Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “clonal dynamics”

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 73 records · Page 4Linked to original sources
PubMed2006

Angioimmunoblastic T-cell lymphoma with supervening Epstein-Barr virus-associated large B-cell lymphoma.

Patients with angioimmunoblastic T-cell lymphoma can have profound immune dysfunction and immunodeficiency. Epstein-Barr virus-driven B-cell lymphoid proliferation can occur in angioimmunoblastic T-cell lymphoma, as in other immunodeficiency states. However, few cases of Epstein-Barr virus-positive B-cell lymphoma arising in patients with preexisting angioimmunoblastic T-cell lymphoma have been reported. We report a case of angioimmunoblastic T-cell lymphoma in which diffuse large B-cell lymphoma developed 56 months after the diagnosis of angioimmunoblastic T-cell lymphoma. The patient survived for 9 years after the initial diagnosis of angioimmunoblastic T-cell lymphoma, and molecular studies performed on multiple biopsy specimens during this period revealed the dynamic nature of clonal lymphoid expansion. Epstein-Barr virus latent membrane protein 1 and Epstein-Barr virus-encoded RNA were detected in the diffuse large B-cell lymphoma, suggesting that Epstein-Barr virus may have played a role in the pathogenesis of the diffuse large B-cell lymphoma.

Aged↗
PubMed2006

Rapid emergence of enfuvirtide resistance in HIV-1-infected patients: results of a clonal analysis.

OBJECTIVES: To study the dynamics of enfuvirtide (T-20) resistance development in HIV-1-infected subjects. PATIENTS AND METHODS: Clonal analysis of gp41 sequences was performed on serial samples obtained from HIV-1-infected subjects with early virologic failure of T-20-based regimens. RESULTS: Enfuvirtide resistance mutations at codons 36 to 45 in the first heptad repeat of gp41 emerged within 2 weeks in most subjects and were associated with the return of plasma HIV-1 RNA level toward baseline by weeks 4 to 8. Mutations at codons 36 (G36E, G36D, or G36S) and 38 (V38A, V38G, or V38M) were the most commonly detected resistance mutations at week 2. Mutations at codons 40 (Q40H) and 43 (N43D) were more prevalent at week 4 than at week 2 and seemed to emerge more slowly than mutations at codons 36 and 38. CONCLUSIONS: The rapid emergence of mutations associated with T-20 resistance in the absence of a fully suppressive antiretroviral regimen demonstrates a low genetic barrier to resistance and underscores the importance of combining T-20 with other active drugs when constructing regimens for highly treatment-experienced patients.

Amino Acid Sequence↗
PubMed1984

Dynamic heterogeneity and metastasis.

Parallel clonal populations grown to small defined sizes were used to quantitate rates of generation of metastatic cells. In murine KHT fibrosarcoma and B16 melanoma lines, metastatic cells are generated at effective rates of 10(-5) per cell per generation, or greater. These variant cells are unstable, and are apparently lost at very high rates. It thus appears that metastases could arise from unstable variants, and that rapid rates of change in some phenotypes may be an important feature of malignant progression. We have called such rapid variations dynamic heterogeneity. This may be a useful concept for further investigating aspects of tumor heterogeneity.

Animals↗
PubMed2026

Phylogenetic distribution and longitudinal persistence of plasmids in Mycobacterium abscessus.

Mycobacterium abscessus, a non-tuberculous mycobacterium, is a cause of severe respiratory infections, notably in individuals with underlying lung conditions. Its high levels of intrinsic and acquired antimicrobial resistance make it particularly difficult to treat and horizontally acquired genetic elements may facilitate the spread of resistance. A small number of plasmids have been identified in this species, but their distribution, transmission dynamics across subspecies and clonal lineages remain poorly characterized. We analysed short-read genomic data from 3,060 M. abscessus isolates, including longitudinal samples, to characterize plasmid diversity and dynamics. Using a graph-based pan-genome approach, we identified 28 plasmids, including 15 previously unreported plasmids, mapped their distribution onto the species phylogeny and assessed their functional potential. Overall, 23.1% of isolates carried at least one plasmid, with higher prevalence in dominant circulating clones (DCCs) compared with non-DCCs. Plasmid carriage varied across subspecies and clonal backgrounds, and plasmids encoded numerous genes which may be linked to bacterial adaptation. Several plasmids persisted across multiple time points within individual patients, suggesting they can be highly stable over the course of a chronic infection.

