Paola Bonetti

Nucleophosmin Is Required for DNA Integrity and p19Arf Protein Stability

ABSTRACT Nucleophosmin (NPM) is a nucleolar phosphoprotein that binds the tumor suppressors p53 and p19Arf and is thought to be indispensable for ribogenesis, cell proliferation, and survival after DNA damage. The NPM gene is the most frequent target of genetic alterations in leukemias and lymphomas, though its role in tumorigenesis is unknown. We report here the first characterization of a mouse NPM knockout strain. Lack of NPM expression results in accumulation of DNA damage, activation of p53, widespread apoptosis, and mid-stage embryonic lethality. Fibroblasts explanted from null embryos fail to grow and rapidly acquire a senescent phenotype. Transfer of the NPM mutation into a p53-null background rescued apoptosis in vivo and fibroblast proliferation in vitro. Cells null for both p53 and NPM grow faster than control cells and are more susceptible to transformation by activated oncogenes, such as mutated Ras or overexpressed Myc. In the absence of NPM, Arf protein is excluded from nucleoli and is markedly less stable. Our data demonstrate that NPM regulates DNA integrity and, through Arf, inhibits cell proliferation and are consistent with a putative tumor-suppressive function of NPM.

Delocalization and destabilization of the Arf tumor suppressor by the leukemia-associated NPM mutant.

One third of acute myeloid leukemias (AMLs) are characterized by the aberrant cytoplasmic localization of nucleophosmin (NPM) due to mutations within its putative nucleolar localization signal. NPM mutations are mutually exclusive with major AML-associated chromosome rearrangements and are frequently associated with a normal karyotype, suggesting that they are critical during leukemogenesis. The underlying molecular mechanisms are, however, unknown. NPM is a nucleocytoplasmic shuttling protein that has been implicated in several cellular processes, including ribosome biogenesis, centrosome duplication, cell cycle progression, and stress response. It has been recently shown that NPM is required for the stabilization and proper nucleolar localization of the tumor suppressor p19(Arf). We report here that the AML-associated NPM mutant localizes mainly in the cytoplasm due to an alteration of its nucleus-cytoplasmic shuttling equilibrium, forms a direct complex with p19(Arf), but is unable to protect it from degradation. Consequently, cells or leukemic blasts expressing the NPM mutant have low levels of cytoplasmic Arf. Furthermore, we show that expression of the NPM mutant reduces the ability of Arf to initiate a p53 response and to induce cell cycle arrest. Inactivation of p19(Arf), a key regulator of the p53-dependent cellular response to oncogene expression, might therefore contribute to leukemogenesis in AMLs with mutated NPM.

The BET Bromodomain Inhibitor OTX015 Affects Pathogenetic Pathways in Preclinical B-cell Tumor Models and Synergizes with Targeted Drugs.

Purpose: In cancer cells, the epigenome is often deregulated, and inhibition of the bromodomain and extra-terminal (BET) family of bromodomain-containing proteins is a novel epigenetic therapeutic approach. Preliminary results of an ongoing phase I trial have reported promising activity and tolerability with the new BET bromodomain inhibitor OTX015. Experimental Design: We assessed the preclinical activity of OTX015 as single agent and in combination in mature B-cell lymphoma models and performed in vitro and in vivo experiments to identify the mechanism of action and the genetic features associated with sensitivity to the compound. Results: OTX015 showed antiproliferative activity in a large panel of cell lines derived from mature B-cell lymphoid tumors with median IC50 of 240 nmol/L, without significant differences among the different histotypes. In vitro and in vivo experiments showed that OTX015 targeted NFKB/TLR/JAK/STAT signaling pathways, MYC- and E2F1-regulated genes, cell-cycle regulation, and chromatin structure. OTX015 presented in vitro synergism with several anticancer agents, especially with mTOR and BTK inhibitors. Gene expression signatures associated with different degrees of sensitivity to OTX015 were identified. Although OTX015 was mostly cytostatic, the compound induced apoptosis in a genetically defined subgroup of cells, derived from activated B-cell–like diffuse large B-cell lymphoma, bearing wtTP53, mutations in MYD88, and CD79B or CARD11. Conclusions: Together with the data coming from the ongoing phase I study, the in vitro and in vivo data presented here provide the basis for further clinical investigation of OTX015 as single agent and in combination therapies. Clin Cancer Res; 21(7); 1628–38. ©2015 AACR.

