Evidence supporting somatic assembly of the DNA segments (minigenes), coding for the framework, and complementarity-determining segments of immunoglobulin variable regions

Analysis of immunoglobulin organization and complexity in mink (Neovison vison)

Mink are susceptible to viruses such as SARS-CoV-2, H1N1 and H9N2, so they are considered a potential animal model for studying human viral infections. Therefore, it is important to study the immune system of mink. Immunoglobulin (Ig) is an important component of humoral immunity and plays an important role in the body's immune defense. In this study, we described the gene loci structure of mink Ig germline by genome comparison, and analysed the mechanism of expression diversity of mink antibody library by 5'RACE and next-generation sequencing (NGS). The results were as follows: the IgH, Igκ and Igλ loci of mink were located on chromosome 13, chromosome 8 and chromosome 3, respectively, and they had 25, 36 and 7 V genes, 3, 5 and 7 J genes and 10 DH genes, respectively. Mink Ig heavy chain preferred the IGHV1, IGHD2 and IGHJ4 subgroups, κ chain mainly use the IGKV1, IGKJ1 and IGHL4 subgroups, and λ chain mainly use the IGLV3 and IGLJ3 subgroups. Linkage diversity analysis revealed that N nucleotide insertion was the main factor affecting the linkage diversity of mink Igs. On the mutation types of mink Ig Somatic Hypermutation (SHM), the high mutation types of heavy chain were mainly G > A, C > T, T > C, A > G, C > A, G > T, A > C, and T > G; the high mutation types of κ chain were G > A and T > C; and the high mutation types of λ chain were G > A and A > G. The objective of this study was to analyse the loci structure and expression diversity of Ig in mink. The results contribute to our comprehension of Ig expression patterns in mink and were valuable for advancing knowledge in mink immunogenetics, exploring the evolution of adaptive immune systems across different species, and conducting comparative genomics research.

Comparative analysis of primer sets for the assessment of clonality in feline lymphomas

Introduction

Lymphomas are among the most important and common malignant tumors in cats. Differentiating lymphomas from reactive lymphoid proliferations can be challenging, so additional tools such as clonality assessment by PCR are important in diagnosis finding. Several PCR assays have been developed to assess clonality in feline lymphomas. For T-cell lymphomas TRG (T-cell receptor gamma) genes are the preferred target whereas for B-cell lymphomas most primer sets target immunoglobulin heavy chain (IGH) genes. Here we compare commonly used diagnostic primer sets for the assessment of clonality in feline lymphomas under controlled conditions (i.e., identical sample set, PCR setup, amplicon detection system).

Methods

Formalin-fixed and paraffin-embedded samples from 31 feline T-cell lymphomas, 29 B-cell lymphomas, and 11 non-neoplastic controls were analyzed by PCR combined with capillary electrophoresis.

Results and discussion

We show that the combination of the primer sets published by Weiss et al. and Mochizuki et al. provided the best results for T-cell clonality, i.e., correctly assigns most populations as clonal or polyclonal. For B-cell clonality, the combination of the primer sets by Mochizuki et al. and Rout et al. gave the best results when omitting the Kde gene rearrangement due to its low specificity. This study rigorously evaluated various primer sets under uniform experimental conditions to improve accuracy of lymphoma diagnostic and provides a recommendation for achieving the highest diagnostic precision in lymphoma clonality analysis.

Similarity measurements of B cell receptor repertoire in baseline mice showed spectrum convergence of IgM

BACKGROUND

The B cell receptor (BCR) repertoire is highly diverse among individuals. Poor similarity of the spectrum among inbred baseline mice may limit the ability to discriminate true signals from those involving specific experimental factors. The repertoire similarity of the baseline status lacks intensive measurements.

RESULTS

We measured the repertoire similarity of IgH in blood and spleen samples from untreated BALB/c and C57BL/6J mice to investigate the baseline status of the two inbred strains. The antibody pool was stratified by the isotype of IgA, IgG and IgM. Between individuals, the results showed better convergence of CDR3 and clonal lineage profiles in IgM than in IgA and IgG, and better robustness of somatic mutation networks in IgM than in IgA and IgG. It also showed that the CDR3 clonotypes and clonal lineages shared better in the spleen samples than in the blood samples. The animal batch differences were detected in CDR3 evenness, mutated clonotype proportions, and maximal network degrees. A cut-off of 95% identity in the CDR3 nucleotide sequences was suitable for clonal lineage establishment.

