Computational Biology in Acute Myeloid Leukemia with CEBPA Abnormalities

__Abstract__ In the last decade, tiling-array and next-generation sequencing technologies allowed quantitative measurements of different cellular processes, such as mRNA expression, genomic changes including deletions or amplifications, DNA-methylation, chromatin modifications or Protein-DNA-binding interactions. Using these technologies, thousands of features can now be measured simultaneously in a patient cell sample. The use of for instance mRNA expression profiles or DNA-methylation profiles have already provided new insight into the molecular biology of patients with Acute Myeloid Leukemia (AML). AML is a blood cell malignancy, in which primitive myeloid cells have been transformed and accumulate in the bone marrow and blood. Different forms of AML exist with different molecular abnormalities that associate with distinct responses to therapy. Many subgroups with comparable mRNA expression or DNA-methylation patterns were identified. These studies also revealed the existence of novel previously undefined AML subtypes. Among those was a group of patients with a mutation in a gene called CEBPA. CEBPA is a gene that encodes the transcription factor CCAAT Enhancer Binding Protein Alpha (C/EBPα), which controls the expression of genes in myeloid progenitor cells. Mutated CEBPA encodes a dysfunctional C/EBPα-protein, which consequently results in aberrant control of “target genes”. In this thesis we focus particularly on the role of CEBPA. We studied the predictive and prognostic relevance of mutated CEBPA, and analyzed in a genome wide fashion the mRNA expression, DNA-methylation and the protein-DNA-binding levels corresponding to (mutated) CEBPA in AML. For the analysis of protein-DNA-binding, we developed a novel statistical methodology. With this statistical methodology we studied the fundamental role of (mutant) C/EBPα binding and the effect on gene expression levels. We also integrated gene expression with DNA-methylation profiles of hundreds of AML patients and revealed the existence of two previously unidentified AML subtypes

Could conscious sedation with midazolam for dental procedures be an alternative to general anesthesia?

Aim: The aim of our study was to evaluate the likelihood that conscious sedation (CS) with intravenous midazolam could become an alternative modality to general anesthesia (GA) for dental procedures.Materials and Methods: In our study, 58 and 47 American Society of Anesthesiologists (ASA).1 pediatric patients, aged 2.12 (mean 6) years, underwent dental procedures and minor oral surgical procedures under GA and CS with intravenous midazolam, respectively. The two groups were evaluated in terms of vital signs, duration of the treatment procedure, patient behavior, and the treatment comfort experienced by the physicians.Results: The oxygen saturation level was significantly lower (GA: 99.0 } 0.30, CS: 98.4 } 1.02; P < 0.001) and the duration of the treatment procedure was significantly shorter (P < 0.001) in the sedation group compared with the GA group. The physicians encountered various difficulties during implementation of the treatment strategy in cases wherethey used CS. Minor oral surgical procedures and tooth extraction  processes requiring no saline irrigation, however, could be performed successfully under CS.Conclusions: In cases requiring multiple dental management issues, the sedation method was not found to be a useful alternative to GA.Key words: Conscious sedation, general anesthesia, pediatric dentistr

Physical routes for the synthesis of kesterite

This paper provides an overview of the physical vapor technologies used to synthesize Cu2ZnSn(S,Se)4 thin films as absorber layers for photovoltaic applications. Through the years, CZT(S,Se) thin films have been fabricated using sequential stacking or co-sputtering of precursors as well as using sequential or co-evaporation of elemental sources, leading to high-efficient solar cells. In addition, pulsed laser deposition of composite targets and monograin growth by the molten salt method were developed as alternative methods for kesterite layers deposition. This review presents the growing increase of the kesterite-based solar cell efficiencies achieved over the recent years. A historical description of the main issues limiting this efficiency and of the experimental pathways designed to prevent or limit these issues is provided and discussed as well. Afinal section is dedicated to the description of promising process steps aiming at further improvements of solar cell efficiency, such as alkali doping and bandgap grading1. R Caballero and M León acknowledge financial support via the Spanish Ministry of Science, Innovation and Universities project (WINCOST, ENE2016-80788-C5-2-R) and thank H2020 EU Programme under the project INFINITE-CELL (H2020-MSCA-RISE-2017-777968). 2. S Canulescu and J Schou acknowledge the support from Innovation Fund Denmark. 3. D-H Kim acknowledges financial support via the DGIST R&D Program of the Ministry of Science and ICT, KOREA (18-BD-05). 4.C. Malerba acknowledges the support from the Italian Ministry of Economic development in the framework of the Operating Agreement with ENEA for the Research on the Electric System. 5.A Redinger acknowledges financial support via the FNR Attract program, Project : SUNSPOT, Nr.11244141. 6. E Saucedo thanks H2020 EU Programme under the projects STARCELL (H2020-NMBP-03-2016-720907) and INFINITE-CELL (H2020-MSCA-RISE-2017-777968), the Spanish Ministry of Science, Innovation and Universities for the IGNITE project (ENE2017-87671-C3-1-R), and the European Regional Development Funds (ERDF, FEDER Programa Competitivitat de Catalunya 2007–2013). IREC belong to the SEMS (Solar Energy Materials and Systems) Consolidated Research Group of the ‘Generalitat de Catalunya’ (Ref. 2017 SGR 862). 7. Taltech acknowledges financial support via the Estonian Ministry of Education and Research funding project IUT19-28 and the European Union Regional Development Fund, Project TK141. 8. B Vermang has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 Research and Innovation Programme (Grant Agreement No 715027

