Title: Blood Metabolites, Mitochondrial Biofunction, and Cervical Cancer: A Bidirectional
Mendelian Randomization Study
Version: 0 Date: 05 Feb 2025
Reviewer's report:
PEER REVIEWER ASSESSMENTS:
OBJECTIVE - Full research articles: is there a clear objective that addresses a testable research
question(s) (brief or other article types: is there a clear objective)?
No - there are major issues
DESIGN - Is the current approach (including controls and analysis protocols) appropriate for
the objective?
No - there are major issues
EXECUTION - Are the experiments and analyses performed with technical rigor to allow
confidence in the results?
No - there are major issues
STATISTICS - Is the use of statistics in the manuscript appropriate?
No - there are issues with the statistics in the study
INTERPRETATION - Is the current interpretation/discussion of the results reasonable and not
overstated?
No - there are major issues
OVERALL MANUSCRIPT POTENTIAL - Is the current version of this work technically
sound? If not, can revisions be made to make the work technically sound?
Maybe - with major revisions
PEER REVIEWER COMMENTS:
GENERAL COMMENTS: The manuscript by Yang et al. tries to establish a causal link between
certain metabolites and mitochondria-related pathways with cervical cancer by recurring to the
Finnish database. The Mendelian randomization statistics are adequate but they have serious
limitations that are well documented in the literature. Authors ignore these limitations and just
over-interpretated the results. Some decisions on threshold values are not clearly explained and
are critical. So, I advise a major revision before the manuscript be submitted for publication.
REQUESTED REVISIONS:
1- In Introduction: Most authors state that alterations in metabolism observed in cancer are
mostly associated with tumour changes during its development, while a direct causation has
been very hard to establish. Information on this debate should be included in the discussion.
2- Material and Methods: Authors never refer the number of samples in the analysed cohorts.
And why did they decide to split the cohorts instead of considering a general cervical cancer
cohort? Depending on sample size, maybe one total cohort would be statistically more robust
than 3 partial cohorts. Authors should explain this decision. Also, how many SNPs were
analysed; were they from microchip (mostly common variants) or whole genome data? This
information should be provided to readers, whom should not need to check this information in
the Finish website.
3- For the selection of the instrumental variable, “The GWAS SNPs related to blood metabolites
and mitochondrial biofunction that were statistically significant were used as IVs, with a
threshold of P<5×10-5”. This threshold seems too permissive, allowing that many variants that
are not significantly associated with the phenotype to be included in the metabolite analyses.
Usually, the significance threshold for GWAS is at the level of 10-8 (see for instance table
1 from Carter et al. 2023 “Why caution should be applied when interpreting and promoting
findings from Mendelian randomisation studies”). Again, needed information is missing about
the essential GWAS studies from which authors gathered the “instrumental variables” used in
their analyses. Authors must explain the permissive threshold.
4- The results section is not properly presented. It is mostly a tedious description of the results
for each metabolite. Authors should include an initial results section commenting if significant
results for a certain metabolite were confirmed or not by various MR tests. If not (as it seems),
authors should comment that results must be considered with extreme caution. Authors ended
up only reporting results for IVW test in the main text – clarify why.
5- The Discussion is also not properly presented. A section on the limitations of reproducibility
of results by the 3 tested methods should be included. If IVW is considered more robust that
the other two, a discussion on this should be included and properly supported by references.
Discussions for each “causal” metabolite should be discussed in cancer context and not in terms
of general health.
6- The tests should be replicated in another European cervical cancer cohort. Can the authors
comment on availability of such a replication cohort?
ADDITIONAL REQUESTS/SUGGESTIONS:
I have already indicated these revisions in my previous comments