CONCLUSIONS

Our findings reveal a natural landscape of BCR repertoire similarities between baseline mice and provide a solid reference for designing studies of mouse BCR repertoires.

Simultaneous affinity maturation and developability enhancement using natural liability-free CDRs

Affinity maturation is often a necessary step for the development of potent therapeutic molecules. Many different diversification strategies have been used for antibody affinity maturation, including error-prone PCR, chain shuffling, and targeted complementary-determining region (CDR) mutation. Although effective, they can negatively impact antibody stability or alter epitope recognition. Moreover, they do not address the presence of sequence liabilities, such as glycosylation, asparagine deamidation, aspartate isomerization, aggregation motifs, and others. Such liabilities, if present or inadvertently introduced, can potentially create the need for new rounds of engineering, or even abolish the value of the antibody as a therapeutic molecule. Here, we demonstrate a sequence agnostic method to improve antibody affinities, while simultaneously eliminating sequence liabilities and retaining the same epitope binding as the parental antibody. This was carried out using a defined collection of natural CDRs as the diversity source, purged of sequence liabilities, and matched to the antibody germline gene family. These CDRs were inserted into the lead molecule in one or two sites at a time (LCDR1-2, LCDR3, HCDR1-2) while retaining the HCDR3 and framework regions unchanged. The final analysis of 92 clones revealed 81 unique variants, with each of 24 tested variants having the same epitope specificity as the parental molecule. Of these, the average affinity improved by over 100 times (to 96 pM), and the best affinity improvement was 231-fold (to 32 pM).

Humanization of Murine Neutralizing Antibodies against Human Herpesvirus 6B

Exanthem subitum is a common childhood illness caused by primary infection with human herpesvirus 6B (HHV-6B). It is occasionally complicated by febrile seizures and even encephalitis. HHV-6B reactivation also causes encephalitis, especially after allogeneic hematopoietic stem cell transplantation. However, no adequate antiviral treatment for HHV-6B has yet been established. Mouse-derived monoclonal antibodies (MAbs) against the HHV-6B envelope glycoprotein complex gH/gL/gQ1/gQ2 have been shown to neutralize the viral infection. These antibodies have the potential to become antiviral agents against HHV-6B despite their inherent immunogenicity to the human immune system. Humanization of MAbs derived from other species is one of the proven solutions to such a dilemma. In this study, we constructed chimeric forms of two neutralizing MAbs against HHV-6B to make humanized antibodies. Both showed neutralizing activities equivalent to those of their original forms. This is the first report of humanized antibodies against HHV-6B and provides a basis for the further development of HHV-6B-specific antivirals.IMPORTANCE Human herpesvirus 6B (HHV-6B) establishes lifelong latent infection in most individuals after the primary infection. Encephalitis is the most severe complication caused by both the primary infection and the reactivation of HHV-6B and is the cause of considerable mortality in patients, without any established treatments to date. The humanization of the murine neutralizing antibodies described in this research provided a feasible way to reduce the inherent immunogenicity of the antibodies without changing their neutralizing activities. These newly designed chimeric antibodies against HHV-6B have the potential to be candidates for antivirals for future use.

Effects of spaceflight on the immunoglobulin repertoire of unimmunized C57BL/6 mice

Spaceflight has been shown to suppress the adaptive immune response, altering the distribution and function of lymphocyte populations. B lymphocytes express highly specific and highly diversified receptors, known as immunoglobulins (Ig), that directly bind and neutralize pathogens. Ig diversity is achieved through the enzymatic splicing of gene segments within the genomic DNA of each B cell in a host. The collection of Ig specificities within a host, or Ig repertoire, has been increasingly characterized in both basic research and clinical settings using high-throughput sequencing technology (HTS). We utilized HTS to test the hypothesis that spaceflight affects the B-cell repertoire. To test this hypothesis, we characterized the impact of spaceflight on the unimmunized Ig repertoire of C57BL/6 mice that were flown aboard the International Space Station (ISS) during the Rodent Research One validation flight in comparison to ground controls. Individual gene segment usage was similar between ground control and flight animals, however, gene segment combinations and the junctions in which gene segments combine was varied among animals within and between treatment groups. We also found that spontaneous somatic mutations in the IgH and Igκ gene loci were not increased. These data suggest that space flight did not affect the B cell repertoire of mice flown and housed on the ISS over a short period of time.

