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PubMed1993

Immunoglobulin clonality analysis. Resolution of ambiguities in immunofixation electrophoresis results by high-resolution, two-dimensional electrophoretic analysis of paraprotein bands eluted from agarose gels.

This article describes evaluation of the clonality of origin of immunoglobulin (Ig) chains by strategies that include qualitative analysis of paraproteins with high-resolution, two-dimensional electrophoresis (2DE) and silver staining. This approach is helpful in evaluating specimens in which standard immunoelectrophoresis or immunofixation electrophoresis (IFE) techniques do not provide definitive Ig typing results. One method the authors developed involves a "band elution" procedure, in which proteins present in high-resolution agarose gel electrophoresis bands are cut from the agarose gel, eluted with a denaturing buffer, and subjected to 2DE. The microheterogeneity patterns of the Ig light chains, heavy chains, or both are evaluated for their relationship regarding mass, charge, and, by inference, number of genes of origin. When necessary, determination of charge relationships may be aided by urea-mediated carbamylation of lysine residues, which introduces single-charge shifts to the individual protein subunits. Overall, these adjunctive techniques are particularly useful in cases with multiple bands of identical immunologic types (eg, several IgG1 bands) on IFE before and after sulfhydryl reduction (with dithiothreitol or 2-mercaptoethanol). The authors present procedural details and examples of the 2DE band elution patterns of serum and urine samples from four patients with B-cell dyscrasias, including the first reported case of POEMS syndrome with biclonal gammopathy, to the best of their knowledge.

Adult↗

PubMed1981

Clonal analysis of the integration and expression of endogenous avian retroviral DNA acquired by exogenous viral infection.

Rous-associated virus-0 is one of several endogenous avian retroviruses that are transmitted vertically and that can be isolated from different inbred lines of chickens. These viruses, referred to here as induced-leukosis viruses bearing a subgroup E glycoprotein (ILV-E), are all closely related. Clonal populations of fibroblasts from line 15B and line 100 inbred chickens have been examined for the presence and expression of exogenously acquired ILV-E sequences. Restriction enzyme analysis of uniform populations of line 15B fibroblasts, prepared by cloning cells either before or after infection with ILV-E, indicates that viral sequences were inserted at multiple sites within the cell genome. Analysis of 49 clonal populations of line 100 fibroblasts containing between one and five copies of exogenous ILV-E sequences demonstrated that each clone was characterized by a unique set of viral DNA insertions within the cell genome. The expression of the exogenous ILV-E sequences within these fibroblast clones was examined by using reverse transcriptase activity as a measure of virus production. Some clones produced an amount of virus equivalent to that produced by an equal number of the uncloned ILV-E-infected parental fibroblasts. Other clones produced 5- to 10-fold less virus. Still other clones produced no detectable virus at all. Among nine clones derived from cells containing a single copy of the ILV-E provirus, the level of virus production differed more than 100-fold. DNA from these clones was analyzed with several different restriction endonucleases to characterize the location and arrangement of the ILV-E sequences. All nine clones consisted of cells that appeared to contain a complete provirus inserted (i) in a different site within the cellular DNA and (ii) in an orientation that was colinear with the viral genomic RNA. It was observed that several cleavage sites potentially affected by methylation were equally available for cleavage in all clones regardless of the level of viral production.

Animals↗

PubMed2005

Clonality analysis by HUMARA assay in Spanish females with essential thrombocythemia and polycythemia vera.

Analysis of the human androgen receptor gene (HUMARA) allows clonality to be assessed in essential thrombocythemia (ET) and polycythemia vera (PV). We studied clonality in 44 patients with ET, 18 with PV and in 64 healthy controls. The X-chromosome inactivation pattern was analyzed by HUMARA-polymerase chain reaction on DNA from purified granulocytes, T lymphocytes and the CD3- fraction of mononuclear cells.

Adult↗

PubMed1994

Clonal analysis of primary marrow stroma: functional homogeneity in support of lymphoid and myeloid cell lines and identification of positive and negative regulators.

