CD44 Expression in Clear Cell Renal Cell Carcinoma (ccRCC) Correlates with Tumor Grade and Patient Survival and Is Affected by Gene Methylation.

Clear cell RCC (ccRCC) represents the most common type of kidney cancer, with surgery being the only potential curative treatment. Almost one-third of ccRCC patients relapse either locally or as cases of distant metastases. Several biomarkers have been employed in order to separate ccRCC patients with better prognosis or to predict treatment outcomes, with limited results. CD44 is a membrane glycoprotein with multiple roles in normal development but also cancer. Recently, the CD44 standard isoform has been implicated in tumor progression and the metastasis cascade through microenvironment interactions. Here, through CD44 immunohistochemical staining of ccRCC patient samples and TCGA data analysis, we sought to elucidate the expression patterns (mRNA and protein) of CD44 in clear cell RCC and correlate its expression with clinicopathological parameters. We were able to show that CD44 expression presents a positive association with tumor grade and overall survival, predicting a worse patient outcome in ccRCC. In addition, our data indicate that the CD44 mRNA upregulation can be attributed to reduced gene methylation, implicating epigenetic gene regulation in ccRCC development and progression.

Analysis of RANK-c interaction partners identifies TRAF3 as a critical regulator of breast cancer aggressiveness.

Breast cancer is a highly heterogeneous disease both at the histological and molecular levels. We have previously shown that RANK-c is a regulator of NF-κB signaling and exerts a suppressive effect on aggressive properties of ER negative breast cancer cells, while there is an opposite effect on ER positive cell lines. In order to identify molecular determinants that govern the opposing function of RANK-c in breast cancer cells we employed the two cell lines with the highest degree of phenotypic divergence upon RANK-c-expression (SKBR3 and BT474) and identified proteins that interact with RANK-c by affinity-enrichment mass spectrometry (AE-MS) analysis. Annotating enriched proteins with NF-κB signaling pathway revealed TRAF3 as an interacting partner of RANK-c in SKBR3 cell protein lysates, but not in BT474 breast cancer cells in which RANK-c induces cell aggressiveness. To determine the role of TRAF3 in the phenotype of BT474-RANK-c cells, we reconstructed the TRAF3/RANK-c interaction both in parental BT474 and RANK-c expressing cells and tested for aggressive properties through colony formation, migration and invasion assays. TRAF3 forced expression was able to reverse BT474 phenotypic changes imposed by RANK-c, rendering cells less aggressive. Finally, TRAF3 gene expression data and TRAF3 immunohistochemical (IHC) analysis on breast cancer samples indicated that TRAF3 expression correlates with Overall Survival (OS), Recurrence Free Survival (RFS) and several clinicopathological parameters (histological grade, proliferation index) of breast cancer disease.

Coarse-Grained Model Incorporating Short- and Long-Range Effective Potentials for the Fast Simulation of Micelle Formation in Solutions of Ionic Surfactants.

A coarse-grained model comprising short- and long-range effective potentials, parametrized with the iterative Boltzmann inversion (IBI) method, is presented for capturing micelle formation in aqueous solutions of ionic surfactants using as a model system sodium dodecyl sulfate (SDS). In the coarse-grained (CG) model, each SDS molecule is represented as a sequence of four beads while each water molecule is modeled as a single bead. The proposed CG scheme involves ten potential energy functions: four of them describe bonded interactions and control the distribution functions of intramolecular degrees of freedom (bond lengths, valence angles, and dihedrals) along an SDS molecule while the other six account for intermolecular interactions between pairs of SDS and water beads and control the radial distribution functions. The nonbonded effective potentials between coarse-grained SDS molecules extend up to about 12 nm and capture structural and morphological features of the micellar solution both at short and long distances. The long-range component of these potentials, in particular, captures correlations between surfactant molecules belonging to different micelles and is essential to describe ordering associated with micelle formation. A new strategy is introduced for determining the effective potentials through IBI by using information (target distribution functions) extracted from independent atomistic simulations of a micellar reference system (a salt-free SDS solution at total surfactant concentration cT equal to 103 mM, temperature T equal to 300 K, and pressure P equal to 1 atm) obtained through a multiscale approach described in an earlier study. It employs several optimization steps for bonded and nonbonded interactions and a gradual parametrization of the short- and long-range components of the latter, followed by reparametrization of the bonded ones. The proposed CG model can reproduce remarkably accurately the microstructure and morphology of the reference system within only a few hours of computational time. It is therefore very promising for future studies of structural and morphological behavior of various liquid surfactant formulations.

