ERBB4-Mediated Signaling Is a Mediator of Resistance to PI3K and BTK Inhibitors in B-cell Lymphoid Neoplasms

BTK and PI3K inhibitors are among the drugs approved for the treatment of patients with lymphoid neoplasms. Although active, their ability to lead to long-lasting complete remission is rather limited, especially in the lymphoma setting. This indicates that tumor cells often develop resistance to the drugs. We started from a marginal zone lymphoma cell line, Karpas-1718, kept under prolonged exposure to the PI3Kδ inhibitor idelalisib until acquisition of resistance, or with no drug. Cells underwent transcriptome, miRNA and methylation profiling, whole-exome sequencing, and pharmacologic screening, which led to the identification of the overexpression of ERBB4 and its ligands HBEGF and NRG2 in the resistant cells. Cellular and genetic experiments demonstrated the involvement of this axis in blocking the antitumor activity of various BTK/PI3K inhibitors, currently used in the clinical setting. Addition of recombinant HBEGF induced resistance to BTK/PI3K inhibitors in parental cells and in additional lymphoma models. Combination with the ERBB inhibitor lapatinib was beneficial in resistant cells and in other lymphoma models already expressing the identified resistance factors. An epigenetic reprogramming sustained the expression of the resistance-related factors, and pretreatment with demethylating agents or EZH2 inhibitors overcame the resistance. Resistance factors were also shown to be expressed in clinical specimens. In conclusion, we showed that the overexpression of ERBB4 and its ligands represents a novel mechanism of resistance for lymphoma cells to bypass the antitumor activity of BTK and PI3K inhibitors and that targeted pharmacologic interventions can restore sensitivity to the small molecules.

Abstract 394: ERBB4-mediated signaling is a mediator of resistance to BTK and PI3K inhibitors in B cell lymphoid neoplasms

Background: Marginal zone lymphoma (MZL) is an indolent yet incurable B cell malignancy. Two BTK inhibitors, ibrutinib and zanubrutinib, are FDA approved for relapsed/refractory MZL patients. PI3K inhibitors have also shown clinical activity. The identification of the mechanisms of resistance can provide useful information to optimize the use of the agents. We previously reported an IL6 driven MZL model of PI3K inhibitors resistance developed by prolonged exposure to the PI3Kδ inhibitor idelalisib (Arribas, Haematologica 2022). Here, we present the detailed characterization of a second model with resistance to both BTK and PI3K inhibitors.

Methods: MTT assay. RNA-Seq, whole exome sequencing, miRNA and methylation profiling. FACS and ELISA analyses.

Results: Resistant cells, developed by continuous exposure of the cell line Karpas1718 to idelalisib, showed resistance to various inhibitors of BTK (ibrutinib, zanubrutinib, acalabrutinib and pirtobrutinib) and PI3K (idelalisib, duvelisib, copanlisib and umbralisib). No mutations affecting BTK, PLCG2 or CXCR4 were identified in resistant cells, which had higher expression of genes involved in ERBB signaling (HBEGF, NRG2, ERBB4), cell proliferation (PBK, MKI67, TCL1A) and DNA recombination (RAG1, RAG2) than parental cells. We confirmed cell surface ERBB4 up-regulation, and the cytoplasmatic expression and secretion of its ligand HBEGF in resistant cells, which led to increased levels of p-AKT and p-ERK. The miRNAs miR-29c and let-7c, known negative regulators of the HBEGF-ERBB axis, were fully methylated and down-regulated in resistant compared to parental cells. ERBB4 genetic silencing improved sensitivity to PI3Kδ inhibitor, and exposure to let-7c or miR-29c mimics decreased secreted HBEGF and recovered sensitivity to PI3K inhibitors in resistant cells. Addition of recombinant HBEGF (rHBEGF) induced resistance to BTK and to PI3K inhibitors in parental cells and in other lymphoma models including mantle cell lymphomas and diffuse large B cell lymphomas (DLBCL). The rHBEGF induced resistance was reverted adding the ERBB inhibitor lapatinib. To extend our findings to the clinical context, using two MZL and one DLBCL expression datasets, we showed HBEGF and ERBB4 expression in clinical specimens. Finally, HBEGF levels appeared elevated in the serum of CLL patients with primary or acquired resistance to PI3Kδ or to BTK inhibitors, compared to patients responding to the drugs and paired for similar clinical features.

