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Results for “clonal modeling”

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At least 127 records · Page 7Linked to original sources
PubMed1999

The interval between courses of high-dose chemotherapy with stem cell rescue: therapeutic hypotheses.

The interval between courses of chemotherapy have classically been kept to a minimum in order to maximize dose intensity. Certain clinical observations suggest that longer intervals, particularly in the high-dose setting, may be more effective. This is based in part on the evidence that resistance is reversible over time and that the interval should be sufficient to allow for such a reversal. Clinical evidence for such reversibility include the following. In metastatic breast cancer, double or double high-dose stem cell rescue (HD-SCR) studies involving a minimal interval, have not, at least as yet, been shown to be superior to single HD-SCR. In Hodgkin's disease, response after relapse correlates directly with duration of time to relapse. In a comparative study of metastatic breast cancer, early HD-SCR preceded by daunorubicin induction was inferior to delayed HD-SCR. The latter was not preceded by induction chemotherapy. In a comparative study of childhood ALL, patients randomized to delayed (4 month interval) intensification had a significantly superior survival as compared to patients randomized to immediate (1 month interval) intensification. Taken together, these clinical observations indicate that resistance is reversible and that optimization of the interval must take this into account. Cytokinetic modeling of those clinical studies also found that delayed HD-SCR could result in a superior effect. Cytokinetic models of minimal residual tumor which were also examined included the Skipper exponential model, the Norton-Simon model which emphasizes the Gompertzian effect, the clonal evolution model, and the Retsky-Demisheli model which derives from a bimodal relapse pattern above. Biological and clinical data have resulted in a clinical protocol in the CALGB wherein patients with metastatic breast cancer are randomly allocated to (1) a single HD-SCR arm; (2) a double HD-SCR with a 5-week interval; and (3) a double HD-SCR arm with a 16 week interval.

Antineoplastic Agents↗
PubMed1987

Proliferative potential of human fibroblasts: an inverse dependence on cell size.

Human foreskin fibroblast-like cells were separated on the basis of DNA content and cell size by fluorescence-activated cell sorting. Subpopulations of "large" or "small" cells with the same (G1) DNA content were clonally expanded and found to contain predominantly nondividing or highly proliferative cells, respectively. From the rate of clonal growth, we deduce that small cells divide faster than large cells. Intermediate-sized cells were found to yield primarily smaller ("attenuated") clones. The clonal data can be incorporated into a previously reported kinetic model of clonal attenuation. This version of the model postulates that small "stem" cells yield larger daughters which have only a limited proliferative potential. We also postulate that a progressive increase in cell size can account for the decreasing concentration of DNA polymerase alpha, which has been reported in older cultures.

Cell Division↗
PubMed1990

A cell culture model for T lymphocyte clonal anergy.

T lymphocytes respond to foreign antigens both by producing protein effector molecules known as lymphokines and by multiplying. Complete activation requires two signaling events, one through the antigen-specific receptor and one through the receptor for a costimulatory molecule. In the absence of the latter signal, the T cell makes only a partial response and, more importantly, enters an unresponsive state known as clonal anergy in which the T cell is incapable of producing its own growth hormone, interleukin-2, on restimulation. Our current understanding at the molecular level of this modulatory process and its relevance to T cell tolerance are reviewed.

Animals↗
PubMed2002

Multistage carcinogenesis and radiation.

We will briefly review the concept of multistage carcinogenesis and the mathematical models built on this idea, including a class of models recently developed to describe the pathogenesis of colon cancer. The simplest model that explicitly accounts for cell proliferation kinetics is the two-stage clonal expansion model. It has been applied to a number of experimental and epidemiological data sets and has generated several thought-provoking hypotheses, especially as they relate to the role of promotion in radiation-induced carcinogenesis. The model generates hazard functions (used to estimate age-specific cancer incidence) that are not always intuitive because of the stochastic nature of the clonal expansion process involved. However, the model does make specific predictions depending on whether initiation, promotion or malignant conversion is affected by a carcinogen. A recent analysis of a large cohort of radiation workers exemplifies this behaviour.

