Biased immunoglobulin heavy variable (IGHV) gene usage and distinctive B-cell receptor (BCR) features have been reported in chronic lymphocytic leukaemia (CLL), which may reflect clonal selection by antigens during disease development. Furthermore, the IGHV gene mutation status distinguishes two clinical entities of CLL, where patients with unmutated IGHV genes have an inferior prognosis compared to those with mutated IGHV genes. Recently, one subgroup of CLL patients expressing the IGHV3-21 gene was found to display highly similar immunoglobulin (IG) gene features, even within the heavy chain complementarity-determining region 3 (HCDR3). Patients in this subgroup typically had a poor prognosis. In paper I, we aimed to identify further subgroups with restricted BCR features among 346 CLL cases. Six subsets were defined which carried virtually identical BCRs in terms of rearranged heavy and light chain (LC) IG genes and CDR3 length and composition. In paper II, we investigated 90 IGHV3-21 cases from diverse geographical locations. We confirmed the highly restricted HCDR3 characteristics in 56% of patients and a biased usage of the IGLV3-21 gene in 72% of cases. Survival analysis also confirmed the poor outcome of this group, irrespective of IGHV gene mutation status and geographical origin. Papers III and IV involved a large-scale analysis of IGH and IG kappa and lambda (IGK/L) gene rearrangements, to define subsets with ‘stereotyped’ BCRs and also to systematically examine the somatic hypermutation (SHM) features of the IG genes in CLL. We studied a cohort of 1967 IGH and 891 IGK/L gene sequences from 1939 patients from 6 European institutions. Over 5300 IGH and ~4700 IGK/L sequences from non-CLL B cells were used as a control data set. In total, 110 CLL stereotyped subsets were defined according to HCDR3 homology. Striking IGK/L gene biases were also evident within subsets, along with distinctive K/LCDR3 features, such as length and amino acid composition. At cohort level, the patterns of mutation appeared to be consistent with that of a canonical SHM mechanism. However, at a subgroup level, certain stereotyped subsets, e.g. IGHV3-21/IGLV3-21 and IGHV4-34/IGKV2-30 CLL, deviated from this pattern. Furthermore, recurrent ‘stereotyped’ mutations occurred in cases belonging to subsets with restricted HCDR3s, in both IGHV and IGK/LV genes, which were subset- and CLL-biased when compared to non-CLL B cells. In conclusion, our findings implicate antigen selection as a significant factor in the pathogenesis of CLL, particularly in cases carrying stereotyped BCRs. The presence of stereotyped mutations throughout the VH and VL domain also indicates involvement of IG regions other than the CDR3 in antigen recognition. Finally, biased IGK/L gene usage and specific K/LCDR3 features are strong indications that LCs are crucial in shaping the specificity of leukemic BCRs, in association with defined heavy chains.

B cells produce a diverse array of antibody specificities that are of low affinity during the initial phase of a humoral immune response. However, somatic hypermutation of the rearranged V region in the immunoglobulin locus generates new antibody affinities, accompanied by the selection of B cells that produce superior antibody affinities. Somatic hypermutation is initiated by the conversion of G:C base pairs to G:U lesions by the enzyme activation induced cytosine deaminase. Left unrepaired, G:U lesions will give rise to transition mutations at G:C base pairs, but are converted to transition and transversion mutations at G:C and A:T base pairs by the paradoxical participation of the base excision repair and mismatch repair pathways. The mismatch repair pathway, which evolved to correct errors produced during DNA replication, is co-opted by hypermutating B cells to produce A:T mutations via the processing of G:U lesions. This process requires the mismatch repair components Msh2, Msh6, and Exo1, but is additionally dependent upon the translesional DNA polymerase eta, a known A:T mutator, and on ubiquitinated PCNA, an initiator of translesion synthesis. The presence of certain types of lesions in the template strand during DNA replication leads to the activation of translesion synthesis. I propose that a similar mechanism operates during somatic hypermutation to activate translesion synthesis and recruit DNA polymerase eta. Our model suggests that mismatch repair-generated single-stranded DNA tracts contain abasic sites produced as a result of uracil excision by uracil-N-glycosylase. Synthesis opposite abasic sites activates translesion synthesis and results in the recruitment of polymerase eta and the subsequent production of A:T mutations. In this thesis, I present data from hypermutating murine B cells and the B cell line Ramos to support this model, demonstrating that the base excision repair and mismatch repair pathways cooperate during somatic hypermutation to generate A:T mutations. In addition, I explore the role of the Mre11-Rad50-Nbs1 complex in its contribution to A:T mutations in Ramos cells. Taken together, these studies demonstrate that conversion of classical DNA repair pathways into mutation-generating processes is driven by the unique environment of the V region in hypermutating B cells.

