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At least 1,495 records · Page 83

Discovery and Development of a Small-Molecule Inhibitor Targeting the GAS41 YEATS Domain in Nonsmall Cell Lung Cancer

Abstract GAS41 is frequently overexpressed in Non-Small Cell Lung Cancer (NSCLC). GAS41 contains a YEATS domain, which recognizes acetylated lysine residues on histones to recruit protein complexes and facilitate transcription. Suppression of GAS41 in NSCLC models inhibits cellular proliferation and markedly reduces tumor growth in mouse xenografts, justifying the development of small-molecule inhibitors. We have employed structure-based design and medicinal chemistry optimization to discover DLG-41, a submicromolar inhibitor binding to the GAS41 YEATS domain. DLG-41 potently disrupts the association of GAS41 YEATS with chromatin in mammalian cells and inhibits the proliferation of NSCLC cell lines with submicromolar potency without significantly affecting normal lung fibroblasts. DLG-41 induces more effective growth inhibition in A549 versus GAS41-knockout cells, demonstrating on-target activity. DLG-41 treatment upregulates the CDKN1A gene and downregulates pathways associated with lung cancer cell identity, tumor migration, and invasion. DLG-41 is a promising chemical probe for targeting GAS41 protein in NSCLC models and has potential for future development.

Listunov, Dymytrii [University of Michigan , , , ,↗

Allosteric inhibition of SHP2 phosphatase inhibits cancers driven by receptor tyrosine kinases

The non-receptor protein tyrosine phosphatase SHP2, encoded by PTPN11, has an important role in signal transduction downstream of growth factor receptor signalling and was the first reported oncogenic tyrosine phosphatase1. Activating mutations of SHP2 have been associated with developmental pathologies such as Noonan syndrome and are found in multiple cancer types, including leukaemia, lung and breast cancer and neuroblastoma1, 2, 3, 4, 5. SHP2 is ubiquitously expressed and regulates cell survival and proliferation primarily through activation of the RAS–ERK signalling pathway2, 3. It is also a key mediator of the programmed cell death 1 (PD-1) and B- and T-lymphocyte attenuator (BTLA) immune checkpoint pathways6, 7. Reduction of SHP2 activity suppresses tumour cell growth and is a potential target of cancer therapy8, 9. Here we report the discovery of a highly potent (IC50 = 0.071 μM), selective and orally bioavailable small-molecule SHP2 inhibitor, SHP099, that stabilizes SHP2 in an auto-inhibited conformation. SHP099 concurrently binds to the interface of the N-terminal SH2, C-terminal SH2, and protein tyrosine phosphatase domains, thus inhibiting SHP2 activity through an allosteric mechanism. SHP099 suppresses RAS–ERK signalling to inhibit the proliferation of receptor-tyrosine-kinase-driven human cancer cells in vitro and is efficacious in mouse tumour xenograft models. Together, these data demonstrate that pharmacological inhibition of SHP2 is a valid therapeutic approach for the treatment of cancers.

59 BASIC BIOLOGICAL SCIENCES↗

Iron addiction: a novel therapeutic target in ovarian cancer

Ovarian cancer is a lethal malignancy that has not seen a major therapeutic advance in over 30 years. We demonstrate that ovarian cancer exhibits a targetable alteration in iron metabolism. Ferroportin (FPN), the iron efflux pump, is decreased, and transferrin receptor (TFR1), the iron importer, is increased in tumor tissue from patients with high grade but not low grade serous ovarian cancer. A similar profile of decreased FPN and increased TFR1 is observed in a genetic model of ovarian cancer tumor-initiating cells (TICs). The net result of these changes is an accumulation of excess intracellular iron and an augmented dependence on iron for proliferation. A forced reduction in intracellular iron reduces the proliferation of ovarian cancer TICs in vitro, and inhibits both tumor growth and intraperitoneal dissemination of tumor cells in vivo. Some mechanistic studies demonstrate that iron increases metastatic spread by facilitating invasion through expression of matrix metalloproteases and synthesis of interleukin 6 (IL-6). Here, we show that the iron dependence of ovarian cancer TICs renders them exquisitely sensitive in vivo to agents that induce iron-dependent cell death (ferroptosis) as well as iron chelators, and thus creates a metabolic vulnerability that can be exploited therapeutically.

