Methylene Blue Increases Active Mitochondria and Cellular Survival Through Modulation of miR16–UPR Signaling Axis

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

Garcia-Padilla et al highlighted an interesting role of Methylen Blue (MB) in regulating mitochondrial function in two different in vitro models of cardiomyocytes, also offering a potential mechanism of action. Overall, the manuscript is well-written and designed. However, there are many critical issues to consider. Below you can find some suggestions that might improve your work.

• Materials and Methods:
• This section should be detailed as much as possible to ensure experimental reproducibility. Indeed, many experimental details are missing. For example, experimental conditions are unclear (e.g., treatment time with MB or H₂O₂). Better explain what is meant by “different experimental conditions” in lane 93.
• Statistical analysis should redone more properly. Authors applied only the t-test even where it is not the most appropriate statistical test.
• Supplementary table 1:

Although the primers used with their sequences have been reported, the only species reported is the murine one. Were the same primers used for the human cell line as well?

 

• Results:
• The main problem is related to the cell lines used. Even if argued in the discussion, it is difficult to find a real explanation for the species-specific effects. Rather, there is a real concern in the HL1 cell line. As authors showed in Figure 2E, the HL1 cells seem to be very suffering already at baseline (% apoptosis of about 60%). It could be that the lack of effect on this cell line is related to the cells used. On the contrary, the effects on the AC16 cell line are interesting.
• Authors discuss about the co-treatment with MB and H₂O₂. To be able to assert of a protective effect of MB, perhaps it would be better to carry out a pre-treatment with MB and then a treatment with H₂O₂. Moreover, authors should specify the reason why they test only one concentration and why they did not perform a dose-response. Again, the experimental conditions are not clear.
• Lane 187-189: authors speculated that the “co-treatment with MB and H₂O₂ results in the reversion of miR-16 upregulation observed in H₂O₂ treatment in HL1”. The SD reported in Figure 2A is very high and, again, the t-test is not appropriate.
• Authors should use a different normalization control for qRT-PCR. As reported by Musyaju et al “ The levels of GAPDH in the mitochondria are low at the basal condition, but they are elevated under stressed conditions, such as exposure to DNA-damaging oxidative stress[16,48]. Thus, post-TBI oxidative stress can induce rapid phosphorylation of GAPDH in neuronal mitochondria and increase GAPDH activity. When GAPDH activity spikes, it induces pro-apoptotic mitochondrial membrane permeabilization via an association with VDAC” (org/10.1016/j.ab.2023.115301). Moreover, the protein expression levels of the same markers (SOD1, SOD2, PRDX etc..) may be even more indicative.
• Figure:
• Figure 2:

Lane 215: add that the observed results are from qPCR.

Lane 218-219: Panel E and F are inverted.

• Discussion:
• Lane 234-238: Authors speculated about the protective effect of MB that should “be explained by the observed ability of MB to restore […], thereby preventing the collapse of the mitochondrial membrane potential”. In this perspective, authors should perform a TMRM assay.
• Limitations: Although limitations of the study have been reported, the main limitation is the in vitro cell model used, which, if adjusted, could yield promising results.

Author Response

Dear Reviewer, thank you very much for your valuable feedback. Below you will find point-by-point answer to your queries.

Materials and Methods:

This section should be detailed as much as possible to ensure experimental reproducibility. Indeed, many experimental details are missing. For example, experimental conditions are unclear (e.g., treatment time with MB or H2O2). Better explain what is meant by “different experimental conditions” in lane 93.

This point has been addressed. Following your suggestion, the corresponding changes have been made to improve the experimental reproducibility of all experiments.

Statistical analysis should redone more properly. Authors applied only the t-test even where it is not the most appropriate statistical test.

This point has been addressed. Following your suggestion, ANOVA test have been applied to check the statistical significance of our results.

Supplementary table 1:

Although the primers used with their sequences have been reported, the only species reported is the murine one. Were the same primers used for the human cell line as well?

We deeply regret our mistake. When uploading documents to the journal's web application, we attached a previous file that did not show the human primers. Indeed, the human primers are different from the mouse ones because the gene sequences are not the same. We have corrected this error by attaching the table with both human and mouse primers.

