GLIOTRAIN students undertake interdisciplinary and intersectoral secondments in Year 3 of the programme

ESR Kieron White (RCSI) undertook a secondment from October 2019 – January 2020 at INSERM, who had recently joined the consortium as a Partner. Here, Kieron applied the Microenvironment Cell Populations-counter (MCP-counter) computational method on sequencing data generated from the GLIOTRAIN biobank samples. This computational technique allows researchers to assess the tumour microenvironment (TME) in cancers, including GBM. The TME is the complex mixture of tumour cells and other “normal” body cells, such as immune cells, and those that make up blood vessels. Interactions between these cells are thought to greatly influence the effect of drugs on treatment of tumours and also the prognosis for patients. This work will support the identification of novel therapeutic strategies targeting the GBM TME. INSERM is a world-leading health science institute, and this secondment provided Kieron with an excellent opportunity to expand his training and specifically to receive top-class training in the MCP-counter method as well as in other wet-lab techniques such as immunohistochemistry .

Romain Tching Chi Yen is based in a commercial organisation (ITTM) and his project is largely computer based. To provide Romain with experience in an academic research institution, he undertook a short secondment to Beneficiary EMC . During this secondment, Romain was actively involved in the generation and analysis of sequencing data with a special focus on an academic (clinical research) laboratory. He undertook GBM tumour whole genome expression data analysis, relating this to drug response of cell cultures derived from the same tumours. Moreover, Romain had the opportunity to work with transcriptomics expression data in order to identify markers that might explain the observed heterogeneity in response to treatment, in various experimental set-ups. It was planned that Romain would return to EMC in March 2020 to undertake some drug screening experiments for wet-lab training, however this was unfortunately a casualty of COVID-19 and has been postponed for now.

In January 2020, ESR Ioannis Ntafoulis (EMC) commenced a secondment at Partner TEVA Nederland. TEVA is a multinational pharmaceutical company who invest in research and development of generic medicines and biopharmaceuticals. One aspect of TEVAs repertoire is drug repurposing, where drugs approved for one disease or indication are tested to see if they might work to treat another disease. It is this aspect that is important for Ioannis’ project. Whilst on secondment (which was unfortunately cut short due to COVID-19) Ioannis was learning about the process of drug repurposing from a pharmaceutical company perspective.

Commencing in January 2020 and currently ongoing remotely, ESR Yahaya Yabo is on secondment to Beneficiary ITTM. His secondment began with an introduction to the business model of the company and the various projects currently ongoing. These projects cut across the different areas of specialization of ITTM such as data curation, hosting, analysis and visualisation. Yahaya’s work at ITTM began with training on tranSMART and test running of the GLIOTRAIN database, identifying glitches that were fixed before it became accessible to the members of the consortium. Following training on the disease maps, Yahaya has been involved in the GBM disease map project, mainly reviewing the entries made by ITTM ESR Romain, who is the developer of the map. The GBM disease map project aims to provide a well annotated, high quality representation of genetic alterations, networks and pathways involved in GBM.

ESR Jenny Weng (VIB) began a secondment at Partner Oncurious in February 2020. The aim of her secondment was to acquire skills in therapeutic antibody design and implementation for pharmacological studies. Unfortunately the secondment was curtailed due to COVID-19, but she is planning to return when restrictions and safety advice allow. During her time at Oncurious Jenny learned about the workflow of nanobody production, and focused on repertoire cloning and library construction, clone selection by bacterial display, and also learned how to use automated workstation to do nanobody purification. Nanobodies are small antibody fragments that are currently evolving as potential therapeutic tools.