59 BASIC BIOLOGICAL SCIENCES↗

Employing antineutrino detectors to safeguard future nuclear reactors from diversions

The Non-Proliferation Treaty and other non-proliferation agreements are in place worldwide to ensure that nuclear material and facilities are used only for peaceful purposes. Antineutrino detectors, sensitive to reactor power and fuel changes, can complement the tools already at the disposal of international agencies to safeguard nuclear facilities and to verify the States' compliance with the agreements. Recent advancement in these detectors has made it possible to leverage them to reduce the likelihood of an undetected diversion of irradiated nuclear material. We study the sensitivity of antineutrino monitors to fuel divergence from two reactor types: a traditional light-water reactor and an advanced sodium-cooled reactor design, a likely candidate for future deployment. The analysis demonstrates that a variety of potential diversion scenarios can be detected by such a system. We outline recent developments in monitoring capabilities and discuss their potential security implications to the international community.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

High-affinity Cu(I) chelator PSP-2 as potential anti-angiogenic agent

Copper is an essential trace metal that has been implicated in angiogenesis, the formation of new blood vessels. As tumor growth relies on establishing a functional capillary network for blood supply, copper chelation therapy may hold promise as an anti-cancer strategy by suppressing angiogenesis. To test the anti-angiogenic effect of PSP-2, a recently developed high affinity Cu(I) chelator with low zeptomolar dissociation constant, we utilized the endothelial cancer cell line EAhy926 and assessed changes in cell migration, proliferation, and tube formation in Matrigel. In addition, sprouting was assessed by the chicken and sheep aortic ring assay, and vascular pattern formation was studied in the chorioallantoic membrane of chicken embryos (CAM assay). While incubation with PSP-2 resulted in selective depletion of cellular copper levels, cell migration was not affected and the proliferating activity was even slightly increased. Moreover, the endothelial tube formation assay revealed significant morphological changes in the presence of PSP-2, with thicker tubular walls and an overall decreased meshes area. Similarly, the aortic ring assay and CAM assay showed that PSP-2 evokes significantly longer sprouts with smaller angles at branching points. Altogether, PSP-2 exhibits significant bioactivity at concentrations as low as 5 μM, rendering it a promising anti-angiogenic agent. As EAhy926 cells exhibit both endothelial and tumorigenic properties, the anti-angiogenic effect of PSP-2 might potentially translate also into anticancer activity.

60 APPLIED LIFE SCIENCES↗

Catalyst carbonylation: a hidden, but essential, step in reaction initiation

The proliferation of increasingly useful reactions for hydrogen transfer in organic synthesis has included the introduction of many new homogeneous catalysts into the organic synthesis lexicon. Unlike the proliferation of palladium-based cross-coupling reactions in which the mechanism is generally conserved, we are learning that these emerging hydrogen transfer catalysts have a rich diversity of mechanisms for catalyst activation, speciation, C–H bond cleavage and formation, and ultimately deactivation. We find that an underappreciated commonality in the catalytic activation for some of these systems is the generation of a (carbonyl)metal group, which dominates the downstream speciation of the catalyst system. In this mini-review we highlight a few well-documented cases of this phenomenon as food for thought for those who are designing new catalytic systems to introduce into this dynamic and impactful area.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A model with competition between the cell lines in leukemia under treatment

The evolution of leukemia is modeled with a delay differential equation model of four cell populations: two populations (healthy and leukemic) ) of stem-like cells involving a larger category consisting of proliferating stem and progenitor cells with self-renew capacity and two populations (healthy and leukemic) of mature cells, considering the competition of healthy vs. leukemic cell populations and three types of division that a stem-like cell can exhibit: self-renew, asymmetric division and differentiation. In the model it is assumed that the treatment acts on the proliferation rate of the leukemic stem cells and on the apoptosis of stem and mature cells. The emphasis in this model is on establishing relevant parameters for chronic and acute manifestations of leukemia. Stability of equilibria is investigated and sufficient conditions for local asymptotic stability will be given using a Lyapunov-Krasovskii functional.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Dynamics of protein aggregation and oligomer formation governed by secondary nucleation

