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Results for “germline sequencing”

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PubMed1994

Unravelling human T-cell receptor junctional region sequences.

Careful analysis of functional V delta 2-J delta 1 and V gamma 9-J gamma 1.2 rearrangements of peripheral T-lymphocytes showed high frequencies of leucine and valine at a fixed position in the V delta 2-J delta 1 junctional regions. This phenomenon remained unnoticed in the numerous published junctional regions for over several years. Because comparable preferential motifs might also occur in junctional regions of other T-cell populations in health and disease, more precise analysis of junctional region diversity is needed. For this reason we describe general guidelines for identification of the various elements in TcR junctional regions: D-gene-derived nucleotides (in case of TcR-beta and TcR-delta genes), P-region nucleotides, N-region nucleotides, and deletion of nucleotides by trimming of the rearranged gene segments. In addition, we summarized the known genomic germline sequences of rearranging TcR gene segments, which are necessary for proper application of the general guidelines. Subsequent analysis of the majority of published TcR junctional regions, allowed us to determine the composition and average insertion and deletion of nucleotides in genomic junctional regions. Because the protein junctional region instead of the genomic junctional region determines the actual specificity of TcR chains, the amino acid composition of the protein junctional regions of different types of TcR gene rearrangements was determined. This revealed some unexpected characteristics, such as the virtual absence of cysteine in all functional TcR junctional regions and increased or decreased frequencies of particular amino acid residues in specific TcR junctional regions. Application of the guidelines in combination with the summarized TcR germline sequences may contribute to uniformity in the analysis of junctional regions and may lead to important information concerning TcR specificity.

Amino Acid Sequence↗

PubMed1993

Restriction fragment length polymorphisms and single germline coding region sequence in VH18/2, a duplicated gene encoding autoantibody.

In this study, we analyze the restriction fragment length polymorphisms of VH18/2, a gene encoding the heavy chain of an anti-DNA antibody, and correlate that with the germline sequence of the gene's coding region. Oligonucleotides probes complementary to the CDR1 and to both the 5' and 3' halves of the CDR2 gene segments were hybridized under stringent conditions to genomic DNA digested with XbaI, and yielded polymorphic bands of 26, 24 and 18 kb with all three probes. Individuals had either one, two, or three bands in common in their genomic DNA, indicating duplication of VH18/2 genes at two sites within the IgH locus. While it is difficult to say which of the three polymorphic gene segments constitute an allelic pair, the 26 and 24 kb fragments were the most commonly seen (97% of individuals had one or both). VH18/2 is known to be over-represented in the expressed repertoire with very little nucleotide divergence from the germline sequence. In order to determine whether the observed RFLPs are due to sequence polymorphism of the VH18/2 coding region, and whether differences in the expressed genes arise from somatic mutation, size-selected genomic DNA containing the gene was cloned and sequenced. A single coding region sequence was found in the germline. The results of this study suggest that overexpression of VH18/2 may in part be due to its duplication. Like other genes encoding autoantibody, which are well conserved, nonpolymorphic and expressed early in programmed immunologic development, VH18/2 may be instrumental in the establishment or regulation of the immune repertoire.

Antibodies, Antinuclear↗

PubMed2003

IGHV1, IGHV5 and IGHV7 subgroup genes in the rhesus macaque.

The diversity of the antibody response is achieved, in part, by rearrangement of different immunoglobulin (Ig) genes. The Ig heavy chain is made up of a variable region (IGHV), a diversity region (IGHD) and a joining region (IGHJ). Human germline IGHV genes have been grouped into seven multigene subgroups. Size and usage of these subgroups is not equal, the IGHV3 subgroup is the most commonly used (36%), followed by IGHV1/7 (26%), then IGHV4, IGHV5, IGHV2, IGHV6 (15%, 12%, 4%, 3% respectively). The rhesus macaque (Macaca mulatta) is a useful non-human primate model for studies of infection and the database of germline Ig genes for the macaque is gradually growing to become a useful tool in the study of B-cell responses. The proportions of IGHV subgroup usage in the macaque are similar to those in man. Representatives from IGHV3 and IGHV4 subgroups for the macaque have been published, as have germline sequences of the IGHD and IGHJ genes. However, to date there have been no sequences published from the second largest IGHV subgroup, IGHV1. We report the isolation and sequencing of a genomic fragment containing an IGHV1 gene from the macaque. Polymerase chain reaction (PCR) primers designed from this sequence enabled us to amplify and sequence 25 new IGHV1 germline genes. We also isolated two IGHV7 genes, using the same primers, and two IGHV5 genes, using human IGHV5 primers.

