Evidence for the placenta-brain axis: multi-omic kernel aggregation predicts intellectual and social impairment in children born extremely preterm

• Published in: Molecular autism Vol. 11; no. 1; pp. 97 - 16
• Main Authors: Santos, Jr, Hudson P, Bhattacharya, Arjun, Joseph, Robert M, Smeester, Lisa, Kuban, Karl C K, Marsit, Carmen J, O'Shea, T Michael, Fry, Rebecca C
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 11-12-2020; BioMed Central; BMC
• Subjects: Adult; Age; Algorithms; Autism; Biomarkers - metabolism; Brain - metabolism; Brain research; Case-Control Studies; Child; Cognition; Complications and side effects; CpG Islands - genetics; Deoxyribonucleic acid; Development and progression; Developmental neurology; Differential expression analysis; DNA; DNA methylation; Epigenome-wide association; Female; Genome-Wide Association Study; Genomes; Genomics; Health aspects; Humans; Infant, Extremely Premature - metabolism; Infant, Newborn; Intellectual Disability - genetics; Intelligence Tests; Male; Mental retardation; MicroRNAs - genetics; MicroRNAs - metabolism; Multi-omic aggregation; Multivariate Analysis; Pediatric research; Pervasive developmental disorders; Physiological aspects; Placenta; Placenta - metabolism; Placental gene regulation; Pregnancy; Premature birth; Premature Birth - genetics; Prenatal neurodevelopmental programming; Psychologists; Quality control; Risk factors; RNA, Messenger - genetics; RNA, Messenger - metabolism; Social and cognitive impairment; Social Behavior; United States; Prenatal neurodevelopmental programming; Placental gene regulation; Epigenome-wide association; Social and cognitive impairment; Differential expression analysis; Multi-omic aggregation
• ISSN: 2040-2392; 2040-2392
• DOI: 10.1186/s13229-020-00402-w

Children born extremely preterm are at heightened risk for intellectual and social impairment, including Autism Spectrum Disorder (ASD). There is increasing evidence for a key role of the placenta in prenatal developmental programming, suggesting that the placenta may, in part, contribute to origins of neurodevelopmental outcomes.
We examined associations between placental transcriptomic and epigenomic profiles and assessed their ability to predict intellectual and social impairment at age 10 years in 379 children from the Extremely Low Gestational Age Newborn (ELGAN) cohort. Assessment of intellectual ability (IQ) and social function was completed with the Differential Ability Scales-II and Social Responsiveness Scale (SRS), respectively. Examining IQ and SRS allows for studying ASD risk beyond the diagnostic criteria, as IQ and SRS are continuous measures strongly correlated with ASD. Genome-wide mRNA, CpG methylation and miRNA were assayeds with the Illumina Hiseq 2500, HTG EdgeSeq miRNA Whole Transcriptome Assay, and Illumina EPIC/850 K array, respectively. We conducted genome-wide differential analyses of placental mRNA, miRNA, and CpG methylation data. These molecular features were then integrated for a predictive analysis of IQ and SRS outcomes using kernel aggregation regression. We lastly examined associations between ASD and the multi-omic-predicted component of IQ and SRS.
Genes with important roles in neurodevelopment and placental tissue organization were associated with intellectual and social impairment. Kernel aggregations of placental multi-omics strongly predicted intellectual and social function, explaining approximately 8% and 12% of variance in SRS and IQ scores via cross-validation, respectively. Predicted in-sample SRS and IQ showed significant positive and negative associations with ASD case-control status.
The ELGAN cohort comprises children born pre-term, and generalization may be affected by unmeasured confounders associated with low gestational age. We conducted external validation of predictive models, though the sample size (N = 49) and the scope of the available out-sample placental dataset are limited. Further validation of the models is merited.
Aggregating information from biomarkers within and among molecular data types improves prediction of complex traits like social and intellectual ability in children born extremely preterm, suggesting that traits within the placenta-brain axis may be omnigenic.