Abstract
Motivation
Genome-wide association studies (GWAS) are a powerful method to detect even weak associations between variants and phenotypes; however, many of the identified associated variants ...are in non-coding regions, and presumably influence gene expression regulation. Identifying potential drug targets, i.e. causal protein-coding genes, therefore, requires crossing the genetics results with functional data.
Results
We present a novel data integration pipeline that analyses GWAS results in the light of experimental epigenetic and cis-regulatory datasets, such as ChIP-Seq, Promoter-Capture Hi-C or eQTL, and presents them in a single report, which can be used for inferring likely causal genes. This pipeline was then fed into an interactive data resource.
Availability and implementation
The analysis code is available at www.github.com/Ensembl/postgap and the interactive data browser at postgwas.opentargets.io.
•Safe handling of lithium should be demonstrated in support of DONES licensing.•LiFIRE facility will study lithium ignition under conditions relevant for DONES.•Outcomes from LiFIRE campaign will ...support DONES fire protection requirements.•Preliminary design and experimental campaign of LiFIRE facility are presented.
In the DEMO-Oriented NEutron Source (DONES) facility, it is expected to use a considerable amount of lithium at an average temperature higher than 300 °C. It is well known that lithium can produce exothermic reactions with several media, generating corrosive and toxic (upon burning) reaction products and with the potential risk of mobilizing radionuclides in little amounts. As a result, lithium represents a hazardous material which must be safely handled under normal operation and, especially, potential accident conditions which involve lithium spills and radioactive releases.
Although the burning behavior of lithium has been studied for several decades, there is still a wide dispersion of data regarding its actual ignition temperature. Generally, measurements of the spontaneous or induced ignition temperature of a leakage of molten lithium, pool/spray type, depend on several factors such as metal purity, gas atmosphere composition and relative humidity, sample size or geometrical aspects, and even different treatments, apparatus, and techniques used.
A dedicated experimental facility, called “LiFIRE”, is currently under development at the National Fusion Laboratory of CIEMAT with the purpose to quantitatively support the DONES safety analysis on the fire risk in case of lithium leakages, based on the Defense-in-Depth principle, i.e. prevention, detection and mitigation.
The assessment of radiation fields in the lithium loop pipes and dump tank during the operation were performed for International Fusion Materials Irradiation Facility – DEMO-Oriented NEutron Source ...(IFMIF-DONES) in order to obtain the radiation dose-rate maps in the component surroundings. Variance reduction techniques such as weight window mesh (produced with the ADVANTG code) were applied to bring the statistical uncertainty down to a reasonable level. The biological dose was given in the study, and potential shielding optimization is suggested and more thoroughly evaluated. The MCNP Monte Carlo was used to simulate a gamma particle transport for radiation shielding purposes for the current Li Systems’ design. In addition, the shielding efficiency was identified for the Impurity Control System components and the dump tank. The analysis reported in this paper takes into account the radiation decay source from and activated corrosion products (ACPs), which is created by d-Li interaction. As a consequence, the radiation (resulting from ACPs and Be-7) shielding calculations have been carried out for safety considerations.
Most cancers preserve functional retinoblastoma (Rb) and may, therefore, respond to inhibition of D-cyclin-dependent Rb kinases, CDK4 and CDK6. To date, CDK4/6 inhibitors have shown promising ...clinical activity in breast cancer and lymphomas, but it is not clear which additional Rb-positive cancers might benefit from these agents. No systematic survey to compare relative sensitivities across tumor types and define molecular determinants of response has been described. We report a subset of cancers highly sensitive to CDK4/6 inhibition and characterized by various genomic aberrations known to elevate D-cyclin levels and describe a recurrent CCND1 3′UTR mutation associated with increased expression in endometrial cancer. The results suggest multiple additional classes of cancer that may benefit from CDK4/6-inhibiting drugs such as abemaciclib.
•A wide range of sensitivity to abemaciclib is observed among Rb+ tumor cells•CDKN2A mutant cancers show only intermediate sensitivity to CDK4/6 inhibition•D-cyclin activating features are associated with highly sensitive cells•About 5% of endometrial cancers bear a stabilizing mutation in the CCND1 3′UTR
Gong et al. identify a subset of cancers highly sensitive to CDK4/6 inhibition, which are characterized by various genomic aberrations known to elevate D-cyclin levels but not by CDKN2A mutations. They also identify a recurrent CCND1 3′UTR mutation associated with increased CCND1 expression in endometrial cancer.
Loss-of-function mutations in the retinoblastoma gene
are common in several treatment-refractory cancers such as small-cell lung cancer and triple-negative breast cancer. To identify drugs synthetic ...lethal with
mutation (
), we tested 36 cell-cycle inhibitors using a cancer cell panel profiling approach optimized to discern cytotoxic from cytostatic effects. Inhibitors of the Aurora kinases AURKA and AURKB showed the strongest
association in this assay. LY3295668, an AURKA inhibitor with over 1,000-fold selectivity versus AURKB, is distinguished by minimal toxicity to bone marrow cells at concentrations active against
cancer cells and leads to durable regression of
tumor xenografts at exposures that are well tolerated in rodents. Genetic suppression screens identified enforcers of the spindle-assembly checkpoint (SAC) as essential for LY3295668 cytotoxicity in RB1-deficient cancers and suggest a model in which a primed SAC creates a unique dependency on AURKA for mitotic exit and survival. SIGNIFICANCE: The identification of a synthetic lethal interaction between
and AURKA inhibition, and the discovery of a drug that can be dosed continuously to achieve uninterrupted inhibition of AURKA kinase activity without myelosuppression, suggest a new approach for the treatment of RB1-deficient malignancies, including patients progressing on CDK4/6 inhibitors.
