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 55 records · Page 3Linked to original sources
PubMed2025

Integrating multi-omics approaches in acute myeloid leukemia (AML): Advancements and clinical implications.

Acute myeloid leukemia (AML) is a highly heterogeneous and aggressive hematologic malignancy characterized by clonal proliferation of myeloid precursors. Despite significant advancements in genomic profiling and targeted therapies, patient outcomes remain suboptimal due to disease complexity, resistance mechanisms, and high relapse rates. The integration of multi-omics approaches-spanning genomics, epigenomics, transcriptomics, proteomics, and metabolomics-has revolutionized AML research, offering a comprehensive understanding of leukemogenesis, tumor heterogeneity, and therapeutic vulnerabilities. Recent studies leveraging high-throughput sequencing, mass spectrometry, and advanced computational tools have uncovered novel biomarkers, clonal evolution dynamics, and microenvironmental interactions that drive AML progression and resistance. For instance, single-cell multi-omics has revealed chemotherapy-resistant leukemic stem cell populations, while proteogenomic analyses have identified actionable targets such as MCL1 and metabolic dependencies like OXPHOS. Clinically, integrated omics platforms are refining risk stratification, minimal residual disease (MRD) monitoring, and personalized therapy selection. However, challenges such as data integration complexity, cost barriers, and ethical considerations remain. This review highlights the transformative potential of multi-omics in AML, emphasizing recent advancements in technology, biomarker discovery, and therapeutic innovation. By bridging the gap between molecular insights and clinical practice, multi-omics integration promises to redefine AML management, paving the way for precision oncology and improved patient outcomes.

Humans↗
PubMed2006

Cutting Edge: IL-12 inversely regulates T-bet and eomesodermin expression during pathogen-induced CD8+ T cell differentiation.

Cytokines are critical determinants for specification of lineage-defining transcription factors of CD4+ T cell subsets. Little is known, however, about how cytokines regulate expression of T-bet and eomesodermin (Eomes) in effector and memory CD8+ T cells. We now report that IL-12, a signature of cell-mediated immunity, represses Eomes while positively regulating T-bet in effector CD8+ T cells during infection with Listeria monocytogenes. After resolution of infection and abatement of IL-12 signaling, Eomes expression rises whereas T-bet expression declines in memory CD8+ T cells. Eomes becomes derepressed in effector cells by ablation of IL-12 signaling. In the absence of IL-12, the dynamics of clonal expansion and contraction are also perturbed. Together, these results reveal how a pathogen-associated signal, such as IL-12, could act as a switch, regulating appropriate clonal growth and decline while, in parallel, shaping a unique pattern of fate-determining transcription factors.

Animals↗
PubMed1987

Facilitation of emergence of multidrug-resistant state by alteration of tumor environment: implications from competitive ecology models.

The presence of multidrug-resistant (MDR) cells in a solid tumor constitutes a major problem in cancer therapy. Current thinking suggests that the resistant phenotype arises de novo during the tumor's evolution via somatic mutation mechanisms. The proportion of MDR cells, once established, may be enriched during therapy as a consequence of differential cell kill. Michelson et al have developed mathematical models of these phenomena to gain an insight into the dynamics of clonal subpopulation emergence in general and MDR emergence in particular, and I now show that one unexpected consequence of therapy may be the facilitation of MDR emergence due to damage inflicted on the host. The therapeutic damage to the host is modeled as a decreased ability to carry a specific tumor burden.

Antineoplastic Agents↗
PubMed1982

Dynamics of B cell repertoire formation: normal patterns of clonal turnover are altered by ligand interaction.

The dynamics of B cell repertoire formation was examined by defining the kinetics and clonal composition of the influenza hemagglutinin- (HA) responsive BALB/c repertoire at 1 and 2 wk of age. Although the size and diversity of the HA-responsive repertoire remain constant during this period, the clonal composition changes significantly. These findings indicate a rapid and regular turnover of clonal specificities within the emerging primary repertoire. In addition, the effect of ligand exposure on this process was analyzed by characterizing the repertoire of 2-wk-old BALB/c mice that had been immunized with virus during their first week of life. This treatment markedly alters the normal kinetics and turnover of the emerging repertoire. First, many clonotypes that normally arise between 1 and 2 wk of age fail to be expressed in detectable numbers. Second, several clonotypes that are normally only transiently expressed at 1 wk of age are preferentially expanded and preserved within the responsive B cell pool. In conjunction, these results demonstrate that a) the primary repertoire is characterized by rapid and regular turnover in clonotype composition, b) antigenic exposure perturbs the normal kinetics and pattern of this turnover, and c) the exact effects of ligand exposure may depend on the developmental stage at which it occurs.

