Single-cell RNA sequencing reveals the developmental program underlying proximal–distal patterning of the human lung at the embryonic stage

Abstract

The lung is the primary respiratory organ in human, in which the proximal airway and the distal alveoli are responsible for air conduction and gas exchange, respectively. However, the regulation of proximal–distal patterning at the embryonic stage of human lung development is largely unknown. Here we investigated the early lung development of human embryos at weeks 4–8 post fertilization (Carnegie stages 12–21) using single-cell RNA sequencing, and obtained a transcriptomic atlas of 169,686 cells. We observed discernible gene expression patterns of proximal and distal epithelia at week 4, upon the initiation of lung organogenesis. Moreover, we identified novel transcriptional regulators of the patterning of proximal (e.g., THRB and EGR3) and distal (e.g., ETV1 and SOX6) epithelia. Further dissection revealed various stromal cell populations, including an early-embryonic BDNF+ population, providing a proximal–distal patterning niche with spatial specificity. In addition, we elucidated the cell fate bifurcation and maturation of airway and vascular smooth muscle progenitor cells at the early stage of lung development. Together, our study expands the scope of human lung developmental biology at early embryonic stages. The discovery of intrinsic transcriptional regulators and novel niche providers deepens the understanding of epithelial proximal–distal patterning in human lung development, opening up new avenues for regenerative medicine.

Early human fetal lung atlas reveals the temporal dynamics of epithelial cell plasticity

“…Transcription factors enriched in early AT2-like cells included ETV1 and HNF1B , as previously described 55 as well as SOX9 and FOXP2. While ETV5 was previously shown to regulate human distal lung identity 11 and mouse adult lung AT2 identity 56 , here we identify the homologous ETV1 as abundantly expressed in human fetal AT2-like cells. Proximity score analysis showed budtip progenitors and AT2-like cells were closely associated, suggesting these cells may also share regionally the same space ( Fig.…”

“…Airway SMC differentially expressed higher levels of TAGLN, ACTA2, MYH11 , while vascular SMC expressed IGFBP7, MEF2C, EGFL6 , both similarly reported in other studies 9 . Transcription factors differentially expressed in airway and vascular SMC included the zinc finger E-box binding homeobox 1 ( ZEB1), a core EMT transcription factor 11 , and the ETS variant transcription factor ( ETV1) , which regulates cell growth, proliferation and differentiation, respectively. Chondrocytes differentially expressed many of the collagen genes including COL2A1, COL11A1, COL9A 1 and the transcription factor CAMP Responsive Element Binding Protein 3 Like 2 ( CREB3L2 known regulate chondrocyte development.…”

“…Recent sequencing datasets from a small collection of normal human fetal lungs obtained from early to mid-gestation fetuses, have highlighted some novel cell types and cell lineage trajectories 9,11 that are unique to human fetal development. Unfortunately, following up on these observations and their potential impact in post-natal lung function is hindered by lack of experimentally tractable models.…”

Early human fetal lung atlas reveals the temporal dynamics of epithelial cell plasticity

“…Airway SMC differentially expressed higher levels of TAGLN, ACTA2, MYH11, while vascular SMC expressed IGFBP7, MEF2C, EGFL6, both similarly reported in other studies 9 . Transcription factors differentially expressed in airway and vascular SMC included the zinc finger E-box binding homeobox 1 (ZEB1), a core EMT transcription factor 11 , and the ETS variant transcription factor (ETV1), which regulates cell growth, proliferation and differentiation, respectively. Chondrocytes differentially expressed many of the collagen genes including COL2A1, COL11A1, COL9A1 and the transcription factor CAMP Responsive Element Binding Protein 3 Like 2 (CREB3L2 known regulate chondrocyte development.…”

“…Understanding the molecular and cellular networks that drive the formation of the respiratory system during fetal development may provide important insight into the regenerative processes during repair and potentially identify developmental origins of postnatal lung disease/disorders. Recent sequencing datasets from a small collection of normal human fetal lungs obtained from early to mid-gestation fetuses, have highlighted some novel cell types and cell lineage trajectories 9,11 that are unique to human fetal development. Unfortunately, following up on these observations and their potential impact in post-natal lung function is hindered by lack of experimentally tractable models.…”