kuo. Targeting Trop-2 with sacituzumab govitecan (IMMU-132) suppresses the tumor growth in diffuse large B 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 1912.

Abstract 4019: Development of mRNA chimeric antigen receptor T cells targeting MET in aggressive B-cell lymphomas

Abstract Multiple versions of CAR T cells targeting the cell surface protein CD19 are approved by the FDA to treat refractory B-cell malignancies. However, durable remissions range from 60% in B-cell leukemias to 40% in B-cell lymphomas. Major reasons for resistance to CD19-CAR treatment relate to heterogeneous or loss of CD19 expression. In addition, CD19-CAR leads to B-cell depletion which increases the risk for infection. These limiting factors necessitate research into alternative targets for CAR therapy against B-cell lymphomas.Using a large data set from clinical trials, we found that approximately 30-70% of diffuse large B-cell lymphomas (DLBCL) express MET. We hypothesize that these MET-positive B-cell lymphomas can potentially be targeted with chimeric antigen receptor (CAR) T-cells against MET receptor. We constructed a second-generation anti-MET-CAR by fusing the scFv fragment of an anti-MET monoclonal antibody with the human CD28 hinge/transmembrane/cytoplasmic domain and CD3ζ cytoplasmic domain. Stable MET-CAR Jurkat cells showed increased CD69 expression upon stimulation by MET-positive lymphoma cell lines such as Karpas-422 and OCI-LY3. Using primary human T cells, we further demonstrated that the mRNA MET-CAR T-cells mediated cytotoxicity against DLBCL cell lines. Of note, while CD19-CAR T-cells showed only low level of cytotoxicity against the CD19-/MET+ OCI-LY3 cell line, MET-CAR T cell was able to mediate substantial tumor cell lysis.In summary, the preliminary data demonstrate that MET-CAR is capable of mediating cytotoxicity against MET-positive DLBCL. Some cell lines such as OCI-LY3 are negative for CD19 but positive for MET expression, and MET-CAR is capable of mediating cell lysis while CD19-CAR is ineffective. These results suggest that some large B-cell lymphomas negative for CD19, either intrinsic or secondary to loss of CD19 as a result of resistance mechanism, may show MET expression and will likely benefit from MET-targeted immunotherapy. Citation Format: Po-Han Chen, Rianna Raghunandan, Markus Muschen, Samuel G. Katz. Development of mRNA chimeric antigen receptor T cells targeting MET in aggressive B-cell lymphomas [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 4019.

Abstract 463: The small nucleolar RNA SNORD46 and SNORD72 have tumor suppressor activity in diffuse large B cell lymphoma

Abstract Background. Following the identification of an 11q24.3 gain upregulating the ETS factors ETS1 and FLI1 in diffuse large B cell lymphoma (DLBCL) (Bonetti et al. Blood 2013), we observed the anti-lymphoma activity of blocking the protein-protein interaction of ETS factors with RNA helicases, using YK-4-279 and its clinical derivative TK-216 (Spriano, Chung et al. CCR 2019). DLBCL cells exposed to the two small molecule inhibitors presented a significant upregulation of small nucleolar RNAs (snoRNAs). Besides their primary functions in rRNA processing, snoRNAs are often deregulated in cancers, with microRNA-like actions and direct interaction with proteins. Here, we characterized SNORD46 and SNORD72, the two snoRNAs most upregulated cells after YK-4-279 and TK-216 and mapped to the 1p34.1 locus recurrently lost in DLBCL. Methods. Real-time PCR, immunoblotting, and shRNA silencing were conducted based on established protocols. RNA-Protein Interaction Prediction (RPISeq) was used to calculate the interaction probabilities of snoRNAs with proteins of interest. The prediction was made using both the Random Forest (RF) and the Support Vector Machine (SVM) classifiers, using a stringent threshold of >0.6. Results. The time-dependent changes of SNORD46 and 74 were validated with real-time PCR in the U2932 activated B cell-like (ABC) DLBCL cell line exposed to YK- 4-279 for 4 or 8 h. Upregulation of SNORD46 and 74 were significantly upregulated compared to their host genes upon YK-4-279 treatment, suggesting these snoRNAs have different functions from the genes in which they are encoded. Across 48 lymphoma cell lines, SNORD74 was more expressed in ABC DLBCL than in the remaining cell lines (P 0.03) or GCB DLBCL (P 0.05), while SNORD46 did not differ. Stable lentiviral-based overexpression of SNORD46 and 74, U2932 ABC DLBCL demonstrated that both SNORD46 and SNORD74 overexpression impaired growth while SNORD92, the control did not SNORD74 overexpression inhibited pAKT-Ser473, suggesting it could exert its anti-tumor effect by negatively impacting BCR signaling. Since constitutive BCR is the main driver for the pathogenesis in ABC DLBCL, we studied the impact of BCR signaling on SNORD46 and 74 expressions. IgM stimulation downregulated the snoRNAs in U2932 and TMD8 ABC DLBCL cell lines at 1 and 2.5 h poststimulation, with a more substantial effect for SNORD74. Furthermore, the snoRNAs were upregulated in four ABCs and four GCB DLBCLs cell lines exposed to the PI3K/mTOR inhibitor bimiralisib. Bioinformatic analysis indicated the possible binding of SNORD46 and especially of SNORD74 to BCR signaling molecules (SYK, LYN, BTK, PI3Kδ, IRAK4, IRAK1, CARD11), RNA helicases (RHA, DDX21, DDX5) and essential DLBCL proteins (BCL6, IRF4). Conclusions. SNORD46 and SNORD74 exert tumor suppressor activity in DLBCL cells, possibly as negative regulators of the BCR signaling. Citation Format: Elaine YL Chung, Filippo Spriano, Sara Napoli, Giulio Sartori, Luciano Cascione, Francesco Bertoni. The small nucleolar RNA SNORD46 and SNORD72 have tumor suppressor activity in diffuse large B 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 463.

