We are looking for a highly motivated project student with a specific interest in bioinformatics, omics profiling and immunology, to join our highly cooperative group at the Department of Clinical Neuroscience at Karolinska Institutet. Our group strives to unveil molecular mechanisms underlying Multiple Sclerosis (MS), a leading cause of progressive disability in young adults, and we currently have an opening for a student to join our project focusing on “Epigenetic regulation of the Human Leukocyte Antigen locus.”
Background of the project: The Human Leukocyte Antigen (HLA) locus is commonly involved in immunemediated conditions, such as MS, where the HLA-DR15 haplotype has been identified as a major genetic risk factor. Recent studies have highlighted that expression levels of HLA genes in antigen presenting cells (APCs), play a role in disease development. We have further demonstrated that epigenetic mechanisms, such as methylation of DNA, regulate expression of the gene in APCs from MS patients (Kular et al.). However, the mechanisms that drive the association of the HLA locus with MS are still not fully unraveled.
In the suggested project, we aim to decipher the epigenetic landscape of the HLA locus using a targeted approach, referred to as SureSelect Methyl-Seq Capture, which we, in collaboration with Agilent Technologies, have designed to specifically enrich the HLA class II locus and proximal promoters of immune- related genes (Kalomoiri et al.). We plan to apply this methodology to APCs in vitro to study epigenetic changes during activation. The project student will gain experience with processing of Methyl-Seq methylation data, which includes QC, read filter, mapping of reads to the reference genome, deduplication, and estimation of DNA methylation levels, differential methylation analysis and biological interpretation using gene ontology and Ingenuity Pathway analysis and Cytoscape. The project student will be introduced to compute servers and HPC environment for data analysis and primarily use R, Bash and Python languages. There will also be a possibility to join the library preparation process in the lab.
Supervisor team and learning environment: The Principal Supervisor Prof. Maja Jagodic, has wide expertise in neuroimmunology and functional (epi)genomics of MS. Co-supervisor Dr. Maria Needhamsen, a Senior Research Infrastructure Specialist, will assist the bioinformatics analyses and PhD Student Maria Kalomoiri, who conducted the experiments and generated the data, will support pathway analysis and interpretation of the results. The Jagodic group consists of approximately 15 members with a mix of experimental and bioinformatic skills located at the Center for Molecular Medicine (CMM), Karolinska Institutet in Solna. The student will furthermore have the possibility to join weekly meetings with the Karolinska Neuroimmunology & MS network (KNIMS, ca. 70 members), bioinformatics team, journal clubs, seminars etc.
Join us! Please contact head of bioinformatics team, maria.needhamsen@ki.se, with your motivation letter and CV.
Project start: Spring semester 2025