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PubMed2006

[Clonality study of palmar fibromatosis].

OBJECTIVE: To study the clonality of palmar fibromatosis by molecular genetic analysis of X chromosome inactivation pattern at a polymorphic site of human androgen receptor gene (HUMARA). METHODS: Twelve female cases of palmar fibromatosis were enrolled into this study. Hematoxylin and eosin-stained sections of paraffin-embedded, formalin-fixed tissues were microdissected by laser capture microdissection technology in order to obtain the proliferative spindle cells. Tumor cells isolated from rectal adenocarcinoma in a female patient were used as positive control. The genomic DNAs were extracted with phenol and chloroform, digested with methylation-sensitive restriction endonuclease HpaII, and amplified by polymerase chain reaction (PCR) using primers targeted to a highly polymorphic short tandem repeat of HUMARA. The amplimers were separated on vertical 8% non-denaturing polyacrylamide gels and the patterns were visualized with ethidium bromide stain. RESULTS: The methodology for clonality analysis was validated in the positive control using rectal adenocarcinoma cells. Among the 12 cases studied, PCR amplification failed in 3 samples and 1 sample showed homozygosity which was not suitable for further analysis. Eight samples were successfully amplified and showed a random X chromosome inactivation pattern, suggesting polyclonality in these lesions. CONCLUSIONS: Palmar fibromatosis is a polyclonal condition and should be considered as a form of non-neoplasmic fibroblastic proliferation.

Actins↗
PubMed2003

Design and standardization of PCR primers and protocols for detection of clonal immunoglobulin and T-cell receptor gene recombinations in suspect lymphoproliferations: report of the BIOMED-2 Concerted Action BMH4-CT98-3936.

In a European BIOMED-2 collaborative study, multiplex PCR assays have successfully been developed and standardized for the detection of clonally rearranged immunoglobulin (Ig) and T-cell receptor (TCR) genes and the chromosome aberrations t(11;14) and t(14;18). This has resulted in 107 different primers in only 18 multiplex PCR tubes: three VH-JH, two DH-JH, two Ig kappa (IGK), one Ig lambda (IGL), three TCR beta (TCRB), two TCR gamma (TCRG), one TCR delta (TCRD), three BCL1-Ig heavy chain (IGH), and one BCL2-IGH. The PCR products of Ig/TCR genes can be analyzed for clonality assessment by heteroduplex analysis or GeneScanning. The detection rate of clonal rearrangements using the BIOMED-2 primer sets is unprecedentedly high. This is mainly based on the complementarity of the various BIOMED-2 tubes. In particular, combined application of IGH (VH-JH and DH-JH) and IGK tubes can detect virtually all clonal B-cell proliferations, even in B-cell malignancies with high levels of somatic mutations. The contribution of IGL gene rearrangements seems limited. Combined usage of the TCRB and TCRG tubes detects virtually all clonal T-cell populations, whereas the TCRD tube has added value in case of TCRgammadelta(+) T-cell proliferations. The BIOMED-2 multiplex tubes can now be used for diagnostic clonality studies as well as for the identification of PCR targets suitable for the detection of minimal residual disease.

Chromosome Aberrations↗
PubMed2025

Combined somatic mutation and transcriptome analysis reveals region-specific differences in clonal architecture in human cortex.

The human cerebral cortex is specialized into regions, but little is known about how human cellular lineages shape cortical regional variation and neuronal cell-type distribution during development. Here, we map single-cell lineages of human cortical regions and neuronal subtypes using >1,000 somatic single-nucleotide variants (sSNVs) identified from deep bulk whole-genome sequencing and analyzed over 25 regions and >72,000 single cells. In the fronto-parietal cortex, sSNVs are rarely restricted, marking neuron-generating clones that disperse into neighboring regions. In contrast, the primary visual cortex harbors 30%-70% more sSNVs than the neighboring secondary visual cortex. Clones at this border exhibit more restricted dispersion, suggesting late developmental lineage segregation. Single-nucleus sSNV and whole-transcriptome analysis reveal glutamatergic neuron clones with modest regional restrictions that share low-mosaic sSNVs with some GABAergic neurons, suggesting a recent dorsal cortical progenitor. Our analysis reveals human-specific cortical lineage patterns, regional differences in clonal patterns, and late divergence of some glutamatergic/GABAergic lineages.

