Talk:Granata 2022 Abstract Bioblast

Comment by the Reviewers and Author

Donnelly Chris 2022-05-30

• A reservation about the abstract in this format would be that the third paragraph is rather dense with information. It could benefit from breaking up/condensing some of this to align with the main point. In particular the first sentence of this paragraph is four lines long and mentions that increases in mitochondrial content drive increases in mitochondrial content. I'm not sure this makes sense, but I may be wrong.

AUTHOR’S RESPONSE (2022-06-04): I would like to thank the Reviewer for providing feedback and improving the abstract. I have now corrected the discrepancy pointed out by the Reviewer, thank you. I have also reduced the length of the first sentence of the 3rd paragraph, as requested, and I removed one sentence from the same paragraph, as suggested, given that the brief time allowed for the presentation will likely not allow me to include these slides.

Moreno-Sanchez Rafael 2022-06-01

• This study analyzes the exercise-induced mitochondrial adaptations in human skeletal muscle by applying a multi-omics experimental approach. The results concisely summarized seem interesting and deserve to be published. However, a couple of issues appear to require clarification. One is the apparent non-linear or non-proportional relationship found between the OXPHOS enzyme contents and the respective mRNA levels. This is not surprising, and it has been documented (doi: 10,1111/febs.13535). If this is what it was observed, then it should be clearly stated in the abstract. Other relationships might be established, and described in the abstract, such as that between enzyme content and activity, or enzyme activity and pathway flux.

• The second minor issue is regarding the approach used. It is mentioned that a multi-omics approach was used, together with “classical biological techniques”, in which metabolic pathway fluxes (fluxomics) and enzyme activities (kinetomics) were assessed. These last two experimental approaches may also be classified as omics approaches.

AUTHOR’S RESPONSE (2022-06-04): I would like to thank the Reviewer for providing feedback and improving the abstract. Specifically to the two issues raised, the first one may have been a misunderstanding as in the abstract I do not mention the presence of a non-proportional relationship between OXPHOS enzymes content and their respective mRNA levels, as stated by the Reviewer. Neither in the abstract nor in the published paper, had we investigated linearity/proportionality between transcript and proteomic changes post-training for the OXPHOS subunits, nor for any other protein functional class. As to the second point, the Reviewer raises a valid point; however, given the limited number of enzyme activities (5 enzymes in total) and metabolic pathway fluxes (a single protocol with 6 reads) investigated, it feels safer to refer to it as “classic biological techniques” rather than kinetomics and fluxomics, respectively. Moreover, the definition “classic biological techniques” was also used to encompass, SDS-PAGE and BN-PAGE analysis, and was intended as a broad term to separate it from the 3 omics techniques used.

Version 1

Mitochondrial health is implicated in multiple diseases and ageing, and is therefore an important determinant of an individual’s quality of life [1]. Exercise training is an accessible and inexpensive therapeutic intervention that is extensively used to prevent, treat, and manage several lifestyle diseases [2], by enhancing mitochondrial biogenesis and improving mitochondrial bioenergetics. However, the intricacy of exercise training-induced mitochondrial adaptations remains, for the most part, unknown.

By utilizing a multi-omics approach integrated with classic biological mitochondrial techniques we performed an in-depth investigation of the effects of three different and sequential volumes of high-intensity interval training on the mitochondrial transcriptome, proteome, and lipidome in human skeletal muscle (N=10) [3].

We first confirmed that changes in mitochondrial respiration, content, and enzymatic activity, as well as supercomplex formation and the content of selected subunits of the OXPHOS system mirrored, for the most part, the changes in training volume, and that these changes were driven by the overall increase in mitochondrial content, as previously demonstrated [4]. Subsequently, by combining the power of 3 omics techniques with biochemical and in silico normalization, we removed the bias arising from the training-induced increase in mitochondrial content to unearth an intricate and previously undemonstrated network of differentially prioritized mitochondrial adaptations. We show that changes in hundreds of transcripts, proteins, and lipids are not stoichiometrically linked to the overall increase in mitochondrial content. Our findings indicate that enhancing electron flow to the OXPHOS system is more important to improve ATP generation than increasing the contents of the OXPHOS machinery, and do not support the hypothesis that training-induced supercomplex reorganization enhances mitochondrial bioenergetics [3].

Our study provides an analytical approach allowing unbiased and in-depth investigation of training-induced mitochondrial adaptations that challenges our current understanding and calls for careful reinterpretation of previous findings.