Transcriptional Profiling of Malignant Melanoma Reveals Novel and Potentially Targetable Gene Fusions.

Invasive melanoma is the deadliest type of skin cancer, with 101,110 expected cases to be diagnosed in 2021. Recurrent BRAF and NRAS mutations are well documented in melanoma. Biologic implications of gene fusions and the efficacy of therapeutically targeting them remains unknown. Retrospective review of patient samples that underwent next-generation sequencing of the exons of 592 cancer-relevant genes and whole transcriptome sequencing for the detection of gene fusion events and gene expression profiling. Expression of PDL1 and ERK1/2 was assessed by immunohistochemistry (IHC). There were 33 (2.6%) cases with oncogenic fusions (14 novel), involving BRAF, RAF1, PRKCA, TERT, AXL, and FGFR3. MAPK pathway-associated genes were over-expressed in BRAF and RAF1 fusion-positive tumors in absence of other driver alterations. Increased expression in tumors with PRKCA and TERT fusions was concurrent with MAPK pathway alterations. For a subset of samples with available tissue, increased phosphorylation of ERK1/2 was observed in BRAF, RAF1, and PRKCA fusion-positive tumors. Oncogenic gene fusions are associated with transcriptional activation of the MAPK pathway, suggesting they could be therapeutic targets with available inhibitors. Additional analyses to fully characterize the oncogenic effects of these fusions may support biomarker driven clinical trials.

A Method to Reuse Archived H&E Stained Histology Slides for a Multiplex Protein Biomarker Analysis.

Archived Hematoxylin and Eosin (H&E) stained pathology slides are routinely stored to index formalin-fixed paraffin-embedded (FFPE) sample tissue blocks. FFPE blocks are clinically annotated human tumor specimens that can be valuable in studies decades after the tissue is collected. If stored properly, they have the potential to yield a valuable number of serial sectioned slides for diagnostic or research purposes. However, some retrospective studies are limited in scope because the tissue samples have been depleted or not enough material is available in stored blocks for serial sections. The goal of these studies was to determine if archived H&E-stained slides can be directly reutilized by optimizing methods to de-stain and then re-stain the H&E stained slides to allow the detection of several biomarkers of interest using a conjugated antibody with chromogen multiplex immunohistochemistry procedure. This simple but innovative procedure, combined with image analysis techniques, demonstrates the ability to perform precise detection of relevant markers correlated to disease progression in initially identified tumor regions in tissue. This may add clinical value in retaining H&E slides for further use.

Gene Editing of α6 Integrin Inhibits Muscle Invasive Networks and Increases Cell-Cell Biophysical Properties in Prostate Cancer.

Human prostate cancer confined to the gland is indolent (low-risk), but tumors outside the capsule are aggressive (high-risk). Extracapsular extension requires invasion within and through a smooth muscle-structured environment. Because integrins respond to biomechanical cues, we used a gene editing approach to determine if a specific region of laminin-binding α6ß1 integrin was required for smooth muscle invasion both in vitro and in vivo. Human tissue specimens showed prostate cancer invasion through smooth muscle and tumor coexpression of α6 integrin and E-cadherin in a cell-cell location and α6 integrin in a cell-extracellular matrix (ECM) distribution. Prostate cancer cells expressing α6 integrin (DU145 α6WT) produced a 3D invasive network on laminin-containing Matrigel and invaded into smooth muscle both in vitro and in vivo. In contrast, cells without α6 integrin (DU145 α6KO) and cells expressing an integrin mutant (DU145 α6AA) did not produce invasive networks, could not invade muscle both in vitro and in vivo, and surprisingly formed 3D cohesive clusters. Using electric cell-substrate impedance testing, cohesive clusters had up to a 30-fold increase in normalized resistance at 400 Hz (cell-cell impedance) as compared with the DU145 α6WT cells. In contrast, measurements at 40,000 Hz (cell-ECM coverage) showed that DU145 α6AA cells were two-fold decreased in normalized resistance and were defective in restoring resistance after a 1 µmol/L S1P challenge as compared with the DU145 α6WT cells. The results suggest that gene editing of a specific α6 integrin extracellular region, not required for normal tissue function, can generate a new biophysical cancer phenotype unable to invade the muscle, presenting a new therapeutic strategy for metastasis prevention in prostate cancer. SIGNIFICANCE: This study shows an innovative strategy to block prostate cancer metastasis and invasion in the muscle through gene editing of a specific α6 integrin extracellular region.