Humans↗
PubMed1998

Gamma/delta T cell lymphoma presenting in the subcutaneous tissue and small intestine in a patient with capillary leak syndrome.

Peripheral T cell neoplasms originating from gamma/delta T cells are rarely reported, despite the development of hepatosplenic lymphoma from gamma/delta T cells. We report a case of multiple generated gamma/delta T cell lymphomas presenting in the subcutaneous tissue and small intestine in a patient with accompanying capillary leak syndrome. The patient, a 43-year-old male presented with remarkable systemic edema, pleural effusion, and ascites. Widespread tumors were evident in the subcutaneous tissue and in the small intestine. A biopsy revealed anaplastic large cell lymphoma in these lesions. Phenotypic examination showed that the neoplastic cells were positive for the surface markers CD3 and TCR delta, but negative for CD4, CD8 and TCR beta. Genomic analysis revealed a clonal rearrangement of the TCR genes encoding the gamma, delta, and beta chains. A polymerase chain reaction analysis of the gene encoding the TCR delta chain showed that the rearrangement occurred between V delta 3 and J delta 1, suggesting that neoplastic cells were generated in the early stages of T cell differentiation.

Adult↗
PubMed1993

Lysogenic phage in Salmonella enterica serovar heidelberg (Salmonella Heidelberg): implications for organism tracing.

A phage typing system using a group of 11 closely related phage (as judged by Southern analysis and restriction fragment length polymorphism analysis) was able to distinguish at least six phage types in Salmonella heidelberg of human and animal origin. Restriction fragment length polymorphism analysis using cosmid probes from S. heidelberg confirmed that most S. heidelberg isolates belong to a single 'clonal' group. Southern analysis using DNA isolated from each of the testing phage group showed that phage types 4, 5 and 6 carry closely related endogenous or lysogenic phage. Induction of a lysogenic phage Hlp-4 (Heidelberg lysogenic phage) from type 4 could become lysogenic and convert phage types 1 and 3 to phage type 4 and phage type 5 to a non-typable phenotype.

Bacteriophage Typing↗
PubMed2000

Allelotype analysis of flow-sorted breast cancer cells demonstrates genetically related diploid and aneuploid subpopulations in primary tumors and lymph node metastases.

Flow cytometric DNA content measurements have demonstrated extensive DNA ploidy heterogeneity in primary breast carcinomas. However, little is known at the molecular level about the clonal relationship between these tumor cell subpopulations, or about the molecular genetic changes associated with aneuploidization. We have used flow cytometric cell sorting to dissect some of this complexity by isolating clonal subpopulations in breast carcinomas for comparative molecular genetic analysis. Clonal subpopulations were isolated from 12 primary breast carcinomas and 5 lymph node metastases from 4 cases based on DNA content and cytokeratin 8/18 labeling. DNA from these clones was screened for allelic imbalances with 92 polymorphic microsatellite markers mapped to 39 different chromosome arms. Diploid and aneuploid populations were concurrently present in 11 out of 12 primary tumors. The DNA ploidy status of primary tumors was identical to that of the related lymph node metastases. Allelic imbalance was present in 10 out of 11 diploid clones (mean, 3.4 +/- 4.2). All allelic imbalances observed in the diploid clones recurred in the cognate aneuploid clones, but were, in the latter, accompanied by additional allelic imbalances at other loci and/or chromosome arms (mean, 10.9 +/- 5.8). In only two of the four metastatic cases did the allelotypes of metastatic clones show small differences relative to their cognate primary tumors. The primary diploid tumor clone recurred in all lymph node metastases. This study indicates that the majority of allelic imbalances in breast carcinomas are established during generation of DNA ploidy diversity. Recurrence of the allelic imbalances in diploid clones in the aneuploid clones suggests linear tumor progression, whereas the simultaneous presence of early diploid and advanced aneuploid clones in both primary and metastatic tumor sites suggests that acquisition of metastatic propensity can be an early event in the genetic progression of breast cancer.

