Abstract
BackgroundThe inability to analyze gene expression in living neurons from Angelman (AS) and Duplication 15q (Dup15q) syndrome subjects has limited our understanding of these disorders at the molecular level.MethodHere, we use dental pulp stem cells (DPSC) from AS deletion, 15q Duplication, and neurotypical control subjects for whole transcriptome analysis. We identified 20 genes unique to AS neurons, 120 genes unique to 15q duplication, and 3 shared transcripts that were differentially expressed in DPSC neurons vs controls.ResultsCopy number correlated with gene expression for most genes across the 15q11.2-q13.1 critical region. Two thirds of the genes differentially expressed in 15q duplication neurons were downregulated compared to controls including several transcription factors, while in AS differential expression was restricted primarily to the 15q region. Here, we show significant downregulation of the transcription factors FOXO1 and HAND2 in neurons from 15q duplication, but not AS deletion subjects suggesting that disruptions in transcriptional regulation may be a driving factor in the autism phenotype in Dup15q syndrome. Downstream analysis revealed downregulation of the ASD associated genes EHPB2 and RORA, both genes with FOXO1 binding sites. Genes upregulated in either Dup15q cortex or idiopathic ASD cortex both overlapped significantly with the most upregulated genes in Dup15q DPSC-derived neurons.ConclusionsFinding a significant increase in both HERC2 and UBE3A in Dup15q neurons and significant decrease in these two genes in AS deletion neurons may explain differences between AS deletion class and UBE3A specific classes of AS mutation where HERC2 is expressed at normal levels. Also, we identified an enrichment for FOXO1-regulated transcripts in Dup15q neurons including ASD-associated genes EHPB2 and RORA indicating a possible connection between this syndromic form of ASD and idiopathic cases.
Highlights
The inability to analyze gene expression in living neurons from Angelman (AS) and Duplication 15q (Dup15q) syndrome subjects has limited our understanding of these disorders at the molecular level
We performed fluorescent in situ hybridization (FISH) analysis on dental pulp stem cells (DPSC) cell lines from all subjects whose samples were used for mRNA-seq analysis in order to determine if the AS deletion samples included the BP1-BP2 region and to determine if the 15q duplication samples were duplicated for the BP4-BP5 region
Gene set enrichment analysis (GSEA) of differentially regulated genes we looked for Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and TRANScription FACtor Database (TRANSFAC) enhanced subsets of differentially regulated genes using a rank ordered gene lists for each binomial comparison for each comparison
Summary
The inability to analyze gene expression in living neurons from Angelman (AS) and Duplication 15q (Dup15q) syndrome subjects has limited our understanding of these disorders at the molecular level. The study of neurogenetic syndromes in the laboratory setting is inherently complicated by a lack of easy access to living neurons for gene expression and electrophysiological studies. That these immature neuronal cultures are an excellent resource for gene expression studies in the disease state, especially for neurodevelopmental disorders where the phenotypes appear at or near birth. We recently showed that DPSC maintain an epigenetic landscape more similar to embryonic stem cells than iPSC making them ideal for gene expression studies [6]. The collection of DPSC from individuals with these syndromes is quite easy and non-invasive. Sample collection can even take place through shipments of exfoliated teeth by parents from remote locations where the subjects reside
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