Dynamic changes during the treatment of pancreatic cancer

This manuscript follows a single patient with pancreatic adenocarcinoma for a five year period, detailing the clinical record, pathology, the dynamic evolution of molecular and cellular alterations as well as the responses to treatments with chemotherapies, targeted therapies and immunotherapies. DNA and RNA samples from biopsies and blood identified a dynamic set of changes in allelic imbalances and copy number variations in response to therapies. Organoid cultures established from biopsies over time were employed for extensive drug testing to determine if this approach was feasible for treatments. When an unusual drug response was detected, an extensive RNA sequencing analysis was employed to establish novel mechanisms of action of this drug. Organoid cell cultures were employed to identify possible antigens associated with the tumor and the patient\u27s T-cells were expanded against one of these antigens. Similar and identical T-cell receptor sequences were observed in the initial biopsy and the expanded T-cell population. Immunotherapy treatment failed to shrink the tumor, which had undergone an epithelial to mesenchymal transition prior to therapy. A warm autopsy of the metastatic lung tumor permitted an extensive analysis of tumor heterogeneity over five years of treatment and surgery. This detailed analysis of the clinical descriptions, imaging, pathology, molecular and cellular evolution of the tumors, treatments, and responses to chemotherapy, targeted therapies, and immunotherapies, as well as attempts at the development of personalized medical treatments for a single patient should provide a valuable guide to future directions in cancer treatment

Identification of novel therapeutic targets in the PI3K/AKT/mTOR pathway in hepatocellular carcinoma using targeted next generation sequencing.

Understanding genetic aberrations in cancer leads to discovery of new targets for cancer therapies. The genomic landscape of hepatocellular carcinoma (HCC) has not been fully described. Therefore, patients with refractory advanced/metastatic HCC referred for experimental therapies, who had adequate tumor tissue available, had targeted next generation sequencing (NGS) of their tumor samples using the Illumina HiSeq 2000 platform (Foundation One, Foundation Medicine, MA) and their treatment outcomes were analyzed. In total, NGS was obtained for 14 patients (median number of prior therapies, 1) with advanced/metastatic HCC. Of these 14 patients, 10 (71%) were men, 4 (29%) women, 6 (43%) had hepatitis B or C-related HCC. NGS revealed at least 1 molecular abnormality in 12 patients (range 0-8, median 2). Detected molecular aberrations led to putative activation of the PI3K/AKT/mTOR pathway (n=3 [mTOR, PIK3CA, NF1]), Wnt pathway (n=6 [CTNNA1, CTNNB1]), MAPK pathway (n=2 [MAP2K1, NRAS]), and aberrant DNA repair mechanisms, cell cycle control and apoptosis (n=18 [ATM, ATR, BAP1, CCND1, CDKN2A, CDK4, FGF3, FGF4, FGF19, MCL1, MDM2, RB1, TP53]). Of the 3 patients with molecular aberrations putatively activating the PI3K/AKT/mTOR pathway, 2 received therapies including a mTOR inhibitor and all demonstrated therapeutic benefit ranging from a partial response to minor shrinkage per RECIST (-30%, -15%; respectively). In conclusion, genomic alterations are common in advanced HCC. Refractory patients with alterations putatively activating the PI3K/AKT/mTOR pathway demonstrated early signals of clinical activity when treated with therapies targeting mTOR

Comments on Sweeny and Gliozzi dynamics for simulations of Potts models in the Fortuin-Kasteleyn representation

We compare the correlation times of the Sweeny and Gliozzi dynamics for two-dimensional Ising and three-state Potts models, and the three-dimensional Ising model for the simulations in the percolation prepresentation. The results are also compared with Swendsen-Wang and Wolff cluster dynamics. It is found that Sweeny and Gliozzi dynamics have essentially the same dynamical critical behavior. Contrary to Gliozzi's claim (cond-mat/0201285), the Gliozzi dynamics has critical slowing down comparable to that of other cluster methods. For the two-dimensional Ising model, both Sweeny and Gliozzi dynamics give good fits to logarithmic size dependences; for two-dimensional three-state Potts model, their dynamical critical exponent z is 0.49(1); the three-dimensional Ising model has z = 0.37(2).Comment: RevTeX, 4 pages, 5 figure

Northern Late Winter Planetary Waves: MRO/MARCI Observations and Mars Climate Model Simulations

As does Earth, Mars presents pronounced global atmospheric circulation patterns. Solar differential heating drives mean meridional overturning (Hadley) circulations which are deep and intense, are hemispherically asymmetric, and where a cross-equatorial single cell dominates. Within middle and high latitudes, thermally indirect eddy-driven (Ferrel) circulation cells have been indicated. Differently, however, large-amplitude orography on planetary and continental scales on Mars can force very non-Earth-like hemispheric circulation patterns. Recent observations from the Mars Reconnaissance Orbiter, "Mars Color Imager" (MARCI) instrument are utilized that emphasize water ice clouds in ultra-violet (UV) wavelengths, and these measurements have been binned into "daily global maps" (DGMs) of water-ice cloud optical depth. The presence of large-scale, extratropical quasi-stationary atmospheric wave disturbances in middle and late winter of the northern hemisphere have been found to be present in such DGMs. In combination with such observations, a full-physics Mars global climate model (NASA ARC marsgcm 2.1) is applied to place the observations into context. During late northern winter, it is found that strong, forced Rossby modes (i.e., planetary waves) exist, and with direct correlation to columnintegrated cloud opacity undulating spatial patterns. At this season, zonal wavenumber s = 2 dominates (in contrast to wavenumber s = 1), consistent with MGS/TES analyses at this particular season (Banfield et al., 2003). Large-scale, planetary waves dictate the "coherence" of the northern polar vortex. Fundamentally, such forced planetary waves influence the polar vortex's impermeability (wave-induced) to tracer transport (e.g., dust and water-ice aerosol) and temporal mean water vapor spatial variations. The large-scale dynamical features of such planetary waves will be highlighted and discussed

Targeted therapy of advanced gallbladder cancer and cholangiocarcinoma with aggressive biology: eliciting early response signals from phase 1 trials.

