MeDUsA: A novel system for automated axon quantification to evaluate neuroaxonal degeneration
MeDUsA: A novel system for automated axon quantification to evaluate neuroaxonal degeneration
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DOI：
10.1101/2021.10.25.465674
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发表时间：
2021-10
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通讯作者：
Yohei Nitta;H. Kawai;Jiro Osaka;Satoko Hakeda-Suzuki;Y. Nagai;K. Doubková;Takashi Suzuki;G. Tavosanis;Atsushi Sugie
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作者：
Yohei Nitta;H. Kawai;Jiro Osaka;Satoko Hakeda-Suzuki;Y. Nagai;K. Doubková;Takashi Suzuki;G. Tavosanis;Atsushi Sugie
背景果蝇是研究人类神经退行性疾病（NDs）的理想模式生物，粗糙眼表型（REP）试验是分析异位表达人类疾病基因毒性的一种简便的实验系统。然而，REP和轴突变性（ND的早期体征）之间的关联仍不清楚。为了解决这个问题，我们开发了一种方法来评估轴突变性，通过定量视网膜R7轴突在果蝇的数量;然而，它需要专业知识，是耗时的。因此，需要一种易于使用的软件，可以自动量化轴突变性。我们创建了MeDUsA（一种“使用苍蝇轴突量化变性的方法”），这是一个基于Python的独立可执行计算机程序，它将预先训练的深度学习掩蔽工具与轴突终端计数工具相结合。该软件自动量化来自共焦z堆栈图像系列的轴突数量。使用该软件，我们首次直接证明了当ND的致病因子（αSyn，Tau，TDP-43，HTT）在果蝇眼中表达时，轴突退化。此外，我们比较了神经营养不良的代表性致病基因及其病理等位基因与REP的轴突毒性，发现它们之间没有显着的相关性。结论MeDUsA能快速准确地定量果蝇眼内轴突。通过简化和自动化需要大量专业知识的耗时的手动工作，它使轴突变性的大规模，复杂的研究工作成为可能，例如筛选以确定介导ND疾病蛋白引起的轴突毒性的基因或药物。
Background Drosophila is an excellent model organism for studying human neurodegenerative diseases (NDs), and the rough eye phenotype (REP) assay is a convenient experimental system for analysing the toxicity of ectopically expressed human disease genes. However, the association between REP and axonal degeneration, an early sign of ND, remains unclear. To address this question, we developed a method to evaluate axonal degeneration by quantifying the number of retinal R7 axons in Drosophila; however, it requires expertise and is time-consuming. Therefore, there is a need for an easy-to-use software that can automatically quantify the axonal degeneration. Result We created MeDUsA (a ‘method for the quantification of degeneration using fly axons’), which is a standalone executable computer program based on Python that combines a pre-trained deep-learning masking tool with an axon terminal counting tool. This software automatically quantifies the number of axons from a confocal z-stack image series. Using this software, we have demonstrated for the first time directly that axons degenerate when the causative factors of NDs (αSyn, Tau, TDP-43, HTT) were expressed in the Drosophila eye. Furthermore, we compared axonal toxicity of the representative causative genes of NDs and their pathological alleles with REP and found no significant correlation between them. Conclusions MeDUsA rapidly and accurately quantifies axons in Drosophila eye. By simplifying and automating time-consuming manual efforts requiring significant expertise, it enables large-scale, complex research efforts on axonal degeneration, such as screening to identify genes or drugs that mediate axonal toxicity caused by ND disease proteins.