Amino Acid Sequence↗

PubMed2006

A study of the structural correlates of affinity maturation: antibody affinity as a function of chemical interactions, structural plasticity and stability.

Mutations introduced in an antibody germline sequence as a result of somatic hypermutation could cause its derivatives to have an altered affinity for its target. Affinity maturation favors the selection of the antibodies which exhibit increased affinity. The mutations in 80 high affinity anti-thyroid peroxidase sequences derived from six germlines were analysed in terms of the physicochemical properties of the replacement residues, namely hydrophilicity, size and polarizability, and charge and polarity, in the context of its position and probable solvent accessibility. The effects of these substitutions were evaluated in terms of the resultant increased chemical interactivity potential of the affinity-matured antibodies relative to the germline. The results of the analysis would be useful in the rational design of antibodies and of other proteins for improved binding properties.

Amino Acid Sequence↗

PubMed1988

Structure of extrachromosomal circular DNAs excised from T-cell antigen receptor alpha and delta-chain loci.

Small polydisperse circular (spc) DNA was isolated from mouse thymocytes, fragmented by HindIII digestion and cloned into the vector. Sixty DNA clones were randomly selected from the 10,400 phage library. The average size of insert was one-fifth of the original circular molecule. Twenty spc-DNA clones were homologous to DNA probes derived from T-cell antigen receptor (TCR) alpha-chain loci. We have characterized nine clones by DNA sequencing; they contain new germline sequences of the TCR alpha-chain variable (V alpha) and joining (J alpha) gene segments and the products out of the recombination of a V alpha with a J alpha gene segment. An additional four spc-DNA clones carried a new rearranging gene of the TCR delta-chain that is located between V alpha and J alpha genes. At least nine of 60 DNA clones carried the recombination junction of a heptamer-heptamer head-to-head structure expected from an excised product of V-J joining. This shows that most extrachromosomal circular DNAs in the thymus are formed by a sequence-dependent recombination mechanism. We suggest that a functional T-cell receptor V alpha gene can be constructed by somatic random rearrangements through successive looping-out, excision and deletion.

Animals↗

PubMed2004

Sequence variant in the intron 10 of the RET oncogene in a patient with microfollicular thyroid carcinoma with medullar differentiation: implications for newly generated chi-like sequence.

Sequence alterations in the RET proto-oncogene are becoming increasingly important to clinical assessment of the malignant disease of the thyroid. A spectrum of mutations is necessary to establish comprehensive phenotype to genotype relationship relevant to diagnosis and therapy of thyroid malignancies. We aimed to append to the increasing database of these oncogenic lesions and, therefore, analyzed DNA from tumor tissue and constitutive DNA from a patient with thyroid carcinoma. Mutational screening and sequence characterization of the RET proto-oncogene was performed to include part of the intronic sequences. We report a germline sequence variant in DNA from the patient diagnosed with microfollicular thyroid carcinoma. The carcinoma presented not as fully developed medullar carcinoma (MTC) but as microfollicular carcinoma with tendency to evolve into MTC. We characterized the sequence variant located in the intron 10 of the RET oncogene as an A to G substitution denoted IVS10 + 4G. The described sequence alteration generates a chi-like sequence surrounded by several chi-like sequences with recombinational potential. Such alteration may be involved in the pathogenesis of the microfollicular carcinoma via genome destabilization through homologous recombination in the process of tumor progression. This result further substantiates the importance of the database correlating specific sequence variations in the RET gene with distinct disease phenotypes.

Adenocarcinoma, Follicular↗

PubMed1999

Low prevalence of the APC I1307K sequence in Jewish and non-Jewish patients with inflammatory bowel disease.