Nucleophosmin and its AML-associated mutant regulate c-Myc turnover through Fbw7γ

Mutations leading to aberrant cytoplasmic localization of nucleophosmin (NPM) are the most frequent genetic alteration in acute myelogenous leukemia (AML). NPM binds the Arf tumor suppressor and protects it from degradation. The AML-associated NPM mutant (NPMmut) also binds p19Arf but is unable to protect it from degradation, which suggests that inactivation of p19Arf contributes to leukemogenesis in AMLs. We report here that NPM regulates turnover of the c-Myc oncoprotein by acting on the F-box protein Fbw7γ, a component of the E3 ligase complex involved in the ubiquitination and proteasome degradation of c-Myc. NPM was required for nucleolar localization and stabilization of Fbw7γ. As a consequence, c-Myc was stabilized in cells lacking NPM. Expression of NPMmut also led to c-Myc stabilization because of its ability to interact with Fbw7γ and delocalize it to the cytoplasm, where it is degraded. Because Fbw7 induces degradation of other growth-promoting proteins, the NPM–Fbw7 interaction emerges as a central tumor suppressor mechanism in human cancer.

PRDM1/BLIMP1 is commonly inactivated in anaplastic large T-cell lymphoma.

Anaplastic large cell lymphoma (ALCL) is a mature T-cell lymphoma that can present as a systemic or primary cutaneous disease. Systemic ALCL represents 2% to 5% of adult lymphoma but up to 30% of all pediatric cases. Two subtypes of systemic ALCL are currently recognized on the basis of the presence of a translocation involving the anaplastic lymphoma kinase ALK gene. Despite considerable progress, several questions remain open regarding the pathogenesis of both ALCL subtypes. To investigate the molecular pathogenesis and to assess the relationship between the ALK(+) and ALK(-) ALCL subtypes, we performed a genome-wide DNA profiling using high-density, single nucleotide polymorphism arrays on a series of 64 cases and 7 cell lines. The commonest lesions were losses at 17p13 and at 6q21, encompassing the TP53 and PRDM1 genes, respectively. The latter gene, coding for BLIMP1, was inactivated by multiple mechanisms, more frequently, but not exclusively, in ALK(-)ALCL. In vitro and in vivo experiments showed that that PRDM1 is a tumor suppressor gene in ALCL models, likely acting as an antiapoptotic agent. Losses of TP53 and/or PRDM1 were present in 52% of ALK(-)ALCL, and in 29% of all ALCL cases with a clinical implication.

The lymphoma-associated NPM-ALK oncogene elicits a p16INK4a/pRb-dependent tumor-suppressive pathway

Oncogene-induced senescence (OIS) is a barrier for tumor development. Oncogene-dependent DNA damage and activation of the ARF/p53 pathway play a central role in OIS and, accordingly, ARF and p53 are frequently mutated in human cancer. A number of leukemia/lymphoma-initiating oncogenes, however, inhibit ARF/p53 and only infrequently select for ARF or p53 mutations, suggesting the involvement of other tumor-suppressive pathways. We report that NPM-ALK, the initiating oncogene of anaplastic large cell lymphomas (ALCLs), induces DNA damage and irreversibly arrests the cell cycle of primary fibroblasts and hematopoietic progenitors. This effect is associated with inhibition of p53 and is caused by activation of the p16INK4a/pRb tumor-suppressive pathway. Analysis of NPM-ALK lymphomagenesis in transgenic mice showed p16INK4a-dependent accumulation of senescent cells in premalignant lesions and decreased tumor latency in the absence of p16INK4a. Accordingly, human ALCLs showed no expression of either p16INK4a or pRb. Up-regulation of the histone-demethylase Jmjd3 and de-methylation at the p16INK4a promoter contributed to the effect of NPM-ALK on p16INK4a, which was transcriptionally regulated. These data demonstrate that p16INK4a/pRb may function as an alternative pathway of oncogene-induced senescence, and suggest that the reactivation of p16INK4a expression might be a novel strategy to restore the senescence program in some tumors.

Deregulation of ETS1 and FLI1 contributes to the pathogenesis of diffuse large B-cell lymphoma.

