Title: Investigating genetic links between blood metabolites and preeclampsia
Version: 1 Date: 26 Nov 2023
Reviewer's report:
Dear respected [Authors],
I hope this message finds you well. We appreciate the effort you have put into your manuscript
entitled "[ Causal associations between human blood circulating metabolites and the risk of
preeclampsia]." After a thorough review, we have identified several areas that would benefit
from further clarification and improvement. Below are detailed recommendations to address the
weak points identified in each section of your manuscript:
Title notes:
The title effectively communicates the main focus of the study; however, there is room for
improvement:
1. Precision in Causality Terminology:
- The term "Causal Associations" might be considered slightly vague. To enhance precision,
consider specifying the nature of the causal relationship, such as "Causative Links" or
"Genetically Predicted Causality."
2. Clarity on Blood Circulating Metabolites:
- While the mention of "blood circulating metabolites" is clear, specifying a key metabolite or
class of metabolites in the title could provide more immediate insight into the study focus.
Abstract notes:
1.Explicit Statement of Research Gap:
- The abstract mentions that the causal role of metabolites in preeclampsia hasn't been explored.
It would be beneficial to explicitly state this as a research gap to provide context for the study's
significance.
2. Specifics on Metabolites:
- While the abstract mentions a total of 12 known and 11 unknown metabolites, providing
examples or general categories of these metabolites in the abstract could offer readers a glimpse
into the study's findings without delving into the full paper.
3.Clarity on Validation Results:
- The validation with another metabolites GWAS data is briefly mentioned, but the abstract
could benefit from a clearer statement on the consistency of results between the primary and
validation datasets. Were there any discrepancies?
4.Metabolite Pathway Analysis Significance:
- The abstract mentions glycolysis/gluconeogenesis and arginine biosynthesis as related to PE.
Providing a brief insight into why these pathways are significant or how they contribute to the
understanding of PE would enhance the abstract's impact.
5.Inclusion of Study Limitations:
- It's advisable to include a brief statement about the limitations of the study. For instance, any
potential biases or challenges in the Mendelian Randomization approach.
6.Highlighting Clinical Implications:
- While the abstract mentions potential biomarkers for screening and diagnosis, adding a
sentence on the potential clinical implications of these findings would strengthen the abstract.
7. Final Statement on Contribution:
- The abstract could conclude with a more explicit statement on how the study contributes to the
existing knowledge on preeclampsia, perhaps in the form of a sentence summarizing the novel
insights gained.
The Introduction notes:
- The Introduction section of the manuscript is comprehensive and well-structured, providing a
clear background on preeclampsia (PE), its significance, and the current challenges in diagnosis
and treatment. However, there are a few points that could be addressed to strengthen this section:
1.Clarity in Objectives: While the objectives of the study are mentioned, it would be beneficial
to explicitly state them at the end of the introduction. This can provide readers with a clear
understanding of the study's purpose before delving into the methods.
2.Transition to Metabolomics: The transition from discussing the challenges in PE diagnosis
and treatment to the role of metabolomics could be smoother. Consider adding a sentence or
two that explicitly connects the need for new diagnostic and treatment targets to the potential
role of metabolomics in addressing these challenges.
3. Relevance of Metabolites: Emphasize why metabolites, in particular, are being explored in
relation to PE. Briefly discuss the rationale behind choosing metabolites as potential biomarkers
and how they might offer insights into the pathogenesis of PE.
4. In-text Citations: Some statements, such as those related to the role of metabolomics in
early disease diagnosis, interpretation of pathology, and drug development, would benefit from
specific in-text citations to support these claims.
5. Review of Previous Studies: While the authors touch upon previous studies identifying
metabolite pathways associated with PE, consider integrating a brief review of relevant literature
to provide a context for the readers. This can also help in highlighting the current gaps in
knowledge that the study aims to address.
The Methods and Statistical Analysis notes:
1. Instrumental Variable (IV) Selection:
- The criteria for selecting IVs associated with genetically determined blood metabolites are
mentioned, but it would be beneficial to briefly discuss why these criteria were chosen and their
relevance to the study.
- Consider providing a rationale for the clump distance of 500 kb and how this specific parameter
contributes to the robustness of the instrumental variable selection.
2. MR Analysis:
- While the main MR method used is Inverse Variance Weighted (IVW), it would be useful to
provide a brief justification for choosing this method as the primary screening method.
- Explain the choice of MR Egger and Weighted Median methods as auxiliary methods and
discuss their specific roles in the analysis.