Abstract 5966: PRT2527, a novel highly selective cyclin-dependent kinase 9 (CDK9) inhibitor, has potent antitumor activity in combination with BTK and BCL2 inhibition in various lymphoid malignancies

Abstract CDK9 is a master regulator of transcription that modulates transcription elongation via phosphorylation of RNA polymerase II. Short-term inhibition of CDK9 depletes short-lived transcripts and labile proteins such as MCL1, BFL1 and MYC to promote cancer cell death. We previously described PRT2527, a novel, potent, highly selective CDK9 inhibitor with anti-leukemic activity in various preclinical models. PRT2527 is currently under evaluation in a Phase I clinical trial in patients with relapsed/refractory hematologic malignancies (NCT05159518). Here we demonstrate PRT2527 potently inhibits cancer cell growth and induces cell death in various models of Diffuse Large B Cell Lymphoma (DLBCL), Mantle Cell Lymphoma (MCL) and Chronic Lymphocytic Leukemia (CLL), through depletion of MCL1, BFL1 and MYC. Specifically, we show that brief treatment with PRT2527 (6h) potently induces apoptosis and inhibits proliferation in DLBCL, MCL and CLL cell lines. We also show that the addition of BTK inhibitors (BTKi) or BCL2 inhibitors (BCL2i) potentiates the apoptosis response induced by PRT2527 in vitro and leads to more robust and durable responses including complete tumor regressions in DLBCL CDX and PDX models in vivo. In all studies, the combination of PRT2527 with BTKi or BCL2i is well tolerated. Mechanistically, we show that BTK inhibition upregulates BMF, an endogenous inhibitor of BCL2 and BCL-xL, driving cells towards MCL1 and BFL1 dependency in TMD-8 cells. Concurrent depletion of MCL1 and BFL1 with PRT2527 leads to complete inhibition of Bcl-2- family mediated survival signaling, potently inducing cell death. In similar fashion, Venetoclax-driven BCL2 inhibition also potentiates the anti-tumor activity of PRT2527. Consistent with these findings in vitro, we observe reduced BFL1 and MCL1 as well as increased BMF in tumors of mice treated with BTKi and PRT2527 suggesting complete Bcl-2 family inhibition. We also demonstrate potent induction of apoptosis in peripheral blood mononuclear cells isolated from patients with both treatment-naïve and relapse/refractory CLL following brief treatment with PRT2527 (6h). Co-treatment with BTKi or BCL2i further enhances the apoptotic effect of PRT2527, similarly suggesting combinatorial benefit. Additionally, we characterize the activity of PRT2527 in models of BTKi relapsed/refractory MCL where increased CDK9 dependency has previously been described. In an Ibrutinib-resistant Mino CDX model, we observe increased tumor growth inhibition following treatment with PRT2527 compared to tumors derived from parental Mino cells, suggesting PRT2527 is efficacious in BTKi-resistant MCL. Altogether these data provide a rationale for evaluating PRT2527 in combination with BTK and BCL2 inhibitors for the treatment of patients with relapsed/refractory lymphoid malignancies. Citation Format: Norman Fultang, Ashley M. Schwab, Sophia McAneny-Droz, Diane Heiser, Peggy Scherle, Neha Bhagwat. PRT2527, a novel highly selective cyclin-dependent kinase 9 (CDK9) inhibitor, has potent antitumor activity in combination with BTK and BCL2 inhibition in various lymphoid malignancies [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 5966.

Abstract 3913: Molecular mechanism of action and targets of glucocorticoids in lymphoma therapy

Abstract Prednisone is an anti-inflammatory glucocorticoid (GC) that is cytotoxic for normal and malignant B cells and, on this basis, has long been included in combination chemotherapies to treat aggressive B-cell lymphomas. However, the mechanisms by which GCs kill malignant lymphoma cells still largely remains elusive due to the pleiotropic consequences of GC binding to the glucocorticoid receptor (GR; NR3C1), a ligand-induced transcription factor. This prompted us to search for critical direct targets of GC action with the hypothesis that GCs may inhibit key survival pathways in lymphomas. To determine effector genes that increase glucocorticoid toxicity, we performed genome-wide CRISPR-Cas9 screens in the presence and absence of prednisolone. Screens in cell line models of Burkitt lymphoma (BL) and diffuse large B cell lymphoma (DLBCL) revealed strong synergy between GC treatment and inactivation of genes encoding components of the B cell receptor (BCR) signaling pathway (≥2 SD). To identify direct transcriptional GR targets and binding sites genome-wide, we performed the cleavage under targets and release using nuclease (CUT&RUN) assay and integrated this dataset with RNA-seq upon GC treatment. The pairwise comparison analysis (p<0.05) for GR-bound genes across BL and DLBCL cell lines revealed a significant enrichment of negative regulators of BCR/PI3K signaling and BCR-related tumor suppressors (LAPTM5, KLHL14, ARID5B, DDIT4, DAPP1, INPP5D, and CSK). Interestingly, expression of CSK, an inhibitor of all Src-family kinases (SFKs), was repressed while that of other BCR negative regulators were directly activated by binding of GR. Combinatorial deletion of activated genes counteracted the toxicity of GC up to 83.9%. In contrast, depletion of CSK paradoxically increased the cytotoxic effects of GC in BCR-dependent aggressive lymphoma with decreased proximal BCR signaling. To gain further insights on CSK function in aggressive lymphomas, we performed phospho-proteome and ubiquitinome profiling by treating lymphoma models with a small molecule inhibitor of CSK kinase activity (CSKi). The CSKi treatment initially increased constitutive BCR signaling, as expected, but then triggered exuberant ubiquitination of the LYN, HCK and BLK, leading to their proteasomal degradation. Consequently, the CSKi blocked BCR-dependent NF-κB activation in ABC DLBCL models and BCR-dependent PI3 kinase activation in models of GCB DLBCL and BL. In summary, inhibition of oncogenic BCR signaling is a major mode of action for GCs. Furthermore, small molecule inhibition of CSK kinase activity potentiated the effect of GCs on oncogenic BCR signaling and strongly synergized with GCs in killing ABC and GCB DLBCL models in vitro and preventing the growth of ABC and GCB DLBCL and patient-derived xenografts, warranting the development of clinical-grade CSK inhibitors for the treatment of these aggressive cancers. Citation Format: Jaewoo Choi, Michele Ceribelli, James D. Phelan, Björn Häupl, Da Wei Huang, George W. Wright, Tony Hsiao, Vivian Morris, Francesco Ciccarese, Boya Wang, Sean Corcoran, Sebastian Scheich, Xin Yu, Weihong Xu, Yandan Yang, Hong Zhao, Joyce Zhou, Grace Zhang, Jagan Muppidi, Giorgio Ga Inghirami, Thomas Oellerich, Craig J. Thomas, Wyndham H. Wilson, Louis M. Staudt. Molecular mechanism of action and targets of glucocorticoids in lymphoma therapy [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 3913.

