Evolution of the porcine (Sus scrofa domestica) immunoglobulin kappa locus through germline gene conversion.

Immunoglobulin (IG) gene rearrangement and expression are central to disease resistance and health maintenance in animals. The IG kappa (IGK) locus in swine (Sus scrofa domestica) contributes to approximately half of all antibody molecules, in contrast to many other Cetartiodactyla, whose members provide the majority of human dietary protein and in which kappa locus utilization is limited. The porcine IGK variable locus is 27.9 kb upstream of five IG kappa J genes (IGKJ) which are separated from a single constant gene (IGKC) by 2.8 kb. Fourteen variable genes (IGKV) were identified, of which nine are functional and two are open reading frame (ORF). Of the three pseudogenes, IGKV3-1 contains a frameshift and multiple stop codons, IGKV7-2 contains multiple stop codons, and IGKV2-5 is missing exon 2. The nine functional IGKV genes are phylogenetically related to either the human IGKV1 or IGKV2 subgroups. IGKV2 subgroup genes were found to be dominantly expressed. Polymorphisms were identified on overlapping BACs derived from the same individual such that 11 genes contain amino acid differences. The most striking allelic differences are present in IGKV2 genes, which contain as many as 16 amino acid changes between alleles, the majority of which are in complementarity determining region (CDR) 1. In addition, many IGKV2 CDR1 are shared between genes but not between alleles, suggesting extensive diversification of this locus through gene conversion.

A Proposed New Nomenclature for the Immunoglobulin Genes of Mus musculus.

Mammalian immunoglobulin (IG) genes are found in complex loci that contain hundreds of highly similar pseudogenes, functional genes and repetitive elements, which has made their investigation particularly challenging. High-throughput sequencing has provided new avenues for the investigation of these loci, and has recently been applied to study the IG genes of important inbred mouse strains, revealing unexpected differences between their IG loci. This demonstrated that the structural differences are of such magnitude that they call into question the merits of the current mouse IG gene nomenclatures. Three nomenclatures for the mouse IG heavy chain locus (Igh) are presently in use, and they are all positional nomenclatures using the C57BL/6 genome reference sequence as their template. The continued use of these nomenclatures requires that genes of other inbred strains be confidently identified as allelic variants of C57BL/6 genes, but this is clearly impossible. The unusual breeding histories of inbred mouse strains mean that, regardless of the genetics of wild mice, no single ancestral origin for the IG loci exists for laboratory mice. Here we present a general discussion of the challenges this presents for any IG nomenclature. Furthermore, we describe principles that could be followed in the formulation of a solution to these challenges. Finally, we propose a non-positional nomenclature that accords with the guidelines of the International Mouse Nomenclature Committee, and outline strategies that can be adopted to meet the nomenclature challenges if three systems are to give way to a new one.

Serologic variations in kappa light chains of various Mus species correlate with differences in gene structure.

Kappa light chains were investigated in sera of several groups of wild derived mouse strains by radioimmunological analysis using xenogeneic anti-mouse kappa light chain antibodies. Although the majority of strains tested expressed serologically indistinguishable kappa chains, several significant exceptions were observed. Anti-kappa chain reactivity was not detectable in normal sera of Mus caroli and Mus cervicolor species using specific antiserum. These strains express a variant of the kappa light chain. Some serologic variation was also observed in kappa chains from members of the subgenus Nannomys. Southern blot analyses using C kappa and J kappa probes indicated different patterns of hybridization in strains that were serologically distinguishable. Mus caroli and Mus cervicolor DNAs digested with the enzymes EcoRI or BamHI show variation from BALB/c and most other mouse strains tested in the size of the hybridizing fragments. This correlation between serologic and blotting analyses is no longer found in SJL and SPE strains, which show variation in BamHI cleavage but not at the serological level. The majority of laboratory and wild derived mice analyzed have the same pattern of hybridization. Taken together our results may also have implications for the phylogenetic classification of wild type mouse strains.

Organization and genomic complexity of sheep immunoglobulin light chain gene loci.

