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PubMed2001

Use of multiple primers in RAPD analysis of clonal organisms provides limited improvement in discrimination.

Randomly amplified polymorphic DNA (RAPD) analysis using two or more primers has been reported to provide additional discriminatory ability over one primer used individually. This may be of particular application in epidemiological typing of clonal organisms, such as Shiga toxin-producing E. coli O157, where strain differentiation can be difficult. Using four arbitrary primers individually, and in all possible permutations, E. coli O157 isolates and other arbitrarily chosen E. coli strains were typed using RAPD analysis. For most nonclonal strains, the use of two primers resulted in increased differentiation between isolates; however, more than two primers did not increase further the discriminatory capacity. E. coli O157 isolates that produced virtually identical profiles using one primer did not show increased differentiation when using two or more primers, demonstrating that in some cases, where strains of an organism are highly related, there is limited advantage to using more than one primer in RAPD analysis.

Bacterial Typing Techniques↗

PubMed1998

Analysis of clonal diversity in mouse immunoglobulin heavy chain genes selected for size of the antigen combining site.

Size-diversity of Ig and T cell receptor antigen binding (CDR3) regions can be visualized by "CDR3 fingerprinting", and provides an estimate of B- or T-cell repertoire complexity. The method does not identify clonal diversity, however, which can only be determined by random sequencing of the CDR3s. In this study we demonstrate that a combination of fingerprinting and single strand conformation polymorphism (SSCP) analysis can be used for a rapid estimation of clonal diversity within mouse Ig antigen binding regions selected for size. This application may be useful in the analysis of clonal expansion within B- and T-cell repertoires.

Amino Acid Sequence↗

PubMed1991

X-chromosome inactivation patterns using HPRT and PGK polymorphisms in haematologically normal and post-chemotherapy females.

Clonal analysis using X-chromosome inactivation patterns of the hypoxanthine phosphoribosyl transferase (HPRT) and phosphoglycerate kinase (PGK) genes has been used in the assessment of haematological malignancies. In many analyses normal haemopoietic tissue or constitutive DNA from each individual has not been readily available and it has been assumed that when the ratio of the percentage of the two alleles remaining after differential methylation enzyme digestion is greater than 3/1 then an oligoclonal/monoclonal population of cells is present. We report here in a study of 65 haematologically normal females informative for HPRT or PGK that 15 (23%) had a skewed Lyonization pattern with clonal analysis ratios greater than 3/1. No correlation was observed between age and the X-chromosome inactivation pattern to suggest the detection of pre-malignant clonal states. The incidence was similar in 23 females who had received conventional combination chemotherapy, with six women (26%) having a ratio greater than 3/1. In the majority of individuals therefore, conventional chemotherapy does not appear to alter the patient's X-chromosome inactivation pattern. These results indicate that caution must be exercised in interpreting the results of clonal analysis of any given individual.

Adolescent↗

PubMed1998

Analysis of clonality using X-linked polymorphisms in a patient with multiple myeloma and myelofibrosis.

We describe a patient who presented with a neutrophilic leukocytosis, normal karyotype, and IgA lambda multiple myeloma. One year after diagnosis she developed diffuse myelofibrosis as well as multiple lytic lesions of bone. Given the myeloproliferative features of her case, the clonality of her peripheral leukocytes was determined prior to treatment. Analysis of X-chromosome inactivation at the X-linked human androgen-receptor gene locus (HUMARA) proved that granulopoiesis was polyclonal. Subsequent treatment of the myeloma reversed with myelofibrosis and normalized her WBC count. This is the first case of multiple myeloma with myelofibrosis in which a concomitant clonal myeloproliferative disease was ruled out at a genetic level. The myeloproliferative features in this case are presumed to be induced by cytokines produced by the plasma cell clone.

Clone Cells↗

PubMed2000

Papillary serous carcinoma of the peritoneum: analysis of clonality of peritoneal tumors.

