Search

Aberrations in genes coding for subunits of the BRG1/BRM associated factor (BAF) chromatin remodeling complexes are highly abundant in human cancers. Currently, it is not understood how these mostly loss-of-function mutations contribute to cancer development and how they can be targeted therapeutically. The cancer-type-specific occurrence patterns of certain subunit mutations suggest subunit-specific effects on BAF complex function, possibly by the formation of aberrant residual complexes. Here, we systematically characterize the effects of individual subunit loss on complex composition, chromatin accessibility and gene expression in a panel of knockout cell lines deficient for 22 BAF subunits. We observe strong, specific and sometimes discordant alterations dependent on the targeted subunit and show that these explain intracomplex codependencies, including the synthetic lethal interactions SMARCA4–ARID2, SMARCA4–ACTB and SMARCC1–SMARCC2. These data provide insights into the role of different BAF subcomplexes in genome-wide chromatin organization and suggest approaches to therapeutically target BAF-mutant cancers. The authors generate cell lines deficient for 22 BAF subunits, studying effects on complex composition, chromatin accessibility and gene expression. They identify synthetic lethal interactions between SMARCA4–ARID2, SMARCA4–ACTB and SMARCC1–SMARCC2.

Central nervous system (CNS) tumors with BCOR internal tandem duplications (CNS-BCOR ITD) are aggressive malignancies recently included in the 2021 WHO Classification of CNS tumors. This entity is characterized by ITDs within the PUFD domain of BCOR, potentially interfering with protein-protein interactions and preventing non-canonical polycomb repressive complex 1.1 (ncPRC1.1) complex formation. Additionally, other BCOR alterations like frame shift mutations and gene fusions have been described. However, the underlying molecular mechanisms promoting tumor aggressiveness remain unknown. We established cell models from one patient harboring a BCOR frameshift mutation and another one with a concomitant BCORL1-fusion. Two additional models were derived from a patient with a CNS-BCOR ITD tumor. Multidrug screening uncovered high sensitivity against defined receptor tyrosine kinase (RTK) inhibitors (TKIs). In detail, ponatinib, nintedanib, and dovitinib reduced cell viability at half maximal inhibitory concentrations (IC50) in the low micro-molar range (

International audience; Not available.

T-cell prolymphocytic leukemia (T-PLL) is a rare and aggressive T-lymphoid malignancy usually refractory to current treatment strategies and associated with short overall survival. By applying next-generation functional testing of primary patient-derived lymphoma cells using a library of 106 US Food and Drug Administration (FDA)-approved anticancer drugs or compounds currently in clinical development, we set out to identify novel effective treatments for T-PLL patients. We found that the B-cell lymphoma 2 (BCL-2) inhibitor venetoclax (ABT-199) demonstrated the strongest T-PLL-specific response when comparing individual ex vivo drug response in 86 patients with refractory hematologic malignancies. Mechanistically, responses to venetoclax correlated with protein expression of BCL-2 but not with expression of the BCL-2 family members myeloid cell leukemia 1 (MCL-1) and BCL-XL in lymphoma cells. BCL-2 expression was inversely correlated with the expression of MCL-1. Based on the ex vivo responses, venetoclax treatment was commenced in 2 late-stage refractory T-PLL patients resulting in clinical responses. Our findings demonstrate first evidence of single-agent activity of venetoclax both ex vivo and in humans, offering a novel agent in T-PLL.

Heterozygous inactivating mutations in ribosomal protein genes (RPGs) are associated with hematopoietic and developmental abnormalities, activation of p53, and altered risk of cancer in humans and model organisms. Here we performed a large‐scale analysis of cancer genome data to examine the frequency and selective pressure of RPG lesions across human cancers. We found that hemizygous RPG deletions are common, occurring in about 43% of 10,744 cancer specimens and cell lines. Consistent with p53‐dependent negative selection, such lesions are underrepresented in TP53 ‐intact tumors ( P ≪ 10−10), and shRNA‐mediated knockdown of RPGs activated p53 in TP53 ‐wild‐type cells. In contrast, we did not see negative selection of RPG deletions in TP53 ‐mutant tumors. RPGs are conserved with respect to homozygous deletions, and shRNA screening data from 174 cell lines demonstrate that further suppression of hemizygously deleted RPGs inhibits cell growth. Our results establish RPG haploinsufficiency as a strikingly common vulnerability of human cancers that associates with TP53 mutations and could be targetable therapeutically. ![][1] Hemizygous deletion of ribosomal protein genes (RPGs) is a strikingly common vulnerability of human cancers that associates with TP53 mutations and could be targetable therapeutically. [1]: /embed/graphic-1.gif

