Fetal versus adult PreB or B cells: the human VH repertoire

Ontogeny of the B Cell Receptor Repertoire and Microbiome in Mice

The immune system matures throughout childhood to achieve full functionality in protecting our bodies against threats. The immune system has a strong reciprocal symbiosis with the host bacterial population and the two systems co-develop, shaping each other. Despite their fundamental role in health physiology, the ontogeny of these systems is poorly characterized. In this study, we investigated the development of the BCR repertoire by analyzing high-throughput sequencing of their receptors in several time points of young C57BL/6J mice. In parallel, we explored the development of the gut microbiome. We discovered that the gut IgA repertoires change from birth to adolescence, including an increase in CDR3 lengths and somatic hypermutation levels. This contrasts with the spleen IgM repertoires that remain stable and distinct from the IgA repertoires in the gut. We also discovered that large clones that germinate in the gut are initially confined to a specific gut compartment, then expand to nearby compartments and later on expand also to the spleen and remain there. Finally, we explored the associations between diversity indices of the B cell repertoires and the microbiome, as well as associations between bacterial and BCR clusters. Our results shed light on the ontogeny of the adaptive immune system and the microbiome, providing a baseline for future research.

B cell repertoire in patients with a novel BTK mutation: expanding the spectrum of atypical X-linked agammaglobulinemia

X-linked agammaglobulinemia (XLA) is caused by mutations in the Bruton tyrosine kinase) BTK) gene. Affected patients have severely reduced amounts of circulating B cells. Patients with atypical XLA may have residual circulating B cells, and there are few studies exploring these cells' repertoire. We aimed to study the B cell repertoire of a novel hypomorphic mutation in the BTK gene, using the next generation sequencing (NGS) technology. Clinical data was collected from our clinical records. Real-time PCR was used to determine KREC copies, and NGS was used to determine the immunoglobulin (Ig) heavy chain (IgH) repertoire diversity. Both patients had a relatively mild clinical and laboratory phenotype, residual BTK protein expression, and the same novel mutation in the BTK gene, c.1841 T > C, p. L614P. Signal-joint kappa-deleting recombination excision circles (sj-KREC) for both patients were completely absent reflecting lack of naïve B cells. The intron RSS-Kde coding joints (cj) were significantly reduced, reflecting residual replicating B cells. NGS displayed restricted IgH repertoire with highly uneven distribution of clones, especially for Pt2. We report a novel BTK mutation, c.1841 T > C (p. L614P) that is associated with a relatively mild phenotype. We conclude that the IgH repertoire in atypical XLA is restricted with highly uneven distribution of clones. This phenomenon may be explained by extremely reduced to non-existent levels of BTK in B cells. This report sheds further light on atypical cases of XLA.

B-cell receptor repertoire sequencing in patients with primary immunodeficiency: a review

The advent of next-generation sequencing (NGS) now allows a detailed assessment of the adaptive immune system in health and disease. In particular, high-throughput B-cell receptor (BCR) repertoire sequencing provides detailed information about the functionality and abnormalities of the B-cell system. However, it is mostly unknown how the BCR repertoire is altered in the context of primary immunodeficiencies (PID) and whether findings are consistent throughout phenotypes and genotypes. We have performed an extensive literature search of the published work on BCR repertoire sequencing in PID patients, including several forms of predominantly antibody disorders and combined immunodeficiencies. It is somewhat surprising that BCR repertoires, even from severe clinical phenotypes, often show only mild abnormalities and that diversity or immunoglobulin gene segment usage is generally preserved to some extent. Despite the great variety of wet laboratory and analytical methods that were used in the different studies, several findings are common to most investigated PIDs, such as the increased usage of gene segments that are associated with self-reactivity. These findings suggest that BCR repertoire characteristics may be used to assess the functionality of the B-cell compartment irrespective of the underlying defect. With the use of NGS approaches, there is now the opportunity to apply BCR repertoire sequencing to multiple patients and explore the PID BCR repertoire in more detail. Ultimately, using BCR repertoire sequencing in translational research could aid the management of PID patients by improving diagnosis, estimating functionality of the immune system and improving assessment of prognosis.

Isolator and other neonatal piglet models in developmental immunology and identification of virulence factors

The postnatal period is a ‘critical window’, a time when innate and passive immunity protect the newborn mammal while its own adaptive immune system is developing. Neonatal piglets, especially those reared in isolators, provide valuable tools for studying immunological development during this period, since environmental factors that cause ambiguity in studies with conventional animals are controlled by the experimenter. However, these models have limited value unless the swine immune system is first characterized and the necessary immunological reagents developed. Characterization has revealed numerous features of the swine immune system that did not fit mouse paradigms but may be more generally true for most mammals. These include fetal class switch recombination that is uncoupled from somatic hypermutation, the relative importance of the molecular mechanisms used to develop the antibody repertoire, the role of gut lymphoid tissue in that process, and the limited heavy chain repertoire but diverse IgG subclass repertoire. Knowledge gained from studies of adaptive immunity in isolator-reared neonatal pigs suggests that isolator piglets can be valuable in identification of virulence factors that are often masked in studies using conventional animals.