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Chromosomal instability (CIN) is a hallmark of cancer aggressiveness, providing genetic plasticity and tumor heterogeneity that allows the tumor to evolve and adapt to stress conditions. CIN is ...considered a cancer therapeutic biomarker because healthy cells do not exhibit CIN. Despite recent efforts to identify therapeutic strategies related to CIN, the results obtained have been very limited. CIN is characterized by a genetic signature where a collection of genes, mostly mitotic regulators, are overexpressed in CIN‐positive tumors, providing aggressiveness and poor prognosis. We attempted to identify new therapeutic strategies related to CIN genes by performing a drug screen, using cells that individually express CIN‐associated genes in an inducible manner. We find that the overexpression of targeting protein for Xklp2 (TPX2) enhances sensitivity to the proto‐oncogene c‐Src (SRC) inhibitor dasatinib due to activation of the Yes‐associated protein 1 (YAP) pathway. Furthermore, using breast cancer data from The Cancer Genome Atlas (TCGA) and a cohort of cancer‐derived patient samples, we find that both TPX2 overexpression and YAP activation are present in a significant percentage of cancer tumor samples and are associated with poor prognosis; therefore, they are putative biomarkers for selection for dasatinib therapy.
Previous efforts trying to find a therapeutic strategy using chromosomal instability (CIN) as a biomarker did not yield promising results. We screened a drug library using breast cancer cells overexpressing individual genes, closely associated with CIN, in an inducible manner. We found that overexpression of the CIN‐associated gene TPX2 provides sensitivity to the SRC inhibitor dasatinib, due to an increase in YAP/TAZ transcriptional signaling.
Polo‐like kinase 1 (PLK1) is a serine/threonine kinase that plays multiple and essential roles during the cell division cycle. Its inhibition in cultured cells leads to severe mitotic aberrancies and ...cell death. Whereas previous reports suggested that Plk1 depletion in mice leads to a non‐mitotic arrest in early embryos, we show here that the bi‐allelic Plk1 depletion in mice certainly results in embryonic lethality due to extensive mitotic aberrations at the morula stage, including multi‐ and mono‐polar spindles, impaired chromosome segregation and cytokinesis failure. In addition, the conditional depletion of Plk1 during mid‐gestation leads also to severe mitotic aberrancies. Our data also confirms that Plk1 is completely dispensable for mitotic entry in vivo. On the other hand, Plk1 haploinsufficient mice are viable, and Plk1‐heterozygous fibroblasts do not harbor any cell cycle alterations. Plk1 is overexpressed in many human tumors, suggesting a therapeutic benefit of inhibiting Plk1, and specific small‐molecule inhibitors for this kinase are now being evaluated in clinical trials. Therefore, the different Plk1 mouse models here presented are a valuable tool to reexamine the relevance of the mitotic kinase Plk1 during mammalian development and animal physiology.
Two different mouse strains, a classical gene‐trapping KO and a conditional KO by Cre recombinase excision, demonstrate that the mitotic kinase Plk1 is essential at any stage of the embryonic development, and its depletion leads to mitotic aberrancies and embryonic death. Instead, Plk1 haploinsufficient mice do not show any alteration.
Integration of safety aspects in IFMIF-DONES design is a main objective of EUROfusion and European Commission projects. IFMIF-DONES will be a radioactive facility of the first category, and stringent ...safety objectives must be achieved and demonstrated. A very low acceptable risk for the worker, the public and the environment is the main principle in the design phase. The progress of safety activities is performed iteratively as detailed engineering develops, taking into account the uniqueness of the facility: a high-power deuterons accelerator (125 mA, 40 MeV), a target of flowing liquid lithium, traps for activation products, a dedicated-design module for irradiated samples, a massive shielding cooled room with confinement function, and a number of conventional systems with safety functions. Several phases are developed: (i) identification of sources and materials at risk, radioactive and nonradioactive, subject to potential mobilization, (ii) failure mode analysis and effects of systems, starting at the functional level, and support with probabilistic analysis, (iii) identification of scenarios leading to unacceptable risk if unmitigated, (iv) proposal of layers of defense by means of safety-credited components and design features, (v) deterministic analysis of scenarios in support of requirements, and (vi) definition and demonstration of safety requirements charged to components.