Introduction T-cell prolymphocytic leukemia (T-PLL) is a rare and aggressive T-lymphoid malignancy with poor response to current treatment strategies. We recently demonstrated single agent activity of venetoclax in relapsed/refractory (r/r) T-PLL, however resistance developed on mono-therapy. We here set out to identify partners for an effective combinatorial treatment concept. Methods To overcome bcl-2 inhibitor resistance we utilized primary T-PLL patient samples and applied a combinatorial next-generation functional drug screen for venetoclax and 25 additional therapeutic agents (Fig.1a). Molecular mechanisms of drug combinations were evaluated by BH3-family member profiling and mass spectrometry. Protein expression was assessed by Western Blot and viability by AnnexinV/Hoechst staining. The best scoring combination was evaluated in two late stage r/r T-PLL patients. Results Pairwise combinations screen of venetoclax with candidate small molecule inhibitors and chemotherapeutic drugs on primary T-PLL cells revealed synergistic action of venetoclax with ibrutinib, idelalisib, and 5-azacytidine, and to lower extents Olaparib, Temsirolimus, Ruxolitinib and Belinostat whereas cisplatin antagonized the effect of venetoclax across all patient samples tested (Fig 1b). The combination of venetoclax and ibrutinib resulted in substantial reduction of viability in primary T-PLL cells (Fig 1c). BH3-profiling on primary T-PLL samples with and without ibrutinib treatment demonstrated enhanced overall priming with predominant increase of bcl-2 dependency upon ibrutinib treatment (Fig 1d). Addition of ibrutinib to venetoclax led to decreased phosphorylation of ITK in vivo (Fig 1e). Two patients suffering from r/r T-PLL after failing at least two treatment lines including alemtuzumab were treated with the combination of venetoclax and ibrutinib resulting in significant clinical responses with substantial drops in leukocytosis and LDH as well as substantial clinical improvement (Fig 2a, b). The dynamic BH3 profiling in samples taken from these patients confirmed that the addition of ibrutinib is indeed increasing overall priming and Bcl-2 dependency (Fig 2c, d). Conclusion Our findings suggest efficacy of combinatorial treatment of venetoclax with ibrutinib in T-PLL. Mechanistically, ibrutinib dephosphorylated ITK in T-PLL cells and, furthermore, enhanced BCL2 dependency, both, in-vivo and in-vitro. Patients treated with the combination venetoclax and ibrutinib experienced profound clinical responses which needs further evaluation in an prospective clinical study on a larger cohort of r/r T-PLL patients. Disclosures Herbaux: Abbvie: Honoraria; Janssen: Honoraria; Takeda: Honoraria; BMS: Honoraria; Gilead: Honoraria. Mayerhoefer:Siemens: Research Funding, Speakers Bureau; BMS: Speakers Bureau. Jaeger:Novartis, Roche, Sandoz: Consultancy; AbbVie, Celgene, Gilead, Novartis, Roche, Takeda Millennium: Research Funding; Amgen, AbbVie, Celgene, Eisai, Gilead, Janssen, Novartis, Roche, Takeda Millennium, MSD, BMS, Sanofi: Honoraria; Celgene, Roche, Janssen, Gilead, Novartis, MSD, AbbVie, Sanofi: Membership on an entity's Board of Directors or advisory committees. Davids:AbbVie, Acerta Pharma, Adaptive, Biotechnologies, Astra-Zeneca, Genentech, Gilead Sciences, Janssen, Pharmacyclics, TG therapeutics: Membership on an entity's Board of Directors or advisory committees; AbbVie, Astra-Zeneca, Genentech, Janssen, MEI, Pharmacyclics, Syros Pharmaceuticals, Verastem: Consultancy; Acerta Pharma, Ascentage Pharma, Genentech, MEI pharma, Pharmacyclics, Surface Oncology, TG Therapeutics, Verastem: Research Funding; Research to Practice: Honoraria. Staber:Takeda-Millenium: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; MSD: Honoraria, Speakers Bureau; Celgene: Honoraria, Membership on an entity's Board of Directors or advisory committees; AbbVie: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Roche: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; Janssen: Honoraria, Speakers Bureau; Gilead: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau. OffLabel Disclosure: Ibrutinib - BTK inhibitor Venetoclax - bcl2 inhibitor

