Identification of the regulatory mechanism of ACE2 in COVID-19-induced kidney damage with systems genetics approach

Abstract

Studies showed that SARS-CoV-2 can directly target the kidney and induce renal damage. As the cell surface receptor for SARS-CoV-2 infection, the angiotensin-converting enzyme 2 (ACE2) plays a pivotal role for renal physiology and function. Thus, it is important to understand ACE2 through which pathway influences the pathogenesis of renal damage induced by COVID-19. In this study, we first performed an eQTL mapping for Ace2 in kidney tissues in 53 BXD mice strains. Results demonstrated that Ace2 is highly expressed and strongly controlled by a genetic locus on chromosome 16 in the kidney, with six genes (Dnase1, Vasn, Usp7, Abat, Mgrn1, and Rbfox1) dominated as the upstream modulator, as they are highly correlated with Ace2 expression. Gene co-expression analysis showed that Ace2 co-variates are significantly involved in the renin-angiotensin system (RAS) pathway which acts as a reno-protector. Importantly, we also found that Ace2 is positively correlated with Pdgf family members, particularly Pdgfc, which showed the most association among the 76 investigated growth factors. Mammalian Phenotype Ontology enrichment indicated that the cognate transcripts for both Ace2 and Pdgfc were mainly involved in regulating renal physiology and morphology. Among which, Cd44, Egfr, Met, Smad3, and Stat3 were identified as hub genes through protein-protein interaction analysis. Finally, in aligning with our systems genetics findings, we found ACE2, pdgf family members, and RAS genes decreased significantly in the CAKI-1 kidney cancer cells treated with S protein and receptor binding domain structural protein. Collectively, our data suggested that ACE2 work with RAS, PDGFC, as well as their cognate hub genes to regulate renal function, which could guide for future clinical prevention and targeted treatment for COVID-19-induced renal damage outcomes. KEY MESSAGES: • Ace2 is highly expressed and strongly controlled by a genetic locus on chromosome 16 in the kidney. • Ace2 co-variates are enriched in the RAS pathway. • Ace2 is strongly correlated with the growth factor Pdgfc. • Ace2 and Pdgfc co-expressed genes involved in the regulation of renal physiology and morphology. • SARS-CoV-2 spike glycoprotein induces down-regulation of Ace2, RAS, and Pdgfc.

Keywords: BXD mice; COVID-19; Kidney; PDGF family; RAS; SARS-CoV-2; Transcriptome.

Fig. 1

Expression and eQTL mapping of Ace2 in BXD family. A Bar plots of the Ace2 expression across the BXD kidney. The x-axis shows the BXD strains and the two parental strains. The y-axis shows the normalized log2 expression levels of Ace2. B Manhattan plot of genome-wide Ace2-regulated genomic loci. The x-axis denotes a position on the mouse genome, in megabases (Mb), while the y-axis gives the LRS value, a measurement of the linkage between Ace2 expression and genomic region. The dashed line indicates suggestive and significant genome-wide thresholds. eQTL mapping was conducted with interval mapping on GeneNetwork (www.genenetwork.org). C Scatter plots showing the Pearson correlations between Ace2 expression and six QTL candidate genes. Pearson correlation coefficient r and p are indicated, gene values are log2 transformed

Fig. 2

Ace2 co-variates are enriched in the renin-angiotensin system (RAS) pathway. A RAS pathway. Green represents genes positively correlated with Ace2 expression in the BXD kidney, while red represents reverse regulation. B–G Scatter plots showing the Pearson correlations between Ace2 expression and six RAS pathway genes. Pearson correlation coefficient r and p are indicated, and gene values are log2 transformed

Fig. 3

Ace2 is positively correlated with the growth factor Pdgfc. A volcano plot showing the Pearson correlations between Ace2 expression and 87 growth factors across the BXD mice kidney. Each spot represents a member of the growth factor, with red color indicating a significant correlation with Ace2 expression (p < 0.05). The y-axis and x-axis represent the log10 transformed p value and Pearson correlation coefficient, respectively. B–E scatter plots showing the Pearson correlations between Ace2 expression and Pdgf family members. Pearson correlation coefficient r and p are indicated, gene values are log2 transformed

Fig. 4

Mimic infection of SARS-COV-2 induces down-regulation of RAS and PDGFs in cells. The mRNA level of ACE2 (A–B), the ratio of ACE2/ACE (C–D), the mRNA of genes related to classical RAS pathway (E–F), the mRNA level of PDGFs family (G–H) and its downstream genes (I–J) were analyzed by qRT-PCR. BSA was used as a control; S1 represents recombinant SARS-COV-2 Spike S1 (S1 Subunit) protein; RBD represents recombinant Spike Protein (RBD). N = 3 cases per group. Data represent means ± S.E.M; biological replicates. p < 0.05*, p < 0.01** and p < 0.001 *** by one-way ANOVA followed by unpaired two-tailed Student’s t-test

Fig. 5

Ace2 and Pdgfc co-expressed genes involve in the regulation of renal physiology and morphology. A Protein–protein interaction network of 168 genes related to renal physiology and morphology. All the genes were correlated with Ace2 and Pdgfc expression (p < 0.05 and Lit > 0.3). Red nodes represent hub genes. Network was constructed with string (www.string.org). B Scatter plots showing the Pearson correlations between Ace2/Pdgfc expression and five hub genes. All Pearson correlation p < 0.05, gene values are log2 transformed