Papillary serous carcinoma of the peritoneum (PSCP) is a primary neoplasm of peritoneal origin, and is histologically difficult to differentiate from papillary serous carcinoma of the ovary (PSCO). PSCP is frequently accompanied by many peritoneal tumors, and has been managed as a disseminated disease. In previous reports, however, the clonality of the tumors has not been fully discussed. Recently, the significant roles of the p53 and BRCA1 genes in PSCP have been reported. In this study, we investigated immunohistochemical staining for p53 proteins, and investigated p53 gene mutations, using DNA sequencing analysis, to clarify the clonality of PSCP tumors. Immunohistochemically, all the tumor samples demonstrated nuclear overexpression of p53 proteins, and the DNA sequencing analysis of the p53 gene showed diverse point mutations at codons 167 and 192 in two of four anatomically different tumors. In conclusion, the possibility of polyclonality of PSCP tumors is suggested.

Aged↗

PubMed2004

Functional gene expression analysis of clonal plasma cells identifies a unique molecular profile for light chain amyloidosis.

Immunoglobulin light chain amyloidosis (AL) is characterized by a clonal expansion of plasma cells within the bone marrow. Gene expression analysis was used to identify a unique molecular profile for AL using enriched plasma cells (CD138+) from the bone marrow of 24 patients with AL and 28 patients with multiple myeloma (MM) and 6 healthy controls. Class prediction analysis (PAM) revealed a subset of 12 genes, which included TNFRSF7 (CD27), SDF-1, and PSMA2, that distinguished between these 2 groups with an estimated and observed accuracy of classification of 92%. This model was validated with an independent dataset of 11 patients with AL and 12 patients with MM with 87% accuracy. Differential expression for the most discriminant genes in the 12-gene subset was validated using quantitative real-time polymerase chain reaction and protein expression analysis, which upheld the observations from the micro-array expression data. Functional analyses using a novel network mapping software revealed a number of potentially significant pathways that were dysregulated in patients with AL, with those regulating proliferation, apoptosis, cell signaling, chemotaxis, and migration being substantially represented. This study provides new insight into the molecular profile of clonal plasma cells and its functional relevance in the pathogenesis of light chain amyloidosis.

Aged↗

PubMed2000

Dermatofibroma is a clonal proliferative disease.

Benign fibrous histiocytoma of the skin or dermatofibroma (DF) has been regarded as a fibrohistiocytic tumor. Whether DF is a neoplastic growth or a reactive process has not been settled. Since a neoplastic process is clonal in nature, clonal analysis of DF was conducted to see if DF is a clonal disease. Fresh specimens of 13 DFs and 2 hypertrophic scars obtained from female patients were studied. The adjacent nonlesional skin tissues served as controls. The clonal analysis was based on the methylation pattern of the polymorphic X-chromosome linked androgen-receptor gene (HUMARA). Eight DFs and 1 hypertrophic scar were heterozygous at the androgen receptor gene and could be analyzed. All 8 informative DFs showed a significant reduction in one of the allelic bands compared with the corresponding bands of the nonlesional tissue after Hha I digestion. Therefore, DF is a clonal proliferative disease. In contrast, 1 hypertrophic scar showed a polyclonal pattern of X-chromosome inactivation. We conclude that DF is a clonal disease favoring a neoplastic process.

Alleles↗

PubMed1995

Clonal hematopoiesis as defined by polymorphic X-linked loci occurs infrequently in aplastic anemia.

We evaluated the methylation status of the X-linked gene phosphoglycerate kinase (PGK1) and the DXS 255 locus detected by probe M27 beta to study clonality in acquired aplastic anemia (AA). A total of 30 females were suitable for clonal analysis of peripheral blood polymorphonuclear cells (PMN) and mononuclear cells using a polymerase chain reaction-based procedure in 24 patients and Southern blotting in 9. Overall, 10 of 30 patients exhibited an imbalanced X-inactivation pattern. However, in 4 patients, analysis of constitutional DNA suggested a skewed methylation pattern and 2 further cases had to be excluded because of the lack of an appropriate control. A truly clonal pattern was thus established in 4 of 30 (13%) patients. In 7 patients who later developed clonal disorders of hematopoiesis, X-inactivation analysis did not predict this event in any case. In patients with a paroxysmal nocturnal hemoglobinuria phenotype, there was no correlation between the proportion of phosphatidylinositol glycan anchored protein (PIG-AP)-deficient blood cells and the corresponding X-inactivation pattern. X-inactivation analysis detected clonal hematopoiesis in only 3 of 10 patients with a deficiency in PIG-AP in the cell population under study, but sorting of nucleated cells on the basis of PIG-AP expression showed the clonal nature of PIG-AP-deficient cells. We conclude that the majority of patients with AA show polyclonal hematopoiesis using X-linked clonal analysis, but that minor clonal populations, such as PIG-AP-deficient cells, may not be detected unless sorted cell populations are separately analyzed.

