Peer Review History

Original SubmissionJanuary 14, 2021
Decision Letter - Muhammad Shareef Masoud, Editor

PONE-D-21-01454

Reference genes for mesangial cell and podocyte qPCR gene expression studies under high-glucose and renin-angiotensin-system blocker conditions

PLOS ONE

Dear Dr. Boim,

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Muhammad Shareef Masoud, Ph.D

Academic Editor

PLOS ONE

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Reviewers' comments:

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Comments to the Author

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Reviewer #1: Partly

Reviewer #2: Yes

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Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #1: No

Reviewer #2: Yes

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Reviewer #1: No

Reviewer #2: No

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Reviewer #1: 1: A certain view is implied by the authors regarding to this study but they could be more explicit.

The authors take a rather narrow view of data publication, which I think hinders their analyses. In this study, author need to elaborate further manuscript methodology and results and results should be reconfirmed with other assay as well.

2: Manuscript writeup should improve.

3: Figure legends could not show proper description, So its better to write in detail.

Reviewer #2: In this manuscript entitled Reference genes for mesangial cell and podocyte qPCR gene expression studies under high-glucose and renin-angiotensin-system blocker conditions analyze six genes (HPRT, ACTB, PGAM-1, GAPDH, PPIA, and B2M) using five software applications and the ΔCt method to determine that the best genes to be used for mesangial cell studies with high glucose and angiotensin receptor II blocker are HPRT and ACTB, while in the same conditions, the best combination of genes for podocyte gene expression normalization is HPRT. The study described in the manuscript is interesting however the manuscript can be considered for publication only if the following issues are addressed:

Major Comments

1 Why authors select these six genes (HPRT, ACTB, PGAM-1, GAPDH, PPIA, and B2M). Please elaborate in this article with references

2 Authors should also compare the results of syber green with probe based real time PCR

3. Grammatical errors in all parts of manuscript

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Reviewer #1: No

Reviewer #2: No

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Revision 1

Reviewer #1

• A certain view is implied by the authors regarding to this study but they could be more explicit. The authors take a rather narrow view of data publication, which I think hinders their analyses.

o We would like to thank this Reviewer for the time dedicated to evaluate this manuscript. We have reviewed the introduction and discussion sections to strengthen the background and rationale of our study, especially including previous data published from other groups.

• Results should be reconfirmed with other assay as well.

o We appreciate the Reviewer’s comment. Literature has shown that probe-based PCR can be adequately reproduced by SYBR Green real-time PCR, delivering highly comparable results with TaqMan and other quantitative gene expression methods (Tajadini 2014, 10.4103/2277-9175.127998; Arikawa 2008, 10.1186/1471-2164-9-328). Other than that, our melting curve analysis showed neither unspecific products nor primer dimers. We also made sure to use proper negative controls for all reactions performed. Multiple studies specifically on reference genes have been performed based on SYBR Green assays only (Zhang 2017, 10.3892/ol.2017.7002; Adeola 2018, 10.4314/ejhs.v28i6.9; Hashemi 2021, 10.1016/j.bbrc.2012.09.009; Nygard 2007, 10.1186/1471-2199-8-67; Ahn 2008, 10.1186/1471-2199-9-78; Bokhale 2020, 10.1016/j.dib.2020.105750). Considering all this information, we believe our results are reliable.

• Manuscript writeup should improve.

o We appreciate the Reviewer's suggestion. We submitted the manuscript to standard English grammatical revision before resubmission of this revised manuscript to PLOS ONE.

• Figure legends could not show proper description, So its better to write in detail.

o We agree with the Reviewer’s comment, and we have altered the figure legends by including details, as suggested.

Reviewer #2

• In this manuscript entitled Reference genes for mesangial cell and podocyte qPCR gene expression studies under high-glucose and renin-angiotensin-system blocker conditions analyze six genes (HPRT, ACTB, PGAM-1, GAPDH, PPIA, and B2M) using five software applications and the ΔCt method to determine that the best genes to be used for mesangial cell studies with high glucose and angiotensin receptor II blocker are HPRT and ACTB, while in the same conditions, the best combination of genes for podocyte gene expression normalization is HPRT. The study described in the manuscript is interesting however the manuscript can be considered for publication only if the following issues are addressed.

o We would like to thank this Reviewer's careful reading and attention to our work. We have addressed the issues as the following:

• Why authors select these six genes (HPRT, ACTB, PGAM-1, GAPDH, PPIA, and B2M). Please elaborate in this article with references.

o We agree with the Reviewer’s comment. We have included the rationale of each gene included in our study in the Discussion section, with references.

• Authors should also compare the results of syber green with probe based real time PCR

o We appreciate the Reviewer’s comment. Literature has shown that probe-based PCR can be adequately reproduced by SYBR Green real-time PCR, delivering highly comparable results with TaqMan and other quantitative gene expression methods (Tajadini 2014, 10.4103/2277-9175.127998; Arikawa 2008, 10.1186/1471-2164-9-328). Other than that, our melting curve analysis showed neither unspecific products nor primer dimers. We also made sure to use proper negative controls for all reactions performed. Multiple studies specifically on reference genes have been performed based on SYBR Green assays only (Zhang 2017, 10.3892/ol.2017.7002; Adeola 2018, 10.4314/ejhs.v28i6.9; Hashemi 2021, 10.1016/j.bbrc.2012.09.009; Nygard 2007, 10.1186/1471-2199-8-67; Ahn 2008, 10.1186/1471-2199-9-78; Bokhale 2020, 10.1016/j.dib.2020.105750). Considering all this information, we believe our results are reliable.

• Grammatical errors in all parts of manuscript.

o We appreciate the Reviewer's suggestion. We submitted the manuscript to standard English grammatical revision before resubmission of this revised manuscript to PLOS ONE.

Attachments
Attachment
Submitted filename: Response to Reviewers.docx
Decision Letter - Muhammad Shareef Masoud, Editor

Reference genes for mesangial cell and podocyte qPCR gene expression studies under high-glucose and renin-angiotensin-system blocker conditions

PONE-D-21-01454R1

Dear Dr. Boim,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

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Kind regards,

Muhammad Shareef Masoud, Ph.D

Academic Editor

PLOS ONE

Formally Accepted
Acceptance Letter - Muhammad Shareef Masoud, Editor

PONE-D-21-01454R1

Reference genes for mesangial cell and podocyte qPCR gene expression studies under high-glucose and renin-angiotensin-system blocker conditions

Dear Dr. Boim:

I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department.

If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact onepress@plos.org.

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PLOS ONE Editorial Office Staff

on behalf of

Dr. Muhammad Shareef Masoud

Academic Editor

PLOS ONE

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