Animals↗
PubMed2004

Modeling genetic networks from clonal analysis.

In this report a systematic approach is used to determine the approximate genetic network and robust dependencies underlying differentiation. The data considered is in the form of a binary matrix and represent the expression of the nine genes across the 99 colonies. The report is divided into two parts: the first part identifies significant pair-wise dependencies from the given binary matrix using linear correlation and mutual information. A new method is proposed to determine statistically significant dependencies estimated using the mutual information measure. In the second, a Bayesian approach is used to obtain an approximate description (equivalence class) of network structures. The robustness of linear correlation, mutual information and the equivalence class of networks is investigated with perturbation and decreasing colony number. Perturbation of the data was achieved by generating bootstrap realizations. The results are refined with biological knowledge. It was found that certain dependencies in the network are immune to perturbation and decreasing colony number and may represent robust features, inherent in the differentiation program of osteoblast progenitor cells. The methods to be discussed are generic in nature and not restricted to the experimental paradigm addressed in this study.

Animals↗
PubMed1983

[Nerve cell clonal lines in culture--models for studying the molecular basis of neuropharmacological actions].

Nerve cell lines with stable properties are isolated from neuroblastomas, glioblastomas or pheochromocytomas by periodic cloning using defined culture media. After the action of different drugs, these cells show all morphological and biochemical signs of differentiation and maturation. Depending on the origin of the clone, the cell lines synthesise typical neurotransmitters, which are stored in vesicles. It is demonstrated on cell lines which synthesise catecholamines that noradrenergic and dopaminergic clones are particularly suitable test objects for basic research in neuropharmacology.

Astrocytoma↗
PubMed1998

Statistical models for low dose exposure.

Extrapolation of health risks from high to low doses has received a considerable amount of attention in carcinogenic risk assessment over decades. Fitting statistical dose-response models to experimental data collected at high doses and use of the fitted model for estimating effects at low doses lead to quite different risk predictions. Dissatisfaction with this procedure was formulated both by toxicologists who saw a deficit of biological knowledge in the models as well as by risk modelers who saw the need of mechanistically-based stochastic modeling. This contribution summarizes the present status of low dose modeling and the determination of the shape of dose-response curves. We will address the controversial issues of the appropriateness of threshold models, the estimation of no observed adverse effect levels (NOAEL), and their relevance for low dose modeling. We will distinguish between quantal dose-response models for tumor incidence and models of the more informative age/time dependent tumor incidence. The multistage model and the two-stage model of clonal expansion are considered as dose-response models accounting for biological mechanisms. Problems of the identifiability of mechanisms are addressed, the relation between administered dose and effective target dose is illustrated by examples, and the recently proposed Benchmark Dose concept for risk assessment is presented with its consequences for mechanistic modeling and statistical estimation.

Age Factors↗
PubMed2004

Characterization of Lewis lung clonal variants in a model of syngeneic pulmonary murine metastases.

Lung cancer is the leading cause of cancer-related mortality world-wide. Since the majority of cancer deaths result from metastatic complications, understanding cellular alterations contributing to organ specific metastases is a continuing cancer research goal. Desirable models involve easy, efficient methodologies for development of pulmonary metastases utilizing genetically related syngeneic tumor cell lines varying in clonogenic frequency and growth rate for comparative studies. This work focused on development and characterization of primary and metastatic Lewis lung subclones (LLCC3, LLC1, LLCab) in a histocompatible C57B1/6 model. Surgical resection of primary tumors utilizing these cell lines resulted in reliable development of pulmonary metastases (> 90% of injected mice), while tail-vein injection proved sporadic (20% of injected mice). The preliminary analysis of selected cell-surface molecules indicates potential genetic differences that may underlie phenotypic variations. The combination of subcutaneous resection methodology and variant cell lines results in robust metastatic lung cancer for testing potential therapeutic interventions.

Animals↗
PubMed1996

An exact representation for the generating function for the Moolgavkar-Venzon-Knudson two-stage model of carcinogenesis with stochastic stem cell growth.