Alleles↗
PubMed2004

Identification of Campylobacter jejuni multilocus sequence type ST-21 clonal complex by single-nucleotide polymorphism analysis.

Conserved single-nucleotide polymorphisms (SNPs) which characterize the allelic profile of the major epidemiological lineage ST-21 were identified from the alleles within the current Campylobacter jejuni multilocus sequence typing (MLST) database. Allelic discrimination assays were designed for the detection of SNPs, enabling rapid strain profiling for clonal complex ST-21. This method is suitable for epidemiological investigations and is complementary to full MLST.

Alleles↗
PubMed1992

Histopathologic, immunophenotypic and genotypic analyses in ocular adnexal lymphoproliferative disorders.

This study reports on fourteen biopsies from patients presenting to our orbital and oncology service with ocular adnexal lymphoid proliferations between November 1988 to September 1991. The biopsies were studied using histologic, immunophenotypic and genotypic analyses. By histologic criteria, there were two reactive, five indeterminate and seven lymphomatous lesions. On immunophenotypic analysis, there were two monoclonal and 10 polyclonal lesions in the 12 specimens analysed. Genotypic analysis confirmed the histopathologic diagnoses for the reactive lesions by showing them to be germline. It also confirmed that both the histopathologic lymphomas and immunophenotypically monoclonal lesions were clonally rearranged. Genotypic analysis was able to separate the histologically indeterminate group into two subsets: clonally rearranged, of which there was one, and germline, of which there were four. In addition, it demonstrated that immunophenotypic polyclonality cannot always be equated with genotypic polyclonality as was the situation in four out of 10 lesions in our series. The significance of clonal arrangements in the histologically indeterminate and immunophenotypically polyclonal groups can only be determined by prospective study.

Adult↗
PubMed1993

Clonality of chronic neutrophilic leukaemia associated with myeloma: analysis using the X-linked probe M27 beta.

AIMS: To determine whether myeloid proliferation was monoclonal or polyclonal in a woman with chronic neutrophilic leukaemia and myeloma. METHODS: The X-linked probe, M27 beta was used to determine the clonality of the neutrophil population by analysis of restriction fragment length polymorphisms and X inactivation pattern. RESULTS: A polyclonal pattern of X inactivation was obtained for the neutrophil population in this patient. CONCLUSION: The myeloid expansion in chronic neutrophilic leukaemia associated with myeloma represents a polyclonal reactive response to the plasma cell clone rather than a co-existent myeloproliferative disorder.

Aged↗
PubMed1993

Concordant clonal delineation of methicillin-resistant Staphylococcus aureus by macrorestriction analysis and polymerase chain reaction genome fingerprinting.

Pulsed-field gel electrophoresis of DNA macrorestriction fragments (macrorestriction analysis) allows epidemiologic typing and delineation of genetic relatedness of methicillin-resistant Staphylococcus aureus (MRSA) by indexing variations in the global chromosome architecture. Polymerase chain reaction (PCR)-mediated genome fingerprinting can also discriminate MRSA strains by detecting locally variable DNA motifs. To assess the correlation between these methods, 48 epidemic MRSA strains collected from 20 hospitals over a 10-year period were tested in a blind comparison by (i) macrorestriction analysis with SstII or SmaI endonuclease and (ii) PCR fingerprinting with four primer sets aimed at the mecA gene, enterobacterial repetitive intergenic consensus sequences, and arbitrary sequences. Isolates were discriminated into 22 macrorestriction patterns and 15 PCR fingerprints. MRSA strains belonging to 12 distinct clones by macrorestriction analysis showed 11 distinct PCR genotypes distinguished by multiple band differences. In contrast, 34 of 37 MRSA strains found to be clonally related by macrorestriction analysis clustered in two highly related PCR genotypes that differed by a single DNA fragment (P < 0.0001). These data demonstrate concordant clonal delineation of epidemic MRSA by macrorestriction analysis and PCR fingerprinting and thereby indicate that the rapid PCR assay may be an efficient epidemiologic typing system.

