Drosophila model to clarify the pathological significance of OPA1 in autosomal dominant optic atrophy

Reviewer #1 (Public Review):

Nitta et al, in their manuscript titled, "Drosophila model to clarify the pathological significance of OPA1 in autosomal dominant optic atrophy." The novelty of this paper lies in its use of human (hOPA1) to try to rescue the phenotype of an OPA1 +/- Drosophilia DOA model (dOPA). The authors then use this model to investigate the differences between dominant-negative and haploinsufficient OPA1 variants. The value of this paper lies in the study of DN/HI variants rather than the establishment of the drosophila model per se as this has existed for some time and does have some significant disadvantages compared to existing models, particularly in the extra-ocular phenotype which is common with some OPA1 variants but not in humans. I judge the findings of this paper to be valuable with regards to significance and solid with regards to the strength of the evidence.

Suggestions for improvements:

1. Stylistically the results section appears to have significant discussion/conclusion/inferences in each section with reference to existing literature. I feel that this information would be better placed in the separate discussion section. E.g. lines 149-154

2. I do think further investigation as to why a reduction of mitochondria was noticed in the knockdown. There are conflicting reports on this in the literature. My own experience of this is fairly uniform mitochondrial number in WT vs OPA1 variant lines but with an increased level of mitophagy presumably reflecting a greater turnover. There are a number of ways to quantify mitochondrial load e.g. mtDNA quantification, protein quantification for tom20/hsp60 or equivalent. I feel the reliance on ICC here is not enough to draw conclusions. Furthermore, mitophagy markers could be checked at the same time either at the transcript or protein level. I feel this is important as it helps validate the drosophila model as we already have a lot of experimental data about the number and function of mitochondria in OPA+/- human/mammalian cells.

3. Could the authors comment on the failure of the dOPA1 rescue to return their biomarker, axonal number to control levels. In Figure 4D is there significance between the control and rescue. Presumably so as there is between the mutant and rescue and the difference looks less.

4. The authors have chosen an interesting if complicated missense variant to study, namely the I382M with several studies showing this is insufficient to cause disease in isolation and appears in high frequency on gnomAD but appears to worsen the phenotype when it appears as a compound het. I think this is worth discussing in the context of the results, particularly with regard to the ability for this variant to partially rescue the dOPA1 model as shown in Figure 5.

5. I feel the main limitation of this paper is the reliance on axonal number as a biomarker for OPA1 function and ultimately rescue. I have concerns because a) this is not a well validated biomarker within the context of OPA1 variants b) we have little understanding of how this is affected by over/under expression and c) if it is a threshold effect e.g. once OPA1 levels reach x%. I think this is particularly relevant when the authors are using this model to make conclusions on dominant negativity/HI with the authors proposing that if expression of a hOPA1 transcript does not increase opa1 expression in a dOPA1 KO then this means that the variant is DN. The authors have used other biomarkers in parts of this manuscript e.g. ROS measurement and mito trafficking but I feel this would benefit from something else particularly in the latter experiments demonstrated in figure 5 and 6.

6. Could the authors clarify what exons in Figure 5 are included in their transcript. My understanding is transcript NM_015560.3 contains exon 4,4b but not 5b. According to Song 2007 this transcript produces invariably s-OPA1 as it contains the exon 4b cleavage site. If this is true, this is a critical limitation in this study and in my opinion significantly undermines the likelihood of the proposed explanation of the findings presented in Figure 6. The primarily functional location of OPA1 is at the IMM and l-OPA1 is the primary opa1 isoform probably only that localizes here as the additional AA act as a IMM anchor. Given this is where GTPase likely oligomerizes the expression of s-OPA1 only is unlikely to interact anyway with native protein. I am not aware of any evidence s-OPA1 is involved in oligomerization. Therefore I don't think this method and specifically expression of a hOPA1 transcript which only makes s-OPA1 to be a reliable indicator of dominant negativity/interference with WT protein function. This could be checked by blotting UAS-hOPA1 protein with a OPA1 antibody specific to human OPA1 only and not to dOPA1. There are several available on the market and if the authors see only s-OPA1 then it confirms they are not expressing l-OPA1 with their hOPA1 construct.

Reviewer #2 (Public Review):

The data presented support and extend some previously published data using Drosophila as a model to unravel the cellular and genetic basis of human Autosomal dominant optic atrophy (DOA). In human, mutations in OPA1, a mitochondrial dynamin like GTPase (amongst others), are the most common cause for DOA. By using a Drosophila loss-of-function mutations, RNAi-mediated knockdown and overexpression, the authors could recapitulate some aspects of the disease phenotype, which could be rescued by the wild-type version of the human gene. Their assays allowed them to distinguish between mutations causing human DOA, affecting the optic system and supposed to be loss-of-function mutations, and those mutations supposed to act as dominant negative, resulting in DOA plus, in which other tissues/organs are affected as well.

Based on the lack of information in the Materials and Methods section and in several figure legends, it was not in all cases possible to follow the conclusions of the authors. Similarly, how the knowledge gained could help to "inform early treatment decisions in patients with mutations in hOPA1" (Line 38) cannot be followed.

Reviewer #3 (Public Review):

Nitta et al. establish a fly model of autosomal dominant optic atrophy, of which hundreds of different OPA1 mutations are the cause with wide phenotypic variance. It has long been hypothesized that missense OPA1 mutations affecting the GTPase domain, which are associated with more severe optic atrophy and extra-ophthalmic neurologic conditions such as sensorineural hearing loss (DOA plus), impart their effects through a dominant negative mechanism, but no clear direct evidence for this exists particularly in an animal model. The authors execute a well-designed study to establish their model, demonstrating a clear mitochondrial phenotype with multiple clinical analogs including optic atrophy measured as axonal degeneration. They then show that hOPA1 mitigates optic atrophy with the same efficacy as dOPA1, setting up the utility of their model to test disease-causing hOPA1 variants. Finally, they leverage this model to provide the first direct evidence for a dominant negative mechanism for 2 mutations causing DOA plus by expressing these variants in the background of a full hOPA1 complement.

Strengths of the paper include well-motivated objectives and hypotheses, overall solid design and execution, and a generally clear and thorough interpretation of their results. The results technically support their primary conclusions with caveats. The first is that both dOPA1 and hOPA1 fail to fully restore optic axonal integrity, yet the authors fail to acknowledge that this only constitutes a partial rescue nor do they discuss how this fact might influence our interpretation of their subsequent results. The second caveat is that their effect sizes are small. Statistically, the results indeed support a dominant negative effect of DOA plus-associated variants, yet the data show a marginal impact on axonal degeneration for these variants. The authors might have considered exploring the impact of these variants on other mitochondrial outcome measures they established earlier on. They might also consider providing some functional context for this marginal difference in axonal optic nerve degeneration.

Despite these caveats, the authors provide the first animal model of DOA that also allows for rapid assessment and mechanistic testing of suspected OPA1 variants. The impact of this work in providing the first direct evidence of a dominant negative mechanism is under-stated considering how important this question is in development of genetic treatments for DOA. The authors discuss important points regarding the potential utility of this model in clinical science. Comments on the potential use of this model to investigate variants of unknown significance in clinical diagnosis requires further discussion of whether there is indeed precedent for this in other genetic conditions (since the model is nevertheless so evolutionarily removed from humans).