Comprehensive genomic analysis of Oesophageal Squamous Cell Carcinoma reveals clinical relevance

Abstract Oesophageal carcinoma is the fourth leading cause of cancer-related death in China, and more than 90% of these tumours are oesophageal squamous cell carcinoma (ESCC). Although several ESCC genomic sequencing studies have identified mutated somatic genes, the number of samples in each study was relatively small, and the molecular basis of ESCC has not been fully elucidated. Here, we performed an integrated analysis of 490 tumours by combining the genomic data from 7 previous ESCC projects. We identified 18 significantly mutated genes (SMGs). PTEN, DCDC1 and CUL3 were first reported as SMGs in ESCC. Notably, the AJUBA mutations and mutational signature4 were significantly correlated with a poorer survival in patients with ESCC. Hierarchical clustering analysis of the copy number alteration (CNA) of cancer gene census (CGC) genes in ESCC patients revealed three subtypes, and subtype3 exhibited more CNAs and marked for worse prognosis compared with subtype2. Moreover, database annotation suggested that two significantly differential CNA genes (PIK3CA and FBXW7) between subtype3 and subtype2 may serve as therapeutic drug targets. This study has extended our knowledge of the genetic basis of ESCC and shed some light into the clinical relevance, which would help improve the therapy and prognosis of ESCC patients

Quantum hydrogen-bond symmetrization in the superconducting hydrogen sulfide system.

The quantum nature of the proton can crucially affect the structural and physical properties of hydrogen compounds. For example, in the high-pressure phases of H2O, quantum proton fluctuations lead to symmetrization of the hydrogen bond and reduce the boundary between asymmetric and symmetric structures in the phase diagram by 30 gigapascals (ref. 3). Here we show that an analogous quantum symmetrization occurs in the recently discovered sulfur hydride superconductor with a superconducting transition temperature Tc of 203 kelvin at 155 gigapascals--the highest Tc reported for any superconductor so far. Superconductivity occurs via the formation of a compound with chemical formula H3S (sulfur trihydride) with sulfur atoms arranged on a body-centred cubic lattice. If the hydrogen atoms are treated as classical particles, then for pressures greater than about 175 gigapascals they are predicted to sit exactly halfway between two sulfur atoms in a structure with Im3m symmetry. At lower pressures, the hydrogen atoms move to an off-centre position, forming a short H-S covalent bond and a longer H···S hydrogen bond in a structure with R3m symmetry. X-ray diffraction experiments confirm the H3S stoichiometry and the sulfur lattice sites, but were unable to discriminate between the two phases. Ab initio density-functional-theory calculations show that quantum nuclear motion lowers the symmetrization pressure by 72 gigapascals for H3S and by 60 gigapascals for D3S. Consequently, we predict that the Im3m phase dominates the pressure range within which the high Tc was measured. The observed pressure dependence of Tc is accurately reproduced in our calculations for the phase, but not for the R3m phase. Therefore, the quantum nature of the proton fundamentally changes the superconducting phase diagram of H3S.We acknowledge financial support from the Spanish Ministry of Economy and Competitiveness (FIS2013- 48286-C2-2-P), French Agence Nationale de la Recherche (Grant No. ANR-13-IS10-0003- 392 01), EPSRC (UK) (Grant No. EP/J017639/1), Cambridge Commonwealth Trust, National Natural Science Foundation of China (Grants No. 11204111, 11404148, and 11274136), and 2012 Changjiang Scholars Program of China. Work at Carnegie was supported by EFree, an Energy Frontier Research Center funded by the DOE, Office of Science, Basic Energy Sciences under Award No. DE-SC-0001057. Computer facilities were provided by the PRACE project AESFT and the Donostia International Physics Center (DIPC).This is the author accepted manuscript. The final version is available from Nature Publishing Group via http://dx.doi.org/10.1038/nature1717

Effect of external beam radiation therapy versus transcatheter arterial chemoembolization for non-diffuse hepatocellular carcinoma (≥ 5 cm): a multicenter experience over a ten-year period

