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FORSCHUNGSINSTITUT FUR MOLEKULARE PATHOLOGIE GESELLSCHAFT MBH

Country: Austria

FORSCHUNGSINSTITUT FUR MOLEKULARE PATHOLOGIE GESELLSCHAFT MBH

40 Projects, page 1 of 8
  • Funder: European Commission Project Code: 740349
    Overall Budget: 2,500,000 EURFunder Contribution: 2,500,000 EUR

    Antibody-secreting cells consisting of short-lived proliferating plasmablasts and long-lived quiescent plasma cells are essential for the acute response to infection and long-term protection of the host against pathogens. Only a few regulators (Blimp1, IRF4, XBP1, Aiolos, Ikaros and E-proteins) have been implicated in the transcriptional control of antibody-secreting cells, and their target genes, with the exception of Blimp1 and E-proteins, are still unknown. This proposal aims to systematically identify key players in the development and function of antibody-secreting cells by using the CRISPR/Cas9 and Cre/loxP methods. For this, we improved existing protocols to extend the duration of in vitro plasmablast differentiation and showed that Rosa26(Cas9/+) B cells infected with Blimp1 or Xbp1 sgRNA-expressing retroviruses recapitulated the Blimp1 and Xbp1 mutant phenotypes in this proof-of-principle experiment. Moreover, Cre retrovirus-mediated deletion of Irf4, Ikaros and Aiolos strongly impaired plasmablast differentiation in this optimized system. To discover new regulators of plasma cell differentiation, CRISPR/Cas9-based screens will be performed with pooled sgRNA libraries targeting all known upregulated genes in plasmablasts and plasma cells, followed by individual validation of the best hits. Selected top-ranked genes will be analyzed in vivo by conditional mutagenesis with newly generated, plasma cell-specific Cre lines. Regulated target genes of IRF4, Ikaros, Aiolos, XBP1 and the XBP1-regulated transcription factor Bhlha15 will be identified in plasmablasts by ChIP- and RNA-seq analyses. Target genes with potentially interesting functions will be further characterized by CRISPR/Cas9- or Cre/loxP-mediated mutagenesis. These experiments will provide fundamentally new insight into the molecular mechanisms controlling the development and function of antibody-secreting cells, which are the essential effector cells of humoral immunity.

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  • Funder: European Commission Project Code: 693949
    Overall Budget: 2,500,000 EURFunder Contribution: 2,500,000 EUR

    During S-phase newly synthesized “sister” DNA molecules become physically connected. This sister chromatid cohesion resists the pulling forces of the mitotic spindle and thereby enables the bi-orientation and subsequent symmetrical segregation of chromosomes. Cohesion is mediated by ring-shaped cohesin complexes, which are thought to entrap sister DNA molecules topologically. In mammalian cells, cohesin is loaded onto DNA at the end of mitosis by the Scc2-Scc4 complex, becomes acetylated during S-phase, and is stably “locked” on DNA during S- and G2-phase by sororin. Sororin stabilizes cohesin on DNA by inhibiting Wapl, which can otherwise release cohesin from DNA again. In addition to mediating cohesion, cohesin also has important roles in organizing higher-order chromatin structures and in gene regulation. Cohesin performs the latter functions in both proliferating and post-mitotic cells and mediates at least some of these together with the sequence-specific DNA-binding protein CTCF, which co-localizes with cohesin at many genomic sites. Although cohesin and CTCF perform essential functions in mammalian cells, it is poorly understood how cohesin is loaded onto DNA by Scc2-Scc4, how cohesin is positioned in the genome, how cohesin is released from DNA again by Wapl, and how Wapl is inhibited by sororin. Likewise, it is not known how cohesin establishes cohesion during DNA replication and how cohesin cooperates with CTCF to organize chromatin structure. Here we propose to address these questions by combining biochemical reconstitution, single-molecule TIRF microscopy, genetic and cell biological approaches. We expect that the results of these studies will advance our understanding of cell division, chromatin structure and gene regulation, and may also provide insight into the etiology of disorders that are caused by cohesin dysfunction, such as Down syndrome and “cohesinopathies” or cancers, in which cohesin mutations have been found to occur frequently.

