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

PLoS Genet. 2019 Jun 14;15(6):e1007721. doi: 10.1371/journal.pgen.1007721. eCollection 2019 Jun.

Abstract

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 of 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. Using an optimized LSR-seq high throughput method, we now show that AID-mediated LSR is evolutionarily conserved and also actively occurs in humans, providing an activation-induced cell death pathway in multiple conditions of B-cell activation. LSR either focuses on the functional IgH allele or is bi-allelic, and its signature is mainly detected when LSR is ongoing while it vanishes from fully differentiated plasma cells or from "resting" blood memory B-cells. 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 although TLR ligation appeared the most efficient. Molecular analysis of breakpoints and junctions confirms that LSR is AID-dependent and reveals junctional sequences somehow similar to CSR junctions but with increased usage of microhomologies.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alleles
  • Animals
  • B-Lymphocytes / immunology*
  • Cell Differentiation / genetics
  • Cytidine Deaminase / genetics*
  • Cytidine Deaminase / immunology
  • Gene Targeting
  • Humans
  • Immunoglobulin Switch Region / genetics*
  • Immunoglobulin Switch Region / immunology
  • Immunoglobulins / immunology*
  • Lymphoid Tissue / immunology
  • Mice
  • Palatine Tonsil / immunology
  • Palatine Tonsil / metabolism
  • Plasma Cells / immunology
  • Plasma Cells / metabolism
  • Receptors, Antigen, B-Cell / genetics
  • Receptors, Antigen, B-Cell / immunology
  • Regulatory Sequences, Nucleic Acid

Substances

  • Immunoglobulins
  • Receptors, Antigen, B-Cell
  • AICDA (activation-induced cytidine deaminase)
  • Cytidine Deaminase

Grants and funding

This work was supported by grants to MC from Association pour la Recherche sur le Cancer (PGA120150202338), Agence Nationale de la Recherche (ANR grant 16-CE15-0019-01), Institut National du Cancer (INCa grant #9363), Ligue Nationale contre le Cancer and Région Aquitaine-Limousin-Poitou-Charente. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.