The formation of aggregates in many protein systems can be significantly accelerated by secondary nucleation, a process where existing assemblies catalyse the nucleation of new species. In particular, secondary nucleation has emerged as a central process controlling the proliferation of many filamentous protein structures, including molecular species related to diseases such as sickle cell anemia and a range of neurodegenerative conditions. Increasing evidence suggests that the physical size of protein filaments plays a key role in determining their potential for deleterious interactions with living cells, with smaller aggregates of misfolded proteins, oligomers, being particularly toxic. It is thus crucial to progress towards an understanding of the factors that control the sizes of protein aggregates. However, the influence of secondary nucleation on the time evolution of aggregate size distributions has been challenging to quantify. This difficulty originates in large part from the fact that secondary nucleation couples the dynamics of species distant in size space. Here, we approach this problem by presenting an analytical treatment of the master equation describing the growth kinetics of linear protein structures proliferating through secondary nucleation and provide closed-form expressions for the temporal evolution of the resulting aggregate size distribution. We show how the availability of analytical solutions for the full filament distribution allows us to identify the key physical parameters that control the sizes of growing protein filaments. Furthermore, we use these results to probe the dynamics of the populations of small oligomeric species as they are formed through secondary nucleation and discuss the implications of our work for understanding the factors that promote or curtail the production of these species with a potentially high deleterious biological activity.

60 APPLIED LIFE SCIENCES↗

Growth control of Saccharomyces cerevisiae through dose of oxygen atoms

To investigate the dose-dependent effects of neutral oxygen radicals on the proliferation as well as the inactivation of microorganisms, we treated suspensions of budding yeast cells with oxygen radicals using an atmospheric-pressure oxygen radical source, varying the fluxes of O({sup 3}P{sub j}) from 1.3 × 10{sup 16} to 2.3 × 10{sup 17 }cm{sup −2} s{sup −1}. Proliferation was promoted at doses of O({sup 3}P{sub j}) ranging from 6 × 10{sup 16} to 2 × 10{sup 17 }cm{sup −3}, and suppressed at doses ranging from 3 × 10{sup 17} to 1 × 10{sup 18 }cm{sup −3}; cells were inactivated by O({sup 3}P{sub j}) doses exceeding 1 × 10{sup 18 }cm{sup −3}, even when the flux was varied over the above flux range. These results showed that the growth of cells was regulated primarily in response to the total dose of O({sup 3}P{sub j})

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

The chromatin remodeler ADNP regulates neurodevelopmental disorder risk genes and neocortical neurogenesis

Although chromatin remodelers are among the most important risk genes associated with neurodevelopmental disorders (NDDs), the roles of these complexes during brain development are in many cases unclear. Here, we focused on the recently discovered ChAHP chromatin remodeling complex. The zinc finger and homeodomain transcription factor ADNP is a core subunit of this complex, and de novoADNPmutations lead to intellectual disability and autism spectrum disorder. However, germlineAdnpknockout mice were previously shown to exhibit early embryonic lethality, obscuring subsequent roles for the ChAHP complex in neurogenesis. To circumvent this early developmental arrest, we generated a conditionalAdnpmutant allele. Using single-cell transcriptomics, cut&run-seq, and histological approaches, we show that during neocortical development, Adnp orchestrates the production of late-born, upper-layer neurons through a two-step process. First, Adnp is required to sustain progenitor proliferation specifically during the developmental window for upper-layer cortical neurogenesis. Accordingly, we found that Adnp recruits the ChAHP subunit Chd4 to genes associated with progenitor proliferation. Second, in postmitotic differentiated neurons, we define a network of risk genes linked to NDDs that are regulated by Adnp and Chd4. Taken together, these data demonstrate that ChAHP is critical for driving the expansion of upper-layer cortical neurons and for regulating neuronal gene expression programs, suggesting that these processes may potentially contribute to NDD etiology.

