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Title: Global gene expression kinetics of early human lung development modeled by directed differentiation of human PSCs using an NKX2-1GFP iPSC reporter      
ID:
PRJNA325535
description:
It has been postulated that during human fetal development all cells of the lung epithelium derive from an embryonic endodermal NKX2-1+ precursor, however, this hypothesis has not been formally tested due to an inability to purify or track this theorized cell for detailed characterization. Here we engineer and developmentally differentiate NKX2-1GFP reporter pluripotent stem cells (PSCs) in vitro to generate and isolate a human primordial lung progenitor that expresses NKX2-1 but is initially devoid of markers of differentiated lung lineages. As these progenitors move through the earliest moments of lung lineage specification from definitive endoderm they can be imaged in real time or isolated for time-series global transcriptomic profiling. We performed microarray analysis of 5 timepoints of human iPSC to lung directed differentiation compared to week 21 human fetal lung and Neural NKX2-1+ cell controls. These profiles indicate that evolutionarily conserved, stage-dependent developmental gene signatures are expressed in primordial human lung progenitors. Using a TALEN-targeted fluorescent reporter to purify iPSC-derived lung progenitors (C17 NKX2-1GFP) we analyzed cells at major developmental time points in vitro (undifferentiated iPSC, definitive endoderm, anterior foregut endoderm and sorted NKX2-1GFP+ and NKX2-1GFP- cells on day 15 and day 28 of the protocol). We also differentiated NXK2-1GFP iPSC in a neural protocol and isolated neural NKX2-1GFP+ cells. Approximately 90% pure human fetal lung epithelial cells from week 21 embryos were used as controls. Overall design: We prepared time series microarray expression profiles representing the following 5 key stages of iPSC lung-directed differentiation: undifferentiated iPSC (day 0), sorted CXCR4+ definitive endoderm (day 3), anterior foregut-like endoderm (day 6), sorted NKX2-1GFP+ and NKX2-1GFP- primordial progenitors (day 15), sorted NKX2-1GFP+ and NKX2-1GFP- differentiated cells (day 28). For positive and negative controls we included primary distal fetal lung epithelial cells (21 weeks of human gestation) and forebrain-like iPSC-derived neural NKX2-1GFP+ cells. Biological triplicates of all samples except human fetal lung were prepared. Biological triplicates were used for each sample except human fetal lung control samples where biological duplicates from one embryo (“uncultured naïve lung epithelium”) and a singlicate from a different embryo (“differentiated AT2 cells”) were prepared. Fetal lung samples were prepared using previously described protocols that result in approximately 90% epithelial cells. Global gene expression in all 27 samples was analyzed by Affymetrix GeneChip Human Gene 2.0 ST arrays
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landingpage: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA325535
authentication:
none
authorization:
none
ID:
pmid:28463226
name:
Homo sapiens
ncbiID:
ncbitax:9606
abbreviation:
NCBI
homePage: http://www.ncbi.nlm.nih.gov
ID:
SCR:006472
name:
National Center for Biotechnology Information
homePage: http://www.ncbi.nlm.nih.gov/bioproject
ID:
SCR:004801
name:
NCBI BioProject