CSReport: A New Computational Tool Designed for Automatic Analysis of Class Switch Recombination Junctions Sequenced by High-Throughput Sequencing

Boyer, François; Boutouil, Hend; Dalloul, Iman; Dalloul, Zeinab; Cook-Moreau, Jeanne; Aldigier, Jean-Claude; Carrion, Claire; Hervé, Bastien; Scaon, Erwan; Cogné, Michel; Péron, Sophie

doi:10.4049/jimmunol.1601924

Cited by 23 publications

(22 citation statements)

References 17 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In addition to raw data processing, V(D)J gene assignment, and clonotype identification, Ag receptor gene repertoire studies require additional sequence analysis extending from diversity profiles to clonal architecture, CDR3 length and characteristics, clonal dynamics (if temporal samples are analyzed), and clonotype comparisons between different lymphoid populations/ individuals/disease entities. The complexity of the data generated would argue for concomitant analysis via independent existing pipelines (87)(88)(89)(90)(91)(92) or newly published ones (93,94).…”

Section: Computational Repseq Analysismentioning

confidence: 99%

High-Throughput Immunogenetics for Clinical and Research Applications in Immunohematology: Potential and Challenges

Langerak

Brüggemann

Davi

et al. 2017

The Journal of Immunology

View full text Add to dashboard Cite

Analysis and interpretation of Ig and TCR gene rearrangements in the conventional, low-throughput way have their limitations in terms of resolution, coverage, and biases. With the advent of high-throughput, next-generation sequencing (NGS) technologies, a deeper analysis of Ig and/or TCR (IG/TR) gene rearrangements is now within reach, which impacts on all main applications of IG/TR immunogenetic analysis. To bridge the generation gap from low- to high-throughput analysis, the EuroClonality-NGS Consortium has been formed, with the main objectives to develop, standardize, and validate the entire workflow of IG/TR NGS assays for 1) clonality assessment, 2) minimal residual disease detection, and 3) repertoire analysis. This concerns the preanalytical (sample preparation, target choice), analytical (amplification, NGS), and postanalytical (immunoinformatics) phases. Here we critically discuss pitfalls and challenges of IG/TR NGS methodology and its applications in hemato-oncology and immunology.

show abstract

Section: Computational Repseq Analysismentioning

confidence: 99%

High-Throughput Immunogenetics for Clinical and Research Applications in Immunohematology: Potential and Challenges

Langerak

Brüggemann

Davi

et al. 2017

The Journal of Immunology

View full text Add to dashboard Cite

show abstract

“…As previously described for mouse LSR, we identified human LSR junctions by nested PCR in DNA from B-cell samples [4]. The specificity of the read-out for these PCR assays was improved by replacing the final hybridization step of PCR products, initially done with specific probes[4]), with high-throughput sequencing adapted from our recently described CSR evaluation algorithm, CSReport [22]. Sequence determination thus precisely mapped the breakpoint sites.…”

Section: Lsr Occurs At Multiple Sites Within the Whole Extent Of Bothmentioning

confidence: 99%

Locus Suicide Recombination actively occurs on the functionally rearranged IgH allele in B-cells from inflamed human lymphoid tissues

