A functional yeast survival screen of tumor-derived cDNA libraries designed to identify anti-apoptotic mammalian oncogenes

Yeast cells can be killed upon expression of pro-apoptotic mammalian proteins. We have established a functional yeast survival screen that was used to isolate novel human anti-apoptotic genes overexpressed in treatment-resistant tumors. The screening of three different cDNA libraries prepared from metastatic melanoma, glioblastomas and leukemic blasts allowed for the identification of many yeast cell death-repressing cDNAs, including 28% of genes that are already known to inhibit apoptosis, 35% of genes upregulated in at least one tumor entity and 16% of genes described as both anti-apoptotic in function and upregulated in tumors. These results confirm the great potential of this screening tool to identify novel anti-apoptotic and tumor-relevant molecules. Three of the isolated candidate genes were further analyzed regarding their anti-apoptotic function in cell culture and their potential as a therapeutic target for molecular therapy. PAICS, an enzyme required for de novo purine biosynthesis, the long non-coding RNA MALAT1 and the MAST2 kinase are overexpressed in certain tumor entities and capable of suppressing apoptosis in human cells. Using a subcutaneous xenograft mouse model, we also demonstrated that glioblastoma tumor growth requires MAST2 expression. An additional advantage of the yeast survival screen is its universal applicability. By using various inducible pro-apoptotic killer proteins and screening the appropriate cDNA library prepared from normal or pathologic tissue of interest, the survival screen can be used to identify apoptosis inhibitors in many different systems

Identification of New Genes Involved in Human Adipogenesis and Fat Storage

Since the worldwide increase in obesity represents a growing challenge for health care systems, new approaches are needed to effectively treat obesity and its associated diseases. One prerequisite for advances in this field is the identification of genes involved in adipogenesis and/or lipid storage. To provide a systematic analysis of genes that regulate adipose tissue biology and to establish a target-oriented compound screening, we performed a high throughput siRNA screen with primary (pre)adipocytes, using a druggable siRNA library targeting 7,784 human genes. The primary screen showed that 459 genes affected adipogenesis and/or lipid accumulation after knock-down. Out of these hits, 333 could be validated in a secondary screen using independent siRNAs and 110 genes were further regulated on the gene expression level during adipogenesis. Assuming that these genes are involved in neutral lipid storage and/or adipocyte differentiation, we performed InCell-Western analysis for the most striking hits to distinguish between the two phenotypes. Beside well known regulators of adipogenesis and neutral lipid storage (i.e. PPARγ, RXR, Perilipin A) the screening revealed a large number of genes which have not been previously described in the context of fatty tissue biology such as axonemal dyneins. Five out of ten axonemal dyneins were identified in our screen and quantitative RT-PCR-analysis revealed that these genes are expressed in preadipocytes and/or maturing adipocytes. Finally, to show that the genes identified in our screen are per se druggable we performed a proof of principle experiment using an antagonist for HTR2B. The results showed a very similar phenotype compared to knock-down experiments proofing the “druggability”. Thus, we identified new adipogenesis-associated genes and those involved in neutral lipid storage. Moreover, by using a druggable siRNA library the screen data provides a very attractive starting point to identify anti-obesity compounds targeting the adipose tissue

Genome-wide siRNA screening reveals several host receptors for the binding of human gut commensal Bifidobacterium bifidum

Bifidobacterium spp. are abundant gut commensals, especially in breast-fed infants. Bifidobacteria are associated with many health-promoting effects including maintenance of epithelial barrier and integrity as well as immunomodulation. However, the protective mechanisms of bifidobacteria on intestinal epithelium at molecular level are poorly understood. In this study, we developed a high-throughput in vitro screening assay to explore binding receptors of intestinal epithelial cells for Bifidobacterium bifidum. Short interfering RNAs (siRNA) were used to silence expression of each gene in the Caco-2 cell line one by one. The screen yielded four cell surface proteins, SERPINB3, LGICZ1, PKD1 and PAQR6, which were identified as potential receptors as the siRNA knock-down of their expression decreased adhesion of B. bifidum to the cell line repeatedly during the three rounds of siRNA screening. Furthermore, blocking of these host cell proteins by specific antibodies decreased the binding of B. bifidum significantly to Caco-2 and HT29 cell lines. All these molecules are located on the surface of epithelial cells and three out of four, SERPINB3, PKD1 and PAQR6, are involved in the regulation of cellular processes related to proliferation, differentiation and apoptosis as well as inflammation and immunity. Our results provide leads to the first steps in the mechanistic cascade of B. bifidum-host interactions leading to regulatory effects in the epithelium and may partly explain how this commensal bacterium is able to promote intestinal homeostasis.Peer reviewe

The Yin and Yang of nucleic acid-based therapy in the brain.

