Detection of activating estrogen receptor gene (ESR1) mutations in single circulating tumor cells

Purpose: Early detection is essential for treatment plans before onset of metastatic disease. Our purpose was to demonstrate feasibility to detect and monitor estrogen receptor 1 (ESR1) gene mutations at the single circulating tumor cell (CTC) level in metastatic breast cancer (MBC). Experimental Design: We used a CTC molecular characterization approach to investigate heterogeneity of 14 hotspot mutations in ESR1 and their correlation with endocrine resistance. Combining the CellSearch and DEPArray technologies allowed recovery of 71 single CTCs and 12 WBC from 3 ER-positive MBC patients. Forty CTCs and 12 WBC were subjected to whole genome amplification by MALBAC and Sanger sequencing. Results: Among 3 selected patients, 2 had an ESR1 mutation (Y537). One showed two different ESR1 variants in a single CTC and another showed loss of heterozygosity. All mutations were detected in matched cell-free DNA (cfDNA). Furthermore, one had 2 serial blood samples analyzed and showed changes in both cfDNA and CTCs with emergence of mutations in ESR1 (Y537S and T570I), which has not been reported previously. Conclusions: CTCs are easily accessible biomarkers to monitor and better personalize management of patients with previously demonstrated ER-MBC who are progressing on endocrine therapy. We showed that single CTC analysis can yield important information on clonal heterogeneity and can be a source of discovery of novel and potential driver mutations. Finally, we also validate a workflow for liquid biopsy that will facilitate early detection of ESR1 mutations, the emergence of endocrine resistance and the choice of further target therapy. ©2017 AACR

Cellular Structures of Carbon Nanotubes in a Polymer Matrix Improve Properties Relative to Composites with Dispersed Nanotubes

A new processing method has been developed to combine a polymer and single wall carbon nanotubes (SWCNTs) to form electrically conductive composites with desirable rheological and mechanical properties. The process involves coating polystyrene (PS) pellets with SWCNTs and then hot pressing to make a contiguous, cellular SWCNT structure. By this method, the electrical percolation threshold decreases and the electrical conductivity increases significantly as compared to composites with a well-dispersed SWCNTs. For example, a SWCNT / PS composite with 0.5 wt% nanotubes and made by this coated particle process (CPP) has an electrical conductivity of ~ 3 x 10-4 S/cm, while a well-dispersed composite made by a coagulation method with the same SWCNT amount has an electrical conductivity of only ~ 10-8 S/cm. The rheological properties of the composite with a macroscopic cellular SWCNT structure are comparable to PS, while the well-dispersed composite exhibits a solid-like behavior, indicating that composites made by this new CPP method are more processable. In addition, the mechanical properties of the CPP-made composite decrease only slightly, as compared with PS. Relative to the common appoach of seeking better dispersion, this new fabrication method provides an important alternative means to higher electrical conductivity in SWCNT / polymer composites. Our straightforward particle coating and pressing method avoids organic solvents and is suitable for large-scale, inexpensive processing using a wide variety of polymer and nanoparticles

Temperature Dependence of Thermal Conductivity Enhancement in Single-walled Carbon Nanotube/polystyrene Composites

The thermal conductivity of single-walled carbon nanotube (SWCNT)/polystyrene composites, prepared by a method known to produce a uniform distribution of SWCNT bundles on the micrometer length scale, was measured in the temperature range from approximately 140 to 360 K. The thermal conductivity enhancement (50% for 1 mass % at 300 K) is reasonably constant above room temperature but is reduced at the lower temperatures. This result is consistent with the expected, large contribution of interfacial thermal resistance in SWCNT/polymer composites. Enhancements in electrical conductivity show that 1 mass % loading is in the region of the electrical percolation threshold

Simulations and electrical conductivity of percolated networks of finite rods with various degrees of axial alignment

We present a three-dimensional simulation and calculation of electrical conductivity above the filler percolation threshold for networks containing finite, conductive cylinders as a function of axial orientation (S) and aspect ratio (L/D). At a fixed volume fraction and L/D, the simulations exhibit a critical degree of orientation, S-c, above which the electrical conductivity decreases dramatically. With increasing filler concentration and aspect ratio, this critical orientation shifts to higher degrees of alignment. Additionally, at a fixed volume fraction and L/D, the simulated electrical conductivity displays a maximum at slight uniaxial orientation, which is less pronounced at higher volume fractions and aspect ratios. Our approach can be used as a predictive tool to design the optimal filler concentration and degree of orientation required to maximize electrical conductivity in polymer nanocomposites with conductive cylindrical fillers of finite dimension

