Integrated genomic characterization of oesophageal carcinoma

Oesophageal cancers are prominent worldwide; however, there are few targeted therapies and survival rates for these cancers remain dismal. Here we performed a comprehensive molecular analysis of 164 carcinomas of the oesophagus derived from Western and Eastern populations. Beyond known histopathological and epidemiologic distinctions, molecular features differentiated oesophageal squamous cell carcinomas from oesophageal adenocarcinomas. Oesophageal squamous cell carcinomas resembled squamous carcinomas of other organs more than they did oesophageal adenocarcinomas. Our analyses identified three molecular subclasses of oesophageal squamous cell carcinomas, but none showed evidence for an aetiological role of human papillomavirus. Squamous cell carcinomas showed frequent genomic amplifications of CCND1 and SOX2 and/or TP63, whereas ERBB2, VEGFA and GATA4 and GATA6 were more commonly amplified in adenocarcinomas. Oesophageal adenocarcinomas strongly resembled the chromosomally unstable variant of gastric adenocarcinoma, suggesting that these cancers could be considered a single disease entity. However, some molecular features, including DNA hypermethylation, occurred disproportionally in oesophageal adenocarcinomas. These data provide a framework to facilitate more rational categorization of these tumours and a foundation for new therapies.ope

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

The effect of culture on Corporate Governance Practices in Nigeria

This study focuses on the effect of culture on the application of corporate governance practices in Nigeria. Corporate governance has been receiving serious attention in emerging markets over the past two decades. But relatively little attention has been given to the study on corporate governance in a country study. The current situations in Nigerian public and private sectors such as the corporate scandal resulting from Lever Brothers Nigeria plc, Siemens, Shell, Halliburton, and Cadbury Nigeria plc, have shown that the issue of fraud, corruption, and corporate scandals cannot be overlooked. Most top management, as this study argues, bring in beliefs acquired from their early childhood into their senior management roles and responsibilities. This study adopts a grounded theory and reports on the effect of culture on the implementation of corporate governance in Nigeria. Based on the interview with 32 staffs, this study identifies the effect of culture that shapes corporate governance and they include abuse of power by top management, weak legal framework, poor recruitment and ineffective control. Although having efficient corporate governance is worth pursuing, this depends on the power of top management, the strength of internal control procedures and the legal framework put in place by management

Comprehensive molecular characterization of the hippo signaling pathway in cancer

Hippo signaling has been recognized as a key tumor suppressor pathway. Here, we perform a comprehensive molecular characterization of 19 Hippo core genes in 9,125 tumor samples across 33 cancer types using multidimensional “omic” data from The Cancer Genome Atlas. We identify somatic drivers among Hippo genes and the related microRNA (miRNA) regulators, and using functional genomic approaches, we experimentally characterize YAP and TAZ mutation effects and miR-590 and miR-200a regulation for TAZ. Hippo pathway activity is best characterized by a YAP/TAZ transcriptional target signature of 22 genes, which shows robust prognostic power across cancer types. Our elastic-net integrated modeling further reveals cancer-type-specific pathway regulators and associated cancer drivers. Our results highlight the importance of Hippo signaling in squamous cell cancers, characterized by frequent amplification of YAP/TAZ, high expression heterogeneity, and significant prognostic patterns. This study represents a systems-biology approach to characterizing key cancer signaling pathways in the post-genomic era

Numerical and Experimental Investigation of Transient Two-phase Flow Phenomena in Concentrated Solar Power Plants with Direct Steam Generation

