Abstract
Synchronicity is observed in many biological systems, including development, as seen in vertebrate body axis formation, fly eye development, and development of the social amoeba D. discoideum. Despite its prevalence, quantitative analyses of synchronicity at the single-cell level remain rare. Here we show that synchronicity in D. discoideum is mediated by early cAMP signaling. Using single-cell RNA sequencing (scRNA-seq), we quantify transcriptome similarities between individual cells during development. We show that synchronicity first declines upon starvation but then increases with the onset of cAMP-pulse signaling. Synchronicity remains stable throughout development and differs between prespore and prestalk cells. Genetic perturbations of cAMP production and response reveal that cAMP signaling is essential for establishing and maintaining synchronicity, as its absence leads to highly asynchronous development. These findings highlight the role of cAMP signaling in coordinating transcriptomic and morphological synchronicity, and establish scRNA-seq as a tool for quantitative analysis of developmental synchronicity.
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Data availability
Raw sequencing reads and processed data have been deposited in the NCBI Gene Expression Omnibus (GEO) under accession number GSE305468. It is available from Zenodo with the DOI 10.5281/zenodo.1848190764. The numerical source data underlying the graphs are available in Supplementary Data 1 (Fig. 2); Supplementary Data 2 (Supplementary Fig. 1); and Supplementary Data 3 (Supplementary Fig. 2a and Fig. 2). All other data and materials are available from the corresponding author on reasonable request.
Code availability
Custom code and reproducible workflows are available at https://github.com/lenatr99/scRNA_dicty, including pipelines for 10x preprocessing, UCE embeddings, UMAP/Leiden clustering, fluorescent-tag assignment, prespore/prestalk classification, synchronicity scoring with bootstrap confidence intervals, and figure generation. The repository includes step-by-step instructions and environment files to enable full reproducibility. It is available from Zenodo with the DOI 10.5281/zenodo.1848180865.
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Acknowledgements
This research was supported by the National Science Foundation (grant number 2319686) through the Integrative Organismal Systems program, as well as by the Slovenian Research and Innovation Agency (grants numbers L2-60154 and P2-0209).
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G.S. conceived the study. G.S., R.C., and M.K.-K. designed the experiments. M.K.-K. performed most of the experiments and data collection, with additional data collected by P.L. and sample processing assistance from Y.L. L.T. led the data analysis and software development, with contributions from M.K.-K. and close guidance from B.Z. G.S. wrote the manuscript. All authors revised and edited the manuscript. G.S., R.C. and B.Z. supervised the project. M.K.-K. and L.T. contributed equally to this work. G.S. and B.Z. jointly oversaw key aspects of the research.
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Katoh-Kurasawa, M., Trnovec, L., Lehmann, P. et al. Early cAMP signaling orchestrates single-cell synchronicity throughout Dictyostelium development. Commun Biol (2026). https://doi.org/10.1038/s42003-026-09806-5
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DOI: https://doi.org/10.1038/s42003-026-09806-5
