Hunting for the chromosomal genes that break the heart

(Press-News.org) Three copies of chromosome 21 causes Down syndrome (DS), and roughly half of children born each year in the United States with DS—approximately 2,600—also have congenital heart defects (CHDs).

What is not known is exactly why the genes on too many copies of chromosome 21 wreak such devastating effects.

In a new paper published in the journal Nature, a team of scientists, including first and co-corresponding author  Sanjeev S. Ranade, PhD, assistant professor in the Center for Cardiovascular and Muscular Diseases and Center for Data Science and Artificial Intelligence at Sanford Burnham Prebys, identify a nuclear binding protein as a key contributor to trisomy 21-related CHDs.

“What our paper did was address a major unresolved question: Yes, three copies of chromosome 21 causes DS, but why? What are the genes on chromosome 21 that are bad if you have them in three copies? How in the world do you try to find those genes?”

Approximately 40,000 children (1 percent) are born in the U.S with CHDs. There are multiple suspected causes, from maternal infections during pregnancy and maternal behaviors like smoking, to environmental exposures, such as pollutants.

Fifteen percent of CHD cases involve chromosomal abnormalities, most often trisomy 21 in which the newborn has a third or extra copy of chromosome 21. Down syndrome is most commonly caused by trisomy 21, and half of all children born with DS have CHDs, specifically a 1,000-fold increase in atrioventricular canal (AVC) defects.

Such defects disrupt the junctions between the heart’s atria (the organ’s two upper chambers that receive blood) and ventricles (the two lower chambers that receive blood from the atria and pump it to body and lungs).

The AVC harbors unique myocardial cells essential to development of the critical valves required to maintain normal blood transfer and flow within the heart, but how trisomy 21 directly affects DS-associated CHDs has not been deciphered.

In their new paper, Ranade and colleagues focus on High Mobility Group Nucleosome Binding Protein 1 or HMGN1, a ubiquitous and critical protein used to bind and build nucleosomes, the basic repeating units of chromatin, which in turn packages DNA into the cell nucleus, regulates gene expression and facilitates DNA replication and repair.

“What we did was use a really cutting edge version of clustered regularly interspaced short palindromic repeats technology called CRISPR activation (CRISPRa) to see if we could increase the levels of chromosome 21 genes, then convert or reprogram a normal cell into looking like a Down Syndrome cell,” said Ranade.

“We did this for 66 chromosome 21 genes and then showed that an epigenetic gene—HMGN1—was a bad guy if you had three copies.”

In their experiments using human pluripotent stem cells and mouse models of DS, the researchers found when too much HMGN1 is present (as in trisomy 21) developing AVC cardiomyocytes shift toward an abnormal state. When one HMGN1 allele in trisomic cells was deleted using CRISPR technology, normal gene expression was restored. In the mouse model, reduction of HMGN1 rescued valvuloseptal defects, leading to fewer mice with holes in their heart.

“We’re hoping that our approach in this paper lays out a roadmap for finding genes driving other kinds of defects, such as intellectual disability or in bone formation, seen in children with Down syndrome,” said Ranade. “Ultimately, once we find the players that drive disease, we believe we can use that information to find drugs that could help people with Down syndrome.”

Deepak Srivastava of the Gladstone Institutes and UC San Francisco is senior and co-corresponding author.

Additional authors include:

Feiya Li, Sean Whalen, Angelo Pelonero, Lin Ye, Yu Huang, Abigail Brand, Tomohiro Nishino, Rahul Mital, Ryan M. Boileau, Frances Koback, Arun Padmanabhan, Victoria Yu, Alexander F. Merriman, Langley Grace Wallace, Annie Nguyen, Nikolaos Poulis, Mauro W. Costa, Casey A. Gifford and Katherine S. Pollard, all at Gladstone Institutes and/or UC San Francisco; and Bastien Cimarosti and Diana Presas-Ramos at Sanford Burnham Prebys.

The study was supported by funding from the National Institutes of Health, National Heart, Lung, and Blood Institute, the Roddenberry Foundation, the L.K. Whittier Foundation, Additional Ventures, the Younger Family Fund, Clark and Sharon Winslow, the American Heart Association, the Japan Society for the Promotion of Science Overseas Research Fellowship, the Michael Antonov Charitable Foundation, the Frank A. Campini Foundation and the Sarnoff Cardiovascular Research Foundation.

The study’s DOI is 10.1038/s41586-025-09593-9.

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