Adolescent↗

PubMed1997

A three-way ribotyping scheme for Salmonella serotype Typhimurium and its usefulness for phylogenetic and epidemiological purposes.

Ribotyping of Salmonella serotype Typhimurium strains was optimised as a tool for epidemiological and phylogenetic purposes. Of five restriction endonucleases evaluated on a series of 84 isolates, HincII, SalI and PvuII were the most useful, generating 13, 9 and 9 ribotypes with 17, 11 and 18 polymorphic restriction sites, and attaining a discrimination index (DI) of 0.81, 0.53 and 0.59, respectively. The combination of results from tests with the three enzymes provided further discrimination (19 ribotypes, DI=0.84). It proved useful for clonal analysis, defining 19 clonal lines with a remarkable degree of genetic heterogeneity, that were grouped into two major clusters (including 12 and 7 lines, respectively) at a significance level of 0.65. When the attributes of this system were compared with those of phage typing, it was found that ribotyping showed higher typability and sensitivity, supporting its use as an appropriate molecular method. In tracing the molecular epidemiology of Typhimurium strains in Asturias, six lines were found that could be considered endemic and were represented by organisms implicated in salmonellosis throughout the period of study; another four lines included organisms isolated from meat, water or both.

Animals↗

PubMed1979

Suppressor mutations causing partial reversion in the amiA region of Pneumococcus.

Mutants of an aminopterin-resistant strain of pneumococcus possessing four different suppressor genes have been isolated after mutagenesis with 5-BUdR. The suppressed strains exhibit a partial revertant phenotype since the parental aminopterin resistance remained unchanged but the associated sensitivity to an excess concentration of the branched chain amino acids L-isoleucine, L-valine and L-leucine was diminished almost to the level of the wild-type strain C13. The suppressor mutations had therefore dissociated the two properties associated with a mutation in the amiA cistron, namely aminopterin resistance and isoleucine sensitivity. The suppressor genes reduced the sensitivity to isoleucine of a number of amiA mutants, but had no effect on the level of resistance to a number of unrelated genes conferring resistance to other antibacterial substances. The suppressor mutations themselves did not confer resistance to aminopterin. Mapping of the suppressor mutations by recombination analysis and by clonal analysis showed them to be intragenic lying in the region near to the amiA-r19, amiA-r23, amiA-r17 loci.

Aminopterin↗

PubMed1989

Myeloproliferative disorders: usefulness of X-linked probes in diagnosis.

Myeloproliferative disorders are neoplasms of the pluripotent hematopoietic stem cell. Accurate diagnosis and distinction from reactive processes can be difficult therein with cytogenetic analysis only being useful in a minority of patients. Use of X-linked restriction fragment length polymorphism and methylation analysis has enabled clonal analysis to be performed in up to 50% of females, significantly increasing the proportion of analyzable patients over methods dependent on glucose-6-phosphate dehydrogenase heterozygosity. Using hypoxanthine phosphoribosyl transferase and phosphoglycerate kinase probes, we have demonstrated monoclonality of peripheral blood leukocytes in three females with myeloproliferative disorders who had uninformative chromosomal analysis. This technique greatly enhances the diagnosis of early myeloproliferative disorder.

Adult↗

PubMed1993

Randomly amplified polymorphic DNA analysis of clonal population structure and geographic variation in a freshwater bryozoan.