Base Sequence↗
PubMed2003

Systemic mastocytosis with associated clonal hematological non-mast-cell lineage disease: analysis of clinicopathologic features and activating c-kit mutations.

The majority of patients with systemic mastocytosis with associated clonal, hematological non-mast cell lineage disease (SM-AHNMD) have a myeloid stem cell malignancy including myelodysplastic syndromes (MDS), myelodysplastic/myeloproliferative disorders, acute myeloid leukemia (AML), or chronic myeloproliferative disease. The clinicopathologic features of SM-AHNMD have not been fully characterized. We describe seven cases of this entity: 3 with MDS, 3 with AML, and 1 with chronic myelomonocytic leukemia. In the majority of cases, SM was diagnosed concurrently with the myeloid malignancy and aberrant mast cell morphology was observed. The commonly described c-kit enzymatic site mutation Asp816Val was detected only in 2 cases, while 3 patients carried the Asp816His mutation. Among the 3 cases with AML, 2 patients carried the translocation t(8;21). On the basis of our results and other reported cases, there appears to be a specific association between SM and AML with t(8;21). Concurrent occurrence of SM may define a subset of patients with de novo AML and other myeloid malignancies who have an adverse prognosis. As clinically effective tyrosine kinase inhibitors that inhibit enzymatic-type c-kit mutations are being developed, detection of mast cell proliferation associated with myeloid malignancy may have important therapeutic implications.

Adult↗
PubMed2002

Accessory cell tumour: a clinicopathological study of 16 aggressive tumours containing EBV-positive Hodgkin and Reed-Sternberg-like giant cells.

AIMS: Lymph nodes contain non-lymphoid accessory cells including follicular dendritic cells and interdigitating dendritic cells. Functionally, these cells belong to the category of immune accessory cells involved in antigen presentation to B or T-lymphocytes. Neoplastic proliferation of these cells is very uncommon. We present here the clinicopathological features of 16 cases of accessory cell tumour. METHODS AND RESULTS: We performed electron microscopic and immunohistochemical examinations, and used in-situ hybridization for EBV-encoded RNA (ISH-EBV) to detect the EBV genome in 11 cases, and Southern blot analysis to assess EBV clonality in two cases. Tumour cells were composed of oval-to-spindle cells arranged in diffuse, vague storiform, fascicular and sometimes whorled patterns in a background of small lymphocytes. In all cases, binucleated or multinucleated Hodgkin and Reed-Sternberg-like giant cells were encountered. Staining for CD68 was positive in all cases. CD21, CD35, Ki-M4p, Ki-FDC1p, and S100 exhibited variable reactivity. ISH-EBV yielded positive labelling in seven of 11 cases, of which five exhibited EBV only in Hodgkin and Reed-Sternberg-like giant cells. Southern blot analysis showed clonality of EBV terminal repeats (EBV-TR) in the two cases examined. Electron microscopic examination showed that many of the tumour cells had numerous interwoven long villous cell processes connected by occasional desmosomes. Many tumours were very refractory to chemotherapy and radiation, with a few exceptions, and half of the cases classified initially as stage IV. A short survival time, of 10 months or less, was observed in seven of 16 patients. CONCLUSIONS: Our study identified more aggressive behaviour of accessory cell tumours. Our results suggest that EBV may potentially induce activation of accessory cells to form Hodgkin and Reed-Sternberg-like giant cells, which correspond with poor prognosis.

Adult↗
PubMed1985

Immunoglobulin G, A, and M--clonal restriction in multiple sclerosis cerebrospinal fluid and serum--analysis by two-dimensional electrophoresis.