Characterization of the naive murine antibody repertoire using unamplified high-throughput sequencing

Antibody specificity and diversity are generated through the enzymatic splicing of genomic gene segments within each B cell. Antibodies are heterodimers of heavy- and light-chains encoded on separate loci. We studied the antibody repertoire from pooled, splenic tissue of unimmunized, adult female C57BL/6J mice, using high-throughput sequencing (HTS) without amplification of antibody transcripts. We recovered over 90,000 heavy-chain and over 135,000 light-chain immunoglobulin sequences. Individual V-, D-, and J-gene segment usage was uniform among the three mouse pools, particularly in highly abundant gene segments, with low frequency V-gene segments not being detected in all pools. Despite the similar usage of individual gene segments, the repertoire of individual B-cell CDR3 amino acid sequences in each mouse pool was highly varied, affirming the combinatorial diversity in the B-cell pool that has been previously demonstrated. There also was some skewing in the V-gene segments that were detected depending on chromosomal location. This study presents a unique, non-primer biased glimpse of the conventionally housed, unimmunized antibody repertoire of the C57BL6/J mouse.

Site-Specifically Labeled Immunoconjugates for Molecular Imaging--Part 1: Cysteine Residues and Glycans

Due to their remarkable selectivity and specificity for cancer biomarkers, immunoconjugates have emerged as extremely promising vectors for the delivery of diagnostic radioisotopes and fluorophores to malignant tissues. Paradoxically, however, these tools for precision medicine are synthesized in a remarkably imprecise way. Indeed, the vast majority of immunoconjugates are created via the random conjugation of bifunctional probes (e.g., DOTA-NCS) to amino acids within the antibody (e.g., lysines). Yet antibodies have multiple copies of these residues throughout their macromolecular structure, making control over the location of the conjugation reaction impossible. This lack of site specificity can lead to the formation of poorly defined, heterogeneous immunoconjugates with suboptimal in vivo behavior. Over the past decade, interest in the synthesis and development of site-specifically labeled immunoconjugates—both antibody-drug conjugates as well as constructs for in vivo imaging—has increased dramatically, and a number of reports have suggested that these better defined, more homogeneous constructs exhibit improved performance in vivo compared to their randomly modified cousins. In this two-part review, we seek to provide an overview of the various methods that have been developed to create site-specifically modified immunoconjugates for positron emission tomography, single photon emission computed tomography, and fluorescence imaging. We will begin with an introduction to the structure of antibodies and antibody fragments. This is followed by the core of the work: sections detailing the four different approaches to site-specific modification strategies based on cysteine residues, glycans, peptide tags, and unnatural amino acids. These discussions will be divided into two installments: cysteine residues and glycans will be detailed in Part 1 of the review, while peptide tags and unnatural amino acids will be addressed in Part 2. Ultimately, we sincerely hope that this review fosters interest and enthusiasm for site-specific immunoconjugates within the nuclear medicine and molecular imaging communities.

Human 4F5 single-chain Fv antibody recognizing a conserved HA1 epitope has broad neutralizing potency against H5N1 influenza A viruses of different clades

Influenza A viruses present a significant threat to public health worldwide. High-affinity human scFv antibodies against a conserved epitope can potentially provide immunity to diverse viruses and protect against future pandemic viruses. A library of phage-displayed human scFv containing 6.0×10(8) members was generated from lymphocytes of H5N1 virus vaccinated individuals. Using the recombinant H5N1 virus hemagglutinin ectodomain (HA1), 4F5 scFv was identified with neutralizing activity against both clade 2 and 9 H5N1 viruses. In embryonated chicken eggs, the antiviral activity of 4F5 scFv conferred a 100% survival rate and at least a 62.5% survival rate against different clades of H5N1 viruses by pre-treatment and post-treatment, respectively. 4F5 scFv belongs to the VH-3-43 family according to the IMGT database, and a peptide (76)WLLGNP(81) containing half of an α-helix in HA1 was identified as the binding pocket. The conserved binding epitope of this novel broadly neutralizing scFv may become key in the design and implementation of vaccines or RNA interference against H5N1 viruses.

