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PubMedDate not supplied

New mechanisms of viral persistence in primary human immunodeficiency virus (HIV) infection.

Viruses, including the Human Immunodeficiency Virus (HIV), have evolved multiple strategies to overcome host immune defenses, allowing them to persist in the host. Molecular and cellular approaches were simultaneously used to provide sensitive and unbiased delineation of the diversity and dynamics of the immune response, and to study the relative compartimentalization of HIV-specific CTL clones in patients undergoing primary HIV infection. This approach revealed that some HIV-specific CTL clones can be deleted in presence of high levels of antigen, a phenomenon analogous to high-dose tolerance or clonal exhaustion described in murine models of persistent viral infections. Also, HIV-specific CTL clones were found to accumulate preferentially in peripheral blood as compared to lymph nodes, even though the large majority of viral replication during primary HIV infection takes place within lymph nodes. These two mechanisms may decrease the effectiveness of the host cell-mediated immune responses, and favor the establishment of virus persistence during primary HIV infection.

Animals↗
PubMed2025

Unusual relapse dynamics in EGFR-mutated lung adenocarcinoma uncovered by genomic profiling: Insights from a case report.

Synchronous or metachronous multiple NSCLCs challenge clinical practice, particularly in distinguishing multiple separate primary lung cancers (SPLC) from intrapulmonary metastasis (IPM) for accurate staging and management. Here, we present a unique case of three resected lung adenocarcinomas (LUAD) from a single patient collected at different time points, all harboring the same EGFR p.L858R somatic driver mutation but exhibiting distinct clonal trajectories. Whole exome sequencing (WES) analysis revealed that the first tumor was an independent primary tumor, while the latter two tumors were clonally related. Our findings highlight the complexity of tumor progression and provide insights into clonal heterogeneity. This report underscores the importance of genomic profiling for discriminating SPLC from IPM and emphasizes that the detection of a single shared driver mutation is not sufficient to prove metastasis.

Humans↗
PubMed2026

Repeated emergence and fitness heterogeneity of KPC-33 in ST11 Klebsiella pneumoniae under ceftazidime-avibactam pressure.

Ceftazidime-avibactam (CZA) is an important therapeutic option for infections caused by Klebsiella pneumoniae carbapenemase (KPC)-producing Klebsiella pneumoniae. However, CZA exposure also selects for emergent KPC variants. Their in vivo evolutionary patterns, fitness consequences, and underlying molecular mechanisms remain unclear. We performed a longitudinal multiomics analysis of 35 clonally related ST11 KPC-producing K. pneumoniae isolates collected from eight hospitalized patients during clinical follow-up, most of whom had received CZA therapy. Whole-genome sequencing, antimicrobial susceptibility testing, in vitro competition assays, enzyme kinetic analysis, and transcriptomic sequencing were used to systematically characterize the within-host evolutionary dynamics of KPC variants and the fitness heterogeneity of KPC-33. Multiple KPC variants were identified during longitudinal follow-up, among which KPC-33 was the most frequently detected. Among the seven patients who received CZA treatment, KPC-33 was detected in longitudinal isolates from four patients. It was also identified in patient P3, who had not received CZA, whereas other variants were only sporadically identified. Biochemical analysis showed that KPC-33 exhibited an altered kinetic profile relative to KPC-2, characterized by reduced catalytic turnover and altered substrate affinity. KPC-33 did not exhibit a uniform and pronounced fitness defect but instead showed marked strain-dependent heterogeneity. Strains with higher competitive fitness generally showed only limited transcriptional changes, whereas those with lower fitness were accompanied by broader transcriptional remodeling. In this longitudinal cohort, KPC-33 was repeatedly detected, predominantly under CZA-associated selective conditions. Its fitness consequences were clearly strain background dependent and may be associated with the extent of transcriptional remodeling. These findings provide new evidence for understanding the in vivo evolution of CZA resistance.

KPC-33↗
PubMed1998

Bacterial genetics and strain variation.

An entire genome sequence will provide valuable information, but the genome of only one individual will limit interpretation of that information. Knowledge concerning genome variation in both eukaryotic and prokaryotic organisms such as Mycobacterium tuberculosis is likely to yield information of equal value and provide fundamental insights concerning the function of the genome. The variability in the genome between individual strains may be small and well defined, but it may cause large phenotypic changes (e.g. point mutations causing drug resistance). Clinical and epidemiological observations have led to the development of hypotheses, assumptions and models concerning disease dynamics. However, genome variation studied by molecular epidemiology has made new insights possible, which have allowed us to examine prevailing dogmas concerning tuberculosis. Recent results suggest that historical dogmas may well hold true in some communities, but not all. The information gathered from studying strain variation can be used for modelling disease dynamics, prediction of epidemics, policy planning and for monitoring the outcome of new interventions, as well as for gaining insight into the life processes of the organism. However, molecular epidemiology has its own limitations, some of which result from our lack of understanding of genome variation. We need further information in order to understand clonality and evolution of this organism so that our use of molecular tools in epidemiology and drug development may become more relevant and accurate.

