Sex-specific DNA methylation signatures of autism spectrum disorder in newborn blood

Background Autism spectrum disorder (ASD) comprises a group of neurodevelopmental conditions currently diagnosed by behavioral assessment in childhood, although neuropathology begins during gestation. A poorly understood male bias for ASD diagnosis is thought to be due to both biological sex differences and cultural biases against female diagnosis of ASD. Identification of molecular biomarkers of ASD likelihood in newborns would provide more objective screening and early intervention. Epigenetic dysregulation has been reported in multiple tissues from newborns who are later diagnosed with ASD, but this is the first study to investigate sex-specific DNA methylation signatures for ASD in newborn blood, an accessible and widely banked tissue. Methods DNA methylation was assayed from ASD and typically developing (TD) newborn blood (discovery set n = 196, replication set n = 90) using whole genome bisulfite sequencing (WGBS) . Sex-stratified differentially methylated regions (DMRs) were assessed for replication, comparisons by sex, overlaps with DMRs from other tissues, and enrichment for biological processes and SFARI ASD-risk genes. Results We found that newborn blood ASD DMRs from both sexes significantly replicated in an independent cohort and were enriched for hypomethylation in ASD compared to TD samples, as well as location in promoters, CpG islands and CpG shores. Comparing females and males, we found that most DMRs with sex differences amongst TD individuals were also found in ASD individuals, plus many additional DMRs with sex differences that were only found in those with ASD. Newborn blood DMRs from females were enriched for the X chromosome and both sexes showed significant overlap with DMRs from umbilical cord blood and placenta but not post-mortem cortex. DMRs from all tissues were enriched for neurodevelopmental processes (females) and SFARI ASD-risk genes (females and males). Limitations This study is primarily limited by sample sizes, particularly amongst females. Conclusions Overall, we found a highly replicated sex-specific DNA methylation signature of ASD in newborn blood that showed support for the female protective effect and convergence with epigenetic and genetic signatures of ASD in newborns. These results demonstrate the utility of newborn blood in ASD screening and emphasizes the importance of sex-stratification in future studies.