Stromal cells play an important role in regulating early hematopoiesis. How stromal cells exert their different functions and the factors that regulate stromal cells themselves remain to be elucidated definitively, however. We describe here a limiting dilution assay for primary stroma colonies from murine marrow. This system permits a critical analysis of stromal cell function and regulation on the clonal level. We report that stroma formation was dependent on an activity secreted by the long-term cultured stromal line AC-3.U. Differential ultrafiltration of AC-3.U supernatant (SN) suggests that this potentially novel activity is represented by molecules with apparent molecular weights (m.w.) of > 100 < 300 kD and > 300 kD. In contrast to the AC-3.U activity, hydrocortisone (HC) acts as a negative regulator of stroma colony formation. We used the stroma colony assay to analyze potential stromal cell heterogeneity. We found that most, if not all, primary stromal colonies supported expansion of both myeloid and lymphoid cell lines. In contrast, long-term cultured stromal cell lines differed not only among lines, but also on the level of sublines, in their ability to sustain myeloid and lymphoid cells. This intraclonal variation suggests that the heterogeneity of cell lines can be a reflection of ongoing culture adaptation. The functional homogeneity of primary stromal colonies, together with their susceptibility to regulators, indicates that the performance of primary stroma is subject to external control. The establishment of a clonal assay system has paved the way to analyze the molecules that regulate primary stroma and thereby hematopoietic cells.

Animals↗

PubMed2004

Clonality analysis of T cells mediating acute and chronic rejection in kidney allografts.

The clonality of T-cell populations mediating acute and chronic rejection (AR and CR, respectively) of kidney allografts was ascertained by investigating the diversity of TCRBV genes expressed by allograft-infiltrating T cells. Both oligoclonality and polyclonality cases were found in biopsy specimens of AR as well as CR. These results indicated that the T-cell clonality in each specimen did not correlate directly with the mode of rejection. When AR and CR specimens were compared, however, the CR specimen group was significantly more polyclonal (or less oligoclonal) than the AR group. This result may reflect the higher chance of epitope spreading in the more slowly progressing CR than in AR.

Clone Cells↗

PubMed2006

PCR-based clonality analysis of B-cell lymphomas in paraffin-embedded tissues: diagnostic value of immunoglobulin kappa and lambda light chain gene rearrangement investigation.

Polymerase chain reaction (PCR)-based analysis, employed for detecting immunoglobulin heavy chain (IgH) gene rearrangements, has become a diagnostic tool widely used in the investigation of B-cell lymphomas, but the overall sensitivity of these methods does not exceed 80%, notably in germinal center (GC) and post-GC B-cell origin lymphomas. Many PCR strategies devised for detecting immunoglobulin light chain (IgL) gene rearrangements have been developed to enhance the clonality detection rates. However, the feasibility of these methods in routine clinical diagnosis using paraffin-embedded tissues has not yet been investigated sufficiently. We studied a large series of 108 cases of B-cell lymphomas, as well as 20 reactive lymphoid tissues using degenerate primers to amplify immunoglobulin kappa (Igkappa) and lambda (Iglambda) light chain genes. B-cell clonality was further investigated using semi-nested PCR for IgH gene rearrangements. B-cell clonality was detected in 74%, 56.5%, and 43.5% of cases using IgH, Igkappa, and Iglambda PCR, respectively. By combining these methods, the clonality detection rate increased to 93.5%. Only polyclonal patterns were noted in reactive lymphoid samples. We concluded that in addition to the established methods for IgH analysis, a PCR-based approach for IgL gene rearrangements analysis improves the clonality detection rate in over 90% of B-cell lymphoma cases using routine histological specimens with poor preservation of the genomic DNA.

Clone Cells↗

PubMed1999

Clonality analysis using X-chromosome inactivation at the human androgen receptor gene (Humara). Evaluation of large cohorts of patients with chronic myeloproliferative diseases, secondary neutrophilia, and reactive thrombocytosis.

