Development cell by cell - Science Magazine

With a trio of techniques, scientists are tracking embryo development in stunning detail.

A representation of cell lineages in a zebrafish embryo, color-coded by time. The first cells are gray; by 6 hours (gold), three major branches have formed.
IMAGE: JEFFREY FARRELL AND YIQUN WANG/SCHIER LAB/HARVARD UNIVERSITY

From at least the time of Hippocrates, biologists have been transfixed by the mystery of how a single cell develops into an adult animal with multiple organs and billions of cells. The ancient Greek physician hypothesized that moisture from a mother's breath helps shape a growing infant, but now we know it is DNA that ultimately orchestrates the processes by which cells multiply and specialize. Now, just as a music score indicates when strings, brass, percussion, and woodwinds chime in to create a symphony, a combination of technologies is revealing when genes in individual cells switch on, cueing the cells to play their specialized parts. The result is the ability to track development of organisms and organs in stunning detail, cell by cell and through time. Science is recognizing that combination of technologies, and its potential for spurring advances in basic research and medicine, as the 2018 Breakthrough of the Year.

Driving those advances are techniques for isolating thousands of intact cells from living organisms, efficiently sequencing expressed genetic material in each cell, and using computers, or labeling the cells, to reconstruct their relationships in space and time. That technical trifecta “will transform the next decade of research,” says Nikolaus Rajewsky, a systems biologist at the Max Delbrück Center for Molecular Medicine in Berlin. This year alone, papers detailed how a flatworm, a fish, a frog, and other organisms begin to make organs and appendages. And groups around the world are applying the techniques to study how human cells mature over a lifetime, how tissues regenerate, and how cells change in diseases.

The ability to isolate thousands of individual cells and sequence each one's genetic material gives researchers a snapshot of what RNA is being produced in each cell at that moment. And because RNA sequences are specific to the genes that produced them, researchers can see which genes are active. Those active genes define what a cell does.

That combination of techniques, known as single-cell RNA-seq, has evolved over the past few years. But a turning point came last year, when two groups showed it could be done on a scale large enough to track early development. One group used single-cell RNA-seq to measure gene activity in 8000 cells extracted at one time point from fruit fly embryos. About the same time, another team profiled gene activity of 50,000 cells from one larval stage of the nematode Caenorhabditis elegans. The data indicated which proteins, called transcription factors, were guiding the cells to differentiate into specialized types.

This year, those researchers and others performed even more extensive analyses on vertebrate embryos. Using a variety of sophisticated computational methods, they linked single-cell RNA-seq readouts taken at different time points to reveal the turning on and off of sets of genes that defined the types of cells formed in those more complex organisms. One study uncovered how a fertilized zebrafish egg gives rise to 25 cell types; another monitored frog development through early stages of organ formation and determined that some cells begin to specialize earlier than previously thought. “The techniques have answered fundamental questions regarding embryology,” says Harvard University stem cell biologist Leonard Zon.

Researchers interested in how some animals can regrow limbs or whole bodies have also turned to single-cell RNA-seq. Two groups studied gene expression patterns in aquatic flatworms called planaria—among biology's champion regenerators—after they had been cut into pieces. The scientists discovered new cell types and developmental trajectories that emerged as each piece regrew into a whole individual. Another group traced the genes that switched on and off in axolotls, a type of salamander, that had lost a forelimb. The researchers found that some mature limb tissue reverted to an embryonic, undifferentiated state and then underwent cellular and molecular reprogramming to build a new limb.

Because cells must be removed from an organism for single-cell sequencing, that technique alone can't show how those cells interact with their neighbors or identify the cells' descendants. But by engineering markers into early embryonic cells, researchers can now track cells and their progeny in living organisms. At least one team exposes early embryos to mobile genetic elements that carry genes for different colored fluorescent tags, which randomly settle into the cells, imparting different colors to each cell lineage. Other teams have harnessed the gene-editing technique called CRISPR to mark the genomes of individual cells with unique barcodelike identifiers, which are then passed on to all their descendants. The gene editor can make new mutations in progeny cells while retaining the original mutations, enabling scientists to track how lineages branch off to form new cell types.

By combining those techniques with single-cell RNA-seq, researchers can both monitor the behavior of individual cells and see how they fit into the organism's unfolding architecture. Using that approach, one team determined the relationships of more than 100 cell types in zebrafish brains. The researchers used CRISPR to mark early embryonic cells, then isolated and sequenced 60,000 cells at different time points to track gene activity as the fish embryo developed.

Other groups are applying similar techniques to track what happens in developing organs, limbs, or other tissues—and how those processes can go wrong, resulting in malformations or disease. “It's like a flight recorder, where you are watching what went wrong and not just looking at a snapshot at the end,” says Jonathan Weissman, a stem cell biologist at the University of California, San Francisco. “We can ask questions at a resolution that was just not possible before.”

Although those technologies cannot be used directly in developing human embryos, researchers are applying the approaches to human tissues and organoids to study gene activity cell by cell and characterize cell types. An international consortium called the Human Cell Atlas is 2 years into an effort to identify every human cell type, where each type is located in the body, and how the cells work together to form tissues and organs. Already, one project has identified most, if not all, kidney cell types, including ones that tend to become cancerous. Another effort has revealed the interplay between maternal and fetal cells that allows pregnancy to proceed. And a collaboration of 53 institutions and 60 companies across Europe, called the LifeTime consortium, is proposing to harness single-cell RNA-seq in a multipronged effort to understand what happens cell by cell as tissues progress toward cancer, diabetes, and other diseases.

High-resolution movies of development and disease will only get more compelling. Papers already posted online extend development studies to ever-more-complex organisms. And researchers hope to combine single-cell RNA-seq with new microscopy techniques to see where in each cell its distinctive molecular activity takes place and how neighboring cells affect that activity.

The single-cell revolution is just starting.

People's Choice

Our readers weigh in with their picks for the top breakthrough of 2018

Visitors to Science's website are in agreement with the magazine's reporters and editors: Development cell by cell is the Breakthrough of the Year.

We invited online readers to vote on a dozen candidates for the breakthrough. The first round of voting narrowed the choices to four, and a second round, in which more than 12,000 votes were cast, determined the top People's Choice.

The combination of techniques that enables scientists to track development at the cellular level, in stunning detail and over time, was the clear winner. The approval of a gene-silencing drug after 20 years of development took second place, followed by the detection of a neutrino traced to a source outside our galaxy. The fourth contender, a set of images of the fruit fly brain showing individual synapses, just missed Science's top 10.