Abstract 4911: PAIRWISE: Deep learning-powered personalized medicine approach identifies actionable drug combinations in B cell lymphoma

Abstract Combination drug therapies offer promise for improving cancer treatment. However, identifying actionable drug combinations for specific cancer subtypes and individual patients remains challenging due to the vast number of possibilities. Existing approaches like high-throughput screening (HTS) and rule-based drug additions have limitations in their ability to predict clinically translatable synergistic combinations. Therefore, advanced machine learning focused on patient-centric modelling have the potential to optimize combination therapies. PAIRWISE is a patient-centric deep learning-powered drug combination recommendation platform. Given gene expression along with chemical structures and targets from a set of two drugs being applied, the output is the binary combination outcome. PAIRWISE introduces a new approach of representing tumor genomics using the unsupervised pretraining design on 11K TCGA tumors. The power of PAIRWISE is derived from knowledge-guided transfer learning by learning from in vitro experiments with drug-drug-cell interactions and cellular heterogeneity. PAIRWISE can accurately predict combination synergy with area under the curve (AUC) > 0.85 across 10 tissue types in a large dataset of 200K in vitro drug combinations and significantly outperform all state-of-the-art methods. Diffuse large B cell lymphoma (DLBCL) is the most common B cell non-Hodgkin lymphoma and remains incurable in around 40% of patients. Finding optimal combination therapy for each DLBCL patient is a critical unmet need. As independent validation, we applied PAIRWISE to an external HTS study of Bruton Tyrosine Kinase inhibitor (BTKi) combinations (Griner et al., 2014), confirming the reproducibility and accuracy of high-confidence predictions (AUC = 0.72). PAIRWISE was also applied to transcriptomic data of 29 DLBCL cell lines (Bal et al., 2022) and predicted BTKi-containing combinations across ABC subtypes with higher synergy scores than GCB (P = 0.02). This is consistent with expected better overall efficacy of BTK inhibitors in ABC subtype (Younes et al., 2019; Davis et al., 2010; Wilson et al., 2015). To predict opportunities in DLBCL, PAIRWISE was used to identify BTKi partners for an additional 211 anti-cancer drugs using 562 published ex vivo DLBCL samples (Schmitz et al., 2018). PAIRWISE effectively identified novel DLBCL sub-population with significantly higher response scores for predicted BTKi combinations and favorable survival. Notably, patients predicted as responsive had significantly better outcomes upon first-line chemotherapy treatments than non-responsive ones (P < 0.0001). Collectively, we demonstrate that PAIRWISE is a highly efficient and generalizable framework that enables confident predictions of pairwise drug combinations at disease subtype level, with the potential of informing treatment options and clinical trial design. Citation Format: Chengqi Xu, Jake Cohen-Setton, Zhouyang Shen, Marta Milo, Ilkay US, Ben Sidders, Jude Fitzgibbon, Heng Pan, Olivier Elemento, Krishna Bulusu. PAIRWISE: Deep learning-powered personalized medicine approach identifies actionable drug combinations in B 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 4911.

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.

Chidamide enhances T-cell-mediated anti-tumor immune function by inhibiting NOTCH1/NFATC1 signaling pathway in ABC-type diffuse large B-cell lymphoma

Chidamide (CS055/HBI-8000, tucidinostat) has shown promising effects in the clinical treatment of various hematologic tumors. Diffuse large B-cell lymphoma (DLBCL) has shown highly heterogeneous biological characteristics. There are complex mechanisms of the role of chidamide in DLBCL for in-depth study. It is essential to probe further into the mechanism of drug-tumor interactions as a guide to clinical application and to understand the occurrence and progression of DLBCL. In vitro and in vivo models were utilized to determine the effects of chidamide on signaling pathways involved in the DLBCL tumor microenvironment. The experimental results show that chidamide inhibited the proliferation of DLBCL cell lines in a dose- and time-dependent manner, and down-regulated the expression of NOTCH1 and NFATC1 in DLBCL cells as well as decreased the concentration of IL-10 in the supernatant. In addition, chidamide significantly lowered the expression of PD1 or TIM3 on CD4+T cells and CD8+T cells and elevated the levels of IL-2, IFN-γ, and TNF-α in the serum of animal models, which augmented the function of circulating T cells and tumor-infiltrating T cells and ultimately significantly repressed the growth of tumors. These findings prove that chidamide can effectively inhibit the cell activity of DLBCL cell lines by inhibiting the activation of NOTCH1 and NFATC1 signaling pathways. It can also improve the abnormal DLBCL microenvironment in which immune escape occurs, and inhibit immune escape. This study provides a new therapeutic idea for the exploration of individualized precision therapy for patients with malignant lymphoma.

