ATLAS Biolabs GmbH

Berlin, Germany

ATLAS Biolabs GmbH

Berlin, Germany

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Lemaire M.,Yale University | Fremeaux-Bacchi V.,Assistance Publique Hopitaux de Paris | Schaefer F.,University of Heidelberg | Choi M.,Yale University | And 29 more authors.
Nature Genetics | Year: 2013

Pathologic thrombosis is a major cause of mortality. Hemolytic-uremic syndrome (HUS) features episodes of small-vessel thrombosis resulting in microangiopathic hemolytic anemia, thrombocytopenia and renal failure. Atypical HUS (aHUS) can result from genetic or autoimmune factors that lead to pathologic complement cascade activation. Using exome sequencing, we identified recessive mutations in DGKE (encoding diacylglycerol kinase É) that co-segregated with aHUS in nine unrelated kindreds, defining a distinctive Mendelian disease. Affected individuals present with aHUS before age 1 year, have persistent hypertension, hematuria and proteinuria (sometimes in the nephrotic range), and develop chronic kidney disease with age. DGKE is found in endothelium, platelets and podocytes. Arachidonic acid-containing diacylglycerols (DAG) activate protein kinase C (PKC), which promotes thrombosis, and DGKE normally inactivates DAG signaling. We infer that loss of DGKE function results in a prothrombotic state. These findings identify a new mechanism of pathologic thrombosis and kidney failure and have immediate implications for treating individuals with aHUS. © 2013 Nature America, Inc. All rights reserved.


Huebner A.K.,University Hospital Jena | Gandia M.,Hospital Universitario Ramon y Cajal | Gandia M.,Research Center Biomedica En Red Of Enfermedades Raras Ciberer | Frommolt P.,University of Cologne | And 23 more authors.
American Journal of Human Genetics | Year: 2011

The fact that hereditary hearing loss is the most common sensory disorder in humans is reflected by, among other things, an extraordinary allelic and nonallelic genetic heterogeneity. X-chromosomal hearing impairment represents only a minor fraction of all cases. In a study of a Spanish family the locus for one of the X-chromosomal forms was assigned to Xp22 (DFNX4). We mapped the disease locus in the same chromosomal region in a large German pedigree with X-chromosomal nonsyndromic hearing impairment by using genome-wide linkage analysis. Males presented with postlingual hearing loss and onset at ages 3-7, whereas onset in female carriers was in the second to third decades. Targeted DNA capture with high-throughput sequencing detected a nonsense mutation in the small muscle protein, X-linked (SMPX) of affected individuals. We identified another nonsense mutation in SMPX in patients from the Spanish family who were previously analyzed to map DFNX4. SMPX encodes an 88 amino acid, cytoskeleton-associated protein that is responsive to mechanical stress. The presence of Smpx in hair cells and supporting cells of the murine cochlea indicates its role in the inner ear. The nonsense mutations detected in the two families suggest a loss-of-function mechanism underlying this form of hearing impairment. Results obtained after heterologous overexpression of SMPX proteins were compatible with this assumption. Because responsivity to physical force is a characteristic feature of the protein, we propose that long-term maintenance of mechanically stressed inner-ear cells critically depends on SMPX function. © 2011 The American Society of Human Genetics.


Grant
Agency: European Commission | Branch: FP7 | Program: MC-ITN | Phase: FP7-PEOPLE-2012-ITN | Award Amount: 3.80M | Year: 2012

DNA is tightly wrapped around histones to form chromatin, a highly dynamic structure that can adopt different conformations with contrasting degrees of compaction. Essential processes of DNA metabolism, such as DNA repair, replication or transcription operate in the context of chromatin and higher order chromosomal organization. Understanding how modulation of chromatin structure and repair influence cell fate decisions in development and disease or how genome surveillance factors interact with the chromatin structure to safeguard the genome is an emerging question that represents a major challenge for human health. The objectives of the aDDRess ITN are: 1. to establish a European research platform of excellence in the proposed field, 2. to create a Network dedicated for the training of ESR/ERs promoting their independent careers and prospects and 3. to transform our current collaborations into a stronger intellectual and training network with links to the industry. In addressing these aims, we have put forward a multidisciplinary approach to study this central thematic area at the molecular, cellular and systems level by assembling a group of scientists with cross disciplinary expertise and capabilities. This integrated approach is likely to provide a solid groundwork on genome maintenance and chromatin dynamics driven by DNA damage.


