bioRxiv Science⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2021.09.14.460349

Predicting Individual Cell Division Events from Single-Cell ERK and Akt Dynamics

Stern, A. D.·Smith, G. R.·Santos, L. C.·Sarmah, D.·Zhang, X.·Lu, X.·Iuricich, F.·Pandey, G.·Iyengar, R.·Birtwistle, M. R.
View original source ↗Export metadata ↓

Abstract

Predictive determinants of stochastic single-cell fates have been elusive, even for the well-studied mammalian cell cycle. What drives proliferation decisions of single cells at any given time? We monitored single-cell dynamics of the ERK and Akt pathways, critical cell cycle progression hubs and anti-cancer drug targets, and paired them to division events in the same single cells using the non-transformed MCF10A epithelial line. Following growth factor treatment, in cells that divide both ERK and Akt activities are significantly higher within the S-G2 time window ([~]8.5-40 hours). Such differences were much smaller in the pre-S-phase, restriction point window which is traditionally associated with ERK and Akt activity dependence, suggesting unappreciated roles for ERK and Akt in S through G2. Machine learning algorithms show that simple metrics of central tendency in this time window are most predictive for subsequent cell division; median ERK and Akt activities classify individual division events with an AUC=0.76. Surprisingly, ERK dynamics alone predict division in individual cells with an AUC=0.74, suggesting Akt activity dynamics contribute little to the decision driving cell division in this context. We also find that ERK and Akt activities are less correlated with each other in cells that divide. Network reconstruction experiments demonstrated that this correlation behavior was likely not due to crosstalk, as ERK and Akt do not interact in this context, in contrast to other transformed cell types. Overall, our findings support roles for ERK and Akt activity throughout the cell cycle as opposed to just before the restriction point, and suggest ERK activity dynamics are substantially more important than Akt activity dynamics for driving cell division in this non-transformed context. Single cell imaging along with machine learning algorithms provide a better basis to understand cell cycle progression on the single cell level.

Explore related subjects

systems biologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Stern, A. D., Smith, G. R., Santos, L. C., Sarmah, D., Zhang, X., Lu, X., Iuricich, F., Pandey, G., Iyengar, R., Birtwistle, M. R.. 2021-09-14. Predicting Individual Cell Division Events from Single-Cell ERK and Akt Dynamics. https://doi.org/10.1101/2021.09.14.460349

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

KEEP EXPLORING

Related preprints

bioRxiv2026

Low-fidelity simulator selection for multi-fidelity inference of epithelial vertex models

Vertex models link cell division, neighbour exchange, and intercellular forces to epithelial tissue form through parameters such as junctional line tension and perimeter contractility. Bayesian inference of these parameters from data quantifies their uncertainty, but for stochastic models of proliferating tissues it requires many costly simulations. Multi-fidelity simulation-based inference reduces this cost by training on many runs of a cheaper, less accurate ('low-fidelity') simulator before refining with a few full ('high-fidelity') runs. Low-fidelity versions can be constructed in several ways, for example by stopping simulations early, coarsening the timestep, or averaging fewer replicates, but it is unclear which to choose before committing to costly training. To address this, we introduce PRISM (Paired Ranking Index for Simulator Matching), a screen that compares each candidate with the full simulator on paired runs, scoring agreement in cell-packing statistics against cost. For a vertex model of a proliferating tissue, PRISM flags stopping early as unreliable before training; once trained, this choice can produce confidently wrong parameter estimates. By contrast, a coarser timestep, within the range tested, is cheap and accurate; while fewer replicates are accurate but too costly. Using a screened low-fidelity simulator, multi-fidelity inference outperforms approximate Bayesian computation and neural-network inference trained on full simulations alone, at matched cost and with well-calibrated uncertainty. The same pattern recurs for a second vertex model fitted to published Drosophila pupal-wing imaging data, although there stopping halfway proves safe. Together, our findings suggest that which approximations are safe depends on the model, and that screening them before training makes multi-fidelity inference of tissue mechanics practical.

systems biology↗
bioRxiv2026

Calibrating developmental dynamics from single-cell atlases: lineage paths outrun least-action routes

Single-cell atlases infer developmental dynamics from destructive snapshots, yet how far realized lineage paths depart from such inferred dynamics has never been measured with controls. We introduce LADD (Least-Action Developmental Dynamics), a measurement framework that learns a stochastic developmental vector field from time-series single-cell RNA-seq and computes minimum-action and minimum-time paths, together with a three-layer calibration protocol that separates genuine path deviation from the generic cost of centroid measurement, and we compare its forecasting component with optimal-transport and flow-matching methods. In the lineage-resolved Caenorhabditis elegans atlas, the raw action ratio of observed lineage-centroid trajectories to optimal paths is 3.79, yet forward-simulated ensembles of the learned model itself score 2.07, leaving a genuine excess of about two-fold. In zebrafish (Danio rerio), the observed ratio sits entirely at the model's floor. Three mechanisms that could explain the residual deviation (detours, flow-opposition, and fate-map complexity) are each excluded; what remains is speed, with lineages moving 30-43% faster along the learned flow. We report validity boundaries for temporal resolution, cross-species comparison, and energetic interpretation, delimiting where action-based trajectory comparisons are meaningful.

systems biology↗
bioRxiv2026

Choice of annotation data significantly impacts automated reconstruction of genome-scale metabolic networks

Genome-scale metabolic models are valuable tools for studying metabolism in many applications, such as metabolic engineering or understanding human disease. However, curated models are available for only a limited number of organisms, and generating high-quality models for additional organisms remains a challenge. To help address this challenge, several software tools have been developed that can produce draft models in an automated fashion, but the quality of these draft models lags behind manually curated ones. Thus, there is still a need to improve these tools. Previous work has focused primarily on developing better methods for each step in the reconstruction process, such as gene annotation and gap-filling. Here, we focus on the data that underlies these methods, such as known connections between protein sequence and function. We find that changing the source of reconstruction data has a substantial impact on the contents and predictions of generated models. In fact, the source of data can have a bigger impact than the choice of reconstruction method. Additionally, we show that the reconstruction process is sensitive to the accuracy of gene annotations in the reconstruction data. Finally, we demonstrate the importance of having functional annotation data from an organism that is closely related to the one for which a model is being built. These observations highlight the importance of reconstruction data and identify principles that should be considered when selecting data for reconstruction tools.

systems biology↗