Reviewer’s report
Title: 
Alterations in MicroRNA Gene Expression Profile in Liver Transplant
Patients with Hepatocellular Carcinoma
Version: 
1 
Date: 
31 Oct 2020
Reviewer's report:
Dear Editor,
BMC Gastroenterology.
The manuscript "Alterations in microRNA gene expression profile in liver
transplant patients with hepatocellular Carcinoma" by Afshari A, et al is a nice
effort to grasp the molecular basis of transplant rejection in HCC patients. Novel
and easily accessible biomarkers of acute rejection could facilitate early
detection and effective clinical management in LT rejected patients. Authors
report the down-regulation of two miRNAs (miR194-5p, miR584as-3p) and
upregulation of 
miR4449 and miR-3158-5p in liver transplant rejected patients
and claim these to be candidate biomarkers for LT rejection in HCC patients.
However, authors need to address some serious concerns. I am asking for a
Revision.
1. To be consistent with the conclusions authors are drawing, the essential
microarray data representing 14 transplant patients need to be represented in Fig.
3. Fig. 3 shows profiles of just 2 individuals as mentioned in the figure legend.
This data is the foundation of the entire data.
2. It would be useful authors 
refer to a 2017 manuscript by Miyaaki Hisamitsu,
et al, Annals of Transplantation, reporting the intrahepatic miRNA profiles in
liver 
transplant patients with viral co-infections. Miyaki et al report fold changes
in expression from 2 to 44 fold using same miRNA microarray techniques. 
3. Authors in table 2 show fold and log2-fold change in differentially expressing
miRNA candidates. It is not clear how the fold change was calculated. Due to the
biological heterogeneity and experimental variabilities, generally fold change < 2
is not considered significant. All values in table 2 represent < 2 fold changes.
4. Figure 4 shows the real time qPCR validation of the microarray data. Again it
is not clear how the fold change was calculated in qPCR assays. Compared to <2
microarray fold changes, authors report 8 and 70 fold up-regulation in miR 4449
and miR 
3158-5p, respectively and 2 and 40 fold down regulation in miR 194-5p
and miR 548as-3p. Authors need to explain why are relative changes not
consistent.
5. The layout of the figures need to be modified for effective representation of
data. For example Fig. 2 could be combined with modified Figure 3, etc. Fig 2,
showing matrix plot is not clear. Two rows are labeled and one is left to wonder
what the middle two rows are.
6. Small grammer/typos like line 50 pg1, line 4, page 2 need to be fixed. What is
Simple Expressed analysis?
7. Reference 31 lacks the journal info.
In summary, It is an interesting study but needs to be reviewed before it is
deemed fit for publication.
Thanks,
Aejaz 
Publons Reviewer Recognition
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Yes
Declaration of competing interests
Please complete a declaration of competing interests, considering the following
questions:
1
. 
Have you in the past five years received reimbursements, fees, funding, or
salary from an organisation that may in any way gain or lose financially
from the publication of this manuscript, either now or in the future?
2
. 
Do you hold any stocks or shares in an organisation that may in any way
gain or lose financially from the publication of this manuscript, either now
or in the future?
3
. 
Do you hold or are you currently applying for any patents relating to the
content of the manuscript?
4
. 
Have you received reimbursements, fees, funding, or salary from an
organization that holds or has applied for patents relating to the content of
the manuscript?
5
. 
Do you have any other financial competing interests?
6
. 
Do you have any non-financial competing interests in relation to this
paper?
If you can answer no to all of the above, write 'I declare that I have no competing
interests' below. If your reply is yes to any, please give details below.
I declare that I have no competing interests
Reviewer Publication Consent.
 I agree for my report to be made available
under an Open Access Creative Commons CC-BY License (
http://creativecommons.org/licenses/by/4.0
) if this manuscript is accepted for
publication. Any comments that I do not wish to be included in the published
report have been included as confidential comments to the editor, which will not
be published.
If you are not happy for us to publish this report, please contact the editorial
office before completing the review.