Production of a neutralizing mouse-human chimeric antibody against botulinum neurotoxin serotype E

A mouse-human chimeric antibody that can neutralize botulinum neurotoxin serotype E (BoNT/E) was developed. Variable regions of heavy and light chains obtained using a mouse hybridoma clone (E9-4) cDNA, which was selected on the basis of neutralizing activity against BoNT/E, were fused with the upstream regions of the constant counterparts of human kappa light and gamma 1 heavy chain genes, respectively. CHO-DG44 cells were transfected with these plasmids and a mouse-human chimeric antibody (EC94) was purified to examine binding and neutralizing activity against BoNT/E. EC94 exhibited the same levels of binding activities against BoNT/E as those of a parent mouse monoclonal antibody and neutralized more than 4,000 LD(50)/mg antibody. This chimeric antibody seems to be a useful candidate for infant botulism in which the use of passive immunotherapy is not planned so as to avoid serious events such as anaphylactic shock. We designed shuffling chimeric antibodies with replacement of V(H) or V(L) of EC94 with that of a chimeric antibody (AC24) that possessed neutralizing activity against BoNT/A. These shuffling antibodies did not exhibit neutralizing activity against either BoNT/E or BoNT/A.

Evidence for the murine IgH mu locus acting as a hot spot for intrachromosomal homologous recombination

Homologous recombination accomplishes the exchange of genetic information between two similar or identical DNA duplexes. It can occur either by gene conversion, a process of unidirectional genetic exchange, or by reciprocal crossing over. Homologous recombination is well known for its role in generating genetic diversity in meiosis and, in mitosis, as a DNA repair mechanism. In the immune system, the evidence suggests a role for homologous recombination in Ig gene evolution and in the diversification of Ab function. Previously, we reported the occurrence of homologous recombination between repeated, donor and recipient alleles of the Ig H chain mu gene C (Cmu) region residing at the Ig mu locus in mouse hybridoma cells. In this study, we constructed mouse hybridoma cell lines bearing Cmu region heteroalleles to learn more about the intrachromosomal homologous recombination process. A high frequency of homologous recombination (gene conversion) was observed for markers spanning the entire recipient Cmu region, suggesting that recombination might initiate at random sites within the Cmu region. The Cmu region heteroalleles were equally proficient as either conversion donors or recipients. Remarkably, when the same Cmu heteroalleles were tested for recombination in ectopic genomic positions, the mean frequency of gene conversion was reduced by at least 65-fold. These results are consistent with the murine IgH mu locus behaving as a hot spot for intrachromosomal homologous recombination.

Development of more efficacious antibodies for medical therapy and diagnosis

Two procedures for improving the efficacy of medically important antibodies are described. The first procedure is designed to reduce the immunogenicity of nonhuman antibodies to the barest minimum--the "humanization" is accomplished by transplanting only the specificity-determining residues of the nonhuman antibody onto a human antibody template. The second procedure is designed to permit the easy production of multispecific/multivalent antibodies via heterodimer formation of electrostatically complementary Fc regions.

Affinity maturation of lymphocyte receptors and positive selection of T cells in the thymus

In this review we have re-evaluated the dominant paradigm that TcR V genes do not somatically mutate. We highlight the many structural and functional similarities between Ig and TcR antigen-specific receptors on B and T cells. We have reviewed the factors influencing the somatic and germline evolution of IgV regions in B cells, have evaluated in detail various models which could be invoked to explain the pattern of variation in both transcribed and non-transcribed segments of germline IgV-gene DNA sequences, and applied this perspective to the TcR V beta and V alpha genes. Whilst specific TcRs recognize a complex of a short antigenic peptide bound to MHC Class I or II glycoprotein, and Ig receptors can recognize both oligopeptides and conformational determinants on undegraded polypeptides, they both employ heterodimer variable regions (Fabs) utilizing all three CDRs in epitope binding. We conclude that a plausible case can be made for the possibility that rearranged TcR V genes may undergo some type of somatic hypermutation process during T-cell development in the thymus (concurrent with or after the positive selection phase) thus allowing a repertoire of TvR alpha beta heterodimers to be both positively and negatively selected by the same set of ligands (self MHC + self peptide) in the thymus.

Possible use of similar framework region amino acid sequences between human and mouse immunoglobulins for humanizing mouse antibodies

We have previously noted that a specific amino acid sequence could form the second framework region of human, mouse and rabbit immunoglobulin light chains, suggesting that this sequence has been preserved for 80 million years. Through divergent evolution, each species has acquired a different set of framework region sequences; however, these sets still share a few similar or identical amino acid sequences. In the present study, we have identified such sequences for all four framework regions between human and mouse immunoglobulin light and heavy chains. They may be useful in humanizing or reshaping mouse or rat antibodies for therapeutic applications in human patients.

