Lizhen Wu1, Vipul Shukla2,6, Anurupa Devi Yadavalli1, Ravi K. Dinesh1,7, Dijin Xu3, Anjana Rao2,4,5 and David G. Schatz1 1Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut 06520, USA; 2Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, California 92037, USA; 3Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut 06510, USA; 4Department of Pharmacology, Moores Cancer Center, University of California at San Diego, La Jolla, California 92093, USA; 5Consortium for Regenerative Medicine, La Jolla, California 92037, USA Corresponding author: david.schatzyale.edu

↵Present addresses: 6Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; 7Department of Pathology, Stanford University, Palo Alto, CA 94305, USA.

Abstract

Somatic hypermutation (SHM) produces point mutations in immunoglobulin (Ig) genes in B cells when uracils created by the activation-induced deaminase are processed in a mutagenic manner by enzymes of the base excision repair (BER) and mismatch repair (MMR) pathways. Such uracil processing creates DNA strand breaks and is susceptible to the generation of deleterious deletions. Here, we demonstrate that the DNA repair factor HMCES strongly suppresses deletions without significantly affecting other parameters of SHM in mouse and human B cells, thereby facilitating the production of antigen-specific antibodies. The deletion-prone repair pathway suppressed by HMCES operates downstream from the uracil glycosylase UNG and is mediated by the combined action of BER factor APE2 and MMR factors MSH2, MSH6, and EXO1. HMCES's ability to shield against deletions during SHM requires its capacity to form covalent cross-links with abasic sites, in sharp contrast to its DNA end-joining role in class switch recombination but analogous to its genome-stabilizing role during DNA replication. Our findings lead to a novel model for the protection of Ig gene integrity during SHM in which abasic site cross-linking by HMCES intercedes at a critical juncture during processing of vulnerable gapped DNA intermediates by BER and MMR enzymes.

Received January 30, 2022. Accepted March 29, 2022.