Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “clonal evolution”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,351 records · Page 75Linked to original sources
PubMed1994

Immunity and inflammation: the cosmic view.

This paper presents an overview of the evolution of defence reactions in multicellular animal life. The co-evolution of hosts and pathogens provides the context to describe the major features of defence reactions and the countermeasures they evoke in their targets. Three major types of solutions to the riddle of self-non-self discrimination are discussed briefly: non-clonal recognition mediated by lectins, the preferential accumulation of C3 in microbial surfaces and vertebrate clonal immunity. Vertebrate immunity is described as a specialized type of inflammation against infectious agents that evolved in response to countermeasures successfully used by intracellular pathogens against non-specific defences.

Animals↗
PubMed1990

Structural similarity between a primitive chordate membrane heterodimer and lymphocyte antigen receptors.

Botryllus schlosseri is a colonial tunicate that shared a common ancestor with the lineage leading to mammals about 450 million years ago, and flourishes today along the California coast. Prior studies of Botryllus populations have demonstrated the presence of a co-dominantly expressed, highly polymorphic histocompatibility locus (Fu/HC) controlling the acceptance (fusion) or rejection of new individuals into a parabiotic colony. Intercolonial blood cell contact, and recognition of self/not self, precedes both fusion and rejection reactions. Efforts to understand the evolution of the immune system necessitate study of cell surface molecules involved in cell-cell recognition events in primitive species. In mammals, birds, amphibians, and fishes clonally distributed lymphocyte surface molecules that are responsible for antigen recognition (B cell immunoglobulins and T cell receptors) can be distinguished by the disulfide linkage that pairs two or more polypeptides containing constant and variable regions. We have identified a disulfide-linked, heterodimeric (alpha beta) cell surface molecule in Botryllus with biochemical resemblance to mammalian lymphocyte antigen receptors. Observed charge variants of constituent chains of the tunicate protein described here do not correlate with Fu/HC allelic diversity. Both chains of this heterodimer can be resolved into several isoforms which are not based upon post-translational carbohydrate or phosphate additions. Comparisons of iodinated tryptic peptides from two beta chain isomorphs reveal one distinct and several common peptides.

Animals↗
PubMed2004

Application of combined immunofluorescence and fluorescence in situ hybridization on paraffin-embedded sections to characterize T-cell lymphoma with EBV-infected B-cell blasts.

Combined immunofluorescence (IF) and fluorescence in situ hybridization (FISH) on formalin-fixed, paraffin-embedded tissue sections were used to examine lymph node tissue from two patients diagnosed with T-cell lymphoma with Epstein-Barr virus (EBV)-infected B-cell blasts. The majority of cells within the samples comprised T-cells staining positively for CD3. In addition, both patients had a population of large pleiomorphic cells that were positive for the B-cell marker CD20 and for EBV LMP-1. Standard PCR clonality testing of the nodes revealed both immunoglobulin heavy chain (IGH) and T-cell receptor (TCR) clonal rearrangements in one patient, although in the other case monoclonality was demonstrated only for TCRG. Cytogenetics of cultured lymphocytes from nodal tissue revealed two apparently unrelated abnormal clones in both patients. Combined IF and FISH revealed that these phenomena reflected two abnormal populations of B- and T-cells rather than reactive B-cell hyperplasia or biphenotypic evolution from a common ancestral lymphoma. True B-cell malignancy probably emerged within a preexisting but unrelated T-cell lymphoma. This is the first study to relate the phenotype of the abnormal cells in such cases to specific clonal populations of cells, and it demonstrates a method that may easily be introduced into a diagnostic cytogenetics laboratory with access to standard pathology laboratory resources.

Antigens, CD20↗
PubMed2005

Human herpesvirus 8 infection in patients with cutaneous lymphoproliferative diseases.

