Reviewer’s report
Title: 
Expression of Cyr61 is associated with Clinical Course in Patients with
Crohn’s Disease
Version: 
1 
Date: 
25 Oct 2020
Reviewer's report:
The study entitled "Expression of Cyr61 is associated with Clinical Course in
Patients with Crohn's Disease" aimed to quantify protein and gene expression of
Cyr61 in CD biopsies compared to normal mucosa from controls. Age- and sex-
matched groups (each n=43) were selected for comparison using a propensity
score. Samples were extracted from FFPE blocks stored in the pathological
archive and collected in 2018-2019. Immunohistochemistry (IHC) was used to
evaluate the protein expression and a semi-quantitative score was calculated
based on staining intensity (low or high) and percentage of stained area.
Depending on the obtained score, patients were distributed in 3 groups (tertiles)
and their clinical outcome (recurrence) was evaluated. 
Results showed higher expression of Cyr61 in CD patients compared to controls.
However, worse clinical outcome was associated with lower Cyr61 expression. 
Several important issues and limitations should be addressed before publication. 
METHODS:
1. Methods should be better described. First, site (ileal or colonic) and
inflammatory activity of CD biopsies included in the analysis should be reported.
Site of control biopsies should be specified too. 
2. The evaluation of the staining intensity is subjective, even when done by an
experienced pathologist. It could be better to have the opinion of at least 2
different readers. 
3. Did you use an automatic calculator of the percentage of the stained area? Did
you use a specific program or application, such as ImageJ? Please, specify. 
4. RNA used for gene expression was obtained from 11 active and inactive CD
biopsies already used in a previously published paper: were paired samples
(active and inactive in the same patients?) Why only 11 among 32 patients
described in the previous study were selected? And how did you select the
samples to be included in this new study? Methods and results on gene
expression should be mentioned in the abstract too. 
5. Clinical and endoscopic disease activity scores (CDAI, SES-CD and CDEIS)
were measured at the time of colonoscopy. Did you retrieve these scores from
medical records? Or did you calculate them retrospectively? In the latter case, it
could be very imprecise and not methodologically correct (CDAI can be
calculated only prospectively, because it requires the collection of daily status of
the patient for 7 days). Also, retrospective calculation of the endoscopic scores
(SES-CD and CDEIS) may be very approximate. Such important limitations
should be mentioned in the discussion. 
RESULTS
1. second page, line 14: please, change "higher" with "lower".
2. Figure 1 should be mentioned in the results and not in the methods. Moreover,
it should be more appropriate to show representative images of control and CD,
and not 2 such different pictures both from CD patients. It is confusing. 
DISCUSSION
1. please, add a section on study limitations
2. possible explanation of study finding is not mentioned. Which should be the
role of Cyr61 in CD pathogenesis? Your results suggest that Cyr61 increases in
CD, but it is reduced in patients with future relapse. How do you explain such
conflicting findings? 
CONCLUSION
1. Based on the methods and the results of this study, the sentence "in the future,
the possible therapeutic role of Cyr61 should be considered" is completely
inappropriate. More detailed or functional experiments were not included in your
study and increased Cyr61 expression (as presented in this paper) may be just a
consequence of inflammation and may not have any active role in pro-
inflammatory pathways and pathogenesis. 
Publons Reviewer Recognition
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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
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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?
No
Are the methods sufficiently described to allow the study to be repeated?
Yes
Is the use of statistics and treatment of uncertainties appropriate?
Yes
Is the presentation of the work clear?
Yes
Are the images in this manuscript (including electrophoretic gels and blots) free
from apparent manipulation?
Yes
Reviewer’s report
Title: 
Expression of Cyr61 is associated with Clinical Course in Patients with
Crohn’s Disease
Version: 
1 
Date: 
25 Oct 2020
Reviewer's report:
The study entitled "Expression of Cyr61 is associated with Clinical Course in
Patients with Crohn's Disease" aimed to quantify protein and gene expression of
Cyr61 in CD biopsies compared to normal mucosa from controls. Age- and sex-
matched groups (each n=43) were selected for comparison using a propensity
score. Samples were extracted from FFPE blocks stored in the pathological
archive and collected in 2018-2019. Immunohistochemistry (IHC) was used to
evaluate the protein expression and a semi-quantitative score was calculated
based on staining intensity (low or high) and percentage of stained area.
Depending on the obtained score, patients were distributed in 3 groups (tertiles)
and their clinical outcome (recurrence) was evaluated. 
Results showed higher expression of Cyr61 in CD patients compared to controls.
However, worse clinical outcome was associated with lower Cyr61 expression. 
Several important issues and limitations should be addressed before publication. 
METHODS:
1. Methods should be better described. First, site (ileal or colonic) and
inflammatory activity of CD biopsies included in the analysis should be reported.
Site of control biopsies should be specified too. 
2. The evaluation of the staining intensity is subjective, even when done by an
experienced pathologist. It could be better to have the opinion of at least 2
different readers. 
3. Did you use an automatic calculator of the percentage of the stained area? Did
you use a specific program or application, such as ImageJ? Please, specify. 
4. RNA used for gene expression was obtained from 11 active and inactive CD
biopsies already used in a previously published paper: were paired samples
(active and inactive in the same patients?) Why only 11 among 32 patients
described in the previous study were selected? And how did you select the
samples to be included in this new study? Methods and results on gene
expression should be mentioned in the abstract too. 
