MeDUsA: A novel system for automated axon quantification to evaluate neuroaxonal degeneration

Abstract

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.

A Quantitative Model of Sporadic Axonal Degeneration in the Drosophila Visual System

“…6 D” ), suggesting that apoptotic cell death had not started at a time point at which axonal degeneration was at full pace ( Fig. 3 H , H' , J , K ; Nitta et al, 2021 ). Nuclear morphology was similar between controls and light-exposed flies ( Fig.…”

“…We then used the surface function to recreate a compact 3D mask of R7 termini based on the manually drawn regions. In an accompanying study, we developed a software enabling automated mask creation, which was partially used in this study and is described in detail in Nitta et al (2021) . After mask creation, we isolated the signal of the mask using the mask channel function.…”