The post-genomic era has unveiled the existence of a large repertory of non-coding RNAs and repetitive elements that play a fundamental role in cellular homeostasis and dysfunction. These may represent unprecedented opportunities to modify gene expression at the right time in the correct space in vivo, providing an almost unlimited reservoir of new potential pharmacological agents. Hijacking their mode of actions, the druggable genome can be extended to regulatory RNAs and DNA elements in a scalable fashion. Here, we discuss the state-of-the–art of nucleic acid-based drugs to treat neurodegenerative diseases. Beneficial effects can be obtained by inhibiting (Yin) and increasing (Yang) gene expression, depending on the disease and the drug target. Together with the description of the current use of inhibitory RNAs (small inhibitory RNAs and antisense oligonucleotides) in animal models and clinical trials, we discuss the molecular basis and applications of new classes of activatory RNAs at transcriptional (RNAa) and translational (SINEUP) levels

Modelling and genetic correction of liver genetic diseases

The urea cycle is a set of biochemical reactions that converts highly toxic ammonia into urea for excretion. Deficiencies in any of the genes of the cycle can be life-threatening, with liver transplantation currently being the only definitive treatment. However, the scarcity of donor organs dictates the investigation of alternative treatments, which requires appropriate disease models, in vitro and in vivo, that faithfully recapitulate the disease pathology. Recent advancements in the field of genome engineering make interventions in the genetic code less challenging, thereby assisting in the generation of such tools, as well as raising the potential for genetic correction of these conditions. The research conducted in this thesis centres around two broad aims: the investigation of disease models and genetic correction of inherited liver disorders. Induced pluripotent stem cells (iPSC) hold great potential both for disease modelling and as a source of cells for cell therapy. However, their generation through cell reprogramming is sometimes challenging and inefficient. Therefore, in PAPER I we sought to optimize the reprogramming procedure by introducing modifications to the currently existing protocols, and managed to increase the reprogramming efficiency. IPSC could theoretically differentiate into any cell type, including hepatocytes. In order to assess the level of differentiation of the hepatocyte-like cells (HLC) generated from stem cell sources, comparisons with authentic primary liver tissues are necessary. To this end, in PAPER II we created gene expression profiles of fetal and mature (post-natal) liver tissues from a significant number of individuals. The dataset can serve as an accurate and simple assessment tool to evaluate and compare HLC, generated in different laboratories, to authentic human liver tissues. If HLC resemble the functions observed in mature primary hepatocytes, they could be used as in vitro disease models. In addition, programmable nucleases can be applied to either correct or introduce disease-causing of interest in the genome. In PAPER III, we generated iPSC from a patient with a pathogenic variant in the ornithine transcarbamylase (OTC) gene, the most common UCD, corrected the genetic defect and differentiated the cells into HLC. The correction was molecularly, as well as phenotypically confirmed by the restoration of urea cycle function. The thesis also focuses on the investigation of in vivo disease models of UCD. Specifically, in PAPERS IV and V we created liver-humanized mice with hepatocytes from patients with UCD, OTC deficiency (OTCD) or carbamoyl phosphate synthetase 1 deficiency (CPS1D). Highly repopulated animals faithfully recapitulated the clinical manifestations of the disease observed in patients, including hyperammonemia which is considered a hallmark of these UCD. Furthermore, in PAPER V, we investigated the efficacy and safety of ex vivo gene editing of primary OTCD hepatocytes. Ureagenesis was restored in vitro in edited cells, as well as in vivo as mice liver-repopulated with genetically engineered cells partially or completely reversed all markers of the disease investigated. Finally, extensive gene expression and deep sequencing analysis revealed no unspecific mutagenesis effected by the programmable nucleases, pointing out the safety of the application. In conclusion, the research work conducted in this thesis demonstrates the prospects that iPSC and humanized mice possess for the generation of models of liver genetic diseases, in vitro and in vivo. Furthermore, the emergence of genome editing technologies further enhances the aforementioned potentials, as well as raises possibilities for the treatment of liver genetic defects through genome manipulation