Abstract P04: Role of glucocorticoid receptor in normal and malignant germinal center B cells

Abstract We have reported that super-enhancers (SEs) are specifically hypermutated by Activation-Induced Deaminase (AID)-induced Aberrant Somatic Hypermutation in >90% of diffuse large B cell lymphoma (DLBCL) cases (Bal et al. Nature 2022). Analysis of 122 primary DLBCL biopsies and cell lines identified more than 80 SEs that are recurrently hypermutated, with an average of 12 hypermutated SE/case. Hypermutated SEs are predominantly linked to genes encoding regulators of B cell development and well-known lymphoma oncogenes, including BCL6, BCL2 and CXCR4. We showed that specific hotspot mutations prevent binding and transcriptional downregulation by transcriptional repressors leading to target gene dysregulation. Among these, hypermutation of the SEs linked to BCL2 and CXCR4 abrogates the binding of the glucocorticoid receptor (GR)/transcription factor encoded by NR3C1. As a result, BCL2 and CXCR4 escape GR-mediated transcriptional repression leading to their de-regulated expression in germinal center (GC) B cells. Together with the observation that the NR3C1 gene is genetically inactivated in a small fraction of DLBCL, and the relevance of glucocorticoid-based therapy in DLBCL, these results prompted a comprehensive analysis of the role of GR in normal and malignant B cells. We report that GR is detectable in the nucleus of the great majority of GC B cells, suggesting that it is active as a transcription factor. Similarly, DLBCL primary cases (including GCB-, ABC- and unclassified DLBCL) display GR nuclear expression. Analysis of a conditional GC-specific Nr3c1 knock-out (KO) mouse model showed that GC B cells form normally in the absence of Nr3c1. However, the transcriptional profile of Nr3c1-KO GC B cells was significantly altered compared to wild-type cells. By integrating the GR binding profile obtained in normal human GC B cells with the transcripts differentially expressed in Nr3c1-KO GC B cells, we identified a set of about 2,000 genes that are directly modulated by GR during the GC reaction. Pathway enrichment analysis showed that GR controls several signaling pathways, suggesting a modulatory role on the BCR and CXCR4 pathways. In addition, GR targets display a significant overlap with the BCL6 transcriptional network, suggesting a cooperative role in GC B cell development. Notably, GR was shown to regulate pathways involved in plasma cell differentiation, while repressing targets associated with memory B cell development. In DLBCL cases, several NR3C1 binding sites are recurrently targeted by mutations, suggesting that genetic impairment of GR activity is heterogeneous and extends beyond CXCR4 and BCL2. Together, these data support a role for the glucocorticoid pathway in GC physiology. Recurrent inactivation of the NR3C1 gene or part of its transcriptional regulatory program may contribute to DLBCL pathogenesis, with implications for presently unknown specific roles of glucocorticoids in the therapeutic regimens for DLBCL. Citation Format: Clarissa Corinaldesi, Antony B Holmes, Elodie Bal, Laura Pasqualucci, Katia Basso, Riccardo Dalla-Favera. Role of glucocorticoid receptor in normal and malignant germinal center B cells [abstract]. In: Proceedings of the Blood Cancer Discovery Symposium; 2024 Mar 4-6; Boston, MA. Philadelphia (PA): AACR; Blood Cancer Discov 2024;5(2_Suppl):Abstract nr P04.

Development and validation of a combined cuproptosis and immunogenic cell death prognostic model for diffuse large B-cell lymphoma.

Diffuse large B-cell lymphoma (DLBCL) is the most common type of non-Hodgkin lymphoma worldwide with a high degree of heterogeneity. Cuproptosis and immunogenic cell death (ICD) have been considered to be vital for tumor progression. However, current understanding of cuproptosis and immunogenic cell death in DLBCL is still very limited. We aim to explore a prognostic model combining cuproptosis and immunogenic cell death in DLBCL. Pearson's correlation analysis was utilized to acquire lncRNAs associated with cuproptosis and immunogenic cell death. Prognostic biomarker identification and model construction involved the use of univariate Cox regression, least absolute shrinkage and selection operator (LASSO) Cox regression, and multivariate Cox regression. We assessed the predictive capability of the risk model by conducting Kaplan-Meier analysis and time-dependent ROC analysis. The analysis and comparison of immune infiltration and drug sensitivity were conducted in this study. Moreover, RT-qPCR was employed to validate the expression of lncRNAs associated with cuproptosis and immunogenic cell death in DLBCL cell lines. We identified 4 prognosis-related lncRNAs (ANKRD10-IT1, HOXB-AS1, LINC00520 and LINC01165) that were correlated with cuproptosis and immunogenic cell death. The model was verified to have a good and independent predictive ability in the prognostic prediction of DLBCL patients. Moreover, significant difference was observed in immune infiltration and drug sensitivity between high- and low-risk groups. Our discoveries could enhance the comprehension of the role of cuproptosis and ICD in DLBCL, potentially offering novel viewpoints and knowledge for personalized and precise treatment of DLBCL individuals.

Bifunctional Inhibitor Reveals NEK2 as a Therapeutic Target and Regulator of Oncogenic Pathways in Lymphoma.

