Recombination-based mechanisms for somatic hypermutation

Immunoglobulin somatic hypermutation: double-strand DNA breaks, AID and error-prone DNA repair

Somatic hypermutation (SHM) is critical for antibody affinity maturation and the generation of memory B cells. Somatic mutations consist mainly of single nucleotide changes with rare insertions and deletions. Such changes would be introduced during error-prone repair of lesions involving single-strand DNA breaks (SSBs) or, more likely, double-strand DNA breaks (DSBs), as DSBs occur exclusively in genes that have the potentials to undergo SHM. In the human, such genes include Ig V, BCL6, and c-MYC. In these germline genes, DSBs are blunt. In rearranged Ig V, BCL6, and translocated c-MYC genes, blunt DSBs are processed to yield resected DNA ends. This process is dependent on the expression of activation-induced cytidine deaminase (AID), which is selectively expressed upon CD40-signaling in hypermutating B cells. CD40-induced and AID-dependent free 5'- and 3'-staggered DNA ends critically channel the repair of DSBs through the homologous recombination (HR) repair pathway. During HR, the modulation of critical translesion DNA polymerases, as signaled by cross-linking of the B cell receptor (BCR) for antigen, leads to the insertions of mismatches, i.e., mutations. The nature of DSBs, the possible roles of AID in the modification of DSBs and that of the translesion DNA polymerases zeta and iota in the subsequent repair process that lead to the insertions of mutations are discussed here within the context of an integrated model of SHM.

Recombinant DRB sequences produced by mismatch repair of heteroduplexes during cloning in Escherichia coli

Recombinant chimeric sequences originating from a mixture of the sequences of two different alleles are frequently found after amplification and cloning in Escherichia coli of exon 2 of the major histocompatibility complex (MHC) DRB genes. Several authors have suggested that the recombinant molecules result from in vitro recombination during PCR; nevertheless, a clear experimental demonstration of this hypothesis is lacking. In order to understand the mechanism producing the chimeric sequences, we set up a simple experiment based on the different restriction patterns of parental and recombinant sequences. Our data demonstrate that in the analysed case most of the recombinant variants were not produced by in vitro recombination during PCR, but were the result of the mismatch repair of heteroduplex molecules during cloning in E. coli. The high mutation rate in the alpha-helix region of DRB expressed genes, both after cloning in E. coli and after the germ-line differentiation process in vertebrates, suggests that the observed mutations are the result of similar gene conversion processes, probably favoured by chi-dependent microrecombination events.

Bcl-2 rescues the germinal center response but does not alter the V gene somatic hypermutation spectrum in MSH2-deficient mice

Ab V genes in mice deficient for the postreplication mismatch repair factor MutS homolog (MSH2) have been reported to display an abnormal bias for hypermutations at G and C nucleotides and hotspots. We previously showed that the germinal center (GC) response is severely attenuated in MSH2-deficient mice. This suggested that premature death of GC B cells might preclude multiple rounds of hypermutation necessary to generate a normal spectrum of base changes. To test this hypothesis, we created MSH2-deficient mice in which Bcl-2 expression was driven in B cells from a transgene. In such mice, the elevated levels of intra-GC apoptosis and untimely GC dissolution characteristic of MSH2-deficient mice are suppressed. However, the spectrum of hypermutation is unchanged. These data indicate that the effects of MSH2 deficiency on GC B cell viability and the hypermutation process are distinct.

Gene conversion-like sequence transfers between transgenic antibody V genes are independent of RAD54

Homology-based Ig gene conversion is a major mechanism for Ab diversification in chickens and the Rad54 DNA repair protein plays an important role in this process. In mice, although gene conversion appears to be rare among endogenous Ig genes, Ab H chain transgenes undergo isotype switching and gene conversion-like sequence transfer processes that also appear to involve homologous recombination or gene conversion. Furthermore, homology-based DNA repair has been suggested to be important for somatic mutation of endogenous mouse Ig genes. To assess the role of Rad54 in these mouse B cell processes, we have analyzed H chain transgene isotype switching, sequence transfer, and somatic hypermutation in mice that lack RAD54. We find that Rad54 is not required for either transgene switching or transgene hypermutation. Furthermore, even transgene sequence transfers that are known to require homology-based recombinations are Rad54 independent. These results indicate that mouse B cells must use factors for promoting homologous recombination that are distinct from the Rad54 proteins important in homology-based chicken Ab gene recombinations. Our findings also suggest that mouse H chain transgene sequence transfers might be more closely related to an error-prone homology-based somatic hypermutational mechanism than to the hyperconversion mechanism that operates in chicken B cells.