Cellular Senescence in Normal Mammary Gland and Breast Cancer. Implications for Cancer Therapy.

Cellular senescence (CS) is a major homeostatic biological process, which plays a key role in normal tissue development and provides protection from stressful cell insults. The role of CS in mammary-gland development and breast cancer is not well understood. While there is a lack of experimental data on the role of CS in the development of the pre-pubertal mammary gland, there is evidence for a biphasic senescence response in adult normal-mammary-epithelial cells, where the bypass of the first senescence barrier (M0) seems to be a key step in the development of premalignant lesions, with genetic abnormalities that resemble in situ breast carcinoma. Further, there is accumulating evidence for the role of cellular senescence in breast-cancer response, regarding treatment and patient outcome. Here, we review the current literature on cellular senescence, in epithelial-mammary cells, breast-cancer cells, and breast-tumor-microenvironment-resident cells. Furthermore, we discuss its putative role in breast-cancer response, regarding treatment and disease progression. In addition, we provide preliminary evidence of CS in breast-cancer-microenvironment cells, such as tumor-associated fibroblasts and tumor-infiltrating lymphocytes, by employing the novel GL13 lipofuscin stain, as a marker of cellular senescence.

The phase behaviour of cetyltrimethylammonium chloride surfactant aqueous solutions at high concentrations: an all-atom molecular dynamics simulation study.

We explore the phase behaviour of aqueous solutions of the cetyltrimethyl ammonium chloride (CTAC) surfactant and in particular the transition from the micellar phase (L1) to the hexagonal columnar phase (H1) by employing all-atom (AA) molecular dynamics (MD) simulations for six CTAC concentrations in the range of 34.1 wt% to 70.5 wt%, at the temperature of 318 K and pressure of 1 atm. For the concentrations considered, we examine the spontaneous occurrence of the H1 phase by testing a number of plausible values for the linear density (molecules per unit length) along the cylindrical columns. Using large simulation cells and starting from random initial configurations, the MD simulations demonstrate that the micellar phase occurs for concentrations up to 50.0 wt%, with CTAC molecules self-assembling into a mixture of spherical and rod-like micelles. At even higher concentrations, the system self-organizes into the H1 phase in accordance with the available experimental data. For the analysis of the MD trajectories, we devise a clustering algorithm based on Voronoi tesselation which enables (a) the thorough characterization of the shape and structure of both molecules and assemblies, and (b) the investigation of the positional and orientational order in the system that are further scrutinised using radial pair correlation functions and X-ray diffraction patterns. Our work paves the way for the investigation of the phase behaviour at high concentrations of other surfactants.

Field-induced anti-nematic and biaxial ordering in binary mixtures of discotic mesogens and spherical magnetic nanoparticles.

Using computer simulations we explore the equilibrium structure and response to external stimuli of complex magnetic hybrids consisting of magnetic particles in discotic liquid crystalline matrices. We show that the anisotropy of the liquid crystalline matrix (either in the nematic or in the columnar phase) promotes the collective orientational ordering of self-assembled magnetic particles. Upon applying an external homogeneous magnetic field in an otherwise isotropic state, the magnetic particles self-assemble into linear-rodlike-chains. At the same time structural changes occur in the matrix. The matrix transforms from an isotropic to a non-conventional anti-nematic state in which the symmetry axis of the discs is, on average, perpendicular to the magnetic field. In addition, a stable biaxial nematic state is found upon applying an external field to an otherwise uniaxial discotic nematic state. These observed morphologies constitute an appealing alternative to binary mixtures of rigid rod-disc system and indicate that non-trivial biaxial ordering can be obtained in the presence of a uniaxial external stimulus.

Quantitative Prediction of the Structure and Viscosity of Aqueous Micellar Solutions of Ionic Surfactants: A Combined Approach Based on Coarse-Grained MARTINI Simulations Followed by Reverse-Mapped All-Atom Molecular Dynamics Simulations.

We address the problem of the quantitative prediction of micelle formation in dilute aqueous solutions of ionic surfactants using sodium dodecyl sulfate (SDS) as a model system through a computational approach that involves three steps: (a) execution of coarse-grained simulations based on the MARTINI force field (with slightly modified parameters to afford the formation of large micelles); (b) reverse mapping of the final self-assembled coarse-grained configuration into an all-atom configuration; and (c) final relaxation of this all-atom configuration through short-time (on the order of a few tens of nanoseconds), detailed isothermal-isobaric molecular dynamics simulations using the CHARMM36 force field. For a given concentration of the solution in SDS molecules, the modified MARTINI-based coarse-grained simulations lead to the formation of large micelles characterized by mean aggregation numbers above the experimentally observed ones. However, by reintroducing the detailed chemical structure through a strategy that solves a well-defined geometric problem and re-equilibrating, these large micellar aggregates quickly dissolve to smaller ones and equilibrate to sizes that perfectly match the average micelle size measured experimentally at the given surfactant concentration. From the all-atom molecular dynamics simulations, we also deduce the surfactant diffusivity DSDS and the zero-shear rate viscosity, η0, of the solution, which are observed to compare very favorably with the few experimental values that we were able to find in the literature.