Expression of the serine/threonine kinase never in mitosis gene A (NIMA)-related kinase 2 (NEK2) is essential for entry into mitosis via its role in facilitating centrosome separation. Its overactivity can lead to tumorigenesis and drug resistance through the activation of several oncogenic pathways, including AKT. Although the cancer-enabling activities of NEK2 are documented in many malignancies, including correlations with poor survival in myeloma, breast, and non-small cell lung cancer, little is known about the role of NEK2 in lymphoma. Here, in tumors from patients with diffuse large B-cell lymphoma (DLBCL), the most common, aggressive non-Hodgkin lymphoma, we found a high abundance of NEK2 mRNA and protein associated with an inferior overall survival. Using our recently developed NEK2 inhibitor, NBI-961, we discovered that DLBCL cell lines and patient-derived cells exhibit a dependency on NEK2 for their viability. This compromised cell fitness was directly attributable to efficient NEK2 inhibition and proteasomal degradation by NBI-961. In a subset of particularly sensitive DLBCL cells, NBI-961 induced G2/mitosis arrest and apoptosis. In contrast, an existing indirect NEK2 inhibitor, INH154, did not prevent NEK2 autophosphorylation, induce NEK2 proteasomal degradation, or affect cell viability. Global proteomics and phospho-proteomics revealed that NEK2 orchestrates cell-cycle and apoptotic pathways through regulation of both known and new signaling molecules. We show the loss of NEK2-sensitized DLBCL to the chemotherapy agents, doxorubicin and vincristine, and effectively suppressed tumor growth in mice. These studies establish the oncogenic activity of NEK2 in DLBCL and set the foundation for development of anti-NEK2 therapeutic strategies in this frequently refractory and relapse-prone cancer.

Targeting HDACs for diffuse large B-cell lymphoma therapy

Histone deacetylases (HDACs) are involved in tumorigenesis and progression, however, their role in diffuse large B-cell lymphoma (DLBCL) is not well understood. In this study, we examined the expression levels, mutations, and clinical significance of HDACs in DLBCL. Additionally, we investigated the therapeutic potential of Chidamide, a novel HDAC inhibitor, to provide scientific evidence for targeting HDACs in DLBCL patients. We extracted transcriptome data of DLBCLs––including 47 lymph node samples and 337 whole-blood-cell controls––from The Cancer Genome Atlas. Bioinformatic analyses of HDAC expression, mutation, and correlation with the clinical significance of DLBCL patients were performed with the Gene Expression Profiling Interactive Analysis, GENEMANIA, and web-based software including cBioPortal and WebGestalt. To examine the therapeutic effect of Chidamide, DLBCL cell lines (WSU-DLCL-2 and DB cells) were employed. Cell proliferation and apoptosis were analyzed with Cell Counting Kit-8 and flow cytometry assays. The impact of Chidamide treatment was also analyzed by RNA sequencing of treated DB cells. Western blot was used to explore the molecular mechanism of the cytotoxicity of Chidamide on DLBCL cell lines. The expression of some HDACs (HDAC1, 2, 3, 4, 6, 7, 8, and 9) were significantly higher in the lymph node samples of DLBCL than that in whole-blood-cell controls. Moreover, we found that the mutation rate of HDACs was also higher in DLBCL tissues, although the overall survival of DLBCL patients was not associated with HDAC expression. Chidamide was found to have a cytotoxic effect on DLBCL cells in a dose-dependent manner, while transcriptome analysis and western blot revealed that using it for treatment impacted several biological processes, including PI3K/AKT signaling, mTOR signaling, the cell cycle, and apoptosis pathways. Alterations of HDAC genes, including enhanced expression and mutations, are positively related to DLBCL. Targeting HDACs with specific inhibitors such as Chidamide may represent a potential therapeutic approach for DLBCL patients.

Analysis and Investigation of Bioinformatics and Epigenetics Reveal the Underlying Mechanisms by which FLOT2 Modulates the Progression of Diffuse Large B-cell Lymphoma.

Diffuse large B-cell lymphoma (DLBCL) poses a significant threat to the quality of life for people worldwide. Regrettably, effective treatment strategies for this disease remain elusive in clinical practice due to the unclear understanding of its molecular mechanisms. Therefore, this study was devised to address these issues and identify novel diagnostic, therapeutic, and prognostic biomarkers for DLBCL. Gene expression and clinical data for DLBCL patients were retrieved from The Cancer Genome Atlas (TCGA) database, and relevant clinical data, tumor mutational burden (TMB), and gene expression levels were extracted. Bioinformatics analysis was conducted to screen for differentially expressed genes (DEGs). The prognostic significance of flotillin-2 (FLOT2) was assessed using Kaplan-Meier survival analysis. Quantitative real-time polymerase chain reaction (qRT-PCR) and Western blot analyses were employed to evaluate mRNA and protein levels of the genes. Cell proliferation, apoptosis, and invasion were assessed using cell counting kit-8 (CCK-8) assay, flow cytometry analysis, and Transwell assay, respectively. Our bioinformatics analysis revealed that FLOT2 was significantly overexpressed in DLBCL tissues compared to normal tissues, a finding corroborated by subsequent immunohistochemistry staining, qRT-PCR, and Western blot analyses. To elucidate its biological functions, shRNAs targeting FLOT2 were transfected into DLBCL cell lines (LY-3 and U2932), resulting in suppressed cell proliferation and invasion, while promoting apoptosis. Furthermore, a positive correlation between TMB and FLOT2 expression in DLBCL was observed. Subsequently, quanTIseq was utilized to calculate the immune score and assess FLOT2 gene expression. In DLBCL, FLOT2 gene expression was found to be associated with T cell CD4+ (non-regulatory) (p < 0.01), monocytes (p < 0.05), and uncharacterized cells (p < 0.05). Regarding immune checkpoint markers, including the cluster of differentiation 274 (CD274), cytotoxic T lymphocyte-associated antigen-4 (CTLA4), hepatitis A virus cellular receptor 2 (HAVCR2), lymphocyte activation gene-3 (LAG3), programmed cell death protein 1 (PDCD1), programmed cell death 1 ligand 2 (PDCD1LG2), Siglec-15 (SIGLEC15), and T cell immunoreceptor with Ig and ITIM domains (TIGIT), our analysis indicated that in DLBCL, FLOT2 exhibited a relationship only with TIGIT (p < 0.05). In summary, FLOT2 functions as an oncogene and is linked to DLBCL prognosis and the tumor microenvironment. Targeting FLOT2 deletion emerges as a novel strategy to impede DLBCL aggressiveness by inhibiting cell proliferation and invasion, ultimately inducing apoptotic cell death.