Characterisation of new potential vaccine candidates against infections caused by Staphylococcus aureus

Due to the rapid emergence of S. aureus strains resistant to multiple antibiotics and the therewith increased mortality rates, the development of alternative strategies to prevent and treat S. aureus infections is of great clinical and economical importance. Based on the results concerning both monovalent active and passive immunisation, it is getting obvious that only multivalent vaccine strategies might confer full protection from S. aureus related infections. Furthermore, due to their short term applicability and potential composition of immunoglobulins of different isotypes and functionalities, strategies based on passive immunisation are particularly advantageous. Using an intravenous immunoglobulin preparation (IVIG) as source of naturally occurring S. aureus specific IgGs, a significant inhibition of staphylococcal growth was observed in vitro. Thus, confirming the bacteriostatic effect on S. aureus as observed using human serum in the 1970s. Since this inhibitory effect was not observed upon treatment with IVIG depleted of S. aureus - specific IgGs (dSaIVIG), bacteriostasis is triggered solely by S. aureus specific IgGs. In order to analyse the underlying mechanism, gene expression profiling was conducted, using a S. aureus-seven genome PCR-product microarray. Comparison of IVIG to dSaIVIG treated samples led to the identification of 236 differentially expressed genes over the course of bacteriostasis. In contrast, IVIG compared to PBS treated samples as additional control resulted in 78 genes with altered expression. Only 13 genes were identified by both sets of microarrays, indicating a strong difference between the two applied controls. Moreover, the most prominent signature representing genes related to iron uptake and metabolism was only identified by comparison of IVIG to dSaIVIG samples. qPCR on iron related genes not only verified the microarray results, but also indicated that the iron signature was derived from dSaIVIG, thus not representing the mechanism underlying bacteriostasis. Due to the lack of a reliable signature the mechanism underlying bacteriostasis could not be characterised. Additionally, we aimed to enlarge the repertoire of potential candidates for a polyvalent vaccine. For this purpose a novel subtractive proteomic approach (SUPRA) on anchorless cell wall (ACW) proteins of S. aureus was developed. This method is based on immunodetection of in vivo expressed, immunogenic proteins separated by 2D gelelectrophoresis with either complete IVIG or dSaIVIG. Proteins immunoreactive with IVIG but not, or to a lesserextent using dSaIVIG were identified by MALDI-TOF analysis. SUPRA led to the identification of 37 new potential vaccine candidates among ACW proteins. Three of these, BT1, BT2 and BT3 were characterised in this study. The surface localisation of these antigens was confirmed by flow cytometry using specific antibodies enriched from IVIG. Purified IgGs for each antigen mediated opsonophagocytosis and subsequent opsonophagocytic killing by human neutrophils. However, when used for monovalent immunisation of BalbC mice only BT1 and BT3 conferred significant protection against lethal S. aureus challenge in a murine model of sepsis. Despite the protective potential upon monovalent immunisation a bivalent vaccination using BT1 and BT3 did not exhibit a synergistic protective effect, most likely due to the reduced amount of antigen used for immunisation. Among the six so far investigated vaccine candidates identified by SUPRA, three conferred protection against lethal challenge with S. aureus (hp2160, BT1 and BT3) and two led to a reduction of bacterial load in organs (eno and oxo). Therefore, SUPRA represents a valuable tool for the identification of promising vaccine candidates for subsequent use in a multicomponent vaccine against S. aureus

Étude du rôle des effecteurs de type III évolutivement conservés chez deux bactéries colonisatrices du xylème

