Homologous Pairing of Chromosome 15q11-q13 Is Associated with Significant Disruption of Gene Expression in Human Maternal Chromosome 15 Microcell Transfered Neurons

Background: Autism is a common neurodevelopmental disorder characterized by abnormalities in social, communicative, and behavioral functioning. Although the etiology of autism remains largely unknown, cytogenetic and genetic studies have suggested that autism may be influenced by genomic imprinting of 15q11-q13, through maternal copy number gains of 15q11-q13 occurring in 1-3% of autism cases. In this study, we focused on the homologous pairing of 15q11-q13 in human neuronal cells.  Homologous pairing of 15q11-q13 was previously observed to be deficient in Rett Syndrome (RTT), Angelmann Syndrome (AS), and autism brain (Thatcher et al, 2005), and altered in maternal 15 q duplication (idic15) brain (Hogart et al, 2009).

Objectives: Our aim is to understand how the homologous pairing of 15q11-q13 is organized in the mammalian brain and associated with gene expression within the paired regions. Therefore, we investigated the impact of an extra human chromosome 15 on normal maternal to paternal 15q11-q13 interactions in a cell culture model.

Methods: Towards the dissection of the molecular basis of the imprinted gene cluster, we have previously established monochromosomal hybrids containing individual human chromosomes of defined parental origin. Human chromosomes in the monochromosomal hybrids were tagged with pSV2bsr, which confers blasticidin S (BS) resistance, so that the marked chromosomes could be successfully transferred into mammalian cells. In this study, to model 15q11-q13 maternal duplication in a neuronal cell line, a paternal or maternal copy of human chromosome 15 was transferred into the human SH-SY5Y neuronal cells by microcell fusion. Then, FISH analysis was performed using probes to SNRPN and GABRB3 to compare how the homologous alleles of 15q11-q13 are organized in human neuronal cells with a paternal or maternal copy of human chromosome 15.

Results: SH-SY5Y cells show an increase in the percentage of 15q11–q13 paired alleles following induced differentiation with 16 nM PMA. In contrast, homologous pairing of 15q11-q13 was disrupted in human neuronal cells with an extra maternal copy of human chromosome 15. Moreover, gene expression analysis of 15q11-q13 transcripts demonstrated significantly decreased expression of SNRPN, GABRB3, CHRNA7 transcripts despite increased maternal dosage.

Conclusions: We observed that homologous pairing of 15q11-q13 was deficient in human neuronal cells with extra copy of human chromosome 15. Interestingly, extra copies of genes are predicted to lead to increased expression, however our study revealed that gene expression can be altered in unexpected ways through epigenetic changes resulting from increased maternal 15q11-13 dosage, similar to what has been previously observed in a human brain sample with maternal 15q duplication and disrupted homologous pairing. Molecular investigation of gene expression in our autism model cells with an extra copy of 15q11-q13 provides insight into the potential complexities of other copy number variations in autism.