If you wish, you can include your name in your published report. Please note
you must decide whether to include your name at the start of the process and
confirm this decision whenever prompted. If you change your decision later, we
will not be able to publish your name.
I agree to the terms of the CC-BY 4.0 license; please 
do not
 publish my name
with my report. (default)
Is the study design appropriate to answer the research question (including the use
of appropriate controls), and are the conclusions supported by the evidence
presented?
Yes
Are the methods sufficiently described to allow the study to be repeated?
No
Is the use of statistics and treatment of uncertainties appropriate?
Yes
Is the presentation of the work clear?
No
Are the images in this manuscript (including electrophoretic gels and blots) free
from apparent manipulation?
Yes
Reviewer’s report
Title: 
Alterations in MicroRNA Gene Expression Profile in Liver Transplant
Patients with Hepatocellular Carcinoma
Version: 
1 
Date: 
31 Oct 2020
Reviewer's report:
Dear Editor,
BMC Gastroenterology.
The manuscript "Alterations in microRNA gene expression profile in liver
transplant patients with hepatocellular Carcinoma" by Afshari A, et al is a nice
effort to grasp the molecular basis of transplant rejection in HCC patients. Novel
and easily accessible biomarkers of acute rejection could facilitate early
detection and effective clinical management in LT rejected patients. Authors
report the down-regulation of two miRNAs (miR194-5p, miR584as-3p) and
upregulation of 
miR4449 and miR-3158-5p in liver transplant rejected patients
and claim these to be candidate biomarkers for LT rejection in HCC patients.
However, authors need to address some serious concerns. I am asking for a
Revision.
1. To be consistent with the conclusions authors are drawing, the essential
microarray data representing 14 transplant patients need to be represented in Fig.
3. Fig. 3 shows profiles of just 2 individuals as mentioned in the figure legend.
This data is the foundation of the entire data.
2. It would be useful authors 
refer to a 2017 manuscript by Miyaaki Hisamitsu,
et al, Annals of Transplantation, reporting the intrahepatic miRNA profiles in
liver 
transplant patients with viral co-infections. Miyaki et al report fold changes
in expression from 2 to 44 fold using same miRNA microarray techniques. 
3. Authors in table 2 show fold and log2-fold change in differentially expressing
miRNA candidates. It is not clear how the fold change was calculated. Due to the
biological heterogeneity and experimental variabilities, generally fold change < 2
is not considered significant. All values in table 2 represent < 2 fold changes.
4. Figure 4 shows the real time qPCR validation of the microarray data. Again it
is not clear how the fold change was calculated in qPCR assays. Compared to <2
microarray fold changes, authors report 8 and 70 fold up-regulation in miR 4449
and miR 
3158-5p, respectively and 2 and 40 fold down regulation in miR 194-5p
and miR 548as-3p. Authors need to explain why are relative changes not
consistent.
5. The layout of the figures need to be modified for effective representation of
data. For example Fig. 2 could be combined with modified Figure 3, etc. Fig 2,
showing matrix plot is not clear. Two rows are labeled and one is left to wonder
what the middle two rows are.
6. Small grammer/typos like line 50 pg1, line 4, page 2 need to be fixed. What is
Simple Expressed analysis?
7. Reference 31 lacks the journal info.
In summary, It is an interesting study but needs to be reviewed before it is
deemed fit for publication.
Thanks,
Aejaz 
Publons Reviewer Recognition
. Springer Nature can send verification of this
review directly to Publons (a subsidiary of Clarivate Analytics). If you would
like to take advantage of this service, please click on the “Yes” option below.