Sheep is the representative of the artiodactyla and is an agriculturally important animal, but limited knowledge is available with regard to its immunoglobulin genes and their expression mechanisms in the sheep. Based on the recently released sheep genome, we have characterized the genomic organization of the sheep immunoglobulin light gene loci. The sheep Igλ locus, located on chromosome 17, contains 2Cλ segments each preceded by a Jλ, but the Cλ2 appears to be a pseudogene. A total of 42 Vλ segments (14 potentially functional genes, 1 ORF and 27 pseudogenes) were identified. In contrast, the Igκ locus on chromosome 3 contains only a single Cκ gene, 3 Jk segments and 13 Vκ segments (8 potentially functional genes and 5 pseudogenes). Analysis of junctions of the recombined VJ transcripts revealed a restricted Vλ4-Jλ1-Cλ1 recombination and Vk6-Jk3-Cκ recombination, respectively encode most of λ and κ chain antibody repertoire in the sheep despite more potential germline encoded combinatorial diversity. Therefore, the sheep may use gene conversion in combination with somatic hypermutation for antibody repertoire formation.

A general method allowing the design of oligonucleotide primers to amplify the variable regions from immunoglobulin cDNA.

The amplification of variable regions of immunoglobulins by reverse transcription polymerase chain reaction (RT-PCR) has become an invaluable technique either for the cloning of monoclonal antibodies (mAbs), or for the building of single-chain fragment variable (ScFv) libraries. Numerous applications have been described either for studying the antigen-antibody interactions or for medical purposes, with the recent development of recombinant antibodies for therapeutic use. Several publications by different groups have reported primer sequences to perform such amplification, but the strategy used to design these primers, and particularly the way of performing the necessary alignments, generally appear poorly detailed. In the present work, we propose a rational method of designing primers in order to amplify the variable region of heavy chain (VH) and variable region of light chain (VL) domains for framework 1 (FR1) of immunoglobulins. The described sets of primers have been designed to hybridize with the entire VH and VL mouse repertory without modification of amino acids since amino acids of framework 1 play a role in the folding, and thus in the functionality, of recombinant antibody. These primers have been applied to the cloning of monoclonal antibodies previously produced in the laboratory. This approach can be extended to other species or members of the immunoglobulin superfamily.

Human kappa light chain subgroup analysis with synthetic peptide-induced antisera.

All human kappa light chains belong to one of four subgroups, classified according to their amino acid sequences or by reactivity with adsorbed heteroantisera. The structural basis for the subgroup distinction by antisera is unknown. Therefore, to create anti-kappa subgroup antibodies with predefined specificity, we immunized rabbits with synthetic peptides which correspond to sequences within the first framework region of prototype kappa I, II, III, and IV light chains. The peptide-induced antisera recognized primary sequence-dependent kappa subgroup determinants. They correctly predicted the amino acid sequence in the first framework region of two kappa light chains. By Western immunoblotting and enzyme-linked immunoassay the antisera also identified previously typed, monoclonal light chains of different subgroups with complete specificity. These reagents, define a site of kappa subgroup distinction and represent a potent tool for the characterization of light chain heterogeneity.

The immunological characterization of human antibodies to factor VIII isolated by immuno-affinity chromatography.

Nine human antibodies to factor VIII were isolated from haemophilic plasmas by affinity chromatography and gel filtration and six were subsequently subjected to immunological characterization. Three partially purified preparations were similarly characterized. Eight of the antibodies were characterized as being exclusively IgG and one preparation was found to contain IgM. Seven of the antibodies contained only a single light chain type, four being of type lambda and three of type kappa. Two antibody preparations contained both kappa and lambda light chains. In four of the preparations, only a single heavy chain sub-class could be demonstrated, three of IgG3 and one of IgG4. Of the remainder, three were a mixture of IgG3 and IgG4 sub-classes and one contained both IgG2 and IgG4. IgG sub-classification could not be achieved with the IgM-containing preparation. These results demonstrate a restricted heterogeneity of light and heavy chains in human antibodies to factor VIII.

