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PubMed2006

Molecular evolution of typical enteropathogenic Escherichia coli: clonal analysis by multilocus sequence typing and virulence gene allelic profiling.

Enteropathogenic Escherichia coli (EPEC) infections are a leading cause of infantile diarrhea in developing nations. Typical EPEC isolates are differentiated from other types of pathogenic E. coli by two distinctive phenotypes, attaching effacement and localized adherence. The genes specifying these phenotypes are found on the locus of enterocyte effacement (LEE) and the EPEC adherence factor (EAF) plasmid. To describe how typical EPEC has evolved, we characterized a diverse collection of strains by multilocus sequence typing (MLST) and performed restriction fragment length polymorphism (RFLP) analysis of three virulence genes (eae, bfpA, and perA) to assess allelic variation. Among 129 strains representing 20 O-serogroups, 21 clonal genotypes were identified using MLST. RFLP analysis resolved nine eae, nine bfpA, and four perA alleles. Each bfpA allele was associated with only one perA allele class, suggesting that recombination has not played a large role in shuffling the bfpA and perA loci between separate EAF plasmids. The distribution of eae alleles among typical EPEC strains is more concordant with the clonal relationships than the distribution of the EAF plasmid types. These results provide further support for the hypothesis that the EPEC pathotype has evolved multiple times within E. coli through separate acquisitions of the LEE island and EAF plasmid.

Adhesins, Bacterial↗
PubMed1987

Clonal analysis of the anti-DNA repertoire of murine B lymphocytes.

The present studies characterize at the clonal level the repertoire of lipopolysaccharide-responsive murine B lymphocytes committed to the production of antibodies reactive with denatured DNA. This repertoire is vast in normal mice as 1-5% of total mitogen-induced antibody-forming cell clones secreted denatured DNA-reactive antibodies when the splenocyte donors were CBA (Ighj), BALB/c (Igha), C57BL/6 (Ighb), CBA nu/nu, and C57BL/6 nu/nu athymic mice. The autoimmune NZB (Ighe) strain did not display elevated proportions of anti-denatured DNA antibody-forming cell precursors. Cross-reactions shown by CBA anti-denatured DNA antibodies suggest that many antibodies might derive significant binding energy from interaction with the bases or similar hydrophobic moieties. Cross-reactions with other tested polynucleotides were frequent, but cross-reactions with phospholipids and phosphocholine were undetectable. Most anti-DNA antibodies bound preferentially or exclusively to single-stranded denatured DNA as compared to double-stranded native DNA. The frequency of anti-denatured DNA antibody-forming cell precursors among CBA peritoneal cells was not elevated. Fluorescence-activated cell sorter-selected Ly-1-positive NZB splenic B cells were not enriched, and Ly-1 negative B cells were not depleted of anti-DNA antibody-forming cell precursors. These results show that antibody-forming cell precursors specific for denatured DNA are not restricted to the Ly-1 positive B-cell subset.

Animals↗
PubMed1995

Clonal analysis of peripheral blood and haemopoietic colonies in patients with aplastic anaemia and refractory anaemia using the polymorphic short tandem repeat on the human androgen-receptor (HUMARA) gene.

The clonalities in white blood cells (WBC) of blood and nucleated bone marrow cells from patients with refractory anaemia and aplastic anaemia were examined by polymerase chain reaction (PCR) methods using the polymorphic short tandem repeat (STR) on the human androgen-receptor gene (HUMARA). Peripheral blood samples were obtained from 12 female patients, six with aplastic anaemia (AA) and six with refractory anaemia (RA). Peripheral blood was fractionated into granulocytes, lymphocytes, T lymphocytes and B lymphocytes. DNA was extracted from each fraction. Bone marrow samples were obtained from seven female patients (three with AA and four with RA). Sorted CD34 positive cells were cultured in a semisolid culture system. DNA was extracted from a 14-day haemopoietic colony. The clonal pattern was assessed using HUMARA gene STR polymorphism and the differential methylation pattern of nearby cytosine residues by PCR methods. Four of six (67%) AA and two of six (33%) RA patients had a monoclonal proliferating pattern in their granulocytes. The ratio of the numbers of minority colonies per majority colonies (m/M ratio) was examined for seven patients (three AA and four RA). In patients who had a clonal haemopoietic pattern in peripheral WBC the ratio was under 0.4 but not zero. In contrast, patients exhibiting a polyclonal pattern had an m/M ratio above 0.8. We concluded that some normal or heterogenous haemopoietic clones, not only MDS but also AA, may remain in the bone marrow, although almost all colonies were derived from a single pathogenic clone when the clonality pattern exhibited monoclonality in peripheral blood analysis.

