Charting a DNA Repair Roadmap for Immunoglobulin Class Switch Recombination

Abstract

Immunoglobulin (Ig) class switch recombination (CSR) is the process occurring in mature B cells that diversifies the effector component of antibody responses. CSR is initiated by the activity of the B cell-specific enzyme activation-induced cytidine deaminase (AID), which leads to the formation of programmed DNA double-strand breaks (DSBs) at the Ig heavy chain (Igh) locus. Mature B cells use a multilayered and complex regulatory framework to ensure that AIDinduced DNA breaks are channeled into productive repair reactions leading to CSR, and to avoid aberrant repair events causing lymphomagenic chromosomal translocations. Here, we review the DNA repair pathways acting on AID-induced DSBs and their functional interplay, with a particular focus on the latest developments in their molecular composition and mechanistic regulation. Breaking the B Cell Genome to Diversify Antibody ResponsesOur immune system is able to generate a diverse repertoire of antibodies (or Igs, see Glossary) that can collectively recognize and efficiently dispose of an impressive number of pathogens. Antibodies are produced by terminally differentiated B lymphocytes known as plasma cells, and can use different routes to eliminate pathogens. These alternative effector functions are specified by the antibody isotypes (or classes) [1]. A mature B lymphocyte diversifies the class of antibody it expresses via the process of Ig CSR [2,3]. CSR replaces the constant portion of the IgM heavy chain with one of the alternative isotypes (IgG, IgA, or IgE), thus changing the antibody effector function without altering its specificity [1]. At the molecular level, CSR is a somatic recombination reaction that occurs via the programmed formation and repair of DNA double-strand breaks (DSBs) within the Ig heavy chain (Igh) locus (Figure 1) [2,3]. The temporary disruption of genome integrity that CSR entails places the process at the crossroads between the establishment of protective immunity, and the need to maintain genome stability. The inability to introduce or repair these programmed DSBs is responsible for primary antibody deficiencies (CSR immunodeficiencies) [4,5]. Conversely, CSR-dependent DSBs can be the substrate of aberrant repair reactions leading to chromosomal translocations, which are a hallmark of several mature B cell lymphomas [6]. Therefore, isotype diversification is a fundamental aspect of mature B lymphocyte physiology with important implications in health and disease. In view of the recent COVID-19 pandemic, which has brought to worldwide attention the crucial health and societal roles played by protective immunity, a comprehensive understanding of the processes contributing to humoral responses is particularly timely. In this review, we describe the functional interplay between DNA repair pathways operating on CSR DSBs, and we highlight the recent developments on the molecular composition and mechanistic aspects of their regulation. Since CSR has been extensively investigated in mice, we refer primarily to the mouse Igh locus and to the ...

Exonuclease 1 (EXO1) is a Potential Prognostic Biomarker and Correlates with Immune Infiltrates in Lung Adenocarcinoma

“…Accordingly, EXO1 played vital roles in immunoglobulin maturation and antibody diversity through class switching recombination and somatic hypermutation. 59 , 60 Therefore, aberrant overexpression of EXO1 may result in the dysfunction of immunoglobulin maturation and reduction of antibody diversity, which may further decrease the infiltrating B cell levels. 34 Furthermore, B cell depletion impaired CD4+ T cell activation and clonal expansion in mice whereas CD8+ T cell activation was not affected.…”

ATR kinase activity promotes antibody class switch recombination in B cells through cell cycle regulation without suppressing DSB resection and microhomology usage

“…In the regard, in B cell deficient for cNHEJ factors, CSR efficiency dramatically decreased to 30% of that of wild‐type (WT) cells but is not completely abolished, suggesting the existence of alternative pathway (A‐EJ) in the absence of c‐NHEJ 17–20 . AID‐initiated DSBs also activate ATM‐dependent DDR process, and it has been clear in literatures that mature B cells deficiency for ATM and its downstream substrates H2AX, 53BP1, Rif1, and so on, significantly reduced CSR efficiency with elevated DSB end resection and use of short sequence homology in joining junctions 16,19,21,22 . Meanwhile, prior studies had suggested that stimulated Lig4‐deficient B cells exhibited elevated S region 5′−3′ DSB resection that exposes single‐stranded overhang DNA for microhomology (MH) annealing 21 .…”

“…CSR replaces the initially expressed IgM molecules on mature B cells with one of the IgG/IgE/IgA constant region exons 12,13 . It is initiated by activation‐induced cytosine deaminase (AID)‐introduced DNA lesions in donor and acceptor long repetitive switch (S) regions (Sm and Sx respectively) that are subsequently converted to DSBs, and completed by the rejoining of DSBs by the core NHEJ factors Xrcc4/Ligase4 with assistance from the Ku70/80 complex and DNA‐PKcs to hold broken ends from falling apart 14–16 . In the regard, in B cell deficient for cNHEJ factors, CSR efficiency dramatically decreased to 30% of that of wild‐type (WT) cells but is not completely abolished, suggesting the existence of alternative pathway (A‐EJ) in the absence of c‐NHEJ 17–20 .…”

Protection of nascent DNA at stalled replication forks is mediated by phosphorylation of RIF1 intrinsically disordered region

“…At the molecular level, CSR is mediated by a deletional recombination reaction at the Ig heavy chain locus (Igh) that replaces the constant (C) gene for the basal IgM isotype with one of the downstream C genes encoding a different Ig class (Yewdell and Chaudhuri, 2017). The reaction is initiated by the formations of multiple programmed DSBs at internally repetitive DNA stretches, known as switch (S) regions, preceding the recombining C regions (Saha et al, 2021). Productive CSR events occur via protection of DSBs from nucleolytic resection, which enables NHEJ-mediated inter-S-region repair (Boboila et al, 2012;Saha et al, 2021).…”