Age Factors↗
PubMed2025

Doblin: inferring dominant clonal lineages from high-resolution DNA barcoding time series.

MOTIVATION: The lineage dynamics and history of cells in a population reflect the interplay of evolutionary forces they experience, including mutation, drift, and selection. When the population is polyclonal, lineage dynamics also manifest the extent of clonal competition among co-existing mutational variants. If the population exists in a community of other species, the lineage dynamics could also reflect the population's ecological interaction with the rest of the community. Recent advances in high-resolution lineage tracking via DNA barcoding, coupled with next-generation sequencing of bacteria, yeast, and mammalian cells, allow for precise quantification of clonal dynamics in these organisms. RESULTS: In this work, we introduce Doblin, an R suite for identifying dominant barcode lineages based on high-resolution lineage tracking data. We first benchmarked Doblin's accuracy using lineage data from evolutionary simulations, showing that it recovers the clones' identity and relative fitness in the simulation. Next, we applied Doblin to analyze clonal dynamics in laboratory evolutions of Escherichia coli populations undergoing antibiotic treatment and in colonization experiments of the gut microbial community. Doblin's versatility allows it to be applied to lineage time-series data across different experimental setups. AVAILABILITY AND IMPLEMENTATION: Doblin is available on CRAN (https://CRAN.R-project.org/package=doblin) and Github (https://github.com/dagagf/doblin).

DNA Barcoding, Taxonomic↗
PubMed1999

Dynamics and requirements of T cell clonal expansion in vivo at the single-cell level: effector function is linked to proliferative capacity.

The adoptive transfer of TCR-transgenic T cells into syngeneic recipients allows characterization of individual T cells during in vivo immune responses. However, the proliferative behavior of individual T cells and its relationship to effector and memory function has been difficult to define. Here, we used a fluorescent dye to dissect and quantify T cell proliferative dynamics in vivo. We find that the average Ag-specific CD4+ T cell that undergoes division in vivo generates >20 daughter cells. TCR and CD28 signals cooperatively determine the degree of primary clonal expansion by increasing both the proportion of Ag-specific T cells that divide and the number of rounds of division the responding T cells undergo. Nonetheless, despite optimal signaling, up to one-third of Ag-specific cells fail to divide even though they show phenotypic evidence of Ag encounter. Surprisingly, however, transgenic T cells maturing on a RAG-2-/- background exhibit a responder frequency of 95-98% in vivo, suggesting that maximal proliferative potential requires either a naive phenotype or allelic exclusion at the TCRalpha locus. Finally, studies reveal division cycle-dependent expression of markers of T cell differentiation, such as CD44, CD45RB, and CD62L, and show also that expression of the cytokines IFN-gamma and IL-2 depends primarily on cell division rather than on receipt of costimulatory signals. These results provide a quantitative assessment of T cell proliferation in vivo and define the relationship between cell division and other parameters of the immune response including cytokine production, the availability of costimulation, and the capacity for memory.

Adoptive Transfer↗
PubMedDate not supplied

[Variability of the clonal structure of Yersinia pseudotuberculosis population under different conditions].

In a series of experiments the dynamics of the clonal structure of Y. pseudotuberculosis population was evaluated by cytopathogenicity in soil extract, as well as in associations with blue-green algae (cyanobacteria) and infusoria, under different temperature conditions. In all variants of experiments made at low environmental temperature (10 degrees C) a considerable part of Y. pseudotuberculosis clones (25-40%) was found to be cytopathogenic, while at 22 degrees C such clones were absent or had low cytopathogenicity. At the same time experiments made under the same temperature conditions (10 degrees C) showed the variability of the clonal structure of the bacterial population in different associations and sterile soil extract, as well as at different periods of the experiments. At low temperatures Y. pseudotuberculosis virulent (cytopathogenic) clones, in contrast to avirulent ones, were characterized by the presence of virulence plasmid p45, as well as high urease and catalase activity. The results of the experiments are discussed from the viewpoint of the clonal concept of bacterial populations and their pathogenicity.

