RR:C19 Evidence Scale rating by reviewer:
Not informative. The flaws in the data and methods in this study are sufficiently serious that they do not substantially justify the claims made. It is not possible to say whether the results and conclusions would match that of the hypothetical ideal study. The study should not be considered as evidence by decision-makers.
This manuscript used single-cell RNA-Seq analyses to characterize a group of SARS-CoV-2 entry factors in human endometrium. They calculate the percentages of endometrial cells expressing SARS-CoV-2 entry factors from their analysis. I think that the data generated here is new. However, my concern is the entire lack of clarity of data analysis and some conclusions are often too speculative and not really supported by analytical data. While the claims are not strongly supported, they may yield some insight by the data and methods used. Decision-makers should consider the claims in this study not actionable (except to prompt further research). My major concerns are following:
While the identification of cells expressing ACE2 and TMPRSS2 during menstrual cycle is most important finding of the manuscript, this paper fails to convey the molecular signature of those cells.
This paper does not show the quality control of generated scRNA-seq data.
Data transparency is another issue with this manuscript. This paper does not describe how the datasets were analyzed and just cites a recently published paper.
This paper considers a few genes, e.g. ACE2, TMPRSS2, CTSB, or CTSL. With the available transcriptomic datasets, one may also dissect the other factors that are associated with SARS-CoV-2 entry into a host cell. For instance, TMPRSS4 and FURIN are also potential proteases.
While showing the low expression or lesser percent of cells expressing a given gene, this paper does not consider the limitations of Fluidigm C1 and Chromium 10X single-cell RNA-seq datasets e.g., drop-outs.
There is literature that show that TMPRSS2 can cleave the “spike” from neighbor cells so a co-expression of ACE2 and TMPRSS2 in a host cell is not necessarily the only way how SARS-CoV-2 enters.
TSNE plots show the early, mid, and late stages of the menstrual cycle but not the cell types. However, the paper shows the expression of chosen genes in a few cell types.
There are better ways to illustrate the expression or co-expression of analyzed genes than is shown in this manuscript.
The manuscript is short, well-structured, and well-writtenl however with the above concerns, I do not think that it has the ability to speak to key audiences.