Science & Technology - Other Topics↗

Conformation-specific inhibitors of activated Ras GTPases reveal limited Ras dependency of patient-derived cancer organoids

The small GTPases H, K, and NRAS are molecular switches indispensable for proper regulation of cellular proliferation and growth. Several mutations in the genes encoding members of this protein family are associated with cancer and result in aberrant activation of signaling processes caused by a deregulated recruitment of downstream effector proteins. In this study, we engineered variants of the Ras-binding domain (RBD) of the C-Raf proto-oncogene, Ser/Thr kinase (CRAF). These variants bound with high affinity with the effector-binding site of Ras in an active conformation. Structural characterization disclosed how the newly identified RBD mutations cooperate and thereby enhance affinity with the effector-binding site in Ras compared with WT RBD. The engineered RBD variants closely mimicked the interaction mode of naturally occurring Ras effectors and acted as dominant-negative affinity reagents that block Ras signal transduction. We report experiments with cancer cells showed that expression of these RBD variants inhibits Ras signaling, reducing cell growth and inducing apoptosis. Using these optimized RBD variants, we stratified patient-derived colorectal cancer organoids with known Ras mutational status according to their response to Ras inhibition. These results revealed that the presence of Ras mutations was insufficient to predict sensitivity to Ras inhibition, suggesting that not all of these tumors required Ras signaling for proliferation. In summary, by engineering the Ras/Raf interface of the CRAF-RBD, we identified potent and selective inhibitors of Ras in its active conformation that outcompete binding of Ras-signaling effectors.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Where did the tumor start? An inverse solver with sparse localization for tumor growth models

In this work, we present a numerical scheme for solving an inverse problem for parameter estimation in tumor growth models for glioblastomas, a form of aggressive primary brain tumor. The growth model is a reaction–diffusion partial differential equation (PDE) for the tumor concentration. We use a PDE-constrained optimization formulation for the inverse problem. The unknown parameters are the reaction coefficient (proliferation), the diffusion coefficient (infiltration), and the initial condition field for the tumor PDE. Segmentation of magnetic resonance imaging (MRI) scans drive the inverse problem where segmented tumor regions serve as partial observations of the tumor concentration. Like most cases in clinical practice, we use data from a single time snapshot. Moreover, the precise time relative to the initiation of the tumor is unknown, which poses an additional difficulty for inversion. We perform a frozen-coefficient spectral analysis and show that the inverse problem is severely ill-posed. We introduce a biophysically motivated regularization on the structure and magnitude of the tumor initial condition. In particular, we assume that the tumor starts at a few locations (enforced with a sparsity constraint on the initial condition of the tumor) and that the initial condition magnitude in the maximum norm is equal to one. We solve the resulting optimization problem using an inexact quasi-Newton method combined with a compressive sampling algorithm for the sparsity constraint. Our implementation uses PETSc and AccFFT libraries. We conduct numerical experiments on synthetic and clinical images to highlight the improved performance of our solver over a previously existing solver that uses standard two-norm regularization for the calibration parameters. The existing solver is unable to localize the initial condition. Our new solver can localize the initial condition and recover infiltration and proliferation. In clinical datasets (for which the ground truth is unknown), our solver results in qualitatively different solutions compared to the two-norm regularized solver.

97 MATHEMATICS AND COMPUTING↗

In situ tumor model for longitudinal in silico imaging trials

Abstract Objective.In this article, we introduce a computational model for simulating the growth of breast cancer lesions accounting for the stiffness of surrounding anatomical structures.Approach.In our model, ligaments are classified as the most rigid structures while the softer parts of the breast are occupied by fat and glandular tissues As a result of these variations in tissue elasticity, the rapidly proliferating tumor cells are met with differential resistance. It is found that these cells are likely to circumvent stiffer terrains such as ligaments, instead electing to proliferate preferentially within the more yielding confines of the breast’s soft topography. By manipulating the interstitial tumor pressure in direct proportion to the elastic constants of the tissues surrounding the tumor, this model thus creates the potential for realizing a database of unique lesion morphology sculpted by the distinctive topography of each local anatomical infrastructure. We modeled the growth of simulated lesions within volumes extracted from fatty breast models, developed by Graffet alwith a resolution of 50μm generated with the open-source and readily available Virtual Imaging Clinical Trials for Regulatory Evaluation (VICTRE) imaging pipeline. To visualize and validate the realism of the lesion models, we leveraged the imaging component of the VICTRE pipeline, which replicates the siemens mammomat inspiration mammography system in a digital format. This system was instrumental in generating digital mammogram (DM) images for each breast model containing the simulated lesions.Results.By utilizing the DM images, we were able to effectively illustrate the imaging characteristics of the lesions as they integrated with the anatomical backgrounds. Our research also involved a reader study that compared 25 simulated DM regions of interest (ROIs) with inserted lesions from our models with DM ROIs from the DDSM dataset containing real manifestations of breast cancer. In general the simulation time for the lesions was approximately 2.5 hours, but it varied depending on the lesion’s local environment.Significance.The lesion growth model will facilitate and enhance longitudinal in silico trials investigating the progression of breast cancer.