OBJECTIVE: To investigate the prevalence of human herpesvirus 8 (HHV-8; Kaposi sarcoma-associated herpesvirus) infection in patients with lymphoproliferative skin diseases such as large-plaque parapsoriasis (LPP) and mycosis fungoides compared with inflammatory cutaneous conditions or healthy control subjects. DESIGN: A survey study was undertaken in 123 subjects with various clinical conditions. SETTING: All patients had been seen in the Dermatology Department of the San Gallicano Dermatology Institute, Rome, Italy, in the last 2 years. PATIENTS: Forty-five patients with inflammatory or autoimmune cutaneous diseases, 50 healthy control subjects, 10 patients with LPP, 12 patients with mycosis fungoides, and 6 patients with classic Kaposi sarcoma were included in the study. MAIN OUTCOME MEASURES: The prevalence of HHV-8 infection was investigated with serologic studies using the gold standard assay based on body cavity-based B-cell lymphoma-1 cells latently infected with HHV-8. The presence of HHV-8 conserved sequence, corresponding to open reading frame 26, was also assessed in the peripheral blood and lesion tissue samples from patients with lymphoproliferative cutaneous diseases with nested polymerase chain reaction. The presence and distribution of cell types infected with HHV-8 in the lesion tissues was determined with immunohistochemical staining with the monoclonal antibody directed against the latent nuclear antigen-1 of HHV-8 encoded by open reading frame 73. RESULTS: In healthy control subjects and patients with inflammatory skin diseases, 13.9% were found to have antibody against HHV-8, consistent with the seroprevalence population in Italy. A highly significant association of HHV-8 infection and LPP was found (100%) compared with mycosis fungoides (25%). The peripheral blood mononuclear cells in 8 of 10 patients with LPP were found to harbor viral sequences at nested polymerase chain reaction, whereas none of them had a detectable serum viral load. All LPP lesion tissue samples were positive for HHV-8-encoded open reading frame 26, and the presence of HHV-8-infected cells was confirmed by immunohistochemistry profiles performed on paraffin-embedded tissues from 4 of 10 patients. The positive cell types included endothelial cells and the infiltrating dermal lymphocytes, characteristic hallmarks of LPP. Analysis of T-cell receptor gamma chain rearrangements in lesion tissue from our patients confirmed the lack of a significant association between T-cell clonality and LPP. CONCLUSION: These data suggest that HHV-8 may play a role in the onset of LPP, a disease whose cause and evolution are still undefined and which has often been considered the early stage of mycosis fungoides.

Adult↗
PubMed1998

Microevolution during epidemic spread of Neisseria meningitidis.

Similar to many other naturally transformable bacteria, Neisseria meningitidis has yielded many examples where horizontal genetic exchange has resulted in genetic variation of individual strains. Epidemic strains are purified of genetic variants due to bottlenecks during the spread from country to country, resulting in clonal descent. Occasionally, clonal replacement also occurs during epidemic spread. These processes occur rapidly in serogroup A meningococci; such that after their descent from a common ancestor, clonally related bacteria have diversified at numerous loci within the last decades.

Disease Outbreaks↗
PubMed1993

Ring chromosome 12 resulting from nonrandom telomeric associations with the short arm of chromosome 15 in a cerebellar astrocytoma.

Ring chromosome 12 was found in an untreated cerebellar astrocytoma apparently resulting from nonrandom telomeric associations involving the short arm of chromosome 15, and both the long and short arms of chromosome 12. The clonal nonrandom telomeric associations of 15p to both ends of the chromosome 12 were transitory, but appear to be the precursor lesion in the evolution to ring chromosome 12 in this tumor. A multistep process in the formation of a ring chromosome resulting from nonrandom telomeric associations to both telomeres is illustrated.

Astrocytoma↗
PubMed2005

Treatment of myelodysplastic syndrome with a DNA methyltransferase inhibitor: lack of evidence for induction of chromosomal instability.

In several large phase II trials, low-dose treatment with the azanucleoside 5-aza-2'-deoxycytidine (decitabine, DAC) resulted in complete hematologic and cytogenetic responses in 23 and 31% of MDS patients, respectively. The question of induction of chromosomal instability by this demethylating agent was addressed by serial karyotypic analyses. 53/122 DAC-treated patients had all normal metaphases at time of treatment start. In 46/53 patients, sequential cytogenetic analyses were performed. 9/46 patients (20%) acquired clonal chromosomal abnormalities during follow-up (4/9 transient). 8/9 abnormalities were gains or losses of entire chromosomes. The rate and pattern of cytogenetic evolution are thus not higher than in historical MDS cohorts not receiving specific treatment.