Production and characterization of the monoclonal antibody against SGP120, a novel serum protein.

A monoclonal antibody designated B1.9.E-2 was produced and characterized to facilitate study of the immunizing antigen-a serum glycoprotein of 120 kDa (sgp 120) of unknown function. The antibody, produced in mice, reacts with 1-2 epitopes located in the N-terminal region of the sgp 120 molecule. The affinity of the reaction, as determined by Scatchard analysis, is Ka = 1.13 x 10(10) I/M and is of a hydrophobic nature. The monoclonal antibody can be purified to a high degree by a modified caprylic acid method and by protein G FPLC chromatography column. B1.9.E-2 does not trigger the complement cascade, as determined by C3 RIA and immune complex solubilization assays. Both affinity purified (C4b Sepharose) and chromatographically isolated (using jacqualine agarose) sgp 120 were recognized by B1.9.E-2. The monoclonal antibody can be utilized for affinity purification of sgp 120, for detection of intact or cleaved sgp 120 in biological samples of healthy and ill individuals, and for the number of functional and neutralization assays aimed at resolving the physiologic role of sgp 120.

Nomenclature of the human immunoglobulin kappa (IGK) genes.

'Nomenclature of the Human Immunoglobulin Kappa (IGK) Genes', the 17th report of the 'IMGT Locus in Focus' section, provides the first complete list of all the human IGK genes. In the most frequent haplotypes, the human IGK locus spans 1,820 kb and the IGKV genes are organized in two clusters separated by 800 kb. In those haplotypes where both the proximal and distal IGKV clusters are present, the total number of human IGK genes per haploid genome is 82 (107 genes if the orphons are included) of which 37-41 are functional. If only the proximal IGKV cluster is present, which is found in a rare haplotype, the total number of genes per haploid genome is 46 (71 genes if the orphons are included) of which 23-25 genes are functional. IMGT/HUGO gene names and definitions of the human IGK genes on chromosome 2p11.2, and IGK orphons on chromosomes 1, 2, 15, and 22 are provided with the gene functionality and the number of alleles according to the rules of the IMGT Scientific chart, with the accession numbers of the IMGT reference sequences, and the accession ID of the Genome Database GDB and NCBI LocusLink databases in which all the IMGT human IGK genes have been entered. The tables are available at the IMGT Marie-Paule page from IMGT, the international ImMunoGeneTics database (http://imgt.cines.fr:8104) created by Marie-Paule Lefranc, Université Montpellier II, CNRS, France.

Support vector machines with selective kernel scaling for protein classification and identification of key amino acid positions.

MOTIVATION: Data that characterize primary and tertiary structures of proteins are now accumulating at a rapid and accelerating rate and require automated computational tools to extract critical information relating amino acid changes with the spectrum of functionally attributes exhibited by a protein. We propose that immunoglobulin-type beta-domains, which are found in approximate 400 functionally distinct forms in humans alone, provide the immense genetic variation within limited conformational changes that might facilitate the development of new computational tools. As an initial step, we describe here an approach based on Support Vector Machine (SVM) technology to identify amino acid variations that contribute to the functional attribute of pathological self-assembly by some human antibody light chains produced during plasma cell diseases. RESULTS: We demonstrate that SVMs with selective kernel scaling are an effective tool in discriminating between benign and pathologic human immunoglobulin light chains. Initial results compare favorably against manual classification performed by experts and indicate the capability of SVMs to capture the underlying structure of the data. The data set consists of 70 proteins of human antibody kappa1 light chains, each represented by aligned sequences of 120 amino acids. We perform feature selection based on a first-order adaptive scaling algorithm, which confirms the importance of changes in certain amino acid positions and identifies other positions that are key in the characterization of protein function.

Prognostic significance of immunologic phenotype in hairy cell leukemia: does it exist?