Molecular simulation of the high temperature phase behaviour of α-unsubstituted sexithiophene.

We examine the high-temperature phase behaviour of α-unsubstituted sexithiophene (α-6T) by means of Molecular Dynamics (MD) and Monte Carlo (MC) simulations using a recently developed state-of-the-art algorithm based on internal bridging moves. In the MD simulations, a realistic fully flexible united-atom model is used. In the MC simulations, a stiffer version of this united-atom model is implemented by restricting atoms on thiophene rings to remain strictly co-planar by employing holonomic constraints for all bond lengths and intra-ring bond bending angles; on the other hand, inter-ring torsion and bond bending angles are considered to be fully flexible subject to suitable potential energy functions. The MD simulations, which are started from the isotropic (Iso) phase at a relatively high temperature (above 700 K) and continued to lower temperatures under isobaric conditions using a very large simulation cell containing 8960 α-6T molecules, show four phase transitions: an isotropic-to-nematic (Iso-to-Nem) at 640 K, a nematic-to-smectic A (Nem-to-SmA) at 630 K, a smectic A-to-smectic C (SmA-to-SmC) at 620 K demonstrating smectic polymorphism, and a SmC-to-crystal-like (SmC-to-Cry) at 600 K. In the corresponding MC simulations, no Nem phase is observed; the system, as it is isobarically cooled down to lower temperatures from its Iso phase, undergoes directly a transition to a SmC phase at 690 K. This is attributed to the stiffer nature of the forcefield employed in these simulations. Both methods (MD and MC) shed light on the type and degree of molecular self-assembly, orientational and positional ordering as a function of temperature, and manifestation of liquid crystalline behaviour of α-6T. We provide a thorough characterization of structural ordering in all mesophases observed, in terms of several measures (radial correlation functions, orientational order parameters and X-ray diffraction patterns). According to the results, at the phase transition temperatures, drastic configurational changes take place driving α-6T molecules to positionally-ordered phases accompanied by self-assembly into characteristic layers which, in turn, are self-organized into macroscopic smectic phases. Our methodology opens up the way to exploring the rich phase behaviour and anisotropic ordering of the condensed phases of several longer (and perhaps more complex) thiophene-based polymers.

Orientational order and translational dynamics of magnetic particle assemblies in liquid crystals.

Implementing extensive molecular dynamics simulations we explore the organization of magnetic particle assemblies (clusters) in a uniaxial liquid crystalline matrix comprised of rodlike particles. The magnetic particles are modelled as soft dipolar spheres with diameter significantly smaller than the width of the rods. Depending on the dipolar strength coupling the magnetic particles arrange into head-to-tail configurations forming various types of clusters including rings (closed loops) and chains. In turn, the liquid crystalline matrix induces long range orientational ordering to these structures and promotes their diffusion along the director of the phase. Different translational dynamics are exhibited as the liquid crystalline matrix transforms either from isotropic to nematic or from nematic to smectic state. This is caused due to different collective motion of the magnetic particles into various clusters in the anisotropic environments. Our results offer a physical insight for understanding both the structure and dynamics of magnetic particle assemblies in liquid crystalline matrices.

Colloidal Suspensions of Rodlike Nanocrystals and Magnetic Spheres under an External Magnetic Stimulus: Experiment and Molecular Dynamics Simulation.

Using experiments and molecular dynamics simulations, we explore magnetic field-induced phase transformations in suspensions of nonmagnetic rodlike and magnetic sphere-shaped particles. We experimentally demonstrate that an external uniform magnetic field causes the formation of small, stable clusters of magnetic particles that, in turn, induce and control the orientational order of the nonmagnetic subphase. Optical birefringence was studied as a function of the magnetic field and the volume fractions of each particle type. Steric transfer of the orientational order was investigated by molecular dynamics (MD) simulations; the results are in qualitative agreement with the experimental observations. By reproducing the general experimental trends, the MD simulation offers a cohesive bottom-up interpretation of the physical behavior of such systems, and it can also be regarded as a guide for further experimental research.