Aged↗
PubMed2002

Haplotype exclusion and receptor editing: irreconcilable differences?

Features of antibody genes and their regulation hinder two properties thought to be critical for clonal selection: haplotype exclusion and receptor diversity. These properties include: (1) the retention of multiple independent L-chain isotypes, which compounds the problem of allelic exclusion with one of isotype exclusion; (2) the process of receptor editing, in which recombination continues in cells already expressing antigen receptors; and (3) non-random associations and quasi-ordered rearrangements of the elements that generate light chain genes, which promote editing at the expense of allelic exclusion and receptor diversification. In contrast, heavy chain gene structure seems to promote haplotype exclusion and receptor diversity. It appears that requirements of receptor selection, such as the need for receptor editing as an immune tolerance mechanism and positive selection as a quality control checkpoint for receptor functionality, impose independent selections that shape the organization and regulation of the antibody genes. Despite these features, B cell development still achieves a significant level of phenotypic haplotype exclusion, suggesting that there is indeed significant selection for antibody monospecificity that is accommodated along with receptor editing. Thus, the immune system achieves both receptor selection and clonal selection, despite their partly antagonistic mechanisms.

Alleles↗
PubMed2001

In search of the origin of the thymus: the thymus and GALT may be evolutionarily related.

The thymus is the major primary immune tissue for the production of functional T lymphocytes in vertebrates. However, its evolutionary origin is unknown. It has recently been shown that the generation of local T cells also occurs in gut-associated lymphoid tissues (GALT). This suggests that the thymus and GALT have similar functions and that they might be evolutionarily related. We discuss the possibility that the thymus may have evolved from mucosa-associated lymphoid tissues (MALT) located in the gill region in early vertebrates. Various facts supporting this proposal are summarized.

Animals↗
PubMed1990

Inducible morphology, heterochrony, and size hierarchies in a colonial invertebrate monoculture.

Conditional or inducible strategies are a powerful tool for analyzing the evolution of aggressive behavior. Structures such as stolons and nematocyst-laden tentacles, induced to deter encroachment by competitors, are proportionately better represented in clonal and colonial marine invertebrates than in aclonal animals. Stolons can be produced by colonies of Membranipora membranacea (Bryozoa) within 48 hr after contact with conspecifics. Absolute size and relative size of interacting colonies determine whether stolons will be produced. Although individual stolons are eventually overgrown by conspecifics, they reduce the size of affected zooids by 27%. Since stolon production is primarily a strategy of large colonies, we suggest that stolons function to limit space occupied by small colonies and may also trigger early and localized reproduction. Thus large colonies can surround multiple small mates and, because they reproduce only locally where induced by contact with small colonies, still maintain high growth rates on free colony perimeters. Stolons appear to be juvenilized zooids and to originate through a process of heterochrony. These induced facultative polymorphisms may be one pathway by which fixed polymorphisms arise in colonial invertebrates. We attribute the unique production of inducible structures against competitors by clonal and colonial invertebrates to both unusually high levels of development plasticity and an energetically favorable architecture for perimeter defense.

Journal Article↗
PubMed1996

Salmonella typhi contains identical intervening sequences in all seven rrl genes.

Salmonella typhi Ty2 rrl genes contain intervening sequences (IVSs) in helix-25 but not in helix-45 on the basis of observed 23S rRNA fragmentation caused by IVS excision. We have confirmed this and shown all seven IVSs to be identical by isolating genomic DNA fragments containing each of the seven rrl genes from S. typhi Ty2 by use of pulsed-field gel electrophoresis; each rrl gene was amplified by PCR in the helix-25 and helix-45 regions and cycle sequenced. Thirty independent wild-type S. typhi strains, tested by genomic PCR and DraI restriction, also have seven rrl genes with helix-25 IVSs and no helix-45 IVSs. We propose that IVS homogeneity in S. typhi occurs because gene conversion drives IVS sequence maintenance and because adaptation to human hosts results in limited clonal diversity.

Base Sequence↗
PubMed2003

Pulmonary Langerhans cell histiocytosis: emerging concepts in pathobiology, radiology, and clinical evolution of disease.