Your name, email address, title of the reviewed manuscript, name of the journal,
and date of your review submission (the “Review Data”) will then be transmitted
to Publons upon publication of the manuscript. If you have already registered at
Publons, they will notify you of the receipt of this review and update your profile
as per your settings and their policy. If you are not registered with Publons, you
will receive an email from them asking you to register in order for them to be
able to recognize your review on your new profile page. Publons may use the
Review Data to generate derivative metadata for the benefit of Publons and you
as a reviewer, carefully considering the sensitivity of such information. For
example, Publons may verify your record as a reviewer by updating your profile
published on its webservice if you have registered for such service or help
editors to identify candidate reviewers. Please find the details of processing in
Publons’ privacy policy 
https://publons.com/about/terms
Yes
Declaration of competing interests
Please complete a declaration of competing interests, considering the following
questions:
1
. 
Have you in the past five years received reimbursements, fees, funding, or
salary from an organisation that may in any way gain or lose financially
from the publication of this manuscript, either now or in the future?
2
. 
Do you hold any stocks or shares in an organisation that may in any way
gain or lose financially from the publication of this manuscript, either now
or in the future?
3
. 
Do you hold or are you currently applying for any patents relating to the
content of the manuscript?
4
. 
Have you received reimbursements, fees, funding, or salary from an
organization that holds or has applied for patents relating to the content of
the manuscript?
5
. 
Do you have any other financial competing interests?
6
. 
Do you have any non-financial competing interests in relation to this
paper?
If you can answer no to all of the above, write 'I declare that I have no competing
interests' below. If your reply is yes to any, please give details below.
I declare that I have no competing interests
Reviewer Publication Consent.
 I agree for my report to be made available
under an Open Access Creative Commons CC-BY License (
http://creativecommons.org/licenses/by/4.0
) if this manuscript is accepted for
publication. Any comments that I do not wish to be included in the published
report have been included as confidential comments to the editor, which will not
be published.
If you are not happy for us to publish this report, please contact the editorial
office before completing the review.
If you wish, you can include your name in your published report. Please note
you must decide whether to include your name at the start of the process and
confirm this decision whenever prompted. If you change your decision later, we
will not be able to publish your name.
I agree to the terms of the CC-BY 4.0 license; please 
do not
 publish my name
with my report. (default)
Is the study design appropriate to answer the research question (including the use
of appropriate controls), and are the conclusions supported by the evidence
presented?
Yes
Are the methods sufficiently described to allow the study to be repeated?
No
Is the use of statistics and treatment of uncertainties appropriate?
Yes
Is the presentation of the work clear?
No
Are the images in this manuscript (including electrophoretic gels and blots) free
from apparent manipulation?
Yes
Please review this paper.
user
Reviewer’s report
Title: 
Alterations in MicroRNA Gene Expression Profile in Liver Transplant
Patients with Hepatocellular Carcinoma
Version: 
1 
Date: 
31 Oct 2020
Reviewer's report:
Dear Editor,
BMC Gastroenterology.
The manuscript "Alterations in microRNA gene expression profile in liver
transplant patients with hepatocellular Carcinoma" by Afshari A, et al is a nice
effort to grasp the molecular basis of transplant rejection in HCC patients. Novel
and easily accessible biomarkers of acute rejection could facilitate early
detection and effective clinical management in LT rejected patients. Authors
report the down-regulation of two miRNAs (miR194-5p, miR584as-3p) and
upregulation of 
miR4449 and miR-3158-5p in liver transplant rejected patients
and claim these to be candidate biomarkers for LT rejection in HCC patients.
However, authors need to address some serious concerns. I am asking for a
Revision.
1. To be consistent with the conclusions authors are drawing, the essential
microarray data representing 14 transplant patients need to be represented in Fig.
3. Fig. 3 shows profiles of just 2 individuals as mentioned in the figure legend.
This data is the foundation of the entire data.
2. It would be useful authors 
refer to a 2017 manuscript by Miyaaki Hisamitsu,
et al, Annals of Transplantation, reporting the intrahepatic miRNA profiles in
liver 
transplant patients with viral co-infections. Miyaki et al report fold changes
in expression from 2 to 44 fold using same miRNA microarray techniques. 