Xanthomonas campestris pv. campestris (Xcc), l'agent responsable de la pourriture noire chez les Brassicacées, et Ralstonia pseudosolanacearum (Rps), l'agent responsable du flétrissement bactérien chez une large variété d'espèces végétales, sont toutes deux des bactéries dévastatrices s'établissant dans le xylème de leur hôte. Malgré les différences dans leur gamme d'hôtes, leur stratégie infectieuse et leur répertoire d'effecteurs, les souches de référence Xcc8004 et RpsGMI1000 partagent six effecteurs de type III (ET3) définis comme orthologues. Cela offre une excellente opportunité de mener des études comparatives puisqu'il est probable que ces six ET3 ciblent des processus orthologues chez les plantes hôtes, notamment chez Arabidopsis thaliana qui est un hôte commun aux deux pathogènes. Dans une première partie de mon projet de thèse, de potentielles protéines d'Arabidopsis interagissant avec les ET3 de Xcc8004 et RpsGMI1000 ont été identifiées grâce à un criblage par double hybride. Nous avons ainsi pu comparer nos résultats avec des criblages similaires réalisés chez d'autres phytopathogènes afin d'obtenir une vision plus exhaustive de la façon dont les effecteurs interagissent avec le protéome de l'hôte. Cela a permis de générer une base de données interactive intégrant nos résultats ainsi que des données interactomiques Arabidopsis-ET3 déjà publiées : "EffectorK" (www.effectork.org). Dans une deuxième partie du projet, les effets in planta de chacun des ET3 ont été étudiés en générant des lignées transgéniques inductibles d'Arabidopsis. En croisant les résultats de ces deux premières parties, les ET3 candidats les plus prometteurs ont été sélectionnés pour conduire des expériences de caractérisation fonctionnelle, ce qui a constitué la dernière partie de mon travail. Ce projet participe à une meilleure compréhension du rôle biologique des ET3 conservés parmi les bactéries colonisatrices du xylème.Xanthomonas campestris pv. campestris (Xcc), the causal agent of black rot disease on Brassicaceae, and Ralstonia pseudosolanacearum (Rps), the causal agent of bacterial wilt on a wide variety of hosts, are both devastating xylem-colonizing bacteria. Despite their differences in host range, infection strategy and effectome repertoire, reference strains Xcc8004 and RpsGMI1000 share six orthologous type III effectors (T3Es). This provides a valuable opportunity for comparative studies as it is likely that these orthologous T3Es target orthologous processes in the host plants, with focus on Arabidopsis thaliana, common host of both pathogens. In a first part of my PhD project, putative Arabidopsis interactors of Xcc8004 and RpsGMI1000 T3Es were identified by yeast two-hybrid at the effectome-scale. This allowed us to compare our results with similarly screened plant pathogens to acquire a global image of how effectors interfere with the host proteome. This led to the generation of an interactive knowledge database integrating our results with published Arabidopsis-effector interactomic data: "EffectorK" (www.effectork.org). In a second part of the project, the in planta effects of single T3Es were dissected by generating inducible transgenic Arabidopsis lines. Combining results from these two parts, the most promising T3E candidates were selected for further functional characterization, forming the last part of my work. Altogether, this project contributes to a better understanding of the biological role of conserved T3Es among xylem-colonizing bacteria

Cellular droplet microarray: a miniaturized technique for high-throughput screening of small molecules and proteins

