Loss-of-function mutations of the X-chromosome gene UPF3B cause male neurodevelopmental disorders (NDDs) via largely unknown mechanisms. We investigated initially by interrogating a novel synonymous UPF3B variant in a male with absent speech. In silico and functional studies using cell lines derived from this individual show altered UPF3B RNA splicing. The resulting mRNA species encodes a frame-shifted protein with a premature termination codon (PTC) predicted to elicit degradation via nonsense-mediated mRNA decay (NMD). UPF3B mRNA was reduced in the cell line, and no UPF3B protein was produced, confirming a loss-of-function allele. UPF3B is itself involved in the NMD mechanism which degrades both PTC-bearing mutant transcripts and also many physiological transcripts. RNAseq analysis showed that ~1.6% of mRNAs exhibited altered expression. These mRNA changes overlapped and correlated with those we identified in additional cell lines obtained from individuals harbouring other UPF3B mutations, permitting us to interrogate pathogenic mechanisms of UPF3B-associated NDDs. We identified 102 genes consistently deregulated across all UPF3B mutant cell lines. Of the 51 upregulated genes, 75% contained an NMD-targeting feature, thus identifying high-confidence direct NMD targets. Intriguingly, 22 of the dysregulated genes encoded known NDD genes, suggesting UPF3B-dependent NMD regulates gene networks critical for cognition and behaviour. Indeed, we show that 78.5% of all NDD genes encode a transcript predicted to be targeted by NMD. These data describe the first synonymous UPF3B mutation in a patient with prominent speech and language disabilities and identify plausible mechanisms of pathology downstream of UPF3B mutations involving the deregulation of NDD-gene networks.

中文翻译：

---

导致言语障碍的同义 UPF3B 变体表明 NMD 是神经发育障碍基因网络的调节因子。


X 染色体基因UPF3B的功能丧失突变通过很大程度上未知的机制导致男性神经发育障碍 (NDD)。我们最初通过询问一名失语男性的新型同义UPF3B变体进行研究。使用源自该个体的细胞系进行的计算机模拟和功能研究显示UPF3B RNA 剪接发生了改变。由此产生的 mRNA 种类编码带有提前终止密码子 (PTC) 的移码蛋白，预计会通过无义介导的 mRNA 衰减 (NMD) 引发降解。细胞系中UPF3B mRNA 减少，并且不产生 UPF3B 蛋白，证实了功能丧失的等位基因。 UPF3B本身参与 NMD 机制，该机制会降解带有 PTC 的突变转录本和许多生理转录本。 RNAseq 分析显示约 1.6% 的 mRNA 表现出表达改变。这些 mRNA 变化与我们在从携带其他UPF3B突变的个体获得的其他细胞系中发现的变化重叠并相关，使我们能够探究UPF3B相关 NDD 的致病机制。我们在所有UPF3B突变细胞系中发现了 102 个基因持续失调。在 51 个上调基因中，75% 包含 NMD 靶向特征，从而识别出高置信度的直接 NMD 靶标。有趣的是，其中 22 个失调基因编码已知的 NDD 基因，这表明 UPF3B 依赖性 NMD 调节对认知和行为至关重要的基因网络。事实上，我们发现所有 NDD 基因中 78.5% 编码的转录本预计会被 NMD 靶向。 这些数据描述了患有明显言语和语言障碍的患者的第一个同义UPF3B突变，并确定了 UPF3B 突变下游涉及 NDD 基因网络失调的可能病理机制。