Susceptible genes and disease mechanisms identified in frontotemporal dementia and frontotemporal dementia with Amyotrophic Lateral Sclerosis by DNA-methylation and GWAS.

Frontotemporal dementia (FTD) is a neurodegenerative disorder predominantly affecting the frontal and temporal lobes. Genome-wide association studies (GWAS) on FTD identified only a few risk loci. One of the possible explanations is that FTD is clinically, pathologically, and genetically heterogeneous. An important open question is to what extent epigenetic factors contribute to FTD and whether these factors vary between FTD clinical subgroup. We compared the DNA-methylation levels of FTD cases (n = 128), and of FTD cases with Amyotrophic Lateral Sclerosis (FTD-ALS; n = 7) to those of unaffected controls (n = 193), which resulted in 14 and 224 candidate genes, respectively. Cluster analysis revealed significant class separation of FTD-ALS from controls. We could further specify genes with increased susceptibility for abnormal gene-transcript behavior by jointly analyzing DNA-methylation levels with the presence of mutations in a GWAS FTD-cohort. For FTD-ALS, this resulted in 9 potential candidate genes, whereas for FTD we detected 1 candidate gene (ELP2). Independent validation-sets confirmed the genes DLG1, METTL7A, KIAA1147, IGHMBP2, PCNX, UBTD2, WDR35, and ELP2/SLC39A6 among others. We could furthermore demonstrate that genes harboring mutations and/or displaying differential DNA-methylation, are involved in common pathways, and may therefore be critical for neurodegeneration in both FTD and FTD-ALS

Genome-wide association meta-analysis of 78,308 individuals identifies new loci and genes influencing human intelligence

Intelligence is associated with important economic and health-related life outcomes1. Despite intelligence having substantial heritability2 (0.54) and a confirmed polygenic nature, initial genetic studies were mostly underpowered3,4,5. Here we report a meta-analysis for intelligence of 78,308 individuals. We identify 336 associated SNPs (METAL P < 5 × 10−8) in 18 genomic loci, of which 15 are new. Around half of the SNPs are located inside a gene, implicating 22 genes, of which 11 are new findings. Gene-based analyses identified an additional 30 genes (MAGMA P < 2.73 × 10−6), of which all but one had not been implicated previously. We show that the identified genes are predominantly expressed in brain tissue, and pathway analysis indicates the involvement of genes regulating cell development (MAGMA competitive P = 3.5 × 10−6). Despite the well-known difference in twin-based heritability2 for intelligence in childhood (0.45) and adulthood (0.80), we show substantial genetic correlation (rg = 0.89, LD score regression P = 5.4 × 10−29). These findings provide new insight into the genetic architecture of intelligence

An epigenome-wide association study meta-analysis of educational attainment

The epigenome is associated with biological factors, such as disease status, and environmental factors, such as smoking, alcohol consumption and body mass index. Although there is a widespread perception that environmental influences on the epigenome are pervasive and profound, there has been little evidence to date in humans with respect to environmental factors that are biologically distal. Here we provide evidence on the associations between epigenetic modifications-in our case, CpG methylation -and educational attainment (EA), a biologically distal environmental factor that is arguably among the most important life-shaping experiences for individuals. Specifically, we report the results of an epigenome-wide association study meta-analysis of EA based on data from 27 cohort studies with a total of 10 767 individuals. We find nine CpG probes significantly associated with EA. However, robustness analyses show that all nine probes have previously been found to be associated with smoking. Only two associations remain when we perform a sensitivity analysis in the subset of never-smokers, and these two probes are known to be strongly associated with maternal smoking during pregnancy, and thus their association with EA could be due to correlation between EA and maternal smoking. Moreover, the effect sizes of the associations with EA are far smaller than the known associations with the biologically proximal environmental factors alcohol consumption, body mass index, smoking and maternal smoking during pregnancy. Follow-up analyses that combine the effects of many probes also point to small methylation associations with EA that are highly correlated with the combined effects of smoking. If our findings regarding EA can be generalized to other biologically distal environmental factors, then they cast doubt on the hypothesis that such factors have large effects on the epigenome