A germline sequence alteration at codon 1307 of the APC gene (I1307K) has been reported in 6-7% of the Ashkenazi Jewish population in the United States. This alteration is believed to predispose the APC gene to a secondary mutation at the same locus, resulting in an increased risk of colorectal carcinoma. There is an increased risk of colorectal carcinoma in patients with inflammatory bowel disease (IBD), a relatively large proportion of whom are Ashkenazi Jews. We therefore sought to determine whether the I1307K sequence variant occurred in the germline DNA of IBD patients. To our surprise, we found this sequence in only two of 267 patients with IBD (0.7%), occurring in only 1.5% of Jewish IBD patients. The I1307K sequence variant was not found in 67 patients with esophageal cancer, 53 patients with gastric carcinoma (13 MSI-H and 44 MSI-negative), or ten patients with sporadic MSI-H colon cancer. These findings suggest that the I1307K sequence is relatively rare in the germline of Jewish as well as non-Jewish IBD patients. It does not appear to contribute to the increased colorectal cancer risk present in these patients.

Colorectal Neoplasms↗

PubMed2005

Molecular case report: IgVH analysis in acute humoral and cellular liver allograft rejection suggests a selected accumulation of effector B cells and plasma cells.

Acute cellular (CLR) and humoral liver allograft rejection (HLR) are the most important immunological obstacles to successful liver transplantation. In HLR, serum antibodies play the central pathogenetic role. In CLR, CD3+ T lymphocytes drive the destructive immune response. Although CLR and HLR show different clinical symptoms and can be kept apart in most cases, they share histomorphological similarities. In CLR, hepatic B lymphocytes and plasma cells as well as B-cell-activating cytokines have recently been described, indicating that, in addition to T cells, antibody-mediated mechanisms might be involved. To analyze the impact of hepatic B cells in CLR and HLR, the immunoglobulin (Ig) variable (V)-region gene repertoire was determined from tissue of one case of CLR and one case of HLR. Complement deposits and lymphocytic infiltrate were determined using immunohistochemistry. T cells, B lymphocytes and plasma cells could be detected in both cases, whereas C3c and C4d deposits could only be demonstrated in the HLR case. The molecular analysis of 63 V-region genes showed that B cells in both allografts expressed selected V-gene repertoires. All sequences differed from the putative germline sequences by multiple somatic mutations. This suggests a clonal expansion of selected effector B cells in the portal tracts of liver allografts. Locally accumulated B cells and their antibodies might be involved in IgG-mediated complement activation in CLR and HLR.

Adult↗

PubMed1992

Variable region gene analysis of an isotype-switched (IgA) variant of chronic lymphocytic leukemia.

Chronic lymphocytic leukemia of B-cell origin (B-CLL) is generally thought to arise by neoplastic transformation of B lymphocytes, which express CD5 and have features of an early stage of B-cell differentiation. To study isotype-switched B-CLL as a potentially more differentiated variant, we performed genetic and functional immunoglobulin (Ig) gene analysis in two cases of CD5+ B-CLL in which the peripheral blood mononuclear cells (PBMC) secreted predominantly IgA (CLL-249) or IgG (CLL-412) when stimulated with pokeweed mitogen in vitro. By cDNA sequencing and by studies of CLL-heterohybridomas, CLL-249 expresses the heavy chain constant region C alpha as anticipated, while CLL-412 expresses C mu, not C gamma. In CLL-249, the expressed VH gene is 98% homologous to VH26, a germline VH3 gene that occurs frequently in the fetal repertoire, and which has been associated with anti-DNA specificity. The VL gene of CLL-249 is a lambda VL gene for which the germline sequence is not known. In CLL-412, the VH gene is 100% homologous to the VH1 gene of a published anti-DNA antibody (21/28), and is probably a germline gene sequence; the VL gene is 100% homologous to 15AVKI, also a germline gene. The supernatant antibody of the CLL-412 heterohybridoma is an IgM-kappa, which reacts with ssDNA and cardiolipin. The CLL-249 heterohybridoma secreted IgA-lambda, which bound none of the antigens tested, a finding that may be related to amino acid differences from the probable germline V genes. The demonstration of an in vivo isotype-switched variant, such as CLL-249, suggests that B-CLL may be a heterogeneous group of clonal disorders, of which less common variants may have features of more differentiated B-cell stages, such as isotype switching.

