Oral Presentation GENEMAPPERS 2026

Multi-omic analysis identifies accelerated biological aging and methylation dysregulation in pediatric congenital heart disease and neurodevelopmental disorders (#34)

Jamie-Lee M. Thompson 1 2 , Yunkai Gao 1 2 , Eri Iwasawa 3 , Debjani Das 1 2 , Emma Rath 1 2 , Michael Troup 1 2 , David Humphreys 1 2 , Haleh Heydarian 3 , Julia Anixt 3 , Nadine Kasparian 3 , Tanya Froehlich 3 , Jason Tchieu 3 , K. Nicole Weaver 3 , Russell Dale 4 , Sally L. Dunwoodie 1 2 , David S. Winlaw 5 6 , Eleni Giannoulatou 1 2
  1. Victor Chang Cardiac Research Institute, South Brisbane, QLD, Australia
  2. St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
  3. Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
  4. The Children’s Hospital at Westmead, University of Sydney, Sydney, NSW, Australia
  5. Heart Center, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, United States of America
  6. Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America

Background: Neurodevelopmental disorders (NDD) frequently co-occur with congenital heart disease (CHD), yet shared molecular mechanisms remain poorly understood. This study integrated whole genome sequencing, RNA sequencing, and DNA methylation data to identify genetic and epigenetic factors contributing to this comorbidity.

Methods: We recruited 15 probands (2 with CHD only, 2 with CHD+NDD, 11 with NDD only) and their parents. Blood samples from these participants were used for whole genome sequencing, RNA sequencing, and DNA methylation analysis. This data was used to investigate the following: rare variant prioritisation, gene expression, splicing variant validation, mono-allelic expression, epigenetic age acceleration, differentially methylated probes, and methylation-related pathways.

Results: WGS achieved 64% diagnostic yield, identifying pathogenic splicing variants in chromatin remodelling genes SMARCA4 and ARID1B, validated by RNA sequencing. HLHS patients showed dramatic epigenetic age acceleration of 17 years compared to chronological age, significantly greater than NDD-only patients (9.5 years, p=0.006) and controls (7.4 years, p=0.008). Individual methylation analysis revealed four probands with extreme dysregulation. Notably, the two probands carrying de novo variants in chromatin remodelling genes (SMARCA4 and ARID1B) exhibited the most severe methylation dysregulation. These methylation patterns, in conjunction with the pathogenic variants, suggest a diagnosis possibly within or overlapping the Coffin-Siris syndrome spectrum, which likely underlies the NDD phenotype in these patients.

Conclusions: This study provides new insights into the genetic and epigenetic landscape underlying the co-occurrence of neurodevelopmental disorders and congenital heart disease. Through integration of genomic, transcriptomic, and epigenomic data, we identified disease-causing variants and changes in epigenetic regulation that contribute to both conditions.