Conclusions: We characterized a novel B cell lymphoma model of secondary resistance to BTK and PI3K inhibitors. Our results indicate that epigenetic plasticity led to the activation of HBEGF-ERBB signaling sustaining resistance to BTK/PI3K inhibitors, which can be overcome using epigenetic agents and ERBB inhibitors. These therapeutics approaches could be tested in novel clinical trials. AJA, SN: equally contributed.

Citation Format: Alberto J. Arribas, Sara Napoli, Luciano Cascione, Laura Barnabei, Giulio Sartori, Eleonora Cannas, Eugenio Gaudio, Chiara Tarantelli, Afua A. Mensah, Filippo Spriano, Antonella Zucchetto, Francesca M. Rossi, Andrea Rinaldi, Manuel Castro de Moura, Anastasios Stathis, Georg Stussi, Valter Gattei, Jennifer R. Brown, Manel Esteller, Emanuele Zucca, Davide Rossi, Francesco Bertoni. ERBB4-mediated signaling is a mediator of resistance to BTK and PI3K inhibitors in B cell lymphoid neoplasms [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 394.

ERBB4-mediated signaling is a mediator of resistance to BTK and PI3K inhibitors in B cell lymphoid neoplasms

BTK and PI3K inhibitors are among the drugs approved for the treatment of patients with lymphoid neoplasms. Although active, their ability to lead as single agents to long-lasting complete remission is rather limited especially in the lymphoma setting. This indicates that tumor cells often develop resistance to the drugs. Here, we show that the overexpression of ERBB4 and its ligands represents a modality for B cell neoplastic cells to bypass the anti-tumor activity of BTK and PI3K inhibitors and that targeted pharmacological interventions can restore sensitivity to the small molecules. We started from a marginal zone lymphoma (MZL) cell line, Karpas-1718, kept under prolonged exposure to the PI3Kδ inhibitor idelalisib until acquisition of resistance, or with no drug. Cells underwent transcriptome, miRNA and methylation profiling, whole exome sequencing, and pharmacological screening which led to the identification of the overexpression of ERBB4 and its ligands HBEGF and NRG2 in the resistant cells. Cellular and genetic experiments demonstrated the involvement of this axis in blocking the anti-tumor activity of various BTK and PI3K inhibitors, currently used in the clinical setting. Addition of recombinant HBEGF induced resistance to BTK and PI3K inhibitors in parental cells but also in additional lymphoma models. Combination with the ERBB inhibitor lapatinib was beneficial in resistant cells and in other lymphoma models already expressing the identified resistance factors. Multi-omics analysis underlined that an epigenetic reprogramming affected the expression of the resistance-related factors, and pretreatment with demethylating agents or EZH2 inhibitors overcame the resistance. Resistance factors were shown to be expressed in clinical samples, further extending the findings of the study. In conclusions, we identified a novel ERBB4-driven mechanism of resistance to BTK and PI3K inhibitors and treatments that appear to overcome it.

Key points

A mechanism of secondary resistance to the PI3Kδ and BTK inhibitors in B cell neoplasms driven by secreted factors.Resistance can be reverted by targeting ERBB signaling.

The genomic landscape of canine diffuse large B-cell lymphoma identifies distinct subtypes with clinical and therapeutic implications

Diffuse large B-cell lymphoma (DLBCL) is the most common lymphoid neoplasm in dogs and in humans. It is characterized by a remarkable degree of clinical heterogeneity that is not completely elucidated by molecular data. This poses a major barrier to understanding the disease and its response to therapy, or when treating dogs with DLBCL within clinical trials. We performed an integrated analysis of exome (n = 77) and RNA sequencing (n = 43) data in a cohort of canine DLBCL to define the genetic landscape of this tumor. A wide range of signaling pathways and cellular processes were found in common with human DLBCL, but the frequencies of the most recurrently mutated genes (TRAF3, SETD2, POT1, TP53, MYC, FBXW7, DDX3X and TBL1XR1) differed. We developed a prognostic model integrating exonic variants and clinical and transcriptomic features to predict the outcome in dogs with DLBCL. These results comprehensively define the genetic drivers of canine DLBCL and can be prospectively utilized to identify new therapeutic opportunities.