Results:

The main problem is related to the cell lines used. Even if argued in the discussion, it is difficult to find a real explanation for the species-specific effects. Rather, there is a real concern in the HL1 cell line. As authors showed in Figure 2E, the HL1 cells seem to be very suffering already at baseline (% apoptosis of about 60%). It could be that the lack of effect on this cell line is related to the cells used. On the contrary, the effects on the AC16 cell line are interesting.

To confirm whether the effects are a consequence of the HL1 cell lineage or of species differences, we isolated CD1 mouse cardiomyocytes and subjected them to the same treatment. Our results demonstrate that primary cardiomyocytes exhibit the same response as HL1 cells to the different treatments with the exception of peroxiredoxin 5, suggesting that the observed differences may be a consequence of species-specific differences and thus not due to HL1 cell line itself (Supplementary Data 1).

Authors discuss about the co-treatment with MB and H2O2. To be able to assert of a protective effect of MB, perhaps it would be better to carry out a pre-treatment with MB and then a treatment with H2O2. Moreover, authors should specify the reason why they test only one concentration and why they did not perform a dose-response. Again, the experimental conditions are not clear.

We respectfully disagree with the reviewer. The time of half-life of MB is around 12-24 hours while the time of oxidative damage and apoptosis produced by ROS is detectable around 16-24 hours sharing the similar window of action. Therefore a pre-treatment may be less effective than if done at the same time.

Lane 187-189: authors speculated that the “co-treatment with MB and H2O2 results in the reversion of miR-16 upregulation observed in H2O2 treatment in HL1”. The SD reported in Figure 2A is very high and, again, the t-test is not appropriate.

This point has been addressed. Following your suggestion, qPCR analysis have been repeated again reducing considerably the SD of samples. Furthermore, ANOVA test have been performed to enforce the significance of our results.

Authors should use a different normalization control for qRT-PCR. As reported by Musyaju et al “ The levels of GAPDH in the mitochondria are low at the basal condition, but they are elevated under stressed conditions, such as exposure to DNA-damaging oxidative stress[16,48]. Thus, post-TBI oxidative stress can induce rapid phosphorylation of GAPDH in neuronal mitochondria and increase GAPDH activity. When GAPDH activity spikes, it induces pro-apoptotic mitochondrial membrane permeabilization via an association with VDAC” (org/10.1016/j.ab.2023.115301). Moreover, the protein expression levels of the same markers (SOD1, SOD2, PRDX etc..) may be even more indicative.

We respectfully disagree with the reviewer. As the reviewer correctly points out, GAPDH activity changes under oxidative stress. However, this change in activity occurs at the protein level, not at the messenger RNA level. In fact, this normalizer is used in various studies that evaluate the expression of different genes under oxidative stress (Calahorra et al., 2018; Muñoz-Gallardo et al., 2024)

Calahorra J, Martínez-Lara E, De Dios C, Siles E. Hypoxia modulates the antioxidant effect of hydroxytyrosol in MCF-7 breast cancer cells. PLoS One. 2018 Sep 20;13(9):e0203892. doi: 10.1371/journal.pone.0203892. PMID: 30235254; PMCID: PMC6147459.

Muñoz-Gallardo MDM, Garcia-Padilla C, Vicente-Garcia C, Carvajal J, Arenega A, Franco D. miR-195b is required for proper cellular homeostasis in the elderly. Sci Rep. 2024 Jan 8;14(1):810. doi: 10.1038/s41598-024-51256-8. PMID: 38191655; PMCID: PMC10774362.

Figure:

Figure 2:

Lane 215: add that the observed results are from qPCR.

We respectfully disagree with the reviewer. On line 212 we indicate that the data obtained comes from qPCR analysis

Lane 218-219: Panel E and F are inverted.

This point has been addressed. Following your suggestion, changes have been added

Discussion:

Lane 234-238: Authors speculated about the protective effect of MB that should “be explained by the observed ability of MB to restore […], thereby preventing the collapse of the mitochondrial membrane potential”. In this perspective, authors should perform a TMRM assay.