The randomly amplified polymorphic DNA (RAPD) assay was used to identify genetic polymorphisms in three clonal populations of the freshwater bryozoan, Cristatella mucedo, a species with few useful biochemical genetic markers. Of the 19 decamer oligonucleotide primers screened, 13 gave clear, reproducible RAPD profiles. Clonal population structure was evident, and one clone was dominant at each site. Cluster analysis grouped populations from more distant localities separately (Thames Valley and Norfolk), whereas populations from the Thames Valley clustered together. However, even at the regional scale a high degree of relatedness pertained. This work is one of the first RAPD studies of natural populations, and demonstrates the suitability of the technique for examining population structure and geographic variation in clonal taxa.

Animals↗

PubMed1998

Bowenoid papulosis showing polyclonal nature.

Bowenoid papulosis (BP) is characterized clinically by its benign-looking appearance and histologically by the features of high grade squamous intraepithelial lesions (SILs). The external genitalia of young people is a common site of occurrence, and most of the lesions undergo resolution by local treatments or even spontaneously. A strong association between BP and high risk types of human papillomavirus (HPV), especially HPV 16, has been reported and the incorporation of BP into the SIL category is generally accepted, but controversy still exists as to the true nature of BP. We analyzed the clonality of BP lesions occurring on both sides of the vulva of a 15-year-old girl. DNA was subjected to a polymerase chain reaction-based clonal analysis using the highly informative androgen receptor gene (HUMARA) with a nonisotopic modification. The clonal analysis of each BP lesion showed a random X-chromosome inactivation pattern, indicating a polyclonal nature of this disorder. Although monoclonal proliferation of vulvar SIL was recently reported, this is the first report of the polyclonality in a type of SIL diagnosed as BP, supporting a clinicopathologic heterogeneity in SIL of the vulva.

Adolescent↗

PubMed2004

Early TCR-beta and TCR-gamma PCR detection of T-cell clonality indicates minimal tumor disease in lymph nodes of cutaneous T-cell lymphoma: diagnostic and prognostic implications.

The lymph nodes are generally the first extracutaneous manifestation in patients with cutaneous T-cell lymphoma (CTCL); however, their early involvement is difficult to assess. The aim of our study was to define the diagnostic and prognostic value of T-cell clonality analysis for a more precise assessment of lymph node involvement in CTCL. T-cell clonality was determined by 2 independent polymerase chain reaction (PCR) assays, namely a recently developed T-cell receptor-beta (TCR-beta) PCR technique as well as an established TCR-gamma PCR. T-cell clonality was found in 22 of 22 lymph nodes with histologically detectable CTCL involvement as well as in 7 of 14 histologically noninvolved dermatopathic lymph nodes. The clonal T-cell populations in the lymph nodes were in all cases identical to those detected in the corresponding skin lesions, identifying them as the tumor cell population. T-cell clonality was not found in any of the 12 dermatopathic lymph nodes from 12 patients with inflammatory skin diseases. Clonal T-cell detection in 7 of 14 dermatopathic lymph nodes of patients with CTCL was associated with limited survival (74 months; confidence interval [CI], 66-82 months) as in patients with histologically confirmed lymph node involvement (41 months; CI, 35-47 months), whereas all patients without T-cell clonality in the lymph nodes (7 patients) were alive at the last follow-up. Thus, T-cell clonality analysis is an important adjunct in differentiating benign dermatopathic lymphadenitis from early CTCL involvement.

Adult↗

PubMed1986

Conversion of acute undifferentiated leukemia phenotypes: analysis of clonal development.

The cellular origin of acute undifferentiated leukemia (AUL) is still a matter of controversy. We report on two cases in which the diagnosis of AUL was established according to restricted criteria. Blast cells of both patients showed phenotypic conversion during the course of disease. In one case, within 24 days from starting treatment, the leukemic phenotype changed from AUL to acute myelomonocytic leukemia (FAB L1, TdT+ to FAB M4, TdT-). The initial phenotype of this acute leukemia was characterized by the co-expression of both B-lymphoid and myeloid markers on the same cell. Moreover, analysis of esterase isoenzyme pattern showed the whole spectrum of isoenzymes typically seen in myelomonocytic leukemias already at diagnosis, yet blast cells additionally contained all three isoenzymes of beta-hexosaminidase typically seen in AUL. However, examination of immunoglobulin (Ig) heavy chain gene rearrangement initially and after conversion revealed an identical monoclonal configuration of Ig heavy chain sequences in both samples. The second AUL patient relapsed after allogeneic bone marrow transplantation with common ALL-antigen (CALLA) positive acute leukemia. Subsequent Southern blot analysis showed a novel rearranged Ig fragment compared to the analysis before transplantation indicating that the leukemic clones prior to and after transplantation were not identical. No chromosomal abnormalities were observed in both cases. These data support the view that AUL cells originate from a pluripotent stem cell that is capable to differentiate in the myelomonocytic lineage (patient 1), and confirm the value of Ig gene analysis as marker for cellular clonality.

