Homozygous Typing Cells Research Articles

MIC gene polymorphism and haplotype diversity in rhesus macaques

Rhesus macaques (Macaca mulatta) mainly originating from India were analysed for their major histocompatibility complex class I-related (MIC) gene repertoire. Thus far, three distinct genes, designated MIC1, MIC2 and MIC3, have been identified in the rhesus macaque. In addition, an MICD pseudogene has been described mapping apart from the other loci in a telomeric direction. Genomic comparisons and the presence of a characteristic microsatellite in exon 5 suggest that the MIC1 gene is the equivalent of the human MICA gene. Hence, the MIC2 gene, lacking the microsatellite - as do humans -, is considered to be the equivalent of human MICB. The MIC3 gene, a hybrid of MICA and MICB, seems to be generated by a crossing-over event with one breakpoint in intron 3 and accordingly is named MICA/B. Apart from their human counterparts, MICA, MICB and MICA/B cluster in separate branches in the phylogenetic tree, confirming the hybrid character of the MICA/B gene. Population analyses have shown that the various genes display polymorphism, and six MICA, five MICB and three MICA/B alleles have been identified. In the panel of homozygous typing cells, two distinct haplotype configurations have been defined by segregation analyses. Each haplotype comprises an MICB gene in conjunction with either an MICA or an MICA/B gene. Furthermore, the presence of a polymorphic microsatellite in the MICA and MICA/B alleles facilitates speedy and accurate haplotyping.

Identification of two new C4 alleles by DNA sequencing and evidence for a historical recombination of serologically defined C4A and C4B alleles.

Nucleotide polymorphisms of the C4 genes were investigated by direct sequencing of seven different homozygous typing cells from the 10IHW panels. Two novel sequences were identified within the C4d region of the C4 genes. Our sequencing analyses extend previous findings suggesting that a recombination hot spot is likely to have occurred between codon positions 1157 and 1186 within the C4d region. The classification of electrophoretically defined C4A and C4B alleles can be further subtyped by sequencing. Because the central major histocompatibility complex region that carries various copies of the C4 gene has been associated with a range of disorders; further analysis at the sequence level within the C4 locus may provide informative genetic markers for the investigation of disease-associated polymorphisms.

The HLA-DOB gene displays limited polymorphism with only one amino acid substitution.

The HLA-DO molecule is a non-classical class II heterodimer composed of alpha and beta chains. We have previously recognized that all eight of the allelic variations of the HLA-DOA gene represent non-synonymous amino acid substitution. In the present study, to analyze genetic polymorphism and allelic variation of the HLA-DOB gene which may affect the efficiency of class II restricted antigen presentation thereby being involved in the susceptibility of HLA associated diseases, we conducted direct DNA sequencing of HLA-DOB in 36 HLA class II homozygous typing cells and identified six new allelic variations (DOB*0101101, *0101102, *01012, *01022, *0104101 and *0104102) including five single nucleotide polymorphisms with only one amino acid substitution. Furthermore, strong linkage disequilibrium was detected between DOB*01022 and DRB1*1502 only, with no linkage disequilibrium between the DOA and the DOB genes. The HLA-DOB gene has been identified in other mammals, and their nucleotide sequences are well conserved. These facts suggest that limited polymorphism in the DOB gene is profitable to execute their unique function as a co chaperone and so strong selective pressure is operating to prevent generic variation against the DOB molecule interacting with the DM molecule and thus maintaining the specified immunological function of regulating antigen presentation.

MICA genetic polymorphism and linkage disequilibrium with HLA-B in 29 African-American families.