Mice deficient for the type II topoisomerase-like DNA transesterase Spo11 show normal immunoglobulin somatic hypermutation and class switching

Somatic hypermutation in B cells undergoing T cell dependent immune responses generates high affinity antibodies that provide protective immunity. B cells also switch from the expression of immunoglobulin (Ig) M and IgD to that of other Ig classes through somatic DNA recombination. Recent work has implicated DNA strand breaks, possibly DNA double strand breaks (DSB), as the initiating lesions in both class switch recombination and hypermutation, although the etiology of these lesions is not understood. Spo11, a protein structurally related to archaeal type II topoisomerases, generates DSB that initiate meiotic recombination. This characteristic, together with its expression pattern, marks this enzyme as a potential candidate for the initiation of hypermutation, and perhaps also for Ig class switching. To investigate whether Spo11 is involved in these processes, we studied the T cell dependent immune response of Spo11-deficient (Spo11(-/-)) mice against the hapten nitrophenyl (NP). We found that V186.2-bearing IgG1 transcripts had normal levels and patterns of somatic hypermutation. Furthermore, Spo11(-/-) mice showed normal serum levels of all Ig isotypes. These results indicate that Spo11 is not required for Ig hypermutation or class switch recombination.

Gene conversion-like sequence transfers in a mouse antibody transgene: antigen selection allows sensitive detection of V region interactions based on homology

Gene conversion is important for antibody diversification in chickens, rabbits and cows. In mice, however, conversion events appear to be infrequent among endogenous antibody genes. DNA sequence transfer events that resemble gene conversions have been reported for a mouse H chain transgene (VVC(mu)) that contains two closely spaced homologous VDJ segments. Surprisingly, these reported VVC(mu) sequence transfers were found frequently among mouse B cells responding to immunization. Transgene sequence transfers could be occurring at high frequency in responding VVC(mu) B cells or could be occurring at lower frequency with subsequent amplification by preferential antigen selection. To distinguish these possibilities, we have analyzed a second transgene (InVVC(mu)) that is identical to VVC(mu) except that the two VDJ regions have been exchanged in position. We find that transgene sequence transfers are much less frequent among responding B cells in InVVC(mu) mice, demonstrating the importance of selection in the frequent transgene conversions observed in VVC(mu) mice. These results suggest that mice, like other species, can use gene conversion to diversify antibodies. Such diversification events are apparently infrequent, however, and might only be detected among endogenous Ig genes with a favorable arrangement of V genes and an antigenic stimulation that selects cells with conversions. For both VVC(mu) and InVVC(mu) mice, conversion-like sequence transfers are strongly correlated with somatic hypermutation. Based on these results, we hypothesize that, in mice, gene conversions represent infrequent alternative reactions of a homology-based DNA repair process that is central in the somatic hypermutational mechanism.

DNA breaks in hypermutating immunoglobulin genes: evidence for a break-and-repair pathway of somatic hypermutation

To test the hypothesis that immunoglobulin gene hypermutation in vivo employs a pathway in which DNA breaks are introduced and subsequently repaired to produce mutations, we have used a PCR-based assay to detect and identify single-strand DNA breaks in lambda1 genes of actively hypermutating primary murine germinal center B cells. We find that there is a two- to threefold excess of breaks in lambda1 genes of hypermutating B cells, relative to nonhypermutating B cells, and that 1.3% of germinal center B cells contain breaks in the lambda1 gene that are associated with hypermutation. Breaks were found in both top and bottom DNA strands and were localized to the region of lambda1 that actively hypermutates, but duplex breaks accounted for only a subset of breaks identified. Almost half of the breaks in hypermutating B cells occurred at hotspots, sites at which two or more independent breaks were identified. Breaksite hotspots were associated with characteristic sequence motifs: a pyrimidine-rich motif, either RCTYT or CCYC; and RGYW, a sequence motif associated with hypermutation hotspots. The sequence motifs identified at breaksite hotspots should inform the design of substrates for characterization of activities that participate in the hypermutation pathway.

Evolutionary changes in mutation rates and spectra and their influence on the adaptation of pathogens

The evolutionary tuning of mutational processes may play a key role in prokaryotic evolution, particularly among pathogens. In this paper we review the evidence that genetic systems controlling the rate and spectrum of heritable mutations have evolved to optimize levels of adaptive variation and rates of genetic change.

