gmhhope
commented
1 year ago The first figure has many issues. For one, I cannot tell if there is a subfigure f that is missing/omitted, since there is a legend pertaining to a subfigure f but there is no subfigure f panel.
Yes, I cannot see figure 1f either. I think it was originally there and in the final revision the figure was removed. But the trace left behind like the legend. This is typical in the peer review process. Things can get really messy.
Additionally, there is no color code for the red/blue indications
- It is coded for different sex as gender plays significant role in Antibody & T cell immunity, but I do not know if they make it explicit in the first place.
There is also no explanation for why the authors included another time designation in subfigure b in comparison to subfigure a.
Again, this is probably due to samples that are used for testing in different assays. They may just do neutralizing Abs assay for longer period post vaccination but not the anti-S IgG ELISA.
Harsha-Tamtam
Systems vaccinology of the BNT162b2 mRNA vaccine in humans
Main Research Question and Contribution to the fields?
The author's main aim was to characterize the innate immune environment in response to mRNA vaccines, in this case, Pfizer (being the first of its kind). Though the methodologies utilized to illustrate the innate immunity are well known and ubiquitously used, no other authors have shown the results for the hypothesis they have outlined. The authors have gone into well enough depth to affirm correlations, significance, and reasoning(s) for highlighting specific data. Interestingly, the mRNA vaccine is the first vaccination demonstrated to not produce any autoantibodies, an aspect unique to the Pfizer vaccine (potentially mRNA vaccinations in general). Additionally, the authors illustrate that pSTAT and IFN- signaling monocytes/dendritic cells emerge after booster vaccinations.
Methods & Data
The author's sample size was representative of the larger population age and gender ratios. The sample size was adequately large enough (n>32). The authors made use of well characterized cell markers to keep their figures easy to interpret and follow. There are issues with Figure 1 (see confusion section below). Color scale intensities are appropriate and the statistical tests used match with other papers and the intended conveyed message for each figure.
The use of CyToF to tag cells based on lanthanide-bound mass and fluorescence to project cell identity is a modern use of projection analysis. We appreciate the use of UMAP instead of tSNE. Not only does UMAP take less time, but rather than using Gaussian probability, it utilizes the topology of the higher dimensional categorization and reduces it to two dimensions (Nerve Theorem) to keep the dimensionality at its purest form
Authors' interpretation
The author interpretations are mostly well supported by their figures. However, given the novelty of the C8 cluster and their claim that this cluster is unique to mRNA induced vaccinations, they authors did not do justice for their interpretation of the C8 cluster. For example, is the C8 cluster a factor in why antibodies are not seen in mRNA vaccinated individuals? Why was there no ATAC-seq done for these cells, when this method could elucidate genes being regulated that differentiate the C8 clusters from other clusters, and better substantiate the C8 subclusters?
Enhancement or next experiment?
I believe the author should have utilized a prediction UMAP overlay to confirm the cell type clusterings from CyToF. Readers unfamiliar with the cell markers utilized (and a large number at that) would likely want verification that the clusters identified are indeed the cells identified from a database/other well known literature.
Any confusion regarding the paper?
The first figure has many issues. For one, I cannot tell if there is a subfigure f that is missing/omitted, since there is a legend pertaining to a subfigure f but there is no subfigure f panel. Additionally, there is no color code for the red/blue indications (there is, but it is mentioned after Figure 1; this should not be the case, as Figure 1 is the first figure to utilize this color code). There is also no explanation for why the authors included another time designation in subfigure b in comparison to subfigure a. It is also difficult to see the box plots; they should be bolder or darker in color.
Moreover, what is the rationale behind using [cell markers Lin and HLA-DR (see Ext. Data. Fig. 5)? A detailed reason for selection against this lineage is required for better understanding of the latter figures.
You own opinions or critiques
See the above comments for personal opinions regarding improvements to the results/discussion to the paper.
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