5. Clinical and endoscopic disease activity scores (CDAI, SES-CD and CDEIS)
were measured at the time of colonoscopy. Did you retrieve these scores from
medical records? Or did you calculate them retrospectively? In the latter case, it
could be very imprecise and not methodologically correct (CDAI can be
calculated only prospectively, because it requires the collection of daily status of
the patient for 7 days). Also, retrospective calculation of the endoscopic scores
(SES-CD and CDEIS) may be very approximate. Such important limitations
should be mentioned in the discussion. 
RESULTS
1. second page, line 14: please, change "higher" with "lower".
2. Figure 1 should be mentioned in the results and not in the methods. Moreover,
it should be more appropriate to show representative images of control and CD,
and not 2 such different pictures both from CD patients. It is confusing. 
DISCUSSION
1. please, add a section on study limitations
2. possible explanation of study finding is not mentioned. Which should be the
role of Cyr61 in CD pathogenesis? Your results suggest that Cyr61 increases in
CD, but it is reduced in patients with future relapse. How do you explain such
conflicting findings? 
CONCLUSION
1. Based on the methods and the results of this study, the sentence "in the future,
the possible therapeutic role of Cyr61 should be considered" is completely
inappropriate. More detailed or functional experiments were not included in your
study and increased Cyr61 expression (as presented in this paper) may be just a
consequence of inflammation and may not have any active role in pro-
inflammatory pathways and pathogenesis. 
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 after the final decision on the manuscript has been made. 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?
No
Are the methods sufficiently described to allow the study to be repeated?
Yes
Is the use of statistics and treatment of uncertainties appropriate?
Yes
Is the presentation of the work clear?
Yes
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: 
Expression of Cyr61 is associated with Clinical Course in Patients with
Crohn’s Disease
Version: 
1 
Date: 
25 Oct 2020
Reviewer's report:
The study entitled "Expression of Cyr61 is associated with Clinical Course in
Patients with Crohn's Disease" aimed to quantify protein and gene expression of
Cyr61 in CD biopsies compared to normal mucosa from controls. Age- and sex-
matched groups (each n=43) were selected for comparison using a propensity
score. Samples were extracted from FFPE blocks stored in the pathological
archive and collected in 2018-2019. Immunohistochemistry (IHC) was used to
evaluate the protein expression and a semi-quantitative score was calculated
based on staining intensity (low or high) and percentage of stained area.
Depending on the obtained score, patients were distributed in 3 groups (tertiles)
and their clinical outcome (recurrence) was evaluated. 
Results showed higher expression of Cyr61 in CD patients compared to controls.
However, worse clinical outcome was associated with lower Cyr61 expression. 
Several important issues and limitations should be addressed before publication. 
METHODS:
1. Methods should be better described. First, site (ileal or colonic) and
inflammatory activity of CD biopsies included in the analysis should be reported.
Site of control biopsies should be specified too. 
2. The evaluation of the staining intensity is subjective, even when done by an
experienced pathologist. It could be better to have the opinion of at least 2
different readers. 
3. Did you use an automatic calculator of the percentage of the stained area? Did
you use a specific program or application, such as ImageJ? Please, specify. 
4. RNA used for gene expression was obtained from 11 active and inactive CD
biopsies already used in a previously published paper: were paired samples
(active and inactive in the same patients?) Why only 11 among 32 patients
described in the previous study were selected? And how did you select the
samples to be included in this new study? Methods and results on gene
expression should be mentioned in the abstract too. 
5. Clinical and endoscopic disease activity scores (CDAI, SES-CD and CDEIS)
were measured at the time of colonoscopy. Did you retrieve these scores from
medical records? Or did you calculate them retrospectively? In the latter case, it
could be very imprecise and not methodologically correct (CDAI can be
calculated only prospectively, because it requires the collection of daily status of
the patient for 7 days). Also, retrospective calculation of the endoscopic scores
(SES-CD and CDEIS) may be very approximate. Such important limitations
should be mentioned in the discussion. 
RESULTS
1. second page, line 14: please, change "higher" with "lower".
2. Figure 1 should be mentioned in the results and not in the methods. Moreover,
it should be more appropriate to show representative images of control and CD,
and not 2 such different pictures both from CD patients. It is confusing. 
DISCUSSION
1. please, add a section on study limitations
2. possible explanation of study finding is not mentioned. Which should be the
role of Cyr61 in CD pathogenesis? Your results suggest that Cyr61 increases in
CD, but it is reduced in patients with future relapse. How do you explain such
conflicting findings? 
CONCLUSION
1. Based on the methods and the results of this study, the sentence "in the future,
the possible therapeutic role of Cyr61 should be considered" is completely
inappropriate. More detailed or functional experiments were not included in your
study and increased Cyr61 expression (as presented in this paper) may be just a
consequence of inflammation and may not have any active role in pro-
inflammatory pathways and pathogenesis. 
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 after the final decision on the manuscript has been made. 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?
No
Are the methods sufficiently described to allow the study to be repeated?
Yes
Is the use of statistics and treatment of uncertainties appropriate?
Yes
Is the presentation of the work clear?
Yes
Are the images in this manuscript (including electrophoretic gels and blots) free
from apparent manipulation?
Yes
assistant