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Project description:BackgroundAutism spectrum disorder (ASD) involves complex genetics interacting with the perinatal environment, complicating the discovery of common genetic risk. The epigenetic layer of DNA methylation shows dynamic developmental changes and molecular memory of in utero experiences, particularly in placenta, a fetal tissue discarded at birth. However, current array-based methods to identify novel ASD risk genes lack coverage of the most structurally and epigenetically variable regions of the human genome.ResultsWe use whole genome bisulfite sequencing in placenta samples from prospective ASD studies to discover a previously uncharacterized ASD risk gene, LOC105373085, renamed NHIP. Out of 134 differentially methylated regions associated with ASD in placental samples, a cluster at 22q13.33 corresponds to a 118-kb hypomethylated block that replicates in two additional cohorts. Within this locus, NHIP is functionally characterized as a nuclear peptide-encoding transcript with high expression in brain, and increased expression following neuronal differentiation or hypoxia, but decreased expression in ASD placenta and brain. NHIP overexpression increases cellular proliferation and alters expression of genes regulating synapses and neurogenesis, overlapping significantly with known ASD risk genes and NHIP-associated genes in ASD brain. A common structural variant disrupting the proximity of NHIP to a fetal brain enhancer is associated with NHIP expression and methylation levels and ASD risk, demonstrating a common genetic influence.ConclusionsTogether, these results identify and initially characterize a novel environmentally responsive ASD risk gene relevant to brain development in a hitherto under-characterized region of the human genome.
| S-EPMC8848662 | biostudies-literature
Project description:Most autism spectrum disorder (ASD) cases involve complex genetics interacting with perinatal environment, complicating the discovery of common genetic risk. The epigenetic layer of DNA methylation shows dynamic developmental changes and molecular memory of in utero experiences, particularly in placenta, a fetal tissue discarded at birth. However, current array-based methods to identify novel ASD risk genes lack coverage of the most structurally and epigenetically variable regions of the human genome. Here we used whole genome bisulfite sequencing (WGBS) in placenta samples from prospective ASD studies to discover a previously uncharacterized ASD risk gene in a co-methylated block at 22q13.33. Differentially methylated region (DMR) analysis identified 139 DMRs common to ASD in placental samples, including a high-confidence 118 kb hypomethylated block at 22q13.33 that replicated in two additional cohorts and identified the novel transcript NHIP as neuronal hypoxia inducible, placenta associated (gene name approved by HGNC). NHIP characterized by high expression in brain, increased expression following neuronal differentiation or hypoxia in vitro, and minimal expression in ASD placenta. Transient NHIP overexpression in cell lines increased cellular proliferation and altered expression of genes regulating synapses and neurogenesis in response to hypoxia, significantly overlapping with NHIP-associated transcript levels in ASD brain and known ASD risk genes. A common Alu insert near a fetal brain enhancer correlated with NHIP placental and brain expression levels and ASD risk, demonstrating a common genetic influence on DNA methylation levels. Together, these results demonstrate a novel environmentally-responsive ASD risk gene relevant to brain development in a hitherto uncharacterized region of the human genome.
2022-01-16 | GSE178203 | GEO
Project description:Most autism spectrum disorder (ASD) cases involve complex genetics interacting with perinatal environment, complicating the discovery of common genetic risk. The epigenetic layer of DNA methylation shows dynamic developmental changes and molecular memory of in utero experiences, particularly in placenta, a fetal tissue discarded at birth. However, current array-based methods to identify novel ASD risk genes lack coverage of the most structurally and epigenetically variable regions of the human genome. Here we used whole genome bisulfite sequencing (WGBS) in placenta samples from prospective ASD studies to discover a previously uncharacterized ASD risk gene in a co-methylated block at 22q13.33. Differentially methylated region (DMR) analysis identified 139 DMRs common to ASD in placental samples, including a high-confidence 118 kb hypomethylated block at 22q13.33 that replicated in two additional cohorts and identified the novel transcript NHIP as neuronal hypoxia inducible, placenta associated (gene name approved by HGNC). NHIP characterized by high expression in brain, increased expression following neuronal differentiation or hypoxia in vitro, and minimal expression in ASD placenta. Transient NHIP overexpression in cell lines increased cellular proliferation and altered expression of genes regulating synapses and neurogenesis in response to hypoxia, significantly overlapping with NHIP-associated transcript levels in ASD brain and known ASD risk genes. A common Alu insert near a fetal brain enhancer correlated with NHIP placental and brain expression levels and ASD risk, demonstrating a common genetic influence on DNA methylation levels. Together, these results demonstrate a novel environmentally-responsive ASD risk gene relevant to brain development in a hitherto uncharacterized region of the human genome.
