Berlin, Germany
Berlin, Germany

Time filter

Source Type

Grant
Agency: European Commission | Branch: FP7 | Program: NoE | Phase: SEC-2011.7.4-1 | Award Amount: 8.18M | Year: 2012

The EUROFORGEN-NoE proposal aims to develop a network of excellence for the creation of a European Virtual Centre of Forensic Genetic Research. Forensic genetics is a highly innovative field of applied science with a strong impact on the security of citizens. However, the genetic methods to identify offenders as well as the creation of national DNA databases have caused concerns to the possible violation of privacy rights. Furthermore, studies to assess the societal dimension of security following the implementation of even more intrusive methods such as the genetic prediction of externally visible characteristics are highly relevant for their public acceptance. The network includes some of the leading groups in European forensic genetic research. It aims to create a closer integration of existing collaborations, as well as establishing new interactions in the field of security, as all key players are addressed: scientists, stakeholders, end-users, educational centres and scientific societies. Only if a long-term collaborative network can be established it will become possible to connect all scientific groups active in the field of forensic genetics, and to initiate a sustained effort covering all aspects of research. These efforts have to be combined with identifying and selecting the most innovative ideas to meet the challenges of analyzing biological crime scene samples compromised by degradation or indentified as mixtures of traces from multiple human sources. The proposal integrates five working packages. WP 1 is devoted to management and coordination. WP 2 will lead the activities aimed at the creation of the virtual centre of research. WP 3 will carry out exemplar projects as models of collaboration and integration of cutting edge research, later complemented by a competitive call for new research projects. The societal dimension of security as well as the ethical and legal aspects wil be addressed in WP 4, whereas WP 5 is devoted to education and training.


Grant
Agency: European Commission | Branch: H2020 | Program: MSCA-ITN-ETN | Phase: MSCA-ITN-2014-ETN | Award Amount: 2.80M | Year: 2015

The mission of EpiPredict is to train a multidisciplinary cohort of young researchers in a new approach to fully exploit the epigenetics of complex diseases. The 12 early-stage researchers (ESRs) will focus on a narrowly defined case, Tamoxifen-induced resistance in Estrogen Receptor positive (ER\) breast cancer, considering five resistance interacting pathways. Given the frequent Tamoxifen treatment failure, resistance prevention and reversal is an urgent clinical problem that is central in EpiPredict. The EpiPredict intersectorial training programme employs a timely systems medicine approach combining next-generation systematic epigenetic, gene/protein profiling with innovative gene-specific epigenetic interference technologies for iterative computational modelling. Together the ESRs will identify key epigenetic changes underlying Tamoxifen induced resistance. This will provide an important step towards diagnostic markers/tools to predict treatment outcome and response monitoring setting the scene for breast cancer personalized medicine. The fellows will be trained by experts from 6 academic and 2 non-academic beneficiaries and 7 partner organizations (1 academic, 6 non-academic including industrial/socio-public parties) and 5 visiting scientists, from fields ranging from epigenetics to both computation and medicine. Strong involvement of the private sector ensures exploitation of EpiPredict achievements and exposure of the ESRs to an entrepreneurial mindset. The cohort of supradisciplinary researchers represents a new generation of research leaders equipped to address complex diseases whilst taking personalized patient aspects into consideration. They will be equipped to compete successfully and succeed in their personal careers. EpiPredict will boost academia and pharma/biotech environments, providing extra impulses to drive European translational science, systems medicine, pharmaceutical industry, and Medical ICT offering ample job opportunities.


The present invention provides an epigenetic haemogram, also referred to as an epigenetic blood cell count that identifies the quantitative, comprehensive picture of cellular composition in a biological sample, wherein advantageously a normalization standard is used. The normalization standard is a nucleic acid molecule comprising at least one marker-region being specific for each of the blood cells to be detected, and at least one control-region being cell-unspecific, wherein said regions are present in the same number of copies on said molecule and/or a natural blood cell sample of known composition. Furthermore, the present invention relates to a kit and the use of a kit for performing the epigenetic assessment of comprehensive, quantitative cellular composition of a biological sample. The biological sample is derived from e.g. a mammalian body fluid, including peripheral, capillary or venous blood samples or subfractions thereof, such as peripheral blood mononuclear cells or peripheral blood monocytes, or a tissue sample, organ sample, or from frozen, dried, embedded, stored or fresh body fluids or tissue samples.


The present invention provides methods, nucleic acids and molecular markers for the detection of chondrycytes. Specifically, it describes particular genes and genomic regions, in particular the genes FMOD, C15ORF27 and HIF1A, in which DNA methylation patterns are a consistent and characteristic property of different cell types, states and stages of differentiation. The invention is useful in determining the identity, composition, quality and potency of cells and cell populations. Furthermore, the invention will be useful in monitoring the differentiation of cells.