Adult↗
PubMed1996

Tubulogenesis from isolated single cells of adult mammalian kidney: clonal analysis with a recombinant retrovirus.

The adult mammalian kidney tubule epithelium exists in a relatively dormant, slowly replicative state but has a large potential for regenerative morphogenesis following severe ischemic or toxic injury. Under selective serum-free growth conditions, which included epidermal growth factor and retinoic acid, a subpopulation of renal proximal tubule cells isolated from adult rabbit kidney were grown in cell culture. These cells possessed two important characteristics: 1) an ability to differentiate morphogenically into tubule structures when grown in three-dimensional collagen gels and 2) a high capacity for self-renewal, since cell lineage analysis with a recombinant retrovirus demonstrated that in vitro tubulogenesis arose from clonal expansion of a single cell. Thus individual cells in the adult kidney have retained the ability for kidney tubulogenesis in vitro.

Animals↗
PubMed1994

Clonal analysis of glandular stomach carcinogenesis in C3H/HeN<==>BALB/c chimeric mice treated with N-methyl-N-nitrosourea.

The clonal growth of gastric carcinomas was investigated immunohistochemically in C3H<==>BALB/c chimeras using a strain specific antibody. C3H, BALB/c and chimeric mice were given N-methyl-N-nitrosourea 0.5 mg/mice once a week for a total of 10 times by intragastric intubation and observed until week 50. In normal gastric mucosa of the chimeras, each gland was composed entirely of C3H strain specific antigen (CSA)-positive or -negative cells and no mixed glands were found. Cells of all adenomatous hyperplasias and adenocarcinomas in chimeric mice were, in each case, homogeneous for one or other of the parental types, while comprising both surface mucous cell and pyloric gland cell forms. The results clearly suggest that individual cancers are derived from single cells with multi-potential activities and that cellular differentiation of gastric cancer cells occurs secondarily.

Adenocarcinoma↗
PubMed2004

Clonal analysis of individual marrow-repopulating cells after experimental peripheral blood progenitor cell transplantation.

Methods to analyze the clonality of an adverse event in preclinical or clinical retroviral stem cell gene therapy protocols are needed. We analyzed the progeny of retrovirally transduced human peripheral blood progenitor cells (PBPCs) after transplantation and engraftment in immune-deficient mice. The integration site of the provirus serves as a unique tag of the individual transduced PBPC. A plasmid library of junctions between proviral and human genomic DNA was generated. We were able to detect individual transduced cell clones that amounted to 0.14%-0.0001% of chimeric bone marrow cells. This is the first report in which the contribution of individual marrow-repopulating cells to human hematopoiesis is directly quantified.

Animals↗
PubMed1993

Clonal analysis of the expression of multiple transformation phenotypes and tumorigenicity by morphologically transformed 10T1/2 cells.

Seventy-five clonal populations of morphologically transformed 10T1/2 cells were established from independent Type II and Type III foci that were of spontaneous origin or were induced by the carcinogenic agents N-methyl-N'-nitro-N-nitrosoguanidine, benzo(a)pyrene diol epoxide-I, and 3-methylcholanthrene. Clonal populations were characterized for expression of selected transformation phenotypes, including growth to elevated saturation density before cessation of proliferation, anchorage independence, ability to reconstruct foci when plated in the presence of wild-type 10T1/2 cells, and tumorigenicity. Forty-one % of the clonal populations expressed only the phenotype of morphological transformation, while 20% expressed all of the transformation phenotypes, including tumorigenicity, in addition to morphological transformation. The remaining clonal populations expressed varying combinations of one or more of the four transformation phenotypes. Clonal populations expressing almost all of the 16 possible combinations of the transformation phenotypes were observed, suggesting that the individual phenotypes segregated independently. Morphological transformation alone was a poor indicator of tumorigenicity, correctly predicting the tumorigenic potential of only 37% of the clonal populations. Among morphologically transformed clonal populations, coexpression of anchorage independence correctly predicted the tumorigenicity of 81% and coexpression of reconstruction of foci on a confluent lawn of wild-type cells correctly predicted the tumorigenicity of 91%. The probability that a morphologically transformed clonal population was tumorigenic correlated with the total number of transformation phenotypes expressed. Expression of the transformation phenotypes differed between tumorigenic and nontumorigenic clonal populations but not between clonal populations established from Type II and Type III foci. Tumorigenicity varied among transformed clonal populations that were induced by the different carcinogenic agents or were of spontaneous origin but did not differ between clonal populations established from Type II and Type III foci.