BackgroundThe optimal local treatment for HCC with tumor diameter ≥ 5 cm is not well established. This research evaluated the effectiveness of external beam radiation therapy (EBRT) versus transcatheter arterial chemoembolization (TACE) for HCC with tumor diameter ≥ 5 cm.MethodsA total of 1210 HCC patients were enrolled in this study, including 302 and 908 patients that received EBRT and TACE, respectively. Propensity score matching (PSM) was used to identify patient pairs with similar baseline characteristics. Overall survival (OS) was the primary study endpoint.ResultsWe identified 428 patients using 1:1 PSM for survival comparison. Compared with the TACE group, the EBRT group had a significantly longer median OS (mOS) before (14.9 vs. 12.3 months, p = 0.0085) and after (16.8 vs. 11.4 months, p = 0.0026) matching. In the subgroup analysis, compared with the TACE group, the EBRT group had a significantly longer mOS for HCC with tumor diameters of 5-7 cm (34.1 vs. 14.3 months, p = 0.04) and 7-10 cm (34.4 vs. 10 months, p = 0.00065), whereas for HCC with tumor diameters ≥ 10 cm, no significant difference in mOS was observed (11.2 vs. 11.2 months, p = 0.83). In addition, the multivariable Cox analysis showed that Child-A, alkaline phosphatase < 125 U/L, and EBRT were independent prognostic indicators for longer survival.ConclusionEBRT is more effective than TACE as the primary local treatment for HCC with tumor diameter ≥ 5 cm, especially for HCC with tumor diameter of 5-10 cm

Genomic Analyses Reveal Mutational Signatures and Frequently Altered Genes in Esophageal Squamous Cell Carcinoma

Esophageal squamous cell carcinoma (ESCC) is one of the most common cancers worldwide and the fourth most lethal cancer in China. However, although genomic studies have identified some mutations associated with ESCC, we know little of the mutational processes responsible. To identify genome-wide mutational signatures, we performed either whole-genome sequencing (WGS) or whole-exome sequencing (WES) on 104 ESCC individuals and combined our data with those of 88 previously reported samples. An APOBEC-mediated mutational signature in 47% of 192 tumors suggests that APOBEC-catalyzed deamination provides a source of DNA damage in ESCC. Moreover, PIK3CA hotspot mutations (c.1624G>A [p.Glu542Lys] and c.1633G>A [p.Glu545Lys]) were enriched in APOBEC-signature tumors, and no smoking-associated signature was observed in ESCC. In the samples analyzed by WGS, we identified focal (<100 kb) amplifications of CBX4 and CBX8. In our combined cohort, we identified frequent inactivating mutations in AJUBA, ZNF750, and PTCH1 and the chromatin-remodeling genes CREBBP and BAP1, in addition to known mutations. Functional analyses suggest roles for several genes (CBX4, CBX8, AJUBA, and ZNF750) in ESCC. Notably, high activity of hedgehog signaling and the PI3K pathway in approximately 60% of 104 ESCC tumors indicates that therapies targeting these pathways might be particularly promising strategies for ESCC. Collectively, our data provide comprehensive insights into the mutational signatures of ESCC and identify markers for early diagnosis and potential therapeutic targets

American ginseng suppresses Western diet-promoted tumorigenesis in model of inflammation-associated colon cancer: role of EGFR

