Gene expression analysis of human induced pluripotent stem cell-derived neurons carrying copy number variants of chromosome 15q11-q13.1

Abstract

BackgroundDuplications of the chromosome 15q11-q13.1 region are associated with an estimated 1 to 3% of all autism cases, making this copy number variation (CNV) one of the most frequent chromosome abnormalities associated with autism spectrum disorder (ASD). Several genes located within the 15q11-q13.1 duplication region including ubiquitin protein ligase E3A (UBE3A), the gene disrupted in Angelman syndrome (AS), are involved in neural function and may play important roles in the neurobehavioral phenotypes associated with chromosome 15q11-q13.1 duplication (Dup15q) syndrome.MethodsWe have generated induced pluripotent stem cell (iPSC) lines from five different individuals containing CNVs of 15q11-q13.1. The iPSC lines were differentiated into mature, functional neurons. Gene expression across the 15q11-q13.1 locus was compared among the five iPSC lines and corresponding iPSC-derived neurons using quantitative reverse transcription PCR (qRT-PCR). Genome-wide gene expression was compared between neurons derived from three iPSC lines using mRNA-Seq.ResultsAnalysis of 15q11-q13.1 gene expression in neurons derived from Dup15q iPSCs reveals that gene copy number does not consistently predict expression levels in cells with interstitial duplications of 15q11-q13.1. mRNA-Seq experiments show that there is substantial overlap in the genes differentially expressed between 15q11-q13.1 deletion and duplication neurons, Finally, we demonstrate that UBE3A transcripts can be pharmacologically rescued to normal levels in iPSC-derived neurons with a 15q11-q13.1 duplication.ConclusionsChromatin structure may influence gene expression across the 15q11-q13.1 region in neurons. Genome-wide analyses suggest that common neuronal pathways may be disrupted in both the Angelman and Dup15q syndromes. These data demonstrate that our disease-specific stem cell models provide a new tool to decipher the underlying cellular and genetic disease mechanisms of ASD and may also offer a pathway to novel therapeutic intervention in Dup15q syndrome.

Induced pluripotent stem cells for modeling neurological disorders

“…Another study generated iPSCs from patients with duplications of chromosome 15q11-q13.1 (Dup15q syndrome) and were further differentiated into functional neurons. Gene expression analysis was performed and compared to AS neurons, revealing they shared common neuronal pathways disrupted in both Angelman and Dup15q syndromes [110] .…”

An Autism-Linked Mutation Disables Phosphorylation Control of UBE3A

“…UBE3A is the only gene in this region that is consistently expressed from the maternal, but not paternal, allele in mature neurons (Albrecht et al, 1997; Rougeulle et al, 1997; Vu and Hoffman, 1997), suggesting that abnormally elevated levels of UBE3A contribute to autism in 15q11-13 duplication syndrome. However, UBE3A is not the only gene duplicated in this syndrome, and pathogenicity in individuals with paternal 15q11-13 duplication has been reported, raising the possibility that additional genes in the region might increase autism risk (Germain et al, 2014; Urraca et al, 2013). …”

The Genetic and Epigenetic Basis Involved in the Pathophysiology of ASD: Therapeutic Implications

“…So, at least 8% of sporadic ASD cases carried a de novo CNV and they are clarifying the etiology for many cases of autism previously considered idiopathic [31,32]. The de novo nature of these CNVs, together with their absence in the general population, suggests they represent a class of highly deleterious and highly penetrant mutations.…”

“…mRNA-Seq experiments show that there is substantial overlap of differentially expressed genes between 15q11-q13.1 deletion and duplication neurons. UBE3A transcripts can be pharmacologically rescued to normal levels in induced pluripotent stem cell (iPSC)-derived neurons with 15q11-q13.1 duplication [139].…”