New approaches to investigating diversity in adaptive immune receptor genes
Hundreds of genes recombine in a combinatorial manner to make B- and T-cell receptors, which are integral to the adaptive immune system. Researchers in the ImmuneDiversity project are investigating the inter-individual diversity of these genes, which will open up new insights into disease susceptibility, as Professor Gunilla Karlsson Hedestam explains.
There is a high degree of variability in the genes that encode our adaptive immune receptors across the world, yet most genomics studies and databases have historically focused on populations with European ancestry. Researchers in the ERCbacked ImmuneDiversity project are now working to provide a broader picture. “We are running studies looking at major population groups, including people with backgrounds from sub-Saharan Africa, East Asia, South Asia and Europe,” explains Gunilla Karlsson Hedestam, a Professor in the Department of Microbiology, Tumor and Cell Biology at the Karolinska Institutet, the project’s Principal Investigator. “We started with local volunteers with diverse backgrounds who were interested in the study and provided blood samples, and we then extended the studies to samples collected through collaboration with scientists around the world that also include more focused population groups,” she outlines. “Using our high throughput genotyping method, we also analysed the 1,000 Genomes Project collection, which comprises samples from all over the world.”
Immune system variability
A Senior Research Specialist in the group, Dr. Martin Corcoran has developed the new techniques to define germline-encoded variation in antigen receptor genes employed in the ImmuneDiversity project. Together
with others in the group, he carefully validated these techniques using both wet lab approaches and computational methods, work that has taken many years to complete. With these techniques now at hand, researchers can finally study adaptive immune responses with a high degree of accuracy and at a level of detail that is not possible with traditional
lot of parallels between B-cells and T-cells in terms of how their antigen receptors are built up,” says Professor Karlsson Hedestam, with building blocks - V, D and J germline genes - that recombine in a combinatorial manner to make up all B-cell receptors (membrane-bound antibodies) and T-cell receptors. “There are hundreds of V, D and J
repertoires and responses. This variation may influence the level of protection our B- and T-cells provide against infections and may also predispose us to the development of certain immune-mediated diseases. “We know for example that multiple sclerosis (MS) and rheumatoid arthritis involve T-cells and B-cells, we just don’t know why some people develop these diseases. One scenario is that infections induce cross-reactive immune responses that not only target the pathogen but also attack self-tissue, and that variations in adaptive immune system genes predispose people to such mis-directed responses,” outlines Professor Karlsson Hedestam. Two new approaches have been developed in the project to enable researchers to probe deeper into this area, called IgDiscover and ImmuneDiscover; the latter is a high throughput approach which is used to sequence large numbers of people very efficiently. “With ImmuneDiscover we start from DNA samples rather than expressed RNA” explains Professor Karlsson Hedestam. “This approach allows us to generate genetic profiles of thousands of people simultaneously.” By applying this technique
to disease cohorts, the team aims to identify gene variants that make people more vulnerable. “By performing personalized genotyping of B- and T-cell receptor genes, we may be able to piece together more of the puzzle for diseases where adaptive immune responses are known to be involved, such as auto-immune conditions”, says Professor
Karlsson Hedestam. A deeper understanding of whether certain alleles are associated with auto-immune disease would enable researchers to identify high-risk groups. “These could be very important prognostic markers that could then be added to information about the patient’s HLA-type,” says Professor Karlsson Hedestam.
performing personalized
of B- and T-cell receptor genes, we may be able to piece together more of the puzzle for diseases where adaptive immune responses are known to be involved, such as autoimmune conditions”.
sequencing methods. The team focuses on Band T-lymphocyte receptors, both of which play important roles in the body’s response to pathogens and are implicated in numerous immune-mediated diseases. “There are a
genes, most of which are highly polymorphic and some genes are missing altogether in some individuals”, she continues. “We aim to define where the polymorphisms are and the frequency of different gene variants in the population. Alleles of a given V, D or J gene may differ from each other by as little as a single nucleotide, but this can be enough to have functional consequences.”
