TY - JOUR
AU - Satoru Fujii
AU - Scott T. Espenschied
AU - Vibha Anand
AU - Joao Bettencourt-Silva
AU - Yi Han
AU - Go Ito
AU - Akira Koseki
AU - Akihiro Kosugi
AU - James Kozloski
AU - Ryoma Matsumoto
AU - Shanshan Meng
AU - Natasha Mulligan
AU - Ryan J. Musich
AU - Kevin P. Newhall
AU - Eri Oshina
AU - Shuhei Sekiguchi
AU - Yi Wang
AU - Jianying Hu
AU - Matthew Ciorba
AU - L. David Sibley
AU - Ryuichi Okamoto
AU - Thaddeus S. Stappenbeck
AB - Primary cell culture is fast becoming a dominant method for discovery work regarding human disease. Currently, there are no methods to quantitatively benchmark these systems. Here, we apply a uniform in vitro culture system of human intestinal epithelial cells (IECs) to achieve this goal. We previously established methods for long-term two-dimensional (2D) cultivation of mouse IECs using an air–liquid interface (ALI) technique. Here, we further refined these methods for long-term 2D cultivation of human IECs, with histological and molecular features of differentiated intestinal epithelia. Leveraging the power and scalability of a biomedical foundation model (BMFM) trained on single-cell RNA sequencing data (BMFM-RNA), we performed classification tasks to identify cell types across sample sources and to quantitatively benchmark our in vitro differentiated cells against cells collected from patient biopsies. We observed a striking concordance between our in vitro differentiated cells and the corresponding cell types in vivo for multiple differentiated secretory cell types. This approach using BMFM-RNA holds promise to expand our understanding of the regulatory mechanisms, including gene–gene regulation underlying homeostasis and regeneration, as well as the functions of rare and poorly understood lineages within the human intestinal epithelia. Moreover, these methods may be applicable to other organs, model systems, and experimental modalities. We propose that the framework used here can be deployed as a standard benchmarking methodology, ultimately improving the fidelity of primary human culture systems.
BT - Proceedings of the National Academy of Sciences
DA - 2026-03-24
DO - 10.1073/pnas.2520482123
IS - 12
N2 - Primary cell culture is fast becoming a dominant method for discovery work regarding human disease. Currently, there are no methods to quantitatively benchmark these systems. Here, we apply a uniform in vitro culture system of human intestinal epithelial cells (IECs) to achieve this goal. We previously established methods for long-term two-dimensional (2D) cultivation of mouse IECs using an air–liquid interface (ALI) technique. Here, we further refined these methods for long-term 2D cultivation of human IECs, with histological and molecular features of differentiated intestinal epithelia. Leveraging the power and scalability of a biomedical foundation model (BMFM) trained on single-cell RNA sequencing data (BMFM-RNA), we performed classification tasks to identify cell types across sample sources and to quantitatively benchmark our in vitro differentiated cells against cells collected from patient biopsies. We observed a striking concordance between our in vitro differentiated cells and the corresponding cell types in vivo for multiple differentiated secretory cell types. This approach using BMFM-RNA holds promise to expand our understanding of the regulatory mechanisms, including gene–gene regulation underlying homeostasis and regeneration, as well as the functions of rare and poorly understood lineages within the human intestinal epithelia. Moreover, these methods may be applicable to other organs, model systems, and experimental modalities. We propose that the framework used here can be deployed as a standard benchmarking methodology, ultimately improving the fidelity of primary human culture systems.
PY - 2026
EP - e2520482123
T2 - Proceedings of the National Academy of Sciences
TI - Quantifying the fidelity of in vitro human cell culture systems using a biomedical foundation model
UR - https://www.pnas.org/doi/10.1073/pnas.2520482123
VL - 123
Y2 - 2026-03-30
ER -