Review 2: "A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients"

RR:C19 Evidence Scale rating by reviewer:

• Reliable. The main study claims are generally justified by its methods and data. The results and conclusions are likely to be similar to the hypothetical ideal study. There are some minor caveats or limitations, but they would/do not change the major claims of the study. The study provides sufficient strength of evidence on its own that its main claims should be considered actionable, with some room for future revision.

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Review:

Decision-makers should consider the claims in this study actionable with limitations based on the methods and data.

COVID-19 disease has a multi-faceted pathology comprising multi-organ dysfunctions. Understanding tissue-specific molecular and cellular alterations are fundamental to designing better treatments and managing post-COVID-19 conditions. This work extends existing COVID-19 cell atlases to the context of liver function and presents a rich resource of single-nucleus and spatial transcriptional data.

This study consists of a rich, granular single nucleus gene expression dataset, from 17 livers of patients who died from COVID-19. The liver atlas recapitulates the liver composition of five major compartments (hepatocytes, immune/blood, endothelial, mesenchymal, and biliary epithelial cells BEC) and includes rare cells. The authors also generated a high-resolution spatial transcriptomic atlas from 62 Regions of Interest (ROIs) from 4 donors. This allowed them to associate spatially specific pathological functions with potential failures of the COVID-19 liver. The restructured cellular composition and gene expression point to several pathological conditions including hepatocellular injury, ductal reaction, neo-vascular expansion, and fibrogenesis.

The methodologies employed to generate and validate the single-nucleus expression atlas are appropriate, and the integration with the healthy reference data follows current best practices. We also appreciate the use of conventional IF/IHC staining to support the spatial liver atlas and validate the observations. However, while 17 patients were used to generate the dataset, the degree of the cellular and expression changes was not consistently reported per individual. This does not allow a thorough assessment of the frequency of the pathological alterations, and the variability of the effects. Also, as noted by the authors, the study is restricted to the first SARS-CoV-2 variant in a non-vaccinated population. It is unclear how the results demonstrated in this study compare with the current situation. This should be considered in future meta-analyses or integration of this dataset.

Disclaimer: Due to our lack of expertise in liver biology (and COVID-19 disease), we decline the complete evaluation of advanced biological conclusions.