The integrity of eukaryotic genomes is constantly challenged by various endogenous and exogenous insults, whereby DNA double-strand breaks (DSBs) are particularly problematic. DSBs can be repaired by multiple pathways, but only the homologous recombination (HR) pathway ensures error-free repair. HR restores missing information around the lesion based on topological interactions with a homologous region on a distinct DNA molecule. HR-directed repair can function across homologous chromosomes in diploid organisms, but is much more efficient between sister chromatids in replicated chromosomes, indicating an important role of chromosome conformation in repair. Sister chromatids are organized by a dynamic interplay between cohesin-mediated loop extrusion, cohesin-mediated sister linkage, and chromatin-based affinity interactions. How these activities shape sister chromatids to support DNA repair is unclear. The proposed project aims to reveal how sister chromatid conformation governs DSB repair efficiency and pathway choice in human cells and to identify and characterize the key molecular factors regulating chromosome conformation for efficient DSB repair. Understanding how intra- and inter-molecular topological interactions contribute to DNA repair will become possible by using a new chromosome conformation capture technology developed in the hosting lab (sister-chromatid sensitive Hi-C). This technology will be combined with a system for acute DSB induction, automated imaging and genomic profiling of DNA repair factors, and targeted protein degradation of cohesin and its regulators to elucidate topological interactions underlying DSB repair. The proposed project will provide insights into how the core machinery shaping the three-dimensional organization of chromosomes contributes to the maintenance of genome integrity.

Most of our knowledge on human development and physiology is derived from experiments done in animal models. While these experiments have led to a comprehensive understanding of the principles of neurogenesis, animal models often fall short of modelling many of the most common neurological disorders. Recent experiments have revealed characteristic striking differences in brain development between rodents and primates and may provide an explanation for this problem. The goal of this proposal is to use three dimensional organoid cultures derived from pluripotent human stem cells to reveal the human specific aspects of brain development and to analyse neurological disease mechanisms directly in human tissue. We have recently developed a 3D culture method allowing us to recapitulate human brain development during the first trimester of embryogenesis. Using this method, we will define the human specific brain patterning events in order to develop a culture system that can recapitulate essentially any part of the brain. Using a unique combination of cell type specific markers and mutagenic viruses, we will define the transcriptional networks defining specific neuronal subtypes. This will allow us to perform loss-of function genetics in human tissue to define transcription factors necessary for development of individual neuronal subtypes on a genome-wide level. Finally, we will apply the genome wide screening technology to human neurological disorders like microcephaly or schizophrenia to identify factors that can rescue disease phenotypes. This research proposal will provide fundamental insights into the cellular and molecular mechanisms specifying various neuronal subclasses in the human brain and establish technology that can be applied to a variety of cell types and brain regions. The proposed experiments have the potential to yield fundamental insights into human neurological disease mechanisms that can currently not be derived from animal models.

Transferring results from animal models to humans is a major bottleneck in pharmaceutical research. This is particularly true for brain disorders, including neurodegenerative and developmental diseases. Both animal models and conventional cell culture methods fail to recapitulate the complexity of the human brain and there are fundamental differences in developmental and physiological aspects between humans and the commonly used animal models. The high attrition rate of drugs for brain disorders has led major pharmaceutical companies to severely downsize their respective departments. To overcome the inherent limitations of current in vitro and in vivo models for brain disorders, we have generated a proprietary human pluripotent stem cell-derived 3D organoid culture system, termed cerebral organoids. These cerebral organoids are ‘mini brains’ that grow in a petri dish , display discrete but interconnected brain regions and recapitulate features of human brain development. ‘Mini Brains’ can be derived from patient-specific stem cells and represent a unique opportunity for creating specific human disease models in a 3D culture. The aim of the ‘Mini Brain’ project is to investigate the commercial feasibility of cerebral organoids as a new and highly cost-effective tool in the discovery and development of therapies for neurodegenerative and developmental diseases. The use of patient-specific cerebral organoids for drug screening and validation offers an alternative to animal experiments, reducing costs and animal use and improving reliability of results, and has the potential to decrease the cost of drug development, reduce the brain disease burden and increase the rate of approved drugs for brain disorders.

VIP-3 represents a prestigious program that sets new standards in postdoctoral training and will contribute to Europe’s competitiveness in attracting the most talented young scientists worldwide. VIP-3 fellows will be required to move out of their comfort zone and develop unique interdisciplinary or intersectoral projects in two laboratories located at the Vienna BioCenter (VBC), which comprises of 6 research institutions, 4 service companies, a business incubator and 39 biotech companies. VIP-3 will thus attract excellent young scientists to a vibrant, collaborative research community located in one of the most liveable cities in the world. The application and selection process of VIP-3 follows a transparent procedure open to highly motivated and talented young scientists of all nationalities. The candidates’ performance and qualities will be evaluated by external, international, unbiased experts. The application and selection procedures will comply with procedures that ensure gender fairness and equal opportunities. VIP-3 will transform and enhance postdoctoral training and mentorship at the VBC. Each fellow i) will choose two supervisors and a third career-development mentor ii) will have access to a wide network for career opportunities, iii) will gain international and intersectoral exposure through connections to our global associate partner institutions, and vi) may take an up to 6-month ‘secondment’ in a sector of their choice. A leadership program will provide each fellow with skills such as self-assessment, effective communication, conflict management, and project management. All activities are overseen by the VIP-3 Advisory Board (VAB), which has been specifically selected with intersectorality in mind. VIP-3 will prepare the future scientific leaders who will shape where research, innovation and society will head in the years to come within or outside academia.