biostudies-literatureUnknown12(1)Mostofinejad ACanada First Research Excellence FundNatural Sciences and Engineering Research CouncilCanada Research Coordinating CommitteeCanadian Institutes of Health ResearchDirected 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.NPJ systems biology and applications29https://www.ebi.ac.uk/biostudies/studies/S-EPMC12920931biostudies-literatureIn silico modeling of anterior foregut endoderm differentiation towards lung epithelial progenitors.PMC12920931Romero DABrinson DWaddell TKAmon CHMostofinejad AKaroubi GfalseIn silico modeling of anterior foregut endoderm differentiation towards lung epithelial progenitors.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.2026-01-01T00:00:00Z2026 Jan2026-07-09T11:44:34.535Z2026-07-09T10:55:52.076ZS-EPMC129209314158800510.1038/s41540-026-00650-1