International audience; Approved drugs are invaluable tools to study biochemical pathways, and further characterization of these compounds may lead to repurposing of single drugs or combinations. Here we describe a collection of 308 small molecules representing the diversity of structures and molecular targets of all FDA-approved chemical entities. The CeMM Library of Unique Drugs (CLOUD) covers prodrugs and active forms at pharmacologically relevant concentrations and is ideally suited for combinatorial studies. We screened pairwise combinations of CLOUD drugs for impairment of cancer cell viability and discovered a synergistic interaction between flutamide and phenprocoumon (PPC). The combination of these drugs modulates the stability of the androgen receptor (AR) and resensitizes AR-mutant prostate cancer cells to flutamide. Mechanistically, we show that the AR is a substrate for γ-carboxylation, a post-translational modification inhibited by PPC. Collectively, our data suggest that PPC could be repurposed to tackle resistance to antiandrogens in prostate cancer patients.

Central nervous system high-grade neuroepithelial tumor with BCL6-corepressor alteration (CNS HGNET-BCOR) is a recently discovered molecular brain tumor entity characterized by genomic alterations of BCOR, a central component of a non-canonical polycomb repressive complex. However, the underlying oncogenic mechanisms and their consequences for tumor-specific anti-cancer therapy remain widely enigmatic. We systematically analyzed genomics, transcriptomics, and drug-sensitivity patterns in three tumor-derived models (two cell-lines, one primary cell-culture) from three consecutive intracranial CNS HGNET-BCOR metastases of one patient. All models harbored a unique frameshift mutation within BCOR resulting in a truncated protein lacking functionally important c-terminal protein domains. Re-expression of BCOR wild-type in our CNS HGNET-BCOR cell-models resulted in decreased cell proliferation and increased apoptosis. Interestingly, genes downregulated upon re-expression of BCOR wild-type were also derepressed in CNS HGNET-BCOR tumor tissues harboring BCOR-alterations different from our case (e.g. internal tandem duplication in BCOR). Via comparison with a chromatin immunoprecipitation DNA-sequencing dataset, we determined that a significant proportion of the corresponding gene promoters are occupied by BCOR in BCOR wild-type cancer cells. An additional drug-screen demonstrated hypersensitivity of CNS HGNET-BCOR cells against histone deacetylase inhibitors and histone methyltransferase inhibitors. Matching of drug sensitivity patterns to upregulated target-genes determined bortezomib, dasatinib, and crizotinib as promising tumor-specific therapeutics against CNS HGNET-BCOR. Taken together, our results suggest that dysfunction of BCOR-mediated gene repression determines the oncogenic behavior and transcriptomic profile of CNS HGNET-BCOR. Moreover, we provide preliminary results for potential pharmacological interventions against this aggressive tumor type.

