Epigenomic signatures reveal mechanistic clues and predictive markers for autism spectrum disorder
Molecular Psychiatry (2023) https://doi.org/10.1038/s41380-022-01917-9
Autism spectrum disorder (ASD) comprises a heterogeneous group of neurodevelopmental outcomes in children with a commonality in deficits in social communication and language combined with repetitive behaviors and interests. The etiology of ASD is heterogeneous, as several hundred genes have been implicated as well as multiple in utero environmental exposures. Over the past two decades, epigenetic investigations, including DNA methylation, have emerged as a novel way to capture the complex interface of multivariate ASD etiologies. More recently, epigenome-wide association studies using human brain and surrogate accessible tissues have revealed some convergent genes that are epigenetically altered in ASD, many of which overlap with known genetic risk factors. Unlike transcriptomes, epigenomic signatures defined by DNA methylation from surrogate tissues such as placenta and cord blood can reflect past differences in fetal brain gene transcription, transcription factor binding, and chromatin. For example, the discovery of NHIP (neuronal hypoxia inducible, placenta associated) through an epigenome-wide association in placenta, identified a common genetic risk for ASD that was modified by prenatal vitamin use. While epigenomic signatures are distinct between different genetic syndromic causes of ASD, bivalent chromatin and some convergent gene pathways are consistently epigenetically altered in both syndromic and idiopathic ASD, as well as some environmental exposures. Together, these epigenomic signatures hold promising clues towards improved early prediction and prevention of ASD as well genes and gene pathways to target for pharmacological interventions. Future advancements in single cell and multi-omic technologies, machine learning, as well as non-invasive screening of epigenomic signatures during pregnancy or newborn periods are expected to continue to impact the translatability of the recent discoveries in epigenomics to precision public health.
15q11-q13 duplication syndrome (Dup15q) is one of the most common CNVs identified in ASD cases and ASD comorbidity is observed in 85% of Dup15q cases . Due to the same chromosomal breakpoints responsible for large deletions in 15q11-q13, Dup15q syndrome results from duplication that is either extrachromosomal or interstitial . While duplications can occur on either parental chromosome, ASD is only observed in individuals with maternal duplication [63, 64]. The AS gene UBE3A is maternally expressed exclusively in neurons due to the paternal expression of the UBE3A antisense . Because the 15q11-q13 locus is parentally imprinted, the strongest methylation signature observed in Dup15q brain is over a ~7 Mb region that is strikingly hypomethylated on the maternal allele by 20 kb window WGBS analysis, resulting in opposite DNA methylation directions in the 15q11-q13 deletion syndromes AS (hypermethylation) versus PWS (hypomethylation) and a more modest hypomethylation in Dup15q syndrome compared to controls . The opposite pattern of maternal hypermethylation and paternal hypomethylation was observed specifically at CpG islands within the 7 Mb imprinted locus , reminiscent of what is observed on the inactive X chromosome in females . The enrichment of both hypo- and hypermethylated probes over the imprinted 15q11-q13 locus in Dup15q syndrome was replicated in a 450k array analysis of three brain regions . This 450k array study in brain also showed a significant overlap in the epigenomic signature between Dup15q and idiopathic ASD , a finding that was also replicated in a subsequent WGBS analysis of idiopathic ASD, Dup15q syndrome, and Rett syndrome .
Functional follow-up analyses using human neuronal cell line models revealed further insights into the potential mechanism responsible for the epigenomic signature of Dup15q syndrome and how multiple “hits” may impact the strength of the epigenomic signature. A human neuronal cell line model of Dup15q syndrome  was cultured in the presence or absence of the environmental pollutant polychlorinated biphenyl (PCB 95) , which had previously observed to be elevated in Dup15q brain samples compared to controls or idiopathic ASD . Long-term clonal cultures of this Dup15q model acquired a second duplication on 22q12.3-q13.33, resulting in a multi-hit model of two chromosomal duplications plus the environmental exposure. Each additional hit increased the number of differentially methylated genes, mostly hypomethylated, with functions at the synaptic membrane . Because most hypomethylated genes showed decreased expression in long-term cultures, an epigenetic change to chromatin modifications was investigated. Specifically, a known nuclear target of the ubiquitin ligase activity of UBE3A is RING1 , a component of the polycomb regulatory complex 1 (PRC1) repressor that is a ubiquitin ligase for the histone components H2A and H2A.Z . Ubiquitinated H2A.Z is a poised developmental mark of large chromatin domains with lower levels of DNA methylation . As shown in Fig. 1, bivalent H2A.Z marked the Dup15q hypomethylated genes and elevated levels of UBE3A correlated with reduced levels of RING1B. PCB 95 further reduced the levels of H2A.Z . Together, these results suggested a multi-hit intersecting pathway between genetic susceptibility and an environmental exposure observed through the shared epigenomic signature.