Computational identification of the normal and perturbed genetic networks involved in myeloid differentiation and acute promyelocytic leukemia

A dissection of the genetic networks and circuitries is described for two form of leukaemia. Integrating transcription factor binding and gene expression profiling, networks are revealed that underly this important human disease

Ku80 cooperates with CBP to promote COX-2 expression and tumor growth.

Cyclooxygenase-2 (COX-2) plays an important role in lung cancer development and progression. Using streptavidin-agarose pulldown and proteomics assay, we identified and validated Ku80, a dimer of Ku participating in the repair of broken DNA double strands, as a new binding protein of the COX-2 gene promoter. Overexpression of Ku80 up-regulated COX-2 promoter activation and COX-2 expression in lung cancer cells. Silencing of Ku80 by siRNA down-regulated COX-2 expression and inhibited tumor cell growth in vitro and in a xenograft mouse model. Ku80 knockdown suppressed phosphorylation of ERK, resulting in an inactivation of the MAPK pathway. Moreover, CBP, a transcription co-activator, interacted with and acetylated Ku80 to co-regulate the activation of COX-2 promoter. Overexpression of CBP increased Ku80 acetylation, thereby promoting COX-2 expression and cell growth. Suppression of CBP by a CBP-specific inhibitor or siRNA inhibited COX-2 expression as well as tumor cell growth. Tissue microarray immunohistochemical analysis of lung adenocarcinomas revealed a strong positive correlation between levels of Ku80 and COX-2 and clinicopathologic variables. Overexpression of Ku80 was associated with poor prognosis in patients with lung cancers. We conclude that Ku80 promotes COX-2 expression and tumor growth and is a potential therapeutic target in lung cancer

Supersymmetric dS/CFT

We put forward new explicit realisations of dS/CFT that relate ${\cal N}=2$ supersymmetric Euclidean vector models with reversed spin-statistics in three dimensions to specific supersymmetric Vasiliev theories in four-dimensional de Sitter space. The partition function of the free supersymmetric vector model deformed by a range of low spin deformations that preserve supersymmetry appears to specify a well-defined wave function with asymptotic de Sitter boundary conditions in the bulk. In particular we find the wave function is globally peaked at undeformed de Sitter space, with a low amplitude for strong deformations. This suggests that supersymmetric de Sitter space is stable in higher-spin gravity and in particular free from ghosts. We speculate this is a limiting case of the de Sitter realizations in exotic string theories.Comment: V2: references and comments added, typos corrected, version published in JHEP; 27 pages, 3 figures, 1 tabl

Descope of the ALIA mission

The present work reports on a feasibility study commissioned by the Chinese Academy of Sciences of China to explore various possible mission options to detect gravitational waves in space alternative to that of the eLISA/LISA mission concept. Based on the relative merits assigned to science and technological viability, a few representative mission options descoped from the ALIA mission are considered. A semi-analytic Monte Carlo simulation is carried out to understand the cosmic black hole merger histories starting from intermediate mass black holes at high redshift as well as the possible scientific merits of the mission options considered in probing the light seed black holes and their coevolution with galaxies in early Universe. The study indicates that, by choosing the armlength of the interferometer to be three million kilometers and shifting the sensitivity floor to around one-hundredth Hz, together with a very moderate improvement on the position noise budget, there are certain mission options capable of exploring light seed, intermediate mass black hole binaries at high redshift that are not readily accessible to eLISA/LISA, and yet the technological requirements seem to within reach in the next few decades for China

Oncogenic ERBB3 Mutations in Human Cancers

SummaryThe human epidermal growth factor receptor (HER) family of tyrosine kinases is deregulated in multiple cancers either through amplification, overexpression, or mutation. ERBB3/HER3, the only member with an impaired kinase domain, although amplified or overexpressed in some cancers, has not been reported to carry oncogenic mutations. Here, we report the identification of ERBB3 somatic mutations in ∼11% of colon and gastric cancers. We found that the ERBB3 mutants transformed colonic and breast epithelial cells in a ligand-independent manner. However, the mutant ERBB3 oncogenic activity was dependent on kinase-active ERBB2. Furthermore, we found that anti-ERBB antibodies and small molecule inhibitors effectively blocked mutant ERBB3-mediated oncogenic signaling and disease progression in vivo

