All the way from Iran to Germany

After finishing my master’s degree in Iran, I was ready to make a change in my life. I have to say that this was not a spontaneous decision; I was always thinking about living and studying in a different country, enthusiastic about being in a new society and experiencing a new culture. All things considered, Germany is the first choice for many students, and I was no exception.

I was happy to be accepted in the STACCATO (European Industrial Doctorates programme) project available at the PEI (Paul-Ehrlich-Institut). This is an international collaborative project in the field of immunotherapy (my special interest), it offers the opportunity of a secondment in another country, and lots of bioinformatics! Overall, the position in the STACCATO programme covered all my interests.

So I moved to the city of skylines and was ready to start a new chapter in my life. Moving to Germany was both challenging and pleasing. For the first few days I had to do lots of official paperwork which now I know it is typical in Germany, but apart from that I found myself enjoying life in Frankfurt.

During the first days at the Lab, I met my nice colleagues and another ESR, Theofilos Filippos Charitidis. We are both working in the same research group, and since Filip had started his Ph.D. prior to me, he kindly helped me to get oriented in the lab. And we still have close collaboration in our projects, which is indeed encouraging. What specifically attracted my attention on a walking tour around Frankfurt is the mix of both historical buildings and the modern, futuristic skylines. Nevertheless, there are also many attractive natural areas and Frankfurt is a very green city. Soon after starting my PhD, it was Christmas time! Hanging around the warm and shiny Christmas Market was all that a newcomer needs to do in the grey German winter!

But unfortunately, the new year started with a global pandemic and, as for everyone around the world, our work was affected. Soon after the crisis became worse, the work in the lab stopped and we were working from home. But during that period I actually found time to learn more about bioinformatics analysis and got to know some of the software tools in this field, which is very helpful. Luckily, under stringent safety measures, we have now started the lab work and I hope everybody will stay safe.

Now, after sharing a bit of my story, I would like to tell you what this journey is all for….

Amazing CAR T cells!

Chimeric antigen receptor T cells, so-called CAR T cells are considered as an evolutionary type of cancer immunotherapy. So far the FDA has approved CAR T-cell therapy for adult patients with certain types of lymphoma, as well as children and young adults with acute lymphoblastic leukemia. Beyond that, there are many clinical trials ongoing assessing CAR T-cell therapy for other types of blood cancer, as well as research projects regarding their efficacy in the management of solid tumors.

But what are CAR T cells? One can imagine them as intelligent T cells that go throughout the body, recognize tumors, and kill them. CAR T cells are actually genetically manipulated T cells, with the ability to express a chimeric antigen receptor (CAR), specific for a surface protein on cancer cells. So the cells gain the ability to recognize cancer cells via their receptor.

In the process of making T cells intelligent enough to recognize tumor cells we need to send the genetic information of the CARs to the cells, then cells will translate this information for tumor cell recognition. This genetic information is transferred to the cells by specific lentiviruses. The virus binds to the cell and injects its genetic information (which in this case is the CAR gene) into the T cells.

This might sound straightforward but it requires a complicated manufacturing process. T cells are isolated from blood samples and activated in cell culture and subsequently transduced with viral particles. After the expansion of these genetically modified T cells, they can be used for clinical purposes. The lentiviral vectors used for transduction of T cells are mostly pseudotyped with the glycoprotein G of vesicular stomatitis virus (VSV) which mediates a broad tropism and thus CAR gene delivery to various cell types. In the Molecular Biotechnology and Gene Therapy group of Paul-Ehrlich-Institut, which I am working in, receptor-targeted lentiviral vectors have been developed. This type of vectors is designed in a way that they can specifically bind to CD4 or CD8 T cell subtypes and transduce them. These vectors can potentially facilitate CAR T cell production by eliminating the need for previous isolation and manipulation of the cells and also direct in vivo generation of the CAR T cells.

What is the purpose of my project?

Despite the successful results obtained with CAR T cell therapy, still some limitations exist. The complicated generation process of CAR T cells which includes delivery of the CAR gene to the T cells often via lentiviral vectors, can affect the functionality of the cells and decrease the clinical efficacy of CAR T cell therapy. The aim of my project is to have a close look at the CAR T cells after production and perform molecular analysis to get an insight about the alterations of the cells during lentiviral vector mediated gene transfer on their efficacy and functionality.

I will try to dissect the CAR T cell characteristics with single-cell profiling. In particular, single-cell transcriptome analysis will be performed along with barcoded antibodies, enabling a comprehensive immunophenotypic and transcriptomic analysis of the cells. This is important to follow the fate of vector particles sticking to cells, and, because often the RNA levels versus protein levels are not correlative.

During this project, conventional or receptor-targeted lentiviral vectors will be used to transduce T cells. Different transduction and manufacturing conditions of CAR T cells will be applied and the overall effect on the functionality and exhaustion of the cells will be measured. Based on the data obtained in this project, I hope we would be able to find solutions for the optimization of the CAR T cell manufacturing process and ultimately improve the functionality of CAR T cells. After almost 8 months working in the lab and living in my cosy apartment in a nice and green neighborhood of Frankfurt, I can say that so far, Germany has been a place for me to learn and experience many new things, and STACCATO not only supports me in pursuing my Ph.D. career, but also provides me an opportunity to meet great people in the field and be part of an international collective that will broaden my horizons. Along with other research groups in STACCATO and in direct collaboration with other brilliant ESRs, I hope that we will answer some fundamental questions in the field.

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