Mis-spliced transcripts generate de novo proteins in TDP-43-related ALS/FTD.
Mis-spliced transcripts generate de novo proteins in TDP-43-related ALS/FTD.
复制标题
错误剪接的转录本在 TDP-43 相关的 ALS/FTD 中从头生成蛋白质。
DOI：
10.1101/2023.01.23.525149
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发表时间：
2023
期刊：
影响因子：
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通讯作者：
Roberts
中科院分区：
文献类型：
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作者：
Seddighi,Sahba;Qi,YueA;Brown,Anna-Leigh;Wilkins,OscarG;Bereda,Colleen;Belair,Cedric;Zhang,Yongjie;Prudencio,Mercedes;Keuss,MatthewJ;Khandeshi,Aditya;Pickles,Sarah;Hill,SarahE;Hawrot,James;Ramos,DanielM;Yuan,Hebao;Roberts
TDP-43是一种RNA结合蛋白，在基因和病理上与肌萎缩侧索硬化症(ALS)和额颞部痴呆(FTD)有关，它的功能丧失导致在疾病过程中数百个转录本中包含隐蔽的外显子。隐蔽外显子可以促进受影响转录本的降解，通过功能丧失机制有害地改变细胞功能。在这里，我们展示了含有隐藏外显子的mRNA转录本在体外TDP-43缺失的人iPSC来源的神经元中产生从头蛋白，并且在ALS或FTD患者的脑脊液(CSF)样本中发现了从头蛋白。通过对TDP-43缺失的人IPSC来源神经元的协同转录和蛋白质组学研究，我们鉴定了65个多肽，它们映射到12个隐含外显子。在TDP-43缺失的人iPSC来源的神经元中发现的隐蔽外显子可以预测TDP-43蛋白病患者死后脑组织中表达的隐蔽外显子。这些神秘的外显子产生转录本变体，从而产生从头蛋白。我们发现，蛋白质中包含的隐藏肽序列改变了它们与其他蛋白质的相互作用，从而可能改变了它们的功能。最后，我们发现在ALS/FTD谱系疾病患者的脑脊液样本中存在13个基因的18个从头肽。隐匿外显子翻译的证明为TDP-43功能障碍下游的ALS/FTD病理生理学提供了新的机制，并可能提供一种潜在的策略来检测患者脑脊液中TDP-43的功能。
Functional loss of TDP-43, an RNA binding protein genetically and pathologically linked to amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), leads to the inclusion of cryptic exons in hundreds of transcripts during disease. Cryptic exons can promote the 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 found that the inclusion of cryptic peptide sequences in proteins altered their interactions with other proteins, thereby likely altering their function. Last, 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.