The two-stage clonal expansion model of carcinogenesis provides a convenient biologically based framework for the quantitative description of carcinogenesis data. Under this stochastic model, a cancer cell arises following the occurrence of two critical mutations in a normal stem cell. Both normal cells and initiated cells that have sustained the first mutation undergo birth-and-death processes responsible for tissue growth. In this article, a new expression for the probability generating function (pgf) for the two-stage model of carcinogenesis is derived. This characterization is obtained by solving a partial differential equation (pde) satisfied by the pgf derived from the corresponding Kolmogorov forward equation. This pde can be reduced to the hypergeometric differential equation of Gauss, which leads to a closed-form expression for the pgf requiring only the evaluation of hypergeometric functions. This result facilitates computation of the exact hazard function for the two-stage model. Several approximations that are simpler to compute are also given. Numerical examples are provided to illustrate the accuracy of these approximations.

Animals↗
PubMed1987

Evidence for a universal process underlying clonal attenuation.

It is shown by computer simulation that an established commitment model of clonal attenuation can account for clone size distribution data obtained from three vertebrate species--chick, hamster and human--from two evolutionarily divergent classes. The different in vitro replicative lifespans of each cell strain can be explained by differences in cell kinetics. These results suggest that the process of clonal attenuation is qualitatively similar in fibroblasts from all vertebrate species.

Animals↗
PubMed1994

Simulating the process of malignant transformation.

A computationally efficient method for the simulation of carcinogenesis is presented. The underlying model for the process is the two-mutation clonal expansion model with explicit consideration of stochastic growth of malignant tumors. The usual likelihood-based methods of analysis ignore the growth kinetics of malignant tumors. The effect of this oversight on estimation of parameters is explored by simulation.

Animals↗
PubMed1986

Are there differences in the cell cycle of normal and malignant cells? An approach to the analysis of the clonal expansion of cells in malignant epithelial proliferations in situ.

The Williams-Bjerknes model for clonal expansion of transformed cells in epithelia was used to examine a series of related questions about the growth of in situ proliferations in epidermis. Bowens disease, actinic keratosis and lentigo maligna lesions were reconstructed on a three-dimensional basis, and all were found to behave differently: the evidence supported the proposal that the 'carcinogenic advantage' enjoyed by transformed cells was proliferative in nature, and indeed varied between the three lesions. We conclude that the clonal expansion of a single cell, with different proliferative carcinogenic advantage, can explain the three-dimensional appearances of these in situ proliferations; furthermore, the well-known 'multifocality' of in situ epidermal proliferations can also be explained by the clonal expansion of a single transformed cell.

Animals↗
PubMed1988

Examination of the role of cigarette smoke in lung carcinogenesis using multistage models.

The widely used multistage model of Armitage and Doll is fit to the British physician lung cancer data of Doll and Hill under the assumption that cigarette smoke induces the initial and penultimate changes. It is shown that the best fit of this model in continuing smokers gives predictions not in accordance with incidence in ex-smokers and dose-response. A better global fit can be obtained by increasing the number of stages, but this de-emphasizes initiation and is inconsistent with the rise of incidence in nonsmokers. Thus, one should look to other models. A two-stage model with clonal growth in which smoking initiates normal target cells and promotes the clonal growth of just the smoke-initiated cells is proposed. This model is shown to agree with the Doll and Hill data and thus it has empirical plausibility that should encourage biological studies of clonal growth in carcinogenesis.

Adult↗
PubMed1991

Two-stage and Weibull models for carcinogenesis applied to the ED01 discontinued dosing data.

The two-stage clonal expansion model for a single, less-than-lifetime period of dosing is formulated and applied to the liver and bladder tumor data from the ED01 study. The model successfully predicts liver tumor incidence for time points beyond termination of dosing with 2-acetylaminofluorene, but it is unsuccessful for bladder tumor incidence. A discontinued dosing version of the Weibull model is proposed and is shown to predict successfully both liver and bladder tumor incidences for time points after termination of dosing.

