Public Release:  Stanford team develops single cell genomics technique to reverse engineer developing lung

How do embryos form the cells in our lungs, muscles, nerves and other tissues? A new process decodes the genetic instructions that enable the all-purpose cells of the embryo to multiply and transform into the many specialized cell types in the body

Stanford School of Engineering


IMAGE: Stanford researchers use single cell genomics analysis (left) to reverse engineer the development of alveolar sacs in the lung (right). Alveoli are small balloon-like structures at the tips of the... view more

Credit: Barbara Treutlein


Now, in a feat of reverse tissue engineering, Stanford researchers have begun to unravel the complex genetic coding that allows embryonic cells to proliferate and transform into all of the specialized cells that perform a myriad of different biological tasks.

A team of interdisciplinary researchers took lung cells from the embryos of mice, choosing samples at different points in the creature's development cycle. Using the new technique of single-cell genomic analysis, they recorded what genes were active in each cell at each point. Though they studied lung cells, their technique is applicable to any type of cell.

"This lays out a playbook for how to do reverse tissue engineering," said Stephen Quake, the Lee Otterson Professor in the School of Engineering and leader of the research team.

He detailed the experiments in a Nature paper co-authored with Mark Krasnow, a professor of biochemistry at the Stanford School of Medicine and Tushar Desai, an assistant professor of pulmonary and critical care medicine at Stanford.

They used this reverse engineering approach to study the cells in the alveoli - the small balloon-like structures at the tips of the airways. The alveoli serve as docking stations where blood vessels receive oxygen and deliver carbon dioxide.

Barbara Treutlein, a postdoctoral scholar in Quake's lab, together with Doug Brownfield, a postdoctoral researcher in Krasnow lab, isolated 198 lung cells from mouse embryos at three stages of gestation: 14.5 days, 16.5 days and 18.5 days (mice are on average born at 20 days). They also took some lung cells from adult mice.


Their next steps involved newer techniques at the heart of their reverse engineering process.


Quake's lab has pioneered the use of microfluidic chips to study single cells. In this study, they used microfluidic devices to capture their 198 sample lung cells. Then they used single cell genomic sequencing to measure which genes were active in each cell at each time.


Genes direct cellular activity by making or "expressing" a messenger RNA or mRNA. Each mRNA instructs the cell to make a particular protein. Cells are essentially a group of interacting proteins. Therefore knowing which mRNAs are active offers a lens into the function of that cell at the point when it was captured in the microfluidic device.


One important finding involved the development of two important cells types at the tip of the alveoli, where the lung meets blood to perform the gas exchange that keeps us alive.






In addition to studying embryonic development, the technique could be used in clinical settings. For instance researchers could study differences between individual cells in a tumor, improving our understanding of the stages of cancers and leading to better, more targeted therapies.


