Dissecting the chromatin and spatial mechanisms of HMGN1-mediatedcongenital heart defects in down syndrome

The National Heart, Lung, and Blood Institute awarded J. David Gladstone Institutes $131,307 on July 21, 2026, under the Cardiovascular Diseases Research program (CFDA 93.837) to support a K99/R00 career development project investigating chromatin and spatial mechanisms underlying congenital heart defects in Down syndrome.

The research, led by Dr. Feiya Li, dissects how increased dosage of the HMGN1 gene on chromosome 21 alters chromatin structure, gene regulation, and spatial cell signaling to produce atrioventricular canal defects. In the K99 phase, the work determines how HMGN1 dosage influences nucleosome positioning and chromatin accessibility using single-molecule footprinting, and identifies chromatin and protein partners through proteomics and capture mass spectrometry. The R00 phase expands from atrioventricular canal cardiomyocytes to neighboring cell types that build the atrioventricular canal microenvironment, combining Visium HD spatial transcriptomics and multiplex imaging to map how altered HMGN1 dosage disrupts organized cell signaling regions within the developing heart.

Dr. Deepak Srivastava provides mentorship in cardiac development and congenital disease. An advisory committee includes Dr. Vijay Ramani (chromatin structure), Dr. Danielle Swaney (proteomics), Dr. Karin Pelka (spatial transcriptomics), and Dr. Katie Pol.

Performance occurs in San Francisco, California. The period of performance runs from July 21, 2026, through May 31, 2028. The assistance type is a Project Grant.

Abstract

Congenital heart defects (CHD) are the most common developmental abnormalities, affecting ~1% of live births. Aneuploidy accounts for ~15% of CHD, with the most frequent form being trisomy 21 (down syndrome, DS). Nearly half of individuals with DS have CHD, with a >1000-fold enrichment for atrioventricular canal (AVC) defects that disrupt atrial-ventricular boundaries. Although some chromosome 21 genes have been linked to congenital heart disease, how gene dosage imbalance changes chromatin organization and cell communication to produce structural defects remains unclear. This K99/R00 project led by DR. Feiya LI will define how increased dosage of the chromosome 21 gene HMGN1 alters chromatin structure, gene regulation, and spatial cell signaling that lead to heart defects in down syndrome. In the K99 phase, the PI will determine how HMGN1 dosage influences nucleosome positioning and chromatin accessibility using single molecule samosa footprinting, and identify chromatin and protein partners through proteomics and capture mass spectrometry. In the R00 phase, the PI expand the research focus from AVC cardiomyocytes to other cell types that build the environment of AVC. The PI will combine visium HD spatial transcriptomics and multiplex imaging to map how altered HMGN1 dosage disrupts organized cell signaling regions within the developing heart. These studies will build a detailed model linking chromatin dysregulation to tissue level remodeling in aneuploidy related heart disease. The training plan integrates experimental and computational goals under the mentorship of DR. Deepak srivastava, an expert in cardiac development and congenital disease, with guidance from an advisory committee including DR. Vijay ramani for chromatin structure, DR. Danielle swaney for proteomics, DR. Karin pelka for spatial transcriptomics, and DR. Katie pollard for computational modeling. Training will include optimizing protocols for nuclei isolation, refining single molecule footprint data processing, and developing expertise in detecting low abundance nuclear proteins through proteomics. In spatial omics, DR. LI will build skills in segmentation, tissue boundary detection, and spatial domain reconstruction, and will implement and compare computational pipelines to improve accuracy for cardiac tissue data. DR. LI will continue expanding computational analysis skillsets to enable rapid adaptation to emerging techniques and analytical frameworks across evolving multiomic platforms. The gladstone institutes provide a collaborative environment with advanced genomics, proteomics, and imaging facilities and strong institutional support for early career investigators. Supported by this environment and the mentoring team, DR. Feiya LI is well positioned to transition to independence and establish a research program that combines chromatin biology, proteomics, and spatial omics to reveal how gene dosage reshapes chromatin and tissue architecture in CHD and aneuploidy related diseases, bringing in insights to broader cardiovascular diseases frameworks as well.