DNA Damage Response and Repair in Adaptive Immunity

Abstract

The diversification of B-cell receptor (BCR), as well as its secreted product, antibody, is a hallmark of adaptive immunity, which has more specific roles in fighting against pathogens. The antibody diversification is from recombination-activating gene (RAG)-initiated V(D)J recombination, activation-induced cytidine deaminase (AID)-initiated class switch recombination (CSR), and V(D)J exon somatic hypermutation (SHM). The proper repair of RAG- and AID-initiated DNA lesions and double-strand breaks (DSBs) is required for promoting antibody diversification, suppressing genomic instability, and oncogenic translocations. DNA damage response (DDR) factors and DSB end-joining factors are recruited to the RAG- and AID-initiated DNA lesions and DSBs to coordinately resolve them for generating productive recombination products during antibody diversification. Recently, cohesin-mediated loop extrusion is proposed to be the underlying mechanism of V(D)J recombination and CSR, which plays essential roles in promoting the orientation-biased deletional end-joining . Here, we will discuss the mechanism of DNA damage repair in antibody diversification.

Keywords: AID-initiated CSR and SHM; DNA damage repair; RAG-initiated V(D)J recombination; antibody diversification; cohesin-mediated loop extrusion.

FIGURE 1

V(D)J recombination, class switch recombination, and V(D)J exon somatic hypermutation-mediated antibody diversification. (A) Schematic structure of antibody which is composed of two pairs of immunoglobulin heavy (IgH) and light (IgL) chains. The blue box indicates the antibody variable region which binds to antigens. The green box indicates the antibody constant region, where the class switch recombination occurs. The red box indicates the mutated region including CDR1, CDR2, and CDR3 within the V(D)J exon; the yellow dots indicate the mutation sites. (B) Two-step process of RAG-initiated V(D)J recombination in progenitor (pro) B cells. (C) Process of AID-initiated class switch recombination (CSR) in mature B cells before entering the germinal center (GC), termed as pre-GC cells. (D) Process of AID-initiated V(D)J exon somatic hypermutation (SHM) in non-switched and switched GC B cells.

FIGURE 2

Classical non-homologous end-joining (C-NHEJ) joins RAG-initiated recombination signal sequence (RSS) breaks to complete V(D)J recombination. (A) Schematic structure of the IgH locus in mice. There are over one hundred V_H segments, 9–12 D segments, and 4 J_H segments in mouse IgH locus. Each V_H is downstream flanked by 23RSS. Each D is flanked by 12RSS on both sides. Each J_H is upstream flanked by 12RSS. (B) Schematic structure of RAG endonuclease, 12RSS (blue triangles), and 23RSS (red triangles). RAG cleaves the heptamer of RSS sequences. (C–H) C-NHEJ-mediated end-joining process during D to J_H recombination. RAG and HMGB1 bind to a pair of D and J_H segments for cleavage, and the synapsis of D and J_H segments is promoted by loop extrusion-mediated RAG scanning process (C). RAG cuts the synapsed RSSs associated with the D and J_H segments to generate a pair of blunt RSS ends and a pair of hairpin-associated coding ends (D). Ku70/Ku80 complex binds to the RAG-initiated DSBs and recruits DNA-PKcs-Artemis complex to open the coding end-associated hairpins (E). RAG-initiated breaks can further be processed by DNA polymerase λ/μ and terminal deoxynucleotidyl transferase (TdT) (F). XRCC4 and ligase 4 are recruited to the breaks to ligate the processed DNA breaks, and other redundant C-NHEJ factors including XLF, PAXX, and ERCC6L2 are also involved in the ligation step (G).Final D to J_H recombination products include the coding join and RSS join (H).

FIGURE 3

Overview of DNA damage repair process during SHM. (A) AID targets the dC to generate dU within V(D)J exon. (B) FAM72a downregulation promotes base excision repair (BER)- and mismatch repair (MMR)-mediated error-free DNA repair. (C) FAM72a upregulation promotes BER- and MMR-mediated error-prone DNA repair, leading to the mutation of V(D)J exon during SHM.

FIGURE 4

Overview of DNA damage repair process during CSR. (A) FAM72a regulates the error-prone vs. error-free DNA repair during AID-initiated CSR. AID-initiated breaks are converted into double-strand breaks (DSBs) upon high level of FAM72a during CSR. (B) Overview of the DNA damage response (DDR) factors and C-NHEJ in promoting direct end joining during CSR. (C) Overview of the alternative end joining (A-EJ) in promoting DSB end resection and microhomology-mediated end joining during CSR. (C–H) Loop extrusion-mediated CSR model. Loop extrusion promotes CSR center formation (D), acceptor S region activation (E), Sμ–Sx synapsis (F), and deletional end joining (G–H).