Passionate about the transmission of genetic diseases, Roukaya YAAKOUBI is doing her thesis at the Institut Pasteur de Tunis on primary immune deficiencies (PIDs), genetic diseases of the immune system. She is studying more particularly the hyper IgE syndrome, a hereditary combined immune deficiency of B and T lymphocytes which is expressed, among other complex clinical symptoms, by a severe allergy. An exchange between the the Institut Pasteur de Tunis and the Institut Pasteur (Paris), carried out within the framework of the ATUN-DIPs project, allowed her to make a leap forward in her research. She explains.
What led you to study primary immune deficiencies?
Very interested in biology, my university studies in molecular and cellular biology led me to better understand the interconnection and the functioning of living organisms. In particular, immunology, which refers to the study of the immune system, represents for me the best discipline to study for example the reactions between the human body and pathogens. The immune system ensures the fight against aggressive or harmful agents to our organism thanks to its constituents which act to limit this aggression but also contributes to the homeostasis of the organism and to the control of the emergence of allergic, auto-immune diseases or cancers. Nevertheless, a defect affecting one or more components of this system can lead to a failure, and this is when I discovered immune deficiencies.
During my master, I chose to study immune deficiencies for my master's thesis. I did a one year internship in the Laboratory of Transmission, Control and Immunobiology of Infections (LR11IPT02) directed by Pr Mohamed Ridha Barbouche under the supervision of Dr Meriem Ben Ali. During this internship, I aimed to study the particularity of Hyper IgE syndrome in Tunisia. Through this experience, I discovered the importance of genetics in the study of primary immune deficiencies and acquired new skills in immunology. This combination of my two favorite fields (genetics and immunology) revealed even more my passion for research.
What are you working on in the ATUN-DIPs project?
Primary immune deficiencies are a heterogeneous group of over 450 diseases in which a genetic defect in the immune system is responsible for an increased susceptibility to infections that can be associated with allergies, autoimmune manifestations, and sometimes cancers.
Since 2016, I have been conducting my research on Hyper IgE syndrome in the immunology laboratory at the Institut Pasteur de Tunis, directed by Pr Mohamed Ridha Barbouche. Part of my thesis work is part of the ATUN-DIPs project.
Hyper IgE syndrome, which is the PID I am working on, is a hereditary combined immune deficiency of B and T lymphocytes. It is characterized by eczema, recurrent skin and respiratory infections, very high levels of a type of antibody in the body - immunoglobulin E (IgE), frequently associated with allergic manifestations. The objective of my thesis is to characterize the genetic basis of the hyper IgE syndrome in Tunisia and to understand why patients suffering from this disease produce them excessively.
My thesis is divided into two parts:
- Investigation of the genes involved in the hyper IgE syndrome thanks to the sequencing of a panel of genes. At present, 9 genes are involved according to the latest classification of PIDs.
- Understanding of the mechanism of IgE overproduction in patients with hyper IgE syndrome.
What did your internship at the Institut Pasteur in Paris bring you?
In Tunisia, we do not have the same high throughput sequencing equipment as the Institut Pasteur (Paris).
For 2 years I had to sequence gene by gene according to the clinical profile of the patients. This is called the "candidate gene" strategy, which takes more time and is more expensive. However, the best strategy to identify the genetic basis for PIDs is to sequence a set of "panel" genes in one go, especially since some PIDs share clinical signs that are not always due to mutations in the same genes. This is called differential diagnosis. Using this strategy will therefore allow a better definitive diagnosis.
This high throughput sequencing method is a technology not yet available at the Institut Pasteur de Tunis but is currently available at the Biomics laboratory of the Institut Pasteur (Paris). We designed a panel of 300 genes with the whole team working on PIDs at the Institut Pasteur de Tunis, which we sent to the Biomics platform to be sequenced.
Before my internship at the Institut Pasteur (Paris), I followed online training courses on high-throughput sequencing. When I arrived at Biomics, I was able to benefit from additional theoretical training on this subject: sample preparation with index labeling, DNA normalization (same quantity of each sample) and finalization of the construction of the libraries, i.e. the set of DNA fragments that will be sequenced with the Next Generation Sequencing (NGS) sequencer.
At the Institut Pasteur (Paris), I also followed other training courses in RNA sequencing and metagenome, as well as quality management courses that added to my curriculum.
How will you apply your learning back at the Institut Pasteur de Tunis?
Within the framework of the ATUN-DIPs project, a transfer of the acquired skills is planned. Thus, the expertise that I acquired in the preparation of banks in the Biomics laboratory of the Institut Pasteur (Paris), will be transmitted in situ to other colleagues at the Institut Pasteur de Tunis. To this effect, a team from Biomics has also moved to Tunis, within the framework of the European project PhindAccess, to help set up the NGS approach at the genomic platform of the Institut Pasteur de Tunis, which will allow, among other things, the preparation of libraries.
In your opinion, what will be the impact of your internship to improve the diagnosis of primary immune deficiencies in Tunisia?
Once the preparation of the libraries will be possible at the Institut Pasteur de Tunis, we will be able to propose, to the requesting patients, a sequencing of the panel which contains 300 genes known to cause PIDs. This will greatly improve the diagnosis and allow a better management of patients.