Integrin α6ß4E variant is associated with actin and CD9 structures and modifies the biophysical properties of cell-cell and cell-extracellular matrix interactions.

Integrin α6ß4 is an essential, dynamic adhesion receptor for laminin 332 found on epithelial cells, required for formation of strong cell-extracellular matrix (ECM) adhesion and induced migration, and coordinated by regions of the ß4C cytoplasmic domain. ß4E, a unique splice variant of ß4 expressed in normal tissue, contains a cytoplasmic domain of 231 amino acids with a unique sequence of 114 amino acids instead of ß4C's canonical 1089 amino acids. We determined the distribution of α6ß4E within normal human glandular epithelium and its regulation and effect on cellular biophysical properties. Canonical α6ß4C expressed in all basal cells, as expected, while α6ß4E expressed within a subset of luminal cells. α6ß4E expression was induced by three-dimensional culture conditions, activated Src, was reversible, and was stabilized by bortezomib, a proteasome inhibitor. α6ß4C expressed in all cells during induced migration, whereas α6ß4E was restricted to a subset of cells with increased kinetics of cell-cell and cell-ECM resistance properties. Interestingly, α6ß4E presented in "ringlike" patterns measuring ∼1.75 × 0.72 microns and containing actin and CD9 at cell-ECM locations. In contrast, α6ß4C expressed only within hemidesmosome-like structures containing BP180. Integrin α6ß4E is an inducible adhesion isoform in normal epithelial cells that can alter biophysical properties of cell-cell and cell-ECM interactions.

Imaging Anomalous Nematic Order and Strain in Optimally Doped BaFe_{2}(As,P)_{2}.

We present the strain and temperature dependence of an anomalous nematic phase in optimally doped BaFe_{2}(As,P)_{2}. Polarized ultrafast optical measurements reveal broken fourfold rotational symmetry in a temperature range above T_{c} in which bulk probes do not detect a phase transition. Using ultrafast microscopy, we find that the magnitude and sign of this nematicity vary on a 50-100 µm length scale, and the temperature at which it onsets ranges from 40 K near a domain boundary to 60 K deep within a domain. Scanning Laue microdiffraction maps of local strain at room temperature indicate that the nematic order appears most strongly in regions of weak, isotropic strain. These results indicate that nematic order arises in a genuine phase transition rather than by enhancement of local anisotropy by a strong nematic susceptibility. We interpret our results in the context of a proposed surface nematic phase.

The Cohesive Metastasis Phenotype in Human Prostate Cancer.

A critical barrier for the successful prevention and treatment of recurrent prostate cancer is detection and eradication of metastatic and therapy-resistant disease. Despite the fall in diagnoses and mortality, the reported incidence of metastatic disease has increased 72% since 2004. Prostate cancer arises in cohesive groups as intraepithelial neoplasia, migrates through muscle and leaves the gland via perineural invasion for hematogenous dissemination. Current technological advances have shown cohesive-clusters of tumor (also known as microemboli) within the circulation. Circulating tumor cell (CTC) profiles are indicative of disseminated prostate cancer, and disseminated tumor cells (DTC) are found in cohesive-clusters, a phenotypic characteristic of both radiation- and drug-resistant tumors. Recent reports in cell biology and informatics, coupled with mass spectrometry, indicate that the integrin adhesome network provides an explanation for the biophysical ability of cohesive-clusters of tumor cells to invade thorough muscle and nerve microenvironments while maintaining adhesion-dependent therapeutic resistance. Targeting cohesive-clusters takes advantage of the known ability of extracellular matrix (ECM) adhesion to promote tumor cell survival and represents an approach that has the potential to avoid the progression to drug- and radiotherapy-resistance. In the following review we will examine the evidence for development and dissemination of cohesive-clusters in metastatic prostate cancer.

Governance Resilience: The Presbyterian Journey.