The human major histocompatibility complex (MHC) class I chain-related gene A ( MICA) is located 46 kb upstream of HLA-B and encodes a stress-inducible protein which displays a restricted pattern of tissue expression. MICA molecules interact with NKG2D, augmenting the activation of natural killer cells, CD8(+) alpha beta T cells, and gamma delta T cells. MICA allelic variation is thought to be associated with disease susceptibility and immune response to transplants. We investigated MICA allelic variations and linkage disequilibrium with HLA-A, B, and DRB1 loci on 110 parental haplotypes from 29 African-American families. PCR/sequence-specific oligonucleotide probing (SSOP) was used to define MICA polymorphisms in exons 2, 3, and 4. Ambiguous allelic combinations were resolved by sequencing exons 2, 3, and 4. Exon 5 polymorphisms were analyzed by size sequencing. For HLA-A, B and DRB1 typing, low-resolution PCR/SSOP and allelic PCR/sequence-specific priming techniques were used. Twelve MICA alleles were observed, the most frequent of which were MICA*008, MICA*004, and MICA*002, with gene frequencies of 28.2, 26.4, and 25.5%, respectively. Thirty-eight HLA-B- MICA haplotypic combinations were uncovered, 22 of which have not been reported in the HLA homozygous typing cell lines from the 10th International Histocompatibility Workshop. Significant positive linkage disequilibria were found in 8 HLA-B- MICA haplotypes. Furthermore, haplotypes bearing HLA-B*1503, *1801, *4901, *5201, *5301, and *5703 were found to segregate with at least two different MICA alleles. Our results provide new data about MICA genetic polymorphisms in African-Americans, which will form the basis for future studies of MICA alleles in allogeneic stem cell transplantation outcome.

RENAL TUMOR-LIKE PYONEPHROSIS WITH FOREIGN BODY

We report on a male patient who underwent abdominal ultrasound examination because of another disease. Ultrasonography showed a left renal mass, which was suspicious of renal tumor. Computerized tomography (CT) confirmed the suspicion. Nephrectomy was performed. The removed kidney was pyonephrotic and a foreign body was found in the collecting system. The foreign body had been in the kidney for 36 years. The patient had not had any symptoms for more than 3 decades. To our knowledge we report the first case of this kind. CASE REPORT A 56-year-old man was treated for anterior wall myocardial infarction. During treatment an abdominal ultrasound examination showed a 10 cm. hypoechogenic mass with central hyperechogenic structures in the upper pole of the left kidney. CT revealed a well-defined 10 cm. cystic lesion occupying the upper half of the left kidney. The mass had a chunky wall and cystic structures with smaller and bigger calcifications inside them (fig. 1). The structure of the lower half was normal and it had good excretion without dilatation of the collecting system. Renal tumor was strongly suspected. In 1963 the patient had undergone pyeloplasty due to a ureteropelvic junction stricture. According to the report of the operation ,a2t o 3c m.segment of the ureter was resected and a new anastomosis was performed with stenting of the ureter and placement of a transrenal drain. The patient had an acute myocardial infarction in 1998 and 1999. He did not have any voiding symptoms and only slight blunt loin pain, which was thought to be related to rheumatical origin. Fever and loss of body weight were not noted. Physical examination did not reveal any abnormality. Red blood count was 4.3 mmol./L., homozygous typing cells were 0.39, white blood count was 7.0 3 10 9 /l., platelets were 181 10 9 /l., urea was 59 mmol./l. and creatinine was 78 mmol./l., which were all normal. After a complete examination, exploration was performed. The retroperitoneum was explored via a lumbar incision. The fetal head-like kidney was mobilized from its surrounding scarred tissues. The kidney was removed en bloc with its fatty capsule after ligation of the renal pedicle and ureter. After the operation, the removed kidney was cut longitudinally. The parenchyma was only in the lower pole, and above it there was a large sack containing thick, yellowish-red pus. Inside the pus, a textile tissue was found (fig. 2). Convalescence was uneventful. The patient was discharged from the hospital on postoperative day 8. Histological examination demonstrated atrophic renal tissue, chronic interstitial inflammation, scarring in the pelvis and peripelvic fatty tissue, and deteriorated gauze in the collecting system. Postoperatively the patient was symptom-free with no flank pain. Ultrasonography showed normal right kidney and the bed of the left kidney was empty. Laboratory tests were normal. DISCUSSION

Haplotype-specific sequence encoding the protein kinase, interferon-inducible double-stranded RNA-dependent activator in the human leukocyte antigen class II region.