Chronic myeloproliferative diseases (MPDs) are not associated with consistent cytogenetic or molecular abnormalities. Demonstration of clonal cell growth by analysis of X-chromosome inactivation (XCI) patterns in females provides a promising tool for diagnosis. However, this technique can be complicated by excessive lyonization of normal cells mimicking clonal cell growth: We analyzed XCI patterns at the human androgen receptor (HUMARA) locus in 146 healthy females, 65 women with secondary neutrophilia, 31 women with reactive thrombocytosis, and 86 women with chronic MPDs. A skewed XCI pattern with greater than 75% amplification of 1 allele (allele ratio > 3:1) was found in 22 (9.1%) of 242 control subjects. The incidence of skewing was statistically significantly lower in women younger than 30 years (2/73) compared with women older than 60 years (10/53). Of 86 patients with a chronic MPD, 71 (82%) exhibited an allele ratio greater than 3:1, whereas only 10 (12%) of 86 age-matched control subjects showed a skewed XCI pattern. Although statistical evaluation of the data showed a significant difference between patients with a chronic MPD and control subjects, proof of clonality in individual, especially elderly, patients is difficult.

Adolescent↗

PubMed1998

Clonal analysis of intrahepatic B cells from HCV-infected patients with and without mixed cryoglobulinemia.

Clonal rearrangements of Ig heavy chain (IgH) genes and hepatitis C virus (HCV) genomic sequences were assayed on intrahepatic B lymphocytes isolated from HCV chronically infected patients with and without type II mixed cryoglobulinemia (MC). Liver tissue samples from eight patients with and nine without MC were subjected to routine histologic studies, immunophenotyping, and genotypic analysis including IgH V-D-J region gene rearrangements by PCR. RT-PCR, signal amplification by branched DNA assay, and in situ hybridization technique were used to detect and quantitate HCV RNA genomic sequences in selected B cells purified from each tissue sample. Although HCV infection of intrahepatic B cells was shown in all patients both with and without MC, frank B cell monoclonal and oligoclonal patterns were found in only three and four patients with MC, respectively. No monoclonal profile was seen in the noncryoglobulinemic patients, whereas an oligoclonal profile was demonstrated in four of them. No clonalities were shown in HCV-unrelated patients matched for age and severity of liver disease. No obvious difference in HCV genotype distribution was found in relation to the clonal expansion profile. Noncryoglobulinemic patients showing clonal expansion in liver tissue had higher titers of serum rheumatoid factor (RF). Spontaneous production of RF was shown in cell cultures of intrahepatic B cells, suggesting their persistent stimulation in vivo. These data indicate that HCV infection of B cells and B cell clonal expansions occur in the liver microenvironment and preferentially involve RF-producing cells.

Adult↗

PubMed1993

Evidence for limited molecular genetic heterogeneity as defined by allelotyping and clonal analysis in nine metastatic breast carcinomas.

To investigate genetic intratumor heterogeneity, 42 samples of nine primary breast carcinomas and 29 related lymph node metastases were examined for DNA ploidy status, allelotype, and X chromosome inactivation pattern. Two primary breast carcinomas showed DNA index heterogeneity and five contained a single DNA aneuploid tumor stemline, whereas the two remaining primary tumors were solely DNA diploid. Most primary DNA tumor stemlines recurred in lymph node metastases (9 of 11). The allelotype, constructed with 31 different probes mapping to 23 different chromosome arms showed allelic imbalances on nearly all chromosome arms investigated. All tumors contained multiple allelic imbalances (range, 3-12). An allelic imbalance present in a primary tumor was consistently present in all DNA samples of that primary tumor and also in all DNA samples of related lymph node metastases, irrespective of DNA index heterogeneity. X chromosome inactivation pattern analysis with probe M27 beta (DXS255) confirmed the presence of clonal tumor cell populations in these tumors at the time of diagnosis. Densitometry of autoradiograms, which by eye showed retention of heterozygosity, revealed a narrow clustering of allelic imbalance factors between 1.0 and 1.4. In contrast, autoradiograms visually showing an allelic imbalance exhibited a marked interprobe, intertumor and intratumor variation in allelic imbalance factors. No relation between densitometry results and DNA ploidy status was found. Thus, at the time of diagnosis, an advanced primary breast carcinoma consists of a clonal tumor cell population with an established complement of allelic imbalances in all parts of the primary tumor and in the related lymph node metastases. Secondary to the establishment of allelic imbalances, intratumor heterogeneity for the copy number of involved alleles may develop, which in turn probably precedes metastasis.