Cluster Analysis↗
PubMedDate not supplied

Lingering biologic dilemmas about the status of the progenitor cells in myelodysplasia.

Myelodysplastic syndromes (MDS) are considered to be stem cell disorders. High incidence of intramedullary apoptosis has been associated with the peripheral cytopenia and refractory anemia in these disorders. The investigations on the cell of origin in the bone marrow have invariably been hampered by a poor yield of CD34+ cells from these marrows. Interestingly, even though limited in number, these studies raised more questions and dilemmas than providing answers. While the enigma surrounding the clonality of these marrows continues, the controversies regarding incidence of apoptosis, proliferation, and potential of clonogenic expansion may be closer to a settlement. The present review proposes a model depicting interplay between extraneous apoptogenic factors and intracellular apoptosis-susceptibility determinants that contributes significantly toward the progression of MDS and how a shift in dynamics of this interplay may provide grounds to accumulate additional mutations with a probable block in differentiation eventually leading to a leukemic transformation.

Antigens, CD34↗
PubMed2005

Stochastic gene expression in a lentiviral positive-feedback loop: HIV-1 Tat fluctuations drive phenotypic diversity.

HIV-1 Tat transactivation is vital for completion of the viral life cycle and has been implicated in determining proviral latency. We present an extensive experimental/computational study of an HIV-1 model vector (LTR-GFP-IRES-Tat) and show that stochastic fluctuations in Tat influence the viral latency decision. Low GFP/Tat expression was found to generate bifurcating phenotypes with clonal populations derived from single proviral integrations simultaneously exhibiting very high and near zero GFP expression. Although phenotypic bifurcation (PheB) was correlated with distinct genomic integration patterns, neither these patterns nor other extrinsic cellular factors (cell cycle/size, aneuploidy, chromatin silencing, etc.) explained PheB. Stochastic computational modeling successfully accounted for PheB and correctly predicted the dynamics of a Tat mutant that were subsequently confirmed by experiment. Thus, Tat stochastics appear sufficient to generate PheB (and potentially proviral latency), illustrating the importance of stochastic fluctuations in gene expression in a mammalian system.

Biodiversity↗
PubMed2005

Kinetics of T lymphocyte responses to persistent antigens.

Long term sequential study of immune responses in the same individuals is difficult from the time commitment required and the problem of maintaining enough subjects to provide for comparative analysis. We closely studied one hundred women with silicone mammary devices through cross sectional analysis up to 26 years post implantation and a similar sample of women to 6 years post explantation. The T cell index, calculated from tritiated thymidine incorporation during lymphoblast transformation, rose to a post implant peak at 10.5-12.0 years, falling progressively over the next 14.0-15.5 years to values indicative of probable immune quiescence. Post explantation, the index rose over the first 3 years and then sharply declined to within the range for unexposed controls. The shape of these time curves contains considerable information referent cell dynamics for both stimulatory and inhibitory factors and for demonstrating net group effects, appropriate to analysis in the cross sectional perspective. When a subset of four women was studied frequently and sequentially up to 8 years, an internal oscillatory pattern emerged, focusing attention on both the stimulatory and the inhibitory aspects of long term clonal expansion. IL-2 has stimulatory and inhibitory properties at different levels of production and is considered a prime candidate as the essential cytokine. The equations have details, however, which require exploration beyond any such provisional conclusion. The analytic process was aided by normalization of oscillatory data to eliminate subject variability and by Pareto optimization to assess the trend shown by normalization. Pareto analysis revealed two minimally coordinated oscillations, one over time and the other along net clonal expansion or decline of the siloxane specific T lymphocyte clone. The segments of the time related oscillation greatly exceeded the reaction times of cytokines currently known to be active in T cell regulation. Although the ultimate controlling factor(s) may be cytokine or chemokine combinations, the data are compatible with some more basic regulatory factor(s) of cell integrity, including limits on the number of cell divisions which can be sustained in long term immunopathic lesions, among other processes.

Antigens↗
PubMed1991

Second generation immune networks.

