Unique microRNA-profiles in EGFR-mutated lung adenocarcinomas

The findings of mutations and the development of targeted therapies have improved lung cancer management. Still, the prognosis remains poor, and we need to know more about the genetic and epigenetic alterations in lung cancer. MicroRNAs are involved in crucial biological processes like carcinogenesis by regulating gene expression at the post-transcriptional level. In this project, we have studied the microRNA expression of lung adenocarcinomas and corresponding normal lung tissue and correlated the expression with clinical data and EGFR- and KRAS-mutational status. Agilent microarrays have been used, examining microRNA expression in 154 surgically resected lung adenocarcinomas and 20 corresponding normal lung tissue samples. Findings were confirmed by RT-qPCR in the same cohort and in an independent cohort of 103 lung cancer patients. EGFR and KRAS mutation analyses were also performed. 129 microRNAs were significantly differentially expressed in lung adenocarcinomas compared with normal lung tissue, and 17 microRNAs were differentially expressed between EGFR-mutated and EGFR wildtype tumors. We identified microRNAs associated with time to progression. We have identified several aberrantly expressed microRNAs that discriminate lung adenocarcinomas from normal lung tissue, and hence may be potential biomarkers for early detection. We have found microRNAs that are differentially expressed between EGFR-mutated and EGFR wildtype lung adenocarcinomas, suggesting that microRNAs can be used as molecular biomarkers in classification. We hypothesize that microRNA expression can be used as biomarkers for clinical course.

Gene expression signature of non-involved lung tissue associated with survival in lung adenocarcinoma patients

Lung adenocarcinoma patients of similar clinical stage and undergoing the same treatments often have marked interindividual variations in prognosis. These clinical discrepancies may be due to the genetic background modulating an individual's predisposition to fighting cancer. Herein, we hypothesized that the lung microenvironment, as reflected by its expression profile, may affect lung adenocarcinoma patients' survival. The transcriptome of non-involved lung tissue, excised from a discovery series of 204 lung adenocarcinoma patients, was evaluated using whole-genome expression microarrays (with probes corresponding to 28 688 well-annotated coding sequences). Genes associated with survival status at 60 months were identified by Cox regression analysis (adjusted for gender, age and clinical stage) and retested in a validation series of 78 additional cases. RNA-Seq analysis from non-involved lung tissue of 12 patients was performed to characterize the different isoforms of candidate genes. Ten genes for which the loge-transformed hazard ratios expressed the same direction of effect in the discovery (P < 1.0 × 10(-3)) and validation series comprised the gene expression signature associated with survival: CNTNAP1, PKNOX1, FAM156A, FRMD8, GALNTL1, TXNDC12, SNTB1, PPP3R1, SNX10 and SERPINH1. RNA sequencing highlighted the complex expression pattern of these genes in non-involved lung tissue from different patients and permitted the detection of a read-through gene fusion between PPP3R1 and the flanking gene (CNRIP1) as well as a novel isoform of CNTNAP1. Our findings support the hypothesis that individual genetic characteristics, evidenced by the expression pattern of non-involved tissue, influence the outcome of lung adenocarcinoma patients.

Controlled exchange interaction between pairs of neutral atoms in an optical lattice

Ultracold atoms trapped by light offer robust quantum coherence and controllability, providing an attractive system for quantum information processing and for the simulation of complex problems in condensed matter physics. Many quantum information processing schemes require the manipulation and deterministic entanglement of individual qubits; this would typically be accomplished using controlled, state-dependent, coherent interactions among qubits. Recent experiments have made progress towards this goal by demonstrating entanglement among an ensemble of atoms confined in an optical lattice. Until now, however, there has been no demonstration of a key operation: controlled entanglement between atoms in isolated pairs. Here we use an optical lattice of double-well potentials to isolate and manipulate arrays of paired (87)Rb atoms, inducing controlled entangling interactions within each pair. Our experiment realizes proposals to use controlled exchange coupling in a system of neutral atoms. Although 87Rb atoms have nearly state-independent interactions, when we force two atoms into the same physical location, the wavefunction exchange symmetry of these identical bosons leads to state-dependent dynamics. We observe repeated interchange of spin between atoms occupying different vibrational levels, with a coherence time of more than ten milliseconds. This observation demonstrates the essential component of a neutral atom quantum SWAP gate (which interchanges the state of two qubits). Its 'half-implementation', the root SWAP gate, is entangling, and together with single-qubit rotations it forms a set of universal gates for quantum computation.

Sublattice addressing and spin-dependent motion of atoms in a double-well lattice

We load atoms into every site of an optical lattice and selectively spin flip atoms in a sublattice consisting of every other site. These selected atoms are separated from their unselected neighbors by less than an optical wavelength. We also show spin-dependent transport, where atomic wave packets are coherently separated into adjacent sites according to their internal state. These tools should be useful for quantum information processing and quantum simulation of lattice models with neutral atoms.

Preparing and probing atomic number states with an atom interferometer

We describe the controlled loading and measurement of number-squeezed states and Poisson states of atoms in individual sites of a double well optical lattice. These states are input to an atom interferometer that is realized by symmetrically splitting individual lattice sites into double wells, allowing atoms in individual sites to evolve independently. The two paths then interfere, creating a matter-wave double-slit diffraction pattern. The time evolution of the double-slit diffraction pattern is used to measure the number statistics of the input state. The flexibility of our double well lattice provides a means to detect the presence of empty lattice sites, an important and so far unmeasured factor in determining the purity of a Mott state.

Instabilities of a Bose-Einstein condensate in a periodic potential: an experimental investigation

By accelerating a Bose-Einstein condensate in a controlled way across the edge of the Brillouin zone of a 1D optical lattice, we investigate the stability of the condensate in the vicinity of the zone edge. Through an analysis of the visibility of the interference pattern after a time-of-flight and the widths of the interference peaks, we characterize the onset of instability as the acceleration of the lattice is decreased. We briefly discuss the significance of our results with respect to recent theoretical work.

Asymmetric Landau-Zener tunneling in a periodic potential

Using a simple model for nonlinear Landau-Zener tunneling between two energy bands of a Bose-Einstein condensate in a periodic potential, we find that the tunneling rates for the two directions of tunneling are not the same. Tunneling from the ground state to the excited state is enhanced by the nonlinearity, whereas in the opposite direction it is suppressed. These findings are confirmed by numerical simulations of the condensate dynamics. Measuring the tunneling rates for a condensate of rubidium atoms in an optical lattice, we have found experimental evidence for this asymmetry.

Atomic micromotion and geometric forces in a triaxial magnetic trap

Nonadiabatic motion of Bose-Einstein condensates of rubidium atoms arising from the dynamical nature of a time-orbiting-potential (TOP) trap was observed experimentally. The orbital micromotion of the condensate in velocity space at the frequency of the rotating bias field of the TOP was detected by a time-of-flight method. A dependence of the equilibrium position of the atoms on the sense of rotation of the bias field was observed. We have compared our experimental findings with numerical simulations. The nonadiabatic following of the atomic spin in the trap rotating magnetic field produces geometric forces acting on the trapped atoms.