Human fetal, cord blood, and adult lymphocyte progenitors have similar potential for generating B cells with a diverse immunoglobulin repertoire

Several characteristics of the immunoglobulin (Ig) repertoire in fetuses and adults set them apart from each other. Functionally, this translates into differences in the affinity and effectiveness of the humoral immune response between adults and the very young. At least 2 possibilities could explain these differences: (1) fetal and adult lymphocyte progenitors differ significantly in their potential to form a diverse repertoire, and (2) factors extrinsic to the immunoglobulin locus are more influential to the character of the repertoire. To address this we used nonobese diabetic-severe combined immunodeficient-β2 microglobulin knockout (NOD/SCID/β2m-/-) mice reconstituted with human B-cell progenitors to compare the immunoglobulin repertoire potential of human fetal, cord blood, and adult sources. We found nearly identical VH and JH gene segment use and only modest differences in the third complementarity determining region of the immunoglobulin heavy chain (HCDR3). We conclude that the repertoire potential is remarkably similar regardless of the age of the individual from which progenitors are derived. Age-related differences in the immunoglobulin repertoire and variance of B-cell responses to immunization appear to arise from selection rather than from changes in recombination of the immunoglobulin locus itself. From the standpoint of the Ig repertoire, an immune system reconstituted from fetal or neonatal stem cells would likely be as diverse as one generated from adult bone marrow.

Long-term kinetics of adult human antibody repertoires

In healthy humans, antibody repertoires change during ontogeny and senescence. The dynamics of antibody repertoires among adults over a longer period of time in one and the same individual has, however, not been extensively studied. In this study we analysed peripheral blood samples from five healthy adults, taken over a period of 10 weeks and once 9 years later. A competitive, quantitative polymerase chain reaction (PCR) was developed to investigate short and long-term variations in VH gene family repertoires. Serum antibody levels to common self and non-self antigens were determined in samples taken at the same time-points as the cell samples to analyse possible correlations between molecular and serological expression profiles. We found a high degree of stability in the VH gene family repertoire over time as well as between individuals with a Caucasian background. A specific change in the usage of primarily the VH3 and VH5 gene families was observed in one individual at one time-point. The deviating pattern resembled the VH gene family utilization pattern observed in naturally activated B lymphocytes. The fluctuations in VH3 and VH5 gene family expression correlated with the presence of rheumatoid factor in serum. We discuss the possible influence of polyclonal, transient stimulation of B cells on VH gene repertoires, as measured in circulating B cells.

Extensive CDR3H length heterogeneity exists in bovine foetal VDJ rearrangements

Analysis of seven variable-diversity-joining (VDJ) gene rearrangements in B splenocytes from a 125-day-old bovine foetus revealed an extensive heavy-chain complementarity-determining region 3 (CDR3H) length variation (9-56 codons). Indeed, the global CDR3H size spectratyping of foetal VDJ rearrangements substantiated such an extensive heterogeneity and was comparable with that noted in peripheral B lymphocytes of adult cattle. These observations are in contrast to species such as humans with extensive germline combinatorial capability where shorter CDR3H length is noted early during B-cell development. Exceptionally long CDR3H (as in adult cattle) was noted in two foetal VDJ rearrangements encoded by a single germline VH gene. Further, two VH genes (gl.110.20 and BF2B5) were preferentially expressed in the foetal VDJ rearrangements. The DH gene-encoded CDR3H region of foetal VDJ rearrangements is remarkable for repetitive GGT (glycine) and TAT (tyrosine) codons that favour the recruitment of somatic hypermutations. It appears that closely related germline DH genes, preferentially used in the hydrophilic reading frame, encode varying CDR3H lengths early during B-cell ontogeny in cattle. A comparison of germline and expressed VH genes, especially in the CDR1 and CDR2, confirms that somatic hypermutations contribute to immunoglobulin (Ig)M antibody diversification in cattle. The biased nucleotide base use and high occurrence of 'hot-spot' triplet (AGPy; AG pyrimidine base) in the CDRs predisposes to somatic hypermutations. Overall, these observations suggest that extensive CDR3H length heterogeneity, including the generation of exceptionally long CDR3H (up to 56 amino acids), and somatic hypermutations contribute to IgM antibody diversification in cattle. The extensive CDR3H length heterogeneity early during the B-cell development may compensate for constraints imposed on antibody diversification owing to the limited germline sequence diversity of genetic elements in cattle.

