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

Abstract

The molecular underpinnings of organ dysfunction in acute COVID-19 and its potential long-term sequelae are under intense investigation. To shed light on these in the context of liver function, we performed single-nucleus RNA-seq and spatial transcriptomic profiling of livers from 17 COVID-19 decedents. We identified hepatocytes positive for SARS-CoV-2 RNA with an expression phenotype resembling infected lung epithelial cells. Integrated analysis and comparisons with healthy controls revealed extensive changes in the cellular composition and expression states in COVID-19 liver, reflecting hepatocellular injury, ductular reaction, pathologic vascular expansion, and fibrogenesis. We also observed Kupffer cell proliferation and erythrocyte progenitors for the first time in a human liver single-cell atlas, resembling similar responses in liver injury in mice and in sepsis, respectively. Despite the absence of a clinical acute liver injury phenotype, endothelial cell composition was dramatically impacted in COVID-19, concomitantly with extensive alterations and profibrogenic activation of reactive cholangiocytes and mesenchymal cells. Our atlas provides novel insights into liver physiology and pathology in COVID-19 and forms a foundational resource for its investigation and understanding.

Aging impairs cold-induced beige adipogenesis and adipocyte metabolic reprogramming

“…Reads were aligned against the GRCm38 mouse genome assembly and gene counts were obtained, per-droplet, by summarizing exonic and intronic UMIs that overlapped with the GENCODE mouse annotation (release 24) for each gene symbol. In order to adjust for downstream effects of ambient RNA expression within mouse nuclei, we used the ‘remove-background’ module from CellBender ( Pita Juarez et al, 2022 ; version 0.2.0) to remove counts due to ambient RNA molecules from the count matrices and to estimate the true cells. Genes were subsequently filtered such that only genes detected in two or more cells and with at least 6 total counts (across all cells) were retained.…”

Emerging Roles of Spatial Transcriptomics in Liver Research

“…Pita-Juarez et al leveraged the GeoMx DSP Whole Transcriptome Atlas platform to spatially analyze human livers from patients with coronavirus disease 2019 (COVID-19) infection and found that COVID-19-specific liver modulation was observed, such as hepatocyte proliferation in zone 1 and hypoxia and stress response in zone 3. 85 Uzun et al compared liver injury after COVID-19 vaccination (vaccine-induced liver injury [VILI]) with autoimmune hepatitis (AIH), since their clinical presentation to some extent resembles each other, using DSP in conjunction with bulk RNA-sequencing. 86 Bulk RNA-sequencing revealed that interferon gamma pathways were significantly enriched in AIH, whereas mitochondrial metabolism and oxidative stress-related pathways were upregulated in VILI, and DSP suggested that hepatocytes were responsible for these differences.…”

Liver in infections: a single-cell and spatial transcriptomics perspective

“…7 B). Comprehensive single-cell/spatial organ atlases of COVID-19 have been generated from various types of patient samples, including livers, using available scRNA-seq and spatial data [ 166 – 169 ]. By performing scRNA-seq and spatial transcriptomic profiling of livers from 17 COVID-19 patients, hepatocytes were identified as positive for SARS-CoV-2 RNA [ 169 ].…”

“…Comprehensive single-cell/spatial organ atlases of COVID-19 have been generated from various types of patient samples, including livers, using available scRNA-seq and spatial data [ 166 – 169 ]. By performing scRNA-seq and spatial transcriptomic profiling of livers from 17 COVID-19 patients, hepatocytes were identified as positive for SARS-CoV-2 RNA [ 169 ]. Further integrated analysis and comparisons with healthy controls revealed massive changes in cellular composition and gene expression in livers affected by COVID-19, mainly in those exhibiting hepatocellular injury, ductular reactions, pathologic vascular expansion, and fibrogenesis (Fig.…”

“…7 B). This human atlas is fundamental to the investigation and understanding of the liver physiology and pathology in COVID-19 [ 169 ]. ACE2 has also been reported to be significantly expressed in liver cholangiocytes, indicating that the liver might be a target organ for SARS-CoV-2 [ 170 ].…”