The protein kinase, interferon-inducible double-stranded (ds)RNA-dependent activator (PRKRA) is a dsRNA-binding protein which activates a protein kinase participating in the antiviral activity of interferon. Our previous studies indicated that the nucleotide sequence encoding PRKRA, which appeared to be an intronless gene, was present in PAC HS265J14 containing the human leukocyte antigen (HLA) DR subregion. In this study, we further investigated and characterized the PRKRA gene on the human genome by means of Southern blotting and polymerase chain reaction with homozygous typing cell lines for HLA genes. Results indicated that the presence of PRKRA in the DR subregion was dependent on the DR53 group. Consistently, fluorescence in situ hybridization profiles with PRKRA as a probe showed that the hybridization signal on Chromosome (Chr) 6p21.3 was seen only in the samples carrying the DR haplotypes that belonged to the DR53 group. Interestingly, another hybridization signal, which was mapped on Chr 2q31.2-q32.1, was always detected in the samples examined, i.e., even in the samples negative for the DR53 group. The outcome of a sequence-database homology search further indicated that the PRKRA gene with introns appeared to be present in a recently opened draft-sequence, RP11-65L3 (GenBank accession number AC009948), which is located between D2S335 and D2S2257. Together, the data presented here indicate that the PRKRA gene in the DR subregion is a processed pseudogene (PRKRApsi), which could have been generated only on the DR53 common ancestor's genome, and that the master copy of PRKRApsi is most probably present on Chr 2q31.2-q32.1.

Limited polymorphism in the HLA-DOA gene.

The HLA-DO molecule, a heterodimer consisting of two novel members of the class II gene family, DOA and DOB, has recently been suggested to function as an important modulator in the HLA class II restricted antigen presentation pathway by interaction with the HLA-DM molecule. In this study, we have analyzed genetic polymorphism and allelic variation of the HLA-DOA gene in 37 HLA class II homozygous typing cells using the direct DNA sequencing technique. As a result, we recognized at least eight allelic variations, DOA*01011, *0101201, *0101202, *0101203, *01013, *0101401, *0101402 and *01015. None of them, however, result in amino acid substitution. The HLA-DOA gene has been identified in other mammals as well, and the nucleotide sequences were well conserved among these species. These results suggest that the DOA molecule has undergone strong selective pressure to preserve functional structure and conformation required for interaction with the DM molecule, preventing non-synonymous amino acid substitution.

Characterization of LMP polymorphism in homozygous typing cells and a random population

Within the class II region of the MHC are several genes whose products are involved in processing antigen for HLA class I presentation. Two such genes, LMP2 and LMP7, encode products that are incorporated into a multicatalytic proteinase complex which serves as the major pathway for protein degradation for class I peptide presentation. Polymorphic residues have been identified in both LMP2 and LMP7. In this report, we describe an ARMS-PCR method to distinguish LMP7 alleles. We applied this method to characterize these alleles in addition to LMP2 alleles in 50 homozygous typing cells (HTC) as well as in a panel of 110 random individuals. Of the four possible combinations of LMP2 and LMP7, we observed three in the HTC population, while all four were observed in the random population. The frequencies at which allele combinations were observed were similar to that predicted by individual allele frequencies. We also analyzed the possibility of linkage disequilibrium of LMP2 and LMP7 alleles with TAP1, TAP2, and specific HLA class I alleles in both populations. From this data, there seems to be no apparent linkage disequilibrium and no indication that particular combinations of LMP2 and LMP7 have been maintained.

Characterization of 12 microsatellite loci of the human MHC in a panel of reference cell lines

The human genome contains a large number of interspersed microsatellite repeats which exhibit a high degree of polymorphism and are inherited in a Mendelian fashion, making them extremely useful genetic markers. Several microsatellites have been described in the HLA region, but allele nomenclature, a set of broadly distributed controls, and typing methods have not been standardized, which has resulted in discrepant microsatellite data between laboratories. In this report we present a detailed protocol for genotyping microsatellites using a semi-automated fluorescence-based method. Twelve microsatellites within or near the major histocompatibility complex (MHC) were typed in the 10th International Histocompatibility Workshop homozygous typing cell lines (HTCs) and alleles were designated based on size. All loci were sequenced in two HTCs providing some information on the level of complexity of the repeat sequence. A comparison of allele size obtained by genotyping versus that obtained by direct sequencing showed minor discrepancies in some cases, but these were not unexpected given the technical differences in the methodologies. Fluorescence-based typing of microsatellites in the MHC described herein is highly efficient, accurate, and reproducible, and will allow comparison of results between laboratories.

Extended HLA haplotypes in Japanese homozygous typing cells.