Deep RNA sequencing analysis of readthrough gene fusions in human prostate adenocarcinoma and reference samples

<p>Abstract</p> <p>Background</p> <p>Readthrough fusions across adjacent genes in the genome, or transcription-induced chimeras (TICs), have been estimated using expressed sequence tag (EST) libraries to involve 4-6% of all genes. Deep transcriptional sequencing (RNA-Seq) now makes it possible to study the occurrence and expression levels of TICs in individual samples across the genome.</p> <p>Methods</p> <p>We performed single-end RNA-Seq on three human prostate adenocarcinoma samples and their corresponding normal tissues, as well as brain and universal reference samples. We developed two bioinformatics methods to specifically identify TIC events: a targeted alignment method using artificial exon-exon junctions within 200,000 bp from adjacent genes, and genomic alignment allowing splicing within individual reads. We performed further experimental verification and characterization of selected TIC and fusion events using quantitative RT-PCR and comparative genomic hybridization microarrays.</p> <p>Results</p> <p>Targeted alignment against artificial exon-exon junctions yielded 339 distinct TIC events, including 32 gene pairs with multiple isoforms. The false discovery rate was estimated to be 1.5%. Spliced alignment to the genome was less sensitive, finding only 18% of those found by targeted alignment in 33-nt reads and 59% of those in 50-nt reads. However, spliced alignment revealed 30 cases of TICs with intervening exons, in addition to distant inversions, scrambled genes, and translocations. Our findings increase the catalog of observed TIC gene pairs by 66%.</p> <p>We verified 6 of 6 predicted TICs in all prostate samples, and 2 of 5 predicted novel distant gene fusions, both private events among 54 prostate tumor samples tested. Expression of TICs correlates with that of the upstream gene, which can explain the prostate-specific pattern of some TIC events and the restriction of the <it>SLC45A3-ELK4 </it>e4-e2 TIC to <it>ERG</it>-negative prostate samples, as confirmed in 20 matched prostate tumor and normal samples and 9 lung cancer cell lines.</p> <p>Conclusions</p> <p>Deep transcriptional sequencing and analysis with targeted and spliced alignment methods can effectively identify TIC events across the genome in individual tissues. Prostate and reference samples exhibit a wide range of TIC events, involving more genes than estimated previously using ESTs. Tissue specificity of TIC events is correlated with expression patterns of the upstream gene. Some TIC events, such as <it>MSMB-NCOA4</it>, may play functional roles in cancer.</p

31st Annual Meeting and Associated Programs of the Society for Immunotherapy of Cancer (SITC 2016) : part two

Background The immunological escape of tumors represents one of the main ob- stacles to the treatment of malignancies. The blockade of PD-1 or CTLA-4 receptors represented a milestone in the history of immunotherapy. However, immune checkpoint inhibitors seem to be effective in specific cohorts of patients. It has been proposed that their efficacy relies on the presence of an immunological response. Thus, we hypothesized that disruption of the PD-L1/PD-1 axis would synergize with our oncolytic vaccine platform PeptiCRAd. Methods We used murine B16OVA in vivo tumor models and flow cytometry analysis to investigate the immunological background. Results First, we found that high-burden B16OVA tumors were refractory to combination immunotherapy. However, with a more aggressive schedule, tumors with a lower burden were more susceptible to the combination of PeptiCRAd and PD-L1 blockade. The therapy signifi- cantly increased the median survival of mice (Fig. 7). Interestingly, the reduced growth of contralaterally injected B16F10 cells sug- gested the presence of a long lasting immunological memory also against non-targeted antigens. Concerning the functional state of tumor infiltrating lymphocytes (TILs), we found that all the immune therapies would enhance the percentage of activated (PD-1pos TIM- 3neg) T lymphocytes and reduce the amount of exhausted (PD-1pos TIM-3pos) cells compared to placebo. As expected, we found that PeptiCRAd monotherapy could increase the number of antigen spe- cific CD8+ T cells compared to other treatments. However, only the combination with PD-L1 blockade could significantly increase the ra- tio between activated and exhausted pentamer positive cells (p= 0.0058), suggesting that by disrupting the PD-1/PD-L1 axis we could decrease the amount of dysfunctional antigen specific T cells. We ob- served that the anatomical location deeply influenced the state of CD4+ and CD8+ T lymphocytes. In fact, TIM-3 expression was in- creased by 2 fold on TILs compared to splenic and lymphoid T cells. In the CD8+ compartment, the expression of PD-1 on the surface seemed to be restricted to the tumor micro-environment, while CD4 + T cells had a high expression of PD-1 also in lymphoid organs. Interestingly, we found that the levels of PD-1 were significantly higher on CD8+ T cells than on CD4+ T cells into the tumor micro- environment (p < 0.0001). Conclusions In conclusion, we demonstrated that the efficacy of immune check- point inhibitors might be strongly enhanced by their combination with cancer vaccines. PeptiCRAd was able to increase the number of antigen-specific T cells and PD-L1 blockade prevented their exhaus- tion, resulting in long-lasting immunological memory and increased median survival