3. Authors in table 2 show fold and log2-fold change in differentially expressing
miRNA candidates. It is not clear how the fold change was calculated. Due to the
biological heterogeneity and experimental variabilities, generally fold change < 2
is not considered significant. All values in table 2 represent < 2 fold changes.
4. Figure 4 shows the real time qPCR validation of the microarray data. Again it
is not clear how the fold change was calculated in qPCR assays. Compared to <2
microarray fold changes, authors report 8 and 70 fold up-regulation in miR 4449
and miR 
3158-5p, respectively and 2 and 40 fold down regulation in miR 194-5p
and miR 548as-3p. Authors need to explain why are relative changes not
consistent.
5. The layout of the figures need to be modified for effective representation of
data. For example Fig. 2 could be combined with modified Figure 3, etc. Fig 2,
showing matrix plot is not clear. Two rows are labeled and one is left to wonder
what the middle two rows are.
6. Small grammer/typos like line 50 pg1, line 4, page 2 need to be fixed. What is
Simple Expressed analysis?
7. Reference 31 lacks the journal info.
In summary, It is an interesting study but needs to be reviewed before it is
deemed fit for publication.
Thanks,
Aejaz 
Publons Reviewer Recognition
. Springer Nature can send verification of this
review directly to Publons (a subsidiary of Clarivate Analytics). If you would
like to take advantage of this service, please click on the “Yes” option below.
Your name, email address, title of the reviewed manuscript, name of the journal,
and date of your review submission (the “Review Data”) will then be transmitted
to Publons upon publication of the manuscript. If you have already registered at
Publons, they will notify you of the receipt of this review and update your profile
as per your settings and their policy. If you are not registered with Publons, you
will receive an email from them asking you to register in order for them to be
able to recognize your review on your new profile page. Publons may use the
Review Data to generate derivative metadata for the benefit of Publons and you
as a reviewer, carefully considering the sensitivity of such information. For
example, Publons may verify your record as a reviewer by updating your profile
published on its webservice if you have registered for such service or help
editors to identify candidate reviewers. Please find the details of processing in
Publons’ privacy policy 
https://publons.com/about/terms
Yes
Declaration of competing interests
Please complete a declaration of competing interests, considering the following
questions:
1
. 
Have you in the past five years received reimbursements, fees, funding, or
salary from an organisation that may in any way gain or lose financially
from the publication of this manuscript, either now or in the future?
2
. 
Do you hold any stocks or shares in an organisation that may in any way
gain or lose financially from the publication of this manuscript, either now
or in the future?
3
. 
Do you hold or are you currently applying for any patents relating to the
content of the manuscript?
4
. 
Have you received reimbursements, fees, funding, or salary from an
organization that holds or has applied for patents relating to the content of
the manuscript?
5
. 
Do you have any other financial competing interests?
6
. 
Do you have any non-financial competing interests in relation to this
paper?
If you can answer no to all of the above, write 'I declare that I have no competing
interests' below. If your reply is yes to any, please give details below.
I declare that I have no competing interests
Reviewer Publication Consent.
 I agree for my report to be made available
under an Open Access Creative Commons CC-BY License (
http://creativecommons.org/licenses/by/4.0
) if this manuscript is accepted for
publication. Any comments that I do not wish to be included in the published
report have been included as confidential comments to the editor, which will not
be published.
If you are not happy for us to publish this report, please contact the editorial
office before completing the review.
If you wish, you can include your name in your published report. Please note
you must decide whether to include your name at the start of the process and
confirm this decision whenever prompted. If you change your decision later, we
will not be able to publish your name.
I agree to the terms of the CC-BY 4.0 license; please 
do not
 publish my name
with my report. (default)
Is the study design appropriate to answer the research question (including the use
of appropriate controls), and are the conclusions supported by the evidence
presented?
Yes
Are the methods sufficiently described to allow the study to be repeated?
No
Is the use of statistics and treatment of uncertainties appropriate?
Yes
Is the presentation of the work clear?
No
Are the images in this manuscript (including electrophoretic gels and blots) free
from apparent manipulation?
Yes
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