PONE-D-23-40197hnRNP Q/SYNCRIP interacts with LIN28 and modulates the LIN28/let-7 axis in human hepatoma cellsPLOS ONE

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2.Ministry of Science and Technology, Taiwan (MOST 108-2311-B-002-012) 

3.Ministry of Science and Technology, Taiwan (MOST 111-2314-B002-065-MY3)

4.National Taiwan University Hospital (UN108-040)

5.National Taiwan University (109L7224)

6.National Taiwan University (110L7205)

7.National Taiwan University Hospital Yunlin Branch (NTUHYL110.I003)

8.National Taiwan University Hospital Yunlin Branch (NTUHYL111.I009)"

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: Yes

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: No

Reviewer #2: Yes

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3. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: Yes

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4. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: Yes

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5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: This is an interesting study that contains novel results regarding hnRNP Q and the interaction with LIN28.

One of the main findings in the manuscript is that reducing the amount of hnRNP Q resulted in a decrease in LIN28B and TRIM71. These results are shown in figure 2A and supplemental figure 2. I would like to request a little more clarity around these 2 figures. Please include how many reps? What are the quantification numbers? Are the numbers an average or just this rep? Are the reductions significantly different?

The siRNA experiment in supplemental figure 2 did not reduce TRIM71 or LIN28B as much as the shRNA experiments in figure 2a. Since the levels of hnRNP Q were reduced in the si experiments, to about the same levels, I feel like this needs to have a little more explanation than the lines 356-359. A clear explanation of the quantification and statistical analysis may hope to clarify this as well.

Reviewer #2: This is a well written manuscript with a set of thorough experiments with sound conclusions. Just some minor changes that I think should be easy to implement:

1. I think the authors should be careful about making statements like their results are consistent with studies showing LIN28B and TRIM71 promote growth and tumorigenicity when they have not done any experiments to investigate the role of these proteins in growth or tumorigenicity. This is especially misleading in the abstract and needs to be taken out (lines 38-40).

2. For Fig 1 I wonder if all RBPs are sensitive to RNAse A treatment and would show lower amounts in IP. Would be great if they could add another control thats a different RBP. Also what does the asterisk under LIN28B refer to in C/D/E?

3. There are several typos that need to be fixed. Line 24: tumor-suppression miRNA should be 'tumor suppressor'; line 34-35: miRNAs levels should be miRNA levels; line 71: 'oligouridylation following' should be 'oligouridylation followed by'; line 98: the a common G quartet structure. Not sure what the authors are trying to state. There are some others in the manuscript and in the supplementary legends.

4. The authors should try to be specific whenever possible. Instead of stating LIN28 in the abstract, please state LIN28B as the observations in this study relate only to this homolog. Similarly when performing Northern blot, they should state let-7a and not just let-7. In line 488 they say unfavorable prognostic marker for liver cancer- is it really all liver cancer or just HCC- please be specific. In figure legend 5e (Line 569) they again say liver cancer.

5. Please provide as much detail as possible in the figure legends- for e.g. in the legend for Fig 2 they do not explain Alpha-HA. I understand they are referring to antibody to the HA tag but for someone who has not had the chance to read the text, it is not clear.

6. Figure 3E legend (line 531) incorrectly states blot showing increased miR-21 levels upon depletion... what they mean to say is unchanged miR-21 levels.

7. While the authors have established a possible mechanism of how hnRNPQ is regulating LIN28B through let-7, its also possible that there may be other possible explanations- for e.g. LIN28B and hnRNPQ may be both regulated by some common factor that promotes their stability when they come together through their interaction with some common RNA molecule. The authors (to their credit) speculate that hnRNPQ1 could share RNA targets with LIN28B, they then state that since increasing Q2 and Q3 isoforms also restores TRIM71 and LIN28B it is likely that hnRNPQs are involved with let-7 biogenesis. It does seem to be the most logical explanation but other possible mechanisms (such as hnRNPQ regulating LIN28 through MYC) may also be at play.

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Reviewer #1: No

Reviewer #2: Yes: Shubin Shahab

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hnRNP Q/SYNCRIP interacts with LIN28B and modulates the LIN28B/let-7 axis in human hepatoma cells

PONE-D-23-40197R1

Dear Dr. Chan,

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,

Massimo Caputi, PhD

Academic Editor

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Additional Editor Comments (optional):

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #1: All comments have been addressed

Reviewer #2: All comments have been addressed

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2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: (No Response)

Reviewer #2: Yes

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3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: (No Response)

Reviewer #2: Yes

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4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: (No Response)

Reviewer #2: Yes

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5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: (No Response)

Reviewer #2: Yes

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6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: (No Response)

Reviewer #2: Thank you for making the changes. Few more minor suggestions:

Minor grammatical error in lines 562-564. Perhaps say :"Collectively, although other factors may still be involved in how hnRNP Q modulates the LIN28B/let-7 axis, ..."

I would also suggest some minor changes in wording. MTS assay does not necessarily measure proliferation (which is measured by cell cycle entry), but rather "viability". in line 472-473, I would suggesting stating "... increase of let-7 family miRNAs, which in turn would decrease levels of their targets..". Expression implies mRNA transcription. We do not know whether let-7 inhibits transcription/translation or causes degradation of the transcript.

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7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

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Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #1: No

Reviewer #2: Yes: Shubin Shahab

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