Establishing high-throughput methods to study ‘mini-guts’

Jenny Ostrop

Jenny Ostrop, Centre of Molecular Inflammation Research at Trondheim, Norway
Service Providers:
EU-OPENSCREEN, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
Euro-BioImaging EMBL Node

The human gastrointestinal tract is a highly sophisticated organ. The gut epithelium consists of several specialized cell types in a distinct spatial arrangement that enable efficient nutrient uptake and forms a barrier against commensal bacteria and pathogens. CORBEL user Jenny Ostrop from the Centre of Molecular Inflammation Research at NTNU in Trondheim, is using organoids - ‘mini-guts’ that form characteristic crypts and villi - to study the intestinal epithelium. Her scientific interest lies in the differentiation of stem cells into the diverse epithelial cell lineages.

‘We are trying to find the molecular ‘switches’ that determine which cell types develop from the stem cells and how the epithelium is composed’, explains Jenny. The organoids are grown in a collagen matrix and their handling is challenging and time-consuming. Having heard about the CORBEL Open Call for research projects from colleagues, Jenny applied for access to the high-throughput screening facilities at EU-OPENSCREEN. During her visit, Jenny was able to automate several working steps in her experimental pipeline, thereby accelerating the workflow. This allowed her to screen a library of compounds that might influence organoid development for their effect on cell differentiation and organoid composition. As the next step, based on the screening results, Jenny is planning to visit Euro-BioImaging to quantify the three-dimensional morphology of the organoids following certain treatments, using advanced microscopy techniques and automated image analysis.

I would definitely recommend other researchers to apply for access to the European research infrastructures. Their offer means a great chance to use instruments that you would normally not have access to and to benefit from their expertise.
Jenny Ostrop

Screening for active compounds against acute myeloid leukemia

Maria Paola Martelli

Maria Paola Martelli, University of Perugia, Italy

EU-OPENSCREEN, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany

Euro-BioImaging EMBL-Node

Prof. Maria Paola Martelli focuses her research on acute myeloid leukemia (AML) with the aim to translate her findings into novel diagnostic tools and therapies. AML affects the maturation of myeloid blood cells leading to accumulation of abnormal cells and ultimately to bone marrow failure. AML accounts for about 80% of acute leukemia in adults with a grim prognosis in particular for elderly patients, often leaving allogeneic stem cell therapy as the only treatment option.

Prof. Martelli is primarily interested in a genetic alteration, present in about one-third of AML cases. This was discovered by Brunangelo Falini when Martelli was a researcher in his lab and has remained a central research interest throughout her career. This mutation alters the properties of a phosphoprotein, which in its mutant form accumulates in the cytoplasm. Prof. Martelli’s CORBEL project aims to identify small molecule compounds, which attack either the mutated phosphoprotein or a key partner. To this end, the first set of experiments was carried out by Prof. Martelli’s PhD student Roberta Ranieri at the EU-OPENSCREEN Node. Access to EU-OPENSCREEN allowed her to screen their collection of compounds against AML cell lines, which she characterized in her lab together with Dr. Ilaria Gionfriddo (Assistant Professor in Hematology, at Perugia University in Prof. Martelli’s lab). Specifically, two FDA-approved drugs resulting from the screen were proved to be highly effective in our cell models and profitably synergistic with drugs already in use in the AML settings. Those promising combinations will soon be tested in murine preclinical models, prior to being employed in a clinical trial. Selected molecules are now being evaluated using advanced imaging technologies at the Euro-BioImaging EMBL-Node. This project will hopefully be a step towards novel therapy options for AML, which are desperately needed and will have a positive impact on human health.

CORBEL is allowing us access to technologies not available in our lab and to scale-up screening of large compound libraries. This is a big step forward for our project.
- Maria Paola Martelli

Integrating EU-wide cardiovascular research datasets

Adriano Barbosa da Silva

Service Providers:
Adriano Barbosa da Silva, Queen Mary University of London (QMUL), United Kingdom

EATRIS Coordination Office, Amsterdam, The Netherlands

BBMRI Headquarters, Graz, Austria

Euro-BioImaging, Population Imaging Node Rotterdam (BIGR), Rotterdam, The Netherlands

Projects like the UK Biobank aim to improve the prevention, diagnosis and treatment of several diseases, by following the health status of 500,000 volunteer participants, and anonymously capturing changes that could give clues on alterations of health condition, lifestyle or environment that could be associated with the onset of diseases, such as cardiovascular diseases (CVD).