Evolution of immunoglobulin genes: VH families in the amphibian Xenopus

We have isolated multiple independent cDNA clones that represent mRNA sequences of immunoglobulin heavy chains from the spleen of adult Xenopus laevis. These cDNA clones contained constant (C) region sequences that were either Cmu or a separate C region sequence believed to be Cnu. In individual cDNA clones the C region sequences were associated with independent heavy-chain variable region (VH) sequences that were classifiable into five distinct families. Genomic Southern blotting analyses with family-specific probes indicated that the haploid genome contains a minimum of 80 VH gene segments, a number similar to that found in various mammalian species. Multiple JH and putative DH segments were also identified (J, joining; D, diversity). Analyses of 13 independent VHDJH junctions suggest that combinatorial and junctional diversification mechanisms probably arose early in vertebrate evolution. Finally, comparison of Xenopus VH sequences to those from other vertebrates indicated conservation of V region framework residues that are responsible for the tertiary structure of the Fv throughout evolution.

Heavy chain variable region. Multiple gene segments encode anti-4-(hydroxy-3-nitro-phenyl)acetyl idiotypic antibodies

The hapten (4-hydroxy-3-nitrophenyl)acetyl (NP), when conjugated to carrier proteins, elicits a characteristic idiotypic response (NPb) in C57BL/6 mice. The response can be divided serologically into two distinct NPb-positive groups of antibodies. The first group consists of four crossreacting subgroups (I-IV), the second of two subgroups (V, VI). Some antibodies of subgroups I and II have been shown to express the unmutated heavy chain variable region (VH) germline gene 186.2. Antibodies of subgroups V and VI crossreact extensively with the NPa-positive antibodies of BALB/c mice. We sequenced heavy chain complementary DNA from eight hybridomas producing anti-NP antibodies. Six of these belong to subgroups V and VI, and two were NPa-positive hybridomas of BALB/c origin. All sequences were homologous to each other, and differed by approximately 80 basepairs from the 186.2 C57BL/6 germline VH gene. From our sequence and Southern blot analyses we suggest: (a) the NPb idiotypic response is the product of several VH germline genes, (b) some of these genes are very homologous to the gene coding for the BALB/c NPa idiotype, and might represent the C57BL/6 allelic forms of this gene, (c) the diversity regions of NPb and NPa-positive antibodies are diverse in length and amino acid composition, except for the first residue, which is always tyrosine, (d) all four heavy chain joining region gene segments are expressed without mutation. We discuss our data in terms of diversity in the germline VH gene repertoire, as well as diversity created by gene segment-joining events and somatic mutation.

Possible involvement of human D minigenes in the first complementarity-determining region of kappa light chains

The nucleotide sequences of the complementary strands of two human diversity region (D) minigenes, D2 and D4, show stretches of homology with two human variable region kappa chain (V kappa) genes, NG9 and HK101, respectively, in the first complementarity-determining region. In one V kappa sequence, the homology includes the 5' flanking region of D minigenes, which may comprise a recombinase recognition signal. It is thus conceivable that gene conversions involving D minigenes may contribute to V kappa diversity.

Novel immunoglobulin heavy chains are produced from DJH gene segment rearrangements in lymphoid cells

It has been found that most immunoglobulin heavy(H)-chain gene diversity (D) segments carry their own 5' transcriptional promoter element. Transcription of rearrangements which use heavy-chain D and joining (J) segments in B-lymphoid cells ultimately leads to the production of a Dmu messenger RNA which contains the DJH segments linked to the mu heavy-chain constant region. If the D is joined to the JH segment in the appropriate translational reading frame, this Dmu mRNA is translated to yield a short Dmu protein with a variable DJH N-terminus.

Is there a higher level genetic code that directs evolution?

Because the genetic code is redundant for most amino acids, different codons can be used in a given position without altering the structure of the protein for which the gene codes. This flexibility permits information encoding structural, and therefore functional, properties of RNA and DNA to be transmitted simultaneously by a protein-coding sequence of DNA. Among the other messages that might be transmitted, it is proposed, is one modulating the evolution of the DNA itself.

Rearranged immunoglobulin heavy chain variable region (VH) pseudogene that deletes the second complementarity-determining region

We have cloned two rearranged heavy chain variable region (VH) genes from the IgG-producing human cell line CESS. The VH gene, which is linked to the mu chain constant region (C mu) gene, has two deletions at residues 45-62 and 82A-90, the former of which corresponds closely to the second complementarity-determining region (CDR2). These results could indicate that translocation of CDR2 occurred and could give support to the argument that reassortment of the V mini-genes is involved in the generation of hypervariability during evolution. However, the rearranged pseudogene could have also arisen by fortuitous deletion. The other VH gene of CESS is an expressed form and is probably linked to the C gamma gene. The diversity region (D) segments used in these rearranged V genes are less than 38% homologous to known human germline D segments, indicating the presence of more unknown germline D segments.

