The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

The systematic translation of cancer genomic data into knowledge of tumour biology and therapeutic possibilities remains challenging. Such efforts should be greatly aided by robust preclinical model systems that reflect the genomic diversity of human cancers and for which detailed genetic and pharmacological annotation is available. Here we describe the Cancer Cell Line Encyclopedia (CCLE): a compilation of gene expression, chromosomal copy number and massively parallel sequencing data from 947 human cancer cell lines. When coupled with pharmacological profiles for 24 anticancer drugs across 479 of the cell lines, this collection allowed identification of genetic, lineage, and gene-expression-based predictors of drug sensitivity. In addition to known predictors, we found that plasma cell lineage correlated with sensitivity to IGF1 receptor inhibitors; AHR expression was associated with MEK inhibitor efficacy in NRAS-mutant lines; and SLFN11 expression predicted sensitivity to topoisomerase inhibitors. Together, our results indicate that large, annotated cell-line collections may help to enable preclinical stratification schemata for anticancer agents. The generation of genetic predictions of drug response in the preclinical setting and their incorporation into cancer clinical trial design could speed the emergence of 'personalized' therapeutic regimens.     

Heterogeneous pathways and timing of factor departure during translation initiation

The initiation of translation establishes the reading frame for protein synthesis and is a key point of regulation. Initiation involves factor-driven assembly at a start codon of a messenger RNA of an elongation-competent 70S ribosomal particle (in bacteria) from separated 30S and 50S subunits and initiator transfer RNA. Here we establish in Escherichia coli, using direct single-molecule tracking, the timing of initiator tRNA, initiation factor 2 (IF2; encoded by infB) and 50S subunit joining during initiation. Our results show multiple pathways to initiation, with orders of arrival of tRNA and IF2 dependent on factor concentration and composition. IF2 accelerates 50S subunit joining and stabilizes the assembled 70S complex. Transition to elongation is gated by the departure of IF2 after GTP hydrolysis, allowing efficient arrival of elongator tRNAs to the second codon presented in the aminoacyl-tRNA binding site (A site). These experiments highlight the power of single-molecule approaches to delineate mechanisms in complex multicomponent systems.     

Engineered two-dimensional Ising interactions in a trapped-ion quantum simulator with hundreds of spins

The presence of long-range quantum spin correlations underlies a variety of physical phenomena in condensed-matter systems, potentially including high-temperature superconductivity. However, many properties of exotic, strongly correlated spin systems, such as spin liquids, have proved difficult to study, in part because calculations involving N-body entanglement become intractable for as few as N?≈?30 particles. Feynman predicted that a quantum simulator--a special-purpose 'analogue' processor built using quantum bits (qubits)--would be inherently suited to solving such problems. In the context of quantum magnetism, a number of experiments have demonstrated the feasibility of this approach, but simulations allowing controlled, tunable interactions between spins localized on two- or three-dimensional lattices of more than a few tens of qubits have yet to be demonstrated, in part because of the technical challenge of realizing large-scale qubit arrays. Here we demonstrate a variable-range Ising-type spin-spin interaction, J(i,j), on a naturally occurring, two-dimensional triangular crystal lattice of hundreds of spin-half particles (beryllium ions stored in a Penning trap). This is a computationally relevant scale more than an order of magnitude larger than previous experiments. We show that a spin-dependent optical dipole force can produce an antiferromagnetic interaction J(i,j) proportional variant d(-a)(i,j), where 0?≤?a?≤?3 and d(i,j) is the distance between spin pairs. These power laws correspond physically to infinite-range (a = 0), Coulomb-like (a = 1), monopole-dipole (a = 2) and dipole-dipole (a = 3) couplings. Experimentally, we demonstrate excellent agreement with a theory for 0.05???a???1.4. This demonstration, coupled with the high spin count, excellent quantum control and low technical complexity of the Penning trap, brings within reach the simulation of otherwise computationally intractable problems in quantum magnetism.     

Rapid disappearance of a warm, dusty circumstellar disk

Stars form with gaseous and dusty circumstellar envelopes, which rapidly settle into disks that eventually give rise to planetary systems. Understanding the process by which these disks evolve is paramount in developing an accurate theory of planet formation that can account for the variety of planetary systems discovered so far. The formation of Earth-like planets through collisional accumulation of rocky objects within a disk has mainly been explored in theoretical and computational work in which post-collision ejecta evolution typically is ignored, although recent work has considered the fate of such material. Here we report observations of a young, Sun-like star (TYC?8241?2652?1) where infrared flux from post-collisional ejecta has decreased drastically, by a factor of about 30, over a period of less than two years. The star seems to have gone from hosting substantial quantities of dusty ejecta, in a region analogous to where the rocky planets orbit in the Solar System, to retaining at most a meagre amount of cooler dust. Such a phase of rapid ejecta evolution has not been previously predicted or observed, and no currently available physical model satisfactorily explains the observations.