Of 94 hairy cell leukemia (HCL) patients studied for immunologic phenotype of their hairy cells, 89 patients had B cell markers and five patients were both surface immunoglobulin (slg) negative and E rosette negative. Forty of the 77 cases that had the heavy chains individually determined had IgG only (52.0%); 23 others had IgG in addition to other Ig heavy chains. Seventy-nine patients had monoclonal light chains; 65 with kappa chain and 14 with lambda chain. The only significant difference with respect to survival among the various slg groups occurred between the kappa chain and the lambda chain groups. Within the first 46 months after diagnosis of HCL, 20 deaths occurred among the 65 kappa chain patients, whereas the first and only death among the lambda chain patients occurred at 68 months after diagnosis. The only clinical or laboratory parameter that was significantly different between these two immunologic subgroups was the incidence of infections. Among the lambda chain patients, an infectious complication rate of 28.6% was observed subsequent to the diagnosis of HCL, whereas this rate was 68.8% in kappa chain patients (P = .005). The survival of lambda patients was found to exceed that of the kappa patients by the generalized Wilcoxon test (P = .03). However, when the log rank test was used, no significant difference was detected (P = .13).

[The primary structure of a monoclonic immunoglobulin-L-chain of subgroup IV of the kappa type (Bence-Jones protein Len.)]. / Len.)Len

The complete amino acid sequence of Bence-Jones protein Len. was established by sequential analysis of tryptic and chymotryptic peptides. The result of these experiments and the comparative sequence analysis with the other 17 completely determined kappa-proteins is incompatible with the serological typisation of protein Len. as a member of subgroup II: There are 18 positions in protein Len. than cannot be associated with any one of the subgroups kappaI, kappaII or kappaIII. Also the average amino acid exchange rate between protein Len. and these subgroups is in the same range as the average amino acid exchange rate between these subgroups. Therefore Bence-Jones protein Len. is the first completely determined representative of a new IV. kappa-type subgroup. The variability of immunoglobulins follows a structural principle in which the single point mutations responsible for the variability are linked. The present paper contains the exact analysis of the linked point mutations within the so far best-investigated subgroup, kappaI (12 completely sequenced proteins). These linked exchanges allow the arrangement of the kappaI proteins in 4 subgroups and their further subdivision. The regularity of this amino acid sequence pattern can only be explained by an evolutionary origin of antibody variability. On the basis of this evolutionary mechanism the relationship of immunoglobulins can be depicted in a phylogenetic tree. Such a tree was therefore constructed for the 18 completely determined Bence-Jones proteins of kappa-type, for the first time taking into account Bence-Jones protein Len. Its topology is in complete agreement with the results of the comparative sequence analysis.

Chemical typing of human kappa light chain subgroups expressed by human hybrid myelomas.

Hybrids between human spleen cells and the non-secretor NSO mouse myeloma, and also between the rat non-secretor line YB2/O and human peripheral blood cells were prepared. After a month in culture very few hybrids retained the ability to secrete the human kappa light chain. From these, clones could be derived which remained stable over several months of continuous culture. On incorporating [3H]-Leu into the culture medium the cells secrete large amounts of radioactive light chain. It is shown that, even without dialysis, the purity of the preparation is sufficient for an automatic N-terminal sequence analysis at the radioactive level. From the pattern of distribution of leucine in the first twenty-two amino acid residues, it is possible to assign the synthesized light chains to one of the four established human subgroups. The method permits a fast and simple classification of human light chains secreted by hybrid myelomas. Although tested with rodent x human hybrids, we see no reason why the method could not equally apply to human x human hybrids.

Serologic and chemical differentiation of human lambda III light chain variable regions.