Abstract 4735: The histone deacetylase inhibitor pracinostat modulates the transcriptome of diffuse large B-cell lymphoma cells and is active in combination with several targeted agents

Background: Pracinostat (SB939) is a class I, II and IV histone deacetylase inhibitor (HDACi), in phase 3 in combination with azacitidine for acute myeloid leukemia (NCT03151408). We reported a strong preclinical activity as a single agent in lymphomas (Mensah et al, AACR 2018). Interestingly, anti-tumor activity differed between metabolically-defined subtypes of diffuse large B-cell lymphoma (DLBCL): lower in OxPhos than in B cell receptor (BCR) cell lines. Thus, we now report RNA-Seq on OxPhos and BCR DLBCL cell lines treated with pracinostat. We also present results of a combination screening with 9 anti-lymphoma drugs for future clinical development of this HDACi.

Methods: For RNA-Seq, OxPhos (Toledo, Pfeiffer, WSU-DLCL2) and BCR (SU-DHL-4, SU-DHL-6, OCI-LY-1) cell lines were treated with pracinostat or DMSO for 6 hours (h) or 14 days (d). Absolute fold change > 2 with adjusted P <0.01 were used as thresholds.

Combinations (72 h) with 5-azacytidine, ibrutinib, lenalidomide, bendamustine, everolimus, rituximab, idelalisib, bortezomib and copanlisib were evaluated on germinal center B-cell (GCB: SU-DHL-6, VAL) and activated B cell-like (ABC: OCI-LY-10, TMD8) DLBCL using the Chou-Talalay combination index (CI).

Results: At transcriptome level, pracinostat determined a time-dependent modulation of proliferation and cell cycle genes with differences between OxPhos and BCR cell lines.

The more sensitive BCR showed a higher number of modulated genes at both timepoints than the less sensitive OxPhos DLBCL. Moreover, while the upregulated transcripts increased with time in both metabolic clusters [doubled in BCR (1201 vs 591) and almost tripled in OxPhos (330 vs 120)], the opposite was true for downregulated genes in BCR (358 vs 600) but not in less sensitive OxPhos (186 vs 187).

Combinations of pracinostat with ibrutinib [0.37 (0.01 - 0.73)] or lenalidomide [0.29 (0.11 - 0.46)] were synergistic in ABC. Idelalisib [0.67 (0.46 - 0.92)] and everolimus [0.78 (0.57 - 1.11)] were both effective in combination with pracinostat in all ABC and 1 GCB, while rituximab was synergistic in 1 ABC and all GCB [0.61 (0.32 - >1.1)]. Copanlisib [0.87 (0.45 - 0.94)] and 5-azacytidine [0.96 (0.64 - 1.14)] were additive with pracinostat in 3/4 cell lines and were synergistic in the remaining. Combination with bortezomib was beneficial in 3 cell lines [0.94 (0.5 - 1.53)] and bendamustine combined effectively with pracinostat in 2 of the 4 cell lines [1.1 (0.89 - 1.3)].

Conclusions: Modulation of the DLBCL transcriptome by pracinostat occurs already at 6 h, suggestive of a rapid effect of pracinostat on chromatin architecture, but it differs between OxPhos and BCR DLBCL. In terms of combinations, pracinostat addition to other targeted agents was largely beneficial.

Citation Format: Afua A. Mensah, Filippo Spriano, Eugenio Gaudio, Chiara Chiara Tarantelli, Luciano Cascione, Andrea Rinaldi, Emanuela Lovati, Emanuele Zucca, Anastasios Stathis, Claudio Pietra, Francesco Bertoni. The histone deacetylase inhibitor pracinostat modulates the transcriptome of diffuse large B-cell lymphoma cells and is active in combination with several targeted agents [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4735.

Bromodomain and extra-terminal domain inhibition modulates the expression of pathologically relevant microRNAs in diffuse large B-cell lymphoma

Aberrant changes in microRNA expression contribute to lymphomagenesis. Bromodomain and extra-terminal domain inhibitors such as OTX015 (MK-8628, birabresib) have demonstrated preclinical and clinical activity in hematologic tumors. MicroRNA profiling of diffuse large B-cell lymphoma cells treated with OTX015 revealed changes in the expression levels of a limited number of microRNAs, including miR-92a-1-5p, miR-21-3p, miR-155-5p and miR-96-5p. Analysis of publicly available chromatin immunoprecipitation sequencing data of diffuse large B-cell lymphoma cells treated with bromodomain and extra-terminal domain (BET) inhibitors showed that the BET family member BRD4 bound to the upstream regulatory regions of multiple microRNA genes and that this binding decreased following BET inhibition. Alignment of our microRNA profiling data with the BRD4 chromatin immunoprecipitation sequencing data revealed that microRNAs downregulated by OTX015 also exhibited reduced BRD4 binding in their promoter regions following treatment with another bromodomain and extra-terminal domain inhibitor, JQ1, indicating that BRD4 contributes directly to microRNA expression in lymphoma. Treatment with bromodomain and extra-terminal domain inhibitors also decreased the expression of the arginine methyltransferase PRMT5, which plays a crucial role in B-cell transformation and negatively modulates the transcription of miR-96-5p. The data presented here indicate that in addition to previously observed effects on the expression of coding genes, bromodomain and extra-terminal domain inhibitors also modulate the expression of microRNAs involved in lymphomagenesis.