Composite human VK genes and a model of their evolution

A phage library and two cosmid libraries were screened for human VK genes. Two recombinant phage and four cosmid clones were analysed in detail by restriction mapping and sequencing. Each one contained a single VKI sequence. Two of these six sequences are potentially functional VK genes and four are pseudogenes. Two pseudogenes derived from different genomic DNAs are highly homologous and are therefore either allelic variants or the products of a recent duplication event. Comparisons of our sequences with all fully determined human VKI amino acid and DNA sequences reveal identical segments which at first sight appear like minigenes. But these segments do not coincide with the subregions and some of the segments include both, framework and complementarity determining regions (FR, CDR, ref. 2). The findings may be explained by an evolutionary model generating composite genes by gene conversion and selection.

Antigen binding to lymphoid cells from unimmunized mice. VII. Restriction of antigen-binding capacity by maturing B lymphocytes

Neonatal spleen populations have been studied for antigen-binding capacity in an attempt to determine if the frequency of double antigen-binding cells changes as the population matures. Just after birth, the frequencies of total ABC, double ABC and Ig-bearing cells were similar to the frequencies seen in the adult bone marrow. During the first week after birth, the proportion of total ABC and Ig-bearing cells rose sharply so that by 8 days after birth, these cells were about half of adult levels. The proportion of total double ABC, after a brief rise at day 1, remained constant throughout the test period. Thus, the proportion of total ABC which are doubles gradually decreases with age. Sedimentation velocity studies indicate that double ABC's tend to co-sediment with cells which require a period of maturation before they can respond to a thymus-independent antigen in irradiated hosts. Single ABC, on the other hand, tend to co-sediment with cells which are immediately responsive to antigen, or require a shorter maturational period before they become responsive to antigen. All of these data, taken together with our other work, suggest the possibility that multiple ABC are clonally-derived lymphocyte populations which become more restricted in their antigen-binding capacity as they mature.

Variable-region sequences of five human lambda-chain proteins reacting with an idiotypic antibody to the MCG Bence-Jones protein

An antibody to the V-region of BJ protein MCG has been used to detect other human lambda-chains with similar idiotypic specificities. Five such proteins have been found and sequenced. They show relatively strong sequence homologies to some segments of the MCG V-region. The results of this study indicate that L-chains which contain short segments of their V-regions that are identical can be readily detected by the use of appropriate antisera.

Recombination between antibody heavy chain variable-region genes: evidence for gene conversion

The murine hybridoma line B1-8.delta 1 secretes monoclonal IgD lambda 1 antibodies specific for the hapten (4-hydroxy-3-nitrophenyl)acetyl (NP). The variable (V) region of these antibodies is defined by a characteristic pattern of idiotopes. A spontaneous V-region variant (B1-8.V1) with altered idiotope pattern was selected. The structural variation is confined to the V region of the heavy chain. It was shown previously that the variant V region is encoded by a gene that was generated by a crossover between the rearranged VDJ gene of the wild type (B1-8.delta 1) and a neighboring germ-line VH gene. In the present study the nucleotide sequence of coding and flanking regions of the VH gene expressed in variant B1-8.V1 was determined. Wild-type and variant VH genes differ at 15 positions in a region between leader sequence and codon 66. The sequence of the region carrying the substitutions is identical to the sequence of the corresponding region in a neighboring germ-line VH gene. This implies that the variant VH gene was generated by a mechanism of recombination more complicated than single crossover. Gene conversion as the mechanism of the recombination is discussed.

Evolution of immunoglobulin V genes: evidence indicating that recently duplicated human V kappa sequences have diverged by gene conversion

We have analyzed several closely related members of the gene family encoding the variable regions of human immunoglobulin kappa light chains (V kappa genes). Two of these genes differ at a single nucleotide out of 940 bases sequenced, and are believed to be alleles of a locus called HK 101. This substitution results in an amino acid replacement in the first complementarity-determining region of the kappa chain. We also compared the structures of two nonallelic human V kappa loci (HK 101 and HK 137) and found a high degree of sequence homology over a region at least 13.5 kb long. This long block of homology indicates that these two loci arose from a recent gene duplication. The DNA sequences of these two nonallelic V kappa genes exhibit a very unusual distribution of nucleotide substitutions. Seven of the ten substitutions found among 940 bases are clustered in a 39 base stretch encoding the first complementarity-determining region and the second framework region of the protein. We suggest that this cluster of substitutions was generated by a gene conversion in which a small segment of one gene was replaced with the homologous segment from another V kappa gene.