Adult↗

PubMed1997

Molecular analysis of clonality in Kaposi's sarcoma.

BACKGROUND: Kaposi's sarcoma is considered to be an angioproliferative disease associated with a novel herpesvirus (KSHV/HHV8), but the precise pathophysiology of the lesion remains unclear. The study of clonality in Kaposi's sarcoma using X linked DNA polymorphism has been difficult so far, because of a very strong prevalence of the disease in males. AIMS: To study the clonality of Kaposi's sarcoma lesions. METHODS: An assay based on a methyl sensitive restriction digest followed by polymerase chain reaction (PCR) amplification of the highly polymorphic human androgen receptor (HUMARA) gene was used. Tissues from Kaposi's sarcoma lesions and control tissues from the same patients were obtained from seven females, four with classic Kaposi's sarcoma and three with AIDS associated Kaposi's sarcoma. A cutaneous angiosarcoma was also analysed, for comparative purposes, and showed evidence of clonality after HpaII digestion. RESULTS: All patients were heterozygous for the HUMARA polymorphism and informative for analysis. In all patients, including four with a nodular form of Kaposi's sarcoma and more than 70% spindle cells in the lesion, a polyclonal pattern of inactivation could be demonstrated. CONCLUSIONS: The Kaposi's sarcoma lesion is first of all a polyclonal cell proliferation.

Acquired Immunodeficiency Syndrome↗

PubMed2004

Analysis of clonal composition of Mycobacterium tuberculosis isolates in primary infections in children.

The assumption that Mycobacterium tuberculosis infections should be considered clonally homogeneous has been weakened in the last few years. Recent studies have shown (i) the isolation of different M. tuberculosis strains from sequential episodes, (ii) mixed infections by two M. tuberculosis strains, and (iii) genetic variations in M. tuberculosis subpopulations due to microevolution events. Nevertheless, it is unknown whether clonal heterogeneity could be found in the initial steps of M. tuberculosis infection, i.e., the primary infection. In the present study we analyzed the clonal composition of the M. tuberculosis isolates causing primary infections in children. Cultures were clonally homogeneous in most cases (11 of 12). In 1 of the 12 cases (8.3%), clonal heterogeneity among the M. tuberculosis isolates was found by spoligotyping and IS6110-based restriction fragment length polymorphism analysis. This case occurred in a 2-year-old child in whom microevolution events were unlikely and who had no risk factors for overexposure to M. tuberculosis. Clonal heterogeneity should also be considered in primary M. tuberculosis infections, including circumstances in which it is usually unexpected.

Adolescent↗

PubMed1990

Functional analysis of clonally expanded CD8, TCR gamma delta T cells in a patient with chronic T-gamma lymphoproliferative disease.

Leukemic cells from a patient with T-gamma lymphocytosis were found to have the surface phenotype, CD3+, CD4-, CD8+, Leu19+, TCR delta 1+, WT31-. The clonal nature of the TCR gamma delta T cell proliferation was documented by flow cytometry and Southern blot analysis. Morphologically, they were large to medium-sized mature lymphocytes with cytoplasmic granules. Functionally, the cells revealed strong cytotoxic activities against NK-sensitive target cells, but had neither killer T cell activity nor suppressive activity on PWM-driven immunoglobulin synthesis by B cells. Interestingly, both suppressive and cytotoxic T cell activities were recovered with the depletion of CD8+ T cells. These studies may suggest some functions of the CD8+ population of human TCR gamma delta T cells in a normal immune system.

Aged↗