Deficiency in Msh2, a component of the mismatch repair (MMR) system, leads to a ~10-fold increase in the mutation frequency in most tissues. By contrast, Msh2-deficiency in germinal center (GC) B cells decreases the mutation frequency at the IgH V-region, as a dU:dG mismatch produced by AID initiates modifications by MMR resulting in mutations at nearby A:T basepairs. This raises the possibility that GC B cells express a factor that converts MMR into a globally mutagenic pathway. To test this notion, we investigated whether MMR corrects mutations in GC B cells at a gene not mutated by AID. We found that GC B cells accumulate 5-times more mutations than follicular B cells. Notably, the mutation frequency was ~10 times higher in Msh2-/- compared to wildtype GC B cells. These results show that in GC B cells MMR functions normally at an AID-insensitive gene.

Deficiency in Msh2, a component of the mismatch repair (MMR) system, leads to a ~10-fold increase in the mutation frequency in most tissues. By contrast, Msh2-deficiency in germinal center (GC) B cells decreases the mutation frequency at the IgH V-region, as a dU:dG mismatch produced by AID initiates modifications by MMR resulting in mutations at nearby A:T basepairs. This raises the possibility that GC B cells express a factor that converts MMR into a globally mutagenic pathway. To test this notion, we investigated whether MMR corrects mutations in GC B cells at a gene not mutated by AID. We found that GC B cells accumulate 5-times more mutations than follicular B cells. Notably, the mutation frequency was ~10 times higher in Msh2-/- compared to wildtype GC B cells. These results show that in GC B cells MMR functions normally at an AID-insensitive gene.

B cells produce a diverse array of antibody specificities that are of low affinity during the initial phase of a humoral immune response. However, somatic hypermutation of the rearranged V region in the immunoglobulin locus generates new antibody affinities, accompanied by the selection of B cells that produce superior antibody affinities. Somatic hypermutation is initiated by the conversion of G:C base pairs to G:U lesions by the enzyme activation induced cytosine deaminase. Left unrepaired, G:U lesions will give rise to transition mutations at G:C base pairs, but are converted to transition and transversion mutations at G:C and A:T base pairs by the paradoxical participation of the base excision repair and mismatch repair pathways. The mismatch repair pathway, which evolved to correct errors produced during DNA replication, is co-opted by hypermutating B cells to produce A:T mutations via the processing of G:U lesions. This process requires the mismatch repair components Msh2, Msh6, and Exo1, but is additionally dependent upon the translesional DNA polymerase eta, a known A:T mutator, and on ubiquitinated PCNA, an initiator of translesion synthesis. The presence of certain types of lesions in the template strand during DNA replication leads to the activation of translesion synthesis. I propose that a similar mechanism operates during somatic hypermutation to activate translesion synthesis and recruit DNA polymerase eta. Our model suggests that mismatch repair-generated single-stranded DNA tracts contain abasic sites produced as a result of uracil excision by uracil-N-glycosylase. Synthesis opposite abasic sites activates translesion synthesis and results in the recruitment of polymerase eta and the subsequent production of A:T mutations. In this thesis, I present data from hypermutating murine B cells and the B cell line Ramos to support this model, demonstrating that the base excision repair and mismatch repair pathways cooperate during somatic hypermutation to generate A:T mutations. In addition, I explore the role of the Mre11-Rad50-Nbs1 complex in its contribution to A:T mutations in Ramos cells. Taken together, these studies demonstrate that conversion of classical DNA repair pathways into mutation-generating processes is driven by the unique environment of the V region in hypermutating B cells.

The processes of secondary antibody diversification are initiated by the mutagenic, B cell specific enzyme, Activation-Induced Deaminase (AID). AID deaminates deoxycytosine (dC) that is located in single-stranded DNA (ssDNA) in actively transcribed DNA to initiate the processes of somatic hypermutation (SHM), gene conversion (GCV) and class switch recombination (CSR) at the antibody gene loci. These processes lead to high affinity antibodies and antibodies of various effector functions that are required to efficiently neutralize invading pathogens. It is currently unclear how the antibody genes are specifically targeted by AID over other genes. I found that AID is able to mutate a non-immunoglobulin (Ig) transgene independent of its chromosomal integration site at rates that were above background mutation rates, but were ~10-fold lower than at the antibody variable (V) region. This result suggests that AID can mutate non-Ig genes at low rates, which may explain AID’s role in oncogenesis, but nevertheless shows that AID preferentially mutates the Ig locus over other loci. While it is understood that AID specifically deaminates dC bases in ssDNA, the size, distribution and origin of these ssDNA substrates is unknown. By utilizing a unique in situ sodium bisulfite assay to detect regions of ssDNA in intact nuclei, I characterized ssDNA regions and found that they are accurate predictors of AID activity during the processes of SHM and CSR in mammalian B cells and E.coli. Importantly, with the use of E.coli models, I show that these ssDNA substrates are the product of transcription-induced negative-supercoiled DNA that correlates strongly with the mutagenic activity of AID. While several underlying mechanisms exist to prevent the mistargeting of AID, my findings suggest that by simply gaining access to ssDNA that is produced by transcription-induced negative supercoiling, AID has the potential to mutate non-Ig genes, albeit at lower rates than the antibody V-region.