Presbyterian Healthcare Services, based in Albuquerque, New Mexico, is the state's only private, not-for-profit integrated healthcare system. It was founded in 1908 as a sanitorium for tuberculosis patients who came to the arid Southwest in search of a cure. Today, Presbyterian is thriving as a twenty-first-century integrated healthcare system, serving one in three New Mexicans in its statewide hospital system; it also includes a 440,000-member health plan and a 700-plus provider medical group. Presbyterian remains dedicated to its singular purpose of improving the health of the patients, members, and communities it serves. Just as Presbyterian has progressed and grown during its 106-year history, its governance system has evolved over time. Presbyterian has always believed that the New Mexico communities it serves deserve not just good governance but great governance and relies on strong structure and processes to lead it to superior outcomes. The ebb and flow of change, our ability to learn from trial and error, and our commitment to success in spite of obstacles make up the story of Presbyterian's strong governance system.

A pre-postintervention study to evaluate the impact of dose calculators on the accuracy of gentamicin and vancomycin initial doses.

OBJECTIVES: Gentamicin and vancomycin are narrow-therapeutic-index antibiotics with potential for high toxicity requiring dose individualisation and continuous monitoring. Clinical decision support (CDS) tools have been effective in reducing gentamicin and vancomycin dosing errors. Online dose calculators for these drugs were implemented in a London National Health Service hospital. This study aimed to evaluate the impact of these calculators on the accuracy of gentamicin and vancomycin initial doses. METHODS: The study used a pre-postintervention design. Data were collected using electronic patient records and paper notes. Random samples of gentamicin and vancomycin initial doses administered during the 8 months before implementation of the calculators were assessed retrospectively against hospital guidelines. Following implementation of the calculators, doses were assessed prospectively. Any gentamicin dose not within ± 10% and any vancomycin dose not within ± 20% of the guideline-recommended dose were considered incorrect. RESULTS: The intranet calculator pages were visited 721 times (gentamicin=333; vancomycin=388) during the 2-month period following the calculators' implementation. Gentamicin dose errors fell from 61.5% (120/195) to 44.2% (95/215), p<0.001. Incorrect vancomycin loading doses fell from 58.1% (90/155) to 32.4% (46/142), p<0.001. Incorrect vancomycin first maintenance doses fell from 55.5% (86/155) to 33.1% (47/142), p<0.001. Loading and first maintenance vancomycin doses were both incorrect in 37.4% (58/155) of patients before and 13.4% (19/142) after calculator implementation, p<0.001. CONCLUSIONS: This study suggests that gentamicin and vancomycin dose calculators significantly improved the prescribing of initial doses of these agents. Therefore, healthcare organisations should consider using such CDS tools to support the prescribing of these high-risk drugs.

Taking the transformational path.

A new report suggests several paths to delivery system transformation.

Risk of medication safety incidents with antibiotic use measured by defined daily doses.

BACKGROUND: Medication incidents (MIs) account for 11.3 % of all reported patient-safety incidents in England and Wales. Approximately one-third of inpatients are prescribed an antibiotic at some point during their hospital stay. The WHO has identified incident reporting as one solution to reduce the recurrence of adverse incidents. OBJECTIVES: The aim of this study was to determine the number and nature of reported antibiotic-associated MIs occurring in inpatients and to use defined daily doses (DDDs) to calculate the incident rate for the antibiotics most commonly associated with MIs at each hospital. SETTING: Two UK acute NHS teaching hospitals. METHODS: Retrospective quantitative analysis was performed on antibiotic-associated MIs reported to the risk management system over a 2-year period. Quality-assurance measures were undertaken before analysis. The study was approved by the clinical audit departments at both hospitals. Drug consumption data from each hospital were used to calculate the DDD for each antibiotic. MAIN OUTCOME MEASURES: The number of antibiotic-related MIs reported and the incident rate for the 10 antibiotics most commonly associated with MIs at each hospital. RESULTS: Healthcare staff submitted 6,756 reports, of which 885 (13.1 %) included antibiotics. This resulted in a total of 959 MIs. Most MIs occurred during prescribing (42.4 %, n = 407) and administration (40.0 %, n = 384) stages. Most common types of MIs were omission/delay (26.3 %, n = 252), and dose/frequency (17.9 %, n = 172). Penicillins (34.5 %, n = 331) and aminoglycosides (16.6 %, n = 159) were the most frequently reported groups with co-amoxiclav (16.8 %, n = 161) and gentamicin (14.1 %, n = 135) the most frequently reported drugs. Using DDDs to assess the incident rate showed that cefotaxime (105.4/10,000 DDDs), gentamicin (25.7/10,000 DDDs) and vancomycin (23.7/10,000 DDDs) had the highest rates. CONCLUSIONS: This study highlights that detailed analysis of data from reports is essential in understanding MIs and developing strategies to prevent their recurrence. Using DDDs in the analysis of MIs allowed determination of an incident rate providing more useful information than the absolute numbers alone. It also highlighted the disproportionate risk associated with less commonly prescribed antibiotics not identified using MI reporting rates alone.