Amino Acid Sequence↗

PubMed1999

Primary diffuse large B cell lymphoma of the stomach: analysis of somatic mutations in the rearranged immunoglobulin heavy chain variable genes indicates antigen selection.

Gastric low grade MALT lymphomas show a pattern of somatic mutations in their rearranged immunoglobulin genes, indicative of antigen selection. This provides evidence for antigen stimulation in the lymphomagenesis. Gastric diffuse large B cell lymphomas develop secondary to low grade MALT lymphoma or de novo. To study whether antigen-selection is also a feature of primary diffuse large B cell lymphomas, we analysed somatic mutations in the rearranged immunoglobulin heavy chain (IgH) variable genes (VH). The rearranged VH genes of six cases of gastric primary diffuse large B cell lymphoma were amplified from genomic or complementary DNA by a VH gene family-specific polymerase chain reaction method. The PCR products were directly sequenced and were compared to published germline sequences to analyse somatic mutations. Similarly to low grade MALT lymphomas 5/6 primary diffuse large B cell lymphomas show a pattern of somatic mutation in their rearranged VH genes, indicative of antigen selection and suggesting a role for antigens in lymphomagenesis. One case showed bi-allelic VH gene rearrangements, which were non-functional due to extensive deletions. Antigen selection could not be demonstrated or excluded. Antigen selection is a common feature in most analysed primary diffuse large B cell lymphomas, although some heterogeneity in the mechanisms involved in the lymphomagenesis of gastric primary diffuse large B cell lymphomas has not been excluded entirely (case 4).

Aged↗

PubMed2004

A simple and rapid protocol for the sequence determination of functional kappa light chain cDNAs from aberrant-chain-positive murine hybridomas.

This protocol describes the application of a polymerase chain reaction to allow the cloning and sequencing of new functional kappa light chain cDNAs from murine hybridomas co-expressing aberrant endogenous kappa chain mRNAs. The presence of kappa light chain aberrant mRNAs can hinder or even prevent determination of the sequence of functional murine kappa light chain cDNAs amplified by PCR from hybridomas. The method described here employs a panel of kappa primers in the presence of molar excess of a primer complementary to the complementary determining region (CDR) 3 of the known aberrant chain sequence. Analysis of the PCR products reveals two bands for some reactions: one the functional, full-length kappa chain cDNA (approximately 400 bp) and another shorter (approximately 100 bp) band corresponding to short aberrant chain kappa CDR3-constant region. The full-length product is gel purified and cloned prior to sequencing and aligned with V-region germline sequences available in NCBI and GenBank databases. This method is used routinely in our laboratory and demonstrates consistency and reliability for sequence determination of kappa light chain V-gene cDNA of mAbs to diverse antigens. This protocol is a rapid and convenient method for determining the sequence of murine V kappa region genes from hybridomas expressing aberrant kappa chain mRNAs.

Amino Acid Sequence↗

PubMed1995

A human antibody specific for hepatitis C virus core protein: synthesis in a bacterial system and characterization.

The cDNA coding for the Fab fragment of the human B12.F8 antibody (Ab), directed against the putative nucleocapsid component (core protein) of hepatitis C virus (HCV), was cloned in the prokaryotic phagemid vector, pHEN-1, to obtain its expression in Escherichia coli. The functionality and specificity of the recombinant Ab, called B12Fab, were examined by Western blot and ELISA using recombinant HCV core protein as antigen. The specificity of B12Fab was further confirmed by ELISA with the 33-mer peptide epitope recognized by the original whole B12.F8 Ab. By immunofluorescence, the recombinant B12Fab was shown to recognize HCV core protein produced in cells transfected with HCV cDNA, indicating that the recombinant B12Fab is suitable as a diagnostic tool for tissue localization of the virus. The B12Fab also functioned when displayed on phage particles, providing the basis for future experiments of in vitro affinity maturation and selection of mutants. The variable chain coding regions of the recombinant B12Fab clone were sequenced and the V-gene usage was determined by comparison with the V kappa and VH germline sequences. The B12Fab V kappa chain belongs to the subgroup II and shows the highest degree of homology with the A3 germline gene, whereas the sequence of the VH chain is strictly related to that of the Humhv3019b18 gene of the VH3 family. These results are, to our knowledge, the first report of molecular cloning and characterization of a functional human Ab specific for an HCV antigen.