Network approaches have had little impact on immunology because they have addressed the wrong questions. They have concentrated on the regulation of clonal immune responses rather than on the supraclonal properties of the immune system that emerge from its network organization, such as natural tolerance and memory. Theoretical advances, observations in unimmunized mice and humans, and the success of novel therapeutics in autoimmune diseases have recently promoted a new burst of research on the structure, temporal dynamics and metadynamical plasticity of immune networks.

Animals↗
PubMed2001

Plasmodium falciparum parasitaemia described by a new mathematical model.

A new mathematical model of Plasmodium falciparum asexual parasitaemia is formulated and fitted to 35 malaria therapy cases making a spontaneous recovery after primary inoculation. Observed and simulated case-histories are compared with respect to 9 descriptive statistics. The simulated courses of parasitaemia are more realistic than any previously published. The model uses a discrete time-step of 2 days. Its realistic behaviour was achieved by the following combination of features (i) intra-clonal antigenic variation, (ii) large variations of the variants' baseline growth rate, depending on both variant and case, (iii) innate autoregulation of the asexual parasite density, variable among cases, (iv) acquired variant-specific immunity and (v) acquired variant-transcending immunity, variable among cases. Aspects of the model's internal behaviour, concerning variant dynamics, as well as the respective contributions of the three control mechanisms (iii) - (v), are displayed. Some implications for pathogenesis and control are discussed.

Animals↗
PubMed1996

A model of the immune network with B-T cell co-operation. I--Prototypical structures and dynamics.

Hitherto, "second generation" network models of the immune system have all been restricted to B-lymphocytes and the Ig molecules they produce. These models have not so far been able to provide a convincing mechanism for the distinction between a "Central Immune System" (CIS) composed of a connected network of lymphocyte clones which couple with "self" antigens in a tolerant mode, and a "Peripheral Immune System" (PIS) composed of clones with little or no supra-clonal organization and which produce classical immune responses when interacting with "non-self" antigens. Here, we present a new network model which explicitly incorporates B-T cell co-operation. In this model, B-cell activation is dependent on T-cell help, and activated T-cells are down-regulated by engagement of their TCRs by soluble Ig. We discuss the underlying biology on which we base the system of ordinary differential equations which defines the present network model. We then illustrate some basic features of the model by examining several prototypical situations with a small number of clones. Depending on the idiotypic connectivity structure, the model exhibits two distinct modes of coupling with antigens: an "immune response" mode in which T- and B-cell clones grow exponentially; and a "tolerant" mode in which T-cell clones are controlled by inclusion of all TCRs in the repertoire of an idiotypic B-cell network. Finally, we discuss the simplifying assumptions of the present model and argue that its range of validity is indeed the region of the state-space of the system where the discrimination between the CIS and the PIS take place.

B-Lymphocytes↗
PubMed2000

Coculturing diverse clonal populations prevents the early-stage neoplastic progression that occurs in the separate clones.

Most human cancers are of monoclonal origin and display many genetic alterations. In an effort to determine whether clonal expansion itself could account for the large number of genetic alterations, we compared spontaneous transformation in cloned and uncloned populations of NIH 3T3 cells. We have reported that progressive transformation of these cells, which is driven by the stress of prolonged contact inhibition at confluence, occurs far more frequently in cultures of recent monoclonal origin than in their uncloned progenitors. In the present work we asked how coculturing six clones at early and late stages of progression would affect the dynamics of transformation in repeated rounds of confluence. When coculture started with clones in early stages of transformation, marked by light focus formation, there was a strong inhibition of the progression to the dense focus formation that occurred in separate cultures of the individual clones. In contrast, when coculture started after the individual clones had progressed to dense focus formation, there was selection of transformants from the clone producing the largest and densest foci. Mixing the cells of a single clone with a large excess of uncloned cells from a subline that was refractory to transformation markedly decreased the size of dense foci from clones in transit from light to dense focus formation, but had much less effect on foci from clones with an established capacity for dense focus formation. The major finding of protection against progression by coculturing clones in early stages of transformation suggests that the expansion of a rogue clone in vivo increasingly isolates many of its cells from genetically stabilizing interactions with surrounding clones. Such clonal isolation might account for the increase in mutation rates associated with the dysplasia in colorectal adenomas that signifies the transition between benign and malignant growth.

3T3 Cells↗
PubMedDate not supplied

Simple developmental programs of gene expression and cellular composition of lymphoid organs at the origin of natural tolerance.