GeoPCA: a new tool for multivariate analysis of dihedral angles based on principal component geodesics

The GeoPCA package is the first tool developed for multivariate analysis of dihedral angles based on principal component geodesics. Principal component geodesic analysis provides a natural generalization of principal component analysis for data distributed in non-Euclidean space, as in the case of angular data. GeoPCA presents projection of angular data on a sphere composed of the first two principal component geodesics, allowing clustering based on dihedral angles as opposed to Cartesian coordinates. It also provides a measure of the similarity between input structures based on only dihedral angles, in analogy to the root-mean-square deviation of atoms based on Cartesian coordinates. The principal component geodesic approach is shown herein to reproduce clusters of nucleotides observed in an η–θ plot. GeoPCA can be accessed via http://pca.limlab.ibms.sinica.edu.tw

A Survey of Machine Learning Approaches Applied to Gene Expression Analysis for Cancer Prediction

Machine learning approaches are powerful techniques commonly employed for developing cancer prediction models using associated gene expression and mutation data. Our survey provides a comprehensive review of recent cancer studies that have employed gene expression data from several cancer types (breast, lung, kidney, ovarian, liver, central nervous system and gallbladder) for survival prediction,tumor identification and stratification. We also provide an overview of biomarker studies that are associated with these cancer types. The survey captures multiple aspects of machine learning associated cancer studies,including cancer classification, cancer prediction, identification of biomarker genes, microarray, and RNA-Seq data.We discuss the technical issues with current cancer prediction models and the corresponding measurement tools for determining the activity levels of gene expression between cancerous tissues and noncancerous tissues. Additionally, we investigate how identifying putative biomarker gene expression patterns can aid in predicting future risk of cancer and inform the provision of personalized treatment

Relationship Between Dispersion Metric and Properties of PMMA/SWNT Nanocomposites

Particle spatial dispersion is a crucial characteristic of polymer composite materials and this property is recognized as especially important in nanocomposite materials due to the general tendency of nanoparticles to aggregate under processing conditions. We introduce dispersion metrics along with a specified dispersion scale over which material homogeneity is measured and consider how the dispersion metrics correlate quantitatively with the variation of basic nanocomposite properties. We then address the general problem of quantifying nanoparticle spatial dispersion in model nanocomposites of single wall carbon nanotubes (SWNT) dispersed in poly(methyl methacrylate) (PMMA) at a fixed SWNT concentration of 0.5 % using a \u27coagulation\u27 fabrication method. Two methods are utilized to measure dispersion, UV-Vis spectroscopy and optical confocal microscopy. Quantitative spatial dispersion levels were obtained through image analysis to obtain a \u27relative dispersion index\u27 (RDI) representing the uniformity of the dispersion of SWNTs in the samples and through absorbance. We find that the storage modulus, electrical conductivity, and flammability containing the same amount of SWNTs, the relationships between the quantified dispersion levels and physical properties show about four orders of magnitude variation in storage modulus, almost eight orders of magnitude variation in electric conductivity, and about 70 % reduction in peak mass loss rate at the highest dispersion level used in this study. The observation of such a profound effect of SWNT dispersion indicates the need for objective dispersion metrics for correlating and understanding how the properties of nanocomposites are determined by the concentration, shape and size of the nanotubes

Structure of a Chaperone-Usher Pilus reveals the molecular basis of rod uncoiling

Types 1 and P pili are prototypical bacterial cell-surface appendages playing essential roles in mediating adhesion of bacteria to the urinary tract. These pili, assembled by the chaperone-usher pathway, are polymers of pilus subunits assembling into two parts: a thin, short tip fibrillum at the top, mounted on a long pilus rod. The rod adopts a helical quaternary structure and is thought to play essential roles: its formation may drive pilus extrusion by preventing backsliding of the nascent growing pilus within the secretion pore; the rod also has striking spring-like properties, being able to uncoil and recoil depending on the intensity of shear forces generated by urine flow. Here, we present an atomic model of the P pilus generated from a 3.8 Å resolution cryo-electron microscopy reconstruction. This structure provides the molecular basis for the rod’s remarkable mechanical properties and illuminates its role in pilus secretion