Immunoglobulin V region variants in hybridoma cells. II. Recombination between V genes

The mouse hybridoma line B1-8.delta 1 secretes a monoclonal IgD, lambda 1 anti-(4-hydroxy-3-nitrophenyl)acetyl (NP) antibody with defined idiotypic determinants. Two spontaneous V-region variants (B1-8.V1/V2) with altered idiotope pattern were selected and the structural variation was located to the variable region of the heavy chain. The amino acid sequences of the B1-8. delta 1 and variant heavy chain V regions were determined. The variant VH regions are identical. Wild-type and variant VH regions differ in 10 positions. Single amino acid exchanges are found in the first and second framework at positions 20 and 43. The majority of replacements (eight substitutions) is clustered in the second complementary-determining region (CDR 2). There are no differences in CDR 1 and CRD 3 and the JH region. The variant, which at first glance appears to have undergone a series of point mutations, arose by recombination, possibly gene conversion, between the rearranged VDJ gene of the wild-type (B1-8.delta 1) and a neighbouring germ line VH gene encoding all of the substitutions.

Multiple differences between the nucleic acid sequences of the IgG2aa and IgG2ab alleles of the mouse

To compare the structure of IgG2a alleles we have determined the complete DNA sequence of the constant region, coding sequence, and 3' untranslated region of a cDNA clone, pAB gamma 2a-1, which was derived from the C57BL/6 mouse strain (b allotype). This sequence was compared with the corresponding IgG2a DNA sequence of BALB/c origin (a allotype). The DNA sequences showed 10% differences, and the deduced protein sequences differed by about 15%. These differences were not evenly distributed: most differences were in the hinge region, the CH3 domain and the 3' untranslated region. It is evident that many alterations in the IgG2a alleles have occurred since the a and b haplotypes were separated--some of these changes were point mutations but some appear to have resulted from gene conversion of the IgG2ab allele by the IgG2bb allele.

Somatic mutation of immunoglobulin light-chain variable-region genes

A single germline immunoglobulin kappa-variable-region gene, VK167, is rearranged and expressed in two myelomas, MOPC167 and MOPC511. Only this single germline gene displays close homology to the expressed genes. Neither of the rearranged, functional genes, however, has a nucleotide sequence that is identical to the germline VK167 gene. Both active genes display several single-base-pair mutations with respect to the germline sequence. The nucleotide sequence data predict the alteration of a restriction-enzyme-recognition site within the VK167 gene between germline cells and cells producing the MOPC167 light-chain protein. Based on this restriction-site alteration, Southern blot analysis proves unambiguously that no gene present in the germline BALB/c mouse genome contains the exact VK167 nucleotide sequence found in cells committed to MOPC167 antibody production. Instead the alterations found in the expressed MOPC167 and MOPC511 V-region genes have apparently arisen by a process of somatic mutation during cellular differentiation. Since nucleotide alterations are found in framework and hypervariable portions of the variable region, the mechanism of somatic mutation is not limited to hypervariable sequences. In addition, Southern blot hybridization indicates that the observed mutations did not arise by recombinational events, but are single-base-pair substitutions. Based on the distribution of mutations that have been found in expressed immunoglobulin variable-region genes, a model that links the introduction of somatic mutations to DNA replication during the V-J joining event is proposed.

Evidence indicating independent assortment of framework and complementarity-determining segments of the variable regions of rabbit light chains. Delineation of a possible J minigene

Amino acid sequences of rabbit light chains show considerable evidence of independent assortment of framework (FR) and complementarity-determining (CDR) segments. This suggests that they are coded for by independent genetic units (minigaenes) and that individual light chains are assembled somatically by recombining these units. Identical FR sets with multiple members generally comprise chains with different specificities, whereas identical CDR sets tend to have chains of a single specificity. A J segment, which, by analogy with mouse light chains, is made up of the last two residues of CDR3 plus all of FR4, contained 18 different sets and could contribute to diversity generated by CDR3. The longest segment, FR3, had a very large number of sets. Evidence is presented showing that the number of sets could be substantially reduced by permitting FR3 to be formed by two independently assorting segments comprising residues 57-68 and 69-88.

binding constants of levans and D-fructo-oligosaccharides to BALB/c and NZB D-fructan-specific, myeloma proteins, determined by affinity electrophoresis