Das Hochdurchsatz-Screening ist von großer Bedeutung und bildet einen der Eckpfeiler der aktuellen Life-Science-Research wie Biologie, Biotechnologie, Biochemie, Computerwissenschaft, medizinische Chemie und Pharmakologie. Das Interesse an einem Screening mit hohem Durchsatz unter akademischen, mittleren und kleinen Biotech-Unternehmen, staatlichen und gemeinnützigen Screening-Standorten, sowie Auftragsforschungsorganisationen wurde spürbar erhöht, da Hochdurchsatz-Screenings eine effiziente Analyse von einer Vielzahl von Stoffen in kürzester Zeit ermöglicht. Das steigende Interesse an dieser Methode führte zu einer schnellen Entwicklung von Screening-Technologien mit hohem Durchsatz in Kombination mit komplementären Technologien. Die Nachteile herkömmlicher Hochdurchsatz-Screenings beinhalten hohe Kosten und Materialverschwendung, lange Zykluszeiten, geringe Produktivität und die begrenzte Ausbaufähigkeit der existierenden Stoffbibliotheken. Die genannten Nachteile verdeutlichen die Wichtigkeit der Bemühungen zur Entwicklung von verbesserten miniaturisierten und automatisierten Hochdurchsatz-Screening Methoden. Droplet Microarray (DMA) ist eine dieser miniaturisierten Plattformen, welche durch die Vereinigung von Oberflächenchemie, Oberflächenfunktionalisierung und Biologie erschaffen wurde. Die hohe Tröpfchendichte auf DMA senkt die Kosten, Materialverschwendung, Zykluszeit des Screenings und erhöht die Effizienz des Verfahrens, während sie effektiv die Verwendung größerer chemischer und biologischer Bibliotheken unterstützt. Die weitere Entwicklung, Auswertung und Verbesserung der DMAs spielt nicht nur für den Fortschritt der Hochdurchsatz-Screenings eine wichtige Rolle, sondern beherbergt auch unermessliches Potential in pharmalogischen Bereichen und der Stammzellenforschung, in welcher es die Wirksamkeit von Gentransfers und das Kultivieren von undifferenzierten Stammzellen erleichtert. Pharmakologisches Priming (Drug Repurposing) wurde als adjuvante Strategie zur Verbesserung der Effizienz nicht-viraler Genübertragung angesehen. Dennoch ist die facettenreiche Anwendung des pharmakologischen Priming aufgrund der unerschwinglich hohen Kosten für Reagenzien und die Durchführung der Methode unweit verbreitet, was den aufkommenden Drang nach miniaturisierten Plattformen und Drug Repurposing erklärt. Abgesehen von der Dringlichkeit im pharmakologischen Bereich, um klinisches Potenzial zu realisieren, benötigt die Stammzellenforschung auch miniaturisierte Methoden um den Einfluss von Zelloberflächeninteraktionen und Zellkulturmedium auf das Verhalten von Stammzellen und die Effekte von Zusatzstoffen, und Oberflächenbeschichtungen einschließlich oberflächenabsorbierter Proteine auf Stammzellen zu beobachten. Das Ziel für den ersten Teil der Dissertation war es nach kleinen Molekülen (Stoffen) auf DMAs zu suchen, welche transfektionsverstärkende Effekte beinhalten, um eine mögliche Verbesserung in den Bereichen Gentransfer- und Therapie zu bieten. Eine Untersuchung der Einflüsse von 774 Food and Drug Administration (FDA)-zugelassenen Wirkstoffen auf die Transfektionseffizienz mit verschiedenen Zelltypen in miniaturisierter- und hochdurchsatzweise wurde mit Hilfe der DMAs veranlasst. Das Screening der FDA-zugelassenen Arzneimittelbibliothek identifizierte 14 einzelne Verbindungen, die eine zwei- bis fünffache Verbesserung der Transfektion aufwiesen. Diese Treffer wurden verifiziert und in großem Maßstab untersucht. Die Ergebnisse deuten darauf hin, dass der auf DMA basierende Ansatz für das Drug Repurposing beständig ist und zur Untersuchung und Entwicklung wirksamerer nicht-viraler Genübertragungssysteme verwendet werden könnte. Das Ziel des zweiten Abschnitts der Dissertation war es, den Einfluss von Oberflächeneigenschaften und sinkendem Volumen auf die Pluripotenz von human induzierten pluripotenten Stammzellen (hiPSCs) zu bestimmen. Zwei künstliche Oberflächen mit unterschiedlichen chemischen Elementen und deren dazugehörigen DMAs wurden für die Kultivierung und Pluripotenz von hiPSCs in vitro untersucht. Die Oberflächen und DMAs wurden genutzt, um human induzierten pluripotenten Stammzellen in 2 ml und 200 nL-Volumen zu kultivieren. Die Ergebnisse zeigten, dass hiPSCs eine hohe Lebensfähigkeit, sowie die erwartete Morphologie und Pluripotenz in 200 nL Tröpfchen auf Typ A und Typ B DMAs ohne Matrigelbeschichtung nach 24 h Kultivierung aufwiesen. Dies beweist, dass DMAs eine vielseitige und simple Plattform für kurzzeitige und xeno-freie Hochdurchsatz-Screenings von hiPSCs sind. Als Ziel für den dritten Teil der Dissertation wurde das Identifizieren von chemisch definierten Proteinen, welche das Kultivieren und Aufrechterhalten der Plutipotenz von hiPSCs Zellen auf DMAs, sowie Mikrotiterplatten weiter verbessern könnten, angesetzt. Es ist möglich eine Proteinbeschichtung, Zellkultur und Immunfluoreszenzfärbung auf miniaturisierter Ebene parallel mit Hilfe von DMAs durchzuführen, was zu einer Reduzierung von Versuchsfehlern und Verbrauchsmaterialien führt. Auf Grund dessen wurden DMAs als Basis zur Überprüfung von elf verschiedenen Proteinen und deren verwandten binären und ternären Kombinationen (insgesamt 231 verschiedene Gruppen) auf ihre Fähigkeit zur Erhaltung der Pluripotenz von hiPSCs genutzt. Aus diesem Raster wurden zehn Gruppen von ternären Proteinkombinationen identifiziert, welche die Proliferation und das Self-Renewal besser unterstützen könnten als mit Matrigel beschichtete Oberflächen. Die effizientesten Proteinkombinationen des primären Screenings wurden weiterhin in einer Langzeitkultur (fünf Wochen) verifiziert. Zusätzlich wurde die Formation von embryonalen Körperchen der auf den ausgewählten Proteinbeschichtungen kultivierten Zellen erzielt und es folgte die Differenzierung der hiPSCs in drei Keimblätter. Zusammengefasst, wurden DMAs als miniaturisierte Schnellscreening-Plattform verwendet, um mehrere biologische Fragen zu beantworten. Als erstes wurden 776 Wirkstoffe auf Nanoebene untersucht und somit kosten-, zeit- und arbeitssparend verwertet. Vierzehn Stoffe wiesen eine zwei- bis fünffache Verbesserung der Transfektionstechniken auf. Als zweites wurden chemische Komponente von Zellkulturoberflächen und kleinen Volumina (200nl) von Zellkulturmedium gefunden, die zur Erhaltung der Pluripotenz von hiPSCs beitragen. Als letztes wurden zehn Gruppen von ternären Proteinkombinationen identifiziert, welche das Kultivieren von undifferenzierten hiPSCs unterstützen. Zwei von ihnen wurden weiter untersucht, um eine Langzeitkultur von undifferenzierten hiPSCs zu erzielen, gefolgt von ihrer Differenzierung in drei Keimblätter. Eine Zusammenfassung und eine Aussicht auf die Zukunft befinden sich am Ende der Dissertation