Comprehensive analysis of the prognostic implication and immune infiltration of CISD2 in diffuse large B-cell lymphoma.

Diffuse large B-cell lymphoma (DLBCL) is the most common B-cell lymphoma in adults. CDGSH iron sulfur domain 2 (CISD2) is an iron-sulfur protein and plays a critical role of cell proliferation. The aberrant expression of CISD2 is associated with the progression of multiple cancers. However, its role in DLBCL remains unclear. The differential expression of CISD2 was identified via public databases, and quantitative real-time PCR (qRT-PCR) and western blot were used to identifed the expression of CISD2. We estimated the impact of CISD2 on clinical prognosis using the Kaplan-Meier plotter. Meanwhile, the drug sensitivity of CISD2 was assessed using CellMiner database. The 100 CISD2-related genes from STRING obtained and analyzed using the LASSO Cox regression. A CISD2 related signature for risk model (CISD2Risk) was established. The PPI network of CISD2Risk was performed, and functional enrichment was conducted through the DAVID database. The impacts of CISD2Risk on clinical features were analyzed. ESTIMATE, CIBERSORT, and MCP-counter algorithm were used to identify CISD2Risk associated with immune infiltration. Subsequently, Univariate and multivariate Cox regression analysis were applied, and a prognostic nomogram, accompanied by a calibration curve, was constructed to predict 1-, 3-, and 5-years survival probabilities. CISD2 was upregulated in DLBCL patients comparing with normal controls via public datasets, similarly, CISD2 was highly expressed in DLBCL cell lines. Overexpression of CISD2 was associated with poor prognosis in DLBCL patients based on the GSE31312, the GSE32918, and GSE93984 datasets (P<0.05). Nine drugs was considered as a potential therapeutic agents for CISD2. By using the LASSO cox regression, twenty seven genes were identified to construct CISD2Risk, and biological functions of these genes might be involved in apoptosis and P53 signaling pathway. The high CISD2Risk value had a worse prognosis and therapeutic effect (P<0.05). The higher stromal score, immune score, and ESTIMATE score were associated with lowe CISD2Risk value, CISD2Risk was negatively correlated with several immune infiltrating cells (macrophages M0 and M1, CD8 T cells, CD4 naïve T cells, NK cell, etc) that might be correlated with better prognosis. Additionally, The high CISD2Risk was identified as an independent prognostic factor for DLBCL patients using both univariate and multivariate Cox regression. The nomogram produced accurate predictions and the calibration curves were in good agreement. Our study demonstrates that high expression of CISD2 in DLBCL patients is associated with poor prognosis. We have successfully constructed and validated a good prognostic prediction and efficacy monitoring for CISD2Risk that included 27 genes. Meanwhile, CISD2Risk may be a promising evaluator for immune infiltration and serve as a reference for clinical decision-making in DLBCL patients.

M6A-related lncRNAs as potential biomarkers and the lncRNA ELFN1-AS1/miR-182-5p/BCL-2 regulatory axis in diffuse large B-cell lymphoma.

Diffuse large B-cell lymphoma (DLBCL) is the most common lymphoid subtype. However, unsatisfactory survival outcomes remain a major challenge, and the underlying mechanisms are poorly understood. N6-methyladenosine (m6A), the most common internal modification of eukaryotic mRNA, participates in cancer pathogenesis. In this study, m6A-associated long non-coding RNAs (lncRNA) were retrieved from publicly available databases. Univariate, LASSO, and multivariate Cox regression analyses were performed to establish an m6A-associated lncRNA model specific to DLBCL. Kaplan-Meier curves, principal component analysis, functional enrichment analyses and nomographs were used to study the risk model. The underlying clinicopathological characteristics and drug sensitivity predictions against the model were identified. Risk modelling based on the three m6A-associated lncRNAs was an independent prognostic factor. By regrouping patients using our model-based method, we could differentiate patients more accurately for their response to immunotherapy. In addition, prospective compounds that can target DLBCL subtypes have been identified. The m6A-associated lncRNA risk-scoring model developed herein holds implications for DLBCL prognosis and clinical response prediction to immunotherapy. In addition, we used bioinformatic tools to identify and verify the ceRNA of the m6A-associated lncRNA ELFN1-AS1/miR-182-5p/BCL-2 regulatory axis. ELFN1-AS1 was highly expressed in DLBCL and DLBCL cell lines. ELFN1-AS1 inhibition significantly reduced the proliferation of DLBCL cells and promoted apoptosis. ABT-263 inhibits proliferation and promotes apoptosis in DLBCL cells. Invitro and invivo studies have shown that ABT-263 combined with si-ELFN1-AS1 can inhibit DLBCL progression.