Animals↗
PubMed2005

Characterization of vancomycin-resistant Enterococcus faecium isolates from broiler poultry and pig farms in England and Wales.

This study aimed to investigate the occurrence and molecular epidemiology of vancomycin-resistant Enterococcus faecium (VREF) isolates on poultry and pig farms in England and Wales. A total of 217 VREF isolates were obtained from fresh feces and environmental swabs collected from conventional and organic farms. A predominant pulsed-field gel electrophoresis (PFGE) profile was found for each VREF-positive farm, together with less frequent types. All isolates presented the vanA genotype and were esp negative. Seventy-six percent of the VREF isolates were additionally resistant to nine or more antimicrobials, presenting a diverse range of resistance phenotypes. The multiresistance traits did not appear to be specific to individual farms or sample types (i.e., environmental or fecal), nor did they correlate with any specific PFGE type. Ninety-three percent of the isolates were resistant to penicillin, 89% were resistant to tetracycline, 87.5% were resistant to erythromycin, and 50% were resistant to quinupristin-dalfospristin (Synercid). The lack of clonality among these populations may suggest the horizontal transfer of resistance genes and/or a dynamic replacement of clonal lines rather than persistence.

Animal Husbandry↗
PubMed2005

Evolutionary history of contagious asexuality in Daphnia pulex.

Asexual taxa are short-lived, suggesting that transitions to asexuality represent evolutionary dead-ends. However, with high rates of clonal origin and coexistence of asexuals and sexuals via selective asymmetries, asexuality may persist in the long term as a result of a dynamic equilibrium between clonal origin and extinction. Few such systems have been studied in detail. Here, we investigate the evolutionary history of asexual lineages of Daphnia pulex, which are derived from sexual relatives via the inheritance of a dominant female-limited meiosis-suppressing locus and inhabit ponds throughout northeastern North America (NA). Our extensive sampling and subsequent phylogenetic analysis using mitochondrial sequence data reveals a young and genetically diverse asexual assemblage, reflecting high rates of clonal origin due to the contagious nature of asexuality. Yet, asexuality is restricted to two phylogroups (B and C) with historical and/or present associations with northeastern NA and is absent from a northwestern phylogroup (A), supporting a recent northeastern origin of asexuality in this species. Furthermore, macrogeographic patterns of genetic variability indicate that phylogroups B and C recolonized northeastern NA from opposite directions, yet their presently overlapping geographic distributions are similarly divided into an eastern asexual and a western sexual region. We attribute these patterns to a recent contagious spread of asexuality from a northeastern source. If environment-mediated selective asymmetries play no significant role in determining the outcome of competitive interactions between sexuals and asexuals, regions of contact may be setting the stage for continued asexual conquests.

Adaptation, Physiological↗
PubMed1997

Significance of antigen-specific T cell clones in collagen diseases: analyses with a novel T cell clonality evaluation system.

The involvement of antigen-specific T cells in the pathogenesis of collagen diseases is still controversial. The final stages of collagen diseases are usually characterized by the dominance of inflammation. Therefore, antigen non-specific factors, such as inflammatory cytokines, probably play an important role in this process. On the other hand, the methods available to analyze the antigen-specific aspects of the immune response are still limited. Here we review our novel system of T cell clonality analysis based on the idea that activated antigen-specific T cells should form accumulating clones among the lymphocyte population. Using this method, dynamic changes of clonal accumulation of T cells could be evaluated during antigenic stimulation in vivo and in vitro. The significance of antigen-specific T cell clones in collagen diseases is discussed using data obtained from patients with rheumatoid arthritis and systemic lupus erythematosus.

Arthritis, Rheumatoid↗
PubMed2001

Clonality in wild rice (Oryza rufipogon, Poaceae) and its implications for conservation management.