T-Cell Leukemia/Lymphoma 1 (TCL1): An Oncogene Regulating Multiple Signaling Pathways

Almost 30 years ago, Carlo Croce's group discovered the T-Cell Leukemia/Lymphoma 1A oncogene (TCL1A or TCL1). TCL1 protein is normally expressed in fetal tissues and early developmental stage lymphocytes. Its expression is deregulated in chronic lymphocytic leukemia (B-CLL) and most lymphomas. TCL1 plays a central role in lymphomagenesis as a co-activator of AKT kinases and other recently elucidated interacting protein partners. These include ATM, HSP70 and TP63, which were all confirmed as binding partners of TCL1 from co-immunoprecipitation experiments utilizing endogenously expressed proteins. The nature of these interactions highlighted the role of TCL1 in enhancing multiple signaling pathways, including PI3K and NF-κB. Based on its role in the aforementioned pathways and, despite the lack of a well-defined enzymatic activity, TCL1 is considered a potential therapeutic target for TCL1-positive hematological malignancies. This perspective will provide an overview of TCL1A and its interacting partners.

Abstract 799: The novel histone deacetylase inhibitor pracinostat is an effective anti-lymphoma agent

Background. Currently, 3 histone deacetylase inhibitors (HDACi) are clinically approved for the treatment of T-cell lymphomas: vorinostat, romidepsin and belinostat. Pracinostat (SB939) is a class I, II and IV HDACi (Novotny-Diermayr et al, Mol Cancer Ther 2010), in phase 3 in combination with azacitidine for acute myeloid leukemia patients who are unfit to receive intensive remission induction chemotherapy (NCT03151408). Here, we tested it on a large panel of lymphoma cell lines alone or in combination with a BCL2 inhibitor, venetoclax and with 5-azacitidine.

Methods. 60 cell lines derived from T-cell lymphoma (10), diffuse large B cell lymphoma (DLBCL, 25), mantle cell lymphoma (10), marginal zone lymphoma (5), Hodgkin lymphoma (4), chronic lymphocytic leukemia (2), primary mediastinal B-cell lymphoma (1), murine (2) and canine (1) lymphomas were exposed to increasing doses of pracinostat and vorinostat alone or to pracinostat in combination with venetoclax or 5-azacitidine for 72h. Cell proliferation was assessed using the MTT assay. Chou-Talalay index was used to determine synergism. For apoptosis and cell cycle analyses, cells were treated with 250 nM pracinostat for 72h then stained with Annexin V and 7-AAD (apoptosis) or fixed then stained with 7-AAD (cell cycle) before flow cytometry.

Results. All lymphoma subtypes responded well to pracinostat (median IC50 250 nM; 95%C.I., 171-324 nM). Pracinostat compared favorably with vorinostat (306 nM; 95%C.I., 241-363 nM), and the anti-proliferative activity of the two compounds was correlated (R=0.8, P<0.0001).

Comparison of consensus cluster classification DLBCL subgroups showed that BCR DLBCL were more sensitive to HDACi than OxPhos DLBCL (pracinostat median IC50 BCR: 171 nM, OxPhos: 865 nM, P 0.001; vorinostat median IC50 BCR: 246 nM, OxPhos: 829 nM, P 0.01. No differences were observed between the DLBCL subtypes based on the cell of origin.

Pracinostat mostly provoked cell cycle arrest in the S and G2/M phases with S-phase arrest associated with OxPhos and G2/M arrest with BCR DLBCL. Pracinostat caused pronounced apoptosis in 2/8 DLBCL cell lines.