Identification and Characterization of Potential Novel Targets in Thyroid Carcinoma: Evidence of Non-Oncogene Addiction Unveiling Tumor Cell Vulnerabilities

Thyroid cancer is the most frequent endocrine malignancy, with an incidence constantly increasing. Despite well-differentiated thyroid tumors are generally cured by conventional therapy, a fraction of them relapses and progresses towards undifferentiated forms, characterized by a poor prognosis. Target therapies introduced in clinical testing are often unsuccessful; therefore, novel therapeutic strategies are needed. To identify critical nodal points for therapeutic intervention, our laboratory faced the “non-oncogene addiction” (NOA) paradigm, which asserts that the tumorigenic state relies on the activity of genes that are essential to support the phenotype of cancer cells but not required to the same degree for normal cell viability. By screening a siRNA library on normal and tumor thyroid cell lines, we identified 15 genes whose silencing interfered with the growth of tumor but not normal thyroid cells. The overall aim of this project was to validate NOA genes to identify thyroid tumor cell vulnerabilities and to explore their role in the regulation of thyroid tumor cell biology. Among the 15 hit genes, we selected MASTL, Cyclin D1 and COPZ1 for validation studies. We confirmed the growth inhibitory effect of their silencing in tumor but not normal thyroid cells and observed that these effects were common to a panel of thyroid tumor cell lines, irrespective of the histotype or genetic lesion. Functional studies on MASTL demonstrated that its depletion in thyroid tumor cells inhibited cell growth, led to mitotic catastrophe and induced DNA damage and cell death. COPZ1 depletion induced abortive autophagy, endoplasmic reticulum stress and apoptotic cell death in thyroid tumor cells, as well as tumor growth inhibition in vivo. Together, our studies identified MASTL and COPZ1 as vulnerability genes for thyroid tumor cells and provided the rationale for future studies aimed to explore their targeting for potential therapeutic intervention