Engineering↗

Melting, reentrant ordering and peak effect for Wigner crystals with quenched and thermal disorder

Abstract We consider simulations of Wigner crystals in solid state systems interacting with random quenched disorder in the presence of thermal fluctuations. When quenched disorder is absent, there is a well defined melting temperature determined by the proliferation of topological defects, while for zero temperature, there is a critical quenched disorder strength above which topological defects proliferate. When both thermal and quenched disorder are present, these effects compete, and the thermal fluctuations can reduce the effectiveness of the quenched disorder, leading to a reentrant ordered phase in agreement with the predictions of Nelson (1983 Phys. Rev. B 27 2902–14). There are two competing theories for the low temperature behavior, and our simulations show that both capture aspects of the actual response. The critical disorder strength separating ordered from disordered states remains finite as the temperature goes to zero, as predicted by Cha and Fertig (1995 Phys. Rev. Lett. 74 4867–70), instead of dropping to zero as predicted by Nelson. At the same time, the critical disorder strength decreases with decreasing temperature, as predicted by Nelson, instead of remaining constant, as predicted by Cha and Fertig. The onset of the reentrant phase can be deduced based on changes in the transport response, where the reentrant ordering appears as an increase in the mobility or the occurrence of a depinning transition. We also find that when the system is in the ordered state and thermally melts, there is an increase in the effective damping or pinning. This produces a drop in the electron mobility that is similar to the peak effect phenomenon found in superconducting vortices, where thermal effects soften the lattice or break down its elasticity, allowing the particles to better adjust their positions to take full advantage of the quenched disorder.

36 MATERIALS SCIENCE↗

Germanium Detectors in Homeland Security at PNNL

Neutron and gamma-ray detection is used for non-proliferation and national security applications. While lower energy resolution detectors such as NaI(Tl) have their place, high purity germanium (HPGe) also has a role to play. A detection with HPGe is often a characterization due to the very high energy resolution. However, HPGe crystals remain small and expensive leaving arrays of smaller crystals as an excellent solution. PNNL has developed two similar HPGe arrays for two very different applications. One array, the Multisensor Aerial Radiation Survey (MARS) detector is a fieldable array that has been tested on trucks, boats, and helicopters. The CASCADES HPGe array is an array designed to assay samples in a low background environment. The history of HPGe arrays at PNNL and the development of MARS and CASCADES will be detailed in this paper along with some of the other applications of HPGe at PNNL.

arrays↗

Increased SUMOylation of TCF21 improves its stability and function in human endometriotic stromal cells

Abstract Endometriosis is an estrogen-dependent disease. Our previous study demonstrated that elevated levels of transcription factor 21 (TCF21) in endometriotic tissues enhanced steroidogenic factor-1 (SF-1) and estrogen receptor β (ERβ) expression by forming a heterodimer with upstream stimulatory factor 2 (USF2), allowing these TCF21/USF2 complexes to bind to the promoters of SF-1 and ERβ. Furthermore, TCF21 contributed to the increased proliferation of endometriotic stromal cells (ESCs), suggesting that TCF21 may play a vital role in the pathogenesis of endometriosis. SUMOylation is a posttranslational modification that has emerged as a crucial molecular regulatory mechanism. However, the mechanism regulating TCF21 SUMOylation in endometriosis is incompletely characterized. Thus, this study aimed to explore the effect of TCF21 SUMOylation on its expression and regulation in ovarian endometriosis. We found that the levels of SUMOylated TCF21 were increased in endometriotic tissues and stromal cells compared with eutopic endometrial tissues and stromal cells and enhanced by estrogen. Treatment with the SUMOylation inhibitor ginkgolic acid (GA) and the results of a protein half-life assay demonstrated that SUMOylation can stabilize the TCF21 protein. A coimmunoprecipitation (Co-IP) assay showed that SUMOylation probably increased its interaction with USF2. Further analyses elucidated that SUMOylation of TCF21 significantly increased the binding activity of USF2 to the SF-1 and ERβ promoters. Moreover, the SUMOylation motifs in TCF21 affected the proliferation ability of ESCs. The results of this study suggest that SUMOylation plays a critical role in mediating the high expression of TCF21 in ESCs and may participate in the development of endometriosis.

