Search bioRxiv⌕ Search

bioRxiv · 10.1101/2021.10.13.464184

Impact of Variability in Cell Cycle Periodicity on Cell Population Dynamics

Abstract

The cell cycle consists of a series of orchestrated events controlled by molecular sensing and feedback networks that ultimately drive the duplication of total DNA and the subsequent division of a single parent cell into two daughter cells. The ability to block the cell cycle and synchronize cells within the same phase has helped understand factors that control cell cycle and the properties of each individual phase. Intriguingly, when cells are released from a synchronized state, they do not maintain synchronized cell division and rapidly become asynchronous. The rate and factors that control cellular desynchronization remain largely unknown. In this study, using a combination of experiments and simulations, we investigate the desynchronization properties in cervical cancer cells (HeLa) starting from the G1/S boundary following double-thymidine block. Propidium iodide (PI) DNA staining was used to perform flow cytometry cell cycle analysis at regular intervals of 8 hours, and a custom auto-similarity function to assess the desynchronization and quantify the convergence to asynchronous state. In parallel, we developed a single-cell phenomenological model the returns the DNA concentration across the cell cycle stages and fitted the parameters using experimental data. Simulations of population of cells reveal that the cell cycle desynchronization rate is primarily sensitive to the variability of cell cycle duration within a population. To validate the model prediction, we introduced lipopolysaccharide (LPS) to increase cell cycle noise. Indeed, we observed an increase in cell cycle variability under LPS stimulation in HeLa cells, accompanied with an enhanced rate of cell cycle desynchronization. Our results show that the desynchronization rate of artificially synchronized in-phase cell populations can be used a proxy of the degree of variance in cell cycle periodicity, an underexplored axis in cell cycle research.

Source connections

Explore related subjects

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Nowak, C. M., Quarton, T., Bleris, L.. 2021-10-14. Impact of Variability in Cell Cycle Periodicity on Cell Population Dynamics. https://doi.org/10.1101/2021.10.13.464184

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

Large language models complement established workflows for mechanistic model construction and refinement in systems biology

Mechanistic models provide a framework for describing, understanding, and predicting biological processes, but their development requires an interdisciplinary team with expertise in biology, mathematics, and computation. Here we present Octomod, a multi-agent workflow based on large language models (LLMs) that integrates biological knowledge retrieval, model construction, parameter estimation, and hypothesis testing. Built on established software tools, including AMICI and pyPESTO, and community standards, including SBML and PEtab, Octomod supports model development and refinement through natural-language interaction with a user. The agents' proposals must pass defined checks and the user's decision before they are used. Every input, model, check, and decision is recorded, so that model building remains transparent and reproducible. We applied Octomod to four problems. Three used published data and differ in model size and in how much the user guided the run: Octomod constructed a model that matched a published model without user guidance, supported the interactive refinement of a gene-regulatory model, and built models of cell-cell communication that explained the responses of five immune cell types to different stimuli. In the fourth application, on newly generated and unpublished lipidomics data, Octomod helped to determine which processes the measurements could inform, identify unresolved label fluxes, and reduce a supplied model to those processes. Together, these results show how LLMs can strengthen and complement established workflows for constructing and refining biologically informed models.

systems biology↗

A Mathematical Model Connecting Appetite-Driven Food Intake to Metabolic Changes across Diet and GLP-1RA Treatments in Mice

Mouse models are widely used to study obesity and the effects of glucagon-like peptide-1 receptor agonists (GLP-1RAs) on appetite-driven meal responses and eating behaviours. However, connecting these behavioural changes to disease prevention remains limited. One reason is that eating behaviour is often summarised as daily or weekly energy intake, obscuring meal-level dynamics. Here we present a mathematical model of mouse appetite-driven food intake across diets and treatment with the GLP-1RAs semaglutide and exenatide. The model jointly described three studies and passed both qualitative assessments and a statistical {chi}2 test (disagreement<threshold, 348<1111). Predictive performance was subsequently validated using four pre-existing studies and one new study. Finally, the model was used to simulate mouse populations under dietary and GLP-1RA interventions, with predictions showing qualitative agreement with the literature. This work aids preclinical drug discovery, supports mouse study design, and improves understanding of how individual meals accumulate into long-term physiological changes.

systems biology↗

Generalized inference of noise-corrected state variability in single cells

Single-cell omics methods operate at their detection limit and are less conducive to technical controls than mini-bulk approaches, which combine cells of the same type before profiling. To integrate mini-bulk samples with paired split-pool controls more holistically, we built stochprofIC, an algorithm that considers data, noise, and covariates in a distributional-regression framework. We vet stochprofIC with synthetic datasets and compare against an adjusted-variance alternative using mini-bulk data in mouse brains and human breast cancers. The noise-batch corrections provided by stochprofIC enable inference of the single-cell populations comprising the mini-bulk, which are validated repeatedly by RNA FISH in different contexts. We use stochprofIC outputs as input to a systems model of nucleocytoplasmic transport and distinguish heterogeneous trafficking states. Pharmacologic inhibition of a MAP3K11-high state inhibits apoptosis in primary breast-cancer organoids, supporting relevance to phenotypes. By deconvolving changes in location and scale, stochprofIC supports mini-bulking when high-sensitivity and reliability profiles are important.

systems biology↗