Pulmonary Langerhans cell histiocytosis (PLCH) is an uncommon disorder of adult smokers associated with a significant morbidity. Arising from the aberrant accumulation of Langerhans and other immune cells, PLCH tends to cause a relatively isolated pulmonary involvement as compared to other forms of Langerhans cell (LC) and histiocytic disorders. Increased knowledge of cytokine triggers, dendritic cell trafficking, and clonality of LC populations in PLCH have resulted in an improved understanding of the pathobiology of PLCH. High-resolution CT (HRCT) of the chest has led to better appreciation of nodular and cystic radiographic abnormalities characteristic of the disease. Correlation of HRCT abnormalities with lung pathologic changes has led to an improved comprehension of clinical evolution of PLCH. Current clinical predictors for PLCH outcomes remain poor, although long-term follow-up and radiologic monitoring may help to define disease progression. This review discusses advances in PLCH emphasizing the etiopathologic bases of the disease and currently available radiologic modalities for monitoring disease progression.

Histiocytosis, Langerhans-Cell↗
PubMed1998

Antibodies of sharks: revolution and evolution.

The combinatorial immune response is restricted to jawed vertebrates with cartilaginous fishes being the lowest extant species to have the mechanism for diversification and an extensive panoply of immunoglobulins, T-cell receptors and MHC products. Here, we review the molecular events of the "big bang" or rapid evolutionary appearance of the functionally complete combinatorial immune system coincident with the appearance of ancestral jawed vertebrates, suggesting that this event was catalyzed by horizontal transfer of DNA processing systems. We analyze the nature and extent of variable and constant domain diversity among the distinct immunoglobulin sets of carcharhine sharks focusing upon the lambda-like light chains and the mu and omega heavy chains. The detection and isolation of natural antibodies from the blood of unimmunized sharks illustrates a surprising range of recognition specificities and the existence of polyspecificity suggests that the antibody-forming system of sharks offers unique opportunities for studies of immunological regulation. Although the homologies between shark and mammalian immunoglobulins are unequivocal, major differences in segmental gene organization present challenges to our understanding of basic immunological phenomena such as clonal restriction.

Amino Acid Sequence↗
PubMed1993

Molecular evolution of the Escherichia coli chromosome. IV. Sequence comparisons.

DNA sequences have been compared in a 4,400-bp region for Escherichia coli K12 and 36 ECOR strains. Discontinuities in degree of similarity, previously inferred, are confirmed in detail. Three clonal frames are described on the basis of the present local high-resolution data, as well as previous analyses of restriction fragment length polymorphism (RFLP) and of multilocus enzyme electrophoresis (MLEE) covering small regions more widely dispersed on the chromosome. These three approaches show important consistency. The data illustrate the fact that, in the limited context of intraspecific genomic sequence variation, clonality and homology are synonymous. Two estimable quantitative properties are defined: recency of common ancestry (the reciprocal of the log10 of the number of generations since the most recent common ancestor), and the number of nucleotide pairs over which a given recency of common ancestry applies. In principle, these parameters are measures of the degree and physical extent of homology. The small size of apparent recombinational replacements, together with the observation that they occasionally occur in discontinuous series, raises the question of whether they result from the superimposition of replacements of much larger size (as expected from an elementary interpretation of conjugation and transduction in experimental E. coli systems) or via an alternative mechanism. Length polymorphisms of several sorts are described.

Base Sequence↗
PubMed1994

Oligoclonality of tumor-infiltrating lymphocytes from human melanomas.

A PCR-based method that determines VDJ junction size patterns in 24 human TCR V beta subfamilies was used to analyze T cells infiltrating sequential malignant melanoma biopsies for the presence of clonal expansions. Infiltrating T cell populations were found to present clonal expansions over a more or less complex polyclonal background. Two clones from a single patient were sequenced and detected in three different tumor sites (skin biopsies), whereas only one of them was also present in peripheral blood. Biopsies from this patient did not show major repertoire changes during in vivo IL-2 treatment. In contrast, in biopsies from a second patient, the expression of all the detected V beta subfamilies was increased and a larger number of clones expanded, probably as a result of therapy. A similar evolution was found among infiltrating T cells cultured in vitro from a third patient for several weeks in the presence of IL-2, where the largely polyclonal repertoire of fresh T cells (from invaded lymph nodes) was dramatically reduced to mainly clonal expansions in all V beta subfamilies detected. The high resolution method used here enables a rapid, comprehensive, qualitative, and semiquantitative description of the T cell repertoire of heterogeneous cell populations. Its use in conjunction with a functional analysis of clones detected within these populations should provide a better understanding of the evolution of the T cell repertoire among tumor-infiltrating lymphocytes during the progression of the disease and as a response to immunotherapy.

