iR+ Seminar Series: Theory and Applications of Immune Repertoires
The iReceptor Plus Seminar Series highlights the Theory and Applications of immune repertoires. The overall goal of the iReceptor Plus Consortium is to facilitate sharing and analysis of Adaptive Immune Receptor Repertoire Data. These immune repertoires are rapidly increasing in size and importance to all aspects of immunotherapy, and the Consortium is dedicated to improving analysis and curation tools that will allow the entire immunology community to maximize the benefit of these data for biomedical research and patient care. In the seminar series we will invite one senior and one early career scientist each month to present their most exciting and impactful research in this area.
iR+ Seminar Series - February 25, 2021
Keynote Speaker: Ludvig Sollid, University of Oslo
Title: Pathogenic T-cell/B-cell cross-talk in celiac disease: Studies of antigen receptors
Abstract: Adaptive immunity with involvement of antigen-specific T cells and B cells are likely essential in development of autoimmune diseases. Research on the involvement of autoimmune T and B cells is however hampered by the lack of knowledge of the disease driving antigens, particularly in humans. Celiac disease, a common disorder that has autoimmune features and this is caused by a maladapted immune response to cereal gluten proteins, is an exception in this regard. The disease is driven by activation of gluten-reactive CD4+ T cells and it is hallmarked by highly disease specific autoantibodies to the enzyme transglutaminase 2 (TG2) and to deamidated gluten peptides (DGP). I will discuss recent findings on the phenotype of gluten-reactive CD4+ T cells, the usage of disease-relevant T-cell receptors and B-cell receptors as well as the crosstalk between pathogenic T cells and B cells in this instructive human disorder.
Early Career Scientist: Jean-Philippe Buerckert, BISC Global
Title: A Deep Dive into the CDRH3 Landscape of SLE and RA Patients
Abstract: Systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA) are two common polygenic autoimmune diseases characterized by elevated serum autoantibodies against a variety of tissue antigens and progressive damage in multiple organs and tissues. In both diseases, malfunctioning checkpoints result in the loss of self-reactivity control of the adaptive immune receptor repertoires (AIRR) manifesting in the production of autoreactive B-cells.
Here we show how AIRR-seq can be applied to dissect the CDRH3 repertoire from PBMC B-cell isolates. Sampling was performed from 10 SLE and 11 RA patients over two timepoints as well as those of 10 healthy controls yielding a total of about 20,000,000 sequences after filtering.
Globally, our data show increased non-functional BCR rearrangements in both diseases compared to healthy donors. We examined CDRH3 repertoire down to the single amino acid level and found that RA and to a lesser extent SLE patient’s repertoires are characterized by increased amounts of hydrophobic k-mers and amino acids compared to healthy controls.
Collectively, these observations shed new light on the underlying molecular basis of autoreactive B-cells in SLE and RA and indicate a complex cluster of B-cell development defects.
iR+ Seminar Series - March 25, 2021
Keynote Speaker: Corey Watson, University of Louisville
Early Career Scientist: Mamie Wang, Yale University
iR+ Seminar Series - April 22, 2021
Keynote Speaker: Hedda Wardemann, DKFZ
Title: Single-cell based antigen-receptor gene and function analyses of the human immune response to a complex pathogen
Abstract: We have developed a platform for the high-throughput analysis of Ig gene repertoires that preserves natural IgH and IgL gene associations and provides full-length Ig gene sequence information for direct gene cloning and the production of recombinant monoclonal antibodies.
Recently, we have established a similar platform for the amplification and cloning of paired T cell receptor (TCR) alpha and beta chain genes to enable functional assessments of TCRs at single cell level. I will discuss how we use this platform to study the clonal evolution and functional quality of the human immune response to the malaria parasite Plasmodium falciparum with the long-term goal to develop improved vaccine design strategies.
Early Career Scientist: Jared Ostmeyer, UTSW
iR+ Seminar Series - May 27, 2021
Keynote Speaker: David Klatzmann, Sorbonne Universite
Early Career Scientist: TBA
iR+ Seminar Series - June 24, 2021
Keynote Speaker: TBA
Early Career Scientist: TBA
iR+ Seminar Series - January 28, 2021
Keynote Speaker: Steven H. Kleinstein, Yale School of Medicine, New Haven, CT, USA
Title: Analysis of B cell antibody repertoires from next-generation sequencing (in infection, vaccination and autoimmunity)
Abstract: Next-generation sequencing (NGS) technologies have revolutionized our ability to carry out large-scale adaptive immune receptor repertoire sequencing (AIRR-Seq) experiments. AIRR-Seq is increasingly being applied to profile B cell receptor (BCR) repertoires and gain insights into immune responses in healthy individuals and those with a range of diseases. As NGS technologies improve, these experiments are producing ever larger datasets, with tens- to hundreds-of-millions of BCR sequences. Although promising, repertoire-scale data present fundamental challenges for analysis requiring the development of new techniques and the rethinking of existing methods that are not scalable to the large number of sequences being generated .
