STSM Report: Piotr Łacina
STSM Reports Published on 18th February 2020
My name is Piotr Łacina and I am a PhD student supervised by Professor Katarzyna Bogunia-Kubik at Laboratory of Clinical Immunogenetics and Pharmacogenetics of the Hirszfeld Institute of Immunology and Experimental Therapy in Wroclaw, Poland.
My name is Piotr Łacina and I am a PhD student supervised by Professor Katarzyna Bogunia-Kubik at Laboratory of Clinical Immunogenetics and Pharmacogenetics of the Hirszfeld Institute of Immunology and Experimental Therapy in Wroclaw, Poland. I came to Newcastle in July 2019 for three weeks to participate in a short term scientific mission (STSM) for the working group ‘Molecular and Cellular Biomarkers of Chronic Graft versus Host Disease (cGvHD)’ hosted by Professor Anne Dickinson and Dr Rachel Crossland in the Haematological Sciences Department at Newcastle University.
The title of my STSM was “Analysis of miRNA data obtained by Nanostring technology using bioinformatics tools for biomarker detection in cGvHD”. To achieve this goal, I worked with Dr Rachel Crossland and Joanna Wielińska, who performed the experiment using samples from a group of post-transplant patients with and without cGvHD symptoms. During my stay, I processed NanoString output data and analysed it with the use of nSolver, RStudio and Microsoft Excel to find out if it is possible to distinguish cGvHD patients from non-cGvHD patients based solely on miRNA expression profiles.
The STSM was successful and I was able to pinpoint miRNAs with expression profiles in plasma extracellular vesicles (EVs) that were different between the studied groups. Using in silico algorithms, I was able to identify genes potentially targeted by those miRNAs, and signalling pathways associated with them. I also learned much about the NanoString technology which has great potential for identifying diagnostic markers. While we used the technology to study EV miRNA, it can also be used to study mRNA and assess gene expression.
During my stay in Newcastle I also helped in setting up and performing the ‘wet lab’ part of the experiment, i.e. EV isolation, RNA isolation and setting up the NanoString experiment. Furthermore, I had a chance to analyse the isolated EVs through electron microscopy and vesicle tracking by NanoSight. An important aspect of this STSM was also collaboration with other COST members, which could facilitate future joint projects.
In conclusion, I learnt many new techniques related to EV and miRNA data analysis, and applied them to find miRNAs differentially expressed in the plasma of cGvHD patients. Given the increasing number of studies on EVs, these newly acquired skills could help me in future potential projects of this COST action.