Adult↗

PubMed2003

Clonal analysis of B cells in the synovial membrane of patients with rheumatoid arthritis.

OBJECTIVE: To investigate the clonal characteristics of B cells in the synovial membranes of rheumatoid arthritis (RA) patients. METHODS: The clonality of B cells at separate sites of the synovial membrane and other tissues from RA patients were investigated by a reverse transcriptase-polymerase chain reaction with a VH framework 3 consensus primer and a subsequent single-strand conformation polymorphism analysis. RESULTS: Several dominant bands were observed in all synovial membrane samples and some of the dominants bands were common among the 2 or 3 separate regions of each synovial sample. The persistent existence of clonal B cells was observed in metachronous synovial fluid samples. CONCLUSION: Infiltrating B cells are oligoclonal and antigen-driven mechanisms may play a role in the generation of clonal B cells in RA synovium. The stable presence of B cell clones in synovial fluid suggests the involvement of these clones in the perpetuation of the chronic inflammation in RA.

Amino Acid Sequence↗

PubMed1989

Clonal analysis of Hemophilus influenzae isolated from children from Pakistan with lower respiratory tract infections.

The clonal diversity of 105 Hemophilus isolates from the blood of children with lower respiratory tract infection in Pakistan was analyzed. Ten isolates were identified as H. parainfluenzae and 95 as H. influenzae. Of the H. influenzae isolates, 61 (64%) were serotype b and 34 (36%) were nontypable; 95% of the type b isolates were members of a single clonal group (as defined by multilocus enzyme electrophoresis, SDS-PAGE outer membrane protein profile, and biotype). This clone is rarely observed among type b strains recovered from patients with invasive type b disease in the USA or Europe. The nontypable isolates in Islamabad also were clonally restricted: 9 clonal groups were found among 34 isolates, with just 5 clonal groups accounting for most (82%) of the strains. Children infected with type b strains were hospitalized more often than those with nontypable H. influenzae disease (64% vs. 41%, P = .06), but no other clinical or demographic features distinguished children infected by type b and nontypable strains.

Bacterial Outer Membrane Proteins↗

PubMed1985

Clonal analysis of tumorigenicity and paratumorigenic phenotypes in rat liver epithelial cells chemically transformed in vitro.

Clonal subpopulations of a chemically induced tumorigenic rat liver epithelial cell line were analyzed for their cellular, biochemical, and in vitro growth properties and their tumorigenicity after injection into day-old newborn isogeneic rats. The phenotypic properties studied included DNA content; growth rate in culture; activities of gamma-glutamyl transpeptidase, NADH diaphorase, pyruvate kinase, glucose-6-phosphate dehydrogenase, and lactate dehydrogenase; ability to grow in calcium-poor medium; and ability to form colonies in soft agar. The results show that none of these phenotypes cosegregates with tumorigenicity and therefore is not reliable as a "marker" phenotype for neoplastic transformation in cultured rat liver epithelial cells. The poor correlations, either qualitatively or quantitatively, between paratumorigenic phenotypes and tumorigenicity suggest that neoplastic transformation in these cells involves a specific transforming gene locus or loci and that in vitro paratumorigenic phenotypes are merely epiphenomena of neoplastic transformation and progression. This study further reveals that the efficiency of the tumorigenicity assay of cultured rat liver epithelial cells in isogeneic newborn rats can be considerably improved by incubating the cells in medium containing only trace amounts of serum prior to transplantation into the host animals.