Towards a quantitative model of immunogenicity: counting pathways in sequence space

One of the fundamental aims of structural biology is the identification of high-affinity ligands for arbitrary receptors. The maturation of the antibody repertoire elegantly and robustly solves this problem through an evolutionary mechanism comprising repeated cycles of mutation and preferential replication. To understand better the limitations and biases of this process, we developed an interpretation of antibody maturation within the framework of sequence space and fitness landscapes. Several well-described phenomena can be directly derived from this framework, and new predictions can be made. Ultimately, this reconceptualization of the clonal selection process suggests a quantitative, testable model of immunogenicity.

The Human Antibody Response to Porcine Xenoantigens Is Encoded by IGHV3-11 and IGHV3-74 IgVH Germline Progenitors

Preformed and induced Ab responses present a major immunological barrier to the use of pig organs for human xenotransplantation. We generated IgM and IgG gene libraries established from lymphocytes of patients treated with a bioartificial liver (BAL) containing pig hepatocytes and used these libraries to identify IgVH genes that encode human Ab responses to pig xenoantigens. Genes encoded by the VH3 family are increased in expression in patients following BAL treatment. cDNA libraries representing the VH3 gene family were generated, and the relative frequency of expression of genes used to encode the Ab response was determined at days 0, 10, and 21. Ig genes derived from the IGHV3-11 and IGHV3-74 germline progenitors increase in frequency post-BAL. The IGHV3-11 gene encodes 12% of VH3 cDNA clones expressed as IgM Abs at day 0 and 32.4–39.0% of cDNA clones encoding IgM Abs in two patients at day 10. IGHV3-11 and IGHV3-74 genes encoding IgM Abs in these patients are expressed without evidence of somatic mutation. By day 21, an isotype switch occurs and IGHV3-11 IgVH progenitors encode IgG Abs that demonstrate somatic mutation. We cloned these genes into a phagemid vector, expressed these clones as single-chain Abs, and demonstrated that the IGHV3-11 gene encodes Abs with the ability to bind to the gal α (1,3) gal epitope. Our results demonstrate that the xenoantibody response in humans is encoded by IgVH genes restricted to IGHV3-11 and IGHV3-74 germline progenitors. IgM Abs are expressed in germline configuration and IgG Abs demonstrate somatic mutations by day 21.

Altered VH6-D-JH repertoire in human insulin-dependent diabetes mellitus and autoimmune idiopathic thrombocytopenic purpura

We have characterized the peripheral B cell repertoire in T cell-mediated insulin-dependent diabetes mellitus (IDMM) and in B cell-mediated autoimmune idiopathic thrombocytopenic purpura (AITP). The VH6-containing repertoire in adult patients with IDDM or AITP and healthy control subjects was investigated by PCR amplification using VH6- and JH-specific primers. Nucleotide sequence analysis of VH6-D-JH rearrangements showed an abnormally high frequency of somatic mutations in non-functional rearrangements from diabetic (3. 58 %) as well as AITP patients (3.18 %), compared to controls (0.4 % and 1.43 %, respectively; p < 0.05). In contrast, the mutation frequency among functional rearrangements was 2.4 - 3 times lower in patients compared to controls ( p < 0.05). Detailed analysis of the VH6 genes carrying mutations showed that the underlying mechanism for this observation is probably different for the two diseases. Analysis of D- and JH gene usage revealed additional deviations from the normal pattern. Taken together, these results suggest defects in the mechanisms controlling selection of the B cell repertoire in patients with IDDM or AITP.

CDR3 sequences of MALT lymphoma show homology with those of autoreactive B-cell lines

We have examined the CDR3 sequence and adjacent regions of immunoglobulin genes from B-cell lymphoma of mucosa-associated lymphoid tissue (MALT). Twenty-nine sequences (15 sequences from 13 low-grade MALT lymphomas, marginal zone B-cell lymphomas; 7 sequences from 6 high-grade MALT lymphomas; 7 sequences from 7 diffuse large cell lymphomas) were obtained after cloning of the polymerase chain reaction-amplified segments. In the low-grade MALT, high-grade MALT and diffuse large cell lymphomas, the mean length of the CDR3 region was 47.6+/-10.31 (range 21 to 60), 38.71+/-10.37 (range 27 to 57) and 40.86+/-3.34 (range 39 to 48) nucleotides, respectively. The length of the CDR3 region was significantly greater in the low-grade MALT lymphoma group than in the other two groups. CDR3 sequences in lymphoma cell clones of 14 cases showed 60 to 81% homology with autoantibody-associated lymphocyte clones including rheumatoid factor. The incidences of these autoantibody-associated lymphocyte clones were higher in the high-grade MALT (4/6) and diffuse large lymphomas (5/7) than in the low-grade MALT lymphoma (5/13). Cases with more than 70% homology at the nucleotide level were found to have 71 to 82% homology with autoantibodies at the protein level in the low-grade MALT lymphomas (2/13), and 67% homology in the high-grade MALT lymphomas (2/7). These results indicate that MALT lymphomas may be derived from the malignant transformation of autoreactive B-cells.