Amino Acid Sequence↗

PubMedDate not supplied

[Identification of immunoglobulin and T-cell receptor gene rearrangements--prerequisite for monitoring of minimal residual disease in Polish acute lymphoblastic leukemia patients based on European standards. Preliminary results].

OBJECTIVE: Initiation and popularization of routine molecular diagnostics of minimal residual disease (MRD) are currently one of the most urgent challenges in Polish hemato-oncology. The paper is aimed to present preliminary results of identification of immunoglobulin (Ig) and T-cell receptor (TCR) gene rearrangements and quantitative assessment of MRD levels in Polish children with acute lymphoblastic leukemia (ALL). The results are presented in the context of clinical significance of MRD study, current methodology of MRD assessment and standardization process in Western Europe. MATERIAL: DNA isolated from bone marrow / bone marrow mononuclear cells obtained at diagnosis from 26 children (25 B-precursor ALL, 1 T-ALL) aged 1.3-16.5 years. METHODS: PCR-heteroduplex analysis, based on standard BIOMED-1 and BIOMED-2 primer combinations and protocols for detection of rearrangements and clonality assessment; sequencing of clonal PCR products and comparison with germline sequences of Ig/TCR genes for identification of the rearranged genes andjunctional regions; real-time quantitative PCR (RQ-PCR) with the use of TaqMan probes for assessment of follow-up MRD levels (in 11 patients). RESULTS: Clonal TCRG, incomplete TCRD, Vdelta2-Jalpha, TCRB, IGK-Kde and IGH gene rearrangements were detected in 61, 61, 35, 13, 39 and 83% of patients, respectively, which was generally concordant with published data for patients of other European nations. CONCLUSIONS: There is an urgent need to broaden the scope of minimal residual disease study in Poland and to develop Polish standards of MRD diagnostics, based on current European experience and standards.

Adolescent↗

PubMed1993

Differential usage of an Ig heavy chain variable region gene by human B-cell tumors.

A monoclonal anti-idiotypic antibody has been raised that recognizes Igs with heavy chains encoded by a member of the VH4 family, the VH4-21 gene segment. The idiotope (Id) is detectable on a high percentage of early B cells in fetal spleen, and is expressed by certain autoantibodies, particularly cold-reactive anti-red blood cell antibodies. Therefore, it was of interest to investigate usage of this VH gene by neoplastic B cells; 81 chronic lymphocytic leukemias (CLLs) involving CD5+ B cells and 62 B-cell lymphomas of varying histologic type have been analyzed. The Id was expressed by only 3 of 81 (3.7%) of the CLLs, indicating a relatively low usage by these tumors. In contrast, the Id was expressed by 9 of 62 (14.5%) of the lymphomas across a range of histologic types, indicating a differential use of the VH4-21 gene among B-cell neoplasms. For three of the Id-positive lymphomas, each of a different histologic class, the nucleotide sequence of the tumor-derived VH gene was determined; the VH4-21 gene was identified, as expected. The sequence from the CLL was identical to the germline sequence, and the marginal zone lymphoma showed only 3 nucleotide changes, 2 of which gave rise to amino acid substitutions. In contrast, the sequence from the follicular lymphoma showed 29 nucleotide changes giving rise to 14 amino acid substitutions, which were scattered among the CDR and FW regions.

Antibodies, Monoclonal↗

PubMed2006

Antigen-receptor genes of the agnathan lamprey are assembled by a process involving copy choice.

Jawless vertebrates have acquired immunity but do not have immunoglobulin-type antigen receptors. Variable lymphocyte receptors (VLRs) have been identified in lamprey that consist of multiple leucine-rich repeat (LRR) modules. An active VLR gene is generated by the assembly of a series of variable gene segments, including many that encode LRRs. Stepwise assembly of the gene segments seems to occur by replacement of the intervening DNA between the 5' and 3' constant-region genes. Here we report that lamprey (Lethenteron japonicum) assemble their VLR genes by a process involving 'copy choice'. Regions of short homology seemed to prime copying of donor LRR-encoding sequences into the recipient gene. Those LRR-encoding germline sequences were abundant and shared extensive sequence homologies. Such genomic organization permits initiation of copying anywhere in an LRR-encoding module for the generation of various hybrid LRRs. Thus, a vast repertoire of recombinant VLR genes could be generated not only by copying of various LRR segments in diverse combinations but also by the use of multiple sites in an LRR gene segment for priming.

