In the realm of biology, creating a comprehensive map of all cell types within an organism typically requires massive international collaboration and hefty budgets. However, exceptions do exist. According to recent reports from Nature, three researchers took the lead and accomplished this feat in just one year, and at a remarkably low cost.
The trio behind this achievement consists of Chengxiang Qiu and Beth K. Martin from the Department of Genome Sciences at the University of Washington in Seattle, USA, along with Ian C. Welsh from the Jackson Laboratory in the United States. With a budget of only around $370,000, they successfully mapped the developmental trajectory of embryonic mice over a period of 10 days.
This marks the largest mouse embryo map to date, offering insights into how stem cells differentiate into specific cell types, how organs develop, and how an organism changes after birth.
The process of mouse embryo development from day 8 (top left) to birth (bottom right). Image source: C. Qiu et al./Nature
Division of labor in embryonic "tree."
The aforementioned study was published in the journal Nature in February of this year. Chengxiang Qiu, Beth K. Martin, and Ian C. Welsh are the co-first authors of the paper, leading the research and completing the majority of the work.
Chengxiang Qiu is also the corresponding author of the paper, along with Jay Shendure, a geneticist at the University of Washington in Seattle, who is the mentor of Qiu's laboratory. Other authors of the paper contributed to related assistance work.
Qiu and Martin, both members of Jay Shendure's lab, decided to illustrate the single-cell transcriptome of embryonic mice around day 19 of gestation using a new technique called sci-RNA-seq3. This technology, developed in Shendure's lab known for molecular biology innovations, enables high-throughput, multi-sample processing within a lower budget, allowing researchers to decipher the assembly of all messenger RNA (mRNA) within individual cells.
Initially, to demonstrate the application of this technique, Qiu and Martin chose to map the transcriptome of embryonic mice. Since preserving whole cells throughout the study proved challenging, researchers opted to grind entire mouse embryos, isolating the cell nuclei instead. These nuclei were then distributed into separate culture dishes, with distinct molecular labels added to mRNA in each dish.
Subsequently, the nuclei were merged, re-separated, and new labels added to each dish, repeating the process. Ultimately, each cell nucleus acquired a unique set of molecular barcodes, allowing researchers to determine the transcriptome of the cells.
With this method, researchers sequenced the mRNA of these cells, constructing a tree-like model to simulate how one cell type transitions into another.
Initially, Qiu and Martin collected embryos every 24 hours over a span of five days. However, the substantial transcriptional changes between time points made it challenging to track how stem cells differentiated into specific cell types. Shendure likened this to missing frames in a video, resulting in a stop-motion animation rather than a smooth, continuous progression.
To address this, Qiu and Martin collaborated with Welsh from the Jackson Laboratory, a biomedical research and mouse breeding facility based in Bar Harbor, Maine, USA, known for its comprehensive mouse facilities.
Welsh, with expertise in mouse research, collected mouse embryos every 2 to 6 hours. Over 10 days of gestation, he meticulously gathered 83 embryos, rapidly freezing and shipping them to Seattle.
In Seattle, Martin collected the single-cell transcriptomes, which Qiu then mapped onto the tree-like model. This model demonstrated when and how 190 cell types (such as liver cells or bone marrow cells) originated from the embryo.
To enrich this "tree," researchers integrated various data sources, including their own (starting from day 8 of gestation), existing work from Shendure's team, and other studies mapping transcriptomes of these embryos and younger ones. This addition contributed an additional 110,000 cells.
These data formed the "root" of the tree-like model, enabling researchers to trace how early stem cells differentiate into specific types seen in older embryos.
Data-driven tree covering cell types from fertilized egg to pup in the entire mouse development process. Image source: paper.
Fortunate discovery, future outlook
This discovery is significant.
The resulting atlas encompasses transcriptomes from 45 time points of mouse development, available for deeper investigation by developmental biologists. It comprises 12.4 million cells, making it the largest mouse embryonic atlas to date.
According to Bertie G?ttgens, a stem cell biologist at the University of Cambridge in the UK, this research is "impressive on many levels, both in terms of its scale of achievement and the way it has achieved its research goals."
Sarah Teichmann, a cell geneticist at the Wellcome Sanger Institute in the UK and co-founder of the Human Cell Atlas, says this achievement will advance multiple studies, including the ability to compare mouse and human development.
Yonatan Stelzer, an epigeneticist at the Weizmann Institute of Science in Israel, believes this research will be helpful in future efforts to map cell types within individual organs or tissues.
Meanwhile, this discovery also involves a stroke of luck.
Researchers noticed two phenomena. Firstly, the most significant changes in the transcriptome occurred within the first hour after mouse birth. Shendure referred to it as "the most stressful moment in life." Some changes were expected, such as lung and fat cells altering their activity to adapt to the external uterine environment.
Pure luck led to another discovery. Welsh typically used cesarean sections to deliver mouse pups for their research. However, one day, upon returning from lunch, he found an unexpected litter of newborn pups. Upon handling these pups, it was found that their transcriptomes differed significantly from those of pups delivered by cesarean section. Researchers suggest that these differences may explain the impact of birth mode on health outcomes.
However, there are areas for improvement in this study.
Teichmann points out that there is still work to be done on the mouse atlas. For example, some time points have more complete transcriptomes than others, and researchers have not yet separated mice by gender to observe these differences.
It is reported that Shendure's team's next plan is to create single-cell atlases of juvenile and adult mice from conception to death.
Stelzer states that future research on embryos will further explore how cells develop over time, not only tracking them in 3D space but also understanding how they divide and migrate to form a complete mouse.
Stelzer also adds that future research could shed light on some questions, such as how two cells with similar transcriptomes determine whether they develop into the left or right eye.
"However, we are still far from solving the entire embryo puzzle," says Stelzer.
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