Abstract C051: Alteration of protein translation by eIF4A1 inhibition exquisitely primes lymphoma cells to induction of ferroptosis

Abstract Background: Ferroptosis induction as a cancer therapy faces challenges establishing clinical therapeutic windows. Cells employ diverse mechanisms to prevent iron-mediated oxidation of membrane polyunsaturated fatty acids that causes ferroptosis, but populations with low rates of protein synthesis such as hematopoietic stem cells are more susceptible. Therefore, we hypothesized protein synthesis inhibitors might enhance therapeutic ferroptosis induction. Rocaglates, inhibitors targeting eIF4A1, have entered clinical trials with promising potential against diffuse large B-cell lymphoma (DLBCL), which also exhibits pre-clinical susceptibility to ferroptosis induction. Up to 40% of patients with DLBCL, the most common lymphoma type, have poor outcomes requiring new approaches to address these persistent unmet clinical needs. Our results reveal striking synergy of rocaglates, including the clinical compound zotatifin (eFT226), with ferroptosis inducers. TMT-pSILAC and RNA-seq analyses revealed profound deregulation of ferroptotic protection resulting from rocalate effects on protein synthesis. Methods: We used RNA-seq and TMT-pSILAC followed by mass spectrometry to analyze transcriptome and protein output in SU-DHL-10 DLBCL cells treated with zotatifin or DMSO for 24h. Enrichment analyses (Enrichr platform, ChIP-X Enrichment Analysis 3, GSEA) identified differentially expressed genes, proteins and transcription factors. We explored synergy between zotatifin and ferroptosis modulators in DLBCL cell lines and measured a wide variety of associated cellular endpoints including lipid peroxidation, glutathione levels, and glutathione peroxidase 4 (GPX4) expression. Results: TMT-pSILAC translatome assessment during rocaglate exposure revealed expression alteration(log2FC ≥ 1.5) of numerous key proteins involved in oxidative stress (i.e. SDHB, SDHA, TRAP1, SCO1, UQCRH, ETFA, COX7C) and enrichment of factors indicating induction of an antioxidant response (CD98HC, NRF1, ATF2, SP2, and NFE2L). These changes led to high synergy of zotatifin in combination with a wide variety of ferroptosis inducers (Bliss δ synergy score &amp;gt; 10) and antagonism with ferroptosis inhibitors (Bliss δ synergy score &amp;lt; - 10). These results were consistent across multiple DLBCL mouse and human experimental systems, and preliminarily appear present also in models of T-cell lymphomas. Lipid peroxidation levels were significantly enhanced when zotatifin was combined with erastin (p-value &amp;lt; 0.0005). Moreover, zotatifin treatment resulted in elevated levels of reduced glutathione (GSH), an effect overcome by addition of ferroptosis inducers (p-value &amp;lt; 0.005). Consistently, GPX4 expression was also impaired. Conclusions: Rocaglates induce novel alterations in oxidative stress factors and associated response pathways, sensitizing B and T lymphomas to therapeutic ferroptosis induction. These findings provide valuable insights for using rocaglates in combination with ferroptosis induction to overcome heterogeneous resistance pathways in high-risk lymphoma patients. Citation Format: Paola Manara, Alexa Marie Barroso, Abdessamad Youssfi Alaoui, Olivia Barbara Lightfuss, Tyler Andrew Cunningham, Kyle Hoffman, Caroline Alice Coughlin, Jonathan Harry Schatz. Alteration of protein translation by eIF4A1 inhibition exquisitely primes lymphoma cells to induction of ferroptosis [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr C051.

Abstract C144: MEN1703/SEL24, a potent PIM inhibitor, demonstrates promising anti-tumour activity in activated B cell like diffuse large B cell lymphoma, mantle cell lymphoma and marginal zone lymphoma cells

Abstract Background. PIM kinases (PIM1, PIM2, PIM3) are serine threonine kinases that function in multiple biological processes including cell cycle regulation, cell survival and proliferation. They also mediate resistance to anti-tumour agents comprising PI3K inhibitors. PIM1 overexpression and mutations are common in diffuse large B cell lymphoma (DLBCL) and PIM1 overexpression has been validated as a rational therapeutic target particularly in ABC and MCD subtypes. PIM1 overexpression is also found in mantle cell lymphoma (MCL). We investigated the pharmacological inhibition of PIM using the small molecule MEN1703/SEL24 in a large panel of lymphoma cell lines. Methods. Anti-proliferative activity was assessed by MTT assay at 72h: MEN1703/SEL24 was tested in 7 ABC-DLBCL, 19 germinal centre-B cell-like (GCB)-DLBCL, nine MCL, six marginal zone lymphoma (MZL), one primary mediastinal, four MZL ibrutinib-and PI3K-resistant models and one canine lymphoma. Cell cycle and apoptosis assays were done by flow cytometry. RNA-Seq was performed on two ABC- and two GCB-DLBCL cell lines treated with MEN1703/SEL24 or DMSO for 4, 8, 12h, followed by limma and functional annotation analysis with gene set enrichment analysis (GSEA). Results. MEN1703/SEL24 showed anti-proliferative activity in all lymphoma histotypes tested (IC50 median = 593 nM; range = 30 - 10,193 nM). MCL (IC50 median = 108 nM; range = 53 - 412 nM) and ABC-DLBCL (IC50median = 994 nM; range = 30 - 1756 nM) were the most sensitive histotypes; among them OCI-Ly-10 (30 nM) and OCI-Ly-3 (142 nM) had mutated PIM1. GCB-DLBCLs comprised the least sensitive cell lines (IC50 median = 961 nM; range = 252 - 10,193 nM) accounting for 8/11 cell lines with IC50 in the upper percentile. More importantly, MEN1703/SEL24 was active in MZL cell lines with acquired resistance to idelalisib, copanlisib and ibrutinib (IC50 median = 367 nM; range = 273 - 410 nM). MEN1703/SEL24 induced apoptosis in 6/6 cell lines and minor G1 arrest in 1/6 cell lines. In DLBCL cell lines more sensitive to MEN1703/SEL24 treatment, RNA-Seq and GSEA revealed differential modulation of immune, MYC and E2F targets. Conclusions. MEN1703/SEL24 shows robust preclinical activity in B cell lymphomas of different histotypes. RNA-Seq indicates that MEN1703/SEL24 modulates the transcriptome of highly responsive DLBCL cell lines differently from poorly responsive cells, providing novel clues to mechanisms involved in sensitivity to PIM inhibitors and supporting a potential for clinical development in this indication. Citation Format: Afua A. Mensah, Alessandro Ghiringhelli, Giulio Sartori, Filippo Spriano, Chiara Tarantelli, Luciano Cascione, Andrea Rinaldi, Alberto A. Arribas, Daniela Bellarosa, Monica Binaschi, Francesco Bertoni. MEN1703/SEL24, a potent PIM inhibitor, demonstrates promising anti-tumour activity in activated B cell like diffuse large B cell lymphoma, mantle cell lymphoma and marginal zone lymphoma cells [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr C144.

