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PubMed2000

Molecular evolution in the hypervariable regions of fetuin: comparison between human and African green monkey fetuin.

Sequences of fetuin cDNA and its deduced amino acid residues from the African green monkey cell line Vero were found to differ by 7.3% and 12.9%, respectively, from the corresponding human sequences. Most amino acid substitutions were clustered within a small segment of the third domain (D3). Calculations of nonsynonymous and synonymous nucleotide substitution rates suggest that this small segment was mutated under positive selection. cDNAs encoding alpha1-antitrypsin, beta-actin and the sequences of intron 4 of alpha1-antitrypsin gene in human liver and Vero cells were also investigated. The results substantiated the positive selection imposed on the D3 segment.

Actins↗
PubMed1982

Primary structure of the variable part of an amyloidogenic Bence-Jones Protein (Mev.). An unusual insertion in the third hypervariable region of a human kappa-immunoglobulin light chain.

The complete amino acid sequence of the variable region of Bence-Jones protein Mev. from a patient suffering from multiple myeloma and generalized amyloidosis is presented. The amino acid sequence of the Bence-Jones protein Mev. is related to other human kappa-immunoglobulin L-chains of subgroup I. With valine established in Position 191 of the constant region, it is of the Inv (3) allotype. Two types of the Bence-Jones protein Mev. were found, one beginning with the typical N-terminal aspartic acid, and another lacking the N-terminal tripeptide and commencing with methionine in Position 4. A unique insertion of glutamic acid after Position 95 was found in the Bence-Jones protein. This is the position where the V- and J-gene segments join. The J-region of Bence-Jones protein Mev. exhibits some marked differences to the five J-regions recently established by nucleic acid sequencing. This suggests, that there must be considerable polymorphism in human kappa-J-genes. The amyloid fibril protein from the same patient (A Mev.) has also been sequenced up to Position 27. It was found to be identical to the sequence of Bence-Jones protein Mev. commencing with aspartic acid. The molecular mass of the amyloid fibril protein was found to be between 11 000 and 12 000 Da as estimated by gelfiltration and dodecyl sulfate-polyacrylamide electrophoresis.

Amino Acid Sequence↗
PubMed2001

Induction of cross-reactive humoral immune response by immunization with mimotopes of the hypervariable region 1 of the hepatitis C virus.

Hepatitis C Virus (HCV) is a major cause of chronic hepatitis, liver cirrhosis and hepatocellular carcinoma, worldwide, and the development of an effective vaccine represents a high priority goal. The Hyper Variable Region 1 (HVR1) of the second Envelope protein (E2) of HCV contains a principal neutralizing determinant, but it is highly variable among different isolates and it is involved in the escape from host immune response. Thus, to be effective, a vaccine should elicit a cross-reacting humoral response against the majority of viral variants. We show that it is possible to achieve a broadly cross-reactive immune response in rabbits by immunization with mimotopes of the HVR1. selected from a specialized phage library using HCV patients' sera. At least some of the cross-reacting anti-mimotope antibodies, elicited in rabbits, recognize discontinuous epitopes in a manner similar to those induced by the virus in infected patients.

Amino Acid Sequence↗
PubMed2001

Relationship between autoimmune hepatitis and HLA-DR4 and DRbeta allelic sequences in the third hypervariable region in Chinese.

AIM: To analyze the association of HLA-DRB1 with autoimmune hepatitis (AIH) in patients from China. METHODS: In 32 patients and 48 healthy controls, polymerase chain reaction amplification with sequence-specific primers (PCR-SSP) was performed to examine the association of certain alleles or polymorphic sequences of HLA-DRB1 with AIH. RESULTS: HLA-DRB1 typing by PCR-SSP showed that DR4 had a significantly increased frequency among patients with AIH versus healthy control (46.9% versus 20.8%; relative risk = 3.35, P=0.014). In subtypes of DR4, there was a trend of increase in the gene frequency of DRB1 0405 in patients with AIH versus healthy controls (21.9% vs 6.3%, P=0.04, but P(c) =0.08). In addition, a significant increase was found in the alleles frequency encoding QRRAA from the third hyperpolymorphic region of DR4 in the patients with AIH (86.7% of DR4 positive patients vs 40.0% in DR4 positive controls, P=0.016, P(c)=0.028, RR=9.75). CONCLUSION: AIH in Chinese is associated with HLA-DR4. There is a relationship between QRRAA sequence within the third hyperpolymorphic region of the DRB allele and AIH in Chinese.

