Maintaining a stable karyotype is essential for the use of pluripotent stem cells (PSCs) in regenerative medicine and translational and basic research. Although around 10-30% of PSC lines present karyotypic abnormalities, the molecular mechanisms underlying this genomic instability are largely unknown. Centromeres, the chromosomal loci that drive chromosome segregation are central to mitotic fidelity. Maintenance of centromeres in somatic cells is tightly cell cycle coupled, as centromeric chromatin assembly is strictly dependent on G1 phase transition. PSCs have an atypical cell cycle structure with truncated gap phases and proliferate at unusually rapid rates. How this affects mitotic fidelity in general, centromere assembly in particular and consequently, genomic stability is an essential question in reprogramming biology. The aim of this multifaceted project is to determine the mechanisms regulating proper chromosome segregation during somatic cell reprogramming to induced PSCs (iPSCs). By combining fluorescent labelling techniques, high-end microscopy and genome-wide analysis, this project will determine the mechanisms of centromere assembly and inheritance in PSCs, the consequences of genome-wide remodelling of chromatin marks during reprogramming on the stable epigenetic propagation of centromeric chromatin and how functional modulation of key centromere assembly factors affect mitotic fidelity. This project capitalises on the unique combination of the researcher’s experience in stem cell biology and iPSC technology and the extensive expertise in the biology of human mitosis and centromere function of the host lab. The results of this study will provide direct insight into how chromosomal segregation is controlled in PSCs and most importantly during reprogramming, which will advance our understanding of the mechanisms underlying the genomic instability of these cells and contribute to the development of strategies to obtain better and more robust iPSCs.

Centrioles assemble centrosomes and cilia/flagella, critical structures for cell division, polarity, motility and signalling, which are often deregulated in human disease. Centriole inheritance, in particular the preservation of their copy number and position in the cell is critical in many eukaryotes. I propose to investigate, in an integrative and quantitative way, how centrioles are formed in the right numbers at the right time and place, and how they are maintained to ensure their function and inheritance. We first ask how centrioles guide their own assembly position and centriole copy number. Our recent work highlighted several properties of the system, including positive and negative feedbacks and spatial cues. We explore critical hypotheses through a combination of biochemistry, quantitative live cell microscopy and computational modelling. We then ask how the centrosome and the cell cycle are both coordinated. We recently identified the triggering event in centriole biogenesis and how its regulation is akin to cell cycle control of DNA replication and centromere assembly. We will explore new hypotheses to understand how assembly time is coupled to the cell cycle. Lastly, we ask how centriole maintenance is regulated. By studying centriole disappearance in the female germline we uncovered that centrioles need to be actively maintained by their surrounding matrix. We propose to investigate how that matrix provides stability to the centrioles, whether this is differently regulated in different cell types and the possible consequences of its misregulation for the organism (infertility and ciliopathy-like symptoms). We will take advantage of several experimental systems (in silico, ex-vivo, flies and human cells), tailoring the assay to the question and allowing for comparisons across experimental systems to provide a deeper understanding of the process and its regulation.

DNA/RNA molecules adopting the Z-conformation have been known to possess immunogenic properties. However, their biological role and importance has been a topic of debate for many years. The discovery of Z-DNA/RNA binding domains (Zα domains) in varied proteins that are involved in the innate immune response, such as the interferon induced form of the RNA editing enzyme ADAR1 (p150), Z-DNA binding protein 1 (ZBP1), the fish kinase PKZ and the pox-virus inhibitor of interferon response E3L, indicates important roles of Z-DNA/RNA in immunity and self/non-self-discrimination. Such Zα domain-containing proteins recognize Z-DNA/RNA in a conformation-specific manner. Recent studies have implicated these domains in viral recognition. Given these important emerging roles for the Zα domains, it is pivotal to understand the physiologically-relevant nucleic acid substrate for them. In this proposal, we propose to deduce the physiologically relevant substrates for Zα domains from ADAR1 p150 and ZBP1 employing next-generation RNA-seq methodologies. Knowledge on the biochemical and structural aspects of substrate specificity and substrate recognition by these domains would yield important insights into the specific roles these proteins play in the physiological context and would propel efforts at designing effective and specific small-molecule inhibitors against these proteins. Utilizing next-generation virtual ligand screening approaches and high-throughput experimental screening, efforts would be undertaken to discover potential binders/inhibitors of these domains. Small-molecule inhibitors of this domain have potential applications in anti-viral treatments especially against viruses such as influenza and human immunodeficiency virus that have huge human and economic impact as well as in the treatment of autoinflammatory disorders.

The immune system was shaped through evolution, primarily through the selective pressure imposed by pathogens. This led to the emergence of multiple mechanisms that limit the negative impact of pathogens on host health and fitness. The best recognized defense strategy against infections relies on resistance mechanisms that aim at pathogen containment, expulsion or clearance. While crucial for host survival to infection, resistance mechanisms can carry significant trade-offs, often driven by oxidative stress and damage imposed to host parenchyma cells, and in some cases compromising the functional output of host tissues, i.e. immunopathology. Presumably for this reason, resistance mechanisms are coupled to countervailing oxidative stress responses that preserve parenchyma tissue function. These provide tissue damage control without exerting a direct negative impact on pathogens and as such are said to confer disease tolerance to infection. This defense strategy relies on the expression of a number of evolutionary conserved effector genes controlling the pro-oxidant effects of iron and heme, as illustrated for the heme catabolizing enzyme heme oxygenase 1 or the iron sequestering protein ferritin H chain. BILITOLERANCE aims at identifying and characterizing an unexplored and possibly central component of this tissue damage control mechanism that relies on the conversion of the end-product of heme catabolism biliverdin into bilirubin, by biliverdin reductase A (BVRA). The central hypothesis to be tested by BILITOLERANCE is that bilirubin generated by BVRA provides a potent lipophilic anti-oxidant defense mechanism that limits the deleterious effects of lipid peroxidation. Moreover BILITOLERANCE will test the hypothesis that bilirubin also signals via the aryl hydrocarbon receptor (AhR) to modulate the activation of tissue-resident macrophages and promote tissue damage control and disease tolerance to infection.