Comparative Analysis of Differential Cellular Transcriptome and Proteome Regulation by HIV-1 and HIV-2 Pseudovirions in the Early Phase of Infection
, Zsófia Ilona Szojka 1,3, Gergő Kalló 4, Éva Csősz 4, Ajneesh Kumar 2,4, Miklós Emri 5, József Tőzsér 1,4,* and Mohamed Mahdi 1,*
Round 1
Reviewer 1 Report
Comments and Suggestions for AuthorsPlease see attached for detailed suggestions and comments.
Comments for author File: 
Comments.pdf
English writing is good in general.
Author Response
Dear Reviewer, Thank you for your effort and time spent revieweing our manuscript. Please find the attached response.
Author Response File: 
Author Response.docx
Reviewer 2 Report
Comments and Suggestions for AuthorsIn this paper, the authors transduced HEK-293T cells using HIV-1, HIV-2 and GFP mock pseudo virions and then they do RNA-Seq to check the up and down regulated genes after 8-, 12-, and 26-hours transduction. They found there was a difference between the HIV-1 and HIV-2 pseudo virions. They also investigated the difference of proteomics between HIV-1 and HIV-2 transduction in HEK 293T cells. The results showed that HIV-2 significantly downregulated the expression of certain proteins that perhaps benefited its life-cycle and latency, while HIV-1 influenced the cellular level of oxidative stress and proteins involved in cell death. The special comments were listed:
1. It seems the up/down regulated genes in RNA do not match the protein changes. So, what makes the protein expression level change?
2. There is a paper doing exactly the same thing, just early time point, like 2 hours after transducing. So, what is the meaning of doing late time point? Actually, investigating HIV in HEK293T cells, not in primary cells, is not really helpful to understand the mechanisms.
Author Response
Dear reviewer. Thank you indeed for your time and comments regarding our manuscript. Please find attached response to your comments.
Author Response File: Author Response.docx
Reviewer 3 Report
Comments and Suggestions for AuthorsProteo-transcriptomic analyses were employed in this study to determine the differential gene expression and proteomic changes induced by transduction with HIV-1/2 pseudovirions at 8, 12, and 26 hour time points in HEK-293T cells. For a further revision, the following points should be considered.
1. It is important to select key genes and conduct experimental validation, e.g. qRT-PCR, western blot.
2. The RNA was extracted for transcriptome sequencing, which is inconsistent with the description of “genome” in the title and abstract.
3. The functional enrichment analysis can be enhanced by selecting the differentially expressed genes that are shared between the transcriptome and proteome.
SPECIFIC COMMENTS:
L52 Could you provide a more detailed explanation of the term 'RNA genome'.
L106-8 Please rewrite this sentence to clarify.
What’s the meaning of LFC in the caption of Figure 1?
L251-2 ”Meanwhile, HIV-2 differentially regulated the cellular expression of genes which are involved in the cell adhesion, extracellular matrix organization and tissue development.“ is confused.
The words are too small to pick out in Figures 5-7.
L292 a redundant word “however”.
Author Response
Dear Reviewer. Thank you for your input regarding our manuscript. Please find attached response. We hope that you may find it satisfactory.
Author Response File: Author Response.docx
Round 2
Reviewer 1 Report
Comments and Suggestions for AuthorsAll my questions are addressed.
Comments on the Quality of English LanguageEnglish writing is good in general.
Author Response
Dear Reviewer,
We would like to thank you again for your time and valuable comments that have vastly improved our manuscript.
Reviewer 2 Report
Comments and Suggestions for Authors
Thank you for the opportunity to review this revised manuscript. The authors have revised the manuscript in accordance with the comments. Still have one comment.
Do authors analyze 8-hour transcriptomic data with 26-hour proteome since the author said fewer overlapping genes is due to the delay?
Author Response
Dear Reviewer, attached please find our response. Thank you.
Author Response File: Author Response.pdf