Animals↗
PubMed1996

Clonal analysis of human recurrent superficial bladder cancer by immunohistochemistry of P53 and retinoblastoma proteins.

PURPOSE: To investigate the clonal origin of malignant cells in recurrent superficial bladder cancer. MATERIALS AND METHODS: We compared the protein expression of p53 and retinoblastoma (Rb) by immunohistochemistry using antibody P1801 and PMG3-245, respectively, in 13 patients at the time of primary superficial bladder cancer resection (6 Ta and 7 T1) and their 15 corresponding recurrences of disease. Mutations in p53 and Rb were inferred on the basis of immunoperoxidase staining. RESULTS: At the time of initial tumor resection, a p53 mutation was observed in 5 patients (39%) and an Rb mutation was observed in 3 (23%). The p53/Rb mutation status of recurrent bladder cancers completely matched their corresponding primary bladder cancer. CONCLUSIONS: The chance that recurrent bladder cancer originated from independent clones in this study was extremely small (p < 10(-6)). This result strongly supports the monoclonal origin of recurrent superficial bladder cancer.

Carcinoma, Transitional Cell↗
PubMedDate not supplied

Clonal analysis by PCR and RFLP in breast cancer and precancerous lesions. Preliminary data.

In order to investigate the clonality in various benign, precancerous and malignant breast lesions, we analyzed small DNA samples from paraffin sections of various breast lesions by polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) of the X-chromosome-linked phosphoglycerokinase (PGK) gene. DNA from the lesion as well as from the adjacent normal tissue were analyzed in each case. Two restriction endonucleases. Hpa-II, a methylation sensitive restriction enzyme and Bst XI, a restriction endonuclease, which recognizes this polymorphic site on the PGK gene, were used. Of 19 cases, one case of in situ ductal Ca (DCIS), two cases of invasive ductal Ca and one case of multifocal ductal Ca were shown to be monoclonal. Two cases of intraductal papillomas were found to be polyclonal. One case of atypical ductal hyperplasia showed no conclusive findings. Additionally DNA was not yielded from 3 cases and other 7 cases were not informative, derived from females homozygotes. Further study of a larger number of cases is in progress.

Breast Neoplasms↗
PubMed2002

A method for clonal analysis of epidermal growth factor-responsive neural progenitors.

Epidermal growth factor (EGF) responsive neural progenitors are defined by clonal growth from single cells. In previous studies we were unable to obtain clones at single cell densities using trypsinized cells and trituration alone always gave cellular aggregates. Here we report on single cell derived clones using a technique involving trituration of EGF responsive neurospheres, cell filtration, and single cell sorting using a MoFlo high speed fluorescence activated cell sorter. Single cell deposition was confirmed by labeling cells with Hoechst 33342 and Flow-check Fluorospheres, and visualization by fluorescence microscopy. The cells were deposited into liquid medium and grown from single cells in 10-20 ng/ml EGF for 12-14 days. This gave a cloning efficiency of 2.12%+/-0.37. New colonies occurred as late as day 18 post-sort. Tritiated thymidine suicide indicates that a percentage of these cells are cycling. Immunohistochemical analysis for oligodendrocytes, astroglia, and neuronal lineages performed on colonies at 10-14 and 21-28 days gave 39% uni-lineage, 36% bi-lineage, and 25% tri-lineage colonies. A total of five different types of progenitor cells were observed. In individual colonies, oligodendrons predominated with a lesser presence of astroglial or neuronal cell types. This approach establishes a reliable and reproducible method for single cell cloning of neurosphere cells.

Animals↗
PubMed1997

Modification of IgH PCR clonal analysis by the addition of sucrose and cresol red directly to PCR reaction mixes.