For example, a recent study on SARS-CoV2-specific antibody responses published by the group showed that single polymorphisms can change the way B-cell receptors interact with critical neutralizing target epitopes. Thus, each of us has a different collection of V, D and J alleles, which shapes our immune
“By
genotypingSanjana Narang and Martin Corcoran Photograph by Johanna Åkerberg Kassel. Marco Mandolesi. Photograph by Johanna Åkerberg Kassel.
Analysis of B- and T-cell receptor V, D and J gene diversity in populations with different genetic ancestries
IMMUNEDIVERSITY
Defining human adaptive immune gene diversity and its impact on disease
Project Objectives
The aim of the project is to define human population diversity in the hundreds of germline V, D and J genes that encode our B- and T-cell antigen receptors, and to investigate how this diversity influences our responses to infections and vaccination or predisposes to the development of autoimmune diseases.
Project Funding
This project has received funding from the European Union’s Horizon 2020 research and innovation programme under Grant agreement ID: 788016. In addition to the ERC Advanced grant, the work is funded by a Distinguished Professor grant from the Swedish Research Council.
Project Partners
For the work on rheumatoid arthritis, we are collaborating with Drs. Malmström and Padyukov at Karolinska Institutet.
Contact Details
Gunilla B. Karlsson Hedestam Professor
Department of Microbiology, Tumor and Cell Biology
Karolinska Institutet
171 77 Stockholm
Visiting address:
Biomedicum C7, C0767, Solnavägen 9 E: Gunilla.Karlsson.Hedestam@ki.se W: https://ki.se/en/mtc/gunilla-karlssonhedestam-group
Cohort studies
The first priorities for the project were to develop the analytical methods and ensure that they were highly robust, reproducible, and precise. Once this was established, the team moved on to identify new alleles and define the frequencies at which they occur in persons with different population ancestries. This work establishes an important baseline, a picture of normal frequencies, which will provide a basis for comparison with disease cohorts, says Professor Karlsson Hedestam. “We think that with our soon to be completed studies on human populations from our own sample collection and the 1,000 Genome Project samples, we are starting to reach saturation point. We will have found most variants except very infrequent ones,” says Professor Karlsson Hedestam.
In the longer run, information about adaptive immune receptor genotypes could be very useful for clinicians, enabling the stratification of patients into higher and lower-risk groups, while it could also be highly valuable for pharmaceutical companies. It may be possible to specifically target genes associated with a disease for example, with the project helping to lay the foundations for further development in this regard. “There is huge potential in this work, but we must do the groundwork first. These gene regions are extremely complicated, and they cannot be completely sequenced with conventional methods,” stresses Professor Karlsson Hedestam.
Gunilla Karlsson Hedestam received her BSc from Uppsala University in 1990 and PhD from University of Oxford in 1993. After a post-doctoral fellowship at Harvard 1994-1998, she joined Karolinska Institutet where she became tenured Professor in 2012. She is a member of the Royal Swedish Academy of Sciences since 2019.
“This work is now almost complete, and we are ready to start pushing through disease cohorts,” says Professor Karlsson Hedestam. This will involve genotyping samples from patients with specific conditions alongside healthy controls. “We will focus increasingly on cohort studies in the coming years,” she continues. When an association is identified for a given disease, the team will investigate the functional impact of the polymorphism using in vitro cell culture systems and structural analysis to unravel the molecular basis for the effect.
The project’s research also holds relevance to the goal of adapting or tailoring vaccines to the genetic profile of specific populations, as vaccines can be more effective in some areas of the world than others. “If certain allelic variants of genes are needed to produce protective antibodies, and they are present at different frequencies in different populations, it could mean that a vaccine could work well in Europe but less well in Asia,” explains Professor Karlsson Hedestam. A deeper understanding of the genetic background of local populations could enable the development of more tailored and effective vaccines against disease.