Tandem Substitutions in Somatic Hypermutation

Frontiers in Immunology, vol. 12, pp. 807015

Abstract

Upon antigen recognition, activation-induced cytosine deaminase initiates affinity maturation of the B-cell receptor by somatic hypermutation (SHM) through error-prone DNA repair pathways. SHM typically creates single nucleotide substitutions, but tandem substitutions may also occur. We investigated incidence and sequence context of tandem substitutions by massive parallel sequencing of V(D)J repertoires in healthy human donors. Mutation patterns were congruent with SHM-derived single nucleotide mutations, delineating initiation of the tandem substitution by AID. Tandem substitutions comprised 5,7% of AID-induced mutations. The majority of tandem substitutions represents single nucleotide juxtalocations of directly adjacent sequences. These observations were confirmed in an independent cohort of healthy donors. We propose a model where tandem substitutions are predominantly generated by translesion synthesis across an apyramidinic site that is typically created by UNG. During replication, apyrimidinic sites transiently adapt an extruded configuration, causing skipping of the extruded base. Consequent strand decontraction leads to the juxtalocation, after which exonucleases repair the apyramidinic site and any directly adjacent mismatched base pairs. The mismatch repair pathway appears to account for the remainder of tandem substitutions. Tandem substitutions may enhance affinity maturation and expedite the adaptive immune response by overcoming amino acid codon degeneracies or mutating two adjacent amino acid residues simultaneously.

Authors 9

1. Julieta Sepúlveda-Yáñez Aachen Department of Hematology, Leiden University Medical Center

   Leiden University Medical Center · Universidad de Magallanes

   Affiliation as printed

   Department of Hematology, Leiden University Medical Center, Leiden, Netherlands

   School of Medicine, University of Magallanes, Punta Arenas, Chile

2. Diego Álvarez-Saravia

   Universidad de Magallanes

   Affiliation as printed

   School of Medicine, University of Magallanes, Punta Arenas, Chile

3. Bas Pilzecker

   The Netherlands Cancer Institute · Radboud Institute for Molecular Life Sciences

   Affiliation as printed

   Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Nijmegen, Netherlands

   Division of Tumor Biology and Immunology, Netherlands Cancer Institute, Amsterdam, Netherlands

4. Pauline A. van Schouwenburg Aachen Department of Pediatrics, Leiden University Medical Center

   Leiden University Medical Center

   Affiliation as printed

   Department of Pediatrics, Leiden University Medical Center, Leiden, Netherlands

5. Mirjam van der Burg Aachen Department of Pediatrics, Leiden University Medical Center

   Leiden University Medical Center

   Affiliation as printed

   Department of Pediatrics, Leiden University Medical Center, Leiden, Netherlands

6. Hendrik Veelken Aachen Department of Hematology, Leiden University Medical Center

   Leiden University Medical Center

   Affiliation as printed

   Department of Hematology, Leiden University Medical Center, Leiden, Netherlands

7. Marcelo A. Navarrete

   Universidad de Magallanes

   Affiliation as printed

   School of Medicine, University of Magallanes, Punta Arenas, Chile

8. Heinz Jacobs

   The Netherlands Cancer Institute

   Affiliation as printed

   Division of Tumor Biology and Immunology, Netherlands Cancer Institute, Amsterdam, Netherlands

9. Marvyn T. Koning corresponding Aachen Department of Hematology, Leiden University Medical Center

   Leiden University Medical Center

   Affiliation as printed

   Department of Hematology, Leiden University Medical Center, Leiden, Netherlands