This point has been addressed. Because we are currently unable to perform TMRM assays in our laboratory, we have changed the statement referred to by the reviewer to more accurately reflect the results demonstrated in our work.

Limitations: Although limitations of the study have been reported, the main limitation is the in vitro cell model used, which, if adjusted, could yield promising results.

Following the reviewer, we have highlighted the limitation of this study in the discussion: “However, it is important to highlight the limitations of our study since it was carried out in vitro and not in vivo. Fernandes et al. (2024) demonstrated that the timing of MB administration is essential for its protective or detrimental function during heart failure. Further in vivo research is required to contribute to the understanding whether MB can be used as a therapeutic drug to improve mitochondrial response during heart failure. Also, Fernandes et al. (2024) demonstrated that the timing of MB administration and the recurrence of this administration is essential for its protective or detrimental function during heart failure suggesting that MB effect in vivo should be more complex than what was observed in vitro”

Reviewer 2 Report

Comments and Suggestions for Authors

1. Near line 159 there are several genes that are measured.  The authors should make it clear to the reader what these genes are so the reader can understand the functional significance.

2. With the addition of methylene blue, the authors observe and increase in fluorescence.  Is this an increase in the number of mitochondrial showing the signal or a greater signal in the mitochondrial already labelled.

3.  Why were the AC16 and HL1 cell lines chosen?  How well so they reflect what is happening in the heart in a living animal?  Why not use isolated cardiac myocytes?

4. What are the differences between AC16 and HL1?  For example, do they have similar responses to hypoxia, cellular signaling, and mitochondrial responses?  Do they differ from what is seen in the living heart or isolated cardiac myocytes? 

5. The authors should discuss in terms of the current knowledge of the signaling pathways the significance of their findings. The authors should explain the differences in experimental observations in terms of the differences in cellular physiology and signaling in the two cell lines.

6. Is the statement "Taking all our data together, we have demonstrated a protective role of MB against 288 oxidative stress, increasing the survival of mouse and human cardiomyocytes." reasonable or over stated?  The authors should consider making their claim more in line with what was found in the study performed.  Similarly for other such statements in this paragraph and elsewhere.

7. The discussion does not adequately describe other related work and how this supports (or is supported by) or adds to the body of knowledge.  At present is seems more of a summary of results.

Author Response

Dear Reviewer, thank you very much for your valuable feedback. Below you will find point-by-point answer to your queries.

1. Near line 159 there are several genes that are measured.  The authors should make it clear to the reader what these genes are so the reader can understand the functional significance.

Following the reviewer’s recommendation, we have grouped the genes according to their function in the text (Line 159- 166:  i.e:  –SOD1 and SOD2, enzymes that catalyze the dismutation of superoxide into hydrogen peroxide, a less reactive molecule, and oxygen;  PRDX2, 3 and 5, pivotal enzymes that act as scavenging of peroxides; GSR, enzyme that regenerate reduced glutathione (GSH) from oxidized glutathione (GSSG)), thus allowing the neutralization of reactive oxygen species and GPRX1 that primarily functions to reduce hydrogen peroxide to water, thus limiting its harmful effects and modulating ROS-mediated signaling pathways.

2. With the addition of methylene blue, the authors observe and increase in fluorescence. Is this an increase in the number of mitochondrial showing the signal or a greater signal in the mitochondrial already labelled.

Fluorescence observed is provided by MitoTrackerGreen® FM (M7514, Invitrogen, Rockford, IL, USA). This product is used broadly to measure the number of mitochondria and moreover the functional activity of them as described the manufacturer’s datasheet (https://www.thermofisher.com/order/catalog/product/M7514) Furthermore several studies that previously have used this compound by measure of number of mitochondria and activity of them:

