Localization of Cell Receptor-Related Genes of SARS-CoV-2 in the Kidney through Single-Cell Transcriptome Analysis

Abstract

Background: The new coronavirus (SARS-CoV-2), which has been responsible for the recent coronavirus disease 2019 (COVID-19) pandemic, uses the cell receptor angiotensin converting enzyme-2 (ACE2) for entry and the serine protease TMPRSS2 for spike (S) protein priming. Meanwhile, the presence of B⁰AT1 (SLC6A19) may prevent TMPRSS2 from accessing the cutting position on ACE2. Identifying the expression of these cell receptor-related genes of SARS-CoV-2 is critical for understanding the pathogenesis of SARS-CoV-2 in various tissues, especially in the kidney.

Methods: The single-cell transcription datasets of the human cell landscape (HCL) and other relevant single-cell transcription databases were used to analyze the expression of ACE2, TMPRSS2, and SLC6A19 in various organs and tissues, but mainly in the kidney.

Results: ACE2 was significantly expressed in the S1, S2, and S3 segments of proximal tubule (PT) cells. TMPRSS2 was widely expressed in several renal tubule populations extending from the PT cells to the collection system cell type, of which intercalated cells and the distal convoluted tubule cells showed more significant expression than PT cells. Unexpectedly, although expressed on various renal tubule populations, SLC6A19 was mainly enriched in PT cells, in line with ACE2 expression. Although alveolar-type (AT) 2 cells of the lung and intestinal epithelial cells expressed ACE2 as well as PT cells, AT 2 cells significantly expressed TMPRSS2 but not SLC6A19, while all 3 genes were significantly expressed in intestinal epithelial cells.

Conclusions: ACE2 was widely expressed in specific cell subgroups of various human tissues, especially in intestinal epithelial cells, kidney PT cells, and also AT 2 cells of the lung. These 3 types of cells demonstrated significant differences in the distribution of the cell receptor-related genes of SARS-CoV-2, which may indicate the diversity of cell surface structures and differences in the affinity between SARS-CoV-2 and cells.

Keywords: Angiotensin-converting enzyme-2; Proximal tubule cells; SARS-CoV-2; Single-cell transcriptome sequencing.

Fig. 1

ACE2 expression in human cell landscape (HCL). a Two-dimensional t-distributed stochastic neighbor embedding plot displaying major cell clusters in HCL. b Scatter plots showing clusters of cells with ACE2 expression. c Histograms of ACE2 expression in adult tissues in HCL. d, e Histograms represent a subgroup of kidney cells that significantly express ACE2 in “adult kidney−3” (d) and in “fetal kidney-5” (e) in HCL, respectively (reproduced from http://bis.zju.edu.cn/HCL/index.html).

Fig. 2

Expression of genes associated with SARS-CoV-2 entry in single-cell transcriptome sequencing database. a UMAP visualization displaying major cell clusters (22,268 single cells). b Dot plot of LRP2 and CUBN (marker genes of PT cells), ACE2, TMPRSS2, and SLC6A19; dot size represents the fraction of cells expressing a cell type, and color intensity binned count-based expression level amongst expressing cells. c UMAP projection, points colored by detection of ACE2 (left), TMPRSS2 (middle), and SLC6A19 (right). Blue, RNA positive; gray, RNA negative. d Volcano plot displaying differential expression of genes between ACE2+ and ACE2– PT cells. Red, up-regulated genes; blue, down-regulated genes. e Bar plot presenting significantly enriched GO terms obtained from GO enrichment analysis performed with differential expression of genes between ACE2+ and ACE2– PT cells.

Fig. 3

Expression of genes associated with SARS-CoV-2 entry in single-nuclear transcriptome. a Dot plot of LRP2 and CUBN (marker genes of PT cells), ACE2, TMPRSS2, and SLC6A19; dot size represents the fraction of cells expressing each cell type, and color intensity binned count-based expression level amongst expressing cells. b Bar plot presenting significantly enriched GO terms obtained from GO enrichment analysis performed with differential expression of genes between ACE2+ and ACE2– PT cells. c Violin plot showing ACE2, SLC6A19, and TMPRSS2 expression distribution among different cell clusters.

Fig. 4

Expression of genes associated with SARS-CoV-2 entry in a single-cell transcriptome sequencing database of Asians. a Dot plot of LRP2 and CUBN (marker genes of PT cells), ACE2, TMPRSS2, and SLC6A19; dot size represents the fraction of cells expressing each cell type, and color intensity binned count-based expression level amongst expressing cells. b Bar plot presenting significantly enriched GO terms obtained from GO enrichment analysis performed with differential expression of genes between ACE2+ and ACE2– PT cells.

Fig. 5

Expression of genes associated with SARS-CoV-2 entry in the small intestine. a UMAP visualization displaying major cell clusters (14,537 single cells). b Dot plot of marker genes for each cell type and ACE2, TMPRSS2, and SLC6A19; dot size represents the fraction of cells expressing each cell type, and color intensity binned count-based expression level amongst expressing cells. c UMAP projection: points colored by detection of ACE2 (left), TMPRSS2 (middle), and SLC6A19 (right). Blue, RNA positive; gray, RNA negative. d Volcano plot displaying differential expression genes between ACE2+ and ACE2– enterocytes. e Bar plot presenting significantly enriched GO terms obtained from GO enrichment analysis performed with differential expression genes between ACE2+ enterocytes and all other enterocytes (Up), ACE2+/TMPRSS2+ enterocytes, and all other enterocytes (Down).

Fig. 6

Expression of genes associated with SARS-CoV-2 entry in the lung. a UMAP visualization displaying major cell clusters. b Dot plot of 3 marker genes for each cell type and ACE2, TMPRSS2, and SLC6A19; dot size represents the fraction of cells expressing each cell type, and color intensity binned count-based expression level amongst expressing cells. c UMAP projection: points colored by detection of ACE2 (left) and TMPRSS2 (right). Blue, RNA positive; gray, RNA negative.