Treatment of relapsed urothelial bladder cancer with vinflunine: real-world evidence by the Hellenic Genitourinary Cancer Group.

Relapsed urothelial cancer represents an unmet medical need. Vinflunine is a third-generation antimicrotubuline inhibitor and is currently the only approved drug for second-line treatment across the European Union. We conducted a retrospective analysis assessing the efficacy and safety of vinflunine in 71 Greek patients with relapsed urothelial cancer who were treated between 2005 and 2014. An overall 84% of our patients received vinflunine as second-line treatment, 77% had a performance status of Eastern Cooperative Oncology Group scale 0 or 1, and 30% had liver metastasis at the time of vinflunine administration. A median of four cycles of vinflunine were administered (range 1-16). The most common reported adverse events were constipation, fatigue, and anemia. Median progression-free survival was 6.2 months (95% confidence interval: 4.4-8.8) and overall survival was 11.9 months (95% confidence interval: 7.4-21). Two patients (3%) achieved a complete remission, seven a partial remission (10%), and 22 (31%) had stable disease according to an intention-to-treat analysis. Hemoglobin level less than 10 g/dl and Eastern Cooperative Oncology Group performance status greater than 1 were independent adverse prognostic factors. Stratification according to the Bellmunt risk model was also associated with progression-free survival and overall survival in our population. Vinflunine appears to be a safe and effective treatment modality for relapsed urothelial cancer. More effective therapies and more accurate prognostic algorithms should be sought.

Utilization of Systemic Chemotherapy in Advanced Urothelial Cancer: A Retrospective Collaborative Study by the Hellenic Genitourinary Cancer Group (HGUCG).

BACKGROUND: Advanced urothelial cancer (AUCa) is associated with poor long-term survival. Two major concerns are related to nonexposure to cisplatin-based chemotherapy and poor outcome after relapse. Our purpose was to record patterns of practice in AUCa in Greece, focusing on first-line treatment and management of relapsed disease. METHODS: Patients with AUCa treated from 2011 to 2013 were included in the analysis. Fitness for cisplatin was assessed by recently established criteria. RESULTS: Of 327 patients treated with first-line chemotherapy, 179 (55%) did not receive cisplatin. Criteria for unfitness for cisplatin were: Eastern Cooperative Oncology Group (ECOG) performance status (PS) ≥ 2, 21%; creatinine clearance ≤ 60 mL/min, 55%; hearing impairment, 8%; neuropathy, 1%; and cardiac failure, 5%. Forty-six patients (27%) did not fulfill any criterion for unfitness for cisplatin. The main reasons for these deviations were comorbidities (28%) and advanced age (32%). Seventy-four (68%) of 109 patients who experienced a relapse received second-line chemotherapy. The most frequent reason for not offering second-line chemotherapy was poor PS or limited life expectancy (66%). CONCLUSION: In line with international data, approximately 50% of Greek patients with AUCa do not receive cisplatin-based chemotherapy, although 27% of them were suitable for such treatment. In addition, about one third of patients with relapse did not receive second-line chemotherapy because of poor PS or short life expectancy. Enforcing criteria for fitness for cisplatin and earlier diagnosis of relapse represent 2 targets for improvement in current treatment practice for AUCa.

Spontaneous ordering of magnetic particles in liquid crystals: From chains to biaxial lamellae.

Using Monte Carlo computer simulations we explore the self-assembly and ordering behavior of a hybrid, soft magnetic system consisting of small magnetic nanospheres in a liquid-crystalline (LC) matrix. Inspired by recent experiments with colloidal rod matrices, we focus on conditions where the sphere and rod diameters are comparable. Already in the absence of a magnetic field, the nematic ordering of the LC can stabilize the formation of magnetic chains along the nematic or smectic director, yielding a state with local (yet no macroscopic) magnetic order. The chains, in turn, increase the overall nematic order, reflecting the complex interplay of the structure formation of the two components. When increasing the sphere diameter, the spontaneous uniaxial ordering is replaced by biaxial lamellar morphologies characterized by alternating layers of rods and magnetic chains oriented perpendicular to the rod's director. These ordering scenarios at zero field suggest a complex response of the resulting hybrid to external stimuli, such as magnetic fields and shear forces.

Molecular simulation study of polar order in orthogonal bent-core smectic liquid crystals.