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Background: Breast cancer is the second most common cancer worldwide. Pharmacologically targeting cyclin-dependent kinases 4 and 6 (CDK4 & 6) has proven to be a successful ...therapeutic approach in patients with estrogen receptor positive (ER+) breast cancer. Differences in both efficacy and toxicity among the available CDK4 & 6 inhibitors has generated interest in a biological explanation. Abemaciclib is an adenosine triphosphate-competitive, reversible, selective inhibitor of CDK4 & 6 that has shown antitumor activity as a single agent and in combination with standard endocrine therapy (ET), in hormone receptor positive (HR+) metastatic breast cancer patients including those with ET resistance, and in combination with ET in high-risk early breast cancer patients. This study examines attributes of abemaciclib and other CDK4 & 6 inhibitors. Methods: The potency of abemaciclib for CDK4 was evaluated using biochemicals and breast cancer cell-based assays. Additionally, different combinations with an anti-estrogen therapy (e.g., tamoxifen, fulvestrant) were analyzed in an in vitro palbociclib (CDK4 & 6 inhibitor)-resistant breast cancer cell model, as well as in a set of CDK4 & 6 sensitive breast cancer cell models. Using cell-free assays, high content imaging and flow cytometry approaches, a subset of markers were monitored to characterize the phenotype of sensitive cell lines in a continuous dose schedule. Results: In in vitro, cell-free assays, abemaciclib shows selectivity for CDK4 over CDK6, and in cell-based assays, abemaciclib preferentially inhibits the proliferation of cells dependent on the presence of CDK4, not CDK6. Abemaciclib inhibits cell proliferation in a wide range of breast cancer cell lines, showing activity regardless of human epidermal growth factor receptor 2 (HER2) and PI3KCA gene mutation status. Furthermore, in a cell line resistant to palbociclib, abemaciclib in combination with fulvestrant (ET) restores CDK4 & 6 sensitivity, leading to cell senescence and cell death. Finally, in human bone marrow progenitor cells, abemaciclib shows a lesser impact on myeloid maturation than other CDK4 & 6 inhibitors, palbociclib and ribociclib, allowing for continuous dosing. Conclusions: In pre-clinical experiments, abemaciclib is a potent cell growth inhibitor, inhibiting preferentially the CDK4/CyclinD1 complex, leading to cell senescence and cell death. These pre-clinical results support the differentiated safety and efficacy profile of abemaciclib observed in clinical trials.
Abstract
Background: Prostate cancer (PCa) is a leading cause of cancer death in men and represents a substantial public health burden 1. Most PCa are primarily dependent on androgen receptor (AR) ...activity and castration is an effective approach to treat PCa patients. Despite the recent significant treatment advances, PCa inevitably becomes androgen-independent and progresses to the castration-resistant disease state (CRPC), the deadliest form of the disease 2. Progression of the disease to castration-resistance is often mediated by a reactivation of AR signaling pathway 3.
Upon androgen stimulation, expression of D-type cyclin is up-regulated which results in an increased cyclin-dependent kinase 4 and 6 (CDK4/6) activity and stimulation of the cell cycle. 4; Thus, inhibition of CDK4/6 may represent an effective strategy to delay or overcome primary androgen resistance.
Abemacicilb is a CDK4 and CDK6 inhibitor with a clinical safety profile allowing continuous dosing to achieve sustained target inhibition 5. Abemaciclib is FDA-approved for the treatment of patients with hormone receptor (HR)-positive, human epidermal growth factor receptor 2 (HER2)-negative metastatic breast cancer 6,7.
Methods: The anti-proliferative activity of the abemaciclib was evaluated using iodide staining in a panel of 15 PCa cell lines. In order to get new insights on abemaciclib effects, deeper in vitro analysis was carried out in LNCaP, PC-3 and 22RV1, as ADT responding and resistant PCa cell models, respectively. Cell cycle analysis was done by FACS and High Content Imaging; cellular signaling was assessed by Western blotting. Apoptosis was measured by detection of caspase 3 and Tunnel assay. 22RV1 xenograft mouse model was used to evaluate abemaciclib efficacy in vivo.
Results: Anti-proliferative activity of abemaciclib was observed across a panel of PCa cell lines, mainly in hormone receptor positive (AR+) cell lines. Overall, abemaciclib efficiently inhibited CDK4 and CDK6 which prevented the phosphorylation of Rb with the consequent effect in cell cycle and induced a G1 cell cycle arrest. Prolonged treatment promoted a marked senescence phenotype indicated by an increased b-galactosidase staining and morphological changes to result ultimately in apoptosis. In 22RV1 xenograft models, abemaciclib significantly reduced tumor growth. Taken together these data provide insights on sensitivity of PCa models to abemaciclib and its mode of action, demonstrating the potential of this drug for the treatment of prostate cancer patients.
Conclusions: Abemaciclib inhibits proliferation of AR positive prostate cancer cell lines by inducing cell cycle arrest mediated by inhibition of Rb phosphorylation. Abemaciclib is a CDK4/6 inhibitor with potential to treat prostate cancer by blocking cell proliferation leading to induction of senescence and apoptosis.
Citation Format: Raquel Torres-Guzmán, Carmen Baquero, Maria Patricia Ganado, Carlos Marugán, Huimin Bian, Yi Zeng, Ramón Rama, Jian Du, Maria José Lallena. Targeting prostate cancer with the CDK4 and CDK6 inhibitor abemaciclib abstract. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4850.
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