Animals↗

PubMed1994

Clonal analysis of alloreactive T cell responses against the closely related B2705 and B2703 subtypes. Implications for HLA-B27 association to spondyloarthropathy.

Alloreactive responses against closely related HLA-B27 subtypes were compared at the clonal level by fine specificity analysis of anti-B*2705 and anti-B*2703 CTL clones from unrelated HLA-B27- individuals with target cells expressing B*2701 to B*2706, and other HLA Ags. T cell epitope sharing between B*2705 and other subtypes was B*2705 > B*2703 > B*2702 > B*2701 > B*2704 > B*2706, and correlated with their amino acid differences. This suggests that identical or similar peptides, or peptide motifs, can be presented by multiple HLA-B27 subtypes to T cells, a feature that may be critical for the similar linkage of several subtypes to spondyloarthropathies. Other cross-reactions were predominantly with HLA-B61 and HLA-B60. Marked differences were observed in the nature and frequency of clonal reaction patterns among individuals. They correlated with structural features of the HLA-B Ags from each donor, suggesting that anti-HLA-B27 T cell responses are partially determined by the HLA-B phenotype of the responder. Ability to respond to particular HLA-B27-associated epitopes may determine differences in disease susceptibility among HLA-B27+ individuals. The anti-B*2703 and anti-B*2705 responses in the same individual were different. A major feature of anti-B*2703 CTL was that a large majority cross-reacted with B*2705. This can be explained by the effect of the single amino acid change in B*2703 on peptide binding and suggests that the B*2703-bound peptide repertoire is mainly a subset of that bound to B*2705, with few peptides being specifically presented by B*2703 to T cells.

Cross Reactions↗

PubMed1986

Clonal analysis of oligodendrocyte development in culture: evidence for a developmental clock that counts cell divisions.

The clonal development of oligodendrocytes was studied by culturing individual oligodendrocyte--type-2 astrocyte (O-2A) progenitor cells on monolayers of type-1 astrocytes, which stimulate O-2A progenitor cells to divide. Oligodendrocytes developed by a proliferative lineage in which clonal progeny differentiated together after a number of cell divisions. Most O-2A progenitor cells had similar cell cycle times (1-2 days), but their proliferative capacity varied greatly: some divided only once while others divided up to eight times before differentiating. sister cells behaved similarly when recultured separately on astrocyte monolayers. These findings are consistent with the cell-division-counting hypothesis previously proposed to explain the timing of oligodendrocyte differentiation. They also unambiguously establish the phenotype of O-2A progenitor cells in vitro and demonstrate that these cells respond directly to growth factors produced by type-1 astrocyte monolayers.

Animals↗

PubMed2002

A novel, essential control for clonality analysis with human androgen receptor gene polymerase chain reaction.

The most widely used technique for determining clonality based on X-chromosome inactivation is the human androgen receptor gene polymerase chain reaction (PCR). The reliability of this assay depends critically on the digestion of DNA before PCR with the methylation-sensitive restriction enzyme HpaII. We have developed a novel method for quantitatively monitoring the HpaII digestion in individual samples. Using real-time quantitative PCR we measured the efficiency of HpaII digestion by measuring the amplification of a gene that escapes X-chromosome inactivation (XE169) before and after digestion. This method was tested in blood samples from 30 individuals: 2 healthy donors and 28 patients with myelodysplastic syndrome. We found a lack of XE169 DNA reduction after digestion in the granulocytes of two myelodysplastic syndrome patients leading to a false polyclonal X-chromosome inactivation pattern. In all other samples a significant reduction of XE169 DNA was observed after HpaII digestion. The median reduction was 220-fold, ranging from a 9.0-fold to a 57,000-fold reduction. Also paraffin-embedded malignant tissue was investigated from two samples of patients with mantle cell lymphoma and two samples of patients with colon carcinoma. In three of these cases inefficient HpaII digestion led to inaccurate X-chromosome inactivation pattern ratios. We conclude that monitoring the efficiency of the HpaII digestion in a human androgen receptor gene PCR setting is both necessary and feasible.

