Culture impact on the transcriptomic programs of primary and iPSC-derived human alveolar type 2 cells

Darrell N. Kotton1, Carla F. Kim2, Barry R. Stripp3
1Boston University, 2Harvard Medical School, 3Cedars-Sinai Medical Center, *Corresponding author
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Description Dysfunction of alveolar epithelial type 2 cells (AEC2s), the facultative progenitors of lung alveoli, is implicated in pulmonary disease pathogenesis, highlighting the importance of human in vitro models. However, AEC2-like cells in culture have yet to be directly compared to their in vivo counterparts at single-cell resolution. Here, we performed head-to-head comparisons among the transcriptomes of primary (1°) adult human AEC2s, their cultured progeny, and human induced pluripotent stem cell–derived AEC2s (iAEC2s). We found each population occupied a distinct transcriptomic space with cultured AEC2s (1° and iAEC2s) exhibiting similarities to and differences from freshly purified 1° cells. Across each cell type, we found an inverse relationship between proliferative and maturation states, with preculture 1° AEC2s being most quiescent/mature and iAEC2s being most proliferative/least mature. Cultures of either type of human AEC2s did not generate detectable alveolar type 1 cells in these defined conditions; however, a subset of iAEC2s cocultured with fibroblasts acquired a transitional cell state described in mice and humans to arise during fibrosis or following injury. Hence, we provide direct comparisons of the transcriptomic programs of 1° and engineered AEC2s, 2 in vitro models that can be harnessed to study human lung health and disease.
Dataset ID LMEX0000004399
Assay Type Single-cell RNA-seq
Organism Human
Stages Adult
Cell Count 8128
Technology 10x Genomics Chromium Single Cell Gene Expression
Reference Alysandratos, et al. (2023)
External databases GEO: GSE193716
FileDescriptionSize
GSE193716.h5adHDF5 annotated format single-cell data matrix645.7 MB
LungMAP IDAlt IDSpeciesAge Group
LMSP0000001387Primary culturedHomo sapiensAdult
LMSP0000001388Primary freshHomo sapiensAdult
LMSP0000001384iAEC2 3DHomo sapiensAdult
LMSP0000001385iAEC2 3D transwellHomo sapiensAdult
LMSP0000001386iAEC2 3D transwell MRC5Homo sapiensAdult