Whether a worm, a human or a blue whale, all multicellular life begins as a single-celled egg.
From this solitary cell emerges the galaxy of others needed to build an organism, with each new cell developing in the right place at the right time to carry out a precise function in coordination with its neighbors.
This feat is one of the most remarkable in the natural world, and despite decades of study, a complete understanding of the process has eluded biologists.
Now, in three landmark studies published online April 26 in Science, Harvard Medical School and Harvard University researchers report how they have systematically profiled every cell in developing zebrafish and frog embryos to establish a roadmap revealing how one cell builds an entire organism.
Using single-cell sequencing technology, the research teams traced the fates of individual cells over the first 24 hours of the life of an embryo. Their analyses reveal the comprehensive landscape of which genes are switched on or off, and when, as embryonic cells transition into new cell states and types.
A zebrafish egg cell forms a complex embryo in only a few hours. Video by Fengzhu Xiong and Sean Megason
Together, the findings represent a catalog of genetic “recipes” for generating different cell types in two important model species and provide an unprecedented resource for the study of developmental biology and disease.
“With single-cell sequencing, we can, in a day’s work, recapitulate decades of painstaking research on the decisions cells make at the earliest stages of life,” said Allon Klein, HMS assistant professor of systems biology and co-corresponding author of two of the three Science studies.
Biomedically, these baseline resources for how organisms develop are as important as having baseline resources for their genomes, the researchers said.
“With the approaches that we’ve developed, we’re charting what we think the future of developmental biology will be as it transforms into a quantitative, ‘big-data’-driven science,” Klein said.
In addition to shedding new light on the early stages of life, the work could open the door to a new understanding of a host of diseases, said Alexander Schier, the Leo Erikson Life Sciences Professor of Molecular and Cellular Biology at Harvard, and a corresponding author of the third study.
“We foresee that any complex biological process in which cells change gene expression over time can be reconstructed using this approach,” Schier said. “Not just the development of embryos but also the development of cancer or brain degeneration.”
One at a time
Every cell in a developing embryo carries within it a copy of the organism’s complete genome. Like construction workers using only the relevant portion of a blueprint when laying a building’s foundation, cells must express the necessary genes at the appropriate time for the embryo to develop correctly.
In their studies, Klein collaborated with co-authors Marc Kirschner, the HMS John Franklin Enders University Professor of Systems Biology, Sean Megason, HMS associate professor of systems biology and colleagues to analyze this process in zebrafish and western claw-toed frog (Xenopus tropicalis) embryos, two of the most well-studied model species in biology.
The researchers leveraged the power of InDrops, a single-cell sequencing technology developed at HMS by Klein, Kirschner and colleagues, to capture gene expression data from each cell of the embryo, one cell at a time. The teams collectively profiled over 200,000 cells at multiple time points across 24 hours for both species.
"It is almost like going from seeing a few stars to seeing the entire universe” said says Schier.
To map the lineage of essentially every cell as an embryo develops, along with the precise sequence of gene expression events that mark new cell states and types, the teams developed new experimental and computational techniques, including the introduction of artificial DNA bar codes to track the lineage relationships between cells, called TracerSeq.
In the study co-led by Schier, the research team used Drop-Seq—a single-cell sequencing technology developed by researchers at HMS and the Broad Institute of MIT and Harvard—to study zebrafish embryos over 12 hours at high time resolution. Teaming with Aviv Regev, core member at the Broad, Schier and colleagues reconstructed cell trajectories through a computational method they named URD, after the Norse mythological figure who decides all fates.
Schier and colleagues profiled more than 38,000 cells, and developed a cellular “family tree” that revealed how gene expression in 25 cell types changed as they specialize. By combining that data with spatial inference, the team was also able to reconstruct the spatial origins of the various cells types in the early zebrafish embryo.
Recipe for success
In both species, the teams’ findings mirrored much of what was previously known about the progression of embryonic development, a result that underscored the power of the new approaches. But the analyses were unprecedented in revealing in comprehensive detail the cascades of events that take cells from early progenitor or “generalist” states to more specialized states with narrowly defined functions.
For scientists striving to answer questions about human disease, these data could be powerfully illuminating. In regenerative medicine, for example, researchers have for decades aimed to manipulate stem cells toward specific fates with the goal of replacing defective cells, tissues or organs with functional ones. Newly gleaned details about the sequence of gene expression changes that precipitate the emergence of specific cell types can propel these efforts further.
A future foundation
The newly generated data sets and the new tools and technologies developed as part of these studies lay the foundation for a wide spectrum of future exploration, according to the authors.
Developmental biologists can gather more and higher quality data on many species, follow embryos further in time and perform any number of perturbation experiments, all of which can help improve our understanding of the fundamental rules of biology and disease.
“I think these studies are creating a real sense of community, with researchers raising questions and interacting with each other in a way that harkens back to earlier times in the study of embryology,” Kirschner said.
The three studies, Schier said, are an example of how the scientific community can work on complementary questions to answer important questions in biology.
“Instead of competing, our groups were in regular contact over the past two years and coordinated the publication of our studies,” he said. “And it is great how complementary the three papers are—each highlights different ways such complex data sets can be generated, analyzed and interpreted.”
The next conceptual leap, the teams suggest, will be to better understand how cell-fate decisions are made.
“Right now, we have a roadmap, but it doesn’t tell us what the signs are,” Megason said. “What we need to do is figure out the signals that direct cells down certain roads, and what the internal mechanisms are that allow cells to make those decisions.”
Whatever the future holds, these data sets will leave their mark.
“The beauty of working on an organism is that this is it,” Klein said. “Ten, 20 years from now, we can still be sure zebrafish and frogs are going to develop according to the same patterns.”
All three research teams have made their data sets and tools available as interactive, browsable online resources.
This article has been republished from materials provided by Harvard Medical School. Note: material may have been edited for length and content. For further information, please contact the cited source.
References: Wagner, D. E., Weinreb, C., Collins, Z. M., Briggs, J. A., Megason, S. G., & Klein, A. M. (2018). Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo. Science, eaar4362. https://doi.org/10.1126/science.aar4362
Briggs, J. A., Weinreb, C., Wagner, D. E., Megason, S., Peshkin, L., Kirschner, M. W., & Klein, A. M. (2018). The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution. Science, eaar5780. https://doi.org/10.1126/science.aar5780
Farrell, J. A., Wang, Y., Riesenfeld, S. J., Shekhar, K., Regev, A., & Schier, A. F. (2018). Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis. Science, eaar3131. https://doi.org/10.1126/science.aar3131