Each year, 9 months of dreams and anticipation shared by millions of future parents turn to despair and fear when they learn that their child was born with a birth defect; an often devastating event that affects one in 20 children born worldwide. The formation of our organs, our limbs and our face is the result of movements and behaviors carefully choreographed by millions of cells, much like the dancers of a troupe. If even a few cells fail to get into the right position and do their job properly, the end result is a birth defect. Yet how each individual cell knows what to do at precisely the right time and place has been largely a mystery.
In a new study published in the scientific journal Nature, a team of researchers from the Gladstone Institutes, in collaboration with the Luxembourg Center for Systems Biomedicine (LCSB) at the University of Luxembourg, reveals for the first time the full spectrum of cells that assemble to form a heart from the earliest stages of embryo formation. They also discovered how cells are controlled and how a mutation in a single gene can have catastrophic consequences by affecting a small group of cells that make up the organ.
Congenital heart defects are the most common and deadly human birth defects. Thanks to the advent of a powerful new technology known as single-cell RNA sequencing, researchers have finally been able to discern the role of tens of thousands of individual cells during the formation of the heart, which is essential for determining how genetic mutations cause disease. .
“With genome sequencing, we can now more easily find genetic variants that we believe contribute to disease,” said Gladstone President and Principal Investigator Deepak Srivastava, MD, who led the study. “The big challenge is determining the specific cell type in which this variant functions and how these cells are affected. This has been particularly difficult for birth defects, since genetic variants only affect a small subset of the cells of the organ. With single-cell technologies, we can finally begin to unravel the mechanisms behind the defects whose genetic cause we know is known.”
The catalog that Srivastava and his team have compiled contains all the genes that are active during the different stages of heart development and identifies the cells in which they can be found. It represents the first step in establishing the link between a genetic variant and a specific cell type.
“It can tell us, among other things, which subset of cells perform critical functions in specific regions of the heart and which contribute to the underlying cause of a disease associated with genetic mutations,” explained Yvanka De Soysa, graduate student. in Srivastava’s lab and first author of the study.
A rich source of data on cardiac development
To complete the repository, the researchers studied nearly 40,000 individual heart cells from a mouse model of heart development. The technology that made this study possible is single-cell RNA sequencing. This sophisticated method, which has only been commercially available for 3 years in its current form, has allowed scientists to capture data on thousands of individual cells at once.
“This sequencing technique allowed us to see all the different cell types present at different stages of heart development and helped us identify which genes were turned on and off along the way,” said Casey A. Gifford, PhD. scientist at Gladstone who is a senior author on the paper. “We were not only able to discover the existence of unknown cell types, but we also gained a better understanding of the function and behavior of individual cells – information that we could never access before.”
After identifying the many cell types involved in heart development, the team wanted to know how these various cell types are generated. To do this, they teamed up with computational biologists from the LCSB who specialize in using single-cell RNA sequencing data to uncover the molecular motors of different cell types.
“Our group has a long history of developing computational models to understand cell conversion,” explained Antonio Del Sol, head of the computational biology group at LCSB and Ikerbasque research professor at the CIC bioGUNE research center in Bilbao, Spain. “We have the expertise to study entire networks of genes that control cell identity. When we joined the project, we applied our method to predict – without any prior knowledge – which molecular factors govern the fate of these different cells heart.”
A discovery in the making for 20 years
Computer analysis predicted the genes involved in the generation of specific cell types in the heart, providing insight into the function of these cells. The analysis also highlighted a major player, a gene called Hand2 that can control the activity of thousands of other genes, and which Srivastava discovered and named more than two decades ago.
Then, as a young researcher, Srivastava spent years studying the role of this master gene and regulator. He eventually discovered that it is one of the most important genes for the formation of the heart. But a decade ago, when trying to find out how this gene actually affects the heart cells that make up the organ, his work hit a dead end because the scientific tools to continue the research didn’t exist. Today, his efforts have finally been revived thanks to new technologies.
By applying single-cell RNA sequencing, he and his collaborators were able to get a much more detailed and complete picture of how the loss of Hand2 causes different cell populations to be dysregulated.
Mice lacking the Hand2 gene fail to form the chamber of the right ventricle, which pumps blood to the lungs. Surprisingly, the new prediction made by the Luxembourg researchers suggested that Hand2 is not necessary for cells to be instructed to become right ventricular cells, but is essential for the formation of outflow tract cells, the structure where the major outgoing blood vessels of the heart arise.
“It didn’t make sense based on previous findings,” De Soysa said. “However, we found that, in fact, Hand2 has very distinct functions for different cell types.”
The calculation prediction turned out to be correct. The team found that hearts without the Hand2 gene never made outflow tract cells, but made right ventricular cells. In the choreography of the heart, it is not enough for a cell to be made, it must also be placed in the right place in relation to the other “dancers”. Without Hand2, cells from the right ventricle were created but blocked at their origin, failing to move into the developing heart.
“Our collaborative findings have made us change the way we think about heart formation and have shown how disruption of cell fate, migration or survival of a few cells can cause heart malformation,” added De Soysa.
A hopeful future for congenital heart disease treatment
The study revealed the mechanisms by which relatively small populations of cells are affected during development and lead to defects in heart formation. It also represents a discovery that would not have been possible without single-cell RNA sequencing technology.
“Single-cell technologies can tell us about how organs form in ways we couldn’t understand before and can provide the underlying cause of disease associated with genetic variations,” Gifford said. “We revealed subtle differences in very, very small subsets of cells that actually have catastrophic consequences and could easily have been overlooked in the past. This is the first step towards designing new therapies.”
Significantly, the new cardiac cell catalog can now serve scientists and physicians interested in various aspects of cardiac development. Knowing the types of cells involved in normal and abnormal heart formation, the scientific community can begin to devise strategies to correct the genetic variants that cause congenital heart disease.
These findings could also guide therapeutic approaches to help both newborns and the growing adult population with congenital heart disease.
“Through surgeries, we have become very good at keeping most children with heart defects alive,” said Srivastava, who is also a pediatric cardiologist at UCSF Benioff Children’s Hospital and a professor of pediatrics at UC. San Francisco. “The result is that today we have nearly 2.5 million congenital heart disease survivors in the United States.”
When children with a birth defect are lucky enough to survive, the same genetic condition that caused the developmental problem can lead to ongoing difficulties in maintaining a healthy heart throughout life.
“We’re starting to see the long-term consequences in adults, and at the moment we really have no way of treating them,” Srivastava added. “My hope is that if we can understand the genetic causes and the cell types affected, we could potentially intervene soon after birth to prevent their condition from worsening over time.
For Srivastava, the holy grail would be to get such a clear picture of the mechanisms involved in causing congenital heart defects that they could develop preventive strategies for those genetically at risk.
“With folic acid being the best paradigm – pregnant women now take higher levels of this vitamin and can successfully prevent nearly two-thirds of cases of spina bifida,” he said. “The ultimate goal is to create similar public health measures that could reduce the overall incidence of birth defects through prevention. But first, we need to know where and how to intervene.”