Plasmids↗
PubMed2026

Type 1 interferon perturbates clonal competition by reshaping human blood development.

Inflammation accelerates evolutionary dynamics of hematopoietic stem cells (HSCs) in clonal hematopoiesis and myeloid neoplasms. We studied HSCs, progenitors and immune cells from patients with myeloproliferative neoplasms at baseline and following interferon-α (IFNα) treatment, the only therapy to deplete mutated stem cells. We deployed single-cell multiomics methods that distinguish the IFNα effects on mutated stem cells from the admixed wild-type HSCs, with respect to their differentiation, transcriptomes, immunophenotypes and chromatin accessibility. IFNα simultaneously activated HSCs into two polarized states: a lymphoid progenitor expansion associated with an anti-inflammatory state and an inflammatory myeloid progenitor state derived from HSCs. The augmented lymphoid differentiation balanced the typical myeloproliferative-neoplasm-induced myeloid bias, associated with normalized blood counts. Somatic mutations modified the effects of IFNα on HSC differentiation and cell cycle entry rates. Clonal fitness upon IFNα exposure was due to resistance of CALR- or JAK2-mutated stem cells to differentiate into inflammatory myeloid progenitors.

Journal Article↗
PubMed2003

Restricted clonal expression of IL-2 by naive T cells reflects differential dynamic interactions with dendritic cells.

Limited frequencies of T cells express IL-2 in primary antigenic responses, despite activation marker expression and proliferation by most clonal members. To define the basis for restricted IL-2 expression, a videomicroscopic system and IL-2 reporter transgenic model were used to characterize dendritic cell (DC)-T cell interactions. T cells destined to produce IL-2 required prolonged interactions with DCs, whereas most T cells established only transient interactions with DCs and were activated, but did not express IL-2. Extended conjugation of T cells with DCs was not always sufficient to initiate IL-2 expression. Thus, there is intrinsic variability in clonal T cell populations that restricts IL-2 commitment, and prolonged engagement with mature DCs is necessary, but not sufficient, for IL-2 gene transcription.

Animals↗
PubMed2025

Innovative strategies for mitochondrial dysfunction in myeloproliferative neoplasms a step toward precision medicine.

Myeloproliferative neoplasms (MPNs) are clonal disorders of hematopoietic stem cells characterized by aberrant proliferation of myeloid lineages, driven primarily by mutations in JAK2, CALR, and myeloproliferative leukemia, leading to constitutive activation of the JAK-STAT pathway. Emerging evidence highlights mitochondrial dysfunction as a key factor in MPN pathogenesis, contributing to increased reactive oxygen species production, mitochondrial DNA mutations, and dysregulated mitochondrial dynamics, which collectively promote clonal expansion and apoptosis resistance. Targeting mitochondrial pathways has gained attention as a therapeutic strategy, with approaches including mitochondria-targeted antioxidants, metabolic inhibitors, and modulation of mitophagy and mitochondrial fission/fusion dynamics. However, challenges such as drug delivery specificity, therapeutic resistance, and off-target effects remain significant. Recent advances in precision medicine, incorporating genomic, transcriptomic, and proteomic profiling, offer a more personalized approach to MPN treatment by tailoring interventions to individual mutation patterns. Additionally, novel therapeutic strategies, including gene editing technologies, RNA-based therapies, and nanoparticle-mediated drug delivery systems, hold promise for overcoming current treatment limitations. The integration of artificial intelligence in drug discovery and biomarker identification further enhances the potential for targeted therapies. Future research should focus on refining these strategies, developing reliable biomarkers for patient stratification, and exploring combination therapies that enhance treatment efficacy while minimizing adverse effects. By addressing mitochondrial dysfunction as an underlying driver of MPNs, these emerging approaches have the potential to improve disease management, extend patient survival, and enhance quality of life. Also, this new approach of precision medicine allows patient stratification and ensures that treatments are formed according to the individual disease biology of each patient, which results in overall better outcomes.

combination drug therapy↗
PubMed2006

Cancer progression by non-clonal chromosome aberrations.