We have defined extended HLA haplotypes including the HLA class II genes, the non-HLA genes such as TAP1, TAP2 and LMP2, and the (CTG)n microsatellite repeats within the NOTCH4 gene between DRA and 21OH in 33 Japanese HLA homozygous typing cells (HTC). These conserved haplotypes characterized by unique linkage might be maintained as a result of functional co-operation among them in the antigen presentation pathway. These HTCs can be served as an original and ethnic-specific standard panel, providing useful genetic markers in haplotypic diversity, disease association, and anthropology studies.

Characterization of 12 microsatellite loci of the human MHC in a panel of reference cell lines.

The human genome contains a large number of interspersed microsatellite repeats which exhibit a high degree of polymorphism and are inherited in a Mendelian fashion, making them extremely useful genetic markers. Several microsatellites have been described in the HLA region, but allele nomenclature, a set of broadly distributed controls, and typing methods have not been standardized, which has resulted in discrepant microsatellite data between laboratories. In this report we present a detailed protocol for genotyping microsatellites using a semi-automated fluorescence-based method. Twelve microsatellites within or near the major histocompatibility complex (MHC) were typed in the 10th International Histocompatibility Workshop homozygous typing cell lines (HTCs) and alleles were designated based on size. All loci were sequenced in two HTCs providing some information on the level of complexity of the repeat sequence. A comparison of allele size obtained by genotyping versus that obtained by direct sequencing showed minor discrepancies in some cases, but these were not unexpected given the technical differences in the methodologies. Fluorescence-based typing of microsatellites in the MHC described herein is highly efficient, accurate, and reproducible, and will allow comparison of results between laboratories.

Relationship Between Protein Complotypes and DNA Variant Haplotypes: Complotype-RFLP Constellations (CRC)

ABSTRACT: From the study of 52 families and 15 homozygous typing cells, 234 MHC complement haplotypes were characterized for features in the DNA of the complotype region: C2/Sst I (2.75, 2.70, 2.65, and 2.40 kb), BF/Taq I (6.6 and 4.5 kb), C4 5′/ Bgl II (15 and 4.5 kb), C4 5′/ Taq I (7.0, 6.4, 6.0 and 5.4 kb) and C4 3′/ Xba I/ BamH I (11 and 4+7 kb) restriction fragment length polymorphisms (RFLP’s), by the presence or absence of C4A, C4B, CYP21A and CYP21B genes and by duplications. Nineteen (of over 1000 theoretically possible) complotype-RFLP constellations (CRC’s) were found. The 9 CRC’s with two C4 and CYP21 genes were designated A through I. CRC’s Bdup and Ddup were like B and D but had duplicated C4B-CYP21B genes. The remaining CRC’s had deletions of C4 and/or CYP21 genes and were designated Bdel, Cdel and the like. Individual complement alleles and complotypes were not randomly distributed among the CRC’s. Some complotypes, such as SC01, SC02 and FlC30, were restricted to only 1 CRC; others, such as SC31, FC31, and SC30, were found in several CRC’s. Some of the CRC’s contained a single complotype, others contained several. Remarkably, there are about 30 CRC-specified complotypes with frequencies of .01 or higher and 14 of .02 or higher. A number of evolutionary origins of complement alleles and complotypes are suggested by the relationships among CRC’s. Approximate normal frequencies of the undeleted CRC’s were A = .27, B = .19, Bdup = .02, C = .17, D = .07, Ddup = .02, E = .06, F = .05, and G = .02. Thus, CRC’s without deletions accounted for 88% of normal complotypes. Since the frequency of Bdel, with a deletion of C4A, was .12, 10 CRC’s accounted for all observed normal caucasian MHC haplotypes.

Further characterization of hla homozygous typing cell lines at the LMP2 polymorphic codon 60 by an ARMS typing method

LMP2 is a subunit of the 20S proteasome within the cellular cytosolic compartment that is thought to cleave proteins into approximately 9 amino acid long oligopeptides. It is hypothesized that changes in the low molecular mass protease (LMP) gene sequence may alter the activity or specificity in which the LMP genes cleave peptides. Currently, the typing method for LMP2 involves polymerase chain reaction (PCR), restriction enzyme digestion, and gel electrophoresis. To help reduce the cost and cumbersomeness of this method, a new typing method was adapted for the LMP2 gene. To establish this new amplification refractory mutation system (ARMS) typing method, primers have been defined, amplification conditions optimized, and control cell lines sequenced to validate testing parameters. Results are listed for selected 10th and 11th International Histocompatibility Workshop homozygous cell lines.