The present invention relates to a method, in particular an in vitro method for identifying IL-17 expressing T cells in a blood and/or tissue sample derived from a mammal, comprising analysing the methylation status of at least one CpG position in the gene IL-17A, wherein a demethylation of said at least one CpG position in said sample when compared to an analogous position in a non IL-17 blood cell is indicative for a IL-17 positive CD4 positive T cell. The analyses according to the invention can identify IL-17 positive T cells and distinguish them from all other cells in complex samples, such as, for example, other blood cells. The present invention furthermore provides an improved method for quantifying IL-17 positive T cells in complex samples based on a comparison of the IL-17A methylation with a methylation of at least one marker selected from the group of CD3, FOXP3, and/or GAPDH. The method can be performed without a step of purifying and/or enriching cells, preferably in whole blood and/or non-trypsinized tissue.


The present invention relates to a method, in particular an in vitro method, for identifying follicular helper T cells, comprising analyzing the methylation status of at least one CpG position in the mammalian gene region for leukemia inhibitory factor (LIF), wherein a demethylation of said gene region is indicative for a follicular helper T cell, when compared to a non-follicular helper T cell. The analyses according to the invention can identify follicular helper T cells on an epigenetic level and distinguish them from all other cells in complex samples, such as, for example, other blood cells. The present invention furthermore provides an improved method for quantifying follicular helper T cells in complex samples. The method can be performed without a step of purifying and/or enriching cells, preferably in whole blood and/or non-trypsinized tissue.


The present invention relates to a method for identifying a specific type and/or state of a mammalian cell in a sample obtained from a mammal, comprising a) analyzing the relative amount of accessible chromatin in regions that are specific for a cell-type and/or cellular state in the genome of said cell, b) comparing said relative amount of accessible chromatin said in regions with the relative amount of accessible chromatin in regions in the genome of said cell that are unspecific for a cell-type and/or cellular state, and c) deducing the specific type and/or state of said mammalian cell in said sample based on said comparison. Preferably, said identifying further comprises a relative quantification of said specific cell type and/or state based on said comparison. The method can further comprise a diagnosis of a predisposition to a disease or a disease based on said identification. Kits and certain markers in regions of accessible chromatin in the genome are described, too.


The present invention relates to a method, in particular an in vitro method for identifying a subgroup of natural killer cells of a mammal, preferably CD3, non T-lymphocyte derived NK cells, which often express the surface proteins CD56 and/or CD16, comprising analyzing the accessibility of the genomic DNA for OSBPL, such as OSBPL5, to bisulfite conversion and/or the methylation status of at least one CpG position in the genes for OSBPL, such as OSBPL5, in particular in their upstream and/or downstream regulatory regions, the promoter, introns, exons and introns exon borders and other conserved regions of said genes, wherein an increase of the accessibility of the genomic DNA and/or a demethylation in the sample as analyzed is indicative for said subgroup of NK cells. The analyses according to the invention can identify CD56+ cells and distinguish them from all other cells such as, for example, either CD56 and/or CD56 bright cells. The methods of the present invention are useful for the identification, the detection, the quantification and quality assurance and control of NK cells. Furthermore, the present invention relates to a kit for performing the above methods as well as respective uses of the inventive methods or kits. The present invention furthermore provides an improved method for analysing the accessibility of the genomic DNA for OSBPL, such as OSBPL5, to bisulfite conversion and/or an analysis of the methylation status of at least one CpG position in the genes for OSBPL, such as OSBPL5, allowing for a precise analysis of both optimally and even from sub-optimal quality samples, such as non-freshly obtained blood, tissue or serum samples.


The present invention relates to a method, in particular an in vitro method, for identifying CD8 positive subpopulations of a mammal, wherein said method comprises analyzing the bisulfite convertibility of at least one CpG position in the CD8 beta and CD8 alpha cell specific bisulfite convertibility gene region according to SEQ ID No. 1 and 2, wherein a bisulfite convertibility of at least one CpG position in said gene regions is indicative for a CD3+CD8+ and/or CD3+/CD8+ cell. The analyses according to the invention can identify CD3+CD8+ and/or CD3+/CD8+ cells on an epigenetic level and distinguish them from all other cells in complex samples, such as, for example, other blood cells.


The present invention relates to a method, in particular an in vitro method, for identifying CD3CD4 positive T lymphocytes of a mammal, wherein said method comprises analyzing the bisulfite convertibility of at least one CpG position in the CD3^(+)CD4^(+ )T helper cell specific non-methylated bisulfite convertible region according to SEQ ID No. 1, wherein a bisulfite convertibility of at least one CpG position to at least 90%, preferably to at least 91% and more preferably to at least 92% and most preferred to at least 95% in said sample is indicative for a CD4^(+ )T-lymphocyte cell, in particular a CD3^(+ )CD4^(+ )T-lymphocyte cell. The present invention further relates to analyzing the bisulfite convertibility of at least one CpG position in the genes FLJ00060, FLJ38379, PPP6C, CD226, ZBTB7B and TNFAIP8 that are capable of positively identifying CD4 expressing cells in whole blood and segregate between CD4 and CD8 positive CD3 positive cells. Furthermore, the present invention relates to a kit for performing the above methods as well as respective uses thereof.

Loading Epiontis GmbH collaborators
Loading Epiontis GmbH collaborators