Alleles↗
PubMed2000

Preferential recognition of TCR hypervariable regions by human anti-idiotypic T cells induced by T cell vaccination.

T cell responses to myelin basic protein (MBP) are potentially involved in the pathogenesis of multiple sclerosis (MS). Immunization with irradiated MBP-reactive T cells (T cell vaccination) induces anti-idiotypic T cell responses that suppress circulating MBP-reactive T cells. This T cell-T cell interaction is thought to involve the recognition of TCR expressed on target T cells. The study was undertaken to define the idiotypic determinants responsible for triggering CD8+ cytotoxic anti-idiotypic T cell responses by T cell vaccination in patients with MS. A panel of 9-mer synthetic TCR peptides corresponding to complementarity-determining region 2 (CDR2) and CDR3 of the immunizing MBP-reactive T cell clones were used to isolate anti-idiotypic T cell lines from immunized MS patients. The resulting TCR-specific T cell lines expressed exclusively the CD8 phenotype and recognized preferentially the CDR3 peptides. CDR3-specific T cell lines were found to lyze specifically autologous immunizing MBP-reactive T cell clones. The findings suggest that CDR3-specific T cells represented anti-idiotypic T cell population induced by T cell vaccination. In contrast, the CDR2 peptides were less immunogenic and contained cryptic determinants as the CDR2-specific T cell lines did not recognize autologous immunizing T cell clones from which the peptide sequence was derived. The study has important implications in our understanding of in vivo idiotypic regulation of autoimmune T cells and the regulatory mechanism underlying T cell vaccination.

Amino Acid Sequence↗
PubMed1999

[Polymorphism of hypervariable region in D-loop of mitochondrial DNA].

DNA sequences of PCR products from mitochondrial DNA (mtDNA) of 80 healthy Japanese volunteers (40 pairs, mother and child) were determined by the direct sequencing method for polymorphism. Thirty (15 pairs) of 80 samples analyzed showed a T-to-C transition at position 16189 (T16189C) of the C-stretch region in the hyper-variable region of mtDNA. For seven pairs randomly selected from the 15 T16189C pairs (C-stretch) and a single pair without the transition (non C-stretch), PCR products from the D-loop region were cloned and then sequenced. The repeat number of C in the C-stretch region was found to show heteroplasmy by sequencing multiples clones from each mtDNA. Statistical analyses of the distribution patterns of the repeat number revealed no significant differences between the mother and child in each lineage but significant differences between the lineages. The seven lineages could be then classified into four groups. The result of our data confirmed the existence of heteroplasmic polymorphism in the C-stretch region and the inheritance of the heteroplasmy from mother to child. Therefore, the analysis of heteroplasmy is applicable to individual identification.

Child↗
PubMed1992

Peptide sequences from the hypervariable regions of two monoclonal anti-idiotypic antibodies against the thyrotropin (TSH) receptor are similar to TSH and inhibit TSH-increased cAMP production in FRTL-5 thyroid cells.