DNA↗

PubMed1999

Clonal analysis of non-toxigenic Vibrio cholerae O1 associated with an outbreak of cholera.

We examined the clonal relationships among eight clinical isolates of non-toxigenic (NT) V. cholerae O1 associated with a cluster of cases of cholera in Warangal, Andhra Pradesh in south India and compared their relatedness to toxigenic O1 strains of classical and E1Tor biotypes and with O139 Bengal strains of V. cholerae by pulsed-field gel electrophoresis (PFGE). Phylogentic analysis of the NotI restriction fragment length polymorphism showed that all the NT. V. cholerae O1 strains formed a tight cluster with more than 80 per cent similarity. Interestingly, the NT V. cholerae O1 cluster was more closely related to V. cholerae O139 than to classical and E1Tor biotypes of V. cholerae O1 indicating closer genetic relationships between NT V. cholerae 01 and O139 Bengal strains that were isolated during the same time-frame.

Bacterial Typing Techniques↗

PubMed1987

A clonal analysis of Neisseria meningitidis serogroup A.

A typing scheme has recently been developed for Neisseria meningitidis serogroup A based on the clonal population structure of these bacteria. An international strain collection consisting of 423 group A strains isolated from 23 epidemics or outbreaks since 1963, as well as from older epidemics and numerous non-epidemic situations was used in the analysis. Strains were first segregated into electrophoretic types, depending on the combined score for the electrophoretic mobilities of 7 cytoplasmic isoenzymes resolved by starch gel electrophoresis and of 2 outer membrane proteins resolved by sodium dodecyl sulphate polyacrylamide gel electrophoresis. The bacteria were subsequently assigned to one of 21 clones after numerical analysis of their electrophoretic types. The epidemiological value of the typing scheme was assessed by examining case and carrier strains isolated during (1982-83) and subsequent to (1984-85) an epidemic in the Gambia, West Africa. The case isolates, all of which were serogroup A, were of a single clonal type. All serogroup A carrier isolates were also of this clone, while carrier strains of other serogroups showed greater clonal diversity. These results indicate that case strains during an epidemic show little clonal diversity and thus that the typing scheme is of value in distinguishing the etiology of epidemics. A retrospective epidemiological analysis of the strains in the international collection showed that most serogroup A epidemics were associated with a single or predominant clone, although some epidemics were of mixed etiology.(ABSTRACT TRUNCATED AT 250 WORDS)

Africa↗

PubMed1988

Clonal analysis of transplant-associated lymphoproliferations based on the structure of the genomic termini of the Epstein-Barr virus.

The clonal composition of various transplant-associated lymphoproliferations was assessed by means of Southern blot hybridizations using a DNA probe specific for the fused termini of the Epstein-Barr virus (EBV) genome. A single clonal band representing the joined EBV genomic termini was detected in most biopsies, demonstrating the presence of a monoclonal expansion of B lymphocytes carrying EBV DNA. Different configurations of immunoglobulin gene rearrangements and fused EBV genomic termini were frequently observed in tissues from different biopsy sites in individual patients, confirming the multiclonal origins for these lymphomas. In rare specimens, multiple forms of the joined termini were detected within individual lesions, which appeared polymorphous by histologic methods of analysis and polyclonal by immunologic and immunogenetic methods of analysis. These studies confirm that there is a spectrum of EBV-associated disorders of varying clonal composition that may arise in immunosuppressed organ-allograft recipients. The data are consistent with the proposal that the lymphoproliferations initiate as polyclonal expansions of EBV-carrying B cells, which progress to multiclonal lymphomas in most patients. Detection of homogeneous episomal EBV DNA in most lesions supports a primary role for the virus in the pathogenesis of these disorders.

B-Lymphocytes↗