Transcriptome profiling of UPF3B/NMD-deficient lymphoblastoid cells from patients with various forms of intellectual disability

Abstract

The nonsense-mediated mRNA decay (NMD) pathway was originally discovered by virtue of its ability to rapidly degrade aberrant mRNAs with premature termination codons. More recently, it was shown that NMD also directly regulates subsets of normal transcripts, suggesting that NMD has roles in normal biological processes. Indeed, several NMD factors have been shown to regulate neurological events (for example, neurogenesis and synaptic plasticity) in numerous vertebrate species. In man, mutations in the NMD factor gene UPF3B, which disrupts a branch of the NMD pathway, cause various forms of intellectual disability (ID). Using Epstein Barr virus—immortalized B cells, also known as lymphoblastoid cell lines (LCLs), from ID patients that have loss-of-function mutations in UPF3B, we investigated the genome-wide consequences of compromised NMD and the role of NMD in neuronal development and function. We found that ~5% of the human transcriptome is impacted in UPF3B patients. The UPF3B paralog, UPF3A, is stabilized in all UPF3B patients, and partially compensates for the loss of UPF3B function. Interestingly, UPF3A protein, but not mRNA, was stabilised in a quantitative manner that inversely correlated with the severity of patients’ phenotype. This suggested that the ability to stabilize the UPF3A protein is a crucial modifier of the neurological symptoms due to loss of UPF3B. We also identified ARHGAP24, which encodes a GTPase-activating protein, as a canonical target of NMD, and we provide evidence that deregulation of this gene inhibits axon and dendrite outgrowth and branching. Our results demonstrate that the UPF3B-dependent NMD pathway is a major regulator of the transcriptome and that its targets have important roles in neuronal cells.

Application of custom-designed oligonucleotide array CGH in 145 patients with autistic spectrum disorders

“…In patient 2 with autism, speech delay, and abnormal EEG, we have identified a de novo B1.0-Mb deletion in 4q21.23q21.3, harboring only one gene ARHGAP24 that encodes a Rho-GTPase-activating protein, regulating neuronal growth. Nguyen et al 20 showed that deregulation of ARHGAP24 inhibits axon and dendrite outgrowth and branching. A number of overlapping larger-sized deletions, ranging in size between 4.4 and 17.9 Mb have been found in patients with ASDs and DD 9 (case 5; Decipher patients 753, 994, (Table 2).…”

Dendritic spine actin cytoskeleton in autism spectrum disorder

“…ARHGAP24 regulates neuronal morphology. Notably, overexpression of ARHGAP24 in murine hippocampal neurons leading to decreased axon outgrowth, together with a reduction in the number of dendritic termini 293 . This suggests that ARHGAP24 could play a role in the development of dendritic spines but this has not yet been demonstrated.…”

“…ARHGAP24 is a binding partner of filamin A, an F-actin crosslinking protein 292 . ARHGAP24 is a canonical target of the nonsense-mediated mRNA decay (NMD) factor UPF3B that regulates the degradation of mutated transcripts, and mutations in the genes coding for UPF3B have been linked to intellectual disability 293 . ARHGAP24 regulates neuronal morphology.…”

Nonsense-mediated mRNA decay in humans at a glance

“…In humans, two UPF3 paralogs, UPF3 and UPF3X (also called UPF3A and UPF3B, respectively), differently modulate NMD activity (Chan et al, 2009;Kunz et al, 2006;Lykke-Andersen et al, 2000;Serin et al, 2001) in ways that, like UPF1 and another NMD factor, UPF2, have been shown to be crucial for, for example, normal neuronal maturation and development (Colak et al, 2013;Jolly et al, 2013;Laumonnier et al, 2010;Lou et al, 2014;Nguyen et al, 2012Nguyen et al, , 2013Tarpey et al, 2007). UPF3 or UPF3X are generally associated with exon junction complexes (EJCs; see below) that are deposited in the nucleus upstream of newly spliced exon-exon junctions, whereas UPF2 is generally associated with EJCs after newly synthesized mRNAs are exported to the cytoplasm (Kim et al, 2001;Lejeune et al, 2002;Lykke-Andersen et al, 2001).…”