Abstract
Directed differentiation of human induced pluripotent stem cells (iPSCs) into anterior foregut endoderm (AFE) and lung progenitors (LPs) has wide-ranging implications for lung developmental biology, disease modeling, and regenerative medicine. We expand on a previously developed mathematical modeling framework and apply it to the directed differentiation of AFE into LPs. A model-based approach guides experimental design, followed by a multistage model inference process: maximum likelihood estimation based on in vitro data and identifiability analyses to eliminate unidentifiable candidates, thereby guiding model selection. To the authors’ knowledge, this is the first mathematical model of the population dynamics of directed differentiation of AFE into LPs. The model suggests that the overall dynamics are primarily driven by AFE proliferation and differentiation into LPs. In silico experiments predict that daily media change nearly doubles LP yields compared to cultures without media replenishment. Moreover, the model suggests that higher split ratios on day 10 enhance yield per input cell, a measure of differentiation efficiency, by 26%. This work provides a blueprint for refining iPSC-based lung lineage differentiation protocols by combining empirical data and mathematical modeling.
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All data and code used to generate the results in this manuscript are available through https://github.com/amostof/inSilicoAFEPaper.
Code availability
All data and code used to generate the results in this manuscript are available through https://github.com/amostof/inSilicoAFEPaper.
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Acknowledgements
This study is funded in part by a Collaborative Health Research Project (CHRP) grant provided by the Canadian Institutes of Health Research in partnership with the Natural Sciences and Engineering Research Council (158270 to C.H.A. and T.W.). The study is also supported by the New Frontiers in Research Fund Transformation stream (NFRFT-2020-00787 to T.W., C.H.A., G.K., and NFRFT-2022-00447 to C.H.A.), and the University of Toronto’s Medicine by Design initiative, which receives funding from the Canada First Research Excellence Fund (to C.A. and T.W.).
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C.A., D.R., T.W., and G.K. designed and supervised the research. A.M. and D.B. performed research and analyzed data. A.M., D.R., and D.B. took the lead in writing the manuscript. All authors provided critical feedback and helped shape the research and the final manuscript.
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Mostofinejad, A., Romero, D.A., Brinson, D. et al. In silico modeling of anterior foregut endoderm differentiation towards lung epithelial progenitors. npj Syst Biol Appl (2026). https://doi.org/10.1038/s41540-026-00650-1
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DOI: https://doi.org/10.1038/s41540-026-00650-1