In chronic myeloid leukemia (CML) resistance against one or more BCR-ABL1 tyrosine kinase inhibitors (TKI) remains a clinical challenge. Preclinical data suggest that TKI combinations may overcome resistance. We report on a heavily pre-treated 78 year-old female patient with CML who developed multi-resistant blast crisis with bone marrow fibrosis and a Ph- clone. Treatment with ponatinib resulted in blast cell clearance, decrease in fibrosis, and disappearance of BCR-ABL1, but also in severe thrombocytopenia with bleedings requiring platelet transfusions. We therefore switched from ponatinib to bosutinib. During bosutinib, platelet counts recovered. However, after 6 months, BCR-ABL1 mRNA levels increased to > 1%. Therefore, we ´switched back´ to ponatinib, and this was again followed by disappearance of BCR-ABL1 and a decrease in platelets. During the next 2 years, we applied ponatinib and bosutinib in continuous rotation-cycles and added hydroxyurea in order to suppress all sub-clones and to balance between efficacy and potential side effects following the principle of personalized medicine. With this approach the patient remained in complete molecular response and reached normal blood counts and a normal quality of life without vascular or other side effects. In conclusion, TKI rotation is a novel potent approach to suppress multiple resistant sub-clones and to balance between clinical efficacy and side effects in patients with advanced CML. Clinical trials are now warranted to show that TKI-rotation is in general safe and effective in these patients.

Genomically amplified fibroblast growth factor receptor 1 (FGFR1) is an oncogenic driver in defined lung cancer subgroups and predicts sensibility against FGFR1 inhibitors in this patient cohort. The FGFR inhibitor nintedanib has recently been approved for treatment of lung adenocarcinoma and is currently evaluated for small cell lung cancer (SCLC). However, tumor recurrence due to development of nintedanib resistance might occur. Hence, we aimed at characterizing the molecular mechanisms underlying acquired nintedanib resistance in FGFR1-driven lung cancer. Chronic nintedanib exposure of the FGFR1-driven SCLC cell line DMS114 (DMS114/NIN) but not of two NSCLC cell lines induced massive overexpression of the multidrug-resistance transporter ABCB1. Indeed, we proved nintedanib to be both substrate and modulator of ABCB1-mediated efflux. Importantly, the oncogenic FGFR1 signaling axis remained active in DMS114/NIN cells while bioinformatic analyses suggested hyperactivation of the endothelin-A receptor (ETAR) signaling axis. Indeed, ETAR inhibition resensitized DMS114/NIN cells against nintedanib by downregulation of ABCB1 expression. PKC and downstream NFκB were identified as major downstream players in ETAR-mediated ABCB1 hyperactivation. Summarizing, ABCB1 needs to be considered as a factor underlying nintedanib resistance. Combination approaches with ETAR antagonists or switching to non-ABCB1 substrate FGFR inhibitors represent innovative strategies to manage nintedanib resistance in lung cancer.

Breast cancer is genetically heterogeneous, and recent studies have underlined a prominent contribution of epigenetics to the development of this disease. To uncover new synthetic lethalities with known breast cancer oncogenes, we screened an epigenome-focused short hairpin RNA library on a panel of engineered breast epithelial cell lines. Here we report a selective interaction between the NOTCH1 signaling pathway and the SUMOylation cascade. Knockdown of the E2-conjugating enzyme UBC9 (UBE2I) as well as inhibition of the E1-activating complex SAE1/UBA2 using ginkgolic acid impairs the growth of NOTCH1-activated breast epithelial cells. We show that upon inhibition of SUMOylation NOTCH1-activated cells proceed slower through the cell cycle and ultimately enter apoptosis. Mechanistically, activation of NOTCH1 signaling depletes the pool of unconjugated small ubiquitin-like modifier 1 (SUMO1) and SUMO2/3 leading to increased sensitivity to perturbation of the SUMOylation cascade. Depletion of unconjugated SUMO correlates with sensitivity to inhibition of SUMOylation also in patient-derived breast cancer cell lines with constitutive NOTCH pathway activation. Our investigation suggests that SUMOylation cascade inhibitors should be further explored as targeted treatment for NOTCH-driven breast cancer.Oncogene advance online publication, 29 September 2014; doi:10.1038/onc.2014.319.