1. Piantadosi CA, Suliman HB. Mitochondrial transcription factor A induction by redox activation of nuclear respiratory factor 1. J Biol Chem. 2006 Jan 6;281(1):324-33. doi: 10.1074/jbc.M508805200. Epub 2005 Oct 17. PMID: 16230352.
2. Nair VD, McNaught KS, González-Maeso J, Sealfon SC, Olanow CW. p53 mediates nontranscriptional cell death in dopaminergic cells in response to proteasome inhibition. J Biol Chem. 2006 Dec 22;281(51):39550-60. doi: 10.1074/jbc.M603950200. Epub 2006 Oct 23. PMID: 17060322.
3. Alonso-Villa E, Mangas A, Bonet F, Campuzano Ó, Quezada-Feijoo M, Ramos M, García-Padilla C, Franco D, Toro R. The Protective Role of miR-130b-3p Against Palmitate-Induced Lipotoxicity in Cardiomyocytes Through PPARγ Pathway. Int J Mol Sci. 2024 Nov 13;25(22):12161. doi: 10.3390/ijms252212161. PMID: 39596228; PMCID: PMC11594327.

Regarding to the reviewer question, we claim that fluorescence increased associated to MB treatment is due to an increase in activate mitochondrial number

3. Why were the AC16 and HL1 cell lines chosen?  How well so they reflect what is happening in the heart in a living animal?  Why not use isolated cardiac myocytes?
4. What are the differences between AC16 and HL1?  For example, do they have similar responses to hypoxia, cellular signaling, and mitochondrial responses?  Do they differ from what is seen in the living heart or isolated cardiac myocytes? 

The third and fourth questions are answered in this section: We have chosen HL1 cells and AC16 cells because they are mouse cardiomyocytes and human cardiomyoblasts, respectively. Both cell lines have been widely used to study cardiomyocyte responses in vitro and have been validated as appropriate models for studying mitochondrial associated processes. However, as we pointed out in the introduction and discussion of our study, although they are valid models for analyzing oxidative stress and mitochondrial function, they have limitations with respect to in vivo models. Thus, although they largely recapitulate the processes that occur in animal models, future experiments have to be carried out in vivo to continue exploring the role of methylene blue as a possible drug against oxidative stress associated with cardiovascular diseases.

Regarding to the differences between HL1 and AC16, ENCODE project together with different studies have reflected several differences between ROS associated pathways in both cell lines, showing that HL-1 cells exhibit greater resistance to oxidative stress compared to AC-16 cells. This is partly due to the fact that HL-1 cells exhibit high catalase activity (absent in AC-16) and more stable mitochondrial superoxide dismutase (SOD2). Similarly, AC-16 cells are more dependent on the glutathione system and have a lower GSH regenerative capacity compared to HL1 cells. This differential resistance may affect the protective role of MB against oxidative stress, being more necessary and evident in those cells that present a worse defense against oxidative stress such as AC16, as compared to HL1.

Those differences in ROS defense system are in line with our results since we demonstrated a greater protective response of human cells -AC16- treated with methylene blue against oxidative stress compared to mouse HL1 cells.

Furthermore, to confirm whether the effects are different between HL1 and isolated cardiac myocytes, we isolated primary mouse cardiomyocytes and subjected them to the same treatment of HL1. Our results demonstrate that primary cardiomyocytes exhibit the same response as HL1 cells to the different treatments with the exception of peroxiredoxin 5, suggesting that the observed differences may be a consequence of species differences (Supplementary Data 2).

5. The authors should discuss in terms of the current knowledge of the signaling pathways the significance of their findings. The authors should explain the differences in experimental observations in terms of the differences in cellular physiology and signaling in the two cell lines.

Following the reviewer’s recommendation, we have explained the differences in experimental observations in terms of the differences in cellular physiology and signaling in HL1 and AC16. Line 273-284: “On the other hand, the differences we observed between HL1 and AC16 cells may be a consequence of these cells' greater or lesser resistance to oxidative stress. Various studies have shown that HL-1 cells exhibit greater resistance to oxidative stress compared to AC-16 cells. This is partly due to the fact that HL-1 cells exhibit high catalase activity (ab-sent in AC-16) and more stable mitochondrial superoxide dismutase (SOD2). Similarly, AC-16 cells are more dependent on the glutathione system and have a lower GSH regenerative capacity compared to HL1 cells. This differential resistance may affect the protective role of MB against oxidative stress, being more necessary and evident in those cells that present a worse defense against oxidative stress such as AC16 compared to HL1”

6. Is the statement "Taking all our data together, we have demonstrated a protective role of MB against 288 oxidative stress, increasing the survival of mouse and human cardiomyocytes." reasonable or over stated?  The authors should consider making their claim more in line with what was found in the study performed.  Similarly for other such statements in this paragraph and elsewhere.