BTG2 Super-Enhancer Mutations Disrupt TFAP4 Binding and Deregulate BTG2 Expression in Diffuse Large B-Cell Lymphoma

Diffuse Large B-cell Lymphoma (DLBCL), the most frequent lymphoid malignancy, remains incurable in ~40% of patients. Coding-genome sequencing efforts identified several genes/pathways altered in this disease, as well as genetic subgroups of prognostic and therapeutic significance. However, the large non-coding portion of the genome remained largely unexplored. We recently identified a pervasive hypermutation mechanism targeting active super-enhancers (SEs) in &amp;gt;90% of DLBCLs and leading to dysregulation of multiple genes, including well-known lymphoma oncogenes (Bal et al., Nature 2022). This pervasive phenomenon exhibits hallmarks of AID activity, and we provided evidence of its oncogenic relevance by demonstrating that mutational hotspots in the BCL6, BCL2 and CXCR4 SEs impair the binding of specific transcriptional repressors, preventing their negative regulation and creating oncogenic dependencies in DLBCL cells. Here we aimed to define the pathogenic role of non-coding mutations targeting the intragenic SE (iSE) of the BTG2 gene, the second most commonly mutated in DLBCL (39% of samples analyzed, including 36/93 primary cases and 7/29 cell lines). BTG2 encodes a member of the B-cell translocation gene (BTG)/ Transducer of ErbB2.1(TOB) family involved in transcriptional co-activation and modulation of mRNA abundance. BTG2 is also targeted by somatic missense mutations in 6-11% of DLBCL samples, suggesting a major role in the pathogenesis of this disease, which has not been explored. In order to identify functionally relevant BTG2 SE mutations, we first screened an extended panel of 286 DLBCL samples for the presence of mutational clusters targeting predicted transcription factor binding motifs. We identified a 20bp sequence stretch that was significantly hypermutated in these tumors, as compared to other lymphoma types or to non-lymphoid tumors (n=64/286, 22%; vs 0/17 Burkitt Lymphomas; 18/284 Follicular Lymphomas; 1/240 Chronic Lymphocytic Leukemias, and 0/1596 other tumors; p&amp;lt;0.0001, Fisher's exact test). In particular, mutations of the C at position +904 to G or T were exclusively detected in 11% DLBCL samples (32/286, p&amp;lt;0.0001, Fisher's exact test). To define the consequences of BTG2 C904 mutations, we then investigated the impact of reverting the mutation to the wild type nucleotide in 2 mutant DLBCL cell lines, using the CRISPR-Cas9 technology. Correction of the mutation led to a significant counter selection of the corrected clones (~85% reduction in a clone recovery assay, compared to control; p&amp;lt;0.001, Fisher's exact test) and to reduced BTG2 mRNA expression (p&amp;lt;0.01, one-way ANOVA), suggesting oncogenic addiction. In silico motif prediction and in vitro DNA-binding assays using mutant vs wild type oligonucleotides in two different DLBCL cell lines, followed by mass spectrometry, identified the Transcription Factor AP4 (TFAP4) as a protein specifically bound to the wild type, but not to the mutant sequences. TFAP4 is an important regulator of B-cell proliferation and cell fate decisions, which can function as a transcriptional activator or repressor in germinal center B-cells and acts downstream of/in parallel with c-MYC. We confirmed that the C904G and C904T SE mutation impaired TFAP4 binding in isogenic DLBCL cell lines by ChIP-qPCR and led to increased BTG2 expression (p&amp;lt;0.001, one-way ANOVA). Moreover, loss of TFAP4 in CRISPR-Cas9 edited DLBCL cells led to higher BTG2 expression levels, documenting TFAP4 as a direct negative regulator of BTG2 expression (p&amp;lt;0.001, one-way ANOVA). Consistently, single cell analysis of normal GC B cells revealed an inverse correlation between the expression pattern of TFAP4 and BTG2 in cells primed to undergo plasma cell differentiation vs cells committed to dark zone re-entry, suggesting that these two genes may function as a molecular switch in the cell fate decision of GC B cells. The programs modulated by BTG2 and TFAP4 in the GC, and disrupted in tumors carrying deregulated BTG2 alleles, will be presented, as defined by RNA-seq analysis of 3 isogenic GC-derived cell lines followed by interrogation of over 100 clinically annotated primary DLBCL biopsies. Together, these data identify TFAP4 as a novel regulator of BTG2 and reveal a previously unappreciated mechanism by which mutations in the BTG2 SE disrupt this circuit and contribute to lymphomagenesis through deregulating BTG2 expression.