Tracking Cooper pairs in a cuprate superconductor by ultrafast angle-resolved photoemission.

In high-temperature superconductivity, the process that leads to the formation of Cooper pairs, the fundamental charge carriers in any superconductor, remains mysterious. We used a femtosecond laser pump pulse to perturb superconducting Bi(2)Sr(2)CaCu(2)O(8+δ) and studied subsequent dynamics using time- and angle-resolved photoemission and infrared reflectivity probes. Gap and quasiparticle population dynamics revealed marked dependencies on both excitation density and crystal momentum. Close to the d-wave nodes, the superconducting gap was sensitive to the pump intensity, and Cooper pairs recombined slowly. Far from the nodes, pumping affected the gap only weakly, and recombination processes were faster. These results demonstrate a new window into the dynamical processes that govern quasiparticle recombination and gap formation in cuprates.

Gramicidin A backbone and side chain dynamics evaluated by molecular dynamics simulations and nuclear magnetic resonance experiments. II: nuclear magnetic resonance experiments.

Motional properties are important for understanding protein function and are accessible to NMR relaxation measurements. The goal of this study is to investigate the internal dynamics occurring in gramicidin A (gA) channels in order to provide benchmark experimental data for comparison with the results of molecular dynamics simulations. We therefore synthesized several (15)N isotope-enriched gA samples, covering all backbone residues as well as the Trp indole side chains for NMR relaxation experiments. On the basis of the (15)N NMR spectra for labeled gA samples incorporated in sodium dodecylsulfate (SDS) micelles, we determined T(1), T(2), and heteronuclear NOE values for backbone and indole (15)NH groups. The results indicate that the SDS-incorporated gA channel is a constrained structure without an especially "floppy" region. The NMR observables, particularly those for backbone groups, are predicted well by the molecular dynamics simulations in the accompanying article (DOI 10.1021/jp200904d ).

Gramicidin A backbone and side chain dynamics evaluated by molecular dynamics simulations and nuclear magnetic resonance experiments. I: molecular dynamics simulations.

Gramicidin A (gA) channels provide an ideal system to test molecular dynamics (MD) simulations of membrane proteins. The peptide backbone lines a cation-selective pore, and due to the small channel size, the average structure and extent of fluctuations of all atoms in the peptide will influence ion permeation. This raises the question of how well molecular mechanical force fields used in MD simulations and potential of mean force (PMF) calculations can predict structure and dynamics as well as ion permeation. To address this question, we undertook a comparative study of nuclear magnetic resonance (NMR) observables predicted by fully atomistic MD simulations on a gA dimer embedded in a sodium dodecyl sulfate (SDS) micelle with measurements of the gA dimer backbone and tryptophan side chain dynamics using solution-state (15)N NMR on gA dimers in SDS micelles (Vostrikov, V. V.; Gu, H.; Ingólfsson, H. I.; Hinton, J. F.; Andersen, O. S.; Roux, B.; Koeppe, R. E., II. J. Phys. Chem. B2011, DOI 10.1021/jp200906y , accompanying article). This comparison enables us to examine the robustness of the MD simulations done using different force fields as well as their ability to predict important features of the gA channel. We find that MD is able to predict NMR observables, including the generalized order parameters (S(2)), the (15)N spin-lattice (T(1)) and spin-spin (T(2)) relaxation times, and the (1)H-(15)N nuclear Overhauser effect (NOE), with remarkable accuracy. To examine further how differences in the force fields can affect the channel conductance, we calculated the PMF for K(+) and Na(+) permeation through a gA channel in a dimyristoylphosphatidylcholine (DMPC) bilayer. In this case, we find that MD is less successful in quantitatively predicting the single-channel conductance.

High-throughput, high-sensitivity analysis of gene expression in Arabidopsis.

