When a baby is born with a severe heart defect, there is usually no obvious explanation. In the majority of cases the family has no history of such heart problems, and most often the parents carry no known genetic mutations related to the defect that they could have passed along. Recently School of Medicine scientists contributed to a sweeping new search for genetic mutations in children with unexplained heart abnormalities that uncovered several hundred non-inherited mutations that may help shed light on how such problems arise during fetal development.

The new study, published June 13 in the journal Nature, was led by scientists from the School of Medicine as part of a multicenter collaboration that included patients and scientists from seven U.S. centers and from University College London. The study compared the genomes of children with severe congenital heart disease (CHD) to the genomes of their healthy parents to try to determine whether de novo mutations—mutations that, rather than being passed from parent to child, arise spontaneously in egg, sperm, or early embryo cells—are involved in these disorders.

“Because many affected patients are the offspring of healthy parents, we speculated that new mutations might play a significant role in CHD,” says Richard P. Lifton, M.D., Ph.D., chair and Sterling Professor of Genetics, professor of medicine, and a lead author of the study along with Martina Brueckner, M.D., associate professor of pediatrics and genetics. Children with heart defects, they found, were 7.5 times more likely to have damaging de novo mutations in genes expressed in the developing heart than were healthy children, and such mutations appear to contribute to more than 10 percent of all cases. Most interestingly, many of the newly identified mutations affect proteins that orchestrate normal development by helping to turn genes on and off at the proper times by altering the chemical marks on histone proteins, which provide a scaffold that DNA is wrapped around in the cell nucleus. This mechanism is known as epigenetic control.

The scientists analyzed the genomes of 362 trios, each comprising two unaffected parents and one child with severe CHD. These families were participants in the National Institutes of Health–funded Pediatric Cardiac Genomics Consortium; the team also studied the genomes of a control group of 260 parent-child trios with no history of CHD. The study used a rapid and inexpensive method of sequencing all the genes in the genome—called exome sequencing—pioneered at Yale over the last decade. The DNA sequencing for the study was performed at the Yale Center for Genome Analysis at Yale’s West Campus, and the analysis was led by two members of Lifton’s lab: Samir Zaidi ’16, a student in Yale’s M.D./Ph.D. Program, and Murim Choi, Ph.D., a postdoctoral fellow.

When the researchers examined the genes with de novo mutations, they found a common thread. “There’s a pathway that seems to be particularly hit by these de novo mutations, not only in congenital heart diseases, but in autism as well,” says Brueckner. “That suggests that this pathway plays a vital role in diverse aspects of fetal development.”

Ten of the de novo mutations found in CHD patients occurred in genes required for the addition or removal of methyl groups at two sites on one of the histones. These two methylation sites play a critical role in turning genes on and off. Most interestingly, one of these marks activates gene expression, while the other represses expression. In embryonic stem cells and in developing embryos, key developmental genes appear to have both of these marks, and scientists have hypothesized that this methylation pattern is particularly important in the developing embryo, when genes must turn on and off at precise times in particular cell types to ensure proper development.

“As development proceeds, cells become committed to a specific fate by removing either the repressive or the activating marks, resulting in either activation of gene expression or long-term repression,” says Lifton, also a Howard Hughes Medical Institute investigator. “It appears that subtle alteration in the dosage of these histone modifications—either increasing or decreasing methylation—can perturb development. This is particularly interesting because it raises the possibility that environmental perturbations might produce the same outcome in the absence of a mutation.”

CHD is only the second disease for which a large search for de novo mutations has been performed. In 2012, Yale researchers studying autism also found a role for de novo mutations, and the most frequently mutated gene in autism plays a role the same methylation pathway. These findings suggest a broad role of this pathway in the development of the heart and brain, and possibly other organs. The next steps in understanding the process, the scientists say, will be uncovering which genes show altered expression as a consequence of changes in histone methylation.

The team plans to follow up on the genes pinpointed in the study, both those affecting the methylation pathway and those associated with other cellular functions. And since de novo mutations only explain roughly one in 10 cases of CHD, they’re still on the hunt for other causes. “The long-term goal,” Brueckner says, “is to be able to understand these congenital abnormalities well enough that we can tailor medical and surgical care specifically to each individual patient, leading to the best lifetime outcome for the growing population of individuals living with congenital heart disease.”