Monoclonal antibodies, D2 and 4G11, selected by the autoantiidiotypic approach following injection of thyrotropin (TSH) into mice, mimic TSH in binding to receptors on thyroid membranes. Based on TSH receptor transfection studies, D2 and 4G11 show unequivocal specificity for the TSH receptor. To see if the complementary determining regions (CDRs) of these antibodies share any primary sequence similarities to regions of TSH critical for receptor binding, we deduced the primary structure of the variable regions of D2 and 4G11 by sequencing the immunoglobulin mRNA. We found that CDR1 of 4G11K and CDR2 of D2 mu show sequence similarity to regions of TSH alpha and TSH beta that had been previously implicated in the interaction of the hormone with its receptor. We tested the inhibitory effects of synthetic peptides from D2 mu-CDR2 and 4G11K-CDR1 on the binding of the corresponding antibodies to rat thyroid FRTL-5 cells and found an EC50 of 0.1 and 1 microM, respectively. TSH-derived peptides with similarity to D2 mu-CDR2 and 4G11K-CDR1 showed a significant but lesser effect on the binding of 4G11 or D2 to thyroid cells. Additionally, we tested the effects of the CDR peptides and TSH-derived peptides on TSH-stimulated cAMP production in FRTL-5 cells and found that D2 mu-CDR2 and 4G11K-CDR1 inhibited this activity, D2 mu-CDR2 most strongly (EC50 10 microM). Thus, linear sequences from the CDRs of these autoantiidiotypic antibodies with similarity to sequences from both subunits of TSH appear to interact with the TSH receptor. These data support previous studies indicating the complexity of the interaction between TSH and its receptor and advance earlier findings that such immunologic approaches are useful in dissecting receptor-ligand interactions.

Animals↗
PubMed1991

Amplification by the polymerase chain reaction of hypervariable regions of the human genome for evaluation of chimerism after bone marrow transplantation.

We combined the polymerase chain reaction (PCR) with oligonucleotide hybridization as a novel and sensitive technique to evaluate posttransplant chimerism. Specific oligonucleotides for hybridization were synthesized homologous to tandemly repetitive core sequences of regions with a variable number of tandem repeats (VNTRs). Polymorphisms at such loci result from allelic differences in the number of repeats. Primers flanking the repeat region of each of the corresponding VNTRs were used for amplification. Recipient and donor pretransplant DNA and recipient posttransplant DNA were amplified. The resultant fragments were analyzed after gel electrophoresis either by hybridization in-gel or after Southern transfer. To confirm our findings, we also performed standard assays of restriction fragment length polymorphisms (RFLPs). Evaluation of 13 selected cases indicated mixed chimerism (4), complete chimerism (5), recurrence of leukemia (2), and endogenous repopulation of hematopoiesis (2) after marrow transplantation. Sensitivity of the method was determined by mixing various proportions of recipient and donor DNA; the limit of detection of the minor component in a mixture was 0.1%. PCR data correlated with RFLP data in all cases except two in which PCR proved more sensitive than RFLP. PCR amplification of VNTRs combined with oligonucleotide hybridization is a novel technique for documenting posttransplant chimerism and has advantages over RFLP analysis: high sensitivity, use of small amounts of DNA (250 ng), ease of preparation of DNA, elimination of need for restriction enzymes, and the ability to complete studies in 2 days.

Base Sequence↗
PubMed1991

[Use of DNA amplification by PCR in the study of the hypervariable region (VNTR) in a forensic medicine setting. Experience with 2 systems: Apo B and YNZ 22].

The PCR method has been applied to amplify two Variable-number-Tandem-Repeat (VNTR) sequences. The high polymorphism of these VNTR systems can be usefully applied in medical legal fields such as paternity testing and individual identification. The VNTR systems utilized were: ApoB and YNZ 22. The study was conducted on a three-generation family of thirteen members, whose relationship was previously established using conventional blood systems. The results confirm the Mendelian inheritance of the alleles found and the suitability of the PCR method for forensic purposes.

Alleles↗
PubMed1991

Specific amino acid residues in the second hypervariable region of HLA-DQA1 and DQB1 chain genes promote the Ro (SS-A)/La (SS-B) autoantibody responses.