The processes of secondary antibody diversification are initiated by the mutagenic, B cell specific enzyme, Activation-Induced Deaminase (AID). AID deaminates deoxycytosine (dC) that is located in single-stranded DNA (ssDNA) in actively transcribed DNA to initiate the processes of somatic hypermutation (SHM), gene conversion (GCV) and class switch recombination (CSR) at the antibody gene loci. These processes lead to high affinity antibodies and antibodies of various effector functions that are required to efficiently neutralize invading pathogens. It is currently unclear how the antibody genes are specifically targeted by AID over other genes. I found that AID is able to mutate a non-immunoglobulin (Ig) transgene independent of its chromosomal integration site at rates that were above background mutation rates, but were ~10-fold lower than at the antibody variable (V) region. This result suggests that AID can mutate non-Ig genes at low rates, which may explain AID’s role in oncogenesis, but nevertheless shows that AID preferentially mutates the Ig locus over other loci. While it is understood that AID specifically deaminates dC bases in ssDNA, the size, distribution and origin of these ssDNA substrates is unknown. By utilizing a unique in situ sodium bisulfite assay to detect regions of ssDNA in intact nuclei, I characterized ssDNA regions and found that they are accurate predictors of AID activity during the processes of SHM and CSR in mammalian B cells and E.coli. Importantly, with the use of E.coli models, I show that these ssDNA substrates are the product of transcription-induced negative-supercoiled DNA that correlates strongly with the mutagenic activity of AID. While several underlying mechanisms exist to prevent the mistargeting of AID, my findings suggest that by simply gaining access to ssDNA that is produced by transcription-induced negative supercoiling, AID has the potential to mutate non-Ig genes, albeit at lower rates than the antibody V-region.

Malt lymphoma is a malignant disease that can arise in a variety of extra nodal sites. Previous studies indicate that tumour arise from more mature B-cells. Our purpose was to examine the presence of clonality and somatic hypermutation of immunoglobulin (IgVн) of MALT lymphomas. Paraffin-embedded tumour samples from13 MALT lymphoma were subjected to rearrangement analysis, by using PCR, heteroduplex gels and sequence analysis. Successful amplification was seen in 10/13 cases and sequences of IgVн genes were obtained in 6/13, all of them were mutated. The percentage of mutation compared to germline sequences was 1,1% to 8,6% monoclonal rearrangemang. It was demonstrated that 5 of 7 clones were derived from the Vн3 family, 2 from Vн1 and 1 from the Vн 4 family.

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第19228号 / 医博第4027号 / 新制||医||1011(附属図書館) / 32227 / 京都大学大学院医学研究科医学専攻 / (主査)教授 武田 俊一, 教授 竹内 理, 教授 髙田 穣 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

The pathogenesis of lupus and other autoimmune diseases driven by antibody-antigen complexes involves interactions between genetic and environmental factors. The genetic factors can be separated into factors that dysregulate adaptive immunity, innate immunity or cell death. One genetic risk factor that can affect both innate and adaptive immunity is the inhibitory Fcγ receptor, FcγRIIB. Reduced or loss of function mutations in FcγRIIB lead to an increased risk of autoimmunity. Using the murine IgG2a specific B cell receptor (BCR) transgenic (Tg) mouse, AM14, our lab discovered that delivery of nucleic acid ligands via the BCR activates B cells by dual engagement of the BCR and endosomal toll like receptors (TLR) 7 and/or 9. Mechanistic studies interrogating the role of downstream signaling effectors and intracellular trafficking in the attenuation of BCR-TLR responses by FcγRIIB were limited by our inability to deliver immune complexes (IC) to non-Tg B cells or form brightly fluorescent IC. To deliver IC to non-Tg B cells, I developed a BCR adapter (BCRAM) that delivers IC to IgM-positive B cells. To track the uptake and trafficking of IC, I developed a panel of antibodies specific for streptavidin (SA). Complexes formed with biotinylated molecules and fluorescent streptavidin could be delivered to AM14 B cells or macrophages and tracked via flow cytometry and/or confocal microscopy. BCRAM and fluorescent IC were used to understand how FcγRIIB attenuated BCR-TLR responses. I found that both DNA IC and RNA IC responses were enhanced by FcγRIIB ablation. Interestingly, a naturally-occurring somatic mutation in the Fc domain of the nucleic acid-binding antibody PL2-3 prevented regulation by FcγRIIB and reduced binding to activating FcγR. Paradoxically, I found that SHIP-1, a negative regulator activated downstream of FcγRIIB engagement, promoted BCR-TLR9 responses independent of FcγRIIB. I hypothesized that FcγRIIB attenuates BCR-TLR9 responses by interfering with sensing by the endosomal TLRs. Using a pH sensing IC, I found that engagement of FcγRIIB leads to residence of the IC in a higher pH compartment. These findings demonstrate that FcγRIIB regulates the activation of autoreactive B cells by modulating the trafficking of nucleic acid containing IC to TLR7 and TLR9 associated intracellular compartments in B cells.