Increased copy number for methylated maternal 15q duplications leads to changes in gene and protein expression in human cortical samples

Abstract

BackgroundDuplication of chromosome 15q11-q13 (dup15q) accounts for approximately 3% of autism cases. Chromosome 15q11-q13 contains imprinted genes necessary for normal mammalian neurodevelopment controlled by a differentially methylated imprinting center (imprinting center of the Prader-Willi locus, PWS-IC). Maternal dup15q occurs as both interstitial duplications and isodicentric chromosome 15. Overexpression of the maternally expressed gene UBE3A is predicted to be the primary cause of the autistic features associated with dup15q. Previous analysis of two postmortem dup15q frontal cortical samples showed heterogeneity between the two cases, with one showing levels of the GABAA receptor genes, UBE3A and SNRPN in a manner not predicted by copy number or parental imprint.MethodsPostmortem human brain tissue (Brodmann area 19, extrastriate visual cortex) was obtained from 8 dup15q, 10 idiopathic autism and 21 typical control tissue samples. Quantitative PCR was used to confirm duplication status. Quantitative RT-PCR and Western blot analyses were performed to measure 15q11-q13 transcript and protein levels, respectively. Methylation-sensitive high-resolution melting-curve analysis was performed on brain genomic DNA to identify the maternal:paternal ratio of methylation at PWS-IC.ResultsDup15q brain samples showed a higher level of PWS-IC methylation than control or autism samples, indicating that dup15q was maternal in origin. UBE3A transcript and protein levels were significantly higher than control and autism in dup15q, as expected, although levels were variable and lower than expected based on copy number in some samples. In contrast, this increase in copy number did not result in consistently increased GABRB3 transcript or protein levels for dup15q samples. Furthermore, SNRPN was expected to be unchanged in expression in dup15q because it is expressed from the single unmethylated paternal allele, yet SNRPN levels were significantly reduced in dup15q samples compared to controls. PWS-IC methylation positively correlated with UBE3A and GABRB3 levels but negatively correlated with SNRPN levels. Idiopathic autism samples exhibited significantly lower GABRB3 and significantly more variable SNRPN levels compared to controls.ConclusionsAlthough these results show that increased UBE3A/UBE3A is a consistent feature of dup15q syndrome, they also suggest that gene expression within 15q11-q13 is not based entirely on copy number but can be influenced by epigenetic mechanisms in brain.

15q11.2 Proximal Imbalances Associated With a Diverse Array of Neuropsychiatric Disorders and Mild Dysmorphic Features

“…4 It is not difficult to predict that individuals with Prader-Willi syndrome (PWS) and Angelman syndrome (AS) who carry BP1-BP3 deletion are more severely affected than those who carry BP2-BP3 deletion due to haploinsufflciency of the genes within BP1-BP2 region. [5][6][7] However, if BP1-BP2 duplication has pathogenic influence, theoretically it is reasonable to propose the following hypotheses regarding copy number gains involving the proximal region of 15q, such as 15q11.2-q13 interstitial duplications and triplications and supernumerary marker chromosomes 15 [SMC (15)] with variable sizes of the proximal region of 15q: (1) individuals with copy number gains of the BP1-BP3 region derived from either parent of origin should present clinical features due to overdosage of the genes within BP1-BP2 region; (2) individuals with copy number gains of the BP1-BP3 derived from maternal origin should present more severe clinical features than those who carry copy number gains of BP2-BP3 region, as the pathogenic influences should result from both overdosage of the genes within BP1-BP2 region and overexpression of the maternally expressed gene UBE3A [31][32][33] ; and (3) if a SMC(15) contains euchromatic materials derived from BP1-BP2 region only, the individuals carrying the SMC (15) should present variable severities of clinical features depending on the copy numbers of this region, the level of mosaicism, and their distributions. Obviously, further elucidation of the functions of the genes within the BP1-BP2 region will not only reveal the pathogenic effects of the BP1-BP2 deletion or duplication to neurodevelopment but also improve genotype-phenotype correlations for individuals with PWS, AS, and copy number gains of 15q11.2-q13 region.…”

Autism and cerebellar dysfunction: Evidence from animal models

“…GABA receptorb3 (GABARB3) is a putative ASD susceptibility gene [51] whereas 15q duplication (which includes GABARB3) is associated with elevated rates of ASD [52]. Moreover, postmortem samples from ASD patient brains display reductions in GABARB3 levels [3].…”

Autistic disorder phenotype associated to a complex 15q intrachromosomal rearrangement

“…Maternally inherited deletion of this gene causes Angelman syndrome. Overexpression of the maternally expressed gene UBE3A is predicted to be the primary cause of the autistic features associated with dup15q [Scoles et al, 2011].…”