Schneider K.U.,University of Heidelberg | Dietrich D.,Epigenomics AG | Fleischhacker M.,Charité - Medical University of Berlin | Leschber G.,ELK Berlin Chest Hospital | And 11 more authors.
BMC Cancer | Year: 2011

Background: DNA methylation in the SHOX2 locus was previously used to reliably detect lung cancer in a group of critical controls, including 'cytologically negative' samples with no visible tumor cell content, at a high specificity based on the analysis of bronchial lavage samples. This study aimed to investigate, if the methylation correlates with SHOX2 gene expression and/or copy number alterations. An amplification of the SHOX2 gene locus together with the observed tumor-specific hypermethylation might explain the good performance of this marker in bronchial lavage samples.Methods: SHOX2 expression, gene copy number and DNA methylation were determined in lung tumor tissues and matched morphologically normal adjacent tissues (NAT) from 55 lung cancer patients. Quantitative HeavyMethyl (HM) real-time PCR was used to detect SHOX2 DNA methylation levels. SHOX2 expression was assayed with quantitative real-time PCR, and copy numbers alterations were measured with conventional real-time PCR and array CGH.Results: A hypermethylation of the SHOX2 locus in tumor tissue as compared to the matched NAT from the same patient was detected in 96% of tumors from a group of 55 lung cancer patients. This correlated highly significantly with the frequent occurrence of copy number amplification (p < 0.0001), while the expression of the SHOX2 gene showed no difference.Conclusions: Frequent gene amplification correlated with hypermethylation of the SHOX2 gene locus. This concerted effect qualifies SHOX2 DNA methylation as a biomarker for lung cancer diagnosis, especially when sensitive detection is needed, i.e. in bronchial lavage or blood samples. © 2011 Schneider et al; licensee BioMed Central Ltd.


Reiner G.,Justus Liebig University | Bertsch N.,Justus Liebig University | Hoeltig D.,University of Veterinary Medicine Hannover | Selke M.,University of Veterinary Medicine Hannover | And 7 more authors.
Mammalian Genome | Year: 2014

Actinobacillus pleuropneumoniae is among the most important pathogens worldwide in pig production. The agent can cause severe economic losses due to decreased performance, acute or chronic pleuropneumonia and an increased incidence of death. Therapeutics cannot be used in a sustainable manner, and vaccination is not always available, but discovering more about host defence and disease mechanisms might lead to new methods of prophylaxis. The aim of the present study was to detect quantitative trait loci (QTL) associated with resistance/susceptibility to A. pleuropneumoniae. Under controlled conditions, 170 F2 animals of a Hampshire/Landrace family, with known differences in founder populations regarding A. pleuropneumoniae resistance, were challenged with an A. pleuropneumoniae serotype 7 aerosol followed by a detailed clinical, radiographic, ultrasonographic, pathological and bacteriological examination. F2 pigs were genotyped with 159 microsatellite markers. Significant QTL were identified on Sus scrofa chromosomes (SSC) 2, 6, 12, 13, 16, 17 and 18. They explained 6-22 % of phenotypic variance. One QTL on SSC2 reached significance on a genome-wide level for five associated phenotypic traits. A multiple regression analysis revealed a combinatory effect of markers SWR345 (SSC2) and S0143 (SSC12) on Respiratory Health Score, Clinical Score and the occurrence of death. The results indicate the genetic background of A. pleuropneumoniae resistance in swine and provide new insights into the genetic architecture of resistance/susceptibility to porcine pleuropneumonia. The results will be helpful in identifying the underlying genes and mechanisms. © 2014 Springer Science+Business Media.