The establishment of the correct conceptual framework is vital to any scientific discipline including cancer research. Influenced by hematologic cancer studies, the current cancer concept focuses on the stepwise patterns of progression as defined by specific recurrent genetic aberrations. This concept has faced a tough challenge as the majority of cancer cases follow non-linear patterns and display stochastic progression. In light of the recent discovery that genomic instability is directly linked to stochastic non-clonal chromosome aberrations (NCCAs), and that cancer progression can be characterized as a dynamic relationship between NCCAs and recurrent clonal chromosome aberrations (CCAs), we propose that the dynamics of NCCAs is a key element for karyotypic evolution in solid tumors. To support this viewpoint, we briefly discuss various basic elements responsible for cancer initiation and progression within an evolutionary context. We argue that even though stochastic changes can be detected at various levels of genetic organization, such as at the gene level and epigenetic level, it is primarily detected at the chromosomal or genome level. Thus, NCCA-mediated genomic variation plays a dominant role in cancer progression. To further illustrate the involvement of NCCA/CCA cycles in the pattern of cancer evolution, four cancer evolutionary models have been proposed based on the comparative analysis of karyotype patterns of various types of cancer.

Animals↗
PubMed2006

Significant gene order and expression differences in Bordetella pertussis despite limited gene content variation.

Bordetella pertussis, an obligate human pathogen and the agent of whooping cough, is a clonal species, despite the dynamic selection pressures imposed by host immunity and vaccine usage. Because the generation of variation is critical for species evolution, we employed a variety of approaches to examine features of B. pertussis genetic variation. We found a high level of conservation of gene content among 137 B. pertussis strains with different geographical, temporal, and epidemiological associations, using comparative genomic hybridization. The limited number of regions of difference were frequently located adjacent to copies of the insertion element IS481, which is present in high numbers in the B. pertussis chromosome. This repeated sequence appears to provide targets for homologous recombination, resulting in deletion of intervening sequences. Using subtractive hybridization, we searched for previously undetected genes in diverse clinical isolates but did not detect any new genes, indicating that gene acquisition is rare in B. pertussis. In contrast, we found evidence of altered gene order in the several strains that were examined and again found an association of IS481 with sites of rearrangement. Finally, we compared whole-genome expression profiles of different strains and found significant changes in transcript abundance, even in the same strain after as few as 12 laboratory passages. This combination of approaches provides a detailed picture of a pathogenic species with little gene loss or gain but with the capacity to generate variation by rearranging its chromosome and altering gene expression. These findings have broad implications for host adaptation by microbial pathogens.

Bordetella pertussis↗
PubMed1995

[Analysis of heavy chain immunoglobulins gene and T-cell receptor delta gene in children with acute leukemia].

IgH gene, TCR delta gene rearrangements and Tal-1 gene deletion were analysed by using PCR, Southern blot and DNA sequencing methods in newly diagnosed BM samples from children with AL. The DNAs from leukemic cells in 102 children were detected with PCR. The results showed that IgH gene rearrangement mainly occurred in B Precursor ALL (37/49). Six PCR products were further analysed by DNA sequencing. Less homogene and bias of JH gene usage were found in analysed DNA sequences. V delta 2-D delta 3 rearrangement of 78 samples from ALL was analysed with PCR method. V delta 2-D delta 3 rearrangements mainly observed in B precursor ALL and related HAL. V delta 2-D delta 2-N-D delta 3 rearrangement was found in a sequence of PCR product. Three cases of Tal-1 gene deletion were observed in all studied 70 samples of AL. They all were in stage I of thymus differentiation. We conclud that PCR detection of those genes are useful in the diagnosis of clonality of AL, DNA sequencing of PCR products is the base of preparing clonal specific probes, and dynamic analysis of IgH gene rearrangement using PCR may be helpful in detection of residual clones.

Child↗
PubMed2006

Does disturbance enhance genotypic diversity in clonal organisms? A field test in the marine angiosperm Zostera marina.

Physical disturbance has often been invoked to control genotypic diversity in sessile clonal organisms, yet experimental evidence is lacking. I studied the effects of physical disturbance on genet dynamics and genotypic diversity in a clonal marine angiosperm, Zostera marina (eelgrass). In replicated plots of 1 m2, the vegetation canopy was removed in gaps of zero (control), 25%, 50% and 75% of the area (n = 6 replicates). Before removal and during two consecutive years, the genotypic composition was determined using genetic markers (DNA microsatellites) in a 5 x 5 pixel grid per plot. An aggregate index of genet dynamics summarizing recruitment, increase, loss and decrease of clones was maximal at intermediate disturbance levels (quadratic polynomial P = 0.02). Physical disturbance also increased the occurrence of new genotypes, possibly reflecting recruitment (linear model, P < 0.05). Contrary to expectations, there was no competitive advantage of more heterozygous genotypes over less heterozygous ones. In the absence of disturbance, in particular, clones with lower individual heterozygosity were more likely to increase in area over a 1-year time period than more heterozygous ones, while there was no such correlation in plots with disturbance (logistic model, P(disturbance x heterozygosity) = 0.036). Undisturbed plots revealed background recruitment independent of canopy gaps, suggesting that Z. marina exhibits a strategy of continual recruitment. Effects of experimental disturbance (linear or quadratic) on clonal diversity were not detectable. Instead, initial (pretreatment) clonal diversity accounted for between 68% and 91% of the variance in diversity, indicating remarkable resilience of genotypic diversity in the face of physical disturbance.