The association constants for the interaction of BALB/c (UPC 10, Y5476, W3082, and UPC 61) and NZB (PC 3660) myeloma anti-D-fructans in pure form, or in ascitic fluids, with high-molecular-weight levans (Ka) and with such low-molecular-weight compounds as rye-grass levan, inulin, sucrose, and D-fructo-oligosaccharides (Kia) were determined by affinity electrophoresis, measuring the extent of retardation of the D-fructan-specific band by levan and its restoration by the low-molecular-weight compounds and oligosaccharide haptens. With different levans,Ka values ranged from 1.14 X 10(5) TO 1.52 X 10(6) ML/g for PC 3660, 1.35 X 10(5) TO 6.45 X 10(5) mL/g for UPC 10, 1.0 X 10(4) to 7.9 X 10(4) mL/g for Y5476, 7.63 X 10(3) to 6.38 X 10(4) mL/g for W 3082, and 3.35 X 10(3) to 1.54 X 10(4) mL/g for UPC 61. The retarded, D-fructan-specific bands of W3082 and UPC 61 were restored by inulin, having beta-D-(2 leads to)-linkages, and rye-grass levan, having beta-D-(2 leads to 6)-linkages, and those of PC 3660, UPC 10, and Y5476 by rye-grass levan. The Kia values of inulin with W3082 and UPC 61 were 10 times those of rye-grass levan. The Kia values of inulin (3.65 X 10(5) M-1 for W3082, and 4.44 X 10(5) M-1 for UPC 61) were very similar to those of [beta-D-Fruf-(2 leads to 1)]2-beta-D-Fruf-(2 leads to 6)-D-Glc (3) (3.95 X 10(5) M-1 for W3082, and 4.5 X 10(5) M-1 for UPC 61). With sucrose and the D-fructo-oligosaccharides, the order of Kia values of W3082 and UPC 61 was 3 greater than beta-D-Fruf-(2 leads to 1)-beta-D-Fruf-(2 leads to 6)-D-Glc greater than sucrose greater than beta-D-Fruf-(2 leads to 6)-D-Glc. With rye-grass levan, Kia values were 4.25 X 10(5) M-1 for PC 3660, 2.7 X 10(5) M-1 for UPC 10, and 8.77 X 10(4) M-1 for Y5476. These results confirm earlier findings that W3082 and UPC 61 have dual specificity for beta-(2 leads to 1) and beta-(2 leads to 6) D-fructofuranosyl linkages, that PC 3660, Y5476, and UPC 1U have specificity for beta-(2 leads to 6) D-fructofuranosyl linkages, and that the combining sites of W3082 and UPC 61 are most complementary to the tetrasaccharide 3. That W3082 and Y5476 share the same, cross-reacting idiotype, although their combining sites differ in specificity, provides further evidence that these two properties do not run parallel.

Organization of kappa light chain genes in germ-line and somatic tissue

We studied the organization of the kappa light chain genes in germ-line (sperm) and somatic (embryo) tissues. We constructed a plasmid containing a DNA insert coding for the kappa chain MOPC 167 and used the Southern blotting technique to determine the organization of kappa variable and constant region genes. In the haploid genome of the mouse there is only one constant region gene detectable and it has the same organization in sperm and embryo DNAs. There are several variable region genes in sperm and embryo that are related to the Vk167 gene. The organization of the V genes in sperm and embryo DNAs is identical. These results show that there is no rearrangement of variable region genes (or "minigenes") during early embryogenesis.

Some sequence similarities among cloned mouse DNA segments that code for lambda and kappa light chains of immunoglobulins

A comparison between the cloned mouse DNA segments that were found to code for the lambda and kappa light chains of immunoglobulins established that there were seven short nucleotide sequences, two of which matched 6 out of 7, two 7 out of 8, two 8 out of 9, and one 9 out of 10 bases; these sequences were located either at homologous amino acid positions or at positions displaced by four amino acids or less. They all occurred in the framework regions (FRs), five next to the complementarity-determining regions (CDRs). Three of these were unique and did not occur elsewhere in the immunoglobulin nucleotides sequenced thus far or in DNA's of phage phi X174, phage G4, or simian virus 40. Five could serve as sites of joining by recombination or insertion of CDR to FR segments, and the invariant tryptophan that is the first residue of the second FR might serve as a sixth. These sites are consistent with the mini-gene or insertional hypotheses for the generation of antibody diversity but could also serve as points of recognition for a mutator enzyme or could serve to limit somatic mutation to the CDRs.