Correlations were examined between habitat characters and clonal structures determined by the RAPD (random amplified polymorphic DNA) assay in five populations of Oryza rufipogon in China. Nine of 175 decameric primers were used in the study because they reproducibly amplified polymorphisms. The extent of clonality together with the clonal and sexual reproductive strategies varied greatly among the five populations and correlated with the habitats where they occur. The populations under serious disturbance or seasonal drought tended to have small clones with relatively high clonal diversity caused by sexual reproduction, whereas the populations with little disturbance and sufficient supply of water were prone to have large clones with relatively low clonal variation and low sexual reproduction. Therefore, the dynamics of sexual vs. clonal reproduction of this species depended mainly on environmental factors, such as external disturbance and water supply, rather than latitudes indicated by previous study. These results have important implications for in situ conservation of O. rufipogon. Adequate external disturbance and water supply control are essential for maintaining high clone diversity of in situ conserved populations. According to the extent of clonality of the populations examined, we recommend that an interval of >12 m should be required for collecting samples for ex situ conservation and for population genetic studies to capture possible genetic diversity for O. rufipogon in China.

Journal Article↗
PubMedDate not supplied

[A mathematical model of pre-epidemic circulation: an analysis of the mechanisms of oriented transformation].

The probable mechanisms of the regulation of the clonal composition of the infective agent in the course of its pre-epidemic circulation are studied. The mathematical model (in the form of two subsystems) describes asymptomatic circulation and the dynamics of the clonal composition: the beginning of the active circulation of faintly virulent variants, the oriented selection of virulent variants and the fixation of the epidemic variant.

Cloning, Molecular↗
PubMed2005

Evidence for involvement of clonally expanded CD8+ T cells in anticancer immune responses in CLL patients following nonmyeloablative conditioning and hematopoietic cell transplantation.

We have analyzed the clonotype composition of CD8+ T cells following nonmyeloablative (NMA) conditioning and hematopoietic cell transplantation (HCT), of patients with chronic lymphocytic leukemia (CLL). Consecutive analyses of blood samples taken up to 2 years following HCT, demonstrated that CD8+ T-cell clonality was highly dynamic in the early phases after HCT, but became more stable after 4-5 months. Moreover, donor lymphocyte infusion (DLI) given for disease progression in one of the patients led to establishment of recurrent as well as new T-cell clonotypes. This coincided with disease remission, strongly suggesting that these T cells were engaged with anti-CLL cytotoxicity. To examine the functional capacity of stable clonally expanded T cells after HCT, CD8+ T cells isolated post-transplant from the recipients were stimulated ex vivo with CLL cells and subsequently analyzed by FACS for surface expression of the marker for cytotoxic activity, CD107a. Stimulation with CLL cells indeed led to surface expression of CD107a, and clonotype analyses of sorted cells demonstrated that CD107a positive T cells were stably expanded following HCT. Our data suggest that clonally expanded CD8+ T-cell clones participate in the ongoing T-cell response against CLL cells following HCT with NMA conditioning.

CD8-Positive T-Lymphocytes↗
PubMed1998

Progression of spontaneous lymphomas in SJL mice: monitoring in vivo clonal evolution with molecular markers in sequential splenic samples.

