DW-PBJ5-Zijian

[zijian-li1228]

Discussion worksheet

The paper you are working on?

Arunachalam et al.

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Main Research Question, Contribution to the fields?

The authors aimed to study the innate immune response post the prime vs boost doses of Pfizer vaccine against COVID-19. They have successfully identified the distinct innate pathways associated with CD8 T cell and neutralizing antibody responses and demonstrated the potency of mRNA vaccination especially after booster dose.

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Methods & Data

The authors used CyTOF to identify cells clusters affected by vaccination and through a multi-omics approached identified IFNy induced cluster C8 as potential pathway for innate immune response post vaccination

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Authors' interpretation

I agree with the authors interpretation mostly. However there are unanswered questions such as what are the mechanisms for interferon stimulated gene response in C8 (as identified by the authors in Discussion)

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Enhancement or next experiment?

increase cohort size to improve statistical power

The paper focuses on the transcriptome signatures, however since transcription=/=expression, I am wondering if they have done any subsequent proteomics analysis.

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Confusion? Terms you don't understand?

no for now

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Have your own opinions or critiques

They did not discuss statistical analysis in detail in their method section and I'm curious about the statistical approach used for each figure especially how data was processed for GSEA. Also the scale used in Fig2 is very small so I'm wondering if the difference can actually be considered significant.

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I hereby confirm that I have:

• [ ] I am still working on the worksheet
• [x] I have finished the worksheet
• [ ] I have gone through the papers
• [ ] Check your peer if they have similar ideas. If it is, plz add their issue number to your comments.

[gmhhope]

They did not discuss statistical analysis in detail in their method section and I'm curious about the statistical approach used for each figure especially how data was processed for GSEA. Also the scale used in Fig2 is very small so I'm wondering if the difference can actually be considered significant.

• Yes that is a usual conduct from Bali's paper. Reason is that he began his career from experimental immunology. And thus he is not very open to code transparency. I see their GitHub repository and I can only see an iceberg of all the codes used in the analysis.

[gmhhope]

The paper focuses on the transcriptome signatures, however since transcription=/=expression, I am wondering if they have done any subsequent proteomics analysis.

They do provide some data of protein analysis. Well, you usually cannot ask for more if they have already provides a kaleidoscope of fancy methods in one single paper :))