Functional annotation analysis to compare DLBCL with IC50 values < 200 nM (n=12) and DLBCL with IC50 > 400 nM (n=7) revealed an enrichment of mitochondrial metabolic pathways, DNA repair and cell cycle regulation in DLBCL with IC50 >400 nM. Combination with venetoclax was beneficial in 3/3 cell lines, while the addition of 5-azacitidine benefited 2 out of 3 cell lines.

Conclusions. Pracinostat robustly inhibits the proliferation of lymphoma cells with a similar IC50 range to vorinostat. Its anti-proliferative activity can be cytotoxic or cytostatic. Combination of pracinostat with other compounds further inhibits lymphoma cell proliferation. In DLBCL, the OxPhos phenotype and an enrichment of mitochondrial metabolism, DNA repair and cell cycle pathways are associated with a poorer response to pracinostat.

Citation Format: Afua A. Mensah, Filippo Spriano, Eugenio Gaudio, Chiara Tarantelli, Luciano Cascione, Luca Aresu, Emanuela Lovati, Emanuele Zucca, Anastasios Stathis, Claudio Pietra, Francesco Bertoni. The novel histone deacetylase inhibitor pracinostat is an effective anti-lymphoma agent [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 799.

Preclinical evaluation of the BET bromodomain inhibitor BAY 1238097 for the treatment of lymphoma

The epigenome is often deregulated in cancer and treatment with inhibitors of bromodomain and extra-terminal proteins, the readers of epigenetic acetylation marks, represents a novel therapeutic approach. Here, we have characterized the anti-tumour activity of the novel bromodomain and extra-terminal (BET) inhibitor BAY 1238097 in preclinical lymphoma models. BAY 1238097 showed anti-proliferative activity in a large panel of lymphoma-derived cell lines, with a median 50% inhibitory concentration between 70 and 208 nmol/l. The compound showed strong anti-tumour efficacy in vivo as a single agent in two diffuse large B cell lymphoma models. Gene expression profiling showed BAY 1238097 targeted the NFKB/TLR/JAK/STAT signalling pathways, MYC and E2F1-regulated genes, cell cycle regulation and chromatin structure. The gene expression profiling signatures also highly overlapped with the signatures obtained with other BET Bromodomain inhibitors and partially overlapped with HDAC-inhibitors, mTOR inhibitors and demethylating agents. Notably, BAY 1238097 presented in vitro synergism with EZH2, mTOR and BTK inhibitors. In conclusion, the BET inhibitor BAY 1238097 presented promising anti-lymphoma preclinical activity in vitro and in vivo, mediated by the interference with biological processes driving the lymphoma cells. Our data also indicate the use of combination schemes targeting EZH2, mTOR and BTK alongside BET bromodomains.

Abstract B76: Evaluation of the novel BET Bromodomain inhibitor BAY 1238097 in lymphoma models identifies EZH2 and MYD88 mutations as potential biomarkers and the bases for combinations

Introduction. Lymphomas present frequent alterations of proteins involved in the epigenetic regulation of gene expression. BET Bromodomain proteins are epigenetic readers contributing to gene transcription regulation. Here, we present preclinical results on the novel BET Bromodomain inhibitor BAY 1238097, currently in phase I study (NCT02369029), alone and in combination in lymphoma cell lines.

Methods. Cell lines derived from diffuse large B-cell lymphoma (DLBCL, 27), mantle cell lymphoma (MCL, 10), splenic marginal zone lymphoma (3), anaplastic large T cell lymphoma (9), pro-lymphocytic leukemia and primary mediastinal large cell lymphoma (1 each) were exposed to increasing concentrations of BAY 1238097 for 72 h followed by MTT assay. Sensitivity was correlated with baseline gene expression profiles and genetic features. Synergy was assessed with the Chou-Talalay combination index (CI): <0.9, synergism; 0.9-1.1 additive effect; >1.2, no benefit.