2022-01-16 | GSE178204 | GEO
Project description:Most autism spectrum disorder (ASD) cases involve complex genetics interacting with perinatal environment, complicating the discovery of common genetic risk. The epigenetic layer of DNA methylation shows dynamic developmental changes and molecular memory of in utero experiences, particularly in placenta, a fetal tissue discarded at birth. However, current array-based methods to identify novel ASD risk genes lack coverage of the most structurally and epigenetically variable regions of the human genome. Here we used whole genome bisulfite sequencing (WGBS) in placenta samples from prospective ASD studies to discover a previously uncharacterized ASD risk gene in a co-methylated block at 22q13.33. Differentially methylated region (DMR) analysis identified 139 DMRs common to ASD in placental samples, including a high-confidence 118 kb hypomethylated block at 22q13.33 that replicated in two additional cohorts and identified the novel transcript NHIP as neuronal hypoxia inducible, placenta associated (gene name approved by HGNC). NHIP characterized by high expression in brain, increased expression following neuronal differentiation or hypoxia in vitro, and minimal expression in ASD placenta. Transient NHIP overexpression in cell lines increased cellular proliferation and altered expression of genes regulating synapses and neurogenesis in response to hypoxia, significantly overlapping with NHIP-associated transcript levels in ASD brain and known ASD risk genes. A common Alu insert near a fetal brain enhancer correlated with NHIP placental and brain expression levels and ASD risk, demonstrating a common genetic influence on DNA methylation levels. Together, these results demonstrate a novel environmentally-responsive ASD risk gene relevant to brain development in a hitherto uncharacterized region of the human genome.
2022-01-16 | GSE178205 | GEO
Project description:Placental methylome reveals a 22q13.33 brain regulatory gene locus associated with autism.
| PRJNA737741 | ENA
Project description:Placental methylome reveals a 22q13.33 brain regulatory gene locus associated with autism [WGS]
| PRJNA737757 | ENA
Project description:Placental methylome reveals a 22q13.33 brain regulatory gene locus associated with autism [WGBS]
| PRJNA737756 | ENA
Project description:Placental methylome reveals a 22q13.33 brain regulatory gene locus associated with autism [RNA-seq]
| PRJNA737758 | ENA
Project description:Due to the vast clinical and genetic heterogeneity, identification of causal genetic determinants for autism spectrum disorder (ASD) has proven to be complex. Whereas several dozen 'rare' genetic variants for ASD susceptibility have been identified, studies are still underpowered to analyse 'common' variants for their subtle effects. A recent application of genome-wide association studies (GWAS) to ASD indicated significant associations with the single nucleotide polymorphisms (SNPs) on chromosome 5p14.1, located in a non-coding region between cadherin10 (CDH10) and cadherin9 (CDH9). Here we apply an in vivo bacterial artificial chromosome (BAC) based enhancer-trapping strategy in mice to scan the gene desert for spatiotemporal cis-regulatory activities. Our results show that the ASD-associated interval harbors the cortical area, striatum, and cerebellum specific enhancers for a long non-coding RNA, moesin pseudogene1 antisense (MSNP1AS) during the brain developing stages. Mouse moesin protein levels are not affected by exogenously expressed human antisense RNAs in our transgenic brains, demonstrating the difficulty in modeling rather smaller effects of common variants. Our first in vivo evidence for the spatiotemporal transcription of MSNP1AS however provides a further support to connect this intergenic variant with the ASD susceptibility.
| S-EPMC4977510 | biostudies-literature
Project description:How do epigenetic modifications change across species and how do these modifications affect evolution? These are fundamental questions at the forefront of our evolutionary epigenomic understanding. Our previous work investigated human and chimpanzee brain methylomes, but it was limited by the lack of outgroup data which is critical for comparative (epi)genomic studies. Here, we compared whole genome DNA methylation maps from brains of humans, chimpanzees and also rhesus macaques (outgroup) to elucidate DNA methylation changes during human brain evolution. Moreover, we validated that our approach is highly robust by further examining 38 human-specific DMRs using targeted deep genomic and bisulfite sequencing in an independent panel of 37 individuals from five primate species. Our unbiased genome-scan identified human brain differentially methylated regions (DMRs), irrespective of their associations with annotated genes. Remarkably, over half of the newly identified DMRs locate in intergenic regions or gene bodies. Nevertheless, their regulatory potential is on par with those of promoter DMRs. An intriguing observation is that DMRs are enriched in active chromatin loops, suggesting human-specific evolutionary remodeling at a higher-order chromatin structure. These findings indicate that there is substantial reprogramming of epigenomic landscapes during human brain evolution involving noncoding regions.
| S-EPMC5062329 | biostudies-literature