Characterization of a swelling-activated anion conductance in homozygous typing cell hepatoma cells.

Liver cell volume and intracellular ion concentrations are maintained within a narrow physiologic range by regulated changes in membrane ion permeability. These studies of homozygous HTC hepatoma cells, a model liver cell line, evaluate the relationship between cell volume and membrane ion permeability, and assess the possibility that cell swelling allows the efflux of the intracellular osmolite taurine through the opening of a conductive pathway. Cell swelling induced by exposure to hypotonic solutions (203 mOsm) caused a rapid increase in cell volume, followed by recovery toward basal values. Volume recovery was inhibited by Cl- depletion or by exposure to the putative Cl- channel blocker 5-nitro-2-(3-phenylpropyl-amino) benzoic acid (NPPB) (25 micromol/L). Swelling increased the efflux rates of 36Cl (181% +/- 15%, P < .01) and 125I (310% +/- 21%, P < .01). In whole cell patch clamp recordings, cell swelling induced by 1) exposure to hypotonic solution or 2) intracellular perfusion with hypertonic sucrose-containing solutions activated an anion-selective current which was outwardly rectified and showed time-dependent inactivation at depolarizing potentials. The current density at -80 mV increased proportionally with increases in the transmembrane osmotic gradient from basal values of -1 pA/pF to maximal values of 70 pA/pF with 100 mmol/L sucrose in the pipette. Basal taurine permeability was low, but cell swelling increased the efflux of [1,2-3H]taurine to 1,587% +/- 172% of basal levels (P < .05). Intracellular perfusion with hypertonic solutions activated currents carried by anionic taurine, with an estimated taurine/Cl- permeability ratio of .88 +/- .17 for whole cell currents. These studies demonstrate that the HTC membrane anion permeability is closely coupled to changes in cell volume, and that the recovery from swelling depends upon activation of anion-selective conductance pathways permeable to both Cl- and taurine.

Characterization of a swelling-activated anion conductance in homozygous typing cell hepatoma cells

Liver cell volume and intracellular ion concentrations are maintained within a narrow physiologic range by regulated changes in membrane ion permeability. These studies of homozygous HTC hepatoma cells, a model liver cell line, evaluate the relationship between cell volume and membrane ion permeability, and assess the possibility that cell swelling allows the efflux of the intracellular osmolite taurine through the opening of a conductive pathway. Cell swelling induced by exposure to hypotonic solutions (203 mOsm) caused a rapid increase in cell volume, followed by recovery toward basal values. Volume recovery was inhibited by Cl- depletion or by exposure to the putative Cl- channel blocker 5-nitro-2-(3-phenylpropyl-amino) benzoic acid (NPPB) (25 μmol/L). Swelling increased the efflux rates of 36Cl (181% +/- 15%, P < .01) and 125I (310% +/- 21%, P < .01). In whole cell patch clamp recordings, cell swelling induced by 1) exposure to hypotonic solution or 2) intracellular perfusion with hypertonic sucrose-containing solutions activated an anion-selective current which was outwardly rectified and showed time-dependent inactivation at depolarizing potentials. The current density at -80 mV increased proportionally with increases in the transmembrane osmotic gradient from basal values of -1 pA/pF to maximal values of 70 pA/pF with 100 mmol/L sucrose in the pipette. Basal taurine permeability was low, but cell swelling increased the efflux of [1,2-3H]taurine to 1,587% +/- 172% of basal levels (P < .05). Intracellular perfusion with hypertonic solutions activated currents carried by anionic taurine, with an estimated taurine/Cl- permeability ratio of .88 +/- .17 for whole cell currents. These studies demonstrate that the HTC membrane anion permeability is closely coupled to changes in cell volume, and that the recovery from swelling depends upon activation of anion-selective conductance pathways permeable to both Cl- and taurine.(Hepatology 1997 Feb;25(2):403-10)

P568 - Extended HLA haplotypes in Japanese homozygous typing cells

P568 - Extended HLA haplotypes in Japanese homozygous typing cells

Restricted TCR V beta repertoire in the human mixed lymphocyte reaction is determined by the TCR on the responder cell and not by the stimulating antigen on the stimulator cell.

