ESR 3: Gene expression in the HLA complex in autoimmune disease


PhD research



Prof. dr. N. de Vries (Niek)


Dept Clinical Immunology & Rheumatology

Amsterdam Rheumatology and immunology Center (ARC)


Rheumatology & Clinical Immunology & Experimental Immunology


Location AMC | D3-220 | Meibergdreef 9 1105 AZ Amsterdam


T: +31205667765  |  E: This email address is being protected from spambots. You need JavaScript enabled to view it.

Duration: 48 months



Genetic studies in many autoimmune disease have shown a strong association with polymorphisms in HLA class I or II molecules. These molecules continuously present peptides on the surface of antigen presenting cells, i.e. dendritic cells and B cells. T cells exert continuous surveillance of these peptides presented in the context of HLA molecules, which may result in the induction of highly specific adaptive immune responses, e.g. in autoimmunity. Thus, genetic variation in the HLA region is strongly associated with autoimmune disease, and molecules encoded in this region are likely to play a key role in the induction of the specific humoral and/or cellular autoimmunity observed in these autoimmune diseases. Despite this key role, there is a relative lack of knowledge regarding the role of surface expression of HLA alleles, and the role of splice variants in these diseases. In this project we will use state-of-the-art high-throughput sequencing approaches to study the role of gene expression and gene splicing in autoimmune disease.




The PhD candidate will get acquainted with cell selection technologies, existing high-throughput sequencing approaches of the HLA, B cell and T cell receptor genes and existing data analysis methods to study gene expression and splicing. The technologies will be used to study allele-specific gene expression and gene splicing in different relevant cell types in health and disease. 


Our research team

Our team aims to better understand the interactions between HLA-presenting APCs, T-cells and B cells that define specificity in, and regulate the disease-associated adaptive immune responses in autoimmune disease. To this end we study unique biobanked and freshly acquired materials from blood, human lymph nodes, bone marrow and synovial tissue obtained during the pre-clinical and earliest phases of autoimmune disease, e.g. in rheumatoid arthritis and vasculitis. The goal is to improve clinical management of these diseases by developing novel biomarkers and identification of new targets for novel therapies. Our team currently consists of 5 PhD students, 1 postdoc and 2 research technicians. For more information see


The project is a close collaboration with prof. dr. Antoine van Kampen of the The Bioinformatics Laboratory. The team is embedded within the recently established Amsterdam Rheumatology and immunology Center (ARC) and the Amsterdam Infection & Immunity Institute (AI&II). We are involved in several national and international research projects, allowing excellent possibilities for collaborations with other research groups in academia as well as industry.


Your profile

We are looking for a highly motivated and enthusiastic researcher with:

           A master degree Biomedical Sciences, with affinity for Immunology and translational research. Experience with cellular responses and molecular biology and affinity with bioinformatics.

           A flexible, pro-active team spirit with excellent communications skills. You like to show initiative and you have talent for focus and organization

           Proficiency in the English language, both written and verbal.


Our offer

All ARCAID ESRs receive a full employment contract for 4 years, according to the Collective Employment Agreement (CAO) of the Dutch University Medical Centres. The monthly salary based on a 36-hour work starts from €2.422,- with yearly increments to a maximum of € 3.103,-. This 4-year PhD position is funded by the  Marie Skłodowska-Curie actions of the European Union's Horizon 2020 COFUND program under grant agreement No 847551. There is no separate budget available for mobility as it is already included in the ESR salary. ESRs may attend external courses, conferences or workshops. If applicable or required, additional expenses for training and conference participation and the travel to a Partner Organisation will be covered by the project. The ESR salary meets the requirements of the Dutch Immigration Department to allow family members to move to the Netherlands. It is at the convenience of the ESR to decide on this family movement since the Amsterdam UMC will not cover additional expenses regarding mobility of spouse nor for the required accompanying residence permits. In addition to their individual scientific projects, all fellows will have the opportunity to attend international progress meetings, scientific conferences and summer schools. Additionally, they benefit from further continuing education, which includes internships and secondments, a variety of training modules as well as transferable skills courses. See recruitment procedure.

Your application

See recruitment procedure. You can apply using the online application form. For more information about the project you can contact Dr. Niek de Vries.