Ibrahim D.M.,Charité - Medical University of Berlin | Ibrahim D.M.,Max Planck Institute for Molecular Genetics | Hansen P.,Charité - Medical University of Berlin | Rodelsperger C.,Charité - Medical University of Berlin | And 20 more authors.
Genome Research | Year: 2013

Gene regulation by transcription factors (TFs) determines developmental programs and cell identity. Consequently, mutations in TFs can lead to dramatic phenotypes in humans by disrupting gene regulation. To date, the molecular mechanisms that actually cause these phenotypes have been difficult to address experimentally. ChIP-seq, which couples chromatin immunoprecipitation with high-throughput sequencing, allows TF function to be investigated on a genomewide scale, enabling new approaches for the investigation of gene regulation. Here, we present the application of ChIP-seq to explore the effect of missense mutations in TFs on their genome-wide binding profile. Using a retroviral expression system in chicken mesenchymal stem cells, we elucidated the mechanism underlying a novel missense mutation in HOXD13 (Q317K) associated with a complex hand and foot malformation phenotype. The mutated glutamine (Q) is conserved in most homeodomains, a notable exception being bicoid-type homeodomains that have lysine (K) at this position. Our results show that the mutation results in a shift in the binding profile of the mutant toward a bicoid/PITX1 motif. Gene expression analysis and functional assays using in vivo overexpression studies confirm that the mutation results in a partial conversion of HOXD13 into a TF with bicoid/PITX1 properties. A similar shift was not observed with another mutation, Q317R, which is associated with brachysyndactyly, suggesting that the bicoid/PITX1-shift observed for Q317K might be related to the severe clinical phenotype. The methodology described can be used to investigate a wide spectrum of TFs and mutations that have not previously been amenable to ChIP-seq experiments. © 2013 Ibrahim et al.


PubMed | ATLAS Biolabs GmbH, University of Warwick, Innsbruck Medical University and Bioenergy 2020+ GmbH
Type: | Journal: Scientific reports | Year: 2016

Investigations of cellular processes initiated by volatile organic compounds (VOCs) are limited when modelling realistic long-term exposure scenarios at low concentrations. Exposure to indoor VOCs is associated with a range of adverse effects, but data on molecular changes at regulatory threshold limits are lacking. Activity analysis of VOC in vitro can be a valuable complement to inhalation toxicological evaluations. We developed an exposure platform that generates a stable VOC atmosphere and allows the exposure of cells for longer periods. Using formaldehyde as a model analyte, air-liquid interface cultured A549 lung epithelial cells were exposed to critical concentrations of 0.1 and 0.5ppm for 3 days. Owing to the lack of known exposure biomarkers, we applied a genome-wide transcriptional analysis to investigate cellular responses at these sublethal concentrations. We demonstrate a minor overlap of differentially expressed transcripts for both treatment concentrations, which can be further analyzed for their use as exposure biomarkers. Moreover, distinct expression patterns emerge for 0.1 and 0.5ppm formaldehyde exposure, which is reflected in significant enrichment of distinct biological processes. More specifically, metabolism of specific compound classes, lipid biosynthesis and lung-associated functions are affected by lower exposure levels and processes affecting proliferation and apoptosis dominate the higher exposure levels.


Grant
Agency: European Commission | Branch: FP7 | Program: MC-ITN | Phase: FP7-PEOPLE-2012-ITN | Award Amount: 3.65M | Year: 2012

Ageing is an inexorable homeostatic failure of largely unknown aetiology that leads to increased vulnerability to disease limiting the quality of life in the elderly and creating high costs to the society. Until recently, the daunting complexity of the ageing process, the conspicuous lack of tools to study it, and a dearth of experimentally tractable model systems have greatly hindered any hypothesis-driven reductionist approaches to understand the molecular basis of ageing. Whereas molecular and cellular damage is thought to be a cause of ageing and age-related pathologies, little is known about the molecular events that underlie ageing or determine longevity. A large number of progeroid syndromes that are characterized by an early onset of age-related pathology are linked to inborn defects in genome maintenance thus pointing towards damage in (nuclear) DNA as a major culprit of ageing and age-related pathology. DNA damage fuelled by intrinsic and environmental sources of genotoxic insult and by errors of genome maintenance mechanisms invariably accumulates with advancing age. The outcome of DNA damage is diverse and generally adverse: DNA lesions may physically obstruct essential processes including DNA replication and transcription. In addition, DNA damage activates checkpoint responses that lead to a reduction in cell proliferation potential (cellular senescence) or to an increase in cell death. As a result, depending on the type and severity of DNA injuries and the cellular response to DNA damage, these cellular mechanisms impair organ maintenance and function during ageing. The CodAge ITN proposes an integrated approach in studying the role of Chronic DNA damage in Ageing and age-related pathology.