We explore the phase behavior and structure of orthogonal smectic liquid crystals consisting of bent-core molecules (BCMs) by means of Monte Carlo molecular simulations. A simple athermal molecular model is introduced that describes the basic features of the BCMs. Phase transitions between uniaxial and biaxial (antiferroelectric) orthogonal smectics are obtained. The results indicate the presence of local in-plane polar correlations in the uniaxial smectic phase. The macroscopic uniaxial-biaxial transformation is rationalized in terms of local polar correlations giving rise to polar domains. The size of these polar domains grows larger under the action of an external vector field and their internal ordering is enhanced, leading to field-induced biaxial order-disorder transitions.

Tunable structures of mixtures of magnetic particles in liquid-crystalline matrices.

We investigate the self-organization of a binary mixture of similar sized rods and dipolar soft spheres by means of Monte-Carlo simulations. We model interparticle interactions by employing anisotropic Gay-Berne, dipolar and soft-sphere interactions. In the limit of vanishing magnetic moments we obtain a variety of fully miscible liquid crystalline phases including nematic, smectic and lamellar phases. For the magnetic mixture, we find that the liquid crystalline matrix supports the formation of orientationally ordered ferromagnetic chains. Depending on the relative size of the species the chains align parallel or perpendicular to the director of the rods forming uniaxial or biaxial nematic, smectic and lamellar phases. As an exemplary external perturbation we apply a homogeneous magnetic field causing uniaxial or biaxial ordering to an otherwise isotropic state.

Ulcerative colitis six years after colon cancer: only a coincidence?

The association between inflammatory bowel disease and colorectal cancer is well known. Ulcerative colitis is a risk factor for the development of colorectal cancer, and this risk increases with the activity and duration of bowel inflammation. Here we describe the case of a 52-year-old man who developed ulcerative colitis 6 years after the diagnosis and treatment of colon cancer. Although this could be a coincidence, there could be additional possibilities, like pre-existence of quiescent colitis, late effect of therapy, or maybe the existence of common pathogenetic factors contributing to the development of ulcerative colitis and colorectal cancer.

Biaxial mesophase behavior of amphiphilic anisometric colloids: a simulation study.

The phase behavior of amphiphilic anisometric particles is explored using Monte Carlo simulations. The particles are composed of two incompatible laterally attached units: a spherocylinder and a spheroplatelet. A liquid crystalline phase polymorphism is obtained including biaxial nematic, (quasi long range biaxial) calamitic smectic-A, biaxial lamellar and columnar phases. The simulation results demonstrate intriguing phase transitions such as nematic-nematic, discotic nematic to (quasi long range biaxial) calamitic smectic-A, biaxial nematic to uniaxial calamitic smectic-A, and isotropic or discotic nematic to biaxial lamellar phases that possess nematic ordering within the layers. These findings are rationalized in terms of molecular geometry and amphiphilicity of different molecular units. The molecular model can be used as a tool for the prediction of the complex phase behavior that is relevant to liquid crystalline colloids.

Supramolecular nature of the nematic-nematic phase transitions of hard boardlike molecules.

The phase behavior of hard boardlike biaxial particles of relative dimensions close to the clamitic to discotic crossover is explored by means of Monte Carlo molecular simulations. Transitions between two distinct biaxial nematic phases as well as transitions from a biaxial nematic to a uniaxial Sm-A phase are obtained. The formation of anisotropic supramolecular assemblies is demonstrated and is quantified by means of rotationally invariant pair correlation functions.

Molecular simulation of hierarchical structures in bent-core nematic liquid crystals.

The structure of nematic liquid crystals formed by bent-core mesogens (BCMs) is studied in the context of Monte Carlo simulations of a simple molecular model that captures the symmetry, shape, and flexibility of achiral BCMs. The results indicate the formation of (i) clusters exhibiting local smectic order, orthogonal or tilted, with strong in-layer polar correlations and antiferroelectric juxtaposition of successive layers and (ii) large homochiral domains through the helical arrangement of the tilted smectic clusters, while the orthogonal clusters produce achiral (untwisted) nematic states.

Molecular modeling of liquid crystalline self-organization of fullerodendrimers: columnar to lamellar phase transitions driven by temperature and/or concentration changes.

The molecular cubic-block model [ J. Chem. Phys. 2005, 123, 164904 ] is used to study a class of poly(benzyl ether) fullerodendrimers that have recently been reported to form columnar liquid crystal phases. In agreement with experiment, the model-molecules are found to self-assemble into columns which form hexagonal or rectangular lattices. The columnar cross sections are elongated in the rectangular phase. Transitions to the isotropic phase, either directly or through the intermediate formation of smectic phases, have been found. The effects of dissolving small amounts of nonbonded fullerene molecules have been explored. The results predict that the fullerene solutes restrict the range of stability of the columnar phase and may induce transitions from the columnar to the smectic or the isotropic phase.