Self-tolerance is acquired in the embryonic/perinatal period, but new lymphocytes (that will have to distinguish between self and nonself) continue to be produced throughout life, after both self and nonself are present. This makes it impossible for natural tolerance to rely on recessive mechanisms. Recent observations on "dominant tolerance" have led to the hypothesis that natural tolerance is established as a consequence of simple developmental programs for gene expression and cellular composition of primary lymphoid organs. In development, the cellular composition of the thymus is predominantly epithelial, allowing for the positive selection and activation of "high avidity" self-reactive T cells that are not deleted because antigen presentation by haemopoietic cells is limiting. Such T cells, activated in that environment, display effector functions of a regulatory type that are maintained in the periphery upon restimulation by tissue peptides shared with the thymic epithelium. Recent thymic emigrants with specificity for tissue-specific antigens that are absent from the thymus will first encounter their ligands in the context of the "regulatory cell" recognition of ubiquitous peptides and are thus recruited into similar regulatory activities. In contrast, thymic emigrants with specificity for nonself antigens (absent during the perinatal period) are not activated intrathymically, reach the periphery as resting cells, and move out of the time window of susceptibility to functional recruitment. These will react "de novo" upon encounter of the respective antigens and will acquire the class of effector functions determined by the peripheral microenvironment in which they are activated. This strategy, which explains the thymic dependence of peripheral tissue-specific tolerance, may be re-enforced by developmental restrictions in cytokine gene expression, and it will ensure the establishment and maintenance of T-cell tolerance through the dynamic storage of a distributed memory of the embryonic self. B lymphocytes that are produced in the embryonic/perinatal period characteristically rearrange and express a few V-genes very predominantly. These V-genes encode antibodies with unique properties of "connectivity" to other V-regions, making it possible to establish a network that limits clonal expansions and/or terminal differentiation to antibody production. Self-reactive B cells are thus recruited into such a network which, by contributing to the molecular environment of the body and to the selection of emergent repertoires, leads to deletion of connected cells and to the "normalization" of the adult antibody repertoires. Natural autoantibody repertoires in the adult are thus recursively maintained, stable and continuously adjusted to the thresholds of single cell deletion and to the alterations in the body composition. The activity of self-specific regulatory T cells contributes to limiting clonal expansion and inhibiting somatic mutation of self-reactive B cells. This model explains a number of observations that were not included in the "clonal" and "recessive" tolerance views, and offers suggestions on mechanisms in physiological autoimmunity and pathology.

Animals↗
PubMed2026

Genomic instability, postoperative recurrence and therapeutic vulnerabilities in resectable non‑small cell lung cancer (Review).

Resectable non‑small cell lung cancer (NSCLC) is managed largely according to anatomical stage, pathological risk and actionable driver alterations, yet these factors do not fully explain postoperative recurrence. Genomic instability may contribute to recurrence by promoting clonal diversification, intratumoral heterogeneity, occult dissemination, persistence of residual tumor cells, and immune escape. In the present review, chromosomal instability (CIN), copy‑number complexity, whole‑genome doubling, DNA repair defects, replication stress, and extrachromosomal DNA (ecDNA) were critically evaluated using a three‑axis translational framework encompassing biological consequences, potential clinical roles, and strength of evidence. Current evidence suggests that clonal diversity and copy‑number complexity have the clearest near‑term prognostic rationale. By contrast, CIN and whole‑genome doubling are supported more strongly by evolutionary and mechanistic rather than prospective clinical evidence. Defects in DNA repair, replication stress, and ecDNA represent potential therapeutic vulnerabilities, but their clinical relevance remains to be established. To date, no treatment‑predictive biomarkers based on genomic instability have been identified for resectable NSCLC. Direct clinical evidence linking any specific genomic instability feature to the presence or longitudinal dynamics of postoperative molecular residual disease (MRD) remains limited. Postoperative circulating tumor DNA‑defined MRD provides prognostic information more directly related to residual disease but remains assay‑dependent and should not be considered a genomic‑instability phenotype. Therefore, features of genomic instability should remain investigational and should not replace established clinical, pathological, or molecular decision‑making. Their near‑term value lies in refining biological risk models and generating testable hypotheses for biomarker‑defined perioperative trials.

Humans↗
PubMed2000

Cellular automaton of idealized brain tumor growth dynamics.

A novel cellular automaton model of proliferative brain tumor growth has been developed. This model is able to simulate Gompertzian tumor growth over nearly three orders of magnitude in radius using only four microscopic parameters. The predicted composition and growth rates are in agreement with a test case pooled from the available medical literature. The model incorporates several new features, improving previous models, and also allows ready extension to study other important properties of tumor growth, such as clonal competition.

Algorithms↗
PubMed2003

BCR/ABL alters the function of NK cells and the acquisition of killer immunoglobulin-like receptors (KIRs).