High-throughput gene expression analysis of genes expressed during salt stress was performed using a novel multiplexed quantitative nuclease protection assay that involves customized DNA microarrays printed within the individual wells of 96-well plates. The levels of expression of the transcripts from 16 different genes were quantified within crude homogenates prepared from Arabidopsis (Arabidopsis thaliana) plants also grown in a 96-well plate format. Examples are provided of the high degree of reproducibility of quantitative dose-response data and of the sensitivity of detection of changes in gene expression within limiting amounts of tissue. The lack of requirement for RNA purification renders the assay particularly suited for high-throughput gene expression analysis and for the discovery of novel chemical compounds that specifically modulate the expression of endogenous target genes.

Calculated and experimental geometries and infrared spectra of metal tris-acetylacetonates: vibrational spectroscopy as a probe of molecular structure for ionic complexes. Part II.

Following on from our previous work on Sc, Fe, Cr, and Al (Part I; see J. Phys. Chem. A, 105 (2001) 238), the geometries and infrared spectra of the trivalent metal tris-acetylacetonate complexes (M[O2C5H7]3; M = Ti, V, Mn, Co) have been studied both experimentally and theoretically using nonlocal hybrid density functional theory with a split-valence plus polarization basis for the ligand and valence triple-zeta for the metal. Unlike the D3 complexes studied in Part I, those of Ti, V and Mn are candidates for Jahn-Teller distortion due to fractional d-shell occupancy. Using scale factors transferred from Part I, our calculated frequencies are in very good agreement with experimentally observed fundamentals. Our investigation shows that the V and Mn complexes distort to C2 ground states, but D3 Ti tris-acetylacetonate is stable. Further investigation of the weak band observed around 800 cm(-1) in the Fe complex (and present in almost all studied first-row transition metal tris-acetylacetonates), which we were unable to assign theoretically in Part I, supports the argument that this band is not a fundamental but is due to Fermi resonance.

Accurate prediction of proton chemical shifts. II. Peptide analogues.

Proton chemical shifts of eight cyclic amide molecules were measured in DMSO and D2O solutions. The magnetic shieldings of the corresponding aliphatic, aromatic, and amide protons were calculated by Hartree-Fock and DFT, using the 6-311G**, 6-311++G**, and TZVP basis sets. For aliphatic protons, all of these methods reproduce the experimental values in DMSO solutions excellently after linear regression. The Hartree-Fock method tends to give slightly better agreement than DFT. The best performance is given by the HF/6-311G** method, with an rms deviation of 0.068 ppm. The deviations from experimental chemical shifts in D2O solutions are only slightly larger than those in DMSO solutions. This suggests that we can use the calculated gas phase proton chemical shifts directly to predict experimental data in various solvents, including water. For amide protons, which exchange with water and form hydrogen bonds with DMSO, only modest agreement is obtained, as expected. The present studies confirm that the GIAO approach can reach high accuracy for the relative chemical shifts of aliphatic and aromatic protons at a low cost. Such calculations may provide constraints for the conformational analysis of proteins and other macromolecules.

Multiplexed screening assay for mRNA combining nuclease protection with luminescent array detection.

The principles and performance are described for the ArrayPlate mRNA assay, a multiplexed mRNA assay for high-throughput and high-content screening and drug development. THP-1 monocytes grown and subjected to compound treatments in 96-well plates were subjected to a multiplexed nuclease protection assay in situ. The nuclease protection assay destroyed all cell-derived mRNA, but left intact stoichiometric amounts of 16 target-specific oligonucleotide probes. Upon transfer of processed cell lysates to a microplate that contained a 16-element oligonucleotide array at the bottom of each well, the various probe species were separated by immobilization at predefined elements of the array. Quantitative detection of array-bound probes was by enzyme-mediated chemiluminescence. A high-resolution charge-coupled device imager was used for the simultaneous readout of all 1536 array elements in a 96-well plate. For the measurement of 16 genes in samples of 25000 cells, the average standard deviation from well to well within a plate was 8.6% of signal intensity and was 10.8% from plate to plate. Assay response was linear and reproducibility was constant for all detected genes in samples ranging from 1000 to 50000 cells. When THP-1 monocytes were differentiated with phorbol ester and subsequently activated with bacterial lipopolysaccharide that contained different concentrations of dexamethasone, dose-dependent effects of dexamethasone on the mRNA levels of several genes were observed.