Results. BAY 1238097 had a median IC50 of 208 nM (95%C.I., 157-260). Activity was higher in B- than in T-cell lymphomas (P<0.001), while no differences were observed among B-cell tumor types or DLBCL ABC/GCB subtypes. Anti-tumor activity was mainly cytostatic, as evidenced by LC50 values higher than 1 μM in 43/51 cell lines, with G1-S block (3/3 cell lines treated with BAY 1238097, 500nM/72h). However, LC50 values < 1 μM were obtained in 7/51 (14%) cell lines (all DLBCL/MCL) and apoptosis was confirmed in all of them by Annexin-V/7-AAD staining. Mut EZH2 was associated with higher sensitivity in all cell lines (P<0.05) and in GCB-DLBCL (P<0.05). Also, an EZH2 signature from follicular lymphomas with or without mutEZH2 (Guo et al., CCR 2014) was associated with higher sensitivity in GCB-DLBCL (NES = 1.6, P<0.01). Thus, we evaluated the effect of BAY 1238097 on EZH2 activity. The compound (500 nM, 72 h) down-regulated EZH2 protein levels and H3K27me3 in 4/4 DLBCL (2 wt, 2 mut EZH2). We then analyzed publicly available ChIP-Seq data for HBL1 DLBCL treated with the BET bromodomain inhibitor JQ1 (500 nM, 3 h; Ceribelli et al, PNAS 2014): the treatment reduced BRD4 binding to the EZH2 upstream regulatory region, indicating a direct effect of BET Bromodomain inhibitors on the regulation of the EZH2 mRNA. Finally, we assessed the combination of BAY 1238097 with the EZH2-inhibitor DZNep for 72 h in 8 GCB-DLBCL. The combination was synergistic or additive in 4/5 mut EZH2 GCB-DLBCL (WSU-DLCL2, CI = 0.7; KARPAS422, 0.7; SU-DHL6, 1; SU-DHL4, 1.1), while it did not present any benefit in 3/3 GCB-DLBCL cell lines with wt EZH2 (Toledo, CI = 1.3; DOHH2, CI = 1.6; Farage, CI = 3.1).

In ABC-DLBCL L265P-MYD88 (P = 0.05) and high expression of JAK/STAT and IFN signaling genes were positively associated with sensitivity. Since MYD88 is a known target of BET Bromodomain inhibitors (Boi et al, CCR 2015), we assessed the combination of BAY 1238097 with the BTK-inhibitor ibrutinib for 72 h and synergism was observed in 2/2 ABC-DLBCL cell lines harboring L265P-MYD88 (OCI-Ly10, CI = 0.8; TMD8, 0.6). No benefit was observed in 2/2 ABC-DLBCL with wt MYD88 (SU-DHL2, CI = 1.7; U2932, 1.4).

Conclusions. BAY 1238097 was active in preclinical models of mature lymphomas. Mutations in EZH2 and MYD88 appeared as potential biomarkers and suggested rational combinations to be further explored.

Citation Format: Elena Bernasconi, Eugenio Gaudio, Chiara Tarantelli, Luciano Cascione, Ivo Kwee, Andrea Rinaldi, Afua A. Mensah, Anastasios Stathis, Matthias Ocker, Emanuele Zucca, Bernard Haendler, Francesco Bertoni. Evaluation of the novel BET Bromodomain inhibitor BAY 1238097 in lymphoma models identifies EZH2 and MYD88 mutations as potential biomarkers and the bases for combinations. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr B76.

Abstract A129: Novel histone deacetylase inhibitors ITF-A and ITF-B exhibit efficacy in preclinical models of mature B-cell lymphomas

