Somatic hypermutation of immunoglobulin genes

IL21 signaling produces phosphorylated STAT3, which acts together with AP-1 (FOSB:JUND) to activate expression of BCL6, a master regulator of the somatic hypermutation pathway. PAX5 with CREBBP and the MLL3,4 complex activate expression of BACH2. BCL6 and the BACH2:MAFK dimer directly repress expression of PRDM1 (BLIMP) to prevent differentiation and maintain proliferation (Ochiai et al. 2006, 2008, Huang et al. 2014). BCL6 also inactivates mutation-triggered checkpoints in cell division by directly repressing expression of CDKN1A, TP53 (p53, Phan and Dalla-Favera 2004), ATR, and CHEK1. The result is cellular proliferation in which mutations are transmitted at high frequency.

CD40LG signaling and concurrent BCR and TLR4 signaling each act through the canonical and non-canonical NF-kappaB pathways to produce nuclear RELA:NFKB1 and nuclear, cleaved NFKB2:RELB (p52:RELB), respectively, which bind with additional factors to the promoter of the Activation-induced cytosine deaminase gene (AICDA, also called AID) and activate expression (Lee et al. 2006, Tran et al. 2010, reviewed in Zan and Casali 2013).

During somatic hypermutation, the mutations are initiated by AICDA-catalyzed deamination of deoxycytidine residues in DNA (reviewed in Yu 2022). Regions of about 2 kilobases that encode immunoglobulin variable domains undergo mutations at a rate more than a million-fold greater than elsewhere in the genome (reviewed in Heltzel and Gearhart 2020, Lauring and Basu 2024). These regions are targeted for mutation by RNA polymerase II transcription complexes that arrest and accumulate in variable regions of immunoglobulin gene arrays (Ig kappa, Ig Lambda, and Ig heavy chain) and the switch region of the Ig heavy chain gene (reviewed in Heltzel and Gearhart 2020, Lauring and Basu 2024). SUPT5H (SPT5) binds to the arrested RNA polymerase II complexes and recruits AICDA.

AICDA is specific for single-stranded DNA and acts on DNA in the transcription bubble to deaminate deoxycytidine to deoxyuridine. Deoxyuridine is recognized by the UNG2 isoform of UNG of the base excision repair pathway (reviewed in Stratigopoulou et al. 2020); deoxyuridine:deoxyguanidine (U:G) mismatches are recognized by MSH2:MSH6 (MutSalpha) of the mismatch repair pathway (reviewed in Pilzecker and Jacobs 2019, Hao et al. 2024). Unique error-prone versions of these repair pathways are activated through ubiquitinated PCNA, which recruits error-prone DNA polymerases, notably POLH (DNA polymerase eta), POLHI (DNA Polymerase iota), POLZ (DNA polymerse zeta, MAD2L2:POLD2:POLD3:REV3L), and REV1 (reviewed in Zanotti and Gearhart 2016), creating transversions at G and C residues and mutations at A and T residues. Duplication of unrepaired U:G mismatches results in transitions to T:A base pairs.

Germinal center B cells undergo alternating phases of somatic hypermutation and proliferation. During the proliferation phase in mice, the period of G0 of the cell cycle when somatic hypermutation would normally occur is suppressed.