Diagnostic immunoglobulin (Ig) polymerase chain reaction (PCR) clonality analyses need to be simple, reproducible, and rapid. Sucrose and cresol red (gel loading buffer reagents) were added to a routine IgH PCR reaction mix to obviate the need for adding gel loading buffer separately after PCR amplification. Not only did this decrease the time spent after PCR analysis but also gave similar or enhanced IgH PCR product intensity compared with normal IgH PCR conditions on polyacrylamide gel electrophoresis. This procedure was easily adapted to routine PCR analysis without the need for further manipulations or optimisation of the PCR reaction mix, and it increased the reproducibility and specificity of the IgH PCR products.

Clone Cells↗
PubMed1991

Clonal analysis of CD4+/CD8+ T cells in a patient with aplastic anemia.

T cell clones were established from peripheral blood of a patient with severe aplastic anemia. 8 of 18 individual clonal T cell populations stably coexpressed CD4 and CD8 molecules, a phenotype characteristic for thymocytes and a minor subpopulation of circulating T lymphocytes. Analysis of T cell receptor genes revealed identical rearrangements of T cell receptor beta chain genes, suggesting clonality of these T cells. CD4+/CD8+ T cells clones were found to be efficiently cytotoxic towards autologous lymphoblasts. Autocytotoxicity could be blocked by a CD3 MAb, a MAb specific for monomorphic MHC class II determinants, and particularly, by an MHC-DP-specific MAb, suggesting specificity for autologous DP molecules. Perhaps more important, CD4+/CD8+ T cell clones inhibited differentiation of autologous progenitor enriched bone marrow cells in vitro by a direct cell-mediated mechanism. These data suggest that circulating cytotoxic CD4+/CD8+ T cell clones specific for autologous MHC-DP determinants may be involved in hematopoietic failure in some cases of aplastic anemia.

Adult↗
PubMed1989

Clonal analysis of childhood acute lymphoblastic leukemia with "cytogenetically independent" cell populations.

Acute lymphoblastic leukemia (ALL) is generally regarded as a clonal disease in which a single abnormal progenitor cell gives rise to neoplastic progeny. Five of 463 cases of childhood ALL with adequately banded leukemic cells were found to have two cytogenetically independent cell populations. In addition, two of the four cases tested had more than two rearranged immunoglobulin genes and (or) T cell receptor genes. To investigate the clonality of these unusual leukemias, we examined the neoplastic cells for X-linked markers extrinsic to the disease. Leukemic cells from each of the three patients heterozygous for an X-linked, restriction fragment length polymorphism showed a single active parental allele, suggesting that both apparently independent cell populations developed from a common progenitor. These cases provide evidence that leukemogenesis involves a multistep process of mutation and suggest that karyotypic abnormalities may be a late event of malignant transformation.

Alleles↗
PubMed1998

Clonality analysis of hematopoiesis and thrombopoietin levels in patients with essential thrombocythemia.

Essential thrombocythemia (ET) is a myeloproliferative disorder, characterized by sustained thrombocytosis. Diagnosis requires the elimination of all known causes of thrombocytosis. ET is believed to be a clonal disorder, and we investigated the frequency of a clonal hematopoiesis in this disease with the aim of using this as a positive diagnostic criterion. However, a non-random inactivation pattern can be encountered in normal females which mimics clonal hematopoiesis. In addition, the percentage of normal females with skewed lyonization seems higher using techniques based on the difference in DNA methylation, compared to G6PD enzyme polymorphism. Recently, new techniques based on transcript analysis have been developed. We report here the results of clonality studies of hematopoiesis in 53 ET patients using two different techniques based on DNA and RNA polymorphisms, and T-lymphocytes as a control tissue of lyonization. The majority of ET patients showed monoclonal hematopoiesis in the presence of polyclonality of T-lymphocytes. Because all ET patients did not show the same clonal pattern of hematopoiesis, we searched for inappropriate secretion of thrombopoietin (TPO) in patients with polyclonal disease. This assay was performed in 48 patients, of whom 9 showed polyclonal hematopoiesis and 27 monoclonal hematopoiesis. We found no difference in TPO levels between ET patients and normal controls, nor between patients with polyclonal hematopoiesis and those with monoclonal hematopoiesis. Our results confirm the high frequency of monoclonal hematopoiesis in ET, the usefulness of RNA markers, and the possibility of using T-lymphocytes as a control tissue for X-chromosome inactivation patterns. On the other hand, TPO levels are not decreased even in ET patients with high platelet counts, suggesting an increased production or decreased clearance of TPO in this disease.