The use of a restricted TCR repertoire has been reported in antigen-stimulated T cells. We have examined by flow cytometry and polymerase chain reaction the changes in the TCR variable beta (V beta) repertoire as they occur in the mixed leukocyte reaction. The HLA class I-negative lymphoblastoid B cell line, Daudi, an HLA class I-positive variant of the Daudi cell line, and the homozygous typing cell line HTC 9062 were used to stimulate HLA-mismatched responder cells from 8 individuals. The magnitude of HLA incompatibility in various combinations ranged from single DR10 and DR13 differences to full 6-antigen differences at the HLA-A, -B, and -DR loci. Using a panel of 19 V beta-specific oligonucleotide primers, changes in the level of TCR V beta mRNA were assessed. The observed V beta repertoire was not specific for the stimulator cell antigens used. We did not find a correlation between the number of mismatched HLA antigens and the number of V beta elements involved. It rather appeared that individual responder cells displayed a uniform V beta pattern following exposure to single and multiple HLA antigens. We conclude that the V beta repertoire was largely determined by factors associated with the TCR on the responder cells, and not as obviously influenced by the HLA antigen(s) on the stimulator cells.

Anchored PCR cloning of the novel HLA-Cw*0704 allele detected by PCR-SSP.

The novel HLA-Cw*0704 allele, previously detected as the PCR-SSP variant Cw7/8v, has been cloned and sequenced from the homozygous typing cell KRO3/4 after amplification by anchored PCR. The nucleotide sequence of Cw*0704 is closely related to those of other Cw*07 alleles, but carries specific changes in exon 3 consistent with its serological behavior-a short Cw7 cross-reactive with antibodies directed against HLA-Cw8. Some of the substitutions of Cw*0704 have not been previously described for HLA-C but are found in HLA-B alleles and in published C sequences of non-human primates. The new allele carries a novel polymorphism in its 5' untranslated region (5' ut) that could be shared by all Cw*07 alleles. By PCR-SSP, Cw*0704 is a relatively common allele in English Caucasoids at a frequency of 4.6%. It is most often observed on HLA-B44 haplotypes previously described as HLA-C "blank", although linkage disequilibria with other HLA-B specificities have been found.

A description of a new DR allele, DRB1*1113

We have discovered a previously unpublished HLA-DRB1 allele, observed in a patient (SB), his mother, and one sibling. The undefined allele gave sporadic positive reactions with sera in the DR52-associated group. SSOPH analysis utilizing both generic and group specific primers and probes also gave ambiguous results. SB typed clearly as a DRB1*0301 (paternal allele) but the DNA from SB also bound probes specific for DRB1*14 and DRB1*11. Sequencing revealed that the undefined allele was similar to a DRB1*14 allele with a segment of sequence found in DRB1*11 alleles. The patient was MLC reactive with donors who express DRB1*0301, *1401 and *0301, *11 and was nonreactive solely to DRB1*0301 (Dw3) homozygous typing cells.

Rapid DNA crossmatch analysis of HLA class II genotypic polymorphisms by temperature gradient gel electrophoresis in unrelated bone marrow donor selection.

The present paper demonstrates the usefulness of the temperature gradient gel electrophoresis (TGGE) as a precise method for the rapid identification of HLA-DR full matched donors by molecular crossmatch analysis. The resulting TGGE fingerprints are highly diverse for different HLA-DR genotypes and identical for samples with identical HLA-DR type, as shown for a panel of 25 randomly selected PCR-SSO pretyped DNA samples. In addition, TGGE analysis of a panel of homozygous typing cell lines (HTCs) established, that even subtle differences in the DR4 subtypes are detectable by TGGE crossmatch analysis. Furthermore, TGGE crossmatch analysis of unrelated donor/patient pairs demonstrated, that only HLA-DR identical patient/donor combinations showed identical TGGE patterns. Thus crossmatch analysis by TGGE presents a novel basis for a rapid and safe unrelated bone marrow donor selection strategy. Only HLA class I identical donors which also show HLA-DR identity in the TGGE crossmatch test are selected for the final confirmation of the HLA class II genes by a suitable DNA subtyping method.