RNA dysfunction in motor neuron disease: identification of novel changes in transcript processing and localisation through long-read RNA-seq

运动神经元疾病中的 RNA 功能障碍：通过长读长 RNA-seq 识别转录本加工和定位的新变化

• 批准号: MC_PC_MR/S022708/1
• 负责人: Pietro Fratta
• 金额: $ 1.93万
• 依托单位: University College London
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2018
• 资助国家: 英国
• 起止时间: 2018 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=MC_PC_MR%2FS022708%2F1
• 关键词: RNA; dysfunction; motor; neuron; disease

Motor neurons (MNs) are the nerve cells that send signals from the spinal cord to our muscles to enable movement to happen. Amyotrophic lateral sclerosis (ALS), also known as motor neuron disease, is a devastating neurodegenerative disorder which causes progressive loss of MNs, leading to loss of muscle function and paralysis. ALS is incurable and leads to death, usually caused by the inability to breathe, on average only 3 years after diagnosis, with a lifetime risk of about 1 in 400. RNAs are essential molecules that carry the information for making individual proteins from DNA. The correct processing of RNAs is crucial for survival and one of the central players in the disease mechanism of ALS, a protein called TDP-43, is important for the processing of RNA.In order to study and understand ALS disease mechanisms, we have recently generated novel mouse models carrying TDP-43 mutations, which induce features of ALS, including the loss of MNs. These mice allow us, by looking over time, at presymptomatic mice and at mice with ALS, to identify what changes with the progression of disease. We have used RNA-sequencing (RNA-seq) to demonstrate that these mutations cause widespread and novel changes in cell RNA. RNAs can be very long molecules, they reach the size of thousands of base pairs, but the current technology to study RNAs, allows us to sequence small fragments of RNA of up to 150 base pairs. Then, powerful bioinformatics algorithms are used to analyse these results, but, although a lot of information and changes can be detected, the architecture of the long RNAs is reconstructed with a certain degree of uncertainty. One of the limitations in understanding how these changes impact on disease is that we cannot reconstruct the exact composition of the whole-RNA architecture.Very recently novel technologies have been made available to directly understand these long RNAs. Co-applicant Towfique Raj is pioneering the use of this technology to mammalian systems and has developed sophisticated tools for analysis.We here propose to apply this novel technology to our ALS mouse models in order to gain a better understanding of how RNA changes impact on disease. In summary, this project will contribute to understand how changes in TDP-43 impacts on MN RNA and survival. The identification of this information is essential to develop effective therapeutics for motor neuron disorders. Furthermore, this project will allow us to start a novel collaboration to apply this cutting-edge technology to numerous ALS mouse and human cell models, transforming our molecular understanding of ALS.

运动神经元（MN）是将信号从脊髓发送到我们的肌肉以使运动发生的神经细胞。肌萎缩侧索硬化症（ALS），也称为运动神经元疾病，是一种破坏性的神经退行性疾病，其引起MN的进行性丧失，导致肌肉功能丧失和瘫痪。ALS是无法治愈的，并导致死亡，通常是由无法呼吸引起的，平均诊断后仅3年，终生风险约为1/400。RNA是携带从DNA制造单个蛋白质的信息的重要分子。RNA的正确加工对生存至关重要，ALS疾病机制中的核心参与者之一，一种称为TDP-43的蛋白质对RNA的加工至关重要。为了研究和理解ALS疾病机制，我们最近产生了携带TDP-43突变的新型小鼠模型，该突变诱导ALS的特征，包括MN的丢失。这些小鼠使我们能够通过观察症状前小鼠和ALS小鼠的时间来确定疾病进展的变化。我们已经使用RNA测序（RNA-seq）来证明这些突变引起细胞RNA中广泛和新颖的变化。RNA可以是非常长的分子，它们达到数千个碱基对的大小，但目前研究RNA的技术，允许我们对多达150个碱基对的RNA小片段进行测序。然后，使用强大的生物信息学算法来分析这些结果，但是，尽管可以检测到大量信息和变化，但长RNA的结构重建具有一定程度的不确定性。理解这些变化如何影响疾病的局限性之一是我们无法重建整个RNA结构的确切组成。最近，新技术已经可以直接理解这些长RNA。共同申请人Towfique Raj率先将该技术应用于哺乳动物系统，并开发了复杂的分析工具。我们在这里建议将这项新技术应用于我们的ALS小鼠模型，以便更好地了解RNA变化如何影响疾病。总之，该项目将有助于了解TDP-43的变化如何影响MN RNA和生存。这些信息的识别对于开发运动神经元疾病的有效治疗方法至关重要。此外，该项目将使我们能够开始一项新的合作，将这项尖端技术应用于许多ALS小鼠和人类细胞模型，改变我们对ALS的分子理解。

项目成果

TDP-43 loss and ALS-risk SNPs drive mis-splicing and depletion of UNC13A.

• DOI: 10.1038/s41586-022-04436-3
• 发表时间: 2022-03
• 期刊: Nature
• 影响因子: 64.8
• 作者: Brown AL;Wilkins OG;Keuss MJ;Hill SE;Zanovello M;Lee WC;Bampton A;Lee FCY;Masino L;Qi YA;Bryce-Smith S;Gatt A;Hallegger M;Fagegaltier D;Phatnani H;NYGC ALS Consortium;Newcombe J;Gustavsson EK;Seddighi S;Reyes JF;Coon SL;Ramos D;Schiavo G;Fisher EMC;Raj T;Secrier M;Lashley T;Ule J;Buratti E;Humphrey J;Ward ME;Fratta P
• 通讯作者: Fratta P

Mis-spliced transcripts generate de novo proteins in TDP-43-related ALS/FTD.

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
• 发表时间: 2023
• 期刊: bioRxiv : the preprint server for biology
• 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
• 通讯作者: Roberts

HnRNP K mislocalisation is a novel protein pathology of frontotemporal lobar degeneration and ageing and leads to cryptic splicing.

• DOI: 10.1007/s00401-021-02340-0
• 发表时间: 2021-10
• 期刊: Acta neuropathologica
• 影响因子: 12.7
• 作者: Bampton A;Gatt A;Humphrey J;Cappelli S;Bhattacharya D;Foti S;Brown AL;Asi Y;Low YH;Foiani M;Raj T;Buratti E;Fratta P;Lashley T
• 通讯作者: Lashley T

Cell environment shapes TDP-43 function with implications in neuronal and muscle disease.

• DOI: 10.1038/s42003-022-03253-8
• 发表时间: 2022-04-05
• 期刊: Communications biology
• 影响因子: 5.9
• 作者: Šušnjar U;Škrabar N;Brown AL;Abbassi Y;Phatnani H;NYGC ALS Consortium;Cortese A;Cereda C;Bugiardini E;Cardani R;Meola G;Ripolone M;Moggio M;Romano M;Secrier M;Fratta P;Buratti E
• 通讯作者: Buratti E

Transcriptomic analysis of frontotemporal lobar degeneration with TDP-43 pathology reveals cellular alterations across multiple brain regions

TDP-43 病理学对额颞叶变性的转录组分析揭示了多个大脑区域的细胞改变

• DOI: 10.1101/2021.10.06.21264635
• 发表时间: 2021
• 作者: Hasan R