Adolescent↗
PubMed2000

Clonal analysis of the human B-cell repertoire using a heteromobility assay.

A heteromobility duplex tracking assay was developed to analyze B-cell clonality. The assay was based on the genetic variability of B-cell immunoglobulin (Ig) sequences. Binding of amplified (Ig) sequences to a single-stranded radiolabeled Ig DNA probe resulted in the formation of heteroduplexes. The mobilities of these heteroduplexes helped to distinguish clonal B cells.

Antigens, Differentiation, B-Lymphocyte↗
PubMed1998

Clonal analysis by ribotyping of Fusobacterium nucleatum isolates obtained from healthy young adults with optimal plaque control.

Fusobacterium nucleatum is a Gram-negative anaerobic rod implicated in the pathogenesis of periodontal disease. However, this organism has also been frequently identified in high numbers in healthy adults. These observations suggest that the species may comprise different clonal types, some of which may participate in disease. The purpose of the present investigation was to use restriction endonuclease analysis (REA) and ribotyping to characterize F. nucleatum clonal types isolated from healthy young adults with optimal plaque control and investigate the stability of some of these clonal types. A group comprising 11 dental students and 11 dental outpatients with optimal plaque control was sampled. Clonal stability was investigated by sampling the dental student group at baseline and at 16 months. One hundred and thirty-two clinical isolates of F. nucleatum were successfully recovered from 15/22 individuals. For the positive subjects, 29 different clonal types were identified by REA and ribotyping, each subject and site being colonized by 1-4 clonal types. For the dental students, 9 and 15 different clonal types were identified at baseline and 16 months, respectively. None of the students harboured identical clonal types at both sampling times. Our results show that ribotyping is a useful technique for monitoring the distributions of F. nucleatum clonal types and indicate that healthy individuals with optimal plaque control can be colonized by more than one F. nucleatum clonal type and that these clonal types appear to be unstable.

Adult↗
PubMed1999

The cellular ecology of progressive neoplastic transformation: a clonal analysis.

A comparison was made of the competence for neoplastic transformation in three different sublines of NIH 3T3 cells and multiple clonal derivatives of each. Over 90% of the neoplastic foci produced by an uncloned transformed (t-SA') subline on a confluent background of nontransformed cells were of the dense, multilayered type, but about half of the t-SA' clones produced only light foci in assays without background. This asymmetry apparently arose from the failure of the light focus formers to register on a background of nontransformed cells. Comparison was made of the capacity for confluence-mediated transformation between uncloned parental cultures and their clonal derivatives by using two nontransformed sublines, one of which was highly sensitive and the other relatively refractory to confluence-mediated transformation. Transformation was more frequent in the clones than in the uncloned parental cultures for both sublines. This was dramatically so in the refractory subline, where the uncloned culture showed no overt sign of transformation in serially repeated assays but increasing numbers of its clones exhibited progressive transformation. The reason for the greater susceptibility of the pure clones is apparently the suppression of transformation among the diverse membership that makes up the uncloned parental culture. Progressive selection toward increasing degrees of transformation in confluent cultures plays a major role in the development of dense focus formers, but direct induction by the constraint of confluence may contribute by heritably damaging cells. In view of our finding of increased susceptibility to transformation in clonal versus uncloned populations, expansion of some clones at the expense of others during the aging process would contribute to the marked increase of cancer with age.

3T3 Cells↗
PubMed1991

Clonal analysis of transient myeloproliferative disorder in Down's syndrome.

Three Down's syndrome patients with transient myeloproliferative disorder were studied for clonality of the proliferating blast cells using the X chromosome-linked polymorphic gene phosphoglycerate kinase, immunoglobulin heavy chain (IgH) gene and T-cell antigen receptor (TCR) (beta, gamma, delta) genes. None of the three cases showed rearrangements of IgH, TCR beta, gamma, or delta genes, indicating the non-lymphoid nature of the proliferating blast cells. The X chromosome inactivation pattern showed that the cells in the blast population in all of the three cases of transient myeloproliferative disorder were clonal. These data suggest that at least some of this disorder can be due to a spontaneously regressing clone of malignant cells.

Adolescent↗