Lymphomas are among the most common cancers. Despite significant progress made in their treatment, many patients still succumb to disease progression or relapse, or are refractory to current treatment regimens. Recently, the important role of epigenetic pathways in the pathogenesis of lymphomas has been highlighted, with several genes encoding epigenetic modifiers being shown to be selectively and prominently targeted by mutations and genomic aberrations. Histone deacetylase inhibitors (HDACi) are a class of molecules that have shown clinical efficacy in hematological malignancies, including T-cell lymphomas. Here, we have assessed the activity of two novel, class I, IIb, and IV HDACi, ITF-A and ITF-B, from Italfarmaco, in a panel of 29 non-Hodgkin lymphoma cell lines, comprising 21 diffuse large B-cell lymphoma (DLBCL) cell lines, 5 mantle cell lymphoma (MCL) cell lines, and 3 splenic marginal zone lymphoma (SMZL) cell lines. Cells were exposed to increasing concentrations of each HDACi and the MTT assay was performed after 72 hours to determine their cytotoxic and cytostatic effects estimating the IC50 (50%-inhibitory concentration), GI50 (50%-growth inhibition), LC50 (50%-lethal concentration), and TGI (total growth inhibition) values. Both ITF-A and ITF-B showed potent activities in most of the cell lines tested, irrespective of histological type, with the majority of IC50 values being below 100 nM. The median IC50 values were 13 nM (2-103 nM) and 33 nM (5-305 nM), for ITF-B and ITF-A, respectively. Median GI50 was 10 nM (1-63) for ITF-B, and 28 nM (2-217 nM) for ITF-A. The median LC50 values were 117 nM (10-2057 nM) and 42 nM (3-2388 nM) for ITF-A and ITF-B, respectively. The range of TGI values was 5-649 nM with a median of 59 nM for ITF-A, and 2-388 nM, with a median of 20n M for ITF-B. Both ITF-A and ITF-B induced apoptosis in the DLBCL and MCL tested as assessed by Annexin-V/7-AAD staining. Two DLBCL cell lines showing sensitivity to both HDACi, were chosen for further functional studies: DOHH2, a GCB-DLBCL cell line, and TMD8, a non-GCB DLBCL cell line. ITF-A and ITF-B presented both nuclear and cytoplasmic activity, as demonstrated by Western blotting analysis showing increased levels of both acetylated histone H3 and acetyl-α-tubulin following treatment with the two HDACi. Quantitative real-time PCR following 24 hours treatment of both cell lines with the two HDACi showed changes in the expression levels of STAT3, CDKN1A (p21) and MYC, suggesting roles for these genes in mediating the anti-proliferative effects of the two molecules. In conclusion, ITF-A and ITF-B showed promising activity in preclinical models of mature lymphomas and represent two new HDACi worthy of further pre-clinical evaluation as single agents and in combination with other agents.

Citation Information: Mol Cancer Ther 2013;12(11 Suppl):A129.

Citation Format: Afua A. Mensah, Eugenio Gaudio, Ivo Kwee, Andrea Rinaldi, Gianluca Fossati, Anastasios Stathis, Emanuele Zucca, Gianluca Caprini, Francesco Bertoni. Novel histone deacetylase inhibitors ITF-A and ITF-B exhibit efficacy in preclinical models of mature B-cell lymphomas. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr A129.

Large genomic aberrations detected by SNP array are independent prognosticators of a shorter time to first treatment in chronic lymphocytic leukemia patients with normal FISH

BACKGROUND

Genomic complexity can predict the clinical course of patients affected by chronic lymphocytic leukemia (CLL) with a normal FISH. However, large studies are still lacking. Here, we analyzed a large series of CLL patients and also carried out the so far largest comparison of FISH versus single-nucleotide polymorphism (SNP) array in this disease.

PATIENTS AND METHODS

SNP-array data were derived from a previously reported dataset.

RESULTS

Seventy-seven of 329 CLL patients (23%) presented with a normal FISH. At least one large (>5 Mb) genomic aberration was detected by SNP array in 17 of 77 patients (22%); this finding significantly affected TTT. There was no correlation with the presence of TP53 mutations. In multivariate analysis, including age, Binet stage, IGHV genes mutational status and large genomic lesion, the latter three factors emerged as independent prognosticators. The concordance between FISH and SNP array varied between 84 and 97%, depending on the specific genomic locus investigated.

CONCLUSIONS

SNP array detected additional large genomic aberrations not covered by the standard FISH panel predicting the outcome of CLL patients.

Analysis of VH gene sequences using two web-based immunogenetics resources gives different results, but the affinity maturation status of chronic lymphocytic leukaemia clones as assessed from either of the resulting data sets has no prognostic significance

Some cellular and molecular features of chronic lymphocytic leukaemia (CLL) cells that are associated with prognosis may reflect the context within which their progenitors encountered antigen. It follows that the nature of antigen drive in CLL could influence the clinical course and we were prompted to assess the impact, if any, of affinity maturation (an antigen-driven process) on prognosis. Statistical models for assessing affinity maturation status are typically applied to V(H) gene sequence data analysed using a web-based resource like IMGT or VBASE. Since these resources differ with respect to some key relevant features, we evaluated a cohort of CLL cases by applying statistical models to V(H) data derived from both IMGT and VBASE. Important differences between the resulting data sets became apparent. These resulted from database variance and because IMGT and VBASE define complementarity-determining and framework regions (CDRs, FRs) in different ways. Thus, the numbers of mutations identified and their distribution between CDRs/FRs varied between the data sets for the majority of clones. Consequently, two different but overlapping sets of cases with evidence of affinity maturation were defined. Notwithstanding their differences, no significant associations of affinity maturation status with CD38 expression, p53 functional status or survival were identifiable in either data set.