A Boolean approach for novel hypoxia-related gene discovery

Tsering Stobdan; Debashis Sahoo; Gabriel G. Haddad

doi:10.1371/journal.pone.0273524

Peer Review History

Original SubmissionMay 27, 2022
19 Jul 2022 Decision Letter - Junming Yue, Editor PONE-D-22-15421A Boolean approach for novel hypoxia-related gene discoveryPLOS ONE Dear Dr. Haddad, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. Please submit your revised manuscript by Sep 02 2022 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. 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Please confirm the stated datasets are included in paper and/or the uploaded supporting information. [Note: HTML markup is below. Please do not edit.] 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: Partly ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes ****** 3. Have the authors made all data underlying the findings in their manuscript fully available? 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Reviewer #1: Yes ****** 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: The manuscript by Tsering Stobdan et. al. used a Boolean method to identify the hypoxia-responsive genes from online database. The story is simple and interesting; however the manuscript is too primitive and need more work on it before it can be considered for publication. 1. Some information in the parentheses need to be clarified, such as ‘potential therapeutic targets (PAHS-032Z array (Qiagen))’ in the first and second paragraphs of Introduction; ‘it is clear that identification of new or next generation of targets will require data from diverse samples types and enormous sample numbers and a newer method to analyze (Ref).’ in the second paragraph of Introduction. 2. Fig. 1, no error bars in all the 0 h groups. Fig 1I, the induction of ITGAV at 8h and 48 h are too modest, and it is hard to believe the significance. 3. The result of this Boolean method seems depend on the seed gene, have the authors ever tried use another seed gene such as EPO and compare the results from different seed genes? 4. The citations of Fig. S3, Fig. S4 in manuscript do not match the figure legend. 5. Cannot find the figure related with this sentence, ‘VEGFA expression does not change when FAM114A1 is upregulated in breast cell line subpopulation (MDA-MB-231) (Fig S4c)’. ****** 6. 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. If you choose “no”, your identity will remain anonymous but your review may still be made public. 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: Yes: Wenjing Zhang ******** [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0273524.r001
Revision 1
28 Jul 2022 Author Response Reviewer #1: The manuscript by Tsering Stobdan et. al. used a Boolean method to identify the hypoxia-responsive genes from online database. The story is simple and interesting; however the manuscript is too primitive and need more work on it before it can be considered for publication. Response: We agree with the reviewer about the simplicity of the approach. Yet it is a powerful method and this is only possible after we were able to combine a normalized expression of 25,955 human microarray data (obtained from Gene Expression Omnibus (GEO)) in a single database. We also pooled 11,758 mouse microarray data for additional validation. The database is available online (http://hegemon.ucsd.edu/Tools/explore.php?key=global). 1. Some information in the parentheses need to be clarified, such as ‘potential therapeutic targets (PAHS-032Z array (Qiagen))’ in the first and second paragraphs of Introduction; ‘it is clear that identification of new or next generation of targets will require data from diverse samples types and enormous sample numbers and a newer method to analyze (Ref).’ in the second paragraph of Introduction. Response: Thank you. We have updated these parts with appropriate references. 2. Fig. 1, no error bars in all the 0 h groups. Fig 1I, the induction of ITGAV at 8h and 48 h are too modest, and it is hard to believe the significance. Response: Since the bar plots are presented as fold change relative to the 0-hour (room air/21% O2) expression, the expression level at 0-hour is set to a baseline value of ‘1’. For the modest ITGAV levels at 8h and 48h, the average values are close and there is a very small standard deviation. A t-test depicts the differences as statistically significant. We have now added a supplementary table i.e., Table S3, which has the values. 3. The result of this Boolean method seems depend on the seed gene, have the authors ever tried use another seed gene such as EPO and compare the results from different seed genes? Response: We explored ANGPTL4, PPARG, PTGIS and INHBA as potential seed genes, one at a time, because of their higher fold change in HPAECs (microarray platform) when exposed to hypoxia (Table 1 from Manalo et al. Blood. 2005). However, since the basal expression of these genes was low (including EPO) in most of the tissues (Figure S6), we chose VEGFA as a more appropriate seed gene for hypoxia related gene discovery, especially when using endothelial cells for further validation. Interestingly, recently, in response to the Reviewer’s query, when we individually used ANGPTL4, PPARG, PTGIS and INHBA as the seed genes, FAM114A1 was the only common gene in the top 100 Boolean related genes listed for each seed gene (Figure S7). We thank the reviewer for this important comment and we have now added this information in the method section of the manuscript. Figure S6: Basal expression of VEGFA, ANGPTL4, PPARG, PTGIS and INHBA in different tissues as indicated in GTEx database. TPM, Transcript Per Million. Figure S7: Venn diagram indicating the common shared genes (among the top 100 Boolean related genes) when ANGPTL4, PPARG, PTGIS and INHBA, respectively, are used seed genes one at a time. FAM114A1 (red circle) is the common for all seed genes. 4. The citations of Fig. S3, Fig. S4 in manuscript do not match the figure legend. Response: Corrected. 5. Cannot find the figure related with this sentence, ‘VEGFA expression does not change when FAM114A1 is upregulated in breast cell line subpopulation (MDA-MB-231) (Fig S4c)’. Response: This is on Figure S4e – f. Additional details are added to its figure legend. Briefly, the cells (MDA-MB-231) with CXCR4-positive subpopulation (expressing CXCR4) have high level of FAM114A1 when compared with the other two groups i.e., cells with CXCR4-positive subpopulation treated with SDF-1 (CXCR4 treated with SDF-1alpha), ligand for CXCR4, also called CXCL12) for one hour and CXCR4-negative subpopulation (not expressing CXCR4). 6. 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. Response: OK Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0273524.r002
10 Aug 2022 Decision Letter - Junming Yue, Editor A Boolean approach for novel hypoxia-related gene discovery PONE-D-22-15421R1 Dear Dr. Haddad, 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. Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication. An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org. If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. 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. Kind regards, Junming Yue Academic Editor PLOS ONE 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 ******** 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: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes ****** 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: Yes ****** 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: Yes ****** 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) ****** 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. If you choose “no”, your identity will remain anonymous but your review may still be made public. 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: Yes: Wenjing Zhang ******** https://doi.org/10.1371/journal.pone.0273524.r003
Formally Accepted
14 Aug 2022 Acceptance Letter - Junming Yue, Editor PONE-D-22-15421R1 A Boolean approach for novel hypoxia-related gene discovery Dear Dr. Haddad: 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. If we can help with anything else, please email us at plosone@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Junming Yue Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0273524.r004

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