The genetic variability of the VH genes in follicular lymphoma: the impact of the hypermutation mechanism

Follicular lymphoma (FL) cells have inherited an activated hypermutation mechanism from their origin of germinal centre B cells. Based on today's knowledge of the intrinsic properties related to this mechanism and the VH base composition, reconsideration of previous reports should be made on a broader range of samples. The present study examined the mutation pattern of the VH genes expressed by 55 cases of FL. FL VH genes showed evidence of antigenic selection in 30% of cases with 88% carrying a functional sIg and 78.2% showing intraclonal variation. VH family and gene segment utilization was found to be roughly similar to that of normal B lymphocytes. FL VH genes revealed extensive variations. 17% of the VH exons harboured a total of five deletions, three duplications and two insertions as compared to the most homologous germline counterpart. The VH genes of one tumour displayed three populations with varying CDR3 length at diagnosis. At relapse, emergence of a differently mutated gene, additional mutations reminiscent of ongoing mutations or no variation was prominent. From this study the heterogeneity of FLs is well established and ongoing mutations are seen in the scope of the activated status of the hypermutation mechanism rather than antigen-stimulated tumour growth.

Somatic hypermutation and the three R's: repair, replication and recombination

Somatic hypermutation introduces single base changes into the rearranged variable (V) regions of antigen activated B cells at a rate of approximately 1 mutation per kilobase per generation. This is nearly a million-fold higher than the typical mutation rate in a mammalian somatic cell. Rampant mutation at this level could have a devastating effect, but somatic hypermutation is accurately targeted and tightly regulated. Here, we provide an overview of immunoglobulin gene somatic hypermutation; discuss mechanisms of mutation in model organisms that may be relevant to the hypermutation mechanism; and review recent advances toward understanding the possible role(s) of DNA repair, replication, and recombination in this fascinating process.

TdT-accessible breaks are scattered over the immunoglobulin V domain in a constitutively hypermutating B cell line

Searching for an in vitro model for somatic hypermutation, we have identified an IgM-expressing Burkitt lymphoma line that constitutively diversifies its immunoglobulin V domain at high rate during culture. As in in vivo, the mutations are largely nucleotide substitutions with the pattern of substitutions revealing a component of the human hypermutation program that is preferentially targeted to G/C residues. The substitutions frequently create stop codons with IgM-loss variants also being generated by V domain-specific deletions and duplications. However, in transfectants expressing terminal deoxynucleotidyl transferase, many IgM-loss variants additionally arise through short nontemplated nucleotide insertions into the V (but not C) domain. Thus, antibody hypermutation is likely accompanied by DNA strand breaks scattered within the mutation domain.

Localization of Splenic B Cells Activated for Switch Recombination by In Situ Hybridization with Iγ1 Switch Transcript and Rad51 Probes

B cells are activated for switch recombination by signals from Th cells, but the site at which this first occurs in vivo has yet to be identified. By in situ hybridization of splenic sections using riboprobes specific for the Iγ1 switch transcript and Rad51 mRNA, we have visualized B cells that are newly activated for switch recombination and characterized the spatial and temporal patterns of Iγ1 and Rad51 mRNA expression. Within 2 days after immunization with (4-hydroxy-3-nitrophenyl)acetyl-chicken gamma-globulin, expression of Iγ1 switch transcripts and Rad51 mRNA was evident and was localized to B220+ B cells clustered within the T cell-rich periarteriolar lymphoid sheath (PALS) and surrounding follicles. By Ab staining, we have shown previously that cells switching from IgM to IgG expression can be visualized at 3 to 5 days postimmunization and colocalize to clusters of Rad51+ cells. Hybridization of adjacent sections with probes for Cμ and Cγ1 mRNA now shows that switching from μ to γ expression occurs within Rad51+Iγ1+ regions of the PALS and peaks between days 3 and 5. Colocalized expression of Iγ1 and Rad51 transcripts was observed from days 2 through 12 of the immune response. Iγ1 and Rad51 transcripts were down-regulated but still detectable at 12 days postimmunization, when they were evident in peanut agglutinin-positive germinal center B cells. Taken together, these observations show that B cells are first activated for switch recombination in the T cell-rich PALS.

A λ 3′ Enhancer Drives Active and Untemplated Somatic Hypermutation of a λ1 Transgene

Somatic hypermutation is a highly regulated process that targets mutations to the rearranged Ig genes. Little is known about the cis-elements required for somatic hypermutation of the λ light chain gene. We have studied somatic hypermutation of a rearranged λ1 transgene under the control of either a λ2-4 or κ 3′ enhancer. The mutations in the transgenes were analyzed by sequencing DNA amplified from hypermutating Peyer’s patch B cells. The results indicate that the λ 3′ enhancer can drive active hypermutation of a λ1 transgene in Peyer’s patch cells. The λ1 transgene under analysis carried two marked Vλ2 genes immediately upstream that could serve as sequence donors in possible gene conversion events. There was no evidence of sequence transfer to the hypermutated λ1 gene, suggesting that gene conversion is not a major mechanism for somatic hypermutation in mice.