A Multi-Timescale Integrated Operation Model for Balancing Power Generation, Ecology, and Water Supply of Reservoir Operation

In traditional ecological scheduling, a single monthly or daily model will lead to the incomplete transmission of ecological information or increase the complexity of solving problems. Therefore, a multi-timescale nested model (MTNM) is proposed. Although the MTNM can express the daily flow process of environmental flow, the quadratic nested calculation method cannot obtain the optimal solution for the daily scheduling scheme. Targeting the problem that long and short-term objectives cannot obtain the optimal solution at the same time, this paper proposes a multi-timescale integrated model (MTIM) which considers the monthly, 10-day, and daily scale. The model is applied to the Liujiaxia reservoir. The scheduling results show that, compared with the MTNM, the MTIM can better meet the multi-objective demand. In a wet year, when both models can guarantee water supply and ecological demand, the MTIM increases electricity generation by 0.91%. In a dry year, electricity generation can still be increased by 4.35% without sacrificing the ecological and water supply benefits of the lower reaches. In different typical years, the MTIM can improve the contradictory relationship between multi-objective by improving the utilization efficiency of water. The results can improve the decision support for the operation process of other reservoirs with ecological needs

A review of municipal solid waste environmental standards with a focus on incinerator residues

Environmental issues are often neglected until a lapse in the care for environment, which leads to serious human health problem, would then put regulation gaps in the spotlight. Environmental regulations and standards are important as they maintain balance among competing resources and help protect human health and the environment. One important environmental standard is related to municipal solid waste (MSW). Proper MSW management is crucial for urban public health. Meanwhile, the sustainability of landfills is also of concern as increasing volumes of MSW consume finite landfill space. The incineration of MSW and the reuse of incinerated residues help alleviate the burden on landfill space. However, the reuse of MSW incinerator residues must be regulated because they may expose the environment to toxic heavy metal elements. The study of environmental standards from different countries applicable to MSW is not widely published, much less those for incinerated MSW residue reuse. This paper compares extant waste classification and reuse standards pertinent to MSW, and explores the unique recent history and policy evolution in some countries exhibiting high environmental regard and rapid changes, so that policy makers can propose new or revise current MSW standards in other countries

Influence of moisture content and temperature on degree of carbonation and the effect on Cu and Cr leaching from incineration bottom ash

This study investigated the influence of moisture content and temperature on the degree of carbonation of municipal solid waste (MSW) incineration bottom ash (IBA) from two different incineration plants in Singapore. The initial rate of carbonation was affected by the nominal moisture content used. Carbonation temperature seemed to play a part in changing the actual moisture content of IBA during carbonation, which in turn affected the degree of carbonation. Results showed that 2 h of carbonation was sufficient for the samples to reach a relatively high degree of carbonation that was close to the degree of carbonation observed after 1 week of carbonation. Both Cu and Cr leaching also showed significant reduction after only 2 h of carbonation. Therefore, the optimum moisture content and temperature were selected based on 2 h of carbonation. The optimum moisture content was 15% for both incineration plants while the optimum temperature was different for the two incineration plants, at 35 °C and 50 °C. The effect on Cu and Cr leaching from IBA after accelerated carbonation was evaluated as a function of carbonation time. Correlation coefficient, Pearson’s R, was used to determine the dominant leaching mechanism. The reduction in Cu leaching was found to be contributed by both formation of carbonate mineral and reduction of DOC leaching. On the other hand, Cr leaching seemed to be dominantly controlled by pH.Accepted versio