Environment↗
PubMed1987

Trypanosoma cruzi: analysis of the population dynamics of heterogeneous mixtures.

Utilizing the previously reported inter-clonal differences in total DNA/organism, flow cytometry was used to analyze the population dynamics of Trypanosoma cruzi clone mixtures growing in liquid medium or vertebrate cells. The growth of clone mixtures in liquid medium can be described by unique parameters reflecting exponential growth rate (r), stationary phase population density (1/k), and the interaction between the clones (h). The relative numbers of each clone in the population change rapidly with time and the results are in quantitative agreement with mathematical models of competitive population growth. The relationship between the parameters for T. cruzi is such that, in general, there is no dynamic equilibrium with coexistence of clones with different growth rates; under all culture protocols, the faster growing clone will prevail. A computer simulation of the vertebrate cell cycle of T. cruzi suggests that clone mixtures grow relatively independently; the basic attributes of the model were substantiated experimentally. Although wide fluctuations in the proportion of each clone released occurred, the faster growing clone again predominated. Finally, these results underline the importance of working with well-defined clones in the laboratory to avoid inconsistencies and paradoxical results and stress the importance of the rapid isolation of single cell clones from clinical specimens when studying the relationship of the parasite to human disease.

Animals↗
PubMed2000

Repertoire dynamics of autoreactive T cells in multiple sclerosis patients and healthy subjects: epitope spreading versus clonal persistence.

Autoantigen-specific T-lymphocytes are present in patients with autoimmune disease and in normal subjects. Little is currently known about the temporal variation (dynamics) of the immune repertoire of these autoreactive T cells. We analysed the long-term variation of the immune repertoire of T cells specific for myelin basic protein (MBP) in five untreated patients with multiple sclerosis and four normal control subjects over a mean observation period of 6 years. MBP-specific CD4(+) T-cell lines were selected with purified human MBP, and their epitope specificity was mapped with overlapping synthetic peptides. Three distinct patterns of repertoire development were observed. (i) Two patients and three control subjects maintained a broad epitope response with fluctuations over time. (ii) Two patients initially showed a focused response that broadened over the course of 6 years; this finding could be described as intramolecular epitope spreading. (iii) In one patient and one control subject, a strikingly focused response, which was directed to a cluster of nested epitopes in the MBP region 83-102, persisted over time. T-cell receptor Vbeta sequence analysis allowed us to trace individual clones of MBP-specific T cells for up to 7 years in the peripheral circulation in four of the five patients and three of the four controls, suggesting that the long-term persistence of MBP-specific T-cell clones is a common feature of the T-cell repertoire not unique to multiple sclerosis. The persisting MBP-specific T-cell clones were not detectable in the blood of one of the patients by complementarity-determining region (CDR)-3 spectratyping, indicating that their frequency does not exceed 1 in 5000 T cells. The temporal characteristics of the MBP-specific T-cell repertoire described here are relevant to therapeutic strategies targeting autoantigen-specific T cells in multiple sclerosis and other autoimmune diseases.

Adult↗
PubMedDate not supplied

Establishment and application of a novel T cell clonality analysis using single-strand conformation polymorphism of T cell receptor messenger signals.

To identify the existence of antigen specific T cell responses and to follow the changes of these reactions, it is considered useful to evaluate whether certain T cells clonally accumulate in the lymphocyte population. For this purpose, we have established a novel method to analyze T cell clonality using a combination of reverse transcriptase-polymerase chain reaction of T cell receptor beta chain transcripts and single-strand conformation polymorphism (SSCP). Using this method, we obtained a smear-like pattern of electrophoresed DNA from the heterogeneous T cell population. On the other hand, a single T cell clone exhibits a band in the appropriate VP amplification and an accumulated T cell clone in a heterogeneous lymphocyte population is identified as a band in the background smear pattern. If a lymphocyte population was stimulated by an antigen either in vitro or in vivo, several distinct bands were found to be generated in the background smear. Thus, the dynamic changes of T cell clonal responses could be monitored with this method. Analyses of several immunological disorders, including autoimmune diseases, malignant disorders, and transplantations, revealed the involvement of antigen-specific T cell immune responses in these disorders. Furthermore, taking advantage of the reproducible mobility of a band of SSCP gel, we are now able to compare identities of the accumulated T cell clones in different samples without the need for nucleotide sequencing of each clone. Such information can thus elucidate the occurrence of uniform or stable immunological reactions in the host and also suggests that these reactions play an important role in vivo. Therefore, taken together, the above described novel T cell clonality analysis is considered to be useful in studying the T cell immune responses in various fields of immunology.