Alleles↗

PubMed1997

t(14;18) chromosomal translocation in follicular lymphoma: an event occurring with almost equal frequency both at the D to J(H) and at later stages in the rearrangement process of the immunoglobulin heavy chain gene locus.

bcl-2/IgH fusion is considered a genetic error which occurs at the diversity (D) to joining (J(H)) stage of the gene rearrangement process in the immunoglobulin heavy chain (IgH) gene locus. Translocations of the bcl-2 protooncogene to the IgH locus at ontogenetically later IgH gene rearrangements are thought to represent exceptions. In the present study we analysed the junctional nucleotide sequence of 18 bcl-2/IgH fusion genes identifiable by polymerase chain reaction performed on DNA extracted from diagnostic lymph node tissue of 14 follicular lymphoma patients. In all clones studied, segments of variable length were found interposed between bcl-2 and J(H) gene sequences. Nucleotide sequence data analysis and comparisons performed with the corresponding germline sequences using the GenBank/EMBL database revealed the presence of D segments in most of the bcl-2/IgH fusion genes under study (13/18). By the same kind of computer-aided analysis, previously unrecognized D segments were identified in many published junctional sequences. These results suggest that bcl-2/IgH fusion events are very prevalent in rather more differentiated stages in B-cell ontogeny than previously recognized.

Base Sequence↗

PubMed1992

Frequency and DNA sequence of tal-1 rearrangement in children with T-cell acute lymphoblastic leukemia.

Using nested polymerase chain reaction (PCR) a gene rearrangement named tal-1 deletion was found in five of 56 leukemic bone marrow samples from children with T-cell acute lymphoblastic leukemia (ALL). The DNA sequences of the PCR fragments consisted of the known conserved germline sequences in addition to short DNA insertions at the breakpoint region, which were different in each patient. Moreover, one patient was examined at diagnosis and at relapse 11 months later, revealing identical DNA sequences at the rearrangement site. The recombination site of the tal rearrangement therefore may be used as a genetic marker for detecting minimal residual disease in about 10% of T-cell ALL in childhood.

Base Sequence↗

PubMed2000

Production and characterization of monoclonal IgM autoantibodies specific for the T-cell receptor.

Natural autoantibodies to the T-cell receptor (Tcr) have been identified in all human sera. However, titer, epitope specificity, and isotype vary with physiological conditions, autoimmune diseases, and retroviral infections. The levels of anti-Tcr autoantibodies in rheumatoid arthritis (RA) patients are significantly higher than in normal individuals, and the autoantibodies are typically IgM. To obtain detailed information on these autoantibodies, we generated B-cell heterohybridomas secreting monoclonal IgM autoantibodies (mAAbs) from the synovial tissue and peripheral blood of RA patients. We selected clones secreting mAAbs that bound a major Vbeta epitope defined by a synthetic peptide that contains the CDR1 region of the Vbeta 8.1 gene product. From these we isolated a subset of seven mAAbs that bound a recombinant single-chain Valpha/Vbeta construct containing the peptide epitope and, also to JURKAT cells which express Vbeta 8.1. The mAAbs produced by these clones were distinct from each other in their V-region sequences. However, all the V regions were essentially identical to germline sequences in both the heavy and light chains. Heavy-chain CDR3 segments ranged in length from 17 to 26 residues, did not correspond to any known autoantibodies, and showed extensive N-region diversity in the V(D)J junctions. Five monoclonal autoantibodies use VH 3 genes, while the remaining two utilized VH 4 sequences. Light-chain variable regions used were Vkappa3 (two), Vlambda3 (four), and one Vlambda2. These autoantibodies derived their unique features from their CDR3 segments that could not be aligned with any known sequences.

Amino Acid Sequence↗