Antibody Repertoire Development in Fetal and Neonatal Piglets. I. Four VH Genes Account for 80 Percent of VH Usage During 84 Days of Fetal Life

VDJ rearrangement and VH gene usage during fetal development in 35 outbred piglets was examined by PCR amplification of VDJs; VDJs were subsequently characterized by hybridization with VH-specific gene probes and by sequencing. VDJ rearrangement was first seen in the fetal liver on day 30 of a 114-day gestation. Four VH genes (VHA, VHB, VHC, and VHE) accounted for ~80% of all VH gene usage regardless of gestational age, choice of piglet, or lymphoid tissue tested; DHA and DHB were used in &gt;90% of the fetal VDJs examined. Evidence of somatic hypermutation during fetal development was not found. The proportion of the four prominent fetal VH genes did not differ significantly between cDNA and DNA, suggesting the absence of selective B cell differentiation. A comparison of recombination signal sequences, flanking sequences, and framework sequences of these fetal genes with other germline VH genes of swine offered no clue as to their selective usage. N-region additions were prominent on day 40 but not on day 30, suggesting that the onset of terminal deoxynucleotidyltransferase activity occurs after 30 days of fetal development. These collective findings indicate that the preimmune, “natural Ab” repertoire of the fetal piglet is largely restricted to the use of four nonpolymorphic and nonmutated VH genes and two nonmutated DH segments. This suggests that the preimmune repertoire of swine is either highly restricted or almost entirely determined by junctional diversity in complementarity-determining region-3.

Determination of gene usage by differential polymerase chain reaction product hybridization

All swine VH genes belong to a highly homologous family and have identical leader sequences, and the swine VH locus contains a single JH. The small number of VH genes used by the fetus and neonate in the first 6 weeks have unique CDR1 and CDR2 sequences, permitting each to be identified using specific oligonucleotide probes. We have used this system as a model for the development of a rapid method for determining the proportional usage of closely related genes based on differential polymerase chain reaction (PCR) product hybridization (DPPH). The validity of the method is demonstrated using mixtures of PCR product containing known amounts of VH gene DNAs and by comparing data obtained by this method with those obtained by enumeration of individual hybridizing clones from lymphoid tissue and peripheral blood B cells. Since DPPH is at least 100-fold more efficient than the enumeration of individual hybridizing clones, it is especially useful for analyzing large numbers of samples in population studies. The possible extension of this method to the usage of other genes is discussed.

Characterization of the CDR3 region of rearranged alpha heavy chain genes in human fetal liver

The human fetal liver is an early site for B cell development. Pre B cells are first detectable in human fetal life at 8 weeks of gestation, when the rearrangement of the mu heavy chain genes starts. In this study we characterize the CDR3 region of rearranged alpha heavy chain transcripts from four human fetal livers ranging from 8 to 11 weeks of gestation. Each fetal liver showed a limited number of variations in CDR3 sequences compared with adult peripheral blood mononuclear cells (PBMC). Sequence analysis of 91 clones demonstrated that there was no preference for the usage of a certain JH gene segment, whereas a preference for usage of DH family genes, DXP and DLR, was seen in most cases during early fetal life. This is the first study where rearranged alpha heavy chain genes in fetal liver have been characterized. Our data suggest that the usage of JH genes is random, while there is a preference for DH family genes in human fetal liver.

Structure, Diversity, and Repertoire of VH Families in the Mexican Axolotl

The Mexican axolotl VH segments associated with the Igh Cμ and Cυ isotypes were isolated from anchored PCR libraries prepared from spleen cell cDNA. The eight new VH segments found bring the number of VH families in the axolotl to 11. Each VH had the canonical structural features of vertebrate VH segments, including residues important for the correct folding of the Ig domain. The distribution of ser AGC/T (AGY) and TCN codons in axolotl VH genes was biased toward AGY in complementarity-determining region-1 (CDR1) and TCN in framework region-1 (FR1); there were no ser residues in the FR2 region. Thus, the axolotl CDR1 region is enriched in DNA sequences forming potential hypermutation hot spots and is flanked by DNA sequences more resistant to point mutation. There was no significant bias toward AGY in CDR2. Southern blotting using family-specific VH probes showed restriction fragments from 1 (VH9) to 11–19 (VH2), and the total number of VH genes was 44 to 70, depending on the restriction endonuclease used. The VH segments were not randomly used by the Hμ and Hυ chains; VH1, VH6, and VH11 were underutilized; and the majority of the VH segments belonged to the VH7, VH8, and VH9 families. Most of the nine JH segments seemed to be randomly used, except JH6 and JH9, which were found only once in 79 clones.