3.Sensitivity Analyses:
- Provide a more detailed explanation of why MR PRESSO was chosen for detecting potential
pleiotropy and heterogeneity and how it adds value to the sensitivity analyses.
- Clarify the decision-making process for removing significant outliers identified by MR
PRESSO and the impact of these removals on the results.
4. Leave-One-Out Analysis:
- Elaborate on the rationale and significance of the leave-one-out analysis. How does this
analysis contribute to the robustness and reliability of the MR results?
5.Statistical Significance Threshold:
- Provide a brief justification for choosing the Bonferroni corrected threshold of P < 1.02E-4
as the significance level. Discuss why this level was deemed appropriate for controlling for
multiple testing.
6.Validation of Results:
- Clarify the specific procedures involved in the validation of results using another independent
metabolite GWAS dataset. What considerations were taken into account during this validation
process?
7.Data Analysis Software:
- Mention the software versions used for the MR analysis (TwoSampleMR and MR-PRESSO)
and any specific settings or adjustments made during the analysis.
8.Population Representation:
- Acknowledge that the study only includes individuals of European ancestry, and discuss
potential implications or limitations related to the generalizability of the findings to other
populations.
The Results and Discussion notes:
Results notes:
1. Clarity in Reporting:
- In the Results section, it is recommended to provide a clear and concise overview of the main
findings before delving into the detailed results. This helps readers to quickly grasp the key
outcomes of the study.
2.Presentation of Tables and Figures:
- Consider improving the clarity of Tables and Figures by providing concise titles and captions.
Ensure that the information presented in these visual elements is easily understandable without
solely relying on the main text.
3. Validation Results:
- In the validation of results using another metabolite GWAS dataset, provide a more explicit
discussion of the consistency or differences observed between the datasets. Discuss any potential
reasons for variations in results between datasets.
4. Interpretation of Causal Associations:
- When presenting the metabolites causally associated with PE, elaborate on the potential
biological mechanisms or pathways through which these metabolites might influence the
development of PE. This can provide a more insightful interpretation for readers.
Tables and Figures notes:
1. Table 1: Results of pleiotropy and heterogeneity test of the unknown metabolites on PE:
- Complexity of Data Presentation: The table contains multiple metabolic groups, making it
visually dense. Consider breaking it down into sub-tables for each metabolic group to enhance
clarity.
- Abbreviation Clarity: Some abbreviations (e.g., MR PRESSO) lack explanations. Include a
comprehensive legend or footnotes to ensure readers understand these abbreviations.
2. Figure 1: MR estimates of known metabolites on the risk for PE:
- Color and Contrast: The colors used may not be accessible to all readers. Ensure sufficient
contrast for better readability, especially for readers with visual impairments.
- Axis Labeling: The x-axis and y-axis labels should be more descriptive. Clearly state what the
odds ratio (OR) and confidence interval (CI) represent for improved interpretability.
3. Figure 2: Meta-analysis of the causal relationship between metabolites and PE:
- Legends and Labels: The legend should provide a concise explanation of the symbols used.
Additionally, label the axes appropriately for a more intuitive understanding.
-Color Scheme Consistency: Ensure consistency in color usage across different figures to
maintain coherence in data representation.
4. Supplementary Figure S1: MR estimates of unknown metabolites on the risk for PE:
-Consistent Scale: Confirm that the scales on the axes are consistent with those in Figure 1 for
accurate visual comparison between known and unknown metabolites.
5.Supplementary Table S10: Enrichment pathway analysis of causally associated metabolites:
- Formatting Consistency: The formatting of p-values (P) in the table lacks uniformity.
Standardize the presentation of p-values for clarity and precision.
- Heading Clarity: Ensure that column headings clearly indicate the information presented.
Ambiguous headings can lead to misinterpretation.
6. Supplementary Figure S2: The leave-one-out analysis of 12 known metabolites on
preeclampsia when leaving one SNP out:
-Comprehensive Labels: The labels on the plot should be comprehensive, indicating which SNP
is being left out at each point. This ensures transparency in the analysis.
7. Supplementary Table S3: Results of pleiotropy and heterogeneity test of the unknown
metabolites on PE:
-Data Interpretation Assistance: Consider adding additional columns or footnotes to aid readers
in interpreting the results. This could include indicating statistically significant values or
providing a key for interpreting different tests.
Discussion notes:
1.Clinical Relevance:
- Connect the findings to the clinical relevance of identifying metabolites causally associated
with PE. Discuss how these metabolites could potentially serve as diagnostic or prognostic
markers in clinical settings.