Cogné

Dalloul

Boyer

et al. 2018

Preprint

Self Cite

View full text Add to dashboard Cite

B-cell activation yields abundant cell death in parallel to clonal amplification and remodeling of immunoglobulin (Ig) genes by activation-induced deaminase (AID). AID promotes affinity maturation of Ig variable regions and class switch recombination (CSR) in mature B lymphocytes. In the IgH locus, these processes are under control by the 3' regulatory region (3'RR) super-enhancer, a region demonstrated in the mouse to be both transcribed and itself targeted by AID-mediated recombination. Alternatively to CSR, IgH deletions joining Sµ to "like-switch" DNA repeats that flank the 3' super-enhancer can thus accomplish so-called "locus suicide recombination" (LSR) in mouse B-cells. We now show that AID-mediated LSR also actively occurs in humans, and provides an activationinduced cell death pathway in multiple conditions of B-cell activation. LSR deletions either focus on the functional IgH allele or are bi-allelic, since they can only be detected when they are ongoing and their signature vanishes from fully differentiated plasma cells or from "resting" blood memory B-cells, but readily reappears when such memory Bcells are re-stimulated in vitro. Highly diversified breakpoints are distributed either within the upstream (3'RR1) or downstream (3'RR2) copies of the IgH 3' super-enhancer and all conditions activating CSR in vitro also seem to trigger LSR. AUTHOR SUMMARYClass switch recombination, initiated by the activation-induced deaminase enzyme rearranges immunoglobulin (Ig) genes in order to replace expression of IgM by IgG, IgA or IgE. A variant form of this event, locus suicide recombination (LSR), was previously reported in mouse B-lymphocytes and simply deletes all functional Ig constant genes, thus terminating B-cell function. This study first demonstrates that the structure of the human Ig heavy chain locus provides an ideal target for LSR, and is thus actively (but transiently) affected by this deletional process at the activated B-cell stage. LSR then yields recombined genes that do not support B-cell survival and which thus become undetectable among long-lived memory B-cells or plasma cells. INTRODUCTIONHumoral immune responses and immunoglobulin (Ig) production rely on the selection of B-cells harboring antigen (Ag)-specific B-cell receptors (BCRs). This selection implies not only proliferation and differentiation of those cells optimally binding Ag but also elimination of the less efficient or inappropriately activated cells. The latter can be accomplished through various pathways leading to anergy, death-by-neglect or activation-induced cell death (AICD).While AICD pathways have been characterized in detail for T-cells, and notably involve FAS-induced apoptosis, they are less documented in B-cells. A major and unique feature of mature B-cells during Ag-driven responses, is their ability to reshape their genome, and more specifically Ig genes, after activation-induced deaminase (AID)-dependent modifications. Somatic hypermutation (SHM) within germinal centers (GC) can yield cells with higher affinity V d...

show abstract

“…Other tools can be used to define clones in the repertoire (Change-O) (4) or analyze Ag selection (IgAT and BASELINe) (5,7) or CSR (8). We have previously published the ImmunoGlobulin Galaxy (IGGalaxy) tool that allows analysis of V, D, and J gene usage and CDR3 length (9).…”

Section: E Very T and B Cell Expresses A Unique Ag Receptor Calledmentioning

confidence: 99%

Antigen Receptor Galaxy: A User-Friendly, Web-Based Tool for Analysis and Visualization of T and B Cell Receptor Repertoire Data

IJspeert

Schouwenburg

Zessen

et al. 2017

The Journal of Immunology

View full text Add to dashboard Cite

Antigen Receptor Galaxy (ARGalaxy) is a Web-based tool for analyses and visualization of TCR and BCR sequencing data of 13 species. ARGalaxy consists of four parts: the demultiplex tool, the international ImMunoGeneTics information system (IMGT) concatenate tool, the immune repertoire pipeline, and the somatic hypermutation (SHM) and class switch recombination (CSR) pipeline. Together they allow the analysis of all different aspects of the immune repertoire. All pipelines can be run independently or combined, depending on the available data and the question of interest. The demultiplex tool allows data trimming and demultiplexing, whereas with the concatenate tool multiple IMGT/HighV-QUEST output files can be merged into a single file. The immune repertoire pipeline is an extended version of our previously published ImmunoGlobulin Galaxy (IGGalaxy) virtual machine that was developed to visualize V(D)J gene usage. It allows analysis of both BCR and TCR rearrangements, visualizes CDR3 characteristics (length and amino acid usage) and junction characteristics, and calculates the diversity of the immune repertoire. Finally, ARGalaxy includes the newly developed SHM and CSR pipeline to analyze SHM and/or CSR in BCR rearrangements. It analyzes the frequency and patterns of SHM, Ag selection (including BASELINe), clonality (Change-O), and CSR. The functionality of the ARGalaxy tool is illustrated in several clinical examples of patients with primary immunodeficiencies. In conclusion, ARGalaxy is a novel tool for the analysis of the complete immune repertoire, which is applicable to many patient groups with disturbances in the immune repertoire such as autoimmune diseases, allergy, and leukemia, but it can also be used to address basic research questions in repertoire formation and selection.

show abstract

CSReport: A New Computational Tool Designed for Automatic Analysis of Class Switch Recombination Junctions Sequenced by High-Throughput Sequencing

Cited by 23 publications

References 17 publications

High-Throughput Immunogenetics for Clinical and Research Applications in Immunohematology: Potential and Challenges

High-Throughput Immunogenetics for Clinical and Research Applications in Immunohematology: Potential and Challenges

Locus Suicide Recombination actively occurs on the functionally rearranged IgH allele in B-cells from inflamed human lymphoid tissues

Antigen Receptor Galaxy: A User-Friendly, Web-Based Tool for Analysis and Visualization of T and B Cell Receptor Repertoire Data

Contact Info

Product

Resources

About