Precision cardiovascular medicine: artificial intelligence and epigenetics for the pathogenesis and prediction of coarctation in neonates

posted on 05.02.2020 by Ray O. Bahado-Singh, Sangeetha Vishweswaraiah, Buket Aydas, Ali Yilmaz, Nazia M. Saiyed, Nitish K. Mishra, Chittibabu Guda, Uppala Radhakrishna

Background: Advances in omics and computational Artificial Intelligence (AI) have been said to be key to meeting the objectives of precision cardiovascular medicine. The focus of precision medicine includes a better assessment of disease risk and understanding of disease mechanisms. Our objective was to determine whether significant epigenetic changes occur in isolated, non-syndromic CoA. Further, we evaluated the AI analysis of DNA methylation for the prediction of CoA.

Methods: Genome-wide DNA methylation analysis of newborn blood DNA was performed in 24 isolated, non-syndromic CoA cases and 16 controls using the Illumina HumanMethylation450 BeadChip arrays. Cytosine nucleotide (CpG) methylation changes in CoA in each of 450,000 CpG loci were determined. Ingenuity pathway analysis (IPA) was performed to identify molecular and disease pathways that were epigenetically dysregulated. Using methylation data, six artificial intelligence (AI) platforms including deep learning (DL) was used for CoA detection.

Results: We identified significant (FDR p-value ≤ .05) methylation changes in 65 different CpG sites located in 75 genes in CoA subjects. DL achieved an AUC (95% CI) = 0.97 (0.80–1) with 95% sensitivity and 98% specificity. Gene ontology (GO) analysis yielded epigenetic alterations in important cardiovascular developmental genes and biological processes: abnormal morphology of cardiovascular system, left ventricular dysfunction, heart conduction disorder, thrombus formation, and coronary artery disease.

Conclusion: In an exploratory study we report the use of AI and epigenomics to achieve important objectives of precision cardiovascular medicine. Accurate prediction of CoA was achieved using a newborn blood spot. Further, we provided evidence of a significant epigenetic etiology in isolated CoA development.