To address these challenges, we have developed computational tools and methods that we currently make available to the wider scientific community through the Immcantation tool suite. This includes: raw read processing, novel V gene allele detection, subject-specific germline genotype identification, B cell clone assignment, lineage tree construction and analysis, somatic mutation profiling and selection analysis. Along with the underlying computational methodology, this presentation will discuss applications of BCR repertoire sequencing and lineage analysis to infection (Lyme disease, COVID-19 and West Nile Virus), vaccination (Influenza), autoimmunity (Multiple sclerosis, Myasthenia Gravis) and allergy/asthma.
- Yaari G, Kleinstein SH. Practical guidelines for B-cell receptor repertoire sequencing analysis. Genome Med. 2015 Nov 20;7:121. doi: 10.1186/s13073-015-0243-2.
Early Career Scientist: Milena Pavlovic, University of Oslo, Oslo, Norway
Title: immuneML: an open-source ecosystem for machine learning analysis of adaptive immune receptor repertoire data
Abstract: Adaptive immune receptor repertoires (AIRR) are key targets for immunological and pharmacological research as they provide a DNA-sequence record of all past and ongoing adaptive immune responses in health, disease, infection and vaccination. The capacity of machine learning (ML) to learn complex discriminative sequence patterns has led to its increasing use for AIRR-based diagnostics and therapeutics discovery. Previous developments have however been highly heterogeneous in terms of technical solutions, domain assumptions and user-interaction options, hampering transparent comparative evaluation and the ability to explore and select ML methodology most appropriate for a given study.
immuneML addresses these previous concerns by covering all major steps in AIRR ML within an open-source ecosystem and online user interface: AIRR sequence data read-in and encoding, training ML models of antigen specificity or immune state prediction as well as model assessment and interpretation. We demonstrate the broad applicability of immuneML for AIRR ML research by (i) replicating inside immuneML a published large-scale study on AIRR-based immune state prediction, (ii) applying a novel ML method for AIRR-based antigen specificity prediction and (iii) showcasing how immuneML may be used for AIRR ML method benchmarking. immuneML promotes reproducibility, customizability and shareability by (i) providing infrastructure for sharing complete ML workflows and intermediate steps, (ii) useful default parameters and workflows that shield beginners from common ML mistakes, (iii) and a user-friendly design based on the Galaxy framework.
iR+ Seminar Series - November 26, 2020
Keynote: Gunilla Karlsson Hedestam, Karolinska Institutet, Stockholm, Sweden
Title: Generation of a comprehensive database of rhesus and cynomolgus macaque IGH alleles
Abstract: We applied the immunoglobulin (IG) gene inference tool, IgDiscover, to define germline VDJ alleles in 45 macaques of different origins. Our analysis resulted in a comprehensive database comprising 1198 IGHV alleles, of which around 70% were not previously described. Haplotype analysis of the animals revealed a considerable level of structural variation in the IGH locus. This work will facilitate high-quality B cell studies in rhesus and cynomolgus macaques.
Early Career Scientist: Vanessa Mhanna, Sorbonne Universite, Paris, France
Title: Exhaustion of the regulatory T cell receptor repertoire instigates diabetes in NOD mice
Abstract: Non-obese diabetic (NOD) mice spontaneously develop autoimmune diabetes. We aimed to analyze their TCR repertoire to better understand NOD autoimmunity. We performed next-generation sequencing of TCRs from splenocytes of prediabetic NOD and normal B6 mice. We analyzed the repertoire of CD4+ effector T cells (Teffs), CD44low CD62Lhigh naïve regulatory T cells (nTregs) and CD44high CD62Llow activated/memory Tregs (amTregs). These latter are known to respond to self-antigens and to be involved in protection against autoimmune diseases.
NOD and B6 nTreg TCR β repertoires were very diverse and mostly composed of unexpanded clonotypes. In contrast, B6 amTregs contained frequent expanded clonotypes that were lost in NOD amTregs resulting in an increased diversity of their repertoire. This was also seen, albeit to a lesser extent, in NOD Teffs. These observations suggested that NOD mice had lost the amTreg clonotypes that could protect them from diabetes.
As IL-2 administration leads to Tregs expansion and activation, and correlatively to protection from diabetes occurrence, we investigated the effects of IL-2 on NOD TCR repertoires. IL-2 administration to NOD mice restored amTreg clonotype expansions and led to few and no clonotype expansions of nTreg and Teffs, respectively. Noteworthily, IL-2-expanded amTreg and nTreg clonotypes were markedly enriched for islet-antigen specific TCRs.
Altogether, our results establish a causal link between an IL-2-mediated impoverishment of Treg repertoires affecting self‑antigen-specific TCRs and the development of autoimmune disease.