PurposePatients with advanced cholangiocarcinoma (CC) and gallbladder carcinoma (GC) have few therapeutic options for relapsed disease. methods: Given the overall poor prognosis in this population and the availability of novel targeted therapies, we systematically analyzed the characteristics and outcomes for GC and CC patients treated on phase I trials with an emphasis on targeted agents and locoregional therapies.ResultsOf 40 treated patients (GC=6; CC=34; median age, 60 years), 8 (20%) had stable disease (SD) > 6 months, 3 (8%) partial response (PR), on protocols with hepatic arterial drug infusion and anti-angiogenic, anti-HER-2/neu or novel MAPK/ERK kinase (MEK) inhibitors. Median progression-free survival (PFS) on phase I trials was 2.0 months (95% CI 1.7, 2.8) versus 3.0 months (95% CI 2.4, 5.0), 3.0 months (95% CI 2.3, 4.6), and 3.0 months (95% CI 2.4, 3.9) for their first-, second-, and last-line FDA-approved therapy. In univariate analysis, >3 metastatic sites, elevated alanine aminotransferase (ALT) (>56IU/L), serum creatinine (>1.6mg/dL), and CA19-9 (>35U/mL) were associated with a shorter PFS. Mutational analysis revealed mutation in the KRAS oncogene in 2 of 11 patients (18%). The SD >6 months/PR rate of 28% was seen with hepatic arterial infusion of oxaliplatin, and inhibitors of angiogenesis, HER-2/neu or MEK.ConclusionsThe PFS in phase I trials was similar to that of the first, second, and last-line therapy (P=0.95, 0.98, 0.76, respectively) with FDA-approved agents given in the advanced setting, emphasizing a role for targeted agents in a clinical trials setting as potentially valuable therapeutic options for these patients

The Apical Targeting Signal of the P2Y 2 Receptor Is Located in Its First Extracellular Loop

P2Y2 and P2Y4 receptors, which have 52% sequence identity, are both expressed at the apical membrane of Madin-Darby canine kidney cells, but the locations of their apical targeting signals are distinctly different. The targeting signal of the P2Y2 receptor is located between the N terminus and 7TM, whereas that of the P2Y4 receptor is present in its C-terminal tail. To identify the apical targeting signal in the P2Y2 receptor, regions of the P2Y2 receptor were progressively substituted with the corresponding regions of the P2Y4 receptor lacking its targeting signal. Characterization of these chimeras and subsequent mutational analysis revealed that four amino acids (Arg95, Gly96, Asp97, and Leu108) in the first extracellular loop play a major role in apical targeting of the P2Y2 receptor. Mutation of RGD to RGE had no effect on P2Y2 receptor targeting, indicating that receptor-integrin interactions are not involved in apical targeting. P2Y2 receptor mutants were localized in a similar manner in Caco-2 colon epithelial cells. This is the first identification of an extracellular protein-based targeting signal in a seven-transmembrane receptor

Cluster Monte Carlo Simulations of the Nematic--Isotropic Transition

We report the results of simulations of the Lebwohl-Lasher model of the nematic-isotropic transition using a new cluster Monte Carlo algorithm. The algorithm is a modification of the Wolff algorithm for spin systems, and greatly reduces critical slowing down. We calculate the free energy in the neighborhood of the transition for systems up to linear size 70. We find a double well structure with a barrier that grows with increasing system size, obeying finite size scaling for systems of size greater than 35. We thus obtain an estimate of the value of the transition temperature in the thermodynamic limit.Comment: 4 figure

GLIMPSE: I. A SIRTF Legacy Project to Map the Inner Galaxy

GLIMPSE (Galactic Legacy Infrared Mid-Plane Survey Extraordinaire), a SIRTF Legacy Science Program, will be a fully sampled, confusion-limited infrared survey of the inner two-thirds of the Galactic disk with a pixel resolution of \~1.2" using the Infrared Array Camera (IRAC) at 3.6, 4.5, 5.8, and 8.0 microns. The survey will cover Galactic latitudes |b| <1 degree and longitudes |l|=10 to 65 degrees (both sides of the Galactic center). The survey area contains the outer ends of the Galactic bar, the Galactic molecular ring, and the inner spiral arms. The GLIMPSE team will process these data to produce a point source catalog, a point source data archive, and a set of mosaicked images. We summarize our observing strategy, give details of our data products, and summarize some of the principal science questions that will be addressed using GLIMPSE data. Up-to-date documentation, survey progress, and information on complementary datasets are available on the GLIMPSE web site: www.astro.wisc.edu/glimpse.Comment: Description of GLIMPSE, a SIRTF Legacy project (Aug 2003 PASP, in press). Paper with full res.color figures at http://www.astro.wisc.edu/glimpse/glimpsepubs.htm