2-Acetylaminofluorene↗
PubMed1999

Two stage model for carcinogenesis: number and size distributions of premalignant clones in longitudinal studies.

The two stage clonal expansion model of carcinogenesis provides a convenient biologically based framework for the description of toxicologic and epidemiologic data on carcinogenesis. Under this model, a cancer cell is generated following the occurrence of two critical mutations in a single stem cell. Initiated cells that have sustained the first mutation undergo a stochastic birth-death process resulting in clonal expansion of the initiated cell population. In this article, we consider the analysis of longitudinal data on the number and size of premalignant clones, formed by clonal expansion of initiated cells. In particular, the joint distribution of the number of premalignant clones observed at different points in time in the same subject is derived. The application of these results in the statistical analysis of longitudinal data on the number and size of premalignant clones observed in initiation-promotion experiments is indicated.

Animals↗
PubMed2001

Alterations in transcription factor binding at the IL-2 promoter region in anergized human CD4+ T lymphocytes.

BACKGROUND: The mechanisms responsible for the induction of clonal anergy are not well understood. We have utilized an in vitro model of human T cell anergy to explore the perturbations in cell signaling at the level of interleukin (IL)-2 gene transcription and to define the contribution of other cytokines to this effect. METHODS: An in vitro model of clonal anergy was established by using CD4+ T lymphocytes from healthy human donors. Cells were anergized by prestimulation with an anti-CD3 monoclonal antibody (mAb) followed by restimulation 72 hr later with anti-CD3 mAb with or without anti-CD28. RESULTS: CD4+ T cells, anergized with anti-CD3 monoclonal antibody (OKT3) prestimulation, displayed a marked reduction in proliferation (P=0.0036) and IL-2 production (P<0.0001). Co-incubation with IL-10 reduced cellular proliferation in OKT3/CD28 pretreated cells by 19% (P=NS) and reduced IL-2 production by 40% (P=0.0024). Anergized T cells demonstrated a reduced binding activity of the AP-1 complex to the IL-2 promoter. Supershift experiments and Western blots confirmed that the binding of c-Fos, JunB, and JunD, but not of FosB, was reduced in anergized cells. At the sis-inducible element (SIE)-binding region of the c-Fos promoter, Stat3 binding was reduced. CONCLUSIONS: T cell anergy, induced by prestimulation with OKT3, is characterized by reduced proliferation and a profound decrease in IL-2 production. Anergy can be prevented by co-incubation with anti-CD28 and partially re-established by IL-10. Anergy is accompanied by a reduction in AP-1 binding to the IL-2 promoter, with selective reduction in binding of c-Fos, JunB, and JunD. Defective binding for Stat3 at the c-Fos promoter suggests an involvement of the Jak-Stat pathway.

CD4-Positive T-Lymphocytes↗
PubMed2006

Mutation parameters from DNA sequence data using graph theoretic measures on lineage trees.

MOTIVATION: B cells responding to antigenic stimulation can fine-tune their binding properties through a process of affinity maturation composed of somatic hypermutation, affinity-selection and clonal expansion. The mutation rate of the B cell receptor DNA sequence, and the effect of these mutations on affinity and specificity, are of critical importance for understanding immune and autoimmune processes. Unbiased estimates of these properties are currently lacking due to the short time-scales involved and the small numbers of sequences available. RESULTS: We have developed a bioinformatic method based on a maximum likelihood analysis of phylogenetic lineage trees to estimate the parameters of a B cell clonal expansion model, which includes somatic hypermutation with the possibility of lethal mutations. Lineage trees are created from clonally related B cell receptor DNA sequences. Important links between tree shapes and underlying model parameters are identified using mutual information. Parameters are estimated using a likelihood function based on the joint distribution of several tree shapes, without requiring a priori knowledge of the number of generations in the clone (which is not available for rapidly dividing populations in vivo). A systematic validation on synthetic trees produced by a mutating birth-death process simulation shows that our estimates are precise and robust to several underlying assumptions. These methods are applied to experimental data from autoimmune mice to demonstrate the existence of hypermutating B cells in an unexpected location in the spleen.

Algorithms↗