SJL mice are an inbred strain with a high incidence of spontaneous lymphomas of the B-cell type. We used molecular markers of clonality to study the process of tumor progression of SJL lymphomas in vivo. This was accomplished at time intervals ranging from 2 to 116 days by initial partial splenectomy (biopsy) followed by spleen sampling at the time of killing (autopsy). Immunoglobulin heavy chain (IgH) gene rearrangement and murine leukemia virus (MuLV) proviral integration patterns were used to study the clonal identities of the sequential tumor pairs in 11 informative mice by Southern blot hybridization. Of these 11 mice, 5 showed the same number of IgH gene rearrangement bands in the matched biopsy-autopsy samples, indicating the persistence of the original lesions. In 2 of 11 mice, a decrease in the number of IgH gene rearrangement bands was seen, consistent with a process of clonal selection in the original oligoclonal population. Another 2 of 11 mice showed an increase in the IgH gene rearrangement bands, indicating the emergence of either a new unrelated clone or, less likely, a subclone with secondary IgH gene rearrangement. The remaining two mice showed differences between the patterns in biopsy and autopsy samples, as assessed by IgH gene rearrangement and the proviral integration analysis. This finding suggests that the biopsied tumor had regressed and new clones had emerged. Tumor development was also associated with an increase in the number of clonal MuLV insertions in all mice except one, in which no non-germline integration band was detected. Of 11 mice, 5 showed an increase in the extent of tumor involvement by microscopic examination of the biopsy and autopsy samples; 3 showed a decrease, whereas 2 showed no change. A change in tumor morphology toward a more dedifferentiated appearance was found in only 1 of 11 mice. Overall, the results did not show a single paradigm that tumor progression followed, rather they indicated a complex and dynamic process of clonal evolution, which is likely to be a major feature of lymphoma progression in vivo.

Animals↗
PubMed2025

Advances in tumor subclone formation and mechanisms of growth and invasion.

Tumor subclones refer to distinct cell populations within the same tumor that possess different genetic characteristics. They play a crucial role in understanding tumor heterogeneity, evolution, and therapeutic resistance. The formation of tumor subclones is driven by several key mechanisms, including the inherent genetic instability of tumor cells, which facilitates the accumulation of novel mutations; selective pressures from the tumor microenvironment and therapeutic interventions, which promote the expansion of certain subclones; and epigenetic modifications, such as DNA methylation and histone modifications, which alter gene expression patterns. Major methodologies for studying tumor subclones include single-cell sequencing, liquid biopsy, and spatial transcriptomics, which provide insights into clonal architecture and dynamic evolution. Beyond their direct involvement in tumor growth and invasion, subclones significantly contribute to tumor heterogeneity, immune evasion, and treatment resistance. Thus, an in-depth investigation of tumor subclones not only aids in guiding personalized precision therapy, overcoming drug resistance, and identifying novel therapeutic targets, but also enhances our ability to predict recurrence and metastasis risks while elucidating the mechanisms underlying tumor heterogeneity. The integration of artificial intelligence, big data analytics, and multi-omics technologies is expected to further advance research in tumor subclones, paving the way for novel strategies in cancer diagnosis and treatment. This review aims to provide a comprehensive overview of tumor subclone formation mechanisms, evolutionary models, analytical methods, and clinical implications, offering insights into precision oncology and future translational research.

Humans↗
PubMed2000

Antigenic diversity of Plasmodium falciparum and antibody-mediated parasite neutralization.

The malaria parasite Plasmodium falciparum, causing the most severe form of the disease in humans, is characterized by a broad antigenic diversity between different strains and isolates of the parasite. The antigenic diversity reflects on the one hand polymorphisms in allelic gene products and, on the other hand, antigenic variation as a result of expression of alternative genes in multigene families. Using selected polymorphic regions in two merozoite surface antigens, a method for genotyping P. falciparum parasites has been developed. This has resulted in new information on the clonal multiplicity and dynamics of parasite populations. Observations from in vivo and in vitro studies have identified many potential parasite-neutralizing immune responses and several of the target antigens are being explored as vaccine candidates. Studies of antibody-mediated neutralization of parasites in P. falciparum in vitro cultures, with or without leukocytes as effector cells, have been instrumental in identifying potential target antigens for protective immunity and for elucidation of the effects of immune pressure on the dynamics of parasite populations and their antigenic plasticity.

Adult↗
PubMed2006

Applications of cell sorting in biotechnology.

Due to its unique capability to analyze a large number of single cells for several parameters simultaneously, flow cytometry has changed our understanding of the behavior of cells in culture and of the population dynamics even of clonal populations. The potential of this method for biotechnological research, which is based on populations of living cells, was soon appreciated. Sorting applications, however, are still less frequent than one would expect with regard to their potential. This review highlights important contributions where flow cytometric cell sorting was used for physiological research, protein engineering, cell engineering, specifically emphasizing selection of overproducing cell lines. Finally conclusions are drawn concerning the impact of cell sorting on inverse metabolic engineering and systems biology.

Journal Article↗