Diffuse large B-cell lymphoma (DLBCL) is the most common form of human lymphoma. DLBCL is a heterogeneous disease characterized by different genetic lesions. We herein report the functional characterization of a recurrent gain mapping on chromosome 11q24.3, found in 23% of 166 DLBCL cases analyzed. The transcription factors ETS1 and FLI1, located within the 11q24.3 region, had significantly higher expression in clinical samples carrying the gain. Functional studies on cell lines showed that ETS1 and FLI1 cooperate in sustaining DLBCL proliferation and viability and regulate genes involved in germinal center differentiation. Taken together, these data identify the 11q24.3 gain as a recurrent lesion in DLBCL leading to ETS1 and FLI1 deregulated expression, which can contribute to the pathogenesis of this disease.

Abstract 5528: The BET Bromodomain inhibitor OTX015 targets the NFKB, TLR and JAK/STAT pathways and shows pre-clinical activity as single agent and in combination in mature B-cell tumors

Proceedings: AACR Annual Meeting 2014; April 5-9, 2014; San Diego, CA Background: Lymphomas are still incurable in many patients and novel active compounds are actively being sought. We previously reported single agent activity of the BET bromodomain OTX015 in lymphoma cell lines and in vivo (AACR 2012; ICML 2013). Here, we report a study of the mechanism of action of OTX015 and its activity in combination with other anti-cancer compounds. Methods: Cell lines: 22 diffuse large B-cell lymphoma (DLBCL), 4 mantle cell lymphomas, 3 multiple myelomas, 3 splenic marginal zone lymphoma and 1 prolymphocytic leukemia. Anti-proliferative of OTX015 (OncoEthix SA, Switzerland) was assessed by MTT and its cytotoxic activity by Annexin V staining and gene expression profiling (GEP) with Illumina HumanHT-12 Expression BeadChips. Data mining was done with LIMMA, GSEA, Metacore. Synergy was assessed in cells (2-5 cell lines) exposed for 72 h to increasing doses of OTX015 alone or in combination with increasing doses of other agents. MTT assays were performed and Chou-Talalay combination index (CI) calculated. Results: OTX015 (500 nM, 72h) showed cytostatic activity in 29/33 (88%) cell lines and apoptosis in 3/22 (14%). Mutations in genes coding for MYD88 and components of BCR (P=0.027), and ABC signaling phenotypes (P=0.008) were significantly associated with apoptosis induction. We performed GEP on 2 cell lines (SU-DHL-6, SU-DHL-2), treated with DMSO or OTX015 (500 nM) for 1, 2, 4, 8 or 12 hours. Most upregulated genes were histones. MYC target genes were highly significantly enriched among all OTX015 regulated transcripts and MYC was the most frequently downregulated gene. OTX015 also downregulated MYD88, IRAK1, TLR6, IL6, STAT3, and TNFRSF17, members of the NFKB, TLR and JAK/STAT pathways. NFKB target genes (IRF4, TNFAIP3 and BIRC3) were also downregulated (PCR). Immunoblotting and immunohistochemistry showed a reduction of transcriptionally active pSTAT3 in 2 ABC cell lines, and a reduction in nuclear localization of p50 (NFKB1), indicating an inhibitory effect of OTX015 on the canonical NFKB pathway. Finally, IL10 and IL4 production was reduced after 24 hours OTX015 treatment. Synergy was observed with everolimus (median CI=0.1; range 0.1-0.2), ibrutinib in ABC-DLBCL (CI=0.04; 0.02-0.1), idelalisib (CAL101) (CI=0.5; 0.04-2.4), vorinostat (CI=0.5; 0.3-0.6), rituximab (CI=0.5; 0.4-0.5), decitabine (CI=0.6; 0.6-0.7), lenalidomide (CI=0.7; 0.6-0.7), and all-trans retinoic acid (CI=0.4; .1-1.6). Additive effects were observed for combinations with romidepsin (CI=1.08; 1-1.22), bendamustine (CI=0.92; 0.83-1.1), and doxorubicin (CI=0.83; 0.71-0.96). Conclusions: OTX015 is a promising candidate for targeted combination therapies. A phase I study ([NCT01713582][1]) in patients with hematological neoplasias is underway and together with our preclinical data, may support further clinical investigations. Citation Format: Eugenio Gaudio, Elena Bernasconi, Ivo Kwee, Michela Boi, Paola Bonetti, Chiara Tarantelli, Andrea Rinaldi, Monica Testoni, Maurilio Ponzoni, Anastasios Stathis, Georg Stussi, Eugenia Riveiro, Patrice Herait, Emanuele Zucca, Francesco Bertoni. The BET Bromodomain inhibitor OTX015 targets the NFKB, TLR and JAK/STAT pathways and shows pre-clinical activity as single agent and in combination in mature B-cell tumors. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5528. doi:10.1158/1538-7445.AM2014-5528 [1]: /lookup/external-ref?link_type=CLINTRIALGOV&access_num=NCT01713582&atom=%2Fcanres%2F74%2F19_Supplement%2F5528.atom

