Prioritization of genes driving congenital phenotypes of patients with de novo genomic structural variants

Background:Genomic structural variants (SVs) can affect many genes and regulatory elements. Therefore, the molecular mechanisms driving the phenotypes of patients carrying de novo SVs are frequently unknown. Methods:We applied a combination of systematic experimental and bioinformatic methods to improve the molecular diagnosis of 39 patients with multiple congenital abnormalities and/or intellectual disability harboring apparent de novo SVs, most with an inconclusive diagnosis after regular genetic testing. Results: In 7 of these cases (18%), whole-genome sequencing analysis revealed disease-relevant complexities of the SVs missed in routine microarray-based analyses. We developed a computational tool to predict the effects on genes directly affected by SVs and on genes indirectly affected likely due to the changes in chromatin organization and impact on regulatory mechanisms. By combining these functional predictions with extensive phenotype information, candidate driver genes were identified in 16/39 (41%) patients. In 8 cases, evidence was found for the involvement of multiple candidate drivers contributing to different parts of the phenotypes. Subsequently, we applied this computational method to two cohorts containing a total of 379 patients with previously detected and classified de novo SVs and identified candidate driver genes in 189 cases (50%), including 40 cases whose SVs were previously not classified as pathogenic. Pathogenic position effects were predicted in 28% of all studied cases with balanced SVs and in 11% of the cases with copy number variants. Conclusions:These results demonstrate an integrated computational and experimental approach to predict driver genes based on analyses of WGS data with phenotype association and chromatin organization datasets. These analyses nominate new pathogenic loci and have strong potential to improve the molecular diagnosis of patients with de novo SVs

Deficiency of nucleotide excision repair is associated with mutational signature observed in cancer

Nucleotide excision repair (NER) is one of the main DNA repair pathways that protect cells against genomic damage. Disruption of this pathway can contribute to the development of cancer and accelerate aging. Mutational characteristics of NER-deficiency may reveal important diagnostic opportunities, as tumors deficient in NER are more sensitive to certain treatments. Here, we analyzed the genome-wide somatic mutational profiles of adult stem cells (ASCs) from NER-deficient Ercc1−/Δ mice. Our results indicate that NER-deficiency increases the base substitution load twofold in liver but not in small intestinal ASCs, which coincides with the tissue-specific aging pathology observed in these mice. Moreover, NER-deficient ASCs of both tissues show an increased contribution of Signature 8 mutations, which is a mutational pattern with unknown etiology that is recurrently observed in various cancer types. The scattered genomic distribution of the base substitutions indicates that deficiency of global-genome NER (GG-NER) underlies the observed mutational consequences. In line with this, we observe increased Signature 8 mutations in a GG-NER-deficient human organoid culture, in which XPC was deleted using CRISPR-Cas9 gene-editing. Furthermore, genomes of NER-deficient breast tumors show an increased contribution of Signature 8 mutations compared with NER-proficient tumors. Elevated levels of Signature 8 mutations could therefore contribute to a predictor of NER-deficiency based on a patient's mutational profile

Cost-effectiveness of a vocational enablement protocol for employees with hearing impairment; design of a randomized controlled trial

Background: Hearing impairment at the workplace, and the resulting psychosocial problems are a major health problem with substantial costs for employees, companies, and society. Therefore, it is important to develop interventions to support hearing impaired employees. The objective of this article is to describe the design of a randomized controlled trial evaluating the (cost-) effectiveness of a Vocational Enablement Protocol (VEP) compared with usual care. Methods/Design. Participants will be selected with the 'Hearing and Distress Screener'. The study population will consist of 160 hearing impaired employees. The VEP intervention group will be compared with usual care. The VEP integrated care programme consists of a multidisciplinary assessment of auditory function, work demands, and personal characteristics. The goal of the intervention is to facilitate participation in work. The primary outcome measure of the study is 'need for recovery after work'. Secondary outcome measures are coping with hearing impairment, distress, self-efficacy, psychosocial workload, job control, general health status, sick leave, work productivity, and health care use. Outcome measures will be assessed by questionnaires at baseline, and 3, 6, 9, and 12 months after baseline. The economic evaluation will be performed from both a societal and a company perspective. A process evaluation will also be performed. Discussion. Interventions addressing occupational difficulties of hearing impaired employees are rare but highly needed. If the VEP integrated care programme proves to be (cost-) effective, the intervention can have an impact on the well-being of hearing impaired employees, and thereby, on the costs for the company as well for the society. Trial registration. Netherlands Trial Register (NTR): NTR2782. © 2012 Gussenhoven et al; BioMed Central Ltd

Chemoselective hydrogenation of functionalized nitroarenes using supported mo promoted Pt nanoparticles

Keywords: chemoselectivity; heterogeneous catalysis; nanoparticles; platinum; reduction Positive discrimination: Supported MoVI promoted Pt nanoparticles (c-Pt+Mo/C) are successfully applied as catalysts in the chemoselective hydrogenation of functionalized nitroarenes. Mild conditions (30¿°C, 4 bar H2, EtOH) prove sufficient for complete reduction to the corresponding anilines, leaving other functional groups untouched. Turnover numbers of at least 20¿000 show that this catalyst is very tolerant to halogen-containing aromatics

Extensive localization of long noncoding RNAs to the cytosol and mono- and polyribosomal complexes

Contains fulltext : 138006.pdf (publisher's version ) (Open Access)BACKGROUND: Long noncoding RNAs (lncRNAs) form an abundant class of transcripts, but the function of the majority of them remains elusive. While it has been shown that some lncRNAs are bound by ribosomes, it has also been convincingly demonstrated that these transcripts do not code for proteins. To obtain a comprehensive understanding of the extent to which lncRNAs bind ribosomes, we performed systematic RNA sequencing on ribosome-associated RNA pools obtained through ribosomal fractionation and compared the RNA content with nuclear and (non-ribosome bound) cytosolic RNA pools. Results : The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. CONCLUSIONS: Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes

The influence of ebselen on the toxicity of cisplatin in LLC-PK1 cells

LLC-PK1 cells have been used as an in vitro model to study the nephrotoxicity of the antitumor drug cisplatin. A concentration-dependent cytotoxicity of cisplatin, measured as lactate dehydrogenase leakage and amount of protein remaining attached to the culture plate, was observed. At a cisplatin concentration of 0.4 mM cell viability was reduced to 21% after 72 hr. Ebselen, a seleno-organic compound capable of forming selenol intermediates through reaction with thiols, was found to protect LLC-PK1 cells against cisplatin-induced toxicity at low concentrations (5-15 microM). The ebselen-induced protection against cisplatin toxicity in this in vitro test system apparently correlates well with a similar protection previously observed in vivo in mice and rats

BASF NanoSelect (TM) technology : innovative supported Pd- and Pt-based catalysts for selective hydrogenation reactions

An innovative BASF catalyst manufacturing technology (NanoSelect (TM)) is introduced which allows production of heterogeneous catalysts with excellent control over metal crystallite sizes. NanoSelect (TM) technology enabled the development of Pd catalysts which are lead-free Lindlar catalyst replacements in alkyne-to-cis-alkene hydrogenations. NanoSelect (TM) Pt catalysts showed excellent chemoselectivity in substituted nitro-arene hydrogenation reactions without build-up of hydroxylamine intermediates. All NanoSelect (TM) produced catalysts show markedly higher activity per gram of metal leading to ten-fold less use of precious meta