Shared Genetic and Regulatory Architecture of Congenital Heart Disease and Autism Spectrum Disorder Revealed by Cross-Tissue Multi-Omic Integration
6 affiliations
- 1Department of Colorectal Surgery and Oncology and School of Brain Science and Brain Medicine, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China.
- 2Liangzhu Laboratory, MOE Frontier Science Center for Brain Science and Brain-Machine Integration, State Key Laboratory of Brain-Machine Intelligence, Zhejiang University, Hangzhou 311121, China.
- 3The Pennington School, 112 W. Delaware Avenue, Pennington, NJ 08534, USA.
- 4Trinity College of Arts & Sciences, Duke University, Durham, NC 27708, USA.
- 5Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China.
- 6Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, China.
Abstract
Background: Congenital heart disease (CHD) and autism spectrum disorder (ASD) co-occur more frequently than expected, suggesting shared developmental susceptibility. We aimed to identify cross-tissue molecular candidates linking cardiac and neurodevelopmental abnormalities. Methods: CHD- and ASD-associated genes were curated from MalaCards and SFARI Gene, and their intersection was defined as the CHD- and ASD-associated gene set (CAGES). Shared gene enrichment was assessed against the human protein-coding genome. CHD and ASD genome-wide association data were integrated with heart and brain cis-expression quantitative trait loci using Bayesian colocalization and summary data-based Mendelian randomization with HEIDI testing. Candidates were further evaluated using bulk transcriptomics, six machine learning feature selection methods, independent cohorts, and scTenifoldKnk virtual knockout analyses in developing human heart and cerebral cortex. Results: Seventy-three genes were shared between CHD and ASD. CHD7 showed suggestive colocalization for CHD and ASD, while lower genetically predicted CHD7 expression was associated with higher odds of both disorders, with nonsignificant HEIDI tests. MEF2C was downregulated in tetralogy of Fallot myocardium and selected by all six ASD machine learning methods, with consistently lower expression in ASD. CAGES-derived signatures discriminated independent CHD, ASD cord blood, and cortical cohorts. CHD7 virtual knockout analysis identified MEF2C as a computationally predicted regulatory candidate in the prenatal brain, particularly in late-fetal excitatory neurons and intermediate progenitor cells, with cell-type-specific predicted effects also observed in the developing heart. Conclusions: CHD and ASD share molecular susceptibility involving pleiotropic developmental mechanisms. CHD7 and MEF2C emerge as connected cross-tissue candidates across complementary genetically informed, transcriptomic, and developmental regulatory analyses, highlighting prenatal neuronal populations and developmental windows for investigating the heart-brain axis.
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BibTeX
@article{zhu2026shared,
title = {{Shared Genetic and Regulatory Architecture of Congenital Heart Disease and Autism Spectrum Disorder Revealed by Cross-Tissue Multi-Omic Integration}},
author = {Min Zhu and Jingkun Fred Zhang and Stella X Hu and Xuechen Wang and Weize Xu},
journal = {Genes},
year = {2026},
month = sep,
doi = {10.3390/genes17101180},
url = {https://europepmc.org/article/PMC/PMC13704632},
note = {CC BY},
}
RIS
TY - JOUR
TI - Shared Genetic and Regulatory Architecture of Congenital Heart Disease and Autism Spectrum Disorder Revealed by Cross-Tissue Multi-Omic Integration
AU - Min Zhu
AU - Jingkun Fred Zhang
AU - Stella X Hu
AU - Xuechen Wang
AU - Weize Xu
PY - 2026
DA - 2026/09/24
JO - Genes
DO - 10.3390/genes17101180
UR - https://europepmc.org/article/PMC/PMC13704632
AB - Background: Congenital heart disease (CHD) and autism spectrum disorder (ASD) co-occur more frequently than expected, suggesting shared developmental susceptibility. We aimed to identify cross-tissue molecular candidates linking cardiac and neurodevelopmental abnormalities. Methods: CHD- and ASD-associated genes were curated from MalaCards and SFARI Gene, and their intersection was defined as the CHD- and ASD-associated gene set (CAGES). Shared gene enrichment was assessed against the human protein-coding genome. CHD and ASD genome-wide association data were integrated with heart and brain cis-expression quantitative trait loci using Bayesian colocalization and summary data-based Mendelian randomization with HEIDI testing. Candidates were further evaluated using bulk transcriptomics, six machine learning feature selection methods, independent cohorts, and scTenifoldKnk virtual knockout analyses in developing human heart and cerebral cortex. Results: Seventy-three genes were shared between CHD and ASD. CHD7 showed suggestive colocalization for CHD and ASD, while lower genetically predicted CHD7 expression was associated with higher odds of both disorders, with nonsignificant HEIDI tests. MEF2C was downregulated in tetralogy of Fallot myocardium and selected by all six ASD machine learning methods, with consistently lower expression in ASD. CAGES-derived signatures discriminated independent CHD, ASD cord blood, and cortical cohorts. CHD7 virtual knockout analysis identified MEF2C as a computationally predicted regulatory candidate in the prenatal brain, particularly in late-fetal excitatory neurons and intermediate progenitor cells, with cell-type-specific predicted effects also observed in the developing heart. Conclusions: CHD and ASD share molecular susceptibility involving pleiotropic developmental mechanisms. CHD7 and MEF2C emerge as connected cross-tissue candidates across complementary genetically informed, transcriptomic, and developmental regulatory analyses, highlighting prenatal neuronal populations and developmental windows for investigating the heart-brain axis.
SN - 2073-4425
ER -