2.Contradictory Findings:
- If there are conflicting findings or discrepancies with previous studies, address them explicitly
and discuss potential reasons for the differences. This adds depth to the discussion and helps
readers understand the broader context of the study.
3.Generalization to Other Populations:
- Acknowledge the limitation that the study only includes individuals of European ancestry.
Discuss the implications of this limitation for the generalization of findings to other populations
and the potential need for future studies in diverse populations.
4.Limitations and Future Directions:
- Explicitly outline the limitations of the study, including any potential biases or constraints
associated with the MR approach. Discuss avenues for future research that could build upon the
current findings and address these limitations.
5.Integration of Pathway Analysis:
- Integrate the findings from the pathway analysis more cohesively into the discussion. Discuss
how the enriched pathways align with current understanding of PE pathophysiology and whether
they offer novel insights for further investigation.
6.Contextualization of Results:
- Ensure that the results are contextualized within the broader literature on PE. This involves
discussing how the identified metabolites align with or challenge existing knowledge in the field.
The conclusion notes:
1. Restatement of Key Findings:
- While the conclusion briefly summarizes the key findings, consider reinforcing the most critical
results to ensure that readers leave with a clear understanding of the study's main contributions.
Emphasize the novel aspects or insights that emerge from the research.
2.Connection to Research Question and Hypotheses:
- Revisit the initial research question and hypotheses posed at the beginning of the manuscript.
Ensure that the conclusion explicitly ties back to these elements, highlighting how the study's
outcomes address the research question and either support or challenge the initial hypotheses.
3.Clinical Implications:
- Expand on the clinical implications of the findings. Discuss how the identified metabolites or
pathways may contribute to our understanding of the disease (PE) and its potential implications
for diagnosis, treatment, or prevention. This will enhance the practical relevance of the study.
4.Limitations Recap:
- Reiterate the limitations discussed throughout the manuscript in the conclusion. This reinforces
transparency and helps readers understand the boundaries of the study. Consider discussing how
these limitations may influence the generalizability and interpretation of the results.
5.Future Directions:
- Provide a more nuanced discussion of future research directions. Specify potential follow-up
studies, methodological improvements, or additional analyses that could build upon the current
findings. This adds depth to the conclusion and guides researchers interested in extending the
work.
6.Synthesis of Results:
- Synthesize the main results rather than presenting them in isolation. Highlight connections
between different aspects of the study, demonstrating how individual findings contribute to the
overall understanding of the research question.
7. Consideration of Alternative Explanations:
- Acknowledge and discuss alternative explanations for the observed results. This demonstrates
a robust consideration of different perspectives and adds intellectual rigor to the conclusion.
8. Avoidance of Redundancy:
- Ensure that the conclusion does not overly repeat information already presented in the Results
and Discussion sections. Instead, focus on providing a concise synthesis and forward-looking
perspective.
9. Clarity in Implications:
- Be explicit about the implications of the study. Clearly communicate the significance of the
findings and how they advance current knowledge in the field. This will help readers appreciate
the broader impact of the research.
The References notes:
1.Consistency in Citation Style:
- Ensure consistency in the citation style throughout the reference list. For example, some entries
use initials for given names (e.g., Y. Yang), while others provide full names (e.g., G. J. Burton).
Adopt a standardized format for clarity.
2. Journal Article Formatting:
- Check the formatting of journal articles, including the use of italics for journal names, proper
capitalization of article titles, and inclusion of volume and issue numbers. Standardize the
presentation of journal references according to the chosen citation style.
3.DOI or URL Inclusion:
- Include Digital Object Identifiers (DOIs) or URLs for journal articles where applicable. This
provides readers with direct access to the source and enhances the reproducibility of the study.
4. Book Title Italicization:
- Ensure that book titles are italicized for consistency in formatting. This applies to entries such
as [2] where the book title is part of the reference.
5.Full Author List:
- Some entries, such as [6], [7], and [28], use "et al." for additional authors. Consider
providing the full list of authors, especially when the total number is reasonably manageable,
to acknowledge all contributors.
6.Year of Publication:
- Confirm the accuracy of publication years for each reference. Consistent formatting of
publication years enhances the overall professional presentation.
7. Relevance of References:
- Ensure that all references cited in the manuscript are included in the reference list, and vice
versa. This helps maintain coherence between in-text citations and the bibliography.
8.Ordering of References:
- Check the order of references to ensure they align with the citation order in the manuscript.
Sequential numbering facilitates easy cross-referencing.
By addressing these recommendations, your manuscript will not only enhance its clarity and
transparency but also contribute more effectively to the scientific discourse in the field. We look
forward to receiving the revised version of your manuscript.
Best regards,