<p>Abstract</p> <p>Background</p> <p>Western diets increase colon cancer risk. Epidemiological evidence and experimental studies suggest that ginseng can inhibit colon cancer development. In this study we asked if ginseng could inhibit Western diet (20% fat) promoted colonic tumorigenesis and if compound K, a microbial metabolite of ginseng could suppress colon cancer xenograft growth.</p> <p>Methods</p> <p>Mice were initiated with azoxymethane (AOM) and, two weeks later fed a Western diet (WD, 20% fat) alone, or WD supplemented with 250-ppm ginseng. After 1 wk, mice received 2.5% dextran sulfate sodium (DSS) for 5 days and were sacrificed 12 wks after AOM. Tumors were harvested and cell proliferation measured by Ki67 staining and apoptosis by TUNEL assay. Levels of EGF-related signaling molecules and apoptosis regulators were determined by Western blotting. Anti-tumor effects of intraperitoneal compound K were examined using a tumor xenograft model and compound K absorption measured following oral ginseng gavage by UPLC-mass spectrometry. Effects of dietary ginseng on microbial diversity were measured by analysis of bacterial 16S rRNA.</p> <p>Results</p> <p>Ginseng significantly inhibited colonic inflammation and tumorigenesis and concomitantly reduced proliferation and increased apoptosis. The EGFR cascade was up-regulated in colonic tumors and ginseng significantly reduced EGFR and ErbB2 activation and Cox-2 expression. Dietary ginseng altered colonic microbial diversity, and bacterial suppression with metronidazole reduced serum compound K following ginseng gavage. Furthermore, compound K significantly inhibited tumor xenograft growth.</p> <p>Conclusions</p> <p>Ginseng inhibited colonic inflammation and tumorigenesis promoted by Western diet. We speculate that the ginseng metabolite compound K contributes to the chemopreventive effects of this agent in colonic tumorigenesis.</p

Extractive visions : Sweden’s quest for China’s natural resources, 1913–1917

This article scrutinises one of the most fascinating and ambitious cases of Swedish informal empire-building in the industrial age: the skilfully orchestrated attempts by scientists, diplomats, industrial companies and financial institutions to seize control over early Republican China’s most strategic industrial sector–its iron and steel complex. Sweden’s ‘extractive vision’, as we call it, started with the recruitment of Johan Gunnar Andersson, head of the Swedish Geological Survey, as a key advisor to the Chinese government. Contrary to earlier research on Andersson’s Chinese career, which narrowly portrays Andersson as a scientist, we show that he was closely affiliated with the exploitative interests of Swedish industrial and foreign-policy actors. In the end he took the lead in seeking to secure, for Sweden, a quasi-colonial presence in Republican China, centring on large-scale extraction of Chinese iron ore, profit-maximising iron exports throughout the Pacific region and construction and operation of China’s largest steel mills and weapons factories.QC 20201130</p

Key role of subdaily wind variability for tropical surface wind stress

High-frequency observations of surface winds over the open ocean are available only at limited locations. However, these observations are essential for assessing atmospheric influences on the ocean, validating reanalysis products, and building parameterization schemes. By analyzing high-frequency measurements from the Global Tropical Moored Buoy Array, the effects of subdaily winds on the mean surface wind stress magnitude are systematically examined. Subdaily winds account for 12.4% of the total stress magnitude on average. The contribution is enhanced over the Intertropical Convergence Zone and reaches a maximum (28.5%) in the equatorial western Pacific. The magnitude of the contribution is primarily determined by the kinetic energy of subdaily winds. Compared to the buoy observations, the ERA5 and MERRA2 subdaily winds underestimate this contribution by 51% and 63% due to underestimations of subdaily kinetic energy, leading to 7% and 8% underestimations in the total stress magnitude, respectively. Two new gustiness parameterization schemes related to precipitation are developed to account for the effect of subdaily winds, explaining ~80% of the contribution from subdaily winds. Considering the importance of wind stress for ocean-atmosphere interactions, the inclusion of these parametrization schemes in climate models is expected to substantially improve simulations of large-scale climate variability

Complete mitochondrial genome of Accipiter trivirgatus

Crested goshawk (Accipiter trivirgatus) is a diurnal raptor tropical Asia which is a bird species in family Accipitridae. In the present study, we determined its complete mitochondrial genome by PCR-based method. The complete mitochondrial genome was 18,454 bp in length which overall base composition was 31.2% A, 24.4% T, 31.0% C, and 13.4% G. It consisted of the typical structure of 13 PCGs, 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and 2 control regions. All of the PCGs started with ATG codon, except for ND3 which was started with ATC. Most of the genes terminate with codons TAA. The non-coding regions include pseudo-control regions