Following the reviewer’s recommendation, we have considered our claims about our results: Line 308-315: Taking all our data together, we have demonstrated a protective role of MB against oxidative stress by modulating GSR expression gene, increasing the survival of in mouse and human cardiomyocytes and the modulation of SOD2, PRDX,3 and 5 in human cardiomyocytes. Furthermore, we have demonstrated that MB treatment reduce the CHOP pro-apoptotic protein expression reversing the enhanced expression of this protein after an increase in oxidative stress

7. The discussion does not adequately describe other related work and how this supports (or is supported by) or adds to the body of knowledge.  At present is seems more of a summary of results.

Following the reviewer’s recommendation, we have changed our discussion

 

 

Reviewer 3 Report

Comments and Suggestions for Authors

Major comments

1. Authors have validated the gene expression using qPCR. It would be nice to show some protein expression studies using western blot to further strengthen the claims.
2. Cell culture methods are not clear. Number of cells plated for each experiment is not included. How you optimized the concentration of H2O2 and methylene blue? Is there any positive control used other than methylene blue??
3. Results of the cell viability assay is missing. 
4. Correction of grammatical errors and language editing is necessary

Minor comments:

1. line number 17-18, the sentence should rewritten as as "Our results reveal that MB increases active mitochondria, reverses H₂O₂-induced oxidative damage",
2. In the same line, what does it mean that active mitochondria?? Better to rewrite it as "Functional" mitochondria" wherever it is applicable.
3. Y-axis labelling is not appropriate for the figures 1I-1Q.
4. Title of the Fig. 2  is not appropriate. What does it mean that "Viability cellular"?? Y-axis titles should be rewritten in this figures as well. (For example, it was simply written as arbitrary units. Arbitrary units of what?? is it fold change?? Nothing is clear.

Comments on the Quality of English Language

Requires extensive editing

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Round 2

Reviewer 1 Report

Comments and Suggestions for Authors

no further comments

Author Response

Thanks for you valuable comments. I are vey happy to hear that you are satisfied with our manuscript modifications. 

Reviewer 2 Report

Comments and Suggestions for Authors

The clarifications and modifications, requested by this reviewer are not included in the manuscript. I do not understand why the authors clarified in the response but not in the manuscript.  The comments were not made for the reviewer's benefit, but to improve the paper for the rea

The response to comment 6 is inadequate.  The study results do not "demonstrate", this is too strong.  It would be better to say the results "suggest that".  Similarly elsewhere.  The conclusions are too strong.  The article does not show causal relations. Rather, circumstantial evidence that suggest the conclusions.

Author Response

Dear Reviewer, thank you very much for your valuable feedback. Below you will find point-by-point answer to your queries.

The clarifications and modifications, requested by this reviewer are not included in the manuscript. I do not understand why the authors clarified in the response but not in the manuscript.  The comments were not made for the reviewer's benefit, but to improve the paper for the reader

We are very sorry. We fully agree with you that the reviewer's recommendations improve the quality of the work and its understanding by readers and the entire scientific community. It is possible that we made an error during the document upload process, and the attached file is the previous version. We are resending you the new version of the document. To facilitate your review, we have highlighted the recommendations in yellow.

The response to comment 6 is inadequate.  The study results do not "demonstrate", this is too strong.  It would be better to say the results "suggest that".  Similarly elsewhere.  The conclusions are too strong.  The article does not show causal relations. Rather, circumstantial evidence that suggest the conclusions.

Following the reviewer’s recommendation, we have changed “demonstrate” by “suggest that”

Reviewer 3 Report

Comments and Suggestions for Authors

Revisions are acceptable

Comments on the Quality of English Language

NA

Author Response

Thanks for you valuable comments. I are vey happy to hear that you are satisfied with our manuscript modifications.