Immunoglobulin G, A, and M (IgG, IgA, and IgM) were purified from multiple sclerosis (MS) cerebrospinal fluid (CSF) and sera and analyzed by two-dimensional electrophoresis. The light (L)-chains of MS CSF IgG were of limited diversity and dominated by about 30 major spots and many less intense spots. CSF IgG of patients with subacute sclerosing panencephalitis (SSPE) was dominated by 10 to 20 intense L-chain spots. L-chains from patients with fungal, syphilitic, and tuberculous infections of the central nervous system (CNS) ranged from 70 to in excess of 300 spots. The patterns of L-chains in MS CSF and autologous sera were different, indicating amplified synthesis of particular L-chains in MS CNS. Cathodic IgG fractions differing in isoelectric point by 0.1 to 0.3 pH units were isolated. SSPE CSF IgG fractions were dominated by a few L-chain spots, MS CSF fractions contained less than 20 spots, and MS serum fractions contained about 200 spots. MS CSF mu-chains were similar in isoelectric point range to serum but fractionated into discrete spots compared with a diffuse pattern in serum. MS CSF IgA alpha-chain spot overlapped in mobility with serum alpha-chains except a portion of the alpha-chain complex in CSF was shifted cathodically forming discrete spots. The CSF L-chains of both IgM and IgA were completely dissimilar to serum. These studies indicate major limited diversity and compartmentalized CNS synthesis of IgG, IgA, and IgM in MS. The restricted clonal pattern is proposed as consequent to B-cell stimulation by disease-related antigen(s) with limited epitope complexity. The dominance of a small number of L-chains supports results from idiotypic analysis suggesting finite clonal complexity of MS CSF IgG and indicates the feasibility of structural analysis of MS CSF L-chains, particularly amino acid sequence determinations.

Humans↗
PubMed1999

Overview of the role of molecular methods in the diagnosis of malignant lymphomas.

OBJECTIVE: To review the role of molecular genetics in the diagnosis of malignant lymphomas. DATA SOURCES AND STUDY SELECTION: Primary research studies and reviews published in the English literature that focus on molecular genetics and malignant lymphoma, in particular, clonality, chromosomal translocations, tumor suppressor genes, and Hodgkin disease. DATA EXTRACTION AND SYNTHESIS: Molecular genetics has an important role in the assessment of malignant lymphomas. Clonality, detected by Southern blot analysis or the polymerase chain reaction, is helpful for establishing the diagnosis of lymphoma in lesions with ambiguous morphologic and immunophenotypic findings. Southern blot analysis is the "gold standard" for clonality assessment, but the process is labor-intensive and time-consuming. Polymerase chain reaction analysis is more convenient, but a potentially significant false-negative rate exists in the analysis of some antigen receptor genes as a result of using consensus primers and the process of somatic hypermutation. Chromosomal translocations, which result in oncogene activation, occur in many types of B- and T-cell lymphomas, and their detection is helpful in classification as well as in establishing a diagnosis of malignancy. Gene rearrangements and chromosomal translocations also can be used to monitor minimal residual disease. Tumor suppressor genes, although their analysis is relatively less useful for diagnosis, are involved in both pathogenesis and tumor progression and will be more important diagnostically as this field continues to expand. Molecular genetic analysis has played a major role in improving our understanding of Hodgkin disease. CONCLUSIONS: Molecular genetic tests are currently important ancillary tools for the diagnosis and classification of malignant lymphomas, and their role is likely to increase in the future.

Chromosomes↗
PubMed1982

Clonal evolution demonstrated by flow cytometric DNA analysis of a human colonic carcinoma grown in nude mice.

A spontaneous change in DNA content of a human colonic carcinoma grown in nude mice was observed fortuitously. The tumor initially had a G1 cell DNA content of 1.3 times that of normal cells. Flow cytometric DNA analysis showed in transplant generation 56 the appearance of a new subpopulation which in three passages completely overgrew the original population. The DNA content of the new subpopulation was twice that of the original population. The observation supports the hypothesis of clonal evolution of tumor cell populations. The growth rates of the tumor before and after the change showed no significant difference (p greater than 0.05). Cell kinetic factors, therefore, offer no obvious explanation of how the overgrowth took place. It is not known whether the original population disappeared completely or survived as a small population below the detection limit. The heterogeneity created by clonal evolution of a tumor would be less pronounced if old subpopulations often become extinct as new ones emerge. Heterogeneity of human tumors is of clinical importance because the individual subpopulations may have different sensitivity patterns to antineoplastic drugs.