Dr. Adriano Barbosa’s CORBEL project aims to extend the impact of large population studies, such as the UK Biobank, by identifying and collecting additional European CVD datasets that could be analysed in parallel in order to validate insights observed in the UK Biobank on an independent dataset. In this respect it was of critical importance for him to gain access to European Research Infrastructures (RIs) that could help with this task.

A bulk search conducted by BBMRI using their negotiator service towards the BBMRI catalogue of biobanks identified 465 matches. In parallel, EATRIS coordination and support office, through its proprietary database of capacity available within the RI partner institutions, identified five institutions. Further discussions between Adriano and principal investigators at the identified institutions enabled by EATRIS allowed to scale down to two institutions with the datasets fully matching Adriano’s CVD query: Fondazione Ri.MED (Italy) and St. Anne's University Hospital (Czech Republic).

EATRIS helped to establish a Data Protection Agreement between Adriano’s university and Ri.MED via engagement with the respective data protection officers. Additionally, EATRIS supported Adriano with setting up a Memorandum of Understanding between his university and the Czech hospital as a first step to establish the necessary framework to have their data used in the scope of the project.

Through the Euro-BioImaging Node in Rotterdam, preliminary work was performed for the deployment of the imaging archive key for the integration of imaging datasets. Further support will be provided for the extraction of imaging features from the medical imaging data sets allowing QMUL to apply machine learning methods to stratify cardiovascular patients based on machine learning.

CORBEL support during my project was fundamental to address the legal requirements needed prior to data sharing. Without RI support it would have been particularly challenging to liaise with the matched biobanks and make sure that their datasets could be used in my research.
Adriano Barbosa da Silva, Queen Mary University of London (QMUL), United Kingdom

© Photo: Adriano Barbosa da Silva

Revealing the morphological plasticity of a cell in planktonic symbioses

Service Providers:
Euro-BioImaging EMBL Node

EMBRC, CNRS Marine Observatory, Villefranche-sur-mer, France

Symbiosis with photosynthetic cells occurred several times in the evolutionary history of eukaryotes and led to the acquisition of the chloroplast– the organelle that performs photosynthesis. Chloroplast acquisition gave rise to a wide diversity of photosynthetic organisms and is considered to be one of the most important biological innovations in eukaryotes.
Living in symbiosis with microalgae is still a widespread phenomenon in today’s oceanic plankton. These ecological interactions contribute significantly to oceanic primary production and the functioning of marine ecosystems. Large-scale environmental sequencing projects (e.g. Tara-Oceans) have unveiled the worldwide prevalence of these cell-cell symbioses in the oceanic plankton.

Despite their key ecological roles in the oceans, the basic functioning of these symbiotic interactions, as well as the subcellular mechanisms by which a cell can accommodate and engineer an intracellular microalgal cell remain unknown. Dr. Johan Decelle, a young group leader at the University of Grenoble Alpes, who played an active role in the Tara-Ocean expeditions, has focused on revealing these mechanisms in his research. The goal of his project is to unveil the structural architecture of the symbiotic cells, in particular the chloroplasts, using cutting-edge imaging technologies. Working with the CNRS Marine Observatory of Villefranche-sur-mer, which is part of EMBRC, has allowed him to collect his study material despite being based away from the sea with his institute. This site offers a favorable oceanographic context for the presence of symbiotic plankton in near-shore waters, which facilitate experiments on live cells. At the Euro-BioImaging EMBL Node, he used the 3D imaging technique FIB-SEM (Focused Ion Beam scanning electron microscopy) to visualize subcellular modifications of the photosynthetic machinery and the microalgal cell at high imaging volume before and during symbiotic interaction.

What started as a project selected via the CORBEL Open Call developed into a long-term collaboration. All partners agree that this project will improve our knowledge of the functioning of planktonic symbioses and bring new evolutionary insights into chloroplast acquisition in eukaryotes.