Base Sequence↗
PubMed2003

A comparison of directed evolution approaches using the beta-glucuronidase model system.

Protein engineers can alter the properties of enzymes by directing their evolution in vitro. Many methods to generate molecular diversity and to identify improved clones have been developed, but experimental evolution remains as much an art as a science. We previously used DNA shuffling (sexual recombination) and a histochemical screen to direct the evolution of Escherichia coli beta-glucuronidase (GUS) variants with improved beta-galactosidase (BGAL) activity. Here, we employ the same model evolutionary system to test the efficiencies of several other techniques: recursive random mutagenesis (asexual), combinatorial cassette mutagenesis (high-frequency recombination) and a versatile high-throughput microplate screen. GUS variants with altered specificity evolved in each trial, but different combinations of mutagenesis and screening techniques effected the fixation of different beneficial mutations. The new microplate screen identified a broader set of mutations than the previously employed X-gal colony screen. Recursive random mutagenesis produced essentially asexual populations, within which beneficial mutations drove each other into extinction (clonal interference); DNA shuffling and combinatorial cassette mutagenesis led instead to the accumulation of beneficial mutations within a single allele. These results explain why recombinational approaches generally increase the efficiency of laboratory evolution.

Directed Molecular Evolution↗
PubMed2000

Intratumoral genetic heterogeneity and progression of endometrioid type endometrial adenocarcinomas.

OBJECTIVES: Development of genetic heterogeneity is one mechanism whereby tumors may acquire increasing aggressiveness during neoplastic progression. In this study we relate development of intratumoral genetic heterogeneity to invasion and metastatic spread of sporadic endometrioid (type I) endometrial adenocarcinomas. METHODS: Microsatellite unstable adenocarcinomas underwent detailed microsatellite allelotype mapping with reconstruction of neoplastic lineages using maximum parsimony analysis. RESULTS: Within individual patients, tumor allelotypes sometimes varied between regions of histologically identical tumor, indicating that genotypic variation may reflect differences inapparent by histology. Comparison of noninvasive (surface/luminal) with invasive (myometrial invasion or metastasis) carcinoma showed highly related genotypes in 3/8 cases in which the invasive component can be recognized as evolved from the superficial tumor lineage by progressive clonal selection. In 3/8 cases superficial and invasive genotypes independently evolved different sets of altered microsatellites, indicating either divergence at an early stage in tumor evolution or independent selection events. A total of 2/8 cases had random patterns of marker distribution between sampled areas that were not informative in delineating systematic relationships between surface and invasive tumor. CONCLUSIONS: We conclude from these results that endometrial tumor progression may occur through physical extension of existing clones or through creation of new subclones with altered growth properties. The latter occurs in about half of cases, where myometrial invasion may select for particular clones that are poorly represented on the luminal surface.

Alleles↗
PubMed1995

Chromosome rearrangements at telomeric level in hematologic disorders.

Following retrospective screening of our karyotype data from 414 consecutive non-childhood, neoplastic, and preneoplastic hematologic diseases, we have isolated 11 cases with alterations involving one or two chromosome termini, including: a) nonclonal telomeric telomeric associations (tas), b) subclonal terminal rearrangements consisting of additional (add) material of unknown origin fused at the end of the chromosome, c) clonal telomere-centromere fusion (t telcen) with pseudodicentric structure. Most of these abnormalities were present in karyotypes with multiple alterations and associated to an evolutive stage of the disease (9 of 94 cases studied in progression, including three of 22 CML studied in blast crisis). The immunophenotype of the cell populations was lymphoid in eight cases, six of which were NHL, and myeloid, erythroid, and undifferentiated in the other three. More data on telomeric abnormalities may clarify whether there is ubiquitous genomic instability of neoplastic cells or an inborn cell lineage predisposition favoring rearrangements involving telomeres.

Adult↗