Animals↗
PubMed2003

Skew in T-cell receptor usage and clonal T-cell expansion in patients with chronic rejection of transplanted kidneys.

BACKGROUND: It is not known whether alloreactive T cells are involved in chronic rejection of transplanted kidneys. The aim of the present study was to determine the involvement of T cells in the chronic graft rejection. METHODS: T-cell receptor (TCR) variable region alpha-chain and TCR variable region beta-chain repertoires were analyzed in peripheral blood mononuclear cells. T-cell clonalities were analyzed by complementarity-determining region 3 size spectratyping. RESULTS: A significant increase in the frequencies of one or more TCR variable region alpha-chain and TCR variable region beta-chain segments was detected in 13 and 15 of the 24 kidney transplant recipients, respectively. The extent of the skew in the TCR usage was correlated with the levels of clonal T-cell expansion, indicating that the clonally expanding T cells were responsible for the skew in the TCR usage. The levels of the skew in the TCR usage and clonal T-cell expansion were significantly greater in the recipients with a graft failure than in those with a stable graft function ( P=0.0081 and P=0.012, respectively). These results indicate that the clonally expanding T cells in the periphery may be related to graft rejection. The percent increase in the serum creatinine levels, which reflected the deterioration of the kidney functions, was significantly higher in the recipients who showed high levels of clonal T-cell expansion than in those who did not ( P=0.021). CONCLUSIONS: The results demonstrate that clonal T-cell expansion in the periphery has a negative impact on the long-term graft functions, and that analysis of the clonal T-cell expansion in peripheral blood mononuclear cells provide significant information on the fate of the transplanted kidney.

Adolescent↗
PubMed2006

A combination of cytomorphology, cytogenetic analysis, fluorescence in situ hybridization and reverse transcriptase polymerase chain reaction for establishing clonality in cases of persisting hypereosinophilia.

To evaluate the frequency of clonal abnormalities in patients with unexplained persisting eosinophilia we analyzed 40 patients (27 males, 13 females) using cytomorphology, cytogenetic analysis, interphase fluorescence in situ hybridization (FISH), and reverse transcriptase polymerase chain reaction (RT-PCR). Cytogenetic analysis revealed clonal abnormalities in five patients (four of whom were males) including t(8;9)(p21;p24), ins(9;4)(q34;q12q31), del(6)(q24), and trisomy 8 (n=2). RT-PCR confirmed a PCM1-JAK2 fusion underlying the t(8;9). FISH analysis suggested a rearrangement involving PDGFRA in the ins(9;4). A FIP1L1-PDGFRA fusion gene was identified in four male patients by interphase FISH and RT-PCR. These methods in combination demonstrated clonality in 8/40 patients (20%) with a male predominance (6/8; 75%).

Chromosome Mapping↗
PubMed2006

Adult T-cell leukemia development from a human T-cell leukemia virus type I carrier after a living-donor liver transplantation.

Adult T-cell leukemia (ATL) develops in a human T-cell leukemia virus type I (HTLV-I) carrier. The development of malignancy during immunosuppressive treatment following organ transplantation is one of the late fatal complications. We describe the development of three cases of ATL in eight HTLV-I carriers within 164 living-donor liver transplant recipients undergoing immunosuppressive treatment. All three cases were immunosuppressed with tacrolimus. Acute-type ATL was diagnosed at 6, 9, and 25 months after living-donor liver transplantation, based on increased numbers of CD4+25+ lymphocytes exhibiting "flower-like" nuclei, and the elevation of lactate dehydrogenase. Southern blot analysis demonstrated the clonal proliferation of ATL cells in peripheral blood. The ATL cells originated from the recipient, as demonstrated by fluorescence in situ hybridization analysis using sex chromosomal markers. Our observations suggest that immunosuppressive treatment for the prevention of graft rejection after living-donor liver transplantation may induce the development of ATL in an HTLV-I carrier.

Adult↗