‘Learning about these available resources and accessible technologies in Europe was such luck! To have the possibility to go all the way from collecting planktonic cells in the ocean to high-end cutting-edge imaging technologies is a unique opportunity to better understand these ecologically-important cells!’ - Johan Decelle

Investigating Toxin-Antitoxin systems in lactic acid bacteria

CORBEL user Camilla Lazzi works in the Department of Food and Drug of the University of Parma, Italy as a food microbiologist in the research field of lactic acid bacteria. These are microorganisms with a wide ecological distribution and important applications, especially in the food industry. Their activity as fermentation workhorses is highly regulated. A bacterial community can induce death or dormancy of some cells, in response to different stress conditions, resulting in a sacrifice to favor the survival of the entire ecosystem. These responses are often mediated by a Toxin-Antitoxin (TA) system. TA systems are two-component systems that involve a stable toxin, able to kill the cells or confer growth stasis, and an unstable antitoxin which inhibits toxin activity. Little is known about the distribution and function of TA systems in lactic acid bacteria, but the activation of these systems could modulate the bacterial population dynamics. Understanding the mechanism of action could have promising scientific and applicative perspectives in the field of fermented food but also in the study of intestinal microbiota.

With the use of CORBEL facilities, Camilla and the research group of Parma University aim to identify TA systems in wild isolates of Lactobacillus strains, and subsequently characterize the mode of action of the TA systems. They collaborate with two service providers, the Biomedical Research Foundation of the Academy of Athens (BRFAA) and the Institute of Photonic Sciences (ICFO). The results of the sequencing at BRFAA were presented at the 26th ICFMH Conference FoodMicro2018. Furthermore, a postdoc student, Alessia Levante, plans to visit BRFAA to perform the final elaboration of the data with Dr. Giannis Vatsellas and Dr. Periklis Makrythanasis. As a second step, Camilla and the research group at Parma University want to elucidate the function of the newly identified TAs. To this end, they requested the ICFO in Barcelona as service provider to perform high-resolution fluorescence microscopy (PALM microscopy). Also in this case, a PhD student will spend a period of time at the service provider to set up the final experimental procedure in collaboration with Dr. Pablo Loza, Dr. Maria Marsal and Dr. Jordi Andilla.

When we read about the CORBEL open call we thought it was a great opportunity to gain access to important Research Infrastructures with experience that is not at all present in our laboratory. Through this call, we have filled a gap improving our research.
Camilla Lazzi, University of Parma, project leader

Research group of Parma University, Department of Food and Drug (from left to right): Claudia Folli, Stefania Grifone, Korotoum Yabre, Alberto Ferrari, Alessia Levante, Camilla Lazzi (missing: Erasmo Neviani, Barbara Montanini)

Greetings from the Sea – a CORBEL Open Call user reports about her first visit

Prof. Simona Candiani from the University of Genoa is one of our successful applicants, who were selected with her project in the 1st CORBEL Open Call. Her scientific interest addresses certain genes that might play an important role in evolutionary neural development. For her research, she uses amphioxus as a model system.
Simona’s first visit in the framework of her CORBEL access brought her to the marine station at Banyuls-sur-mer, which is the only Mediterranean infrastructure that offers the possibility to collect amphioxus adult. She received training to perform in vitro fertilization of the collected animals to prepare embryo cultures, which will be needed for RNA extraction and whole mount in situ hybridization.

My stay in Banyuls was really useful as I had the opportunity to gain experience with amphioxus egg microinjection – a very challenging technique, as I was warned by several of my colleagues ahead of my trip! Nevertheless, I obtained a few microinjected animals and now I am looking forward to the next steps in my CORBEL project! 

Simona’s visit was facilitated a lot by the administrative support from CORBEL project managers and the technical assistance by local scientific staff.

As second service provider in her project pipeline, Simona requested access to the Advanced Light Microscopy Facility (ALMF) at EMBL Heidelberg. Here, she will receive not only access to the most advanced imaging technologies, but also technical support in developing a suitable imaging protocol. The goal is to reveal the 3D localization of several neural markers in amphioxus, which will eventually help to better characterize the function of the genes of interest in neural differentiation of amphioxus.

S. Candiani performing
amphioxus egg microinjection
model system amphioxus
research vessel Nereis

This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 654248.