Zhu, Jingwen↗

MiR-144 overexpression as a promising therapeutic strategy to overcome glioblastoma cell invasiveness and resistance to chemotherapy

Abstract Glioblastoma (GB) is the most aggressive and common form of primary brain tumor, characterized by fast proliferation, high invasion, and resistance to current standard treatment. The average survival rate post-diagnosis is only of 14.6 months, despite the aggressive standard post-surgery treatment approaches of radiotherapy concomitant with chemotherapy with temozolomide. Altered cell metabolism has been identified as an emerging cancer hallmark, including in GB, thus offering a new target for cancer therapies. On the other hand, abnormal expression levels of miRNAs, key regulators of multiple molecular pathways, have been correlated with pathological manifestations of cancer, such as chemoresistance, proliferation, and resistance to apoptosis. In this work, we hypothesized that gene therapy based on modulation of a miRNA with aberrant expression in GB and predicted to target crucial metabolic enzymes might impair tumor cell metabolism. We found that the increase of miR-144 levels, shown to be downregulated in U87 and DBTRG human GB cell lines, as well as in GB tumor samples, promoted the downregulation of mRNA of enzymes involved in bioenergetic pathways, with consequent alterations in cell metabolism, impairment of migratory capacity, and sensitization of DBTRG cells to a chemotherapeutic drug, the dichloroacetate (DCA). Taken together, our findings provide evidence that the miR-144 plus DCA combined therapy holds promise to overcome GB-acquired chemoresistance, therefore deserving to be explored toward its potential application as a complementary therapeutic approach to the current treatment options for this type of brain tumor.

Cardoso, Ana M. S.↗

Repeated exposure to eucalyptus wood smoke alters pulmonary gene and metabolic profiles in male Long-Evans rats

Abstract Exposure to wildfire smoke is associated with both acute and chronic cardiopulmonary illnesses, which are of special concern for wildland firefighters who experience repeated exposure to wood smoke. It is necessary to better understand the underlying pathophysiology by which wood smoke exposure increases pulmonary disease burdens in this population. We hypothesize that wood smoke exposure produces pulmonary dysfunction, lung inflammation, and gene expression profiles associated with future pulmonary complications. Male Long-Evans rats were intermittently exposed to smoldering eucalyptus wood smoke at 2 concentrations, low (11.0 ± 1.89 mg/m3) and high (23.7 ± 0.077 mg/m3), over a 2-week period. Whole-body plethysmography was measured intermittently throughout. Lung tissue and lavage fluid were collected 24 h after the final exposure for transcriptomics and metabolomics. Increasing smoke exposure upregulated neutrophils and select cytokines in the bronchoalveolar lavage fluid. In total, 3446 genes were differentially expressed in the lungs of rats in the high smoke exposure and only 1 gene in the low smoke exposure (Cd151). Genes altered in the high smoke group reflected changes to the Eukaryotic Initiation Factor 2 stress and oxidative stress responses, which mirrored metabolomics analyses. xMWAS-integrated analysis revealed that smoke exposure significantly altered pathways associated with oxidative stress, lung morphogenesis, and tumor proliferation pathways. These results indicate that intermittent, 2-week exposure to eucalyptus wood smoke leads to transcriptomic and metabolic changes in the lung that may predict future lung disease development. Collectively, these findings provide insight into cellular signaling pathways that may contribute to the chronic pulmonary conditions observed in wildland firefighters.

Toxicology↗