The direct steam generation process in parabolic trough collectors of CSP plants heats and evaporates water to obtain steam that is subsequently superheated to feed a steam turbine. Recently, this process was proven in economic and operational perspectives in the once-through mode to be a promising option for large-scale commercial plants. Nevertheless, knowledge gaps about the two-phase flow could deter the deployment of this type of power plant. The once-through mode implies temperature oscillations at the transition region from two-phase flow to superheated steam that induces thermal stresses in the receiver and could reduce the receiver's lifetime. The uncertainties complicate a reliable economic analysis. The thesis aims to enrich the existing pool of knowledge about the two-phase flow under specific conditions in state-of-the-art parabolic trough facilities with direct steam generation. The objective is to state the relevance of intermittent flows and wavy flows, severe slugging, and flow instabilities regarding the implications at the end of the two-phase flow region by means of advanced numerical and experimental tools. The numerical simulations use the capabilities of a one-dimensional two-fluid model that gives a deeper insight into the two-phase flow compared to the previously used homogeneous equilibrium models. The unique experiments are performed with a single wire-mesh sensor, which measures the local instantaneous void fraction and has been installed in the low-quality region of the DISS test facility at the Plataforma Solar de Almería in Spain for the first time. It is analytically shown that the two-fluid model can identify unstable liquid-gas interfaces in certain conditions that would initiate the transition to a non-stratified flow. The numerical results of intermittent and wavy flow are validated by wire-mesh sensor experiments, suggesting that thermal oscillations at the end of the two-phase flow are linked to the transient two-phase flow pattern in the evaporator. The wire-mesh sensor measures slug flow, roll waves, wavy flow, and stratified-wavy flow in the horizontal receiver pipes within pressures of 30 to 80 bar.In the simulation, severe slugging could not be observed in the U-shaped connection pipes under typical operating conditions - this can mainly be ascribed to high-pressure conditions. The obtained findings enhance the understanding of the evaporation process in the receiver pipes and improve the confidence in this technology. Subsequent research should increase the number of experiments in the low-quality region and extend the measurements towards the high-quality region. These efforts will yield a full collection of reliable and reproducible data for the investigated system that is affected by many and various influencing parameters

Epidemiological study on survival of chronic myeloid leukemia (CML) and Ph+ acute lymphoblastic leukemia (ALL) patients with BCR-ABL T315I mutation.

The BCR-ABL T315I mutation represents a major mechanism of resistance to tyrosine kinase inhibitors (TKIs). The objectives of this retrospective observational study were to estimate overall and progression-free survival for chronic myeloid leukemia in chronic-phase (CP), accelerated-phase (AP), or blastic-phase (BP) and Philadelphia chromosome-positive (Ph)(+) acute lymphoblastic leukemia (ALL) patients with T315I mutation. Medical records of 222 patients from 9 countries were reviewed; data were analyzed using log-rank tests and Cox proportional hazard models. Median age at T315I mutation detection was 54 years; 57% cases were men. Median time between TKI treatment initiation and T315I mutation detection was 29.2, 15.4, 5.8, and 9.1 months, respectively, for CP, AP, BP, and Ph(+) ALL patients. After T315I mutation detection, second-generation TKIs were used in 56% of cases, hydroxyurea in 39%, imatinib in 35%, cytarabine in 26%, MK-0457 in 11%, stem cell transplantation in 17%, and interferon-alpha in 6% of cases. Median overall survival from T315I mutation detection was 22.4, 28.4, 4.0, and 4.9 months, and median progression-free survival was 11.5, 22.2, 1.8, and 2.5 months, respectively, for CP, AP, BP, and Ph(+) ALL patients. These results confirm that survival of patients harboring a T315I mutation is dependent on disease phase at the time of mutation detection

Ponatinib efficacy and safety in Philadelphia chromosome-positive leukemia: final 5-year results of the phase 2 PACE trial

Ponatinib has potent activity against native and mutant BCR-ABL1, including BCR-ABL1T315I. The pivotal phase 2 Ponatinib Ph+ ALL and CML Evaluation (PACE) trial evaluated efficacy and safety of ponatinib at a starting dose of 45 mg once daily in 449 patients with chronic myeloid leukemia (CML) or Philadelphia chromosome–positive acute lymphoblastic leukemia (ALL) resistant/intolerant to dasatinib or nilotinib, or with BCR-ABL1T315I. This analysis focuses on chronic-phase CML (CP-CML) patients (n = 270) with 56.8-month median follow-up. Among 267 evaluable patients, 60%, 40%, and 24% achieved major cytogenetic response (MCyR), major molecular response (MMR), and 4.5-log molecular response, respectively. The probability of maintaining MCyR for 5 years was 82% among responders. Dose reductions were implemented in October 2013 to decrease the risk of arterial occlusive events (AOEs); ≥90% of CP-CML patients who had achieved MCyR or MMR maintained response 40 months after elective dose reductions. Estimated 5-year overall survival was 73%. In CP-CML patients, the most common treatment-emergent adverse events were rash (47%), abdominal pain (46%), thrombocytopenia (46%), headache (43%), dry skin (42%), and constipation (41%). The cumulative incidence of AOEs in CP-CML patients increased over time to 31%, while the exposure-adjusted incidence of new AOEs (15.8 and 4.9 per 100 patient-years in years 1 and 5, respectively) did not increase over time. These final PACE results demonstrate ponatinib provides durable and clinically meaningful responses, irrespective of dose reductions, in this population of heavily pretreated CP-CML patients. This trial was registered at www.clinicaltrials.gov as #NCT01207440