Natural killer (NK) cells decrease in function during chronic myelogenous leukemia (CML) progression from chronic phase to blast crisis, and they can become BCR/ABL(+) late in the disease course. To study this altered function, NK92 cells were transduced with the BCR/ABL oncogene. In contrast to the parental cells, which died when deprived of interleukin 2 (IL-2), p210(+) NK92 cells proliferated and survived indefinitely in the absence of IL-2. BCR/ABL also decreased the natural cytotoxicity of NK92 cells against K562 targets, without affecting IL-2, interferon gamma (IFN-gamma), or tumor necrosis factor alpha (TNF-alpha) production. Although the ABL-specific tyrosine kinase inhibitor imatinib mesylate (STI-571) had no effect on parental NK92 cells, it markedly decreased the growth and survival of IL-2-independent p210(+) NK92 cells. In contrast to the parental cell line, serial analysis of p210(+) NK92 cells detected small populations that clonally expressed one or more killer immunoglobulin-like receptors (KIRs). Unlike the decreased natural cytotoxicity, the function of the activating CD158j receptor remained intact. Southern blotting and hybridization with an enhanced green fluorescence protein (eGFP) probe showed that KIR(-) and KIR(+) NK92 cells were all derived from the same clone, suggesting that KIR acquisition remains dynamic at the maturational stage represented by the NK92 cell line. When tested in primary CD56(+bright) NK cells, p210 induced partial IL-2-independent growth and increased KIR expression similar to findings in NK92 cells. This is the first study to show that BCR/ABL, well known for its effects on the myeloid lineage, can alter the function of lymphoid cells, which may be associated with the defect in innate immunity associated with CML progression.

Benzamides↗
PubMed2006

Deterministic and stochastic regimes of asexual evolution on rugged fitness landscapes.

We study the adaptation dynamics of an initially maladapted asexual population with genotypes represented by binary sequences of length L. The population evolves in a maximally rugged fitness landscape with a large number of local optima. We find that whether the evolutionary trajectory is deterministic or stochastic depends on the effective mutational distance d(eff) up to which the population can spread in genotype space. For d(eff) = L, the deterministic quasi-species theory operates while for d(eff) < 1, the evolution is completely stochastic. Between these two limiting cases, the dynamics are described by a local quasi-species theory below a crossover time T(x) while above T(x) the population gets trapped at a local fitness peak and manages to find a better peak via either stochastic tunneling or double mutations. In the stochastic regime d(eff) < 1, we identify two subregimes associated with clonal interference and uphill adaptive walks, respectively. We argue that our findings are relevant to the interpretation of evolution experiments with microbial populations.

Adaptation, Biological↗
PubMed2000

Dynamics of the reactivity to MBP in multiple sclerosis.

Though many lines of evidence support the importance of myelin basic protein (MBP) in the pathogenesis of experimental autoimmune encephalomyelitis (EAE), its role in multiple sclerosis (MS) is still debated as well as the significance of epitope spreading in disease progression. We characterised the response to MBP in eight MS subjects and three of these were followed over time. In one case, the follow up lasted over a 6-year period. Clonal expansion, clonal persistence and epitope spreading against other MBP determinants was detected irrespective of disease course. In one patient we identified a novel T-cell receptor variable gene (BV28S2) which may be involved in the selection of MBP determinants, as suggested by experiments performed in the presence of mismatched antigen presenting cells (APC) between two subjects compatible for HLA-DR2 subtype but differing for the epitope recognised. Our findings do not sustain a role for the response to MBP effecting on clinical course and suggest that a novel TCR gene may be involved in the recognition of unusual self antigens.

Amino Acid Sequence↗
PubMed1998

Mitochondrial DNA: a tool for populational genetics studies.

Mitochondria are cellular organelles that have the function of the oxidative phosphorilation and the formation of ATP. In humans, the mtDNA is a double-stranded, circular, covalent closed molecule of 16.5 kb. The mtDNA is inherited as a haploid from the mother and heteroplasmy has been found rarely. From a populational perspective, it could be considered as a system of small, sexually isolated demes, or clonal lineages, with an evolutionary rate 5 to 10 times faster than the nuclear genome. All these characteristics make this molecule ideal for evolutionary studies. We present two applications of this molecule in genetical studies. One of these is referred to the Balearic Islands populations, Majorca, Minorca, Ibiza, and Chuetas. The other example is the populational dynamics of the different mitochondrial haplotypes in Drosophila subobscura. We also discuss the importance of nuclear markers to complete these studies as well as the study of the Y chromosome to compensate the bias produced by the study of only the mtDNA.

Animals↗