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Brock, A.

Publications and source records attributed to Brock, A..

22 records · Page 2Linked to original sources

Stochastic Models for Revealing the Dynamics of the Growth of Small Tumor Populations

The widely accepted model of tumor growth assumes tumors grow exponentially at a constant rate during early tumorigenesis when populations are small. The possibility that tumors might exhibit altered slower growth dynamics or even net cell death below a critical tumor size has yet to be fully explored. Deterministic growth models are capable of describing larger populations because population variation becomes small compared with the average, but when the population being modeled is small, the inherent stochasticity of the birth and death process produces significant variation. Recent advances in high throughput data collection allow for precise and sufficiently large data sets needed to capture this variation. Therefore, we present a stochastic modeling framework to describe and test the potential for altered growth dynamics at small tumor populations.

cancer biology↗

Cancer cell population growth kinetics at low densities deviate from the exponential growth model and suggest an Allee effect

Models of cancer cell population expansion assume exponential growth kinetics at low cell densities, with deviations from exponential growth only at higher densities due to limited resources such as space and nutrients. However, recent pre-clinical and clinical observations of tumor initiation or recurrence indicate the presence of tumor growth kinetics in which growth rates scale with cell numbers. These observations are analogous to the cooperative behavior of species in an ecosystem described by the ecological principle of the Allee effect. In preclinical and clinical models however, tumor growth data is limited by the lower limit of detection (i.e. a measurable lesion) and confounding variables, such as tumor microenvironment and immune responses may cause and mask deviations from exponential growth models. In this work, we present alternative growth models to investigate the presence of an Allee effect in cancer cells seeded at low cell densities in a controlled in vitro setting. We propose a stochastic modeling framework to consider the small number of cells in this low-density regime and use the moment approach for stochastic parameter estimation to calibrate the stochastic growth trajectories. We validate the framework on simulated data and apply this approach to longitudinal cell proliferation data of BT-474 luminal B breast cancer cells. We find that cell population growth kinetics are best described by a model structure that considers the Allee effect, in that the birth rate of tumor cells depends on cell number. This indicates a potentially critical role of cooperative behavior among tumor cells at low cell densities with relevance to early stage growth patterns of emerging tumors and relapse.\n\nAuthor SummaryThe growth kinetics of cancer cells at very low cell densities are of utmost clinical importance as the ability of a small number of newly transformed or surviving cells to grow exponentially and thus, to \"take off\" underlies tumor formation and relapse after treatment. Mathematical models of stochastic tumor cell growth typically assume a stochastic birth-death process of cells impacted by limited nutrients and space when cells reach high density, resulting in the widely accepted logistic growth model. Here we present an in-depth investigation of alternate growth models adopted from ecology to describe potential deviations from a simple cell autonomous birth-death model at low cell densities. We show that our stochastic modeling framework is robust and can be used to identify the underlying structure of stochastic growth trajectories from both simulated and experimental data taken from a controlled in vitro setting in which we can capture data from the relevant low cell density regime. This work suggests that the assumption of cell autonomous proliferation via a constant exponential growth rate at low cell densities may not be appropriate for all cancer cell growth dynamics. Consideration of cooperative behavior amongst tumor cells in this regime is critical for elucidating strategies for controlling tumor cell growth.

cancer biology↗

A multi-state model of chemoresistance to characterize phenotypic dynamics in breast cancer

The development of resistance to chemotherapy is a major cause of treatment failure in breast cancer. Although several molecular mechanisms of chemotherapeutic resistance are well studied, a quantitative understanding of the dynamics of resistant subpopulations within a heterogeneous tumor cell population remains elusive. While mathematical models describing the dynamics of heterogeneous cancer cell populations have been proposed, few have been experimentally validated due to the complex nature of resistance that limits the ability of a single phenotypic marker to sufficiently isolate drug resistant subpopulations. In this work, we address this problem with a combined experimental and modeling system that uses drug sensitivity data to reveal the composition of multiple subpopulations differing in their level of drug resistance. We calibrate time-resolved dose-response data to three mathematical models to interrogate the models ability to capture the dynamics of drug. All three models demonstrated an increase in population level resistance following drug exposure. The candidate models were compared by Akaike information criterion and the model selection criteria identified a multi-state model incorporating the role of population heterogeneity and cellular plasticity. To validate the ability of this model to identify the composition of subpopulations, we mixed wild-type MCF-7 and MCF-7/ADR resistant cells at various proportions and evaluated the corresponding model output. Our blinded two-state model was able to estimate the proportions of cell subtypes, with the measured proportions falling within the 95 percent confidence intervals on the parameter estimations and at an R-squared value of 0.986. To the best of our knowledge, this contribution represents the first work to combine experimental time-resolved drug sensitivity data with a mathematical model of resistance development.

systems biology↗

Control of lineage-specific gene expression by functionalized gRNA barcodes

Lineage tracking delivers essential quantitative insight into dynamic, probabilistic cellular processes, such as somatic tumor evolution and differentiation. Methods for high diversity lineage quantitation rely on sequencing the population of DNA barcodes. However, molecular analysis of specific individual lineages is not possible with this approach. To address this challenge, we developed a functionalized lineage tracing tool that enables high diversity lineage tracing and lineage-specific manipulation of gene expression. This modular platform utilizes expressed barcode gRNAs to both track cell lineages and direct lineage specific gene expression.

synthetic biology↗