Grant
Agency: European Commission | Branch: FP7 | Program: CP-FP | Phase: HEALTH.2013.2.2.1-2 | Award Amount: 7.74M | Year: 2014

Postoperative delirium (POD) is characterized by the progressive deterioration of sensory/cognitive function after surgery with incidences of up to 30-80%. It is frequently followed by postoperative cognitive dysfunction (POCD) which tends to persist over time. In elderly patients, POCD resembles chronic dementia and appears to accelerate the cognitive decline in Alzheimer dementia. POD is strongly associated with subsequent dementia after 3.2 and 5.0 years of follow-up: odds ratio = 12.52 [95% CI, 1.86-84.21] corrected for baseline dementia, severity of illness, age. In an aging society like the EU, the socioeconomic implications of POD/POCD are therefore profound. At present no treatment exists and there are no established molecular or imaging biomarkers that allow risk and clinical outcome prediction. We will establish valid biomarkers panels for risk and clinical outcome prediction of POD/POCD in N=1200 surgical patients according to the regulatory requirements of the European Medicines Agency. Thus, a valuable database will be created not yet existing worldwide. Neuroimaging investigations, which directly provide information on brain structure/function, will include structural magnetic resonance imaging (MRI), diffusion tensor imaging (DTI), arterial spin labelling (ASL), functional magnetic resonance imaging with simultaneous electrophysiology (fMRI/EEG) and glutamate MR-spectroscopy (MRS). These investigations will be complemented by genetic/gene expression analyses (sequencing of cholinergic candidate genes/corresponding transcripts) and analyses of plasma and cerebrospinal fluid markers (inflammatory/metabolic). Supported by bioinformatics approaches, integration of neuroimaging data with knowledge from molecular biomarkers (multivariate expert system) is expected to allow patient stratification. This will greatly support decision-making before surgical intervention (balancing benefits and risks) as well as the development of novel therapies in POD/POCD.


Hirsch B.,Charité - Medical University of Berlin | Grunbaum M.,Institute of Pathology | Wagner F.,ATLAS Biolabs GmbH | Bi Y.,Fudan University | And 4 more authors.
Histopathology | Year: 2012

Aims: A20 (TNFAIP3) is a nuclear factor-κB (NF-κB)-inducible component of tumour necrosis factor and Toll-like receptor intracellular signal transduction. It negatively regulates NF-κB, and has been identified as a tumour suppressor. Several studies have described A20 inactivation by deletion of the A20 locus at 6q23, inactivating mutations, and/or methylation of the A20 promoter in various lymphoma entities. Methods and results: We generated a monoclonal antibody against the C-terminus of A20 (Ber-A20) and investigated full-length A20 expression of normal lymphoid tissue and lymphomas for the first time. We identified loss of A20 expression in tumour cells of 24% of classical Hodgkin lymphoma, 27% of diffuse large B-cell lymphoma, 20% of chronic lymphocytic leukaemia, 19% of follicular lymphoma, 13% of mantle cell lymphoma and 8% of primary mediastinal B-cell lymphoma cases by immunohistology. Loss of A20 expression rarely occurred in T-cell non-Hodgkin lymphoma. Conclusions: Our data are in agreement with cytogenetic and molecular analyses. Among 21 cases of ocular adnexal marginal zone lymphomas with known A20 mutation status, we detected complete absence of A20 expression, whereas cases with wild-type A20 were weakly A20-positive. We demonstrate that A20 loss can be detected by immunohistology with a sensitivity similar to that of complex molecular and genetic methods. © 2012 Blackwell Publishing Ltd.

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