Functional loss of TDP-43, an RNA-binding protein genetically and pathologically linked to amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), leads to inclusion of cryptic exons in hundreds of transcripts during disease. Cryptic exons can promote degradation of affected transcripts, deleteriously altering cellular function through loss-of-function mechanisms. Here, we show that mRNA transcripts harboring cryptic exons generated de novo proteins in TDP-43-depleted human iPSC-derived neurons in vitro, and de novo peptides were found in cerebrospinal fluid (CSF) samples from patients with ALS or FTD. Using coordinated transcriptomic and proteomic studies of TDP-43-depleted human iPSC-derived neurons, we identified 65 peptides that mapped to 12 cryptic exons. Cryptic exons identified in TDP-43-depleted human iPSC-derived neurons were predictive of cryptic exons expressed in postmortem brain tissue from patients with TDP-43 proteinopathy. These cryptic exons produced transcript variants that generated de novo proteins. We discovered that inclusion of cryptic peptide sequences in proteins altered their interactions with other proteins, thereby likely altering their function. Finally, we showed that 18 de novo peptides across 13 genes were present in CSF samples from patients with ALS/FTD spectrum disorders. The demonstration of cryptic exon translation suggests new mechanisms for ALS/FTD pathophysiology downstream of TDP-43 dysfunction and may provide a potential strategy to assay TDP-43 function in patient CSF.

中文翻译：

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错误剪接的转录本在 TDP-43 相关的 ALS/FTD 中从头生成蛋白质

TDP-43 是一种 RNA 结合蛋白，在遗传和病理学上与肌萎缩侧索硬化症 (ALS) 和额颞叶痴呆 (FTD) 有关，其功能丧失导致疾病期间数百个转录本中包含隐秘的外显子。隐性外显子可以促进受影响转录物的降解，通过功能丧失机制有害地改变细胞功能。在这里，我们表明，含有隐秘外显子的 mRNA 转录物在体外 TDP-43 耗尽的人 iPSC 衍生神经元中从头生成蛋白质，并且在 ALS 或 FTD 患者的脑脊液 (CSF) 样本中发现了从头肽。通过对 TDP-43 耗尽的人类 iPSC 衍生神经元进行协调的转录组学和蛋白质组学研究，我们鉴定了 65 个映射到 12 个神秘外显子的肽。在 TDP-43 耗尽的人 iPSC 衍生神经元中鉴定出的隐秘外显子可以预测 TDP-43 蛋白病患者死后脑组织中表达的隐秘外显子。这些神秘的外显子产生转录变体，从而产生从头蛋白质。我们发现，蛋白质中包含神秘肽序列会改变它们与其他蛋白质的相互作用，从而可能改变它们的功能。最后，我们发现 ALS/FTD 谱系疾病患者的 CSF 样本中存在跨 13 个基因的 18 个从头肽。神秘外显子翻译的证明提示了 TDP-43 功能障碍下游 ALS/FTD 病理生理学的新机制，并可能提供检测患者 CSF 中 TDP-43 功能的潜在策略。