Human lambda L chains of a major V lambda subgroup, V lambda III, have been differentiated serologically and chemically into three V lambda III sub-subgroups designated V lambda IIIa, V lambda IIIb, and V lambda IIIc. Antisera prepared against lambda III Bence Jones proteins were obtained that recognized distinctive V lambda III-related epitopes expressed by monoclonal lambda III L chains. After appropriate absorption, these reagents were rendered specific for three distinct populations of lambda III proteins--lambda IIIa, lambda IIIb, and lambda IIIc. The antisera were used in comparative immunodiffusion analyses of 28 monoclonal lambda III L chains, 10 of which were classified as lambda IIIa, 4 as lambda IIIb, and 14 as lambda IIIc. The isotypic nature of the three lambda III sub-subgroups was demonstrated serologically through analyses of lambda-chains derived from the serum IgG molecules of normal individuals. The amino acid sequences of five serologically classified lambda III chains, which included members of the three V lambda III sub-subgroups, had been previously determined. This information, in addition to our establishment of the complete (or virtually complete) V region sequence of 15 and the partial sequence of eight other lambda IIIa, lambda IIIb, and lambda IIIc proteins, made it possible to correlate chemical data with serologic classification. Proteins within each of the three serologically-classified lambda III sub-subgroups typically possessed a high degree (approximately 83%) of intra-sub-subgroup sequence homology that included both framework and complementarity determining region residues. Furthermore, within the framework and complementarity determining regions, sub-subgroup-specific residues were identified. Taken together, these data reveal that the human V lambda III genome consists of (at least) three distinct V lambda IIIa, V lambda IIIb, and V lambda IIIc germline genes that encode for lambda IIIa, lambda IIIb, and lambda IIIc L chains, respectively.

Shoulder-pad sign of amyloidosis: structure of an Ig kappa III protein.

While amyloid infiltration of articular structures is rare, the 'shoulder-pad' sign resulting from periarticular soft tissue amyloid deposition is essentially pathognomonic for immunogloblin (Ig) (AL) amyloidosis. We report the characterization of an amyloid protein (GRA) which produced articular amyloid deposits and the shoulder-pad sign. Amyloid fibrils were isolated from soft tissue shoulder mass of a patient with systemic AL amyloidosis. The fibrils were solubilized in guanidine HCl and proteins separated by Sepharose chromatography. Amino acid sequence of fractionated protein was determined after tryptic digestion. Sequence analysis of the major amyloid protein yielded a kappa III Ig light chain structure. The entire variable region (VL) plus the constant region (CL) to residue 207 was identified; but lesser amounts of CL than VL were present. A number of amino acid residues previously not observed in kappa III VL proteins, plus a two amino acid insert (95A, 95B), were identified. Kappa III VL amyloid proteins are rare and may show an increased predilection for soft tissue deposition. While several unique amino acid residues that were identified in protein GRA may contribute to soft tissue amyloid deposition, no definite pattern is obvious from comparison with other reported kappa III amyloid proteins.

Generation of the primary antibody repertoire in rabbits: expression of a diverse set of Igk-V genes may compensate for limited combinatorial diversity at the heavy chain locus.

In mouse and human, generation of combinatorial diversity through use of different heavy and light chain variable region genes in immunoglobulin rearrangements can be a major contributor to the primary antibody repertoire. In rabbits, the contribution of the combinatorial mechanism to heavy chain diversity is minimal, as only a few Igh-V genes are rearranged and expressed. To investigate the contribution of combinatorial diversity toward generation of the rabbit V(kappa) repertoire, we constructed five genomic libraries from rabbit kidney DNA and 1 cDNA library from the bone marrow of a 1-day-old rabbit using a series of polymerase chain reaction-based strategies. Our analyses indicate that most of the sequences that we recovered from our libraries belong to a single family and some are extremely similar. The actual number of germline Igk-V genes is potentially greater than our conservative estimate of at least 39, 28 of which we found expressed as mRNA. The germline Igk-V genes display different lengths of the coding region 3' of Cys 88 ranging from 7 to 12 amino acids, resulting in CDR3 length heterogeneity among functional V(kappa)J(kappa) sequences ranging from 8 to 15 amino acids. Some of the V(kappa)J(kappa) junctions had N and P nucleotide additions. Thus, in contrast to limited combinatorial diversity of its heavy chain, the rabbit can draw upon a diverse set of germline Igk-V genes. The kappa light chain has the potential to be a major contributor toward generation of the antibody specificities of the rabbit pre-immune repertoire.