Abstract 1017: The BRD-inhibitor OTX015 affects proliferation and gene expression of cells derived from mature lymphoid neoplasms.

Proceedings: AACR 104th Annual Meeting 2013; Apr 6-10, 2013; Washington, DC Inhibitors of the BET family members BRD2/3/4 are a promising new class of anti-cancer drugs. Here, we assessed the antitumor activity and the mechanism of action of OTX015, a selective orally bioavailable BRD2/3/4 inhibitor, in cells derived from human mature lymphoid neoplasms. OTX015 was evaluated in 31 B-cell malignancies cell lines: 13 diffuse large B-cell lymphomas (DLBCL), 8 anaplastic large T-cell lymphomas (ALCL), 4 mantle cell lymphomas (MCL), 3 splenic marginal zone lymphomas (SMZL), and 3 multiple myelomas (MM). Anti-proliferative effect was seen in the majority of the cell lines. The median IC50s, calculated at 72h, were: DLBCL, 0.19μM (range 0.07-12.68); ALCL, 0.48μM (0.04-9.1); SMZL, 0.16μM (0.1-0.24); MM, 0.45μM (0.06-0.7); MCL, 2μM (1.22- >15). There were apparently no IC50 differences based on the cell of origin (DLBCL) or ALK-positivity status (ALCL). Apoptosis did not appear as the main effect of the drug, being not observed in 11 cell lines treated with the IC50 defined by MTT test after 72-hour exposure. However, OTX105 determined a dose-dependent G1 cell cycle arrest in 12/12 cell lines (DLBCL, MM and ALCL), and an increased percentage of senescent cells in 3/3 sensitive cell lines (DLBCL and ALCL). MYC mRNA was suppressed in a dose-dependent manner in 4/5 DLBCL, 4/4 ALCL and 2/2 MM cell lines. Down-regulation was usually seen within 1h. Real-time PCR showed that MYC and also NFKB target genes were affected. Gene expression profiling (GEP), using the Illumina HumanHT-12 v4 Expression BeadChip array, was done in 3 sensitive DLBCL cell lines, exposed to DMSO or OTX015 (0.5μM) for 4h and 8h. MYC was the most down-regulated gene. Functional annotation of the down-regulated genes identified an over-representation of genes involved in RNA and DNA metabolism and cell cycle, putative MYC target genes and transcripts reported as down-regulated after treatment with aminopeptidase inhibitors and HDAC-inhibitors. Up-regulated transcripts were enriched of genes coding for proteins involved in chromatin structure, as well as putative MYC target genes and transcripts reported as up-regulated after treatment with HDAC-inhibitors, demethylating agents or aplidine. Also, GEP signature was similar to what reported for the BRD-inhibitor JQ1. In conclusion, OTX015 showed in vitro anti-tumoral activity in a large series of mature lymphoid neoplasms. The activity was largely cytostatic, with cell cycle G1 arrest and induction of senescence. Down-regulation of MYC and its putative targets appeared as the main effect, but it might not be the only mechanism of action, since a few cell lines did not appear to down-regulate MYC after exposure to OTX015, which also induced down-regulation of NFKB target genes and modulation of transcripts similar to what observed with HDAC-inhibitors. The compound appears worth of further investigation as a new promising therapeutic agent in lymphomas. Citation Format: Paola Bonetti, Michela Boi, Elena Bernasconi, Andrea Rinaldi, Ivo Kwee, Eugenio Gaudio, Maurilio Ponzoni, Maria Grazia Tibiletti, Anastasios Stathis, Eugenia Riveiro, Giorgio Inghirami, Emanuele Zucca, Francesco Bertoni. The BRD-inhibitor OTX015 affects proliferation and gene expression of cells derived from mature lymphoid neoplasms. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1017. doi:10.1158/1538-7445.AM2013-1017