Deciphering adaptive immunity using high-throughput genomics and proteomics approaches.
Background: Antibodies are immune glycoproteins that represent a crucial part of the adaptive immune system as they mediate broad protection against viruses, bacteria, and cancer. Moreover, antibodies may serve as a unique source of information on past and current physiological and pathological events in the human body. Dysregulation of the antibody-dependent response can lead to a variety of abnormalities and diseases. Antibodies are found in the secreted form in the blood (antibody phenotype) and membrane-bound on B cells as B-cell receptor (antibody genotype). Thus, investigating the relationship between genomic and phenotypic antibody diversity is of decisive importance for understanding antibody-driven immune protection and disease.
In this project, we aim to establish a robust high-throughput framework for single-cell (SC) genomic and proteomic characterization of antibody repertoires using high-throughput genomic sequencing and mass spectrometry. The generated data will be analyzed using a variety of bioinformatics tools.
Project: The master student will be mainly involved in the generation of libraries for (single-cell) high-throughput sequencing (including all upstream steps), testing of novel sequencing protocols, and preparation of samples for mass spectrometry (LC-MS/MS) analysis. In addition, the student will be able to learn the basics of bioinformatics analysis including sequencing data preprocessing and characterization.
Methods: Blood sampling through venipuncture, isolation of peripheral blood mononuclear cells (PBMC) from whole blood, isolation of B cells from PBMC, single-cell encapsulation using microfluidic devices, mRNA isolation, cDNA synthesis, RT-PCR, template-switching PCR, LC-MS/MS sample preparation, bioinformatics data analysis using the R programming language.
Environment: The project will be performed at the Computational and Systems Immunology research group (Greiff lab), located at the Department of Immunology, Rikshospitalet. The group is led by associate professor Victor Greiff and includes researchers at different carrier stages. We are actively collaborating with other research environments within the immunology field as well as with bioinformatics and computer scientists. The group is young, ambitious, dynamic, and friendly. As a member of the research group, you will be involved in all activities including weekly scientific meetings, journal clubs, project discussions, etc.
What we expect from you: We are looking for a highly motivated person with a passion for science. Previous experience with some of the methods described above is an advantage.
Contact: Contact Dr. Igor Snapkov (firstname.lastname@example.org) or Dr. Victor Greiff (email@example.com) if you have any questions or are interested in joining our team!