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  • Funder: European Commission Project Code: 101032582
    Overall Budget: 186,167 EURFunder Contribution: 186,167 EUR

    In the last decade, we have witnessed tremendous progress in understanding the genetic landscape of acute myeloid leukemia (AML), which has been translated into several approved targeted therapies. Although these therapies are effective initially, most patients eventually develop resistance through a variety of genetic and/or epigenetic mechanisms that remain incompletely understood. While it is widely accepted that transient responses to oncogene-targeted therapeutics into cure will require drug combinations, the pre-clinical and clinical development of rational combination therapies remains challenging. The advent of high-throughput genetic screens and transcriptome profiling methods fundamentally changes the way we can address this problem. The overall goal of this proposal is to apply and integrate these innovative technologies to deeply investigate genetic and gene-regulatory mechanisms in the response to small-molecule inhibitors of FLT3 and the MLL-Menin interaction, which hold promise as targeted therapeutics for more than 50% of AML patients. Using advanced CRISPR/Cas9- and shRNA-based screening platforms, I will systematically identify genes that modify the response to FLT3 and MLL-Menin inhibition. Complementary to functional-genetic screens, I will apply SLAMseq, a scalable time-resolved mRNA profiling method co-developed by the host lab, to dynamically investigate transcriptional programs underlying the primary response and adaptation to FLT3 and MLL-Menin inhibition. Functional-genetic and time-resolved transcriptome profiles will be integrated to select promising candidates for validation and mechanistic follow-up studies in patient AML samples and genetically engineered mouse models. In summary, by providing deep insight into the response to FLT3- and MLL-Menin inhibition, I thrive to identify candidate targets and new concepts for rational combination therapies that would address an unmet clinical need with a clear path towards clinical translation.

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  • Funder: European Commission Project Code: 800247
    Overall Budget: 166,157 EURFunder Contribution: 166,157 EUR

    Mutations in TUBB2B are associated with a range of malformations of cortical development: severe structural brain disorders stemming from abnormal cerebral cortex formation. Functional investigation of TUBB2B mutations will enable us to elucidate distinct pathogenic mechanisms underlying various malformations and advance our understanding of normal brain development. TUBB2B is highly expressed during embryonic brain development. It encodes a major component of microtubules (MTs), which perform essential roles during neuronal proliferation, neuronal migration and cortical organisation. I have obtained preliminary data in non-neuronal cells that suggests certain (but not all) TUBB2B-related malformations result from impaired cell division during neurogenesis. This highlights a potential disease-specific mechanism. I will investigate this hypothesis using state-of-the-art induced pluripotent stem cells (iPSCs) and cerebral organoid (COs) technologies, more relevant to brain development. I will generate iPSCs from fibroblasts obtained from patients with specific TUBB2B genotypes and brain phenotypes. I will use CRISPR/Cas9 genome editing to generate isogenic controls (in addition to a generic wild type line). Mutant and control iPSCs will be differentiated into a neural lineage to study effects of mutations on cell cycle and MT dynamics. Subsequently, differentiated cells will be aggregated into COs; self-organising ‘mini-brains’ that recapitulate human brain development and disease. I will employ immunohistochemistry and microscopy to examine TUBB2B mutation effects on neuronal proliferation, migration and organisation. I will hosted by Dr David Keays (IMP, Vienna). His lab are global leaders in tubulin-gene research and work in close collaboration with the pioneers in CO techniques (Knoblich Lab, IMBA, Vienna). Dissemination and communication of results will impact the scientific community, promote EU-based research and establish me as a reputable figure in the field.

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  • Funder: European Commission Project Code: 704299
    Overall Budget: 166,157 EURFunder Contribution: 166,157 EUR

    The cohesin-complex mediates sister chromatid cohesion from S-phase until mitosis and is involved in the formation of higher-order chromatin structure. To fulfill these vital functions, cohesin is loaded and positioned in the genome by mechanisms that are only poorly understood. In vitro, loading of cohesin on DNA only requires ATP and a loading-complex formed by Scc2-Scc4, while loading in vivo on chromatin is regulated by additional factors. For example, in Xenopus laevis oocytes, cohesin loading strictly depends on pre-replication complexes (pre-RCs), which are formed in telophase/G1. Mechanistic studies are required to understand how cohesin-loading occurs at the molecular level. I will first determine the mechanism by which Scc2-Scc4 loads cohesin on DNA. Using single-molecule FRET and optical tweezers, I will monitor the effect of Scc2-Scc4 on conformational changes of cohesin as it is loaded on a DNA template. After characterizing this minimal loading reaction, I will reconstitute cohesin-loading during telophase/G1 using a purified system. With these experiments I will address why and how loading of cohesin is regulated by the formation of pre-RCs.

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