Polycomb/Trithorax response elements (PRE/TREs) can switch their function reversibly between silencing and activation by mechanisms that are poorly understood. Here we show that a switch in forward and reverse noncoding transcription from the Drosophila melanogaster vestigial (vg) PRE/TRE switches the status of the element between silencing (induced by the forward strand) and activation (induced by the reverse strand). In vitro, both noncoding RNAs inhibit PRC2 histone methyltransferase activity, but, in vivo, only the reverse strand binds PRC2. Overexpression of the reverse strand evicts PRC2 from chromatin and inhibits its enzymatic activity. We propose that the interaction of RNAs with PRC2 is differentially regulated in vivo, allowing regulated inhibition of local PRC2 activity. Genome-wide analysis shows that strand switching of noncoding RNAs occurs at several hundred Polycomb-binding sites in fly and vertebrate genomes. This work identifies a previously unreported and potentially widespread class of PRE/TREs that switch function by switching the direction of noncoding RNA transcription.

Lung cancer accounts for the highest number of cancer-related deaths worldwide. Patient outcome is dismal and approval of targeted compounds is yet restricted to non-small cell lung cancer (NSCLC) histology. In defined subgroups of NSCLC, but also of small cell lung cancer (SCLC), genetically amplified fibroblast growth factor receptor 1 (FGFR1) is an oncogenic driver and inhibition of the FGFR1 signaling axis exerts potent antitumor effects. The FGFR/PDGFR/VEGFR inhibitor (TKI) nintedanib has recently been approved for second-line treatment of lung adenocarcinoma (AC) and is also being investigated in clinical trials for the treatment of SCLC. Despite initial treatment success, tumor recurrence due to acquired drug resistance is anticipated. We therefore aimed at characterizing the molecular mechanisms underlying resistance development of FGFR1-driven lung cancer against nintedanib. One SCLC line (DMS114) and two NSCLC squamous cell carcinoma (SCC) lines (NCI-H1703, NCI-H520) driven by FGFR1 based on gene amplification were selected for nintedanib resistance in vitro. Cytotoxicity was evaluated by MTT and FACS. Intracellular responses to drug exposure were analyzed by qPCR and Western Blot. To compare transcription levels of parental cells with their selected sublines, whole-genome gene expression array was performed. Cross-cytotoxicity profiles were determined by a large-scale anticancer compound screen. ATP-binding cassette (ABC) transporter activity was analyzed by calcein AM efflux- and ATPase assay, intracellular Nintedanib levels were determined by liquid chromatograpy-mass spectrometry (LC-MS). Chronic exposure to the FGFR/PDGFR/VEGFR inhibitor nintedanib led to expression of the ABCB1 multidrug-resistance (MDR) efflux pump in the SCLC cell line DMS114 but not in the NSCLC SCC cell lines NCI-H1703 and NCI-H520. In the nintedanib-selected subline of DMS114 (DMS114/NIN), the FGFR1 signaling axis remained active. Insensitivity of DMS1114/NIN towards Nintedanib was mediated by efflux via ABCB1, revealing Nintedanib as a substrate for this efflux pump. Ponatinib, another non-ABCB1-substrate FGFR inhibitor, retained strong cytotoxic activity. Additionally, DMS114/NIN cells exerted profound and ABCB1-dependent collateral sensitivity against the MDR-selective lanthanum compound KP772. ABCB1 needs to be considered as a factor underlying intrinsic and acquired nintedanib resistance. On one hand, in second-line therapy, chemotherapy-induced MDR might render tumors resistant to Nintedanib. On the other hand, in first-line treatment, high ABCB1 expression in cancer cells or the microvasculature e.g. in clear-cell renal carcinoma or CNS tumors might account for intrinsic Nintedanib resistance. Switching to MDR-selective anticancer compounds or to non-ABCB1-substrate small molecule TKIs in FGFR/PDGFR/VEGFR-driven tumors might be an option to circumvent nintedanib resistance. Citation Format: Bernhard Englinger, Daniela Lötsch, Christine Pirker, Sushilla van Schoonhoven, Bernd Boidol, Charles Lardeau, Stefan Kubicek, Pal Szabó, Gergely Szakacs, Walter Berger. Acquired nintedanib resistance in FGFR1-driven small cell but not non-small cell lung cancer is mediated by ABCB1. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2119.