Lab experience at the Laboratory of Hematology in the Policlinico Hospital University of Milan, Italy – Karol Jacek Kieszkowski

I got the opportunity to do my 2nd lab rotation at the Laboratory of Hematology in the Policlinico Hospital (University of Milan, Milan, Italy).

PI of the laboratory: Prof. Niccolo Bolli

Tutor: Dr. Francesca Lazzaroni

The lab focuses on different hematological conditions, especially the multiple myeloma using different techniques, especially the single cell RNA sequencing.

My experience & learnings:

During my lab rotation, I have learnt many useful research procedures spanning the entire process, i.e. from the biological specimen isolation to data analysis and results interpretation. In particular:

• Bone marrow aspirates mononuclear cells isolation by means of density gradient centrifugation;
• 10x Genomics Single Cell 5′ Gene Expression and V(D)J Profiling with CITE-seq;
• Quality control procedures of nucleic acid samples such as PicoGreen and TapeStation;
• Puregene DNA isolation;
• Basics on R programming language;
• Single cell analysis workflow in R: from data pre-processing (SoupX, DoubletFinder) to cell assignment, differential gene expression analysis and gene set enrichment analysis.

The internship was challenging, considering my lack of previous experience in coding and the aforementioned laboratory procedures. However, the team provided me with relevant resources, such as the papers published by the team that I followed and detailed protocols for each undertaken procedure. Moreover, the researchers working in the lab took their time to explain me all the relevant concepts about the R programming language, not to mention providing me with their own code which served as a vital reference. The whole team was always supportive and eager to clarify any complex concepts.

The rotation helped me develop scientific reasoning. Not only did the lab researchers introduce to me the exciting projects that they were working on, but they also explained to me the role of the single cell gene expression analysis, which is the core part of their studies. It is a very powerful tool that allows us to formulate data-driven hypotheses that can then be validated through subsequent, targeted experiments. For instance, thanks to the single cell analysis, it is possible identify the upregulation of specific gene sets responsible for a given biological pathway. This allows us to draw the hypothesis that this associated biological pathway is involved in the disease’s pathogenesis. This prompts the design of focused studies to evaluate the pathway’s role.

I found this clerkship incredibly formative for my future academic activities. In particular, I would really like to apply the wide range of possibilities of data analysis offered by R programming language to my future final thesis project.