In order to define the HLA-DR and DQ alleles, as well as the specific DQA1 and DQB1 chain genes involved in the anti-Ro/La autoantibody responses, RFLP analysis and sequence-specific oligonucleotide typing was carried out on 58 Caucasians and 48 American blacks with SLE or Sjögren's syndrome and anti-Ro antibodies. Among both Caucasian and black patients, the highest relative risk for the anti-Ro response (both with and without accompanying anti-La) was conferred by heterozygosity for the DQw2.1 (in linkage disequilibrium with HLA-DR3) and DQw6 (a subtype of DQw1) alleles compared with either 269 normal race-matched controls or 80 anti-Ro negative SLE/Sjögren's syndrome patients. Analysis of individual DQA1 and DQB1 chain alleles revealed that DQA1*0501 and DQB1*0201 were most frequent, followed by DQA1 and DQB1 alleles comprising DQw6. In patients not possessing DQw2.1 and/or DQw6 alleles, HLA-DQB1*0302 and HLA-DQA1*0401 (especially in blacks) were significantly increased. Nucleotide sequence analysis of these associated alleles showed that 100% of patients with anti-Ro had a glutamine residue at position 34 of the outermost domain of the DQA1 chain and/or a leucine at position 26 of the outermost domain of the DQB1 chain. Patients with anti-Ro plus La were more likely to have all four of their DQA1/DQB1 chains containing these amino acid residues than either anti-Ro-negative SLE patients or controls. These data implicate specific amino acid residues on both DQA1 and DQB1 chains located in the floor of the Ag binding cleft of the HLA-DQA1:B1 heterodimer and further suggest a role for "gene dosage" in the anti-Ro (+/- La) autoantibody response.

Alleles↗
PubMed1989

[DNA fingerprints and hypervariable regions: genetic marker with many application potentials in medicine and biology].

DNA polymorphisms are based on variations in the nucleotide sequences of the DNA within a given population and are transmitted from parents to offspring by Mendelian inheritance. Most of these mutations are phenotypically silent. Two different types of DNA polymorphisms are restriction fragment length polymorphisms and highly variable regions (HVRs), the latter with many different alleles at a given locus. Molecular probes for HVRs (or DNA minisatellites) can detect a great number of cross-hybridising fragments dispersed throughout the genome. The polymorphic patterns of these fragments are completely individual-specific, hence termed DNA "fingerprints". DNA "fingerprinting" has been shown to be a powerful tool for establishing family relationships, for example in paternity disputes, and for the positive identification of individuals in forensic medicine. The technique may be used to document marrow engraftment in patients who have undergone allogeneic bone marrow transplantation. DNA "fingerprinting" is a new method of assessing clonality in human tumours by identifying clonal somatic mutations in the tumour DNA. Cloning of individual DNA "fingerprint" fragments yields locus-specific HVR probes which, due to their high rate of heterozygosity, are ideal for linkage analysis and prenatal diagnosis in single gene disorders. This is exemplified by adult polycystic kidney disease, which has been found by a 3'alpha-globin-HVR probe to be closely linked to the alpha-globin-gene cluster on chromosome 16p. Locus-specific HVR probes have been used for the molecular diagnosis of clonal chromosomal deletions or loss of heterozygosity at particular loci in a large variety of tumours. These findings are the basis for the identification of anti-oncogenes or putative tumour-suppressor genes in the human genome.

Animals↗
PubMed1986

Genetic analysis of the hypervariable region flanking the human insulin gene.

In order to study the mechanisms for the generation of length diversity within the 5' flanking region of the human insulin gene, we have isolated and sequenced a previously uncharacterized allele. This allele, of a size intermediate between those three already described in the literature, encompasses 1,156 base pairs (bp) and contains 81 reiterated tandem oligonucleotides of 14-15 bp each. Population analysis on 298 independently sampled individuals by Southern blotting of genomic DNA demonstrates that the polymorphic portion of the insulin 5' flanking region varies from 400 to more than 8,000 nucleotides, being encoded by from 30 to over 540 oligomeric repeats. Length variability 5' to the insulin gene is a result primarily of unequal crossing over, which generates an expansion or contraction in the number of tandem repeat units per chromosome. A similar mechanism probably accounts for nondispersed reiterated sequences at other loci in the human genome.

Alleles↗