Study reveals how DNA misfolding causes congenital heart disease
核心洞察
Researchers at Gladstone Institutes (搜索) discovered that the transcription factor TBX5 (搜索) physically folds DNA into the three-dimensional architecture heart cells require to function properly.
Losing even one copy of TBX5 (搜索) triggers a total collapse of the heart's 3D DNA organization across compartments, domains, and chromatin loops, directly causing heart defects.
The findings reframe haploinsufficiency, suggesting many birth defects may arise from the same mechanism: the cell's 3D instruction manual folding incorrectly.
Congenital heart disease (搜索) is the most common birth defect, affecting approximately 1 in 100 babies born each year. One of the many causes of this disorder is having only one functional copy of the gene TBX5 (搜索), instead of two healthy copies inherited from parents. Yet scientists have struggled to understand why one faulty copy of this gene, even in the presence of a second healthy copy, can so drastically derail heart development.
Now, researchers at Gladstone Institutes (搜索) have shown that TBX5 (搜索) plays a role in physically folding DNA into the architecture that heart cells need to function. In a new study published in Science, they found that even losing one copy dismantles this DNA organization, with ripple effects in how countless other genes are used by the cells.
The study reframes how scientists think about a longstanding puzzle in genetics: why losing one copy of a gene, a condition called haploinsufficiency, can cause serious developmental defects.
"TBX5 (搜索) is just one example of a broader class of genes that cause birth defects when only one copy is lost. What's exciting about our findings is they suggest many different birth defects might happen for the same reason: the cell's 3D instruction manual simply gets folded the wrong way," said Benoit Bruneau, PhD, director of the Gladstone Institute of Cardiovascular Disease and senior author of the study.
A close look at DNA folding
Fitting DNA inside a cell is like taking a miles-long instruction manual and packing it into the head of a pin. Because every cell type precisely folds its manual into a unique three-dimensional shape, a heart cell gets different instructions than a brain cell—and therefore functions differently.
The DNA's 3D structure is organized into several layers, including large compartments (like separate binders of the manual), domains (like paragraphs), and chromatin loops (like folding a page so two distant sentences touch). In cells, these loops bring distant genetic switches known as enhancers into physical contact with genes, allowing the cell to turn on the specific instructions it needs.
Researchers already knew that TBX5 (搜索) was a master regulator of heart development—a protein that switches on many genes a heart cell needs to form and function properly. Bruneau's lab had previously shown that losing one copy of TBX5 affects the levels of hundreds of other heart-specific genes. But they did not know exactly how.
Mapping the heart's 3D genome
To investigate, the team combined many advanced techniques to observe how individual cells react differently to the loss of TBX5 (搜索). They coaxed human stem cells—either healthy, lacking one copy of TBX5, or lacking both copies—to mature into heart muscle cells, then used high-resolution 3D mapping to look at DNA loops in unprecedented detail.
Because the study involved millions of data points from thousands of individual cells, they turned to computational models to make sense of the resulting datasets.
"We developed and used different computational models to analyze results from thousands of individual cells," said Katie Pollard, PhD, director of the Gladstone Institute of Data Science and Biotechnology and the other senior author of the study. "That allowed us to finally see how losing this one protein causes the heart's DNA structure to break down on every level."
"Using the custom computational approaches we developed, we were able to see for the first time how the loss of TBX5 (搜索) triggers the total collapse of the heart's 3D DNA organization," said Shuzhen Kuang, PhD, a first author of the study and former bioinformatics fellow in Pollard's lab. "Surprisingly, we discovered this collapse happens at every level of genome organization—compartments, domains, and chromatin loops."
A master architect
The data revealed that as healthy stem cells matured into heart muscle cells, the genome underwent a sweeping reorganization, with large stretches of DNA shifting from inactive to active or vice versa. The team found that TBX5 (搜索) is the main architect behind these structural changes.
The scientists discovered that TBX5 (搜索) acts as a GPS, telling a molecular motor known as cohesin (搜索) exactly where to land on the DNA to build the chromatin loops that connect genes with their enhancers. When there isn't enough TBX5, the DNA misfolds and fails to form necessary loops, preventing vital heart-related genes from being turned on.
"What was striking was how the amount of TBX5 (搜索) matters immensely," said Zoe Grant, PhD, a first author of the study and a postdoctoral researcher in Bruneau's lab. "The more TBX5 you removed, the worse the disruption across every level of genome organization we looked at."
In fact, the study proves that having only half the normal amount of TBX5 (搜索) is enough to cause the DNA structure to misfold, which directly leads to heart defects.
When the researchers looked more closely at individual cells, they discovered that not all heart cells responded identically to TBX5 (搜索) loss. Particular differences could be seen between two distinct types of heart cells—atrial and ventricular—and even between individual cells of the same type.
"This could help explain why people with the same mutation can have different heart defects," Grant said.
A new window into developmental disease
While the study sheds new light on why congenital heart disease (搜索) occurs at a molecular level, the findings could apply to many other developmental disorders.
"We believe we've uncovered a new mechanism of disease," said Bruneau. "We showed that even a small decrease in a single protein can cause the DNA blueprint to fold incorrectly and lead to disease. So, many birth defects currently attributed to genetic mutations may actually be caused by the 3D misfolding of DNA."
The team plans to investigate when during early cardiac development TBX5 (搜索) first begins shaping the genome's architecture, and whether the same principles hold for other proteins that cause birth defects.
The paper, "Dose-dependent sensitivity of human three-dimensional chromatin to a heart disease-linked transcription factor," was published in the journal Science on July 23, 2026. The work was supported by the National Institutes of Health (NHLBI U01 HL157989, UM1HG011585, R01 HL155906), the California Institute for Regenerative Medicine, Additional Venture, Gladstone Institutes (搜索), the Roddenberry Foundation, the Younger Family Fund, UC San Francisco, the Saving tiny Hearts Society, and the National Science Foundation.