Autoimmune Diseases↗
PubMed2004

The malignant transformation event as a clonal transformation of apoptosis to anti-apoptosis pathways and of cell cycle dynamics.

Anti-apoptosis, as a more vital aspect of a whole series of progressive steps in carcinogenesis, would appear primarily a phenomenon of variable nonresponsiveness. Programmed cell death, in addition, would appear to affect the individual cell as attributes also of an integral field phenomenon constituted by clones of tumor cells that grow, proliferate and spread. Various modes of development of anti-apoptosis subsequently involving the development of genetic abnormalities would possibly account for transformation as a neoplastic phenomenon. It is in terms of such pathways as telomeric length preservation, of anti-apoptosis as failed activation of apoptosis, and of failed DNA binding events that clonally selected tumor cells would tend to inherently progress to higher grade and stage and to spread systemically. Moreover, clonal and field events would possibly influence in their turn individual cell cyclical activity and programmed cell pathways in neoplastic transformation. Anti-apoptosis would constitute, in fact, a predicted system of pathways that switch from apoptosis as an essential pathway in malignant transformation. Angiogenesis, as a full series of cascade events of a paracrine/autocrine nature, would also participate with anti-apoptosis in a tumor cell cycle transformation that is self-amplifying. Given different modes of how apoptosis would convert to anti-apoptosis in tumorigenesis, perhaps abnormal cell cycle dynamics might also contribute to the evolving nature of such neoplastic transformation.

Apoptosis↗
PubMed2005

Estimating the number of rate limiting genomic changes for human breast cancer.

We used multistage models that incorporate the age dependent dynamics of normal breast tissue, clonal expansion of intermediate cells and mutational events to fit data for the age-specific incidence of breast cancers in the surveillance, epidemiology, and end results (SEER) registry. Our results suggest that two or three rate limiting events occurring at rates characteristic of point mutation rates for normal mammalian cells set in motion a sequence of other genomic changes that lead with high probability to breast carcinoma.

Adolescent↗
PubMed1989

Kinetic assay of cytotoxic T lymphocyte clones. I. Methodology and data analysis.

A kinetic assay for cytotoxic T lymphocyte (CTL) clones expanded briefly in culture is described. The Hill equation for allosteric kinetics is used to fit curves to dose-response data. In this assay, K0--the target cell concentration required for half-maximal velocity of killing--is determined for clones generated from a population's most frequent CTL precursors. Because each clone's K0 is a constant under given conditions and a description of relative cytolytic efficiency, K0 values can be used to compare the clonal composition of disparate or dynamic populations. The parameter n is the target concentration exponent in the Hill equation and the slope of the line in the Hill plot. This parameter further specifies the shape of a clone's dose response curve, describing a clone's responsiveness to changes in target cell concentration. Because the assay is designed for small, undetermined effector cell concentrations, maximum velocities are not compared. The method described herein requires minimal supplies, equipment, and biological materials.

Animals↗
PubMed1986

Cell lines as an investigational tool for the study of biology of small cell lung cancer.

Tumors, whether they be of clonal or polyclonal origin, are dynamic processes, constantly undergoing alterations, both in vivo and in vitro. However, in many if not most tumors, certain properties are relatively stable. There must be selective advantages for tumor populations to maintain these properties. A careful comparison of the properties of tumors and their cell lines, and correlating these data with the clinical history of the tumor is essential. From such studies we conclude that cell lines are suitable models to study the biology of SCLC and many important contributions would have been impossible without a large comprehensive panel of cell lines. These lines may be suitable for the selection of the best in vitro regimen to treat individual patients from whom the lines